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@article{bart+17sa,
abstract = {Determining the stability of molecules and condensed phases is the cornerstone of atomistic modelling, underpinning our understanding of chemical and materials properties and transformations. Here we show that a machine learning model, based on a local description of chemical environments and Bayesian statistical learning, provides a unified framework to predict atomic-scale properties. It captures the quantum mechanical effects governing the complex surface reconstructions of silicon, predicts the stability of different classes of molecules with chemical accuracy, and distinguishes active and inactive protein ligands with more than 99{\%} reliability. The universality and the systematic nature of our framework provides new insight into the potential energy surface of materials and molecules.},
archivePrefix = {arXiv},
arxivId = {1706.00179},
author = {Bart{\'{o}}k, A.P. Albert P. and De, Sandip and Poelking, Carl and Bernstein, Noam and Kermode, James R. J.R. and Cs{\'{a}}nyi, G{\'{a}}bor and Ceriotti, Michele},




journal = {Science Advances},


pages = {e1701816},
title = {{Machine learning unifies the modeling of materials and molecules}},

volume = {3},
year = {2017}
}
@article{gubs-kusa01mp,
abstract = {A charge perturbation variant of the finite-field method has been used to calculate dipole and quadrupole moments, dipole polarizability, hyper- and principal components of high-order polarizabilities of the water molecule in gas and in liquid phase conditions. Calculations were performed for the ground-state water molecule at the MP2 and MP4 levels of theory. The gas phase values determined allow our methodology for extracting polarizabilities to be tested and a properly balanced, moderate-sized basis set to be selected; the results obtained are in very good agreement with experiment and the most accurate previous theoretical estimates. A local field approach is introduced to mimic the electrostatic environment experienced by a water molecule in the liquid. Within this approach, sets of fixed charges are used to generate the desired electric fields and field gradients. Three different liquid phase models and the corresponding sets of electrical properties are examined. The values obtained from these models and for gas-phase are compared. The magnitudes of the dipole and the quadrupole moments increase moving from gas to liquid phase, where the latter shows greater sensitivity to the choice of liquid model. For a liquid phase water molecule the first hyperpolarizability (beta) and first higher polarizability (A) increase markedly, actually changing sign, the second hyperpolarizability (gamma) also increases but much less dramatically, and components of the second high-order polarizability tensor (B) demonstrate a rearrangement of contributions. The values reported for the hyper- and high-order polarizability tensors are the first such theoretical estimates for liquid water.},
author = {Gubskaya, A V and Kusalik, P G},


isbn = {0026-8976},

journal = {Mol Phys},

pages = {1107--1120},
title = {{The multipole polarizabilities and hyperpolarizabilities of the water molecule in liquid state: an ab initio study}},
volume = {99},
year = {2001}
}
@article{geor-mand10prb,
author = {Georgescu, Ionuţ and Mandelshtam, Vladimir a.},



journal = {Phys. Rev. B},


pages = {94305},
title = {{Molecular dynamics with quantum fluctuations}},

volume = {82},
year = {2010}
}
@article{isob+05jpcb,
abstract = {The hydrogen desorption mechanism in the reaction from LiH + LiNH2 to Li2NH + H2 was examined by thermal desorption mass spectrometry, thermogravimetric analysis, and Fourier transform IR analyses for the products replaced by LiD or LiND2 for LiH or LiNH2, respectively. The results obtained indicate that the hydrogen desorption reaction proceeds through the following two-step elementary reactions mediated by ammonia: 2LiNH2 --{\textgreater} Li2NH + NH3 and LiH + NH3 --{\textgreater} LiNH2 + H2, where hydrogen molecules are randomly formed from four equivalent hydrogen atoms in a hypothetical LiNH4 produced by the reaction between LiH and NH3 according to the laws of probability.},
author = {Isobe, Shigehito and Ichikawa, Takayuki and Hino, Satoshi and Fujii, Hironobu},



journal = {J. Phys. Chem.. B},


pages = {14855--8},
pmid = {16852881},
title = {{Hydrogen desorption mechanism in a Li-N-H system by means of the isotopic exchange technique.}},

volume = {109},
year = {2005}
}
@article{szew05prb,
author = {Szewczyk, A. and Gutowska, M. and Dabrowski, B.},



journal = {Phys. Rev. B},


pages = {224429},
publisher = {American Physical Society},
title = {{Specific heat and phase diagram of heavily doped La1−xSrxMnO3 (0.45⩽x⩽1.0)}},

volume = {72},
year = {2005}
}
@article{vand+05cpc,
author = {VandeVondele, Joost and Krack, Matthias and Mohamed, Fawzi and Parrinello, Michele and Chassaing, Thomas and Hutter, J{\"{u}}rg},



journal = {Comp. Phys. Comm.},



pages = {103--128},
title = {{Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach}},

volume = {167},
year = {2005}
}
@article{fabe+16prl,
author = {Faber, Felix A and Lindmaa, Alexander and von Lilienfeld, O Anatole and Armiento, Rickard},


journal = {Phys. Rev. Lett.},


pages = {135502},
publisher = {American Physical Society},
title = {{Machine Learning Energies of 2 Million Elpasolite {\$}(AB{\{}C{\}}{\_}{\{}2{\}}{\{}D{\}}{\_}{\{}6{\}}){\$} Crystals}},

volume = {117},
year = {2016}
}
@article{Wise1992,
author = {Wise, David S},

pages = {1--16},
title = {{Matrix Algorithms using Quadtrees Technical Report 357 0 Introduction}},
year = {1992}
}
@book{eise-kauz68book,
address = {Oxford (UK)},
author = {Eisenberg, D. and Kauzmann, W.},
publisher = {Oxford University Press},
title = {{The Structure and Properties of Water}},
year = {1968}
}
@inproceedings{kazh+03proc,
author = {Kazhdan, Michael and Funkhouser, Thomas and Rusinkiewicz, Szymon},
booktitle = {Proceedings of the 2003 Eurographics/ACM SIGGRAPH Symposium on Geometry Processing},
isbn = {1-58113-687-0},
pages = {156--164},
publisher = {Eurographics Association},
series = {SGP '03},
title = {{Rotation Invariant Spherical Harmonic Representation of 3D Shape Descriptors}},

year = {2003}
}
@article{rays07prb,
author = {Rayson, M. J},



journal = {Phys. Rev. B},


pages = {153203},
title = {{Low-complexity method for large-scale self-consistent ab initio electronic structure calculations without localization}},

volume = {75},
year = {2007}
}
@article{wilk02npb,
author = {Wilcox, Walter},



journal = {Nucl. Phys. B - Proceedings Supplements},


pages = {1064--1066},
title = {{Heatbath noise methods in lattice QCD}},

volume = {106-107},
year = {2002}
}
@article{bart+13prb2,
author = {Bart{\'{o}}k, Albert P. and Gillan, Michael J. and Manby, Frederick R. and Cs{\'{a}}nyi, G{\'{a}}bor},



journal = {Phys. Rev. B},


pages = {054104},
title = {{Machine-learning approach for one- and two-body corrections to density functional theory: Applications to molecular and condensed water}},

volume = {88},
year = {2013}
}
@article{deby12adp,
author = {Debye, P.},


journal = {Ann. Phys.},

pages = {789--839},
title = {{Zur Theorie der spezifischen W{\"{a}}rmen}},

volume = {344},
year = {1912}
}
@article{chen-siep99tca,
author = {Chen, B and Siepmann, J I},
journal = {Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)},

pages = {87--104},
publisher = {Springer},
title = {{Monte Carlo algorithms for simulating systems with adiabatic separation of electronic and nuclear degrees of freedom}},
volume = {103},
year = {1999}
}
@article{gat96areps,
author = {Gat, J R},

journal = {Annual Review of Earth and Planetary Sciences},

pages = {225--262},
publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA},
title = {{Oxygen and hydrogen isotopes in the hydrologic cycle}},
volume = {24},
year = {1996}
}
@article{hart+96prb,
author = {Hartwigsen, C and Goedecker, S and Hutter, J},

journal = {Phys. Rev. B},

pages = {3641--3662},
publisher = {APS},
title = {{Relativistic separable dual-space Gaussian pseudopotentials from H to Rn}},
volume = {58},
year = {1998}
}
@article{ams;+15prb,
author = {Amsler, Maximilian and Botti, Silvana and Marques, Miguel A. L. and Lenosky, Thomas J. and Goedecker, Stefan},



journal = {Phys. Rev. B},


pages = {14101},
title = {{Low-density silicon allotropes for photovoltaic applications}},

volume = {92},
year = {2015}
}
@article{savi-epst70gca,
author = {Savin, Samuel M and Epstein, Samuel},



journal = {Geochimica et Cosmochimica Acta},


pages = {25--42},
publisher = {Elsevier},
title = {{The oxygen and hydrogen isotope geochemistry of clay minerals}},

volume = {34},
year = {1970}
}
@article{ricc-cicc09molp,
author = {Ricci, Andrea and Ciccotti, Giovanni},



journal = {Mol. Phys.},


pages = {1927--1931},
publisher = {Taylor {\&} Francis},
title = {{Algorithms for Brownian dynamics}},

volume = {101},
year = {2003}
}
@article{agar-dell15jcp,
author = {Agarwal, Animesh and {Delle Site}, Luigi},


journal = {J. Chem. Phys.},


pages = {094102},
title = {{Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water}},

volume = {143},
year = {2015}
}
@article{gonz-abas11jcp,
abstract = {A new flexible water model, TIP4P/2005f, is developed. The idea was to add intramolecular degrees of freedom to the successful rigid model TIP4P/2005 in order to try to improve the predictions for some properties, and to enable the calculation of new ones. The new model incorporates flexibility by means of a Morse potential for the bond stretching and a harmonic term for the angle bending. The parameters have been fitted to account for the peaks of the infrared spectrum of liquid water and to produce an averaged geometry close to that of TIP4P/2005. As for the intermolecular interactions, only a small change in the $\sigma$ parameter of the Lennard-Jones potential has been introduced. The overall predictions are very close to those of TIP4P/2005. This ensures that the new model may be used with the same confidence as its predecessor in studies where a flexible model is advisable.},
author = {Gonz{\'{a}}lez, Miguel a and Abascal, Jos{\'{e}} L F},



journal = {J. Chem. Phys.},


pages = {224516},
pmid = {22168712},
title = {{A flexible model for water based on TIP4P/2005.}},

volume = {135},
year = {2011}
}
@article{fabe+17jctc,
author = {Faber, Felix A. and Hutchison, Luke and Huang, Bing and Gilmer, Justin and Schoenholz, Samuel S. and Dahl, George E. and Vinyals, Oriol and Kearnes, Steven and Riley, Patrick F. and von Lilienfeld, O. Anatole},


journal = {J. Chem. Theory Comput.},


pages = {5255--5264},
title = {{Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error}},

volume = {13},
year = {2017}
}
@article{sain02csda,
abstract = {Multivariate versions of variable bandwidth kernel density estimators can lead to improvement over kernel density estimators using global bandwidth choices. These estimators are more flexible and better able to model complex (multimodal) densities. In this work, two variable bandwidth estimators are discussed: the balloon estimator which varies the smoothing matrix with each estimation point and the sample point estimator which uses a different smoothing matrix for each data point. A binned version of the sample point estimator is developed that, for various situations in low to moderate dimensions, exhibits less error (MISE) than the fixed bandwidth estimator and the balloon estimator. A practical implementation of the sample point estimator is shown through simulation and example to do a better job at reconstructing features of the underlying density than fixed bandwidth estimators. Computational details, including parameterization of the smoothing matrix, are discussed throughout. {\textcopyright} 2002 Elsevier Science B.V. All rights reserved.},
author = {Sain, Stephan R.},



journal = {Computational Statistics {\&} Data Analysis},



pages = {165--186},
pmid = {20826288},
title = {{Multivariate locally adaptive density estimation}},

volume = {39},
year = {2002}
}
@article{chen+10ieee,
abstract = {We address covariance estimation in the sense of minimum mean-squared error (MMSE) when the samples are Gaussian distributed. Specifically, we consider shrinkage methods which are suitable for high dimensional problems with a small number of samples (large p small n). First, we improve on the Ledoit-Wolf (LW) method by conditioning on a sufficient statistic. By the Rao-Blackwell theorem, this yields a new estimator called RBLW, whose mean-squared error dominates that of LW for Gaussian variables. Second, to further reduce the estimation error, we propose an iterative approach which approximates the clairvoyant shrinkage estimator. Convergence of this iterative method is established and a closed form expression for the limit is determined, which is referred to as the oracle approximating shrinkage (OAS) estimator. Both RBLW and OAS estimators have simple expressions and are easily implemented. Although the two methods are developed from different perspectives, their structure is identical up to specified constants. The RBLW estimator provably dominates the LW method for Gaussian samples. Numerical simulations demonstrate that the OAS approach can perform even better than RBLW, especially when n is much less than p . We also demonstrate the performance of these techniques in the context of adaptive beamforming.},
archivePrefix = {arXiv},
arxivId = {0907.4698},
author = {Chen, Yilun and Wiesel, Ami and Eldar, Yonina C. and Hero, Alfred O.},



isbn = {1053-587X},

journal = {IEEE Transactions on Signal Processing},


pages = {5016--5029},
title = {{Shrinkage algorithms for MMSE covariance estimation}},
volume = {58},
year = {2010}
}
@article{fent60iret,
author = {Fenton, L and Fentont, Lawrence F},

journal = {IRE Trans. Comm. Sys.},

pages = {57--67},
publisher = {IEEE},
title = {{The sum of log-normal probability distributions in scatter transmission systems}},
volume = {8},
year = {1960}
}
@article{jose+12jcp,
abstract = {An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations.},
author = {Jose, K. V Jovan and Artrith, Nongnuch and Behler, Jörg},



journal = {J. Chem. Phys.},

pages = {194111},
pmid = {22612084},
title = {{Construction of high-dimensional neural network potentials using environment-dependent atom pairs}},

volume = {136},
year = {2012}
}
@article{louw-baer06cpl,
author = {Louwerse, Manuel J and Baerends, Evert Jan},

journal = {Chem. Phys. Lett.},

pages = {138--141},
title = {{Calculation of pressure in case of periodic boundary conditions}},
volume = {421},
year = {2006}
}
@article{mcko+13jpca,
abstract = {This paper explores the dynamics of a highly rotationally and vibrationally excited radical, CD2CD2OH. The radical is produced from the 193 nm photodissociation of 2-bromoethanol-d4, so it is imparted with high angular momentum and high vibrational energy and subsequently dissociates to several product channels. This paper focuses on characterizing its angular momentum and modeling its effect on the product channels, including the HOD + vinyl-d3 product channel resulting from a frustrated dissociation of the radical originally en route to OH + ethene-d4 that instead results in D atom abstraction. Our impulsive model of the initial photodissociation shows that, for some cases, upward of 200 au of angular momentum is imparted, which greatly affects the dynamics of the competing product channels. Using a permutationally invariant potential energy surface and quasiclassical trajectories, we simulated the dissociation dynamics of CD2CD2OH and compared these results to those of Kamarchik et al. (J. Phys. Chem. Lett. 2010, 1, 3058-3065), who studied the dynamics of CH2CH2OH with zero angular momentum. We found that the recoil translational energy distribution for radicals that dissociated to OH + C2D4 matched experiment closely only when high angular momentum of the initial radical was explicitly included in the trajectory calculations. Similarly, the rate constant for dissociation changes when rotational energy was added to the vibrational energy in the initial conditions. Lastly, we applied the sketch-map dimensionality reduction technique to analyze mechanistic information leading to the vinyl + water product channel. Projecting the ab initio intrinsic reaction coordinates onto the lower dimensional space identified with sketch map offers new insight into the dynamics when one looks at the simulated trajectories in the lower dimensional space. Further analysis shows that the transition path resembles a frustrated dissociation of the OH + ethene radical adduct, followed instead by branching to vinyl + water when the leaving OH group encounters a nearby D atom on the ethene moiety. This characterization is in accord with the one made previously. We show that the transition path bifurcation between the two similar channels occurs at carbon-oxygen distances and oxygen-abstracted deuterium distances of 2-2.5 {\{}{\AA}{\}} controlled by the C-O-D bond angle with large angles preferentially branching to the water plus vinyl product state. The experimental branching ratios were not reproduced by theory, however, due partly to the insufficient quality of the fitted potential surface. We also have evidence of a minor product channel, HD + vinoxy-d3, from our molecular dynamics simulations that allows us to assign the HD signal in prior experimental work.},
author = {McKown, Benjamin G and Ceriotti, Michele and Womack, Caroline C and Kamarchik, Eugene and Butler, Laurie J and Bowman, Joel M},



journal = {J. Phys. Chem.. A},


pages = {10951--10963},
pmid = {24124756},
title = {{Effects of high angular momentum on the unimolecular dissociation of CD2CD2OH: theory and comparisons with experiment.}},

volume = {117},
year = {2013}
}
@article{khal+11nmat,
abstract = {Graphite and diamond have comparable free energies, yet forming diamond from graphite in the absence of a catalyst requires pressures that are significantly higher than those at equilibrium coexistence. At lower temperatures, the formation of the metastable hexagonal polymorph of diamond is favoured instead of the more stable cubic diamond. These phenomena cannot be explained by the concerted mechanism suggested in previous theoretical studies. Using an ab initio quality neural-network potential, we carried out a large-scale study of the graphite-to-diamond transition assuming that it occurs through nucleation. The nucleation mechanism accounts for the observed phenomenology and reveals its microscopic origins. We demonstrate that the large lattice distortions that accompany the formation of diamond nuclei inhibit the phase transition at low pressure, and direct it towards the hexagonal diamond phase at higher pressure. The proposed nucleation mechanism should improve our understanding of structural transformations in a wide range of carbon-based materials.},
author = {Khaliullin, Rustam Z and Eshet, Hagai and K{\"{u}}hne, Thomas D and Behler, J{\"{o}}rg and Parrinello, Michele},



journal = {Nature materials},


pages = {693--7},
pmid = {21785417},
publisher = {Nature Publishing Group},
title = {{Nucleation mechanism for the direct graphite-to-diamond phase transition.}},

volume = {10},
year = {2011}
}
@article{li+93prb,
author = {Li, X P and Nunes, R W and Vanderbilt, D},

journal = {Phys. Rev. B},

pages = {10891--10894},
publisher = {APS},
title = {{Density-matrix electronic-structure method with linear system-size scaling}},
volume = {47},
year = {1993}
}
@article{chin97pla,
author = {Chin, Siu A.},

journal = {Phys. Lett. A},


pages = {344--348},
title = {{Symplectic integrators from composite operator factorizations}},
volume = {226},
year = {1997}
}
@article{mann-hall03prl,
author = {Mann, David and Halls, Mathew},



journal = {Phys. Rev. Lett.},


pages = {195503},
title = {{Water Alignment and Proton Conduction inside Carbon Nanotubes}},

volume = {90},
year = {2003}
}
@article{ceri+13pnas,
abstract = {The hydrogen bond (HB) is central to our understanding of the properties of water. However, despite intense theoretical and experimental study, it continues to hold some surprises. Here, we show from an analysis of ab initio simulations that take proper account of nuclear quantum effects that the hydrogen-bonded protons in liquid water experience significant excursions in the direction of the acceptor oxygen atoms. This generates a small but nonnegligible fraction of transient autoprotolysis events that are not seen in simulations with classical nuclei. These events are associated with major rearrangements of the electronic density, as revealed by an analysis of the computed Wannier centers and (1)H chemical shifts. We also show that the quantum fluctuations exhibit significant correlations across neighboring HBs, consistent with an ephemeral shuttling of protons along water wires. We end by suggesting possible implications for our understanding of how perturbations (solvated ions, interfaces, and confinement) might affect the HB network in water.},
author = {Ceriotti, Michele and Cuny, J{\'{e}}r{\^{o}}me and Parrinello, Michele and Manolopoulos, David E},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {15591--6},
pmid = {24014589},
title = {{Nuclear quantum effects and hydrogen bond fluctuations in water.}},

volume = {110},
year = {2013}
}
@article{zen+15jcp,
abstract = {Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.},
archivePrefix = {arXiv},
arxivId = {1412.2936},
author = {Zen, Andrea and Luo, Ye and Mazzola, Guglielmo and Guidoni, Leonardo and Sorella, Sandro},




journal = {J. Chem. Phys.},


pages = {144111},
pmid = {25877566},
title = {{Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo}},

volume = {142},
year = {2015}
}
@article{ande+98am,
author = {Andersen, S.J. and Zandbergen, H.W. and Jansen, J. and Tr{\AE}holt, C. and Tundal, U. and Reiso, O.},



journal = {Acta Materialia},


pages = {3283--3298},
title = {{The crystal structure of the $\beta$″ phase in Al–Mg–Si alloys}},

volume = {46},
year = {1998}
}
@article{schu+17ncomm,
author = {Sch{\"{u}}tt, Kristof T. and Arbabzadah, Farhad and Chmiela, Stefan and M{\"{u}}ller, Klaus R. and Tkatchenko, Alexandre},



journal = {Nature Comm.},

pages = {13890},
title = {{Quantum-chemical insights from deep tensor neural networks}},

volume = {8},
year = {2017}
}
@article{kauf-baum89jpb,
abstract = {Single-centre partial-wave expansions are derived for several Gaussian-type functions: simple, solid harmonic and spherical Gaussians. Single-centre expansions for the most commonly used Cartesian Gaussians are obtained by expanding these functions in spherical Gaussians. Transformation matrices for expanding Cartesian in spherical Gaussians are given for s, p, d and f type functions. The single-centre expansions are used to calculate the partial-wave decomposition of overlap integrals for all Gaussian-type functions specified. The formulae given are suitable for fast numerical computation and were tested with programs developed for this purpose.},
author = {Kaufmann, K and Baumeister, W},



journal = {Journal of Physics B: Atomic, Molecular and Optical Physics},


pages = {1--12},
title = {{Single-centre expansion of Gaussian basis functions and the angular decomposition of their overlap integrals}},

volume = {22},
year = {1989}
}
@article{bron+93surf,
author = {Bronikowski, M J and Wang, Y and McEllistrem, M T and Hamers, R J},

journal = {Surf. Sci.},
pages = {50},
title = {{Adsorption and dissociation of disilane on Si(001) studied by STM}},
volume = {298},
year = {1993}
}
@article{sade+13jcp,
abstract = {In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint vectors satisfies the properties of a metric and can therefore safely be used to measure dissimilarities between configurations in the high dimensional configuration space. In particular we show that these metrics are a perfect and computationally cheap replacement for the root-mean-square distance (RMSD) when one has to decide whether two noise contaminated configurations are identical or not. We introduce a Monte Carlo approach to obtain the global minimum of the RMSD between configurations, which is obtained from a global minimization over all translations, rotations, and permutations of atomic indices.},
author = {Sadeghi, Ali and Ghasemi, S Alireza and Schaefer, Bastian and Mohr, Stephan and Lill, Markus A and Goedecker, Stefan},



journal = {J. Chem. Phys.},



pages = {184118},
pmid = {24320265},
title = {{Metrics for measuring distances in configuration spaces.}},

volume = {139},
year = {2013}
}
@article{chen-ceri18prb,
abstract = {The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial. As a consequence, all too often the potential energy of the system is used as a proxy, overlooking entropic and anharmonic effects. Here we discuss a combination of different thermodynamic integration routes to obtain the absolute Gibbs free energy of a solid system starting from a harmonic reference state. This approach enables the direct comparison between the free energy of different structures, circumventing the need to sample the transition paths between them. We showcase this thermodynamic integration scheme by computing the Gibbs free energy associated with a vacancy in BCC iron, and the intrinsic stacking fault free energy of nickel. These examples highlight the pitfalls of estimating the free energy of crystallographic defects only using the minimum potential energy, which overestimates the vacancy free energy by 60{\%} and the stacking-fault energy by almost 300{\%} at temperatures close to the melting point.},
archivePrefix = {arXiv},
arxivId = {1710.02815},
author = {Cheng, Bingqing and Ceriotti, Michele},




journal = {Phys. Rev. B},



pages = {054102},
publisher = {American Physical Society},
title = {{Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids}},

volume = {97},
year = {2018}
}
@article{liu+14jacs,
abstract = {Coupled intramolecular and intermolecular vibrational quantum dynamics, using an ab initio potential energy surface, successfully describes the subpicosecond relaxation of the OD and OH stretch fundamental and first overtone of dilute HOD in ice Ih. The calculations indicate that more than one intermolecular mode along with the three intramolecular modes is needed to describe the relaxation, in contrast to a recent study using a phenomenological potential in just two degrees of freedom. Detailed time-dependent relaxation pathways from 6-mode calculations are also given.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Liu, Hanchao and Wang, Yimin and Bowman, Joel M.},



isbn = {1520-5126 (Electronic)$\backslash$r0002-7863 (Linking)},

journal = {J. Chem. Am. Soc. },


pages = {5888--5891},
pmid = {24717075},
title = {{Ab Initio Deconstruction of the Vibrational Relaxation Pathways of Dilute HOD in Ice Ih}},

volume = {136},
year = {2014}
}
@article{gall-piet13jcp,
abstract = {We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.},
author = {Gallet, GA A and Pietrucci, Fabio},



journal = {J. Chem. Phys.},


pages = {74101},
pmid = {23968066},
title = {{Structural cluster analysis of chemical reactions in solution}},

volume = {139},
year = {2013}
}
@article{delb+12jctc,
abstract = {A novel algorithm, based on a hybrid Gaussian and plane waves (GPW) approach, is developed for the canonical second-order M?ller?Plesset perturbation energy (MP2) of finite and extended systems. The key aspect of the method is that the electron repulsion integrals (ia|?{\$}\sigma{\$}) are computed by direct integration between the products of Gaussian basis functions ?{\$}\sigma{\$} and the electrostatic potential arising from a given occupied-virtual pair density ia. The electrostatic potential is obtained in a plane waves basis set after solving the Poisson equation in Fourier space. In particular, for condensed phase systems, this scheme is highly efficient. Furthermore, our implementation has low memory requirements and displays excellent parallel scalability up to 100?000 processes. In this way, canonical MP2 calculations for condensed phase systems containing hundreds of atoms or more than 5000 basis functions can be performed within minutes, while systems up to 1000 atoms and 10?000 basis functions remain feasible. Solid LiH has been employed as a benchmark to study basis set and system size convergence. Lattice constants and cohesive energies of various molecular crystals have been studied with MP2 and double-hybrid functionals. A novel algorithm, based on a hybrid Gaussian and plane waves (GPW) approach, is developed for the canonical second-order M?ller?Plesset perturbation energy (MP2) of finite and extended systems. The key aspect of the method is that the electron repulsion integrals (ia|?{\$}\sigma{\$}) are computed by direct integration between the products of Gaussian basis functions ?{\$}\sigma{\$} and the electrostatic potential arising from a given occupied-virtual pair density ia. The electrostatic potential is obtained in a plane waves basis set after solving the Poisson equation in Fourier space. In particular, for condensed phase systems, this scheme is highly efficient. Furthermore, our implementation has low memory requirements and displays excellent parallel scalability up to 100?000 processes. In this way, canonical MP2 calculations for condensed phase systems containing hundreds of atoms or more than 5000 basis functions can be performed within minutes, while systems up to 1000 atoms and 10?000 basis functions remain feasible. Solid LiH has been employed as a benchmark to study basis set and system size convergence. Lattice constants and cohesive energies of various molecular crystals have been studied with MP2 and double-hybrid functionals.},
author = {{Del Ben}, Mauro and Hutter, J{\"{u}}rg and Vandevondele, Joost},


isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},
pages = {4177--4188},
title = {{Second-order m{\{}{\o}{\}}ller-plesset perturbation theory in the condensed phase: An efficient and massively parallel gaussian and plane waves approach}},
volume = {8},
year = {2012}
}
@book{wale03book,
author = {Wales, David},
publisher = {Cambridge University Press},
title = {{Energy landscapes: Applications to clusters, biomolecules and glasses}},
year = {2003}
}
@article{rome+01jcp,
abstract = {Compton scattering is an experimental technique which probes the electron momentum density. Here we present a method which allows the calculation of the Compton profile using the formalism of the maximally localized Wannier functions. We applied this method to analyze recent experimental measurements of the anisotropy component of the Compton profile which have been interpreted as the signature of the partial covalent character of the hydrogen bond in ice I-h. We are able to reproduce well the experimental results, however we do not find evidence of a covalent nature of the hydrogen bond. In fact our analysis shows that, although the wave functions in ice I-h have a quantum-mechanical, multicenter character, this gives rise to an antibonding, repulsive interaction between neighboring water molecules. Application to our technique to other, nonhydrogen bonded systems, and analysis of the corresponding Compton scattering profile anisotropy, gives further support to our interpretation. (C) 2001 American Institute of Physics.},
author = {Romero, Aldo H. and Silvestrelli, Pier Luigi and Parrinello, Michele},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

mendeley-tags = {electron compton scattering,hydrogen bond},

pages = {115--123},
title = {{Compton scattering and the character of the hydrogen bond in ice Ih}},
volume = {115},
year = {2001}
}
@article{mart02jcp,
author = {Martens, Craig C.},



journal = {J. Chem. Phys.},

pages = {2516--2528},
publisher = {AIP},
title = {{Qualitative dynamics of generalized Langevin equations and the theory of chemical reaction rates}},

volume = {116},
year = {2002}
}
@article{Lim2006,
author = {Lim, Freda and Tok, E. and Kang, H.},



journal = {Phys. Rev. B},


pages = {205333},
title = {{Decomposition of SiH3 to SiH2 on Si(100)-(2×1)}},

volume = {74},
year = {2006}
}
@article{Pilkington1996,
author = {Pilkington, J.R. R and Baden, S.B. B and John, R and Scott, B},



journal = {IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS},


pages = {288--300},
publisher = {IEEE Computer Society},
title = {{Dynamic partitioning of non-uniform structured workloads with spacefilling curves}},

volume = {7},
year = {1996}
}
@article{prak+11jctc,
author = {Prakash, Meher K. and Barducci, Alessandro and Parrinello, Michele},



journal = {J. Chem. Theory Comput.},


pages = {2025--2027},
title = {{Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations}},

volume = {7},
year = {2011}
}
@article{casa+16nc,
author = {Casati, Nicola and Kleppe, Annette and Jephcoat, Andrew P and Macchi, Piero},

journal = {Nature Comm.},

pages = {10901},
publisher = {Springer Nature},
title = {{Putting pressure on aromaticity along with in situ experimental electron density of a molecular crystal}},

volume = {7},
year = {2016}
}
@article{hong-chou98prb,
author = {Hong, S and Chou, M Y},

journal = {Phys. Rev. B},

pages = {13363--13366},
publisher = {APS},
title = {{Role of hydrogen in SiH2 adsorption on Si(100)}},
volume = {58},
year = {1998}
}
@article{jang-voth99jcp,
author = {Jang, Seogjoo and Voth, Gregory a.},



journal = {J. Chem. Phys.},

pages = {2371},
title = {{A derivation of centroid molecular dynamics and other approximate time evolution methods for path integral centroid variables}},

volume = {111},
year = {1999}
}
@article{bloc+90prl,
author = {Bl{\"{o}}chl, Peter and {Van de Walle}, C. and Pantelides, S.},



journal = {Phys. Rev. Lett.},


pages = {1401--1404},
title = {{First-principles calculations of diffusion coefficients: Hydrogen in silicon}},

volume = {64},
year = {1990}
}
@article{mich+13jpcc,
author = {Michel, Kyle Jay and Zhang, Yongsheng and Wolverton, C},



journal = {J. Phys. Chem. C},


pages = {19295},
title = {{Fast Mass Transport Kinetics in B 20 H 16 : A High-Capacity Hydrogen Storage Material}},

year = {2013}
}
@article{glie+17prb,
abstract = {We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian Process (GP) Regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group SO(d) for the relevant dimensionality d. Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe and Si crystalline systems.},
archivePrefix = {arXiv},
arxivId = {1611.03877},
author = {Glielmo, Aldo and Sollich, Peter and {De Vita}, Alessandro},




journal = {Phys. Rev. B},


pages = {214302},
title = {{Accurate interatomic force fields via machine learning with covariant kernels}},

volume = {95},
year = {2017}
}
@article{pred04pre,
author = {Predescu, Cristian},


journal = {Phys. Rev. E},


pages = {066705},
title = {{Reconstruction of thermally symmetrized quantum autocorrelation functions from imaginary-time data}},

volume = {70},
year = {2004}
}
@article{vand97cossms,
author = {Vanderbilt, David},

journal = {Current Opinion in Solid State and Materials Science},

pages = {701--705},
title = {{First-principles based modelling of ferroelectrics}},
volume = {2},
year = {1997}
}
@article{damm+09prl,
author = {Dammak, Hichem and Chalopin, Yann and Laroche, Marine and Hayoun, Marc and Greffet, Jean-Jacques},

journal = {Phys. Rev. Lett.},

pages = {190601},
publisher = {APS},
title = {{Quantum Thermal Bath for Molecular Dynamics Simulation}},
volume = {103},
year = {2009}
}
@article{mora+10pnas,
abstract = {Using quantum simulation techniques based on either density functional theory or quantum Monte Carlo, we find clear evidence of a first-order transition in liquid hydrogen, between a low conductivity molecular state and a high conductivity atomic state. Using the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures near 2,000 K and pressures near 120 GPa. Furthermore, we have determined the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line. The melting line crosses the metalization line at 700 K and 220 GPa using density functional energetics and at 550 K and 290 GPa using quantum Monte Carlo energetics.},
author = {Morales, Miguel a and Pierleoni, Carlo and Schwegler, Eric and Ceperley, D M},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {12799--12803},
pmid = {20566888},
title = {{Evidence for a first-order liquid-liquid transition in high-pressure hydrogen from ab initio simulations.}},

volume = {107},
year = {2010}
}
@article{rapp+03mmta,
author = {Rappaz, M and Jacot, A and Boettinger, W. J.},



journal = {Metallurgical and Materials Transactions A},


pages = {467--479},
title = {{Last-stage solidification of alloys: Theoretical model of dendrite-arm and grain coalescence}},

volume = {34},
year = {2003}
}
@article{cao-voth93jcp,
author = {Cao, Jianshu and Voth, Gregory A},

journal = {J. Chem. Phys.},

pages = {10070--10073},
publisher = {AIP},
title = {{A new perspective on quantum time correlation functions}},
volume = {99},
year = {1993}
}
@article{bai-li06jcp,
abstract = {We present a simple approach to calculate the solid-liquid interfacial free energy. This new method is based on the classical nucleation theory. Using the molecular dynamics simulation, we employ spherical crystal nuclei embedded in the supercooled liquids to create an ideal model of a homogeneous nucleation. The interfacial free energy is extracted by fitting the relation between the critical nucleus size and the reciprocal of the critical undercooling temperature. The orientationally averaged interfacial free energy is found to be 0.302+/-0.002 (in standard LJ unit). The temperature dependence of the interfacial free energy is also obtained in this work. We find that the interfacial free energy increases slightly with increasing temperature. The positive temperature coefficient of the interfacial free energy is in qualitative agreement with Spaepen's analysis [Solid State Phys. 47, FS181 (1994)] and Turnbull's empirical estimation [J. Appl. Phys. 21, 1022 (1950)].},
author = {Bai, Xian-Ming and Li, Mo},



journal = {J. Chem. Phys.},


pages = {124707},
pmid = {16599718},
title = {{Calculation of solid-liquid interfacial free energy: a classical nucleation theory based approach.}},

volume = {124},
year = {2006}
}
@article{behl11pccp,
abstract = {The accuracy of the results obtained in molecular dynamics or Monte Carlo simulations crucially depends on a reliable description of the atomic interactions. A large variety of efficient potentials has been proposed in the literature, but often the optimum functional form is difficult to find and strongly depends on the particular system. In recent years, artificial neural networks (NN) have become a promising new method to construct potentials for a wide range of systems. They offer a number of advantages: they are very general and applicable to systems as different as small molecules, semiconductors and metals; they are numerically very accurate and fast to evaluate; and they can be constructed using any electronic structure method. Significant progress has been made in recent years and a number of successful applications demonstrate the capabilities of neural network potentials. In this Perspective, the current status of NN potentials is reviewed, and their advantages and limitations are discussed.},
author = {Behler, J{\"{o}}rg},



journal = {PCCP},



pages = {17930--55},
pmid = {21915403},
title = {{Neural network potential-energy surfaces in chemistry: a tool for large-scale simulations.}},

volume = {13},
year = {2011}
}
@article{fox+88pra,
author = {Fox, Ronald F and Gatland, Ian R and Roy, Rajarshi and Vemuri, Gautam},


journal = {Phys. Rev. A},

pages = {5938--5940},
publisher = {American Physical Society},
title = {{Fast, accurate algorithm for numerical simulation of exponentially correlated colored noise}},
volume = {38},
year = {1988}
}
@article{baro+01rmp,
author = {Baroni, S and {De Gironcoli}, S and {Dal Corso}, A and Giannozzi, P},
journal = {Rev. Mod. Phys.},

pages = {515},
publisher = {American Physical Society},
title = {{Phonons and related crystal properties from density-functional perturbation theory}},
volume = {73},
year = {2001}
}
@article{past+91pa,
author = {Pastore, G. and Smargiassi, E. and Buda, F.},



journal = {Phys. Rev. A},

pages = {6334--6347},
pmid = {9905763},
publisher = {American Physical Society},
title = {{Theory of ab initio molecular-dynamics calculations}},
volume = {44},
year = {1991}
}
@article{kuma03jom,
author = {Kumar, Sanjay},



journal = {JOM},


pages = {43--47},
title = {{Selective laser sintering: A qualitative and objective approach}},

volume = {55},
year = {2003}
}
@article{stre+06prl,
author = {Streitz, F H and Glosli, J N and Patel, M V},

journal = {Phys. Rev. Lett.},

pages = {225701},
publisher = {APS},
title = {{Beyond Finite-Size Scaling in Solidification Simulations}},
volume = {96},
year = {2006}
}
@incollection{cutu13nips,
abstract = {Optimal transportation distances are a fundamental family of parameterized distances for histograms. Despite their appealing theoretical properties, excellent performance in retrieval tasks and intuitive formulation, their computation involves the resolution of a linear program whose cost is prohibitive whenever the histograms' dimension exceeds a few hundreds. We propose in this work a new family of optimal transportation distances that look at transportation problems from a maximum-entropy perspective. We smooth the classical optimal transportation problem with an entropic regularization term, and show that the resulting optimum is also a distance which can be computed through Sinkhorn-Knopp's matrix scaling algorithm at a speed that is several orders of magnitude faster than that of transportation solvers. We also report improved performance over classical optimal transportation distances on the MNIST benchmark problem.},
archivePrefix = {arXiv},
arxivId = {arXiv:1306.0895v1},
author = {Cuturi, Marco},
booktitle = {Advances in Neural Information Processing Systems 26},
editor = {Burges, C J C and Bottou, L and Welling, M and Ghahramani, Z and Weinberger, K Q},



pages = {2292--2300},
publisher = {Curran Associates, Inc.},
title = {{Sinkhorn Distances: Lightspeed Computation of Optimal Transport}},

year = {2013}
}
@article{casa+14jcp,
author = {Casassa, S. and Baima, J. and Mahmoud, A. and Kirtman, B.},



journal = {J. Chem. Phys.},

pages = {224702},
title = {{Ab initio investigation of electronic and vibrational contributions to linear and nonlinear dielectric properties of ice}},

volume = {140},
year = {2014}
}
@article{gate+90jcp2,
author = {Gates, S M and Greenlief, C M and Beach, D B and Holbert, P A},


journal = {J. Chem. Phys.},

pages = {3144--3153},
publisher = {AIP},
title = {{Decomposition of silane on Si(111)-(7{\{}$\backslash$times{\}}7) and Si(100)-(2{\{}$\backslash$times{\}}1) surfaces below 500{\{}{\^{}}$\backslash$circ{\}}C}},
volume = {92},
year = {1990}
}
@article{chen+02nat,
author = {Chen, P and Xiong, Z and Luo, J and Lin, J and Tan, K L},

journal = {Nature},

pages = {302--304},
publisher = {Nature Publishing Group},
title = {{Interaction of hydrogen with metal nitrides and imides}},
volume = {420},
year = {2002}
}
@article{owen+97ss,
author = {Owen, J.H.G. H G and Miki, K. and Bowler, D.R. R and Goringe, C.M. M and Goldfarb, I. and Briggs, G.A.D. A D},



journal = {Surf. Sci.},



pages = {79--90},
publisher = {Elsevier Science},
title = {{Gas-source growth of group IV semiconductors: I. Si (001) nucleation mechanisms}},

volume = {394},
year = {1997}
}
@article{niel51rmp,
author = {Nielsen, Harald},



journal = {Rev. Mod. Phys.},


pages = {90--136},
title = {{The Vibration-Rotation Energies of Molecules}},

volume = {23},
year = {1951}
}
@article{ceri+14cpc,
author = {Ceriotti, Michele and More, Joshua and Manolopoulos, David E.},



journal = {Comp. Phys. Comm.},

pages = {1019--1026},
publisher = {Elsevier B.V.},
title = {{i-PI: A Python interface for ab initio path integral molecular dynamics simulations}},

volume = {185},
year = {2014}
}
@article{pogs+04msea,
author = {Pogson, S. and Fox, P. and O'Neill, W. and Sutcliffe, C.J. J},



journal = {Materials Science and Engineering: A},

mendeley-tags = {additive manufacturing},


pages = {453--459},
title = {{The direct metal laser remelting of copper and tool steel powders}},

volume = {386},
year = {2004}
}
@article{morr-song03jcp,
author = {Morris, James R. and Song, Xueyu},



journal = {J. Chem. Phys.},

pages = {3920},
title = {{The anisotropic free energy of the Lennard-Jones crystal-melt interface}},

volume = {119},
year = {2003}
}
@article{kuti82prl,
author = {Kuti, Julius},



journal = {Phys. Rev. Lett.},


pages = {183--186},
title = {{Stochastic Method for the Numerical Study of Lattice Fermions}},

volume = {49},
year = {1982}
}
@article{doll68pr,
author = {Dolling, G and Smith, HG G and Nicklow, RM M and Vijayaraghavan, P R and Wilkinson, M K},

journal = {Phys. Rev.},

pages = {970--979},
publisher = {American Physical Society},
title = {{Lattice dynamics of lithium fluoride}},

volume = {168},
year = {1968}
}
@article{buss-parr08cpc,
archivePrefix = {arXiv},
arxivId = {arXiv:0803.4397v1},
author = {Bussi, Giovanni and Parrinello, Michele},


journal = {Comp. Phys. Comm.},

pages = {26},
title = {{Stochastic thermostats: comparison of local and global schemes}},
volume = {179},
year = {2008}
}
@article{haze99jspi,
abstract = {The problem of selecting the bandwidth for optimal kernel density estimation at a point is considered. A class of local bandwidth selectors which minimize smoothed bootstrap estimates of mean-squared error in density estimation is introduced. It is proved that the bandwidth selectors in the class achieve optimal relative rates of convergence, dependent upon the local smoothness of the target density. Practical implementation of the bandwidth selection methodology is discussed. The use of Gaussian-based kernels to facilitate computation of the smoothed bootstrap estimate of mean-squared error is proposed. The performance of the bandwidth selectors is investigated empirically.},
author = {Hazelton, Martin L.},



journal = {Journal of Statistical Planning and Inference},



pages = {37--50},
title = {{An optimal local bandwidth selector for kernel density estimation}},

volume = {77},
year = {1999}
}
@article{ravi-wolv04am,
abstract = {Al-Mg-Si-(Cu) alloys form the basis of a wide variety of commercial precipitation-hardened alloys, and the observed precipitation sequence in these alloys is complex and involves a wide variety of metastable phases (e.g. GP zones, ?????, U1, U2, B???, ?????). Calculations of metastable phase equilibria in these alloys are virtually nonexistent due to the lack of quantitative information on the thermodynamics of the precipitate phases. We have undertaken an extensive, systematic first-principles study of energetics of all the reported precipitate phases of Al-Mg-Si-(Cu) alloys, using density functional-based calculations in both the local density and generalized gradient approximations. Our calculations help clarify the energetics of the metastable precipitate phases, and in certain cases, provide insight into the compositional changes of precipitates during aging. In addition to energetics, we also examine the relative volumes of the various phases, and discuss cases of significant deviation from that of the solid solution. ?? 2004 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.},
author = {Ravi, C. and Wolverton, C.},


isbn = {1359-6454},

journal = {Acta Materialia},



pages = {4213--4227},
title = {{First-principles study of crystal structure and stability of Al/Mg/Si/(Cu) precipitates}},

volume = {52},
year = {2004}
}
@book{chen+08book,
address = {Berlin, Heidelberg},

editor = {Chen, C. and H{\"{a}}rdle, W. and Unwin, A.},
isbn = {978-3-540-33036-3},
publisher = {Springer Berlin Heidelberg},
series = {Springer Handbooks Comp.Statistics},
title = {{Handbook of Data Visualization}},

year = {2008}
}
@article{adel76jcp,
author = {Adelman, S. A.},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pages = {124--130},
publisher = {AIP},
title = {{Fokker--Planck equations for simple non-Markovian systems}},
volume = {64},
year = {1976}
}
@article{ross+02jcp,
author = {Rosso, Lula and Min{\'{a}}ry, Peter and Zhu, Zhongwei and Tuckerman, Mark E},
journal = {J. Chem. Phys.},

pages = {4389},
title = {{On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles}},
volume = {116},
year = {2002}
}
@article{liu-wu13jcp,
author = {Liu, Yu and Wu, Jianzhong},



journal = {J. Chem. Phys.},

pages = {41103},
title = {{Communication: Long-range angular correlations in liquid water}},

volume = {139},
year = {2013}
}
@misc{CPMD,
annote = {From Duplicate 1 (CPMD - )

{\{}C{\}}opyright {\{}IBM{\}} {\{}Corp{\}} 1990-2006, {\{}C{\}}opyright {\{}MPI{\}} f{\{}{\"{u}}{\}}r {\{}Festk{\{}{\"{o}}{\}}rperforschung{\}} {\{}Stuttgart{\}} 1997-2001

From Duplicate 2 (CPMD - )

{\{}{\{}{\}}C{\{}{\}}{\}}opyright {\{}{\{}{\}}IBM{\{}{\}}{\}} {\{}{\{}{\}}Corp{\{}{\}}{\}} 1990-2006, {\{}{\{}{\}}C{\{}{\}}{\}}opyright {\{}{\{}{\}}MPI{\{}{\}}{\}} f{\{}{\{}{\}}{\{}{\"{u}}{\}}{\{}{\}}{\}}r {\{}{\{}{\}}Festk{\{}{\{}{\}}{\{}{\"{o}}{\}}{\{}{\}}{\}}rperforschung{\{}{\}}{\}} {\{}{\{}{\}}Stuttgart{\{}{\}}{\}} 1997-2001},
howpublished = {http://www.cpmd.org/},
title = {{CPMD}}
}
@article{kaat+98jcp,
author = {Kaatz, Philip and Donley, Elizabeth A and Shelton, David P},



journal = {J. Chem. Phys.},


pages = {849--856},
title = {{A comparison of molecular hyperpolarizabilities from gas and liquid phase measurements}},

volume = {108},
year = {1998}
}
@article{mei+98jpcb,
author = {Mei, Hsiao S and Tuckerman, Mark E and Sagnella, Diane E and Klein, Michael L},



journal = {J. Phys. Chem. B},


pages = {10446--10458},
title = {{Quantum Nuclear ab Initio Molecular Dynamics Study of Water Wires}},

volume = {102},
year = {1998}
}
@article{kapi+16jcp2,
abstract = {{\"{i}}¿½ 2016 Author(s). The precise description of quantum nuclear fluctuations in atomistic modelling is possible by employing path integral techniques, which involve a considerable computational overhead due to the need of simulating multiple replicas of the system. Many approaches have been suggested to reduce the required number of replicas. Among these, high-order factorizations of the Boltzmann operator are particularly attractive for high-precision and low-temperature scenarios. Unfortunately, to date, several technical challenges have prevented a widespread use of these approaches to study the nuclear quantum effects in condensed-phase systems. Here we introduce an inexpensive molecular dynamics scheme that overcomes these limitations, thus making it possible to exploit the improved convergence of high-order path integrals without having to sacrifice the stability, convenience, and flexibility of conventional second-order techniques. The capabilities of the method are demonstrated by simulations of liquid water and ice, as described by a neural-network potential fitted to the dispersion-corrected hybrid density functional theory calculations.},
author = {Kapil, Venkat and Behler, J{\"{o}}rg and Ceriotti, Michele},



journal = {J. Chem. Phys.},


pages = {234103},
title = {{High order path integrals made easy}},

volume = {145},
year = {2016}
}
@article{cepe-poll84jcp,
author = {Pollock, E. L. and Ceperley, D. M.},


journal = {Phys. Rev. B},


pages = {2555--2568},
title = {{Simulation of quantum many-body systems by path-integral methods}},

volume = {30},
year = {1984}
}
@article{voth06acr,
abstract = {The excess proton in aqueous media is critical to many aspects of chemistry, biology, and materials science. This species is at the heart of the most elementary of chemical (e.g., acid-base) and biological (e.g., bioenergetics) concepts, yet to this day, it remains mysterious, surprising, and often misunderstood. In this Account, our efforts to describe excess proton solvation and transport through computer modeling and simulation will be described. Results will be summarized for several important systems, as obtained from the multistate empirical valence bond (MS-EVB) approach, which allows for the explicit treatment of (Grotthuss) proton shuttling and charge delocalization.},
author = {Voth, Gregory a},



journal = {Acc. Chem. Res.},



pages = {143--50},
pmid = {16489734},
title = {{Computer simulation of proton solvation and transport in aqueous and biomolecular systems.}},

volume = {39},
year = {2006}
}
@article{ters-hama85prb,
author = {Tersoff, J and Hamann, D R},



journal = {Phys. Rev. B},


pages = {805--813},
publisher = {American Physical Society},
title = {{Theory of the scanning tunneling microscope}},

volume = {31},
year = {1985}
}
@article{rama+15jctc,
abstract = {Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree?Fock methods, at the computational cost of Hartree?Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10{\%} of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy. Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree?Fock methods, at the computational cost of Hartree?Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10{\%} of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.},
annote = {From Duplicate 1 (Big Data Meets Quantum Chemistry Approximations: The $\Delta$-Machine Learning Approach - Ramakrishnan, Raghunathan; Dral, Pavlo O.; Rupp, Matthias; von Lilienfeld, O. Anatole)

NULL},
archivePrefix = {arXiv},
arxivId = {arXiv:1503.04987v1},
author = {Ramakrishnan, Raghunathan and Dral, Pavlo O. and Rupp, Matthias and von Lilienfeld, O. Anatole},



isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},


pages = {2087--2096},
pmid = {26574412},
title = {{Big Data Meets Quantum Chemistry Approximations: The $\Delta$-Machine Learning Approach}},

volume = {11},
year = {2015}
}
@article{beg-niel76prb,
annote = {From Duplicate 1 ( 













































Temperature dependence of lattice dynamics of lithium 7













































- Beg, M M; Nielsen, M )















},
author = {Beg, M. M. and Nielsen, M.},

journal = {Phys. Rev. B},

pages = {4266--4273},
publisher = {American Physical Society},
title = {{Temperature dependence of lattice dynamics of lithium 7}},
volume = {14},
year = {1976}
}
@article{cere+07prb,
author = {Cereda, S and Ceriotti, M and Montalenti, F and Bernasconi, M and Miglio, L},

journal = {Phys. Rev. B},

pages = {235311},
publisher = {APS},
title = {{Quantitative estimate of H abstraction by thermal SiH{\_}3 on hydrogenated Si (001)(2$\backslash$times 1)}},
volume = {75},
year = {2007}
}
@article{stum-sche94prl,
author = {Stumpf, Roland and Scheffler, Matthias},



journal = {Phys. Rev. Lett.},

mendeley-tags = {aluminum},


pages = {254--257},
title = {{Theory of self-diffusion at and growth of Al(111)}},

volume = {72},
year = {1994}
}
@article{parr-rahm81jap,
author = {Parrinello, M.},



journal = {J. Appl. Phys.},

pages = {7182},
title = {{Polymorphic transitions in single crystals: A new molecular dynamics method}},

volume = {52},
year = {1981}
}
@article{klei-hort72jltp,
author = {Klein, ML L and Horton, GK K},

journal = {J. Low Temp. Phys.},

pages = {151--166},
title = {{The rise of self-consistent phonon theory}},

volume = {9},
year = {1972}
}
@article{shel16jcp,
author = {Shelton, David P.},



journal = {J. Chem. Phys.},

pages = {234506},
title = {{Orientation correlation and local field in liquid nitrobenzene}},

volume = {144},
year = {2016}
}
@article{vals-parr14prl,
author = {Valsson, Omar and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {90601},
title = {{Variational Approach to Enhanced Sampling and Free Energy Calculations}},

volume = {113},
year = {2014}
}
@article{habe+10pccp,
abstract = {Proton dissociation and transfer were examined with ab initio molecular dynamics (AIMD) simulations of carbon nanotubes (CNT) functionalized with perfluorosulfonic acid (-CF(2)SO(3)H) groups with 1-3 H(2)O/SO(3)H. The CNT systems were constructed both with and without fluorine atoms covalently bound to the walls to elucidate the effects of the presence of a strongly hydrophobic environment, the fluorine, on proton dissociation, hydration, and stabilization. The simulations revealed that the dissociated proton was preferentially stabilized as a hydrated hydronium cation (i.e., Eigen like) in the fluorinated CNTs but as a Zundel (H(5)O(2)(+)) cation in the nonfluorinated CNTs. This feature is attributed to the fluorine atoms forming hydrogen bonds with the water molecules coordinated to the central hydronium ion.},
author = {Habenicht, Bradley F and Paddison, Stephen J and Tuckerman, Mark E},



journal = {PCCP},



pages = {8728--32},
pmid = {20556301},
title = {{Ab initio molecular dynamics simulations investigating proton transfer in perfluorosulfonic acid functionalized carbon nanotubes.}},

volume = {12},
year = {2010}
}
@article{matu+97jcp,
author = {Matubayasi, Nobuyuki and Wakai, Chihiro and Nakahara, Masaru},



journal = {J. Chem. Phys.},

pages = {9133},
title = {{Structural study of supercritical water. I. Nuclear magnetic resonance spectroscopy}},

volume = {107},
year = {1997}
}
@misc{parr-rahm82book,
annote = {M. Parrinello and A. Rahman, in Monte Carlo Methods in Quantum Problems, edited by M. H. Kalos (Reidel, Dordrecht, 1984), page 105.},
title = {{No Title}}
}
@article{coco-degi05prb,
author = {Cococcioni, Matteo and de Gironcoli, Stefano},



journal = {Phys. Rev. B},


pages = {35105},
title = {{Linear response approach to the calculation of the effective interaction parameters in the LDA+U method}},

volume = {71},
year = {2005}
}
@article{mu-walt11jpcc,
author = {Mu, Bin and Walton, Krista S.},


journal = {J. Phys. Chem. C},


pages = {22748--22754},
title = {{Thermal Analysis and Heat Capacity Study of Metal–Organic Frameworks}},

volume = {115},
year = {2011}
}
@article{liu+91prb,
author = {Liu, Da and Wang, Renhui and Ye, Yiying},



journal = {Phys. Rev. B},

mendeley-tags = {aluminum,chromium},


pages = {4648--4652},
title = {{Stability comparison of several icosahedral structure units of Al-Cr alloys}},

volume = {43},
year = {1991}
}
@article{harp-bern70pra,
author = {Harp, G. and Berne, B.},



journal = {Phys. Rev. A},


pages = {975--996},
title = {{Time-Correlation Functions, Memory Functions, and Molecular Dynamics}},

volume = {2},
year = {1970}
}
@article{gatti+99nature,
author = {Gatti, F and Fontanelli, F and Galeazzi, M and Swift, AM and Vitale, S},


journal = {Nature},

pages = {137--139},
title = {{Detection of environmental fine structure in the low-energy $\beta$-decay spectrum of 187Re}},

volume = {397},
year = {1999}
}
@book{paul60book,
author = {Pauling, Linus},
publisher = {Cornell University Press},
title = {{The nature of the chemical bond and the structure of molecules and crystals: an introduction to modern structural chemistry}},
year = {1960}
}
@article{sawa+97prb,
author = {Sawada, H and Morikawa, Y and Terakura, K and Hamada, N},

journal = {Phys. Rev. B},

pages = {12154--12160},
publisher = {American Physical Society},
title = {{Jahn-Teller distortion and magnetic structures in LaMnO{\_}3 }},
volume = {56},
year = {1997}
}
@article{paxt-katz16am,
abstract = {We calculate the rate coefficient as a function of temperature for lattice diffusion of hydrogen and its isotopes in ??-iron; and also for trapping and escape from a vacancy. We employ Monte-Carlo and molecular dynamics methods based around the Feynman path integral formulation of the quantum partition function. We find large quantum effects including tunnelling at low temperature and recrossing at high temperature due to the finite extent of the particle probability density. In particular these serve to increase the rate of trapping and to decrease the rate of escape at low temperature. Our results also show very clear non classical isotope effects.},
author = {Paxton, Anthony T. and Katzarov, Ivaylo H.},


isbn = {13596454},

journal = {Acta Materialia},

pages = {71--76},
publisher = {Elsevier Ltd},
title = {{Quantum and isotope effects on hydrogen diffusion, trapping and escape in iron}},

volume = {103},
year = {2016}
}
@article{wern+04science,
abstract = {X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen-bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen-bonded tetrahedral structure in ice. Upon heating from 25 degrees C to 90 degrees C, 5 to 10{\%} of the molecules change from tetrahedral environments to two hydrogen-bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed.},
author = {Wernet, Ph and Nordlund, D and Bergmann, U and Cavalleri, M and Odelius, M and Ogasawara, H and N{\"{a}}slund, L a and Hirsch, T K and Ojam{\"{a}}e, L and Glatzel, P and Pettersson, L G M and Nilsson, A},



journal = {Science},



pages = {995--9},
pmid = {15060287},
title = {{The structure of the first coordination shell in liquid water.}},

volume = {304},
year = {2004}
}
@article{ceri+13jctc,
author = {Ceriotti, Michele and Tribello, Gareth A. and Parrinello, Michele},



journal = {J. Chem. Theory Comput.},


pages = {1521--1532},
title = {{Demonstrating the Transferability and the Descriptive Power of Sketch-Map}},

volume = {9},
year = {2013}
}
@article{erre+16nature,
abstract = {The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases of H2O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered sulfur hydride superconductor with a superconducting transition temperature Tc of 203 kelvin at 155 gigapascals-the highest Tc reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula H3S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice. If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H-S covalent bond and a longer H{\textperiodcentered}{\textperiodcentered}{\textperiodcentered}S hydrogen bond in a structure with R3m symmetry. X-ray diffraction experiments confirm the H3S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases. Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for H3S and by 60 gigapascals for D3S. Consequently, we predict that the phase dominates the pressure range within which the high Tc was measured. The observed pressure dependence of Tc is accurately reproduced in our calculations for the phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of H3S.},
archivePrefix = {arXiv},
arxivId = {1512.02933},
author = {Errea, Ion and Calandra, Matteo and Pickard, Chris J. and Nelson, Joseph R. and Needs, Richard J. and Li, Yinwei and Liu, Hanyu and Zhang, Yunwei and Ma, Yanming and Mauri, Francesco},




journal = {Nature},

pages = {81--84},
pmid = {27018657},
publisher = {Nature Publishing Group},
title = {{Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system}},

volume = {532},
year = {2016}
}
@article{mcke+14jcp,
abstract = {This work considers how the properties of hydrogen bonded complexes, X-H⋯Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H⋯O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4 - 3.0 {\AA}, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends.},
author = {McKenzie, Ross H and Bekker, Christiaan and Athokpam, Bijyalaxmi and Ramesh, Sai G},



journal = {J. Chem. Phys.},


pages = {174508},
pmid = {24811647},
title = {{Effect of quantum nuclear motion on hydrogen bonding.}},

volume = {140},
year = {2014}
}
@article{kreu96cm,
author = {Kreuer, Klaus-Dieter},



journal = {Chemistry of Materials},


pages = {610--641},
title = {{Proton Conductivity: Materials and Applications}},

volume = {8},
year = {1996}
}
@article{lin+11prb,
author = {Lin, L and Morrone, J A and Car, R and Parrinello, M},

journal = {Phys. Rev. B},

pages = {220302},
publisher = {APS},
title = {{Momentum distribution, vibrational dynamics, and the potential of mean force in ice}},
volume = {83},
year = {2011}
}
@article{imba+18jcp,
abstract = {Machine learning of atomic-scale properties is revolutionizing molecular modelling, making it possible to evaluate inter-atomic potentials with first-principles accuracy, at a fraction of the costs. The accuracy, speed and reliability of machine-learning potentials, however, depends strongly on the way atomic configurations are represented, i.e. the choice of descriptors used as input for the machine learning method. The raw Cartesian coordinates are typically transformed in "fingerprints", or "symmetry functions", that are designed to encode, in addition to the structure, important properties of the potential-energy surface like its invariances with respect to rotation, translation and permutation of like atoms. Here we discuss automatic protocols to select a number of fingerprints out of a large pool of candidates, based on the correlations that are intrinsic to the training data. This procedure can greatly simplify the construction of neural network potentials that strike the best balance between accuracy and computational efficiency, and has the potential to accelerate by orders of magnitude the evaluation of Gaussian Approximation Potentials based on the Smooth Overlap of Atomic Positions kernel. We present applications to the construction of neural network potentials for water and for an Al-Mg-Si alloy, and to the prediction of the formation energies of small organic molecules using Gaussian process regression.},
archivePrefix = {arXiv},
arxivId = {1804.02150},
author = {Imbalzano, Giulio and Anelli, Andrea and Giofr{\'{e}}, Daniele and Klees, Sinja and Behler, J{\"{o}}rg and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {241730},
title = {{Automatic selection of atomic fingerprints and reference configurations for machine-learning potentials}},

volume = {148},
year = {2018}
}
@article{hwan00surf,
author = {Hwang, G S},
journal = {Surf. Sci.},

pages = {L789},
publisher = {Elsevier Science},
title = {{A channel for dimer flipping on the Si(001) surface}},
volume = {465},
year = {2000}
}
@article{gree+89jvsta,
author = {Greenlief, C Michael and Gates, Stephen M and Holbert, Philip A},



journal = {Journal of Vacuum Science {\&} Technology A: Vacuum, Surfaces, and Films},


pages = {1845},
publisher = {AVS},
title = {{Reaction kinetics of surface silicon hydrides}},

volume = {7},
year = {1989}
}
@article{goed95jcomp,
author = {Goedecker, S},

journal = {J. Comp. Phys.},

pages = {261--268},
publisher = {Academic Press},
title = {{Low Complexity Algorithms for Electronic Structure Calculations}},
volume = {118},
year = {1995}
}
@article{soko-02pre,
author = {Sokolov, I M},

journal = {Phys. Rev. E},

pages = {41101},
publisher = {American Physical Society},
title = {{Solutions of a class of non-Markovian Fokker-Planck equations}},
volume = {66},
year = {2002}
}
@article{stec+14jctc,
abstract = {We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org .$\backslash$nWe demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org .},
archivePrefix = {arXiv},
arxivId = {arXiv:1312.4419v1},
author = {Stecher, Thomas and Bernstein, Noam and Cs{\'{a}}nyi, G{\'{a}}bor},



isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},

pages = {4079--4097},
pmid = {26588550},
title = {{Free energy surface reconstruction from umbrella samples using Gaussian process regression}},
volume = {10},
year = {2014}
}
@article{vand08nm,
abstract = {Whereas structure-property relationships have long guided the discovery and optimization of novel materials, formal quantitative methods to identify such relationships in crystalline systems are beginning to emerge. Among them is cluster expansion, which has been successfully used to parametrize the configurational dependence of important scalar physical properties such as bandgaps, Curie temperatures, equation-of-state parameters and densities of states. However, cluster expansion is currently unable to handle anisotropic properties, a key distinguishing feature of crystalline systems central to the design of modern epitaxial structures and devices. Here, I introduce a tensorial cluster expansion enabling the prediction of fundamental tensor-valued material properties such as elasticity, piezoelectricity, dielectric constants, optoelectric coupling, anisotropic diffusion coefficients, surface energy and stress. As an application, I develop predictive ab initio models of anisotropic properties relevant to the design and optimization of III-V semiconductor epitaxial optoelectronic devices.},
author = {van de Walle, A.},


isbn = {1476-1122},

journal = {Nature Materials},


pages = {455--458},
pmid = {18488033},
title = {{A complete representation of structure–property relationships in crystals}},

volume = {7},
year = {2008}
}
@article{sama+14science,
author = {Samanta, Amit and Tuckerman, Mark E and Yu, T.-Q. and E, W.},



journal = {Science},

pages = {729--732},
title = {{Microscopic mechanisms of equilibrium melting of a solid}},

volume = {346},
year = {2014}
}
@book{all-tild90book,
author = {Allen, M P and Tildesley, D J},
publisher = {Oxford University Press, USA},
title = {{Computer simulation of liquids}},
year = {1990}
}
@article{mart+96molp,
author = {Martyna, Glenn J. and Tuckerman, Mark E. and Tobias, Douglas J. and Klein, Michael L.},



journal = {Mol. Phys.},


pages = {1117--1157},
publisher = {Taylor {\&} Francis},
title = {{Explicit reversible integrators for extended systems dynamics}},

volume = {87},
year = {1996}
}
@article{ozol+05jpcm,
abstract = {An Al-Si solid-state phase diagram is studied using first-principles electronic structure calculations of formation enthalpies and quasiharmonic vibrational free energies. The harmonic vibrational entropy of formation of a Si impurity in fcc Al is predicted to be Delta S-vib = +2.6 k(B) per Si atom, resulting in more than a ten-fold increase in the calculated solubility. Thermal expansion is found to further increase the maximum solubility at T = 850 K by approximately 55{\%}. Surprisingly, when vibrational effects are included, the widely used local-density approximation (LDA) performs poorly in reproducing the experimental solvus boundary, which is overestimated by a factor of ten. This failure is attributed to the neglect of corrections to the calculated LDA impurity enthalpy Delta H stemming from the inhomogeneity of the electronic charge density. These corrections tend to favour the four-fold coordinated diamond structure over the twelve-fold coordinated fcc solid-solution phase. The generalized-gradient approximation (GGA) is found to remove most of the discrepancy between the experimental and calculated Delta H, giving a good agreement with the experimental Al-Si phase diagram.},
author = {Ozoliņ{\v{s}}, V and Sadigh, B and Asta, M},


isbn = {0953-8984},

journal = {J. Phys. Cond. Matt.},


pages = {2197--2210},
title = {{Effects of vibrational entropy on the Al–Si phase diagram}},

volume = {17},
year = {2005}
}
@article{nata+15pccp,
abstract = {We report a reactive neural network potential for protonated water clusters that accurately represents the density-functional theory potential-energy surface.},
author = {{Kondati Natarajan}, Suresh and Morawietz, Tobias and Behler, J{\"{o}}rg},


journal = {Physical Chemistry Chemical Physics},

pages = {8356--8371},
title = {{Representing the potential-energy surface of protonated water clusters by high-dimensional neural network potentials}},

volume = {17},
year = {2015}
}
@article{kraj-parr05prb,
author = {Krajewski, F R and Parrinello, M},

journal = {Phys. Rev. B},
pages = {233105},
title = {{Stochastic linear scaling for metals and nonmetals}},
volume = {71},
year = {2005}
}
@article{habe-mano11jcp,
abstract = {We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable.},
author = {Habershon, Scott and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {224111},
pmid = {22168684},
title = {{Thermodynamic integration from classical to quantum mechanics.}},

volume = {135},
year = {2011}
}
@article{Andersen1983,
author = {Andersen, C},

pages = {24--34},
title = {{Rattle : A “ Velocity ” Molecular Version of the Shake Dynamics Calculations for}},
year = {1983}
}
@article{zwan73jsp,
author = {Zwanzig, Robert},

journal = {J. Stat. Phys.},

pages = {215--220},
publisher = {Springer},
title = {{Nonlinear generalized Langevin equations}},

volume = {9},
year = {1973}
}
@article{loba-voth96jcp,
author = {Lobaugh, J. and Voth, Gregory a.},



journal = {J. Chem. Phys.},

pages = {2056},
title = {{The quantum dynamics of an excess proton in water}},

volume = {104},
year = {1996}
}
@article{baer+13prl,
abstract = {We formulate the Kohn-Sham density functional theory (KS-DFT) as a statistical theory in which the electron density is determined from an average of correlated stochastic densities in a trace formula. The key idea is that it is sufficient to converge the total energy per electron to within a predefined statistical error in order to obtain reliable estimates of the electronic band structure, the forces on nuclei, the density and its moments, etc. The fluctuations in the total energy per electron are guaranteed to decay to zero as the system size increases. This facilitates “self-averaging” which leads to the first ever report of sublinear scaling KS-DFT electronic structure. The approach sidesteps calculation of the density matrix and thus, is insensitive to its evasive sparseness, as demonstrated here for silicon nanocrystals. The formalism is not only appealing in terms of its promise to far push the limits of application of KS-DFT, but also represents a cognitive change in the way we think of electronic structure calculations as this stochastic theory seamlessly converges to the thermodynamic limit.},
annote = {NULL},
archivePrefix = {arXiv},
arxivId = {1304.4053},
author = {Baer, Roi and Neuhauser, Daniel and Rabani, Eran},




journal = {Phys. Rev. Lett.},


pages = {106402},
pmid = {25166686},
title = {{Self-Averaging Stochastic Kohn-Sham Density-Functional Theory}},

volume = {111},
year = {2013}
}
@article{bene+15jcp,
abstract = {In this work we study, by means of molecular dynamics simulations, the$\backslash$nsolid-liquid interface of NaCl under coexistence conditions. By$\backslash$nanalysing capillary waves, we obtain the stiffness for different$\backslash$norientations of the solid and calculate the interfacial free energy by$\backslash$nexpanding the dependency of the interfacial free energy with the solid$\backslash$norientation in terms of cubic harmonics. We obtain an average value for$\backslash$nthe solid-fluid interfacial free energy of 89 +/- 6 mN m(-1) that is$\backslash$nconsistent with previous results based on the measure of nucleation free$\backslash$nenergy barriers {\{}[{\}}Valeriani et al., J. Chem. Phys. 122, 194501 (2005)].$\backslash$nWe analyse the influence of the simulation setup on interfacial$\backslash$nproperties and find that facets prepared as an elongated rectangular$\backslash$nstripe give the same results as those prepared as squares for all cases$\backslash$nbut the 111 face. For some crystal orientations, we observe at small$\backslash$nwave-vectors a behaviour not consistent with capillary wave theory and$\backslash$nshow that this behavior does not depend on the simulation setup. (C)$\backslash$n2015 AIP Publishing LLC.},
author = {Benet, Jorge and MacDowell, Luis G. and Sanz, Eduardo},


isbn = {1089-7690 (Electronic)$\backslash$r0021-9606 (Linking)},

journal = {J. Chem. Phys.},


pages = {134706},
pmid = {25854257},
title = {{Interfacial free energy of the NaCl crystal-melt interface from capillary wave fluctuations}},

volume = {142},
year = {2015}
}
@article{curt+03prl,
abstract = {Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. It is typically addressed with highly accurate quantum mechanical computations on a small set of candidate structures, or with empirical rules that have been extracted from a large amount of experimental information, but have limited predictive power. In this Letter, we transfer the concept of heuristic rule extraction to a large library of ab initio calculated information, and we demonstrate that this can be developed into a tool for crystal structure prediction.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0307262},
author = {Curtarolo, Stefano and Morgan, Dane and Persson, Kristin and Rodgers, John and Ceder, Gerbrand},



isbn = {0031-9007},

journal = {Phys. Rev. Lett.},


pages = {135503},
pmid = {14525315},
primaryClass = {cond-mat},
title = {{Predicting crystal structures with data mining of quantum calculations}},

volume = {91},
year = {2003}
}
@article{gamm+98rmp,
author = {Gammaitoni, Luca and H{\"{a}}nggi, Peter and Jung, Peter and Marchesoni, Fabio},

journal = {Rev. Mod. Phys.},

pages = {223--287},
publisher = {American Physical Society},
title = {{Stochastic resonance}},
volume = {70},
year = {1998}
}
@article{scan-jean03amsci,
author = {Scandolo, S and Jeanloz, R},

journal = {American Scientist},

pages = {516--525},
title = {{The Centers of Planets}},
volume = {91},
year = {2003}
}
@article{andr+13cp,
author = {Andreani, C. and Romanelli, G. and Senesi, R.},



journal = {Chemical Physics},
pages = {106--110},
publisher = {Elsevier B.V.},
title = {{A combined INS and DINS study of proton quantum dynamics of ice and water across the triple point and in the supercritical phase}},

volume = {427},
year = {2013}
}
@article{defo99pc,
author = {de Forcrand, Philippe},



journal = {Parallel Computing},



pages = {1341--1355},
title = {{The MultiBoson method}},

volume = {25},
year = {1999}
}
@article{bako+13pccp,
abstract = {Networks are increasingly recognized as important building blocks of various systems in nature and society. Water is known to possess an extended hydrogen bond network, in which the individual bonds are broken in the sub-picosecond range and still the network structure remains intact. We investigated and compared the topological properties of liquid water and methanol at various temperatures using concepts derived within the framework of graph and network theory (neighbour number and cycle size distribution, the distribution of local cyclic and local bonding coefficients, Laplacian spectra of the network, inverse participation ratio distribution of the eigenvalues and average localization distribution of a node) and compared them to small world and Erdős-R{\{}{\'{e}}{\}}nyi random networks. Various characteristic properties (e.g. the local cyclic and bonding coefficients) of the network in liquid water could be reproduced by small world and/or Erdős-R{\{}{\'{e}}{\}}nyi networks, but the ring size distribution of water is unique and none of the studied graph models could describe it. Using the inverse participation ratio of the Laplacian eigenvectors we characterized the network inhomogeneities found in water and showed that similar phenomena can be observed in Erdős-R{\{}{\'{e}}{\}}nyi and small world graphs. We demonstrated that the topological properties of the hydrogen bond network found in liquid water systematically change with the temperature and that increasing temperature leads to a broader ring size distribution. We applied the studied topological indices to the network of water molecules with four hydrogen bonds, and showed that at low temperature (250 K) these molecules form a percolated or nearly-percolated network, while at ambient or high temperatures only small clusters of four-hydrogen bonded water molecules exist.},
author = {Bak{\'{o}}, Imre and Bencsura, Akos and Hermannson, Kersti and B{\'{a}}lint, Szabolcs and Gr{\'{o}}sz, Tam{\'{a}}s and Chihaia, Viorel and Ol{\'{a}}h, Julianna},



journal = {PCCP},



pages = {15163--15171},
pmid = {23925551},
title = {{Hydrogen bond network topology in liquid water and methanol: a graph theory approach.}},

volume = {15},
year = {2013}
}
@misc{parr-rahm82book,
annote = {M. Parrinello and A. Rahman, in Monte Carlo Methods in Quantum Problems, edited by M. H. Kalos (Reidel, Dordrecht, 1984), page 105.},
title = {{No Title}}
}
@article{shi+07jcp,
author = {Shi, J and Tok, E S and Kang, H C},

journal = {J. Chem. Phys.},
pages = {164713},
publisher = {AIP},
title = {{The dissociative adsorption of silane and disilane on Si (100)-(2$\backslash$times 1)}},
volume = {127},
year = {2007}
}
@article{stre+78mp,
author = {Streett, W.B. B and Tildesley, D.J. J and Saville, G.},



journal = {Mol. Phys.},


pages = {639--648},
title = {{Multiple time-step methods in molecular dynamics}},

volume = {35},
year = {1978}
}
@article{jang-voth97jcp,
author = {Jang, Seogjoo and Voth, Gregory A},


journal = {J. Chem. Phys.},

pages = {9514--9526},
publisher = {AIP},
title = {{Simple reversible molecular dynamics algorithms for Nos{\'{e}}-Hoover chain dynamics}},
volume = {107},
year = {1997}
}
@article{reit+13prl,
author = {Reiter, G F and Deb, Aniruddha and Sakurai, Y and Itou, M and Krishnan, V G and Paddison, S J},


journal = {Phys. Rev. Lett.},

pages = {1--5},
title = {{Anomalous Ground State of the Electrons in Nanoconfined Water}},
volume = {036803},
year = {2013}
}
@article{das+06pnas,
abstract = {The definition of reaction coordinates for the characterization of a protein-folding reaction has long been a controversial issue, even for the "simple" case in which one single free-energy barrier separates the folded and unfolded ensemble. We propose a general approach to this problem to obtain a few collective coordinates by using nonlinear dimensionality reduction. We validate the usefulness of this method by characterizing the folding landscape associated with a coarse-grained protein model of src homology 3 as sampled by molecular dynamics simulations. The folding free-energy landscape projected on the few relevant coordinates emerging from the dimensionality reduction can correctly identify the transition-state ensemble of the reaction. The first embedding dimension efficiently captures the evolution of the folding process along the main folding route. These results clearly show that the proposed method can efficiently find a low-dimensional representation of a complex process such as protein folding.},
author = {Das, P. and Moll, M. and Stamati, H. and Kavraki, L. E. and Clementi, C.},


isbn = {0036040010},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {9885--9890},
pmid = {16785435},
title = {{Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction}},

volume = {103},
year = {2006}
}
@article{anci+97science,
author = {Ancilotto, F. and Chiarotti, G L and Scandolo, S and Tosatti, E},



journal = {Science},


pages = {1288--1290},
publisher = {AAAS},
title = {{Dissociation of Methane into Hydrocarbons at Extreme (Planetary) Pressure and Temperature}},

volume = {275},
year = {1997}
}
@article{conn-will83prb,
author = {Connolly, J. and Williams, a.},



journal = {Phys. Rev. B},


pages = {5169--5172},
title = {{Density-functional theory applied to phase transformations in transition-metal alloys}},

volume = {27},
year = {1983}
}
@article{DeDivitiis1995,
author = {de Divitiis, G.M. M and Frezzotti, R. and Guagnelli, M. and Masetti, M. and Petronzio, R.},



journal = {Nucl. Phys. B},


pages = {274--286},
title = {{The bermions: an approach to lattice QCD dynamical fermions from negative flavour numbers}},

volume = {455},
year = {1995}
}
@article{kaji+17sr,
abstract = {Material informatics (MI) is a promising approach to liberate us from the time-consuming Edisonian (trial and error) process for material discoveries, driven by machine-learning algorithms. Several descriptors, which are encoded material features to feed computers, were proposed in the last few decades. Especially to solid systems, however, their insufficient representations of three dimensionality of field quantities such as electron distributions and local potentials have critically hindered broad and practical successes of the solid-state MI. We develop a simple, generic 3D voxel descriptor that compacts any field quantities, in such a suitable way to implement convolutional neural networks (CNNs). We examine the 3D voxel descriptor encoded from the electron distribution by a regression test with 680 oxides data. The present scheme outperforms other existing descriptors in the prediction of Hartree energies that are significantly relevant to the long-wavelength distribution of the valence electrons. The results indicate that this scheme can forecast any functionals of field quantities just by learning sufficient amount of data, if there is an explicit correlation between the target properties and field quantities. This 3D descriptor opens a way to import prominent CNNs-based algorithms of supervised, semi-supervised and reinforcement learnings into the solid-state MI.},
author = {Kajita, Seiji and Ohba, Nobuko and Jinnouchi, Ryosuke and Asahi, Ryoji},



journal = {Scientific Reports},

pages = {1--9},
publisher = {Springer US},
title = {{A Universal 3D Voxel Descriptor for Solid-State Material Informatics with Deep Convolutional Neural Networks}},

volume = {7},
year = {2017}
}
@article{rous-marx00caej,
author = {Rousseau, Roger and Marx, Dominik},


journal = {Chemistry-A European Journal},


pages = {2982--2993},
title = {{Exploring the electronic structure of elemental lithium: From small molecules to nanoclusters, bulk metal, and surfaces}},

volume = {6},
year = {2000}
}
@article{benn75jcp,
author = {Bennett, Charles H},



journal = {J. Comp. Phys.},


pages = {267--279},
title = {{Mass tensor molecular dynamics}},

volume = {19},
year = {1975}
}
@article{ceri-bern07prb,
abstract = {We have studied diffusion pathways of a silyl radical adsorbed on the hydrogenated Si (100)-(2x1) surface by density-functional theory. The process is of interest for the growth of crystalline silicon by plasma-enhanced chemical vapor deposition. Preliminary searches for migration mechanisms have been performed using metadynamics simulations. Local minima and transition states have been further refined by using the nudged-elastic-band method. Barriers for diffusion from plausible adsorption sites as low as 0.2 eV have been found, but trap states have also been spotted, leading to a more stable configuration, with escape barriers of 0.7 eV. Diffusion among weakly bound physisorbed states is also possible with very low activation barriers ({\textless}50 meV). However, desorption mechanisms (either as SiH3 or as SiH4) from physisorbed or more strongly bound adsorption configurations turn out to have activation energies similar to diffusion barriers. Kinetic Monte Carlo simulations based on ab initio activation energies show that the silyl radical diffuses at most by a few lattice spacing before desorbing at temperatures in the range 300-1000 K.},
author = {Ceriotti, Michele and Bernasconi, Marco},



journal = {Phys. Rev. B},


pages = {245309},
publisher = {APS},
title = {{Diffusion and desorption of SiH3 on hydrogenated H:Si(100)-(2x1) from first principles}},

volume = {76},
year = {2007}
}
@article{cere+07prb,
author = {Cereda, S and Ceriotti, M and Montalenti, F and Bernasconi, M and Miglio, Leo},



journal = {Phys. Rev. B},


pages = {235311},
publisher = {APS},
title = {{Quantitative estimate of H abstraction by thermal SiH3 on hydrogenated Si(001)(2×1)}},

volume = {75},
year = {2007}
}
@article{inou+88jjap,
author = {Inoue, Akihisa and Ohtera, Katsumasa and Tsai, An-Pang and Masumoto, Tsuyoshi},



journal = {Japanese J. Appl. Phys.},

mendeley-tags = {aluminum},


pages = {L479--L482},
title = {{Aluminum-Based Amorphous Alloys with Tensile Strength above 980 MPa (100 kg/mm 2 )}},

volume = {27},
year = {1988}
}
@article{cere+06surf,
author = {Cereda, S and Montalenti, F and Cogoni, M and Branduardi, D and Radny, M W and Smith, P V and Miglio, L},

journal = {Surf. Sci.},

pages = {4445--4453},
publisher = {Elsevier},
title = {{Binding sites for SiH2/Si (001): A combined ab initio, tight-binding, and classical investigation}},
volume = {600},
year = {2006}
}
@article{gaid-gall17jpcl,
author = {Gaiduk, Alex P and Galli, Giulia},



journal = {J. Phys. Chem. Letters},


pages = {1496--1502},
title = {{Local and Global Effects of Dissolved Sodium Chloride on the Structure of Water}},

volume = {8},
year = {2017}
}
@article{stee13jcp,
abstract = {A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Mo{\o}ller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.},
author = {Steele, Ryan P},



journal = {J. Chem. Phys.},


pages = {011102},
pmid = {23822286},
title = {{Multiple-timestep ab initio molecular dynamics with electron correlation.}},

volume = {139},
year = {2013}
}
@article{dahm+90pml,
author = {Dahmen, U. and Hetheringtont, C. J. D. and O'Keefe, M. a. and Westmacottt, K. H. and Mills, M. J. and Daw, M. S. and Vitek, V.},



journal = {Philosophical Magazine Letters},


pages = {327--335},
title = {{Atomic structure of a $\Sigma$99 grain boundary in aluminium: A comparison between atomic-resolution observation and pair-potential and embedded-atom simulations}},

volume = {62},
year = {1990}
}
@article{cere+08prl,
author = {Cereda, S and Zipoli, F and Bernasconi, M and Miglio, L and Montalenti, F},

journal = {Phys. Rev. Lett.},

pages = {46105},
publisher = {APS},
title = {{Thermal-Hydrogen Promoted Selective Desorption and Enhanced Mobility of Adsorbed Radicals in Silicon Film Growth}},
volume = {100},
year = {2008}
}
@article{mccu-pitts43bmb,
author = {McCulloch, Warren S. and Pitts, Walter},



journal = {The Bulletin of Mathematical Biophysics},


pages = {115--133},
title = {{A logical calculus of the ideas immanent in nervous activity}},

volume = {5},
year = {1943}
}
@article{lawr-skin03cpl,
author = {Lawrence, C.P P and Skinner, J.L L},



journal = {Chem. Phys. Lett.},

pages = {472--477},
title = {{Ultrafast infrared spectroscopy probes hydrogen-bonding dynamics in liquid water}},

volume = {369},
year = {2003}
}
@article{paes-voth10jcp,
abstract = {A detailed analysis of the infrared lineshapes corresponding to the intramolecular bond vibrations of HOD in either H(2)O or D(2)O is presented here in order to quantitatively assess the accuracy of centroid molecular dynamics in reproducing the correct features of the infrared spectrum of water at ambient conditions. Through a direct comparison with the results obtained from mixed quantum-classical calculations, it is shown that centroid molecular dynamics provides accurate vibrational shifts and lineshapes when the intramolecular bond stretching vibrations are described by a physically reasonable anharmonic potential. Artificially large redshifts due to a so-called "curvature problem" are instead obtained with an unphysical shifted harmonic potential because the latter allows substantial probability density at zero bond lengths.},
author = {Paesani, Francesco and Voth, Gregory a},



journal = {J. Chem. Phys.},



pages = {014105},
pmid = {20078147},
title = {{A quantitative assessment of the accuracy of centroid molecular dynamics for the calculation of the infrared spectrum of liquid water.}},

volume = {132},
year = {2010}
}
@article{wolv07am,
author = {Wolverton, C.},



journal = {Acta Materialia},



pages = {5867--5872},
title = {{Solute–vacancy binding in aluminum}},

volume = {55},
year = {2007}
}
@article{vill-triz14ejp,
abstract = {The isothermal compressibility of an interacting or non interacting system may be extracted from the fluctuations of the number of particles in a well chosen control volume. Finite size effects are prevalent and should then be accounted for to obtain a meaningful, thermodynamic compressibility. In the traditional computational setup where a given simulation box is replicated with periodic boundary conditions, we study particle number fluctuations outside the box (i.e. when the control volume exceeds the box itself), which bear relevant thermodynamic information. We also investigate the related problem of extracting the compressibility from the structure factor in the small wave-vector limit ({\$}k\backslashto 0{\$}). The calculation should be restricted to the discrete set of wave-vectors {\$}k{\$} that are compatible with the periodicity of the system, and we assess the consequences of considering other {\$}k{\$} values, a widespread error among beginners.},
archivePrefix = {arXiv},
arxivId = {1401.2683},
author = {Villamaina, Dario and Trizac, Emmanuel},




journal = {European Journal of Physics},


pages = {035011},
title = {{Thinking outside the box: fluctuations and finite size effects}},

volume = {35},
year = {2014}
}
@article{herm+13prb,
author = {Hermet, Jessica and Torrent, Marc and Bottin, Fran{\c{c}}ois and Dezanneau, Guilhem and Geneste, Gr{\'{e}}gory},



journal = {Phys. Rev. B},


pages = {104303},
title = {{Hydrogen diffusion in the protonic conductor BaCe{\_}{\{}1−x{\}}Gd{\_}{\{}x{\}}O{\_}{\{}3−x/2{\}} from density functional theory}},

volume = {87},
year = {2013}
}
@article{foil+86prb,
author = {Foiles, S. and Baskes, M. and Daw, M.},



journal = {Phys. Rev. B},

mendeley-tags = {aluminum,eam},


pages = {7983--7991},
title = {{Embedded-atom-method functions for the fcc metals Cu, Ag, Au, Ni, Pd, Pt, and their alloys}},

volume = {33},
year = {1986}
}
@article{kuma+92jcc,
author = {Kumar, S and Rosenberg, J M and Bouzida, D and Swendsen, R H and Kollman, P A and Rosenbergl, John M},

journal = {J. Comp. Chem.},

pages = {1011--1021},
publisher = {Wiley Online Library},
title = {{The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method}},
volume = {13},
year = {1992}
}
@article{kim+17prl,
author = {Kim, Kyung Hwan and Pathak, Harshad and Sp{\"{a}}h, Alexander and Perakis, Fivos and Mariedahl, Daniel and Sellberg, Jonas A. and Katayama, Tetsuo and Harada, Yoshihisa and Ogasawara, Hirohito and Pettersson, Lars G. M. and Nilsson, Anders},



journal = {Phys. Rev. Lett.},

pages = {075502},
title = {{Temperature-Independent Nuclear Quantum Effects on the Structure of Water}},

volume = {119},
year = {2017}
}
@article{vani-mill07jcp,
abstract = {The quantum instanton approximation is used to compute kinetic isotope effects for intramolecular hydrogen transfer in cis-1,3-pentadiene. Due to the importance of skeleton motions, this system with 13 atoms is a simple prototype for hydrogen transfer in enzymatic reactions. The calculation is carried out using thermodynamic integration with respect to the mass of the isotopes and a path integral Monte Carlo evaluation of relevant thermodynamic quantities. Efficient "virial" estimators are derived for the logarithmic derivatives of the partition function and the delta-delta correlation functions. These estimators require significantly fewer Monte Carlo samples since their statistical error does not increase with the number of discrete time slices in the path integral. The calculation treats all 39 degrees of freedom quantum mechanically and uses an empirical valence bond potential based on a molecular mechanics force field.},
author = {Van$\backslash$'$\backslash$icek, Jir$\backslash$'$\backslash$i and Miller, William H and Van{\'{i}}cek, Jir{\'{i}} and Miller, William H},



journal = {J. Chem. Phys.},



pages = {114309},
pmid = {17887839},
title = {{Efficient estimators for quantum instanton evaluation of the kinetic isotope effects: application to the intramolecular hydrogen transfer in pentadiene.}},

volume = {127},
year = {2007}
}
@article{zhan+05am,
author = {Zhang, H. and Upmanyu, M. and Srolovitz, D.J. J},



journal = {Acta Materialia},



pages = {79--86},
title = {{Curvature driven grain boundary migration in aluminum: molecular dynamics simulations}},

volume = {53},
year = {2005}
}
@article{pamu+12prl,
author = {Pamuk, B. and Soler, J. M. and Ram{\'{i}}rez, R. and Herrero, C. P. and Stephens, P. W. and Allen, P. B. and Fern{\'{a}}ndez-Serra, M.-V.},



journal = {Phys. Rev. Lett.},


pages = {193003},
title = {{Anomalous Nuclear Quantum Effects in Ice}},

volume = {108},
year = {2012}
}
@article{wikf-mich14jcp,
archivePrefix = {arXiv},
arxivId = {arXiv:1312.1921v1},
author = {Wikfeldt, K. T. and Michaelides, A.},




journal = {J. Chem. Phys.},

pages = {1--5},
title = {{Communication: Ab initio simulations of hydrogen-bonded ferroelectrics: Collective tunneling and the origin of geometrical isotope effects}},
volume = {140},
year = {2014}
}
@article{huan-vonl16jcp,
annote = {NULL},
author = {Huang, Bing and von Lilienfeld, O Anatole},


journal = {J. Chem. Phys.},

title = {{Communication: Understanding molecular representations in machine learning: The role of uniqueness and target similarity}},

volume = {145},
year = {2016}
}
@article{ropo+16sd,
abstract = {We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca(2+), Ba(2+), Sr(2+), Cd(2+), Pb(2+), and Hg(2+)). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.},
author = {Ropo, Matti and Schneider, Markus and Baldauf, Carsten and Blum, Volker},



journal = {Scientific Data},


pages = {160009},
pmid = {26881946},
title = {{First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids}},

volume = {3},
year = {2016}
}
@article{urey47jcs,
author = {Urey, Harold C.},



journal = {Journal of the Chemical Society (Resumed)},

pages = {562},
title = {{The thermodynamic properties of isotopic substances}},

year = {1947}
}
@article{athe-calv08cpc,
abstract = {The parallel tempering simulation method was recently extended to allow for possible exchanges between non-adjacent replicas. We introduce a multiple-exchange variant which naturally incorporates the information from all replicas when calculating statistical averages, building on the related virtual-move method of Coluzza and Frenkel (ChemPhysChem 2005, 6, 1779). The method is extensively tested on three model systems, namely, a Lennard-Jones cluster exhibiting a finite size phase transition, the Lennard-Jones fluid, and the 2D ferromagnetic Ising model. In all cases, the present method performs significantly better and converges faster than conventional parallel tempering Monte Carlo simulations. The standard deviations are also systematically decreased with respect to virtual moves.},
author = {Ath{\`{e}}nes, Manuel and Calvo, Florent},



journal = {Chemphyschem : a European J. Chem. Phys. and physical chemistry},


pages = {2332--9},
pmid = {18924195},
title = {{Multiple-replica exchange with information retrieval.}},

volume = {9},
year = {2008}
}
@article{zhou+01jcp,
author = {Zhou, Ruhong and Harder, Edward and Xu, Huafeng and Berne, B. J.},



journal = {J. Chem. Phys.},

pages = {2348},
title = {{Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems}},

volume = {115},
year = {2001}
}
@article{enge+15prx,
abstract = {We use extensive first-principles quantum mechanical calculations to show that, although the static lattice and harmonic vibrational energies are almost identical, the anharmonic vibrational energy of hexagonal ice is significantly lower than that of cubic ice. This difference in anharmonicity is crucial, stabilizing hexagonal ice compared with cubic ice by at least 1.4 meV/H2O, in agreement with experimental estimates. The difference in anharmonicity arises predominantly from molecular O-H bond-stretching vibrational modes and is related to the different stacking of atomic layers.},
archivePrefix = {arXiv},
arxivId = {arXiv:1508.02969v1},
author = {Engel, Edgar a. and Monserrat, Bartomeu and Needs, Richard J.},



isbn = {2160-3308},

journal = {Phys. Rev. X},



pages = {021033},
title = {{Anharmonic Nuclear Motion and the Relative Stability of Hexagonal and Cubic ice}},

volume = {5},
year = {2015}
}
@article{buss-parr07pre,
author = {Bussi, G and Parrinello, M},

journal = {Phys. Rev. E},

pages = {56707},
publisher = {APS},
title = {{Accurate sampling using Langevin dynamics}},
volume = {75},
year = {2007}
}
@article{liu-tuck00jcp,
author = {Liu, Yi and Tuckerman, Mark E},

journal = {J. Chem. Phys.},

pages = {1685--1700},
publisher = {AIP},
title = {{Generalized Gaussian moment thermostatting: A new continuous dynamical approach to the canonical ensemble}},
volume = {112},
year = {2000}
}
@article{sind10jctc,
author = {Sindhikara, Daniel J. and Emerson, Daniel J. and Roitberg, Adrian E.},



journal = {J. Chem. Theory Comput.},


pages = {2804--2808},
title = {{Exchange Often and Properly in Replica Exchange Molecular Dynamics}},

volume = {6},
year = {2010}
}
@article{xu+92jpcm,
author = {Xu, C H and Wang, C Z and Chan, C T and Ho, K M},

journal = {J. Phys. Cond. Matt.},
pages = {6047--6054},
publisher = {Institute of Physics Publishing},
title = {{A transferable tight-binding potential for carbon}},
volume = {4},
year = {1992}
}
@article{ilie+97prb,
author = {Iliev, M. N. and Lee, H.-G. G and Popov, V. N. and Sun, Y. Y. and Thomsen, C. and Meng, R. L. and Chu, C. W. and Abrashev, M V},



journal = {Phys. Rev. B},


pages = {2872--2877},
publisher = {American Physical Society},
title = {{Raman spectroscopy of orthorhombic perovskitelike $\backslash$mathrmYMnO{\_}3 and $\backslash$mathrmLaMnO{\_}3}},

volume = {57},
year = {1998}
}
@article{ceri+11jcp,
abstract = {The quantum nature of nuclei plays an important role in the accurate modelling of light atoms such as hydrogen, but it is often neglected in simulations due to the high computational overhead involved. It has recently been shown that zero-point energy effects can be included comparatively cheaply in simulations of harmonic and quasiharmonic systems by augmenting classical molecular dynamics with a generalized Langevin equation (GLE). Here we describe how a similar approach can be used to accelerate the convergence of path integral (PI) molecular dynamics to the exact quantum mechanical result in more strongly anharmonic systems exhibiting both zero point energy and tunnelling effects. The resulting PI-GLE method is illustrated with applications to a double-well tunnelling problem and to liquid water.},
author = {Ceriotti, Michele and Manolopoulos, David E and Parrinello, Michele},


institution = {Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, Lugano, Switzerland. michele.ceriotti@phys.chem.ethz.ch},

journal = {J. Chem. Phys.},



pages = {84104},
pmid = {21361524},
publisher = {AIP},
title = {{Accelerating the convergence of path integral dynamics with a generalized Langevin equation.}},

volume = {134},
year = {2011}
}
@article{haus99unpub,
author = {Haussler, D.},


title = {{Convolution Kernels on Discrete Structures}},
year = {1999}
}
@article{ferg+10pnas,
abstract = {We employ the diffusion map approach as a nonlinear dimensionality reduction technique to extract a dynamically relevant, low-dimensional description of n-alkane chains in the ideal-gas phase and in aqueous solution. In the case of C8 we find the dynamics to be governed by torsional motions. For C16 and C24 we extract three global order parameters with which we characterize the fundamental dynamics, and determine that the low free-energy pathway of globular collapse proceeds by a "kink and slide" mechanism, whereby a bend near the end of the linear chain migrates toward the middle to form a hairpin and, ultimately, a coiled helix. The low-dimensional representation is subtly perturbed in the solvated phase relative to the ideal gas, and its geometric structure is conserved between C16 and C24. The methodology is directly extensible to biomolecular self-assembly processes, such as protein folding.},
author = {Ferguson, Andrew L and Panagiotopoulos, Athanassios Z and Debenedetti, Pablo G and Kevrekidis, Ioannis G},


isbn = {1003293107},

journal = {Proc. Natl. Acad. Sci. USA},



pages = {13597--602},
pmid = {20643962},
title = {{Systematic determination of order parameters for chain dynamics using diffusion maps.}},

volume = {107},
year = {2010}
}
@article{king-vand94prb,
author = {King-Smith, R D and Vanderbilt, David},

journal = {Phys. Rev. B},

pages = {5828--5844},
publisher = {American Physical Society},
title = {{First-principles investigation of ferroelectricity in perovskite compounds}},
volume = {49},
year = {1994}
}
@misc{GAUSSIAN,
annote = {{\{}Wallingford CT: Gaussian, Inc.{\}}},
author = {Frisch, M J and Others},
title = {{{\{}Gaussian 03, 2004 Rev. D 01{\}}}}
}
@article{muel-cede10prb,
author = {Mueller, Tim and Ceder, Gerbrand},



journal = {Phys. Rev. B},


pages = {174307},
title = {{Ab initio study of the low-temperature phases of lithium imide}},

volume = {82},
year = {2010}
}
@unpublished{biblio-car-parrinello,
title = {{No Title}}
}
@article{piet+08prl,
author = {Pietropaolo, A. and Senesi, R. and Andreani, C. and Botti, A. and Ricci, M. a. and Bruni, F.},



journal = {Phys. Rev. Lett.},

pages = {2--5},
title = {{Excess of Proton Mean Kinetic Energy in Supercooled Water}},

volume = {100},
year = {2008}
}
@article{bern-thir86arpc,
author = {Berne, B J and Thirumalai, D},



journal = {Annual Review of Physical Chemistry},


pages = {401--424},
publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA},
title = {{On the Simulation of Quantum Systems: Path Integral Methods}},

volume = {37},
year = {1986}
}
@article{barb+98npb,
author = {Barbour, Ian M and Morrison, Susan E and Klepfish, Elyakum G and Kogut, J B and Lombardo, M P and Kogut, B},

journal = {Nucl. Phys. B},

pages = {220--233},
publisher = {Elsevier},
title = {{Results on finite density QCD}},
volume = {60},
year = {1998}
}
@article{ehle+14jms,
author = {Ehlers, F. J. H. and Wenner, S. and Andersen, S. J. and Marioara, C. D. and Lefebvre, W. and Boothroyd, C. B. and Holmestad, R.},



journal = {Journal of Materials Science},


pages = {6413--6426},
title = {{Phase stabilization principle and precipitate-host lattice influences for Al–Mg–Si–Cu alloy precipitates}},

volume = {49},
year = {2014}
}
@article{wang+12jpcc,
author = {Wang, Jue and Pedroza, Luana S. and Poissier, Adrien and Fern{\'{a}}ndez-Serra, M. V.},



journal = {J. Phys. Chem. C},


pages = {14382--14389},
title = {{Water Dissociation at the GaN(101̅0) Surface: Structure, Dynamics and Surface Acidity}},

volume = {116},
year = {2012}
}
@article{hunt-kear83bcy,
author = {Hunter, I W and Kearney, R E},

journal = {Biological Cybernetics},

pages = {141},
title = {{Generation of random sequences with jointly specified probability density and autocorrelation functions}},
volume = {47},
year = {2000}
}
@article{ling+07ac,
author = {Lingenfelder, Magal$\backslash$'$\backslash$i Magal{\'{i}} and Tomba, Giulia and Costantini, Giovanni and {Colombi Ciacchi}, Lucio and {De Vita}, Alessandro and Kern, Klaus},



journal = {Angewandte Chemie (International ed. in English)},



pages = {4492--4495},
pmid = {17443762},
title = {{Tracking the chiral recognition of adsorbed dipeptides at the single-molecule level.}},

volume = {46},
year = {2007}
}
@article{rait+11jpcm,
author = {Raiteri, Paolo and Gale, Julian D and Bussi, Giovanni},



journal = {J. Phys. Cond. Matt.},


pages = {334213},
title = {{Reactive force field simulation of proton diffusion in BaZrO 3 using an empirical valence bond approach}},

volume = {23},
year = {2011}
}
@article{neug-hess03jcp,
author = {Neugebauer, Johannes and Hess, Bernd a.},



journal = {J. Chem. Phys.},

pages = {7215},
title = {{Fundamental vibrational frequencies of small polyatomic molecules from density-functional calculations and vibrational perturbation theory}},

volume = {118},
year = {2003}
}
@article{liu+13ijt,
abstract = {Multicomponent diffusion in liquids is ubiquitous in (bio)chemical processes. It has gained considerable and increasing interest as it is often the rate limiting step in a process. In this paper, we review methods for calculating diffusion coefficients from molecular simulation and predictive engineering models. The main achievements of our research during the past years can be summarized as follows: (1) we introduced a consistent method for computing Fick diffusion coefficients using equilibrium molecular dynamics simulations; (2) we developed a multicomponent Darken equation for the description of the concentration dependence of Maxwell–Stefan diffusivities. In the case of infinite dilution, the multicomponent Darken equation provides an expression for which can be used to parametrize the generalized Vignes equation; and (3) a predictive model for self-diffusivities was proposed for the parametrization of the multicomponent Darken equation. This equation accurately describes the concentration dependence of self-diffusivities in weakly associating systems. With these methods, a sound framework for the prediction of mutual diffusion in liquids is achieved.},
author = {Liu, Xin and Schnell, Sondre K. and Simon, Jean-Marc and Kr{\"{u}}ger, Peter and Bedeaux, Dick and Kjelstrup, Signe and Bardow, Andr{\'{e}} and Vlugt, Thijs J. H.},


isbn = {0195-928X},

journal = {International Journal of Thermophysics},


pages = {1169--1196},
title = {{Diffusion Coefficients from Molecular Dynamics Simulations in Binary and Ternary Mixtures}},

volume = {34},
year = {2013}
}
@article{mack62jpcs,
author = {Mackenzie, J.K. K and Moore, A.J.W. J W and Nicholas, J.F. F},



journal = {J. Phys. And Chemistry of Solids},


pages = {185--196},
title = {{Bonds broken at atomically flat crystal surfaces - I: Face-centred and body-centred cubic crystals}},

volume = {23},
year = {1962}
}
@article{shim+00jcp,
author = {Shimokawa, S and Namiki, A and N.-Gamo, M. and Ando, T},



journal = {J. Chem. Phys.},

pages = {6916},
publisher = {AIP},
title = {{Temperature dependence of atomic hydrogen-induced surface processes on Ge(100): Thermal desorption, abstraction, and collision-induced desorption}},

volume = {113},
year = {2000}
}
@article{glae-frie02jcp,
author = {Glaesemann, Kurt R and Fried, Laurence E},

journal = {J. Chem. Phys.},

pages = {3020--3026},
publisher = {AIP},
title = {{Improved heat capacity estimator for path integral simulations}},
volume = {117},
year = {2002}
}
@article{hija+18jcp,
abstract = {Stochastic thermostats based on the Langevin equation, in which a system is coupled to an external heat bath, are popular methods for temperature control in molecular dynamics simulations due to their ergodicity and their ease of implementation. Traditionally, these thermostats suffer from sluggish behaviour in the limit of high friction, unlike thermostats of the Nos$\backslash$'e-Hoover family whose performance degrades more gently in the strong coupling regime. We propose a simple and easy-to-implement modification to the integration scheme of the Langevin algorithm that addresses the fundamental source of the overdamped behaviour of high-friction Langevin dynamics: if the action of the thermostat causes the momentum of a particle to change direction, it is flipped back. This fast-forward Langevin equation preserves the momentum distribution, and so guarantees the correct equilibrium sampling. It mimics the quadratic behavior of Nos$\backslash$'e-Hoover thermostats, and displays similarly good performance in the strong coupling limit. We test the efficiency of this scheme by applying it to a 1-dimensional harmonic oscillator, as well as to water and Lennard-Jones polymers. The sampling efficiency of the fast-forward Langevin equation thermostat, measured by the correlation time of relevant system variables, is at least as good as the traditional Langevin thermostat, and in the overdamped regime the fast-forward thermostat performs much better, improving the efficiency by an order of magnitude at the highest frictions we considered.},
archivePrefix = {arXiv},
arxivId = {1804.08913},
author = {Hijazi, Mahdi and Wilkins, David M. D.M. and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {184109},
title = {{Fast-forward Langevin dynamics with momentum flips}},

volume = {148},
year = {2018}
}
@article{lang08cras,
author = {Langevin, P},

journal = {CR Acad. Sci},
pages = {530},
title = {{The theory of Brownian movement}},
volume = {146},
year = {1908}
}
@article{maye+02jms,
author = {Mayers, J and Reiter, G.F F and Platzman, P},



journal = {Journal of Molecular Structure},


pages = {275--282},
title = {{Measurement of proton momentum distributions by eV neutron scattering}},

volume = {615},
year = {2002}
}
@book{stra63book,
address = {New York},
author = {Stratonovich, R L},
publisher = {Gordon and Breach},
title = {{Topics in the Theory of Random Noise}},
volume = {1},
year = {1963}
}
@article{zwan-aila69pr,
author = {Zwanzig, Robert and Ailawadi, Narinder},



journal = {Phys. Rev.},


pages = {280--283},
publisher = {APS},
title = {{Statistical Error Due to Finite Time Averaging in Computer Experiments}},

volume = {182},
year = {1969}
}
@article{thir+94jcp,
author = {Thirumalai, D and Hall, Randall W and Berne, B J},

journal = {J. Chem. Phys.},

pages = {2523--2527},
publisher = {AIP},
title = {{A path integral Monte Carlo study of liquid neon and the quantum effective pair potential}},
volume = {81},
year = {1984}
}
@article{schn-stol78prb,
author = {Schneider, T and Stoll, E},
journal = {Phys. Rev. B},

pages = {1302--1322},
title = {{Molecular-dynamics study of a three-dimensional one-component model for distortive phase transitions}},
volume = {17},
year = {1978}
}
@article{gard88ibm,
author = {Gardiner, C W},

journal = {IBM J. Res. Dev.},
pages = {127},
title = {{Quantum noise and quantum Langevin equations}},
volume = {32},
year = {1988}
}
@article{herr-rami00prb,
author = {Herrero, C P and Ram{\`{i}}rez, R},

journal = {Phys. Rev. B},

pages = {24103},
publisher = {APS},
title = {{Structural and thermodynamic properties of diamond: A path-integral Monte Carlo study}},
volume = {63},
year = {2000}
}
@article{geis+01sci,
abstract = {The dissociation of a water molecule in liquid water is the fundamental event in acid-base chemistry, determining the pH of water. Because of the short time scales and microscopic length scales involved, the dynamics of this autoionization have not been directly probed by experiment. Here, the autoionization mechanism is revealed by sampling and analyzing ab initio molecular dynamics trajectories. We identify the rare fluctuations in solvation energies that destabilize an oxygen-hydrogen bond. Through the transfer of protons along a hydrogen bond "wire," the nascent ions separate by three or more neighbors. If the hydrogen bond wire connecting the two ions is subsequently broken, a metastable charge-separated state is visited. The ions may then diffuse to large separations. If, however, the hydrogen bond wire remains unbroken, the ions recombine rapidly. Because of their concomitant large electric fields, the transient ionic species produced in this case may provide an experimentally detectable signal of the dynamics we report.},
author = {Geissler, P L and Dellago, C and Chandler, D and Hutter, J and Parrinello, M},



journal = {Science},


pages = {2121--2124},
pmid = {11251111},
publisher = {American Association for the Advancement of Science},
title = {{Autoionization in liquid water}},

volume = {291},
year = {2001}
}
@article{tkat+13jcp,
author = {Tkatchenko, Alexandre and Ambrosetti, Alberto and DiStasio, Robert A.},


journal = {J. Chem. Phys.},

pages = {074106},
title = {{Interatomic methods for the dispersion energy derived from the adiabatic connection fluctuation-dissipation theorem}},

volume = {138},
year = {2013}
}
@article{gibe+14jpcb,
abstract = {In this work, we revisit the role of nuclear quantum effects on the structural and electronic properties of the excess proton in bulk liquid water using advanced molecular dynamics techniques. The hydronium ion is known to be a weak acceptor of a hydrogen bond which gives it some hydrophobic character. Quantum effects reduce the degree of this hydrophobicity which facilitates the fluctuations of the protons along the wires compared to the classical proton. Although the Eigen and Zundel species still appear to be dominant motifs, quantum fluctuations result in rather drastic events where both transient autoionization and delocalization over extended proton wires can simultaneously occur. These wild fluctuations also result in a significant change of the electronic properties of the system such as the broadening of the electronic density of states. An analysis of the Wannier functions indicate that quantum fluctuations of neat water molecules result in transient charging with subtle similarities and differences to that of the excess proton.},
author = {Giberti, Federico and Hassanali, A.A. Ali A and Ceriotti, Michele and Parrinello, Michele},



journal = {J. Phys. Chem. B},


pages = {13226--13235},
pmid = {25286281},
title = {{The Role of Quantum Effects on Structural and Electronic Fluctuations in Neat and Charged Water}},

volume = {118},
year = {2014}
}
@article{shar+05prl,
author = {Sharma, Manu and Resta, Raffaele and Car, Roberto},

journal = {Phys. Rev. Lett.},

pages = {187401},
publisher = {American Physical Society},
title = {{Intermolecular Dynamical Charge Fluctuations in Water: A Signature of the H-Bond Network}},
volume = {95},
year = {2005}
}
@article{parl76laa,
author = {Parlett, B.N. N},



journal = {Linear Algebra and its Applications},


pages = {117--121},
title = {{A recurrence among the elements of functions of triangular matrices}},

volume = {14},
year = {1976}
}
@article{mark-ceri18nrc,
abstract = {The approximation underlying most atomistic simulations to treat nuclei classically can lead to large errors and the failure to capture important physical effects. This Review reports on recent developments that enable modelling of quantum nuclei at a computational cost comparable with that of a classical simulation.},
author = {Markland, Thomas E. and Ceriotti, Michele},



journal = {Nature Reviews Chemistry},


pages = {0109},
title = {{Nuclear quantum effects enter the mainstream}},

volume = {2},
year = {2018}
}
@article{perg+09cpc,
author = {Perger, W.F. F and Criswell, J. and Civalleri, B. and Dovesi, R.},



journal = {Comp. Phys. Comm.},


pages = {1753--1759},
publisher = {Elsevier B.V.},
title = {{Ab-initio calculation of elastic constants of crystalline systems with the CRYSTAL code}},

volume = {180},
year = {2009}
}
@incollection{deng-schi03book,
author = {Deng, Xunming and Schiff, EA A},
booktitle = {Handbook of Photovoltaic Science and Engineering},


isbn = {0471491969},
pages = {505----565},
title = {{Amorphous silicon based solar cells}},

year = {2003}
}
@article{bakk-nien02science,
abstract = {We find that the vibrational potential of the O-H stretch vibrations of liquid water shows extreme anharmonicity that arises from the O-H O hydrogen bond interaction. We observe that already in the second excited state of the O-H stretch vibration, the hydrogen atom becomes delocalized between the oxygen atoms of two neighboring water molecules. The energy required for this delocalization is unexpectedly low and corresponds to less than 20{\%} of the dissociation energy of the O-H bond of the water molecule in the gas phase.},
author = {Bakker, H J and Nienhuys, H-K},



journal = {Science},


pages = {587--90},
pmid = {12142533},
title = {{Delocalization of protons in liquid water.}},

volume = {297},
year = {2002}
}
@article{hone+06jcp,
abstract = {The recently introduced approximate many-body quantum simulation method, ring polymer molecular dynamics (RPMD), is compared to the centroid molecular dynamics method (CMD). Comparisons of simulation results for liquid para-hydrogen at two state points and liquid ortho-deuterium at one state point are presented. The calculated quantum correlation functions for the two methods are shown to be in good agreement with one another for a large portion of the time spectrum. However, as the quantum mechanical nature of the system increases, RPMD is less accurate in predicting the kinetic energy of the system than is CMD. A simplified and highly efficient algorithm is proposed which largely corrects this deficiency.},
author = {Hone, Tyler D and Rossky, Peter J and Voth, Gregory a},



journal = {J. Chem. Phys.},


pages = {154103},
pmid = {16674214},
title = {{A comparative study of imaginary time path integral based methods for quantum dynamics.}},

volume = {124},
year = {2006}
}
@article{piet-andr11prl,
author = {Pietrucci, Fabio and Andreoni, Wanda},



journal = {Phys. Rev. Lett.},


pages = {085504},
title = {{Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale}},

volume = {107},
year = {2011}
}
@article{krac05tca,
abstract = {Pseudopotential parameter sets for the elements from H to Kr using the relativistic, norm-conserving, separable, dual-space Gaussian-type pseudopotentials of Goedecker, Teter, and Hutter (GTH) are presented as optimized for the gradient-corrected exchange-correlation functionals of Becke, Lee, Yang, and Parr (BLYP), Becke and Perdew (BP), and Perdew, Burke, and Ernzerhof (PBE). The accuracy and reliability of the GTH pseudopotentials is shown by calculations for a series of small molecules.},
author = {Krack, M},



journal = {Theoretical Chemistry Accounts},



pages = {145--152},
publisher = {Springer},
title = {{Pseudopotentials for H to Kr optimized for gradient-corrected exchange-correlation functionals}},

volume = {114},
year = {2005}
}
@article{pred+05jpcb,
abstract = {We introduce the concept of effective fraction, defined as the expected probability that a configuration from the lowest index replica successfully reaches the highest index replica during a replica exchange Monte Carlo simulation. We then argue that the effective fraction represents an adequate measure of the quality of the sampling technique, as far as swapping is concerned. Under the hypothesis that the correlation between successive exchanges is negligible, we propose a technique for the computation of the effective fraction, a technique that relies solely on the values of the acceptance probabilities obtained at the end of the simulation. The effective fraction is then utilized for the study of the efficiency of a popular swapping scheme in the context of parallel tempering in the canonical ensemble. For large dimensional oscillators, we show that the swapping probability that minimizes the computational effort is 38.74{\%}. By studying the parallel tempering swapping efficiency for a 13-atom Lennard-Jones cluster, we argue that the value of 38.74{\%} remains roughly the optimal probability for most systems with continuous distributions that are likely to be encountered in practice.},
author = {Predescu, Cristian and Predescu, Mihaela and Ciobanu, Cristian V},



journal = {J. Phys. Chem.. B},


pages = {4189--96},
pmid = {16851481},
title = {{On the efficiency of exchange in parallel tempering monte carlo simulations.}},

volume = {109},
year = {2005}
}
@article{laio+05jpcb,
author = {Laio, A and Rodriguez-Fortea, A and Gervasio, F L and Ceccarelli, M and Parrinello, M},

journal = {J. Phys. Chem. B},

pages = {6714--6721},
title = {{Assessing the accuracy of metadynamics}},
volume = {109},
year = {2005}
}
@article{leim+13jcp,
abstract = {A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian motions in some combination. The Baker-Campbell-Hausdorff expansion is used to study sampling accuracy following recent work by the authors, which allows determination of the stepsize-dependent bias in configurational averaging. For harmonic oscillators, configurational averaging is exact for certain schemes, which may result in improved performance in the modelling of biomolecules where bond stretches play a prominent role. For general systems, an optimal method can be identified that has very low bias compared to alternatives. In simulations of the alanine dipeptide reported here (both solvated and unsolvated), higher accuracy is obtained without loss of computational efficiency, while allowing large timestep, and with no impairment of the conformational exploration rate (the effective diffusion rate observed in simulation). The optimal scheme is a uniformly better performing algorithm for molecular sampling, with overall efficiency improvements of 25{\%} or more in practical timestep size achievable in vacuum, and with reductions in the error of configurational averages of a factor of ten or more attainable in solvated simulations at large timestep.},
archivePrefix = {arXiv},
arxivId = {1304.3269},
author = {Leimkuhler, Benedict and Matthews, Charles},




journal = {J. Chem. Phys.},

pmid = {23656109},
title = {{Robust and efficient configurational molecular sampling via Langevin dynamics}},
volume = {138},
year = {2013}
}
@article{Dong1994,
author = {Dong, Shao-Jing and Liu, Keh-Fei},



journal = {Phys. Lett. B},


pages = {130--136},
title = {{Stochastic estimation with Z2 noise}},

volume = {328},
year = {1994}
}
@article{zhan-gall14jcp,
abstract = {We present an analysis of the dipolar correlations in water as a function of temperature and density and in the presence of simple ionic solutes, carried out using molecular dynamics simulations and empirical potentials. We show that the dipole-dipole correlation function of the liquid exhibits sizable oscillations over nanodomains of about 1.5 nm radius, with several isosbestic points as a function of temperature; the size of the nanodomains is nearly independent on temperature and density, between 240 and 400 K and 0.9 and 1.3 g/cm3, but it is substantially affected by the presence of solvated ions. In the same range of thermodynamic conditions, the decay time ($\tau$) of the system dipole moment varies by a factor of about 30 and 1.5, as a function of temperature and density, respectively. At 300 K, we observed a maximum in $\tau$ as a function of density, and a corresponding shallow maximum in the tetrahedral order parameter, in a range where the diffusion coefficient, the pressure and the dielectric constant increase monotonically.},
author = {Zhang, Cui and Galli, Giulia},



journal = {J. Chem. Phys.},


pages = {084504},
pmid = {25173018},
title = {{Dipolar correlations in liquid water}},

volume = {141},
year = {2014}
}
@article{panz-colo94prl,
author = {Panzarini, G. and Colombo, L.},



journal = {Phys. Rev. Lett.},


pages = {1636--1639},
title = {{Hydrogen Diffusion in Silicon from Tight-Binding Molecular Dynamics}},

volume = {73},
year = {1994}
}
@article{kress+98jcamd,
author = {Kress, J D and Goedecker, S and Hoisie, A and Wasserman, H and Lubeck, O and Collins, L A and Holian, B L},

journal = {Journal of Computer-Aided Materials Design},

pages = {295--316},
publisher = {Springer},
title = {{Parallel O (N) tight-binding molecular dynamics of polyethylene and compressed methane}},
volume = {5},
year = {1998}
}
@article{du+94science,
abstract = {Surface vibrational spectroscopy by sum-frequency generation was used to study hydrophobicity at the molecular level at various interfaces: water-surfactant-coated quartz, water-hexane, and water-air. In all cases, hydrophobicity was characterized by the appearance of dangling hydroxyl bonds on 25 percent of the surface water molecules. At the water-quartz interface, packing restrictions force the water surface layer to have a more ordered, ice-like structure. A partly wettable water-quartz interface was also studied.},
author = {Du, Quan and Freysz, Eric and Shen, YR Ron Ron},

journal = {Science},

pages = {----826},
publisher = {American Association for the Advancement of Science},
series = {New Series},
title = {{Surface Vibrational Spectroscopic Studies of Hydrogen Bonding and Hydrophobicity}},

volume = {264},
year = {1994}
}
@article{hass+12jacs,
abstract = {The motion of the excess proton is understood as a process involving interconversion between two limiting states, namely, the Eigen and Zundel cations. Nuclear quantum effects (NQE) and the organization of the surrounding solvent play a significant role in this process. However, little is known about how these factors can change the limiting state in molecular systems and the physicochemical properties of its surrounding hydrogen-bond environment. In this work we use state of the art ab initio molecular dynamics simulations to examine the role of NQE on the nature of the proton in four hydrogen chloride hydrates. We demonstrate that NQE significantly alter the phase space properties of the proton and that the local electronic structure of the proton is an exquisitely sensitive indicator of the limiting state in each of the crystals. We evaluate both the proton momentum distribution and the proton chemical shifts and demonstrate that deep inelastic neutron scattering and solid-state nuclear magnetic resonance experiments can serve as complementary techniques for probing the quantum nature of the proton in hydrogen-bonding systems. We believe that the rich and insightful information we obtain for these acid hydrates provides a motivation for new experimental studies.},
address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
author = {Hassanali, Ali A and Cuny, Jerome J{\'{e}}r{\^{o}}me and Ceriotti, Michele and Pickard, Chris J and Parrinello, Michele},



journal = {J. Chem. Am. Soc. },

pages = {8557--8569},
pmid = {22500856},
publisher = {AMER CHEMICAL SOC},
title = {{The Fuzzy Quantum Proton in the Hydrogen Chloride Hydrates}},

volume = {134},
year = {2012}
}
@article{wan+13jctc,
abstract = {We report the first ab initio simulations of the Raman spectra of liquid water, obtained by combining first principles molecular dynamics and density functional perturbation theory. Our computed spectra are in good agreement with experiments, especially in the low frequency region. We also describe a systematic strategy to analyze the Raman intensities, which is of general applicability to molecular solids and liquids, and it is based on maximally localized Wannier functions and effective molecular polarizabilities. Our analysis revealed the presence of intermolecular charge fluctuations accompanying the hydrogen bond (HB) stretching modes at 270 cm?1, in spite of the absence of any Raman activity in the isotropic spectrum. We also found that charge fluctuations partly contribute to the 200 cm?1 peak in the anisotropic spectrum, thus providing insight into the controversial origin of such peak. Our results highlighted the importance of taking into account electronic effects in interpreting the Raman spectra of liquid water and the key role of charge fluctuations within the HB network; they also pointed at the inaccuracies of models using constant molecular polarizabilities to describe the Raman response of liquid water. We report the first ab initio simulations of the Raman spectra of liquid water, obtained by combining first principles molecular dynamics and density functional perturbation theory. Our computed spectra are in good agreement with experiments, especially in the low frequency region. We also describe a systematic strategy to analyze the Raman intensities, which is of general applicability to molecular solids and liquids, and it is based on maximally localized Wannier functions and effective molecular polarizabilities. Our analysis revealed the presence of intermolecular charge fluctuations accompanying the hydrogen bond (HB) stretching modes at 270 cm?1, in spite of the absence of any Raman activity in the isotropic spectrum. We also found that charge fluctuations partly contribute to the 200 cm?1 peak in the anisotropic spectrum, thus providing insight into the controversial origin of such peak. Our results highlighted the importance of taking into account electronic effects in interpreting the Raman spectra of liquid water and the key role of charge fluctuations within the HB network; they also pointed at the inaccuracies of models using constant molecular polarizabilities to describe the Raman response of liquid water.},
author = {Wan, Quan and Spanu, Leonardo and Galli, Giulia A. and Gygi, Fran??ois},



journal = {J. Chem. Theory Comput.},

pages = {4124--4130},
pmid = {26592405},
title = {{Raman spectra of liquid water from Ab initio molecular dynamics: Vibrational signatures of charge fluctuations in the hydrogen bond network}},
volume = {9},
year = {2013}
}
@article{liu-mill06jcp,
abstract = {The thermal Gaussian approximation (TGA) recently developed by Frantsuzov et al. [Chem. Phys. Lett. 381, 117 (2003)] has been demonstrated to be a practical way for approximating the Boltzmann operator exp(-betaH) for multidimensional systems. In this paper the TGA is combined with semiclassical (SC) initial value representations (IVRs) for thermal time correlation functions. Specifically, it is used with the linearized SC-IVR (LSC-IVR, equivalent to the classical Wigner model), and the "forward-backward semiclassical dynamics" approximation developed by Shao and Makri [J. Phys. Chem. A 103, 7753 (1999); 103, 9749 (1999)]. Use of the TGA with both of these approximate SC-IVRs allows the oscillatory part of the IVR to be integrated out explicitly, providing an extremely simple result that is readily applicable to large molecular systems. Calculation of the force-force autocorrelation for a strongly anharmonic oscillator demonstrates its accuracy, and calculation of the velocity autocorrelation function (and thus the diffusion coefficient) of liquid neon demonstrates its applicability.},
author = {Liu, Jian and Miller, William H},



journal = {J. Chem. Phys.},


pages = {224104},
pmid = {17176131},
title = {{Using the thermal Gaussian approximation for the Boltzmann operator in semiclassical initial value time correlation functions.}},

volume = {125},
year = {2006}
}
@article{Nelder1964,
author = {Nelder, By J A and Meadf, R},
title = {{A simplex method for function minimization}},
year = {1964}
}
@article{bals+96jcp,
abstract = {It has been suggested that principal component analysis can identify slow modes in proteins and, thereby, facilitate the study of long time dynamics. However, sampling errors due to finite simulation times preclude the identification of slow modes that can be used for this purpose. This is demonstrated numerically with the aid of simulations of the protein G-actin and analytically with the aid of a model which is exactly recoverable by principal component analysis. Although principal component analysis usually demonstrates that a set of a small number of modes captures the majority of the fluctuations, the set depends on the particular sampling time window and its width. It has been suggested that principal component analysis can identify slow modes in proteins and, thereby, facilitate the study of long time dynamics. However, sampling errors due to finite simulation times preclude the identification of slow modes that can be used for this purpose. This is demonstrated numerically with the aid of simulations of the protein G-actin and analytically with the aid of a model which is exactly recoverable by principal component analysis. Although principal component analysis usually demonstrates that a set of a small number of modes captures the majority of the fluctuations, the set depends on the particular sampling time window and its width.},
author = {Balsera, M a and Wriggers, W and Oono, Y and Schulten, K},


isbn = {0022-3654},

journal = {J. Phys. Chem.},
pages = {2567--2572},
title = {{Principal Component Analysis and Long Time Protein Dynamics}},

volume = {100},
year = {1996}
}
@article{heyd+10pnas,
abstract = {Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at approximately 200 cm(-1) is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm(-1) approximately 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances.},
author = {Heyden, Matthias and Sun, Jian and Funkner, Stefan and Mathias, Gerald and Forbert, Harald and Havenith, Martina and Marx, Dominik},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {12068--12073},
pmid = {20566886},
title = {{Dissecting the THz spectrum of liquid water from first principles via correlations in time and space.}},

volume = {107},
year = {2010}
}
@misc{EPAPS-sih3deco,
annote = {See EPAPS Document No. ----- for a movie of metadynamics trajectory, and a discussion of Brillouin-zone sampling issues.},
title = {{No Title}}
}
@article{mark+08jpcb,
abstract = {Conditional and time-dependent radial distribution functions reveal the details of the water structure surrounding the hydronium during the proton mobility process. Using this methodology for classical multistate empirical valence bond (MS-EVB) and ab initio molecular dynamics trajectories, as well as quantal MS-EVB trajectories, we supply statistical proof that proton hops in liquid water occur by a transition from the H3O+[3H2O] Eigen-complex, via the H5O2+ Zundel-complex, to a H3O+[3H2O] centered on a neighboring water molecule. In the "resting period" before a transition, there is a distorted hydronium with one of its water ligands at a shorter distance and another at a longer distance than average. The identity of this "special partner" interchanges rapidly within the three first-shell water ligands. This is coupled to cleavage of an acceptor-type hydrogen bond. Just before the transition, a partner is selected by an additional translation of the H3O+ moiety in its direction, possibly enabled by loosening of donor-type hydrogen bonds on the opposite side. We monitor the transition in real time, showing how the average structure is converted to a distorted H5O2+ cation constituting the transitional complex for proton hopping between water molecules.},
author = {Markovitch, Omer and Chen, Hanning and Izvekov, Sergei and Paesani, Francesco and Voth, Gregory a and Agmon, Noam},



journal = {J. Phys. Chem.. B},



pages = {9456--66},
pmid = {18630857},
title = {{Special pair dance and partner selection: elementary steps in proton transport in liquid water.}},

volume = {112},
year = {2008}
}
@article{nguy+18jcp,
abstract = {The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enable routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, BPNN-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.},
archivePrefix = {arXiv},
arxivId = {1802.00564},
author = {Nguyen, Thuong T.T. and Sz{\'{e}}kely, Eszter and Imbalzano, Giulio and Behler, J{\"{o}}rg and Cs{\'{a}}nyi, G{\'{a}}bor and Ceriotti, Michele and G{\"{o}}tz, A.W. Andreas W. and Paesani, Francesco},




journal = {J. Chem. Phys.},


pages = {241725},
title = {{Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions}},

volume = {148},
year = {2018}
}
@article{frau+95prb,
author = {Frauenheim, Th. and Weich, F. and K{\"{o}}hler, Th. and Uhlmann, S. and Porezag, D. and Seifert, G.},



journal = {Phys. Rev. B},



pages = {11492--11501},
title = {{Density-functional-based construction of transferable nonorthogonal tight-binding potentials for Si and SiH}},

volume = {52},
year = {1995}
}
@article{hess+08jctc,
author = {Hess, B and Kutzner, C and van der Spoel, D and Lindahl, E},

journal = {J. Chem. Theory Comput.},

pages = {435--447},
title = {{{\{}GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation{\}}}},
volume = {4},
year = {2008}
}
@article{merz-kupk15cgd,
author = {Merz, Klaus and Kupka, Anna},



journal = {Crystal Growth {\{}{\&}{\}} Design},


pages = {1553--1558},
title = {{Deuterium Perturbs the Molecular Arrangement in the Solid State}},

volume = {15},
year = {2015}
}
@article{tiwa-parr13prl,
author = {Tiwary, Pratyush and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {230602},
title = {{From Metadynamics to Dynamics}},

volume = {111},
year = {2013}
}
@article{sand+07cms,
abstract = {A class of proposed coherent precipitate structures (Guinier-Preston zones) in the Al-Mg-Si alloy are investigated using first-principles density functional theory methods. The cluster expansion method is used to extract effective interaction parameters, providing the means for large scale energy calculations of alloy structures. The Mg1Si1 L10 structure and structures related to the Mg5Si6 ????? phase are studied in more detail, and e.g., precipitate/matrix interface energies are presented. Using direct first-principles calculations we show that the former phase is dynamically unstable and thus must be stabilized by the surrounding Al matrix. Monte Carlo simulations and free-energy techniques are used to study the Al rich side of the phase diagram with the current CE parameters, and kinetic Monte Carlo simulations are used to study clustering in the disordered phase. The implications of our findings are discussed in the framework of classical nucleation theories, and we outline possible nucleation mechanisms. ?? 2007 Elsevier B.V. All rights reserved.},
author = {Sandberg, Nils and Slabanja, Mattias and Holmestad, Randi},


isbn = {0927-0256},

journal = {Computational Materials Science},



pages = {309--318},
title = {{Ab initio simulations of clustering and precipitation in Al–Mg–Si alloys}},

volume = {40},
year = {2007}
}
@article{cahn-hill59jcp,
author = {Cahn, John W. and Hilliard, John E.},



journal = {J. Chem. Phys.},

pages = {688},
title = {{Free Energy of a Nonuniform System. III. Nucleation in a Two-Component Incompressible Fluid}},

volume = {31},
year = {1959}
}
@article{rama-vonl15cijc,
abstract = {We introduce property-independent kernels for machine learning modeling of arbitrarily many molecular properties. The kernels encode molecular structures for training sets of varying size, as well as similarity measures sufficiently diffuse in chemical space to sample over all training molecules. Corresponding molecular reference properties provided, they enable the instantaneous generation of ML models which can systematically be improved through the addition of more data. This idea is exemplified for single kernel based modeling of internal energy, enthalpy, free energy, heat capacity, polarizability, electronic spread, zero-point vibrational energy, energies of frontier orbitals, HOMO- LUMO gap, and the highest fundamental vibrational wavenumber. Models of these properties are trained and tested using 112 kilo organic molecules of similar size. Resulting models are discussed as well as the kernels' use for generating and using other property models.},
archivePrefix = {arXiv},
arxivId = {1502.04563v2},
author = {Ramakrishnan, Raghunathan and von Lilienfeld, O Anatole},




journal = {CHIMIA International Journal for Chemistry},



pages = {182--186},
title = {{Many Molecular Properties from One Kernel in Chemical Space}},

volume = {69},
year = {2015}
}
@article{ceri+10prb,
abstract = {Owing to their small mass, hydrogen atoms exhibit strong quantum behavior even at room temperature. Including these effects in first-principles calculations is challenging because of the huge computational effort required by conventional techniques. Here we present the first ab initio application of a recently developed stochastic scheme, which allows to approximate nuclear quantum effects inexpensively. The proton momentum distribution of lithium imide, a material of interest for hydrogen storage, was experimentally measured by inelastic neutron-scattering experiments and compared with the outcome of quantum thermostatted ab initio dynamics. We obtain favorable agreement between theory and experiments for this purely quantum-mechanical property, thereby demonstrating that it is possible to improve the modeling of complex hydrogen-containing materials without additional computational effort. {\textcopyright} 2010 The American Physical Society.},
author = {Ceriotti, Michele and Miceli, Giacomo and Pietropaolo, Antonino and Colognesi, Daniele and Nale, Angeloclaudio and Catti, Michele and Bernasconi, Marco and Parrinello, Michele},



journal = {Phys. Rev. B},

pages = {174306},
publisher = {American Physical Society},
title = {{Nuclear quantum effects in ab initio dynamics: Theory and experiments for lithium imide}},
volume = {82},
year = {2010}
}
@article{ceri+10jctc,
abstract = {Recently, we have shown how a colored-noise Langevin equation can be used in the context of molecular dynamics as a tool to obtain dynamical trajectories whose properties are tailored to display desired sampling features. In the present paper, after having reviewed some analytical results for the stochastic differential equations forming the basis of our approach, we describe in detail the implementation of the generalized Langevin equation thermostat and the fitting procedure used to obtain optimal parameters. We also discuss the simulation of nuclear quantum effects and demonstrate that by carefully choosing parameters one can successfully model strongly anharmonic solids such as neon. For the reader's convenience, a library of thermostat parameters and some demonstrative code can be downloaded from an online repository.},
author = {Ceriotti, Michele and Bussi, Giovanni and Parrinello, Michele},



journal = {J. Chem. Theory Comput.},


pages = {1170--1180},
publisher = {ACS Publications},
title = {{Colored-Noise Thermostats {\`{a}} la Carte}},

volume = {6},
year = {2010}
}
@article{gree-thom59jcs,
author = {Greenwood, N. N. and Thompson, A},



journal = {Journal of the Chemical Society (Resumed)},
pages = {3485},
title = {{The mechanism of electrical conduction in fused phosphoric and trideuterophosphoric acids}},

volume = {VI},
year = {1959}
}
@article{mill73jpc,
abstract = {Self-diffusion coefficients of tritiated water in normal (HzO) and heavy water (DzO) have been measured over the temperature range 1-45'. The diaphragm-cell technique was used and the results are considered to be probably accurate to *0.2{\%}. The data of Longsworth1{\%}2 for HDO diffusion in both HzO and DzO in conjunction with the tritiated water values measured here have been used to calculate the self-diffusion coefficients of pure normal water (HzO-HzO) and pure heavy water (D20-Dz0). These coefficients have em tabulated and compared with molecular dynamics and nmr data.},
author = {Mills, R},


isbn = {0022-3654},

journal = {J. Phys. Chem.},

pages = {685--688},
title = {{Self-diffusion in normal and heavy water in the range 1-45.deg.}},

volume = {77},
year = {1973}
}
@book{tuck08book,
author = {Tuckerman, Mark},
publisher = {Oxford University Press},
title = {{Statistical Mechanics and Molecular Simulations}},
year = {2008}
}
@phdthesis{kurt14phd,
author = {Kurtuldu, G{\"{u}}ven and Rappaz, Michel},
publisher = {EPFL},
title = {{Influence of Trace Elements on the Nucleation and Solidification Morphologies of Fcc Alloys and Relationship with Icosahedral Quasicrystal Formation}},
year = {2014}
}
@article{day+02jcp,
author = {Day, Tyler J. F. and Soudackov, Alexander V. and Čuma, Martin and Schmitt, Udo W. and Voth, Gregory a.},



journal = {J. Chem. Phys.},

mendeley-tags = {center of excess charge},

pages = {5839},
title = {{A second generation multistate empirical valence bond model for proton transport in aqueous systems}},

volume = {117},
year = {2002}
}
@article{mish+10am,
author = {Mishin, Y. and Asta, M. and Li, Ju},



journal = {Acta Materialia},



pages = {1117--1151},
publisher = {Acta Materialia Inc.},
title = {{Atomistic modeling of interfaces and their impact on microstructure and properties}},

volume = {58},
year = {2010}
}
@book{gard03book,
address = {Berlin},
author = {Gardiner, C W},
edition = {Third},
publisher = {Springer},
title = {{Handbook of Stochastic Methods}},
year = {2003}
}
@article{gast+18jcp,
author = {Gastegger, M. and Schwiedrzik, L. and Bittermann, M. and Berzsenyi, F. and Marquetand, P.},


journal = {J. Chem. Phys.},


pages = {241709},
title = {{wACSF—Weighted atom-centered symmetry functions as descriptors in machine learning potentials}},

volume = {148},
year = {2018}
}
@article{gate+90jcp,
author = {Gates, S M and Greenlief, C M and Beach, D B},

journal = {J. Chem. Phys.},

pages = {7493},
title = {{Decomposition mechanism of SiHx species on Si(100)-2x1 for x-2,3, and 4}},
volume = {93},
year = {1990}
}
@article{Vastenhouw2005,
author = {Vastenhouw, Brendan and Bisseling, Rob H.},



journal = {SIAM Review},



pages = {67--95},
title = {{A Two-Dimensional Data Distribution Method for Parallel Sparse Matrix-Vector Multiplication}},

volume = {47},
year = {2005}
}
@article{marc-grig83jcp,
author = {Marchesoni, F and Grigolini, P},

journal = {J. Chem. Phys.},

pages = {6287},
publisher = {AIP},
title = {{On the extension of the Kramers theory of chemical relaxation to the case of nonwhite noise}},
volume = {78},
year = {1983}
}
@article{fren04pnas,
abstract = {The Markov chain Monte Carlo method is an important tool to estimate the average properties of systems with a very large number of accessible states. This technique is used extensively in fields ranging from physics to genetics and economics. The rejection of trial configurations is a central ingredient in existing Markov chain Monte Carlo simulations. I argue that the efficiency of Monte Carlo simulations can be enhanced, sometimes dramatically, by properly sampling configurations that are normally rejected. This "waste-recycling" of microstates is useful in sampling schemes in which only one of a large set of trial configurations is accepted. It differs fundamentally from schemes that extract information about the density of macrostates from virtual Monte Carlo moves. As a simple illustration, I show that the method greatly improves the calculation of the order-parameter distribution of a two-dimensional Ising model. This method should enhance the efficiency of parallel Monte Carlo simulations significantly.},
author = {Frenkel, Daan},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {17571--5},
pmid = {15591337},
title = {{Speed-up of Monte Carlo simulations by sampling of rejected states.}},

volume = {101},
year = {2004}
}
@article{varv+13prb,
abstract = {Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.},
author = {Varvenne, C{\'{e}}line and Bruneval, Fabien and Marinica, Mihai Cosmin and Clouet, Emmanuel},



journal = {Phys. Rev. B - Condensed Matter and Materials Physics},
pages = {1--7},
title = {{Point defect modeling in materials: Coupling ab initio and elasticity approaches}},
volume = {88},
year = {2013}
}
@article{grim+10jcp,
abstract = {The method of dispersion correction as an add-on to standard Kohn-Sham density functional theory (DFT-D) has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific dispersion coefficients and cutoff radii that are both computed from first principles. The coefficients for new eighth-order dispersion terms are computed using established recursion relations. System (geometry) dependent information is used for the first time in a DFT-D type approach by employing the new concept of fractional coordination numbers (CN). They are used to interpolate between dispersion coefficients of atoms in different chemical environments. The method only requires adjustment of two global parameters for each density functional, is asymptotically exact for a gas of weakly interacting neutral atoms, and easily allows the computation of atomic forces. Three-body nonadditivity terms are considered. The method has been assessed on standard benchmark sets for inter- and intramolecular noncovalent interactions with a particular emphasis on a consistent description of light and heavy element systems. The mean absolute deviations for the S22 benchmark set of noncovalent interactions for 11 standard density functionals decrease by 15{\%}-40{\%} compared to the previous (already accurate) DFT-D version. Spectacular improvements are found for a tripeptide-folding model and all tested metallic systems. The rectification of the long-range behavior and the use of more accurate C(6) coefficients also lead to a much better description of large (infinite) systems as shown for graphene sheets and the adsorption of benzene on an Ag(111) surface. For graphene it is found that the inclusion of three-body terms substantially (by about 10{\%}) weakens the interlayer binding. We propose the revised DFT-D method as a general tool for the computation of the dispersion energy in molecules and solids of any kind with DFT and related (low-cost) electronic structure methods for large systems.},
author = {Grimme, Stefan and Antony, Jens and Ehrlich, Stephan and Krieg, Helge},



journal = {J. Chem. Phys.},


pages = {154104},
pmid = {20423165},
title = {{A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu.}},

volume = {132},
year = {2010}
}
@article{beck88pra,
author = {Becke, A D},

journal = {Phys. Rev. A},

pages = {3098},
publisher = {APS},
title = {{Density-functional exchange-energy approximation with correct asymptotic behavior}},
volume = {38},
year = {1988}
}
@article{inou+87jms,
author = {Inoue, Akihisa and Kimura, Hisamichi and Masumoto, Tsuyoshi},



journal = {Journal of Materials Science},


pages = {1758--1768},
title = {{Formation, thermal stability and electrical resistivity of quasicrystalline phase in rapidly quenched Al-Cr alloys}},

volume = {22},
year = {1987}
}
@article{fens+10pre,
author = {Fensin, Saryu J. and Olmsted, David and Buta, Dorel and Asta, Mark and Karma, Alain and Hoyt, J. J.},



journal = {Phys. Rev. E},


pages = {031601},
title = {{Structural disjoining potential for grain-boundary premelting and grain coalescence from molecular-dynamics simulations}},

volume = {81},
year = {2010}
}
@article{kim+76jap,
author = {Kim, K. Y. and Chhabildas, L. C. and Ruoff, a. L.},



journal = {J. Appl. Phys.},

pages = {2862--2866},
publisher = {AIP},
title = {{Isothermal equations of state for lithium fluoride}},

volume = {47},
year = {1976}
}
@article{dono-grim03pnas,
abstract = {We describe a method for recovering the underlying parametrization of scattered data (m(i)) lying on a manifold M embedded in high-dimensional Euclidean space. The method, Hessian-based locally linear embedding, derives from a conceptual framework of local isometry in which the manifold M, viewed as a Riemannian submanifold of the ambient Euclidean Space R(n), is locally isometric to an open, connected subset $\Theta$ of Euclidean space R(d). Because $\Theta$ does not have to be convex, this framework is able to handle a significantly wider class of situations than the original ISOMAP algorithm. The theoretical framework revolves around a quadratic form H(f) = ∫(M)||H(f)(m)||²(F)dm defined on functions f: M--{\textgreater} R. Here Hf denotes the Hessian of f, and H(f) averages the Frobenius norm of the Hessian over M. To define the Hessian, we use orthogonal coordinates on the tangent planes of M. The key observation is that, if M truly is locally isometric to an open, connected subset of R(d), then H(f) has a (d + 1)-dimensional null space consisting of the constant functions and a d-dimensional space of functions spanned by the original isometric coordinates. Hence, the isometric coordinates can be recovered up to a linear isometry. Our method may be viewed as a modification of locally linear embedding and our theoretical framework as a modification of the Laplacian eigenmaps framework, where we substitute a quadratic form based on the Hessian in place of one based on the Laplacian.},
author = {Donoho, David L and Grimes, Carrie},


isbn = {1031596100},

journal = {Proc. Natl. Acad. Sci. USA},


pages = {5591--5596},
pmid = {16576753},
title = {{Hessian eigenmaps: Locally linear embedding techniques for high-dimensional data}},

volume = {100},
year = {2003}
}
@article{dabro+99prb,
author = {Dabrowski, B and Xiong, X and Bukowski, Z and Dybzinski, R and Klamut, P W and Siewenie, J E and Chmaissem, O and Shaffer, J and Kimball, C W and Jorgensen, J D and Short, S},

journal = {Phys. Rev. B},

pages = {7006--7017},
publisher = {American Physical Society},
title = {{Structure-properties phase diagram for La{\_}1-xSr{\_}xMnO{\_}3 (0.1{\textless} x{\textless} 0.2) }},
volume = {60},
year = {1999}
}
@article{galv-sugi17jctc,
abstract = {The free energy calculations of complex chemical and biological systems with molec-ular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e. importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbour density estimator (NNDE) and the artifi-cial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation},
author = {Galvelis, Raimondas and Sugita, Yuji},



journal = {J. Chem. Theory Comput.},

pages = {2489--2500},
title = {{Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics}},
volume = {13},
year = {2017}
}
@article{cepe-poll86prl,
author = {Ceperley, DM M and Pollock, EL L},



journal = {Phys. Rev. Lett.},


pages = {351--354},
title = {{Path-integral computation of the low-temperature properties of liquid 4He}},

volume = {56},
year = {1986}
}
@article{shel09jcp,
abstract = {The electric field of dissolved ions accounts for the narrow spike at zero frequency shift, with the polarization signature of a polar longitudinal collective mode, in the high resolution hyper-Rayleigh light scattering (HRS) spectrum for liquid water and other polar solvents. This peak in the HRS spectrum probes both the structure factor and the fluctuation time for the ion charge density in solution. The experimental results for KCl-D(2)O solutions are consistent with the Debye-Huckel charge structure factor and determine the diffusion coefficient and static local field factor.},
author = {Shelton, David P},



journal = {J. Chem. Phys.},

mendeley-tags = {SHS,ions in solution,mean-field model},


pages = {114501},
pmid = {19317539},
title = {{Electric field of Ions in solution probed by hyper-Rayleigh scattering.}},

volume = {130},
year = {2009}
}
@article{zen+18pnas,
author = {Zen, Andrea and Brandenburg, Jan Gerit and Klime{\v{s}}, Jiř{\'{i}} and Tkatchenko, Alexandre and Alf{\`{e}}, Dario and Michaelides, Angelos},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {1724--1729},
pmid = {29432177},
title = {{Fast and accurate quantum Monte Carlo for molecular crystals}},

volume = {115},
year = {2018}
}
@article{Moler2003,
author = {Moler, Cleve and {Van Loan}, Charles},



journal = {SIAM Review},



pages = {3--49},
title = {{Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later}},

volume = {45},
year = {2003}
}
@article{gude72jcp,
author = {G{\"{u}}del, H U},

journal = {J. Chem. Phys.},

pages = {4984--4989},
publisher = {AIP},
title = {{Hydrogen Bonds in H[sub 3]Co(CN)[sub 6] and D[sub 3]Co(CN)[sub 6]. Model Calculations}},
volume = {56},
year = {1972}
}
@article{moli+09jpcb,
author = {Molinero, Valeria and Moore, Emily B},



journal = {J. Phys. Chem. B},

pages = {4008--4016},
title = {{Water Modeled As an Intermediate Element between Carbon and Silicon †}},

volume = {113},
year = {2009}
}
@article{suzu95pla,
author = {Suzuki, M},

journal = {Phys. Lett. A},

pages = {425--428},
publisher = {Elsevier},
title = {{Hybrid exponential product formulas for unbounded operators with possible applications to Monte Carlo simulations}},
volume = {201},
year = {1995}
}
@book{bish11book,
author = {Bishop, Christopher M},
isbn = {0387310738},
publisher = {Springer},
title = {{Pattern Recognition and Machine Learning (Information Science and Statistics)}},
year = {2011}
}
@article{bold+03jtac,
author = {Boldyreva, E V and Drebushchak, V A and Drebushchak, T N},



pages = {409--418},
title = {{POLYMORPHISM OF GLYCINE Thermodynamic aspects . Part I . Relative stability of the polymorphs}},
volume = {73},
year = {2003}
}
@article{deri-csan17prb,
abstract = {We introduce a Gaussian approximation potential (GAP) for atomistic simulations of liquid and amorphous elemental carbon. Based on a machine-learning representation of the density-functional theory (DFT) potential-energy surface, such interatomic potentials enable materials simulations with close-to DFT accuracy but at much lower computational cost. We first determine the maximum accuracy that any finite-range potential can achieve in carbon structures; then, using a novel hierarchical set of two-, three-, and many-body structural descriptors, we construct a GAP model that can indeed reach the target accuracy. The potential yields accurate energetic and structural properties over a wide range of densities; it also correctly captures the structure of the liquid phases, at variance with state-of-the-art empirical potentials. Exemplary applications of the GAP model to surfaces of "diamond-like" tetrahedral amorphous carbon (ta-C) are presented, including an estimate of the amorphous material's surface energy, and simulations of high-temperature surface reconstructions ("graphitization"). The new interatomic potential appears to be promising for realistic and accurate simulations of nanoscale amorphous carbon structures.},
archivePrefix = {arXiv},
arxivId = {1611.03277},
author = {Deringer, Volker L. and Cs{\'{a}}nyi, G{\'{a}}bor},




journal = {Phys. Rev. B},


pages = {094203},
title = {{Machine learning based interatomic potential for amorphous carbon}},

volume = {95},
year = {2017}
}
@article{schl-zutt01nature,
abstract = {Mobility--the transport of people and goods - is a socioeconomic reality that will surely increase in the coming years. It should be safe, economic and reasonably clean. Little energy needs to be expended to overcome potential energy changes, but a great deal is lost through friction (for cars about 10 kWh per 100 km) and low-efficiency energy conversion. Vehicles can be run either by connecting them to a continuous supply of energy or by storing energy on board. Hydrogen would be ideal as a synthetic fuel because it is lightweight, highly abundant and its oxidation product (water) is environmentally benign, but storage remains a problem. Here we present recent developments in the search for innovative materials with high hydrogen-storage capacity.},
author = {Schlapbach, Louis and Z{\"{u}}ttel, Andreas},



journal = {Nature},


pages = {353--8},
pmid = {11713542},
title = {{Hydrogen-storage materials for mobile applications.}},

volume = {414},
year = {2001}
}
@article{putr+00jcp,
author = {Putrino, Anna and Sebastiani, Daniel and Parrinello, Michele},


journal = {J. Chem. Phys.},

pages = {7102},
title = {{Generalized variational density functional perturbation theory}},

volume = {113},
year = {2000}
}
@article{zhan+05jpcb,
author = {Zhang, C and Dyer, M and Alavi, A},

journal = {J. Phys. Chem. B},

pages = {22089--22091},
publisher = {Washington, DC: American Chemical Society, c1997-},
title = {{Quantum delocalization of hydrogen in the Li2NH crystal}},
volume = {109},
year = {2005}
}
@article{kulk+90surf,
author = {Kulkarni, S K and Gates, S M and Scott, B A and Sawiri, H H and Kulkami, S K},

journal = {Surf. Sci.},

pages = {13},
title = {{Modulated molecular beam scattering of disilane on silicon}},
volume = {239},
year = {1990}
}
@article{buss+09jcp,
author = {Bussi, Giovanni and Zykova-Timan, Tatyana and Parrinello, Michele},



journal = {J. Chem. Phys.},


pages = {074101},
publisher = {AIP},
title = {{Isothermal-isobaric molecular dynamics using stochastic velocity rescaling}},

volume = {130},
year = {2009}
}
@article{Publishing2011,
author = {Publishing, Blackwell},
pages = {3--23},
title = {{No Title}},
volume = {55},
year = {2011}
}
@article{rodr-laio14science,
abstract = {Cluster analysis is aimed at classifying elements into categories on the basis of their similarity. Its applications range from astronomy to bioinformatics, bibliometrics, and pattern recognition. We propose an approach based on the idea that cluster centers are characterized by a higher density than their neighbors and by a relatively large distance from points with higher densities. This idea forms the basis of a clustering procedure in which the number of clusters arises intuitively, outliers are automatically spotted and excluded from the analysis, and clusters are recognized regardless of their shape and of the dimensionality of the space in which they are embedded. We demonstrate the power of the algorithm on several test cases.},
author = {Rodriguez, Alex and Laio, Alessandro},


isbn = {1095-9203},

journal = {Science (New York, N.Y.)},

pages = {1492--1496},
pmid = {24970081},
title = {{Machine learning. Clustering by fast search and find of density peaks.}},

volume = {344},
year = {2014}
}
@article{diac-shah97peis,
author = {Diaconis, Persi and Shahshahani, Mehrdad},

journal = {Probability in the Engineering and Information Sciences},
pages = {15--32},
title = {{The subgroup algorithm for generating uniform random variables}},
volume = {1},
year = {1987}
}
@article{haye+09jpcb,
abstract = {The mono-, di-, and tetrahydrates of trifluoromethanesulfonic acid, which contain characteristic H(3)O(+), H(5)O(2)(+), and H(9)O(4)(+) structures, provide model systems for understanding proton transport in materials with high perfluorosulfonic acid density such as perfluorosulfonic acid membranes commonly employed in hydrogen fuel cells. Ab initio molecular dynamics simulations indicate that protons in these solids are predisposed to transfer to the water most strongly bound to sulfonate groups via a Grotthuss-type mechanism, but quickly return to the most solvated defect structure either due to the lack of a nearby species to stabilize the new defect or a preference for the proton to be maximally hydrated. Path integral molecular dynamics of the mono- and dihydrate reveal significant quantum effects that facilitate proton transfer to the "presolvated" water or SO(3)(-) in the first solvation shell and increase the Zundel character of all the defects. These trends are quantified in free energy profiles for each bonding environment. Hydrogen bonding criteria for HOH-OH(2) and HOH-O(3)S are extracted from the two-dimensional potential of mean force. The quantum radial distribution function, radius of gyration, and root-mean-square displacement position correlation function show that the protonic charge is distributed over two or more water molecules. Metastable structural defects with one excess proton shared between two sulfonate groups and another Zundel or Eigen type cation defect are found for the mono- and dihydrate but not for the tetrahydrate crystal. Results for the tetrahydrate native crystal exhibit minor differences at 210 and 250 K. IR spectra are calculated for all native and stable defect structures. Graph theory techniques are used to characterize the chain lengths and ring sizes in the hydrogen bond network. Low conductivities when limited water is present may be attributable to trapping of protons between SO(3)(-) groups and the increased probability that protons transfer to waters bridging two different sulfonate groups.},
author = {Hayes, Robin L and Paddison, Stephen J and Tuckerman, Mark E},



journal = {J. Phys. Chem.. B},


pages = {16574--89},
pmid = {19968267},
title = {{Proton transport in triflic acid hydrates studied via path integral car-parrinello molecular dynamics.}},

volume = {113},
year = {2009}
}
@article{smar-sriv05jcp,
abstract = {First-principles pseudopotential calculations, within a simple dynamically constrained scheme, have been performed to investigate the reaction of 0.25 ML coverage of SiH4 and Si2H6 with the Si(001)-(2 x 2) surface. The silane molecule (SiH4) is adsorbed on to the surface at a number of different sites (on dimer, interrow, or intrarow) with varying barrier heights. Two distinct structures, which are similar in energy, arise from the initial dissociative reaction SiH4--{\textgreater}SiH3(silyl) + H, where the dissociated species are adsorbed either on the same dimer components or on adjacent dimer components. Several further decays of silyl from SiH4 are presented in two separate regimes of high and low ambient hydrogen coverages. The decomposition of silyl can form two different bridging structures: an on top or an intrarow bridging structure in both of the two hydrogen coverage regimes. The disilane molecule (Si2H6) is also adsorbed upon this surface with varying energy barriers, resulting in a dissociation reaction where two SiH3 species are adsorbed on one dimer or in an adjacent dimer configuration. Plausible energy reaction paths for the above models are presented. The stability of the SiH2 species is also discussed.},
author = {Smardon, R D and Srivastava, G P},



journal = {J. Chem. Phys.},


pages = {174703},
pmid = {16375553},
title = {{Ab initio surface reaction energetics of SiH4 and Si2H6 on Si(001)-2x2}},

volume = {123},
year = {2005}
}
@article{four+09jacs,
author = {Fournier, Bertrand and Bendeif, El-Eulmi and Guillot, Benoît Benoi$\backslash${\^{}}t and Podjarny, Alberto and Lecomte, Claude and Jelsch, Christian},


journal = {J. Chem. Am. Soc. },


pages = {10929--10941},
publisher = {American Chemical Society ({\{}ACS{\}})},
title = {{Charge Density and Electrostatic Interactions of Fidarestat, an Inhibitor of Human Aldose Reductase}},

volume = {131},
year = {2009}
}
@article{mark-mano08cpl,
author = {Markland, Thomas E and Manolopoulos, David E},

journal = {Chem. Phys. Lett.},

pages = {256},
title = {{A refined ring polymer contraction scheme for systems with electrostatic interactions}},
volume = {464},
year = {2008}
}
@article{jans+99jcp,
abstract = {Molecular dynamics (MD) simulation is used to assess the hyper-Rayleigh scattering (HRS) depolarization ratio of liquid nitrobenzene subject to vertically polarized light. In contrast to previous theoretical work, we have quantified both incoherent and coherent scattering arising from positional and orientational inhomogeneities in the molecular distribution. Although coherent scattering is shown to be much less important than in the case of Rayleigh scattering, it can not be neglected. Therefore, our analysis supports the current practice of working with dilute solutions (for which coherent contributions to HRS are truly negligible) to extract the first molecular hyperpolarizability from HRS measurements. In cases where experiments with pure liquids can not be circumvented, our analysis may be used to separate coherent and incoherent signals. Our work, which uses as input static “gas-phase” (hyper)polarizabilities obtained from ab initio calculations, also provides information on the orientations and magnitudes of the local electric fields experienced by the individual molecules in the liquid. For nitrobenzene it is found that the local fields are largely determined by specific dipolar alignment between neighboring pairs of molecules, with consequences on the HRS signal.},
author = {Janssen, R. H. C. and Theodorou, D. N. and Raptis, S. and Papadopoulos, M. G.},



journal = {J. Chem. Phys.},

pages = {9711},
title = {{Molecular simulation of static hyper-Rayleigh scattering: A calculation of the depolarization ratio and the local fields for liquid nitrobenzene}},

volume = {111},
year = {1999}
}
@article{poma-dell10prl,
author = {Poma, A. B. and {Delle Site}, L.},



journal = {Phys. Rev. Lett.},


pages = {250201},
publisher = {American Physical Society},
title = {{Classical to Path-Integral Adaptive Resolution in Molecular Simulation: Towards a Smooth Quantum-Classical Coupling}},

volume = {104},
year = {2010}
}
@article{chen+16sa,
abstract = {{\textcopyright} The Authors. Electrolytes interact with water in many ways: Changing dipole orientation, inducing charge transfer, and distorting the hydrogen-bond network in the bulk and at interfaces. Numerous experiments and computations have detected short-range perturbations that extend up to three hydration shells around individual ions. We report a multiscale investigation of the bulk and surface of aqueous electrolyte solutions that extends from the atomic scale (using atomistic modeling) to nanoscopic length scales (using bulk and interfacial femtosecond second harmonic measurements) to the macroscopic scale (using surface tension experiments). Electrolytes induce orientational order at concentrations starting at 10 mM that causes nonspecific changes in the surface tension of dilute electrolyte solutions. Aside from ion-dipole interactions, collective hydrogen-bond interactions are crucial and explain the observed difference of a factor of 6 between light water and heavy water. 2016},
author = {Chen, Y. and Okur, H.I. I. and Gomopoulos, N. and Macias-Romero, C. and Cremer, P.S. S. and Petersen, P.B. B. and Tocci, G. and Wilkins, D.M. M. and Liang, C. and Ceriotti, M. and Roke, S.},



journal = {Science Advances},


pages = {e1501891--e1501891},
title = {{Electrolytes induce long-range orientational order and free energy changes in the H-bond network of bulk water}},

volume = {2},
year = {2016}
}
@article{buss+06jacs,
author = {Bussi, G and Gervasio, F L and Laio, A and Parrinello, M},

journal = {J. Chem. Am. Soc. },

pages = {13435--13441},
publisher = {ACS Publications},
title = {{Free-energy landscape for {\{}$\beta${\}} hairpin folding from combined parallel tempering and metadynamics}},
volume = {128},
year = {2006}
}
@article{good-soka86prl,
author = {Goodman, Jonathan and Sokal, Alan},



journal = {Phys. Rev. Lett.},


pages = {1015--1018},
title = {{Multigrid Monte Carlo Method for Lattice Field Theories}},

volume = {56},
year = {1986}
}
@article{swam+11jmr,
author = {Swamy, V T and Ranganathan, S and Chattopadhyay, K},



journal = {J. Mat. Res.},


pages = {539--551},
title = {{Rapidly solidified Al-Cr alloys: Crystalline and quasicrystalline phases}},

volume = {4},
year = {2011}
}
@article{patr+08pccp,
abstract = {An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations (also known as temperature-replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability Pdes. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes (correlation 97{\%}), independent of force field and over a wide temperature range. To facilitate its use, the algorithm has been implemented as a web server at .},
author = {Patriksson, Alexandra and van der Spoel, David},



journal = {PCCP},



pages = {2073--7},
pmid = {18688361},
title = {{A temperature predictor for parallel tempering simulations.}},

volume = {10},
year = {2008}
}
@article{mark-mano08jcp,
abstract = {A quantum simulation of an imaginary time path integral typically requires around n times more computational effort than the corresponding classical simulation, where n is the number of ring polymer beads (or imaginary time slices) used in the calculation. However, this estimate neglects the fact that the potential energies of many systems can be decomposed into a sum of rapidly varying short-range and slowly varying long-range contributions. For such systems, the computational effort of the path integral simulation can be reduced considerably by evaluating the long-range forces on a contracted ring polymer with fewer beads than are needed to evaluate the short-range forces. This idea is developed and then illustrated with an application to a flexible model of liquid water in which the intramolecular forces are evaluated with 32 beads, the oxygen-oxygen Lennard-Jones forces with seven, and the intermolecular electrostatic forces with just five. The resulting static and dynamic properties are within a few percent of those of a full 32-bead calculation, and yet they are obtained with a computational effort less than six times (rather than 32 times) that of a classical simulation. We hope that this development will encourage future studies of quantum mechanical fluctuations in liquid water and aqueous solutions and in many other systems with similar interaction potentials.},
author = {Markland, Thomas E and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {024105},
pmid = {18624514},
title = {{An efficient ring polymer contraction scheme for imaginary time path integral simulations.}},

volume = {129},
year = {2008}
}
@article{shap16mms,
author = {Shapeev, Alexander V.},


journal = {Multiscale Modeling {\&} Simulation},


pages = {1153--1173},
title = {{Moment Tensor Potentials: A Class of Systematically Improvable Interatomic Potentials}},

volume = {14},
year = {2016}
}
@article{alav+94prl,
author = {Alavi, Ali and Kohanoff, Jorge and Parrinello, Michele and Frenkel, Daan},



journal = {Phys. Rev. Lett.},


pages = {2599--2602},
title = {{Ab Initio Molecular Dynamics with Excited Electrons}},

volume = {73},
year = {1994}
}
@article{laio-gerv08rpp,
author = {Laio, A and Gervasio, F L},

journal = {Rep. Prog. Phys.},
pages = {126601},
publisher = {Institute of Physics Publishing},
title = {{Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science}},
volume = {71},
year = {2008}
}
@article{bao+06pre,
author = {Bao, Jing-Dong and Zhou, Yan and L{\"{u}}, Kun},

journal = {Phys. Rev. E (Statistical, Nonlinear, Soft Matter Physics)},

pages = {41125},
publisher = {APS},
title = {{Anomalous diffusion in periodic potentials under self-similar colored noise}},
volume = {74},
year = {2006}
}
@article{enge+18ncomm,
abstract = {{\textcopyright} 2018 The Author(s). Ice is one of the most extensively studied condensed matter systems. Yet, both experimentally and theoretically several new phases have been discovered over the last years. Here we report a large-scale density-functional-theory study of the configuration space of water ice. We geometry optimise 74,963 ice structures, which are selected and constructed from over five million tetrahedral networks listed in the databases of Treacy, Deem, and the International Zeolite Association. All prior knowledge of ice is set aside and we introduce "generalised convex hulls" to identify configurations stabilised by appropriate thermodynamic constraints. We thereby rediscover all known phases (I-XVII, i, 0 and the quartz phase) except the metastable ice IV. Crucially, we also find promising candidates for ices XVIII through LI. Using the "sketch-map" dimensionality-reduction algorithm we construct an a priori, navigable map of configuration space, which reproduces similarity relations between structures and highlights the novel candidates. By relating the known phases to the tractably small, yet structurally diverse set of synthesisable candidate structures, we provide an excellent starting point for identifying formation pathways.},
author = {Engel, E.A. Edgar A and Anelli, Andrea and Ceriotti, Michele and Pickard, Chris J C.J. and Needs, R.J. Richard J},


isbn = {4146701804618},

journal = {Nature Comm.},


pages = {2173},
publisher = {Springer US},
title = {{Mapping uncharted territory in ice from zeolite networks to ice structures}},

volume = {9},
year = {2018}
}
@article{desi11ac,
author = {Desiraju, Gautam R},



journal = {Angewandte Chemie (International ed. in English)},



pages = {52--9},
pmid = {21031379},
title = {{A bond by any other name.}},

volume = {50},
year = {2011}
}
@article{spri+85jcp,
author = {Sprik, Michiel and Klein, Michael and Chandler, David},



journal = {Phys. Rev. B},


pages = {4234--4244},
title = {{Staging: A sampling technique for the Monte Carlo evaluation of path integrals}},

volume = {31},
year = {1985}
}
@article{fren-wise97acm,
author = {Frens, Jeremy D and Wise, David S},



journal = {ACM SIGPLAN Notices},


pages = {206--216},
title = {{Auto-blocking matrix-multiplication or tracking BLAS3 performance from source code}},

volume = {32},
year = {1997}
}
@article{spae94ssp,
abstract = {The essential nature of simple liquids and the ubiquity of fivefold symmetrical local order were confirmed in the analysis of physical models, such as the dense random packing of hard spheres4 or computer-generated ones,5 and formed the basis of a formal},
author = {Spaepen, Frans},



journal = {Solid State Physics - Advances in Research and Applications},

pages = {1--32},
title = {{Homogeneous Nucleation and the Temperature Dependence of the Crystal-Melt Interfacial Tension}},
volume = {47},
year = {1994}
}
@article{egor+97jcp,
author = {Egorov, S. A. and Gallicchio, E. and Berne, B. J.},



journal = {J. Chem. Phys.},

pages = {9312},
title = {{The simulation of electronic absorption spectrum of a chromophore coupled to a condensed phase environment: Maximum entropy versus singular value decomposition approaches}},

volume = {107},
year = {1997}
}
@unpublished{biblio-car-parrinello,
title = {{No Title}}
}
@article{li-brou87jcp,
author = {Li, X P and Broughton, J Q},

journal = {J. Chem. Phys.},
pages = {5094},
title = {{High-order correction to the Trotter expansion for use in computer simulation}},
volume = {86},
year = {1987}
}
@article{mori+90jcp,
author = {Morishige, K. and Kawamura, K. and Kose, A.},



journal = {J. Chem. Phys.},

pages = {5267},
title = {{X-ray diffraction study of the structure of a monolayer methanol film adsorbed on graphite}},

volume = {93},
year = {1990}
}
@article{vand+05jcp,
abstract = {The performance of density functional theory methods for the modeling of condensed aqueous systems is hard to predict and validation by ab initio molecular simulation of liquid water is absolutely necessary. In order to assess the reliability of these tests, the effect of temperature on the structure and dynamics of liquid water has been characterized with 16 simulations of 20 ps in the temperature range of 280-380 K. We find a pronounced influence of temperature on the pair correlation functions and on the diffusion constant including nonergodic behavior on the time scale of the simulation in the lower temperature range (which includes ambient temperature). These observations were taken into account in a consistent comparison of a series of density functionals (BLYP, PBE, TPSS, OLYP, HCTH120, HCTH407). All simulations were carried out using an ab initio molecular dynamics approach in which wave functions are represented using Gaussians and the density is expanded in an auxiliary basis of plane waves. Whereas the first three functionals show similar behavior, it is found that the latter three functionals yield more diffusive dynamics and less structure.},
author = {VandeVondele, Joost and Mohamed, Fawzi and Krack, Matthias and Hutter, J{\"{u}}rg and Sprik, Michiel and Parrinello, Michele},



journal = {J. Chem. Phys.},


pages = {14515},
pmid = {15638682},
title = {{The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water.}},

volume = {122},
year = {2005}
}
@article{polt+18jcp,
author = {Poltavsky, Igor and DiStasio, Robert A. and Tkatchenko, Alexandre},


journal = {J. Chem. Phys.},


pages = {102325},
title = {{Perturbed path integrals in imaginary time: Efficiently modeling nuclear quantum effects in molecules and materials}},

volume = {148},
year = {2018}
}
@article{rems+11jsp,
abstract = {Using concepts from perturbation and local molecular field theories of liquids we divide the potential of the SPC/E water model into short and long ranged parts. The short ranged parts define a minimal reference network model that captures very well the structure of the local hydrogen bond network in bulk water while ignoring effects of the remaining long ranged interactions. This deconstruction can provide insight into the different roles that the local hydrogen bond network, dispersion forces, and long ranged dipolar interactions play in determining a variety of properties of SPC/E and related classical models of water. Here we focus on the anomalous behavior of the internal pressure and the temperature dependence of the density of bulk water. We further utilize these short ranged models along with local molecular field theory to quantify the influence of these interactions on the structure of hydrophobic interfaces and the crossover from small to large scale hydration behavior. The implications of our findings for theories of hydrophobicity and possible refinements of classical water models are also discussed.},
archivePrefix = {arXiv},
arxivId = {1107.5593},
author = {Remsing, Richard C. and Rodgers, Jocelyn M. and Weeks, John D.},




journal = {J. Stat. Phys.},



pages = {313--334},
title = {{Deconstructing Classical Water Models at Interfaces and in Bulk}},

volume = {145},
year = {2011}
}
@article{mart+99jcp,
author = {Martyna, Glenn J and Hughes, Adam and Tuckerman, Mark E},



journal = {J. Chem. Phys.},

pages = {3275},
publisher = {AIP},
title = {{Molecular dynamics algorithms for path integrals at constant pressure}},

volume = {110},
year = {1999}
}
@article{koha+92prb,
author = {Kohanoff, Jorge and Andreoni, Wanda and Parrinello, Michele},



journal = {Phys. Rev. B},


pages = {4371--4373},
publisher = {APS},
title = {{Zero-point-motion effects on the structure of C60}},

volume = {46},
year = {1992}
}
@article{torr-vall99jcp,
author = {Torrie, G.M. M and Valleau, J.P. P},



journal = {J. Comp. Phys.},


pages = {187--199},
title = {{Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling}},

volume = {23},
year = {1977}
}
@article{cour+13jacs,
abstract = {In this work, we report that organocatalyst 1-Bcat-2-PPh2-C6H4 ((1); cat = catechol) acts as an ambiphilic metal-free system for the reduction of carbon dioxide in presence of hydroboranes (HBR2 = HBcat (catecholborane), HBpin (pinacolborane), 9-BBN (9-borabicyclo[3.3.1]nonane), BH3{\textperiodcentered}SMe2 and BH3{\textperiodcentered}THF) to generate CH3OBR2 or (CH3OBO)3, products that can be readily hydrolyzed to methanol. The yields can be as high as 99{\%} with exclusive formation of CH3OBR2 or (CH3OBO)3 with TON (turnover numbers) and TOF (turnover frequencies) reaching {\textgreater}2950 and 853 h(-1), respectively. Furthermore, the catalyst exhibits "living" behavior: once the first loading is consumed, it resumes its activity on adding another loading of reagents.},
author = {Courtemanche, Marc-Andr{\'{e}} and L{\'{e}}gar{\'{e}}, Marc-Andr{\'{e}} and Maron, Laurent and Fontaine, Fr{\'{e}}d{\'{e}}ric-Georges},



journal = {J. Chem. Am. Soc. },


pages = {9326--9},
pmid = {23750670},
title = {{A highly active phosphine-borane organocatalyst for the reduction of CO2 to methanol using hydroboranes.}},

volume = {135},
year = {2013}
}
@article{shep+08jcp,
abstract = {A comparison of chain-of-states based methods for finding minimum energy pathways (MEPs) is presented. In each method, a set of images along an initial pathway between two local minima is relaxed to find a MEP. We compare the nudged elastic band (NEB), doubly nudged elastic band, string, and simplified string methods, each with a set of commonly used optimizers. Our results show that the NEB and string methods are essentially equivalent and the most efficient methods for finding MEPs when coupled with a suitable optimizer. The most efficient optimizer was found to be a form of the limited-memory Broyden-Fletcher-Goldfarb-Shanno method in which the approximate inverse Hessian is constructed globally for all images along the path. The use of a climbing-image allows for finding the saddle point while representing the MEP with as few images as possible. If a highly accurate MEP is desired, it is found to be more efficient to descend from the saddle to the minima than to use a chain-of-states method with many images. Our results are based on a pairwise Morse potential to model rearrangements of a heptamer island on Pt(111), and plane-wave based density functional theory to model a rollover diffusion mechanism of a Pd tetramer on MgO(100) and dissociative adsorption and diffusion of oxygen on Au(111).},
author = {Sheppard, Daniel and Terrell, Rye and Henkelman, Graeme},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pages = {1--10},
pmid = {18397052},
title = {{Optimization methods for finding minimum energy paths}},
volume = {128},
year = {2008}
}
@article{kirk+83science,
abstract = {There is a deep and useful connection between statistical mechanics (the behavior of systems with many degrees of freedom in thermal equilibrium at a finite temperature) and multivariate or combinatorial optimization (finding the minimum of a given function depending on many parameters). A detailed analogy with annealing in solids provides a framework for optimization of the properties of very large and complex systems. This connection to statistical mechanics exposes new information and provides an unfamiliar perspective on traditional optimization problems and methods.},
author = {Kirkpatrick, S and Gelatt, C D and Vecchi, M P},



journal = {Science},


pages = {671--680},
pmid = {17813860},
publisher = {American Association for the Advancement of Science},
series = {New Series},
title = {{Optimization by Simulated Annealing}},

volume = {220},
year = {1983}
}
@article{hall+16jcp,
abstract = {We present efficient finite difference estimators for goal-oriented sensitivity indices with applications to the generalized Langevin equation (GLE). In particular, we apply these estimators to analyze an extended variable formulation of the GLE where other well known sensitivity analysis techniques such as the likelihood ratio method are not applicable to key parameters of interest. These easily implemented estimators are formed by coupling the nominal and perturbed dynamics appearing in the finite difference through a common driving noise, or common random path. After developing a general framework for variance reduction via coupling, we demonstrate the optimality of the common random path coupling in the sense that it produces a minimal variance surrogate for the difference estimator relative to sampling dynamics driven by independent paths. In order to build intuition for the common random path coupling, we evaluate the efficiency of the proposed estimators for a comprehensive set of examples of interest in particle dynamics. These reduced variance difference estimators are also a useful tool for performing global sensitivity analysis and for investigating non-local perturbations of parameters, such as increasing the number of Prony modes active in an extended variable GLE.},
archivePrefix = {arXiv},
arxivId = {1609.02739},
author = {Hall, Eric Joseph and Katsoulakis, Markos A. and Rey-Bellet, Luc},




journal = {J. Chem. Phys.},



pages = {224108},
title = {{Uncertainty quantification for generalized Langevin dynamics}},

volume = {145},
year = {2016}
}
@article{vans-derl01prb,
author = {{Van Swygenhoven}, H. and Derlet, P.},



journal = {Phys. Rev. B},

mendeley-tags = {aluminum},


pages = {224105},
title = {{Grain-boundary sliding in nanocrystalline fcc metals}},

volume = {64},
year = {2001}
}
@article{pond+10jpcb,
abstract = {Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.},
author = {Ponder, Jay W and Wu, Chuanjie and Ren, Pengyu and Pande, Vijay S and Chodera, John D and Schnieders, Michael J and Haque, Imran and Mobley, David L and Lambrecht, Daniel S and DiStasio, Robert A and Head-Gordon, Martin and Clark, Gary N I and Johnson, Margaret E and Head-Gordon, Teresa},



journal = {J. Phys. Chem.. B},



pages = {2549--2564},
pmid = {20136072},
title = {{Current status of the AMOEBA polarizable force field.}},

volume = {114},
year = {2010}
}
@article{hall-bern84jcp,
author = {Hall, Randall W. and Berne, B. J.},


journal = {J. Chem. Phys.},


pages = {3641--3643},
title = {{Nonergodicity in path integral molecular dynamics}},

volume = {81},
year = {1984}
}
@article{barr-rodn11jsp,
author = {Barrat, Jean-Louis and Rodney, David},



journal = {J. Stat. Phys.},



pages = {679--689},
title = {{Portable Implementation of a Quantum Thermal Bath for Molecular Dynamics Simulations}},

volume = {144},
year = {2011}
}
@article{impe+82mp,
author = {Impey, R.W. and Madden, P.A. and McDonald, I.R.},


journal = {Mol. Phys.},


pages = {513--539},
title = {{Spectroscopic and transport properties of water}},

volume = {46},
year = {1982}
}
@article{stum-sche96prb,
author = {Stumpf, R and Scheffler, M},


journal = {Phys. Rev.. B, Condensed matter},

mendeley-tags = {aluminum},


pages = {4958--4973},
pmid = {9984058},
title = {{Ab initio calculations of energies and self-diffusion on flat and stepped surfaces of Al and their implications on crystal growth.}},

volume = {53},
year = {1996}
}
@article{reit+12prb,
author = {Reiter, G. F. and Kolesnikov, a. I. and Paddison, S. J. and Platzman, P. M. and Moravsky, a. P. and Adams, M. a. and Mayers, J.},



journal = {Phys. Rev. B},


pages = {045403},
title = {{Evidence for an anomalous quantum state of protons in nanoconfined water}},

volume = {85},
year = {2012}
}
@article{goed-tete95prb,
author = {Goedecker, S and Teter, M},

journal = {Phys. Rev. B},

pages = {9455--9464},
publisher = {APS},
title = {{Tight-binding electronic-structure calculations and tight-binding molecular dynamics with localized orbitals}},
volume = {51},
year = {1995}
}
@article{reit+02prb,
author = {Reiter, G F and Mayers, J and Noreland, J},

journal = {Phys. Rev. B},

pages = {104305},
publisher = {American Physical Society},
title = {{Momentum-distribution spectroscopy using deep inelastic neutron scattering}},
volume = {65},
year = {2002}
}
@article{spiw-kral11jcp,
abstract = {Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling.},
author = {Spiwok, Vojt{\v{e}}ch and Kr{\'{a}}lov{\'{a}}, Blanka},



journal = {J. Chem. Phys.},



pages = {224504},
pmid = {22168700},
title = {{Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap.}},

volume = {135},
year = {2011}
}
@inproceedings{dach+05ieee,
author = {{Dacheng Tao} and {Xuelong Li} and {Weiming Hu} and Maybank, S. and {Xindong Wu}},
booktitle = {Fifth IEEE International Conference on Data Mining (ICDM'05)},


isbn = {0-7695-2278-5},

pages = {450--457},
publisher = {IEEE},
title = {{Supervised Tensor Learning}},

year = {2005}
}
@article{yan+01jac,
author = {Yan, X.-Y and Chang, Y.a and Xie, F.-Y and Chen, S.-L and Zhang, F and Daniel, S},



journal = {J. Alloys Compd.},

mendeley-tags = {aluminum},


pages = {151--160},
title = {{Calculated phase diagrams of aluminum alloys from binary Al-Cu to multicomponent commercial alloys}},

volume = {320},
year = {2001}
}
@article{gris+18prl,
abstract = {Statistical learning methods show great promise in providing an accurate prediction of materials and molecular properties, while minimizing the need for computationally demanding electronic structure calculations. The accuracy and transferability of these models are increased significantly by encoding into the learning procedure the fundamental symmetries of rotational and permutational invariance of scalar properties. However, the prediction of tensorial properties requires that the model respects the appropriate geometric transformations, rather than invariance, when the reference frame is rotated. We introduce a formalism that can be used to perform machine-learning of tensorial properties of arbitrary rank for general molecular geometries. To demonstrate it, we derive a tensor kernel adapted to rotational symmetry, which is the natural generalization of the smooth overlap of atomic positions (SOAP) kernel commonly used for the prediction of scalar properties at the atomic scale. The performance and generality of the approach is demonstrated by learning the instantaneous electrical response of water oligomers of increasing complexity, from the isolated molecule to the condensed phase.},
archivePrefix = {arXiv},
arxivId = {1709.06757},
author = {Grisafi, Andrea and Wilkins, D.M. David M. and Cs{\'{a}}nyi, G{\'{a}}bor and Ceriotti, Michele},




journal = {Phys. Rev. Lett.},


pages = {036002},
title = {{Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems}},

volume = {120},
year = {2018}
}
@article{piet+09bjp,
author = {Pietropaolo, Antonino and Senesi, Roberto and Andreani, Carla and Mayers, Jerry},



journal = {Braz. J. Phys.	},



pages = {318--321},
title = {{Quantum effects in water: proton kinetic energy maxima in stable and supercooled liquid}},

volume = {39},
year = {2009}
}
@article{moll+13nature,
author = {M{\"{o}}ller, Lars and Sowers, Todd and Bock, Michael and Spahni, Renato and Behrens, Melanie and Schmitt, Jochen and Miller, Heinrich and Fischer, Hubertus},



journal = {Nature Geoscience},

mendeley-tags = {fractionation},


pages = {885--890},
title = {{Independent variations of CH4 emissions and isotopic composition over the past 160,000 years}},

volume = {6},
year = {2013}
}
@article{delb+15jcp,
author = {{Del Ben}, Mauro and Hutter, J{\"{u}}rg and VandeVondele, Joost},



journal = {J. Chem. Phys.},

pages = {102803},
title = {{Forces and stress in second order M{\{}{\o}{\}}ller-Plesset perturbation theory for condensed phase systems within the resolution-of-identity Gaussian and plane waves approach}},

volume = {143},
year = {2015}
}
@article{rapp+99mmta,
author = {Rappaz, M and Drezet, J. -M. and Gremaud, M},



journal = {Metallurgical and Materials Transactions A},


pages = {449--455},
title = {{A new hot-tearing criterion}},

volume = {30},
year = {1999}
}
@article{wein-adda11armr,
author = {Weiner, Steve and Addadi, Lia},


journal = {Annu. Rev. Mater. Res.},


pages = {21--40},
title = {{Crystallization Pathways in Biomineralization}},
year = {2011}
}
@article{flam+09jcp,
abstract = {In a recent article [Pietropaolo et al., Phys. Rev. Lett.100, 127802 (2008)] we discussed the results of a deep inelastic neutron scattering experiment aimed at the measure of mean kinetic energy, {\textless}E(k){\textgreater}, and momentum distribution of protons in supercooled water. The observed excess of proton mean kinetic energy, with respect to theoretical predictions and measurements in water stable liquid and solid phases, suggested a possible link between the anomalous temperature dependence of water density and the temperature dependence of {\textless}E(k){\textgreater}. Nevertheless, the limited number of data did not allow a more quantitative description. Here we report on new measurements, above and below the temperature of maximum density and in the supercooled phase. These show two {\textless}E(k){\textgreater} maxima: The first one, in the supercooled phase in the range of 269-272 K, and a second one at 277 K, the temperature of the maximum density of water.},
archivePrefix = {arXiv},
arxivId = {0901.4273},
author = {Flammini, D and Ricci, M a and Bruni, F},




journal = {J. Chem. Phys.},


pages = {236101},
pmid = {19548768},
title = {{A new water anomaly: the temperature dependence of the proton mean kinetic energy.}},

volume = {130},
year = {2009}
}
@article{liu+04msmse,
author = {Liu, Xiang-Yang and Ercolessi, Furio and Adams, James B},



journal = {Modelling and Simulation in Materials Science and Engineering},

mendeley-tags = {aluminum},


pages = {665--670},
title = {{Aluminium interatomic potential from density functional theory calculations with improved stacking fault energy}},

volume = {12},
year = {2004}
}
@article{bern+00sci,
author = {Berner, R. A. and Petsch, S. T. and Lake, J. A. and Beerling, D. J. and Popp, B. N. and Lane, R. S. and Laws, E. A. and Westley, M. B. and Cassar, N. and Woodward, F. I. and Quick, W. P.},



journal = {Science},


pages = {1630--1633},
title = {{Isotope Fractionation and Atmospheric Oxygen: Implications for Phanerozoic O2 Evolution}},

volume = {287},
year = {2000}
}
@article{gall-parr92prl,
author = {Galli, Giulia and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {3547--3550},
publisher = {APS},
title = {{Large scale electronic structure calculations}},

volume = {69},
year = {1992}
}
@article{ifti+00jcp,
author = {Iftimie, Radu and Salahub, Dennis and Wei, Dongqing and Schofield, Jeremy},



journal = {J. Chem. Phys.},

pages = {4852},
title = {{Using a classical potential as an efficient importance function for sampling from an ab initio potential}},

volume = {113},
year = {2000}
}
@article{roma+14jpcs,
author = {Romanelli, G and Fernandez-Alonso, F and Andreani, C},



journal = {Journal of Physics: Conference Series},
pages = {012003},
title = {{The Harmonic Picture of Nuclear Mean Kinetic Energies in Heavy Water}},

volume = {571},
year = {2014}
}
@article{mach09pre,
author = {Machta, J.},



journal = {Phys. Rev. E},


pages = {056706},
title = {{Strengths and weaknesses of parallel tempering}},

volume = {80},
year = {2009}
}
@article{gasp+16jctc,
abstract = {{\textcopyright} 2016 American Chemical Society. The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the interatomic potential, finding that, in most cases, the qualitative features of the hydrogen-bond network are remarkably robust.},
archivePrefix = {arXiv},
arxivId = {arXiv:1602.03577v1},
author = {Gasparotto, Piero and Hassanali, Ali A.A. and Ceriotti, Michele},




journal = {J. Chem. Theory Comput.},



pages = {1953--1964},
title = {{Probing Defects and Correlations in the Hydrogen-Bond Network of ab Initio Water}},

volume = {12},
year = {2016}
}
@article{balo+06jac,
author = {Balogh, M P and Jones, C Y and Herbst, J F and Hector, L G and Others},

journal = {J. Alloys Compd.},

pages = {326--336},
publisher = {Elsevier},
title = {{Crystal structures and phase transformation of deuterated lithium imide, Li2ND}},
volume = {420},
year = {2006}
}
@article{gome+10jcp,
abstract = {When BaZrO(3) is doped with Y in 12.5{\%} of Zr sites, density functional theory with the PBE functional predicts octahedral distortions within a cubic phase yielding a greater variety of proton binding sites than undoped BaZrO(3). Proton binding sites, transition states, and normal modes are found and used to calculate transition state theory rate constants. The binding sites are used to represent vertices in a graph. The rate constants connecting binding sites are used to provide weights for graph edges. Vertex and color coding are used to find proton conduction pathways in BaZr(0.875)Y(0.125)O(3). Many similarly probable proton conduction pathways which can be periodically replicated to yield long range proton conduction are found. The average limiting barriers at 600 K for seven step and eight step periodic pathways are 0.29 and 0.30 eV, respectively. Inclusion of a lattice reorganization barrier raises these to 0.42 and 0.33 eV, respectively. The majority of the seven step pathways have an interoctahedral rate limiting step while the majority of the eight step pathways have an intraoctahedral rate limiting step. While the average limiting barrier of the seven step periodic pathway including a lattice reorganization barrier is closer to experiment, how to appropriately weight different length periodic pathways is not clear. Likely, conduction is influenced by combinations of different length pathways. Vertex and color coding provide useful ways of finding the wide variety of long range proton conduction pathways that contribute to long range proton conduction. They complement more traditional serial methods such as molecular dynamics and kinetic Monte Carlo.},
author = {Gomez, Maria a and Chunduru, Mythili and Chigweshe, Lorencia and Foster, Leigh and Fensin, S J and Fletcher, Katharyn M and Fernandez, Laura E},



journal = {J. Chem. Phys.},


pages = {214709},
pmid = {20528043},
title = {{The effect of yttrium dopant on the proton conduction pathways of BaZrO3, a cubic perovskite.}},

volume = {132},
year = {2010}
}
@article{borm+03eabe,
author = {B{\"{o}}rm, Steffen and Grasedyck, Lars and Hackbusch, Wolfgang and Bo, Steffen},



journal = {Engineering Analysis with Boundary Elements},



pages = {405--422},
publisher = {Elsevier},
title = {{Introduction to hierarchical matrices with applications}},

volume = {27},
year = {2003}
}
@article{rybk-vand17jpcl,
author = {Rybkin, Vladimir V. and VandeVondele, Joost},


journal = {J. Phys. Chem. Letters},


pages = {1424--1428},
title = {{Nuclear Quantum Effects on Aqueous Electron Attachment and Redox Properties}},

volume = {8},
year = {2017}
}
@article{kreu+95ssi,
author = {Kreuer, K},



journal = {Solid State Ionics},



pages = {157--162},
title = {{H/D isotope effect of proton conductivity and proton conduction mechanism in oxides}},

volume = {77},
year = {1995}
}
@article{chen+13pccp,
abstract = {Proton transport (PT) in bulk liquid water and within a thin water-filled carbon nanotube has been examined using ab initio path-integral molecular dynamics (PIMD). Barrierless proton transfer is observed in each case when quantum nuclear effects (QNEs) are accounted for. The key difference between the two systems is that in the nanotube facile PT is facilitated by a favorable pre-alignment of water molecules, whereas in bulk liquid water solvent reorganization is required prior to PT. Configurations where the quantum excess proton is delocalized over several adjacent water molecules along with continuous interconversion between different hydration states reveals that, as in liquid water, the hydrated proton under confinement is best described as a fluxional defect, rather than any individual idealized hydration state such as Zundel, Eigen, or the so-called linear H7O3(+) complex along the water chain. These findings highlight the importance of QNEs in intermediate strength hydrogen bonds (HBs) and explain why H(+) diffusion through nanochannels is impeded much less than other cations.},
author = {Chen, Ji and Li, Xin-Zheng and Zhang, Qianfan and Michaelides, Angelos and Wang, Enge},



journal = {PCCP},

pages = {6344--6349},
pmid = {23518762},
title = {{Nature of proton transport in a water-filled carbon nanotube and in liquid water.}},

year = {2013}
}
@article{jorg+83jcp,
author = {Jorgensen, WL William L William L and Chandrasekhar, Jayaraman and Madura, Jeffry D and Impey, Roger W and Klein, Michael L},

journal = {The Journal of chemical {\ldots}},

pages = {926},
publisher = {AIP},
title = {{Comparison of simple potential functions for simulating liquid water}},

volume = {79},
year = {1983}
}
@article{rick-haym03jcp,
author = {Rick, Steven W. and Haymet, a. D. J.},



journal = {J. Chem. Phys.},

pages = {9291},
title = {{Dielectric constant and proton order and disorder in ice Ih: Monte Carlo computer simulations}},

volume = {118},
year = {2003}
}
@article{swin+95nsb,
author = {Swindells, Mark B. and MacArthur, Malcolm W. and Thornton, Janet M.},



journal = {Nature Structural Biology},


pages = {596--603},
title = {{Intrinsic {\$}\phi{\$},{\$}\psi{\$} propensities of amino acids, derived from the coil regions of known structures}},

volume = {2},
year = {1995}
}
@article{brou-gilm86jcp5,
author = {Broughton, J Q and Gilmer, G H},



journal = {J. Chem. Phys.},

pages = {5749},
title = {{Molecular dynamics of the crystal–fluid interface. V. Structure and dynamics of crystal–melt systems}},

volume = {84},
year = {1986}
}
@article{rosi+03science,
abstract = {Metal-organic framework-5 (MOF-5) of composition Zn4O(BDC)3 (BDC = 1,4-benzenedicarboxylate) with a cubic three-dimensional extended porous structure adsorbed hydrogen up to 4.5 weight percent (17.2 hydrogen molecules per formula unit) at 78 kelvin and 1.0 weight percent at room temperature and pressure of 20 bar. Inelastic neutron scattering spectroscopy of the rotational transitions of the adsorbed hydrogen molecules indicates the presence of two well-defined binding sites (termed I and II), which we associate with hydrogen binding to zinc and the BDC linker, respectively. Preliminary studies on topologically similar isoreticular metal-organic framework-6 and -8 (IRMOF-6 and -8) having cyclobutylbenzene and naphthalene linkers, respectively, gave approximately double and quadruple (2.0 weight percent) the uptake found for MOF-5 at room temperature and 10 bar.},
author = {Rosi, Nathaniel L and Eckert, Juergen and Eddaoudi, Mohamed and Vodak, David T and Kim, Jaheon and O'Keeffe, Michael and Yaghi, Omar M},



journal = {Science (New York, N.Y.)},


pages = {1127--9},
pmid = {12750515},
title = {{Hydrogen storage in microporous metal-organic frameworks.}},

volume = {300},
year = {2003}
}
@article{deut+06jpcb,
abstract = {Epilayers of single-crystal GaAsPN and GaPN semiconductor samples with varying nitrogen compositions were photoelectrochemically characterized to determine their potential to serve as water splitting photoelectrodes. The band gap and flatband potentials were determined and used to calculate the valence and conduction band edge energies. The band edges for all compositions appear to be too negative by more than 500 mV for any of the materials to effect light-driven water splitting without an external bias. Corrosion analysis was used to establish material stability under operating conditions. GaPN was found to show good stability toward photocorrosion; on the other hand, GaAsPN showed enhanced photocorrosion as compared to GaP.},
author = {Deutsch, Todd G and Koval, Carl a and Turner, John a},



journal = {J. Phys. Chem.. B},


pages = {25297--307},
pmid = {17165975},
title = {{III-V nitride epilayers for photoelectrochemical water splitting: GaPN and GaAsPN.}},

volume = {110},
year = {2006}
}
@article{pan+04jacs,
abstract = {Advancement in hydrogen storage techniques represents one of the most important areas of today's materials research. While extensive efforts have been made to the existing techniques, there is no viable storage technology capable of meeting the DOE cost and performance targets at the present time. New materials with significantly improved hydrogen adsorption capability are needed. Microporous metal coordination materials (MMOM) are promising candidates for use as sorbents in hydrogen adsorption. These materials possess physical characteristics similar to those of single-walled carbon nanotubes (SWNTs) but also exhibit a number of improved features. Here, we report a novel MMOM structure and its room-temperature hydrogen adsorption properties.},
author = {Pan, Long and Sander, Michelle B and Huang, Xiaoying and Li, Jing and Smith, Milton and Bittner, Edward and Bockrath, Bradley and Johnson, J Karl},



journal = {J. Chem. Am. Soc. },


pages = {1308--9},
pmid = {14759166},
title = {{Microporous metal organic materials: promising candidates as sorbents for hydrogen storage.}},

volume = {126},
year = {2004}
}
@article{liu-zhan16jcp,
author = {Liu, Jian and Zhang, Zhijun},



journal = {J. Chem. Phys.},

pages = {034307},
title = {{Path integral Liouville dynamics: Applications to infrared spectra of OH, water, ammonia, and methane}},

volume = {144},
year = {2016}
}
@article{gaus-salm89prd,
author = {Gausterer, H and Salmhofer, M},



journal = {Phys. Rev. D},


pages = {2723--2726},
title = {{Remarks on global Monte Carlo algorithms}},

volume = {40},
year = {1989}
}
@article{tang-scan02jcp,
author = {Tangney, P and Scandolo, S},

journal = {J. Chem. Phys.},
pages = {14},
publisher = {AIP},
title = {{How well do Car{\{}--{\}}Parrinello simulations reproduce the Born{\{}--{\}}Oppenheimer surface?: Theory and examples}},
volume = {116},
year = {2002}
}
@article{hors+96prb,
author = {Horsfield, A P and Godwin, P D and Pettifor, D G and Sutton, A P},

journal = {Phys. Rev. B},

pages = {15773--15775},
publisher = {APS},
title = {{Computational materials synthesis. I. A tight-binding scheme for hydrocarbons}},
volume = {54},
year = {1996}
}
@article{bell-vand00prb,
abstract = {We present an approach to the implementation of the virtual crystal approximation (VCA) for the study of properties of solid solutions in the context of density-functional methods. Our approach can easily be applied to any type of pseudopotential, and also has the advantage that it can be used to obtain estimates of the atomic forces that would arise if the real atoms were present, thus giving insight into the expected displacements in the real alloy. We have applied this VCA technique within the Vanderbilt ultrasoft-pseudopotential scheme to predict dielectric and piezoelectric properties of the Pb(Zr0.5Ti0.5)O-3 solid solution in its paraelectric and ferroelectric phases, respectively. Comparison with calculations performed on ordered alloy supercells and with data on parents compounds demonstrates the adequacy of using the VCA for this perovskite solid solution. In particular, the VCA approach reproduces the anomalous Born effective charges and the large value of the piezoelectric coefficients.},
author = {Bellaiche, L and Vanderbilt, David},

journal = {Phys. Rev. B},

pages = {7877--7882},
publisher = {American Physical Society},
title = {{Virtual crystal approximation revisited: Application to dielectric and piezoelectric properties of perovskites}},

volume = {61},
year = {2000}
}
@article{mish+01prb,
author = {Mishin, Y. and Mehl, M. and Papaconstantopoulos, D. and Voter, A. and Kress, J.},



journal = {Phys. Rev. B},


pages = {224106},
title = {{Structural stability and lattice defects in copper: Ab initio, tight-binding, and embedded-atom calculations}},

volume = {63},
year = {2001}
}
@article{spri91jpc,
author = {Sprik, Michiel},


isbn = {0022365419},

journal = {J. Phys. Chem.},


pages = {2283--2291},
publisher = {American Chemical Society},
title = {{Computer simulation of the dynamics of induced polarization fluctuations in water}},

volume = {95},
year = {1991}
}
@article{schu+18jcp,
author = {Sch{\"{u}}tt, K. T. and Sauceda, H. E. and Kindermans, P.-J. and Tkatchenko, A. and M{\"{u}}ller, K.-R.},


journal = {J. Chem. Phys.},


pages = {241722},
title = {{SchNet – A deep learning architecture for molecules and materials}},

volume = {148},
year = {2018}
}
@article{trau+06science,
author = {Trautt, Z. T. and Upmanyu, M. and Karma, A.},



journal = {Science},


pages = {632--635},
title = {{Interface Mobility from Interface Random Walk}},

volume = {314},
year = {2006}
}
@article{mill-mano05jcp,
abstract = {We have used the ring-polymer molecular dynamics method to calculate approximate Kubo-transformed velocity autocorrelation functions and self-diffusion coefficients for low-pressure liquid para-hydrogen at temperatures of 25 and 14 K. The resulting diffusion coefficients are shown to be consistent with experimental shear viscosities and the established finite-size relation D(L) approximately = D(infinity)-2.837k(B)T6pietaL, where k(B) is the Boltzmann constant, T the absolute temperature, eta the shear viscosity, and L the length of the (cubic) simulation cell. The diffusion coefficients D(L) obtained in simulations with finite system sizes are therefore too small. However, the extrapolation to infinite system size corrects this deficiency and leads to excellent agreement with experimental results. This both demonstrates the influence of system-size effects on quantum mechanical diffusion coefficients and provides further evidence that ring-polymer molecular dynamics is an accurate as well as practical way of including quantum effects in condensed phase molecular dynamics.},
author = {Miller, Thomas F and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {184503},
pmid = {15918725},
title = {{Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics.}},

volume = {122},
year = {2005}
}
@incollection{raml-john14book,
author = {Raml{\o}v, Hans and Johnsen, Johannes L},
booktitle = {Emerging Technologies for Food Processing},
chapter = {29},

edition = {Second Edi},

isbn = {9780124114791},
pages = {539--562},
publisher = {Elsevier},
title = {{Controlling the Freezing Process with Antifreeze Proteins}},

year = {2014}
}
@article{Hwang2000,
author = {Hwang, Gyeong S},
pages = {789--793},
title = {{Surf. Sci. Letters A channel for dimer flipping on the Si ( 001 ) surface}},
volume = {465},
year = {2000}
}
@article{wang+07am,
abstract = {The metastable ?????-Mg5Si6 phase is often the most effective hardening precipitate in Al-rich Al-Mg-Si alloys. Two important factors that control the precipitate morphology are the strain energy and the interfacial energy between the precipitate and the matrix. By means of a first-principles supercell approach and density functional theory calculations, we have studied the interfacial properties between ?????-Mg5Si6 and ??-Al. We carefully construct a large number of interfacial cells in order to elucidate preferred interfacial terminations and orientations, as well as atom alignment and intermixing across the interface. Each of the low-energy interfaces we found possesses two key attributes: a high number of Al-Si bonds across the interface, and a face-centered cubic topological alignment of atoms across those interfaces. Our first-principles results yield quantitative values for the interfacial energies, lattice mismatches and strain energies that can be used in future predictions of precipitate morphologies as a function of size. ?? 2007 Acta Materialia Inc.},
author = {Wang, Y. and Liu, Z.-K. and Chen, L.-Q. and Wolverton, C.},


isbn = {1359-6454},

journal = {Acta Materialia},



pages = {5934--5947},
title = {{First-principles calculations of $\beta$″-Mg5Si6/$\alpha$-Al interfaces}},

volume = {55},
year = {2007}
}
@article{wang+10jcp,
abstract = {Localized molecular orbital energy decomposition analysis and symmetry-adapted perturbation theory (SAPT) calculations are used to analyze the two- and three-body interaction energies of four low-energy isomers of (H(2)O)(6) in order to gain insight into the performance of several popular density functionals for describing the electrostatic, exchange-repulsion, induction, and short-range dispersion interactions between water molecules. The energy decomposition analyses indicate that all density functionals considered significantly overestimate the contributions of charge transfer to the interaction energies. Moreover, in contrast to some studies that state that density functional theory (DFT) does not include dispersion interactions, we adopt a broader definition and conclude that for (H(2)O)(6) the short-range dispersion interactions recovered in the DFT calculations account about 75{\%} or more of the net (short-range plus long-range) dispersion energies obtained from the SAPT calculations.},
author = {Wang, F-F and Jenness, G and Al-Saidi, W a and Jordan, K D},



journal = {J. Chem. Phys.},


pages = {134303},
pmid = {20387929},
title = {{Assessment of the performance of common density functional methods for describing the interaction energies of (H2O)6 clusters.}},

volume = {132},
year = {2010}
}
@article{savi+11prb,
author = {Savin, Alexander V. and Mazo, Mikhail a. and Kikot, Irina P. and Manevitch, Leonid I. and Onufriev, Alexey V.},



journal = {Phys. Rev. B},


pages = {245406},
title = {{Heat conductivity of the DNA double helix}},

volume = {83},
year = {2011}
}
@article{born+09jacs,
abstract = {We have studied the solvation of model peptides at low hydration levels by terahertz absorption spectroscopy. We have recorded the concentration-dependent terahertz absorption coefficients of N-acetyl-glycine-amide (NAGA), N-acetyl-glycine-methylamide (NAGMA), N-acetyl-leucine-amide (NALA), N-acetyl-leucine-methylamide (NALMA), and N-acetyl-tryptophan-amide (NATA) in aqueous solution. We find a dramatic decrease in the THz absorption, if the number of water molecules per solute is less than 18-20. This change is taken as a signature for the breakdown of peptide-water network motions, which supports the hypothesis that a minimum number of hydration waters is required to activate these motions. This is well below a monolayer coverage of the model peptides. It is interesting to note that the required hydration level corresponds to the number of water molecules which are required for biological functionality.},
author = {Born, Benjamin and Weing{\"{a}}rtner, Hermann and Br{\"{u}}ndermann, Erik and Havenith, Martina},



journal = {J. Chem. Am. Soc.},



pages = {3752--3755},
pmid = {19275262},
title = {{Solvation dynamics of model peptides probed by terahertz spectroscopy. Observation of the onset of collective network motions.}},

volume = {131},
year = {2009}
}
@article{stol+99prl,
author = {Stoltze, P and N{\o}rskov, JK K and Landman, U},



journal = {Phys. Rev. Lett.},

mendeley-tags = {aluminum},


pages = {440--443},
title = {{Disordering and Melting of Aluminum Surfaces}},

volume = {61},
year = {1988}
}
@article{upma+06am,
author = {Upmanyu, M. and Srolovitz, D.J. J and Lobkovsky, A.E. E and Warren, J.a. and Carter, W.C. C},



journal = {Acta Materialia},



pages = {1707--1719},
title = {{Simultaneous grain boundary migration and grain rotation}},

volume = {54},
year = {2006}
}
@article{cha+89science,
author = {Cha, Yuan and Murray, Christopher J and Klinman, Judith P},

journal = {Science},

pages = {1325--1330},
publisher = {American Association for the Advancement of Science},
title = {{Hydrogen tunneling in enzyme reactions}},
volume = {243},
year = {1989}
}
@article{kant08prb,
author = {Kantorovich, L},

journal = {Phys. Rev. B},

pages = {94304},
publisher = {APS},
title = {{Generalized Langevin equation for solids. I. Rigorous derivation and main properties}},
volume = {78},
year = {2008}
}
@article{koma+13bjn,
author = {Komarov, Pavel V and Khalatur, Pavel G and Khokhlov, Alexei R},



journal = {Beilstein Journal of Nanotechnology},


pages = {567--587},
title = {{Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport}},

volume = {4},
year = {2013}
}
@article{kraj-parr06prb,
author = {Krajewski, Florian and Parrinello, Michele},



journal = {Phys. Rev. B},


pages = {041105},
title = {{Linear scaling electronic structure calculations and accurate statistical mechanics sampling with noisy forces}},

volume = {73},
year = {2006}
}
@article{skin+13jcp,
abstract = {Four recent x-ray diffraction measurements of ambient liquid water are reviewed here. Each of these measurements represents a significant development of the x-ray diffraction technique applied to the study of liquid water. Sources of uncertainty from statistical noise, Q-range, Compton scattering, and self-scattering are discussed. The oxygen-hydrogen contribution to the measured x-ray scattering pattern was subtracted using literature data to yield an experimental determination, with error bars, of the oxygen-oxygen pair-distribution function, g(OO)(r), which essentially describes the distribution of molecular centers. The extended Q-range and low statistical noise of these measurements has significantly reduced truncation effects and related errors in the g(OO)(r) functions obtained. From these measurements and error analysis, the position and height of the nearest neighbor maximum in g(OO)(r) were found to be 2.80(1) Å and 2.57(5) respectively. Numerical data for the coherent differential x-ray scattering cross-section I(X)(Q), the oxygen-oxygen structure factor S(OO)(Q), and the derived g(OO)(r) are provided as benchmarks for calibrating force-fields for water.},
author = {Skinner, Lawrie B. and Huang, Congcong and Schlesinger, Daniel and Pettersson, Lars G M and Nilsson, Anders and Benmore, Chris J.},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pmid = {23445023},
title = {{Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q-range}},
volume = {138},
year = {2013}
}
@article{bart-csan15ijqc,
author = {Bart{\'{o}}k, Albert P. and Cs{\'{a}}nyi, G{\'{a}}bor},



journal = {International Journal of Quantum Chemistry},


pages = {1051--1057},
title = {{Gaussian approximation potentials: A brief tutorial introduction}},

volume = {115},
year = {2015}
}
@article{cicc-ryck81jsp,
author = {Ciccotti, G and Ryckaert, J P},

journal = {J. Stat. Phys.},

pages = {73--82},
publisher = {Springer},
title = {{On the derivation of the generalized Langevin equation for interacting Brownian particles}},
volume = {26},
year = {1981}
}
@article{tuck+02science,
abstract = {Compared to other ions, protons (H(+)) and hydroxide ions (OH(-)) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural diffusion' the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH(-) can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH(-) hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.},
author = {Tuckerman, Mark E and Marx, Dominik and Parrinello, Michele},



journal = {Nature},


pages = {925--929},
pmid = {12087398},
title = {{The nature and transport mechanism of hydrated hydroxide ions in aqueous solution.}},

volume = {417},
year = {2002}
}
@article{guo+96jcp,
author = {Guo, Yin and Thompson, Donald L and Sewell, Thomas D},

journal = {J. Chem. Phys.},

pages = {576--582},
publisher = {AIP},
title = {{Analysis of the zero-point energy problem in classical trajectory simulations}},
volume = {104},
year = {1996}
}
@article{abra-buss13entr,
abstract = {We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.},
author = {Abrams, Cameron and Bussi, Giovanni},



journal = {Entropy},



pages = {163--199},
title = {{Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration}},

volume = {16},
year = {2013}
}
@article{angi+10prb,
abstract = {The solid-liquid interface free energy $\gamma$sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous approaches to compute $\gamma$sl with atomistic simulations are computationally demanding. We present an approach which is to obtain $\gamma$sl from a free-energy map of the phase transition reconstructed by metadynamics. We apply this to the benchmark case of a Lennard-Jones potential, and the results confirm the most reliable data obtained previously. We demonstrate several advantages of our approach: it is simple to implement, robust and free of hysteresis problems, it allows a rigorous and unbiased estimate of the statistical uncertainty, and it returns a good estimate of the thermodynamic limit with system sizes of a just a few hundred atoms. It is therefore attractive for applications which require more realistic and specific models of interatomic forces. {\textcopyright} 2010 The American Physical Society.},
author = {Angioletti-Uberti, Stefano and Ceriotti, Michele and Lee, P.D. Peter D and Finnis, Mike W M.W.},



journal = {Phys. Rev. B},


pages = {125416},
publisher = {American Physical Society},
title = {{Solid-liquid interface free energy through metadynamics simulations}},

volume = {81},
year = {2010}
}
@article{shen+06nature,
abstract = {Unlike the well-defined long-range order that characterizes crystalline metals, the atomic arrangements in amorphous alloys remain mysterious at present. Despite intense research activity on metallic glasses and relentless pursuit of their structural description, the details of how the atoms are packed in amorphous metals are generally far less understood than for the case of network-forming glasses. Here we use a combination of state-of-the-art experimental and computational techniques to resolve the atomic-level structure of amorphous alloys. By analysing a range of model binary systems that involve different chemistry and atomic size ratios, we elucidate the different types of short-range order as well as the nature of the medium-range order. Our findings provide a reality check for the atomic structural models proposed over the years, and have implications for understanding the nature, forming ability and properties of metallic glasses.},
author = {Sheng, H W and Luo, W K and Alamgir, F M and Bai, J M and Ma, E},



journal = {Nature},


pages = {419--425},
pmid = {16437105},
title = {{Atomic packing and short-to-medium-range order in metallic glasses.}},

volume = {439},
year = {2006}
}
@article{jasi-gate91acr,
author = {Jasinski, Joseph M. and Gates, Stephen M.},



journal = {Acc. Chem. Res.},


pages = {9--15},
title = {{Silicon chemical vapor deposition one step at a time: fundamental studies of silicon hydride chemistry}},

volume = {24},
year = {1991}
}
@inproceedings{ong+04acm,
abstract = {What happens when we do not have a positive definite kernel? It turns out that we can still do learning, in what is now a Krein Space. This paper talks about regression with indefinite kernels.},
address = {New York, New York, USA},
author = {Ong, Cheng Soon and Mary, Xavier and Canu, St{\'{e}}phane and Smola, Alexander J.},
booktitle = {Twenty-first international conference on Machine learning - ICML '04},


isbn = {1581138285},


pages = {81},
publisher = {ACM Press},
title = {{Learning with non-positive kernels}},

year = {2004}
}
@article{kozl+04jpcm,
abstract = {The crystal and magnetic structure of manganite La 0.7 Sr 0.3 MnO 3 has been studied in the pressure range 0{\{}--{\}}7.5{\{}{\~{}}{\}}GPa and the temperature range 4{\{}--{\}}300{\{}{\~{}}{\}}K. The ferromagnetic state of La 0.7 Sr 0.3 MnO 3 remains stable in the whole studied pressure range. The Curie temperature increases as d T C /d P = 4.3{\{}{\~{}}{\}}K{\{}{\~{}}{\}}GPa {\{}-{\}}1 . Unlike the manganites with orthorhombic crystal structure, the pressure-induced increase of T C in La 0.7 Sr 0.3 MnO 3 having the rhombohedral crystal structure of {\#}{\#}IMG{\#}{\#} [http://ej.iop.org/images/0953-8984/16/37/011/cm184790ieqn1.gif] R$\backslash$bar 3c symmetry may be explained by modification of structural parameters only. The difference between the properties of manganites with rhombohedral and orthorhombic structures under high pressure is discussed in terms of the symmetry of MnO 6 octahedra.},
author = {Kozlenko, D P and Goncharenko, I N and Savenko, B N and Voronin, V I},



journal = {J. Phys. Cond. Matt.},


pages = {6755--6762},
title = {{High pressure effects on the crystal and magnetic structure of La 0.7 Sr 0.3 MnO 3}},

volume = {16},
year = {2004}
}
@article{henk-jons00jcp,
author = {Henkelman, G and J{\'{o}}nsson, H},

journal = {J. Chem. Phys.},

pages = {9978},
publisher = {AIP},
title = {{Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points}},
volume = {113},
year = {2000}
}
@article{mice+12jpcc,
author = {Miceli, Giacomo and Guzzo, Matteo and Cucinotta, Clotilde and Bernasconi, Marco},



journal = {J. Phys. Chem. C},


pages = {4311--4315},
title = {{First Principles Study of Hydrogen Desorption from the NaAlH 4 Surface Doped by Ti Clusters}},

volume = {116},
year = {2012}
}
@article{wein+16ncomm,
annote = {NULL},
author = {Weinrauch, I. and Savchenko, I. and Denysenko, D. and Souliou, S. M. and Kim, H.-H. and {Le Tacon}, M. and Daemen, L. L. and Cheng, Y. and Mavrandonakis, A. and Ramirez-Cuesta, A. J. and Volkmer, D. and Sch{\"{u}}tz, G. and Hirscher, M. and Heine, T.},



journal = {Nature Comm.},

pages = {14496},
title = {{Capture of heavy hydrogen isotopes in a metal-organic framework with active Cu(I) sites}},

volume = {8},
year = {2017}
}
@article{hasz09science,
abstract = {The capture of carbon dioxide at the point of emission from coal- or gas-burning power plants is an attractive route to reducing carbon dioxide emissions into the atmosphere. To commercialize carbon capture, as well as transport of liquified carbon dioxide and its storage in exploited oil fields or saline formations, many technological, commercial, and political hurdles remain to be overcome. Urgent action is required if carbon capture and storage is to play a large role in limiting climate change.},
author = {Haszeldine, R Stuart},



journal = {Science (New York, N.Y.)},


pages = {1647--52},
pmid = {19779187},
title = {{Carbon capture and storage: how green can black be?}},

volume = {325},
year = {2009}
}
@article{beye+01jacs,
author = {Beyer, Theresa and Day, Graeme M and Price, Sarah L},


pages = {5086--5094},
title = {{The Prediction, Morphology, and Mechanical Properties of the Polymorphs of Paracetamol - J. Chem. Am. Soc.  (ACS Publications)}},
year = {2001}
}
@article{dell+14ncom,
abstract = {The cryopreservation of cells, tissue and organs is fundamental to modern biotechnology, transplantation medicine and chemical biology. The current state-of-the-art method of cryopreservation is the addition of large amounts of organic solvents such as glycerol or dimethyl sulfoxide, to promote vitrification and prevent ice formation. Here we employ a synthetic, biomimetic, polymer, which is capable of slowing the growth of ice crystals in a manner similar to antifreeze (glyco)proteins to enhance the cryopreservation of sheep and human red blood cells. We find that only 0.1 wt{\{}{\%}{\}} of the polymer is required to attain significant cell recovery post freezing, compared with over 20 wt{\{}{\%}{\}} required for solvent-based strategies. These results demonstrate that synthetic antifreeze (glyco)protein mimics could have a crucial role in modern regenerative medicine to improve the storage and distribution of biological material for transplantation.},
author = {Deller, Robert C and Vatish, Manu and Mitchell, Daniel a and Gibson, Matthew I},



journal = {Nature Comm.},

pages = {3244},
pmid = {24488146},
title = {{Synthetic polymers enable non-vitreous cellular cryopreservation by reducing ice crystal growth during thawing.}},

volume = {5},
year = {2014}
}
@article{bell+18jpcl,
abstract = {The ion-induced long-range orientational order between water molecules recently observed in second harmonic scattering experiments and illustrated with large scale molecular dynamics simulations is quantitatively explained using the Ornstein-Zernike integral equation approach of liquid physics. This general effect, not specific to hydrogen-bonding solvents, is controlled by electroneutrality condition, dipolar interactions and dielectric+ionic screening. As expected, all numerical theories recover the well-known analytical expressions established 40 years ago.},
author = {Belloni, Luc and Borgis, Daniel and Levesque, Maximilien},



journal = {J. Phys. Chem. Letters},

pages = {1985--1989},
title = {{Screened Coulombic Orientational Correlations in Dilute Aqueous Electrolytes}},

year = {2018}
}
@article{chen-ceri17jcp,
abstract = {Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this letter, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory.},
archivePrefix = {arXiv},
arxivId = {arXiv:1610.01322v1},
author = {Cheng, Bingqing and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {034106},
title = {{Bridging the gap between atomistic and macroscopic models of homogeneous nucleation}},

volume = {146},
year = {2017}
}
@article{rich-alth09jcp,
abstract = {We demonstrate that the ring-polymer molecular dynamics (RPMD) method is equivalent to an automated and approximate implementation of the "Im F" version of semiclassical instanton theory when used to calculate reaction rates in the deep-tunneling regime. This explains why the RPMD method is often reliable in this regime and also shows how it can be systematically improved. The geometry of the beads at the transition state on the ring-polymer potential surface describes a finite-difference approximation to the "instanton" trajectory (a periodic orbit in imaginary time beta variant Planck's over 2pi on the inverted potential surface). The deep-tunneling RPMD rate is an approximation to the rate obtained by applying classical transition-state theory (TST) in ring-polymer phase-space using the optimal dividing surface; this TST rate is in turn an approximation to a free-energy version of the Im F instanton rate. The optimal dividing surface is in general a function of several modes of the ring polymer, which explains why centroid-based quantum-TSTs break down at low temperatures for asymmetric reaction barriers. Numerical tests on one-dimensional models show that the RPMD rate tends to overestimate deep-tunneling rates for asymmetric barriers and underestimate them for symmetric barriers, and we explain that this is likely to be a general trend. The ability of the RPMD method to give a dividing-surface-independent rate in the deep-tunneling regime is shown to be a consequence of setting the bead-masses equal to the physical mass.},
author = {Richardson, Jeremy O and Althorpe, Stuart C},



journal = {J. Chem. Phys.},


pages = {214106},
pmid = {19968336},
title = {{Ring-polymer molecular dynamics rate-theory in the deep-tunneling regime: Connection with semiclassical instanton theory}},

volume = {131},
year = {2009}
}
@article{barr-kato13prb,
author = {Barros, Kipton and Kato, Yasuyuki},



journal = {Phys. Rev. B},


pages = {235101},
title = {{Efficient Langevin simulation of coupled classical fields and fermions}},

volume = {88},
year = {2013}
}
@article{evan+94jpcm,
author = {Search, Home and Journals, Collections and Contact, About and Iopscience, My and Address, I P and Evans, A C and Mayers, J and Timms, D N},

journal = {J. Phys. Cond. Matt.},
pages = {4197},
publisher = {IOP Publishing},
title = {{The kinetic energy of lithium-7 above and below the martensitic transformation}},
volume = {6},
year = {1994}
}
@article{mice-bern11jpcc,
author = {Miceli, Giacomo and Bernasconi, Marco},



journal = {J. Phys. Chem. C},


pages = {13496--13501},
title = {{First-Principles Study of the Hydrogenation Process of Li 2 NH}},

volume = {115},
year = {2011}
}
@article{arch-titt95ss,
author = {Archer, Geb and Titterington, Dm},

journal = {Statistica Sinica},

pages = {77--96},
title = {{The iterative image space reconstruction algorithm (ISRA) as an alternative to the EM algorithm for solving positive linear inverse problems}},
volume = {5},
year = {1995}
}
@article{barm+06sm,
author = {Barmak, K. and Kim, J. and Kim, C.-S. and Archibald, W.E. E and Rohrer, G.S. S and Rollett, A.D. D and Kinderlehrer, D. and Ta'asan, S. and Zhang, H. and Srolovitz, D.J. J},



journal = {Scripta Materialia},



pages = {1059--1063},
title = {{Grain boundary energy and grain growth in Al films: Comparison of experiments and simulations}},

volume = {54},
year = {2006}
}
@article{hart+05prl,
abstract = {The technique of high energy x-ray diffraction has been used to measure the temperature variation of hydrogen versus deuterium isotopic quantum effects on the structure of water. The magnitude of the effect is found to be inversely proportional to the temperature, varying by a factor of 2.5 over the range 6 to 45 °C. In addition, the H216O versus H218O effect has been measured at 26 °C and the structural difference shown to be restricted to the nearest neighbor molecular interactions. The results are compared to recent simulations and previously measured isochoric temperature differentials; additionally, implications for H/D substitution experiments are considered.},
author = {Hart, R. T. and Benmore, C. J. and Neuefeind, J. and Kohara, S. and Tomberli, B. and Egelstaff, P. A.},


isbn = {0031-9007},

journal = {Phys. Rev. Lett.},


pages = {047801},
pmid = {15783600},
title = {{Temperature Dependence of Isotopic Quantum Effects in Water}},

volume = {94},
year = {2005}
}
@article{burg-ramb79ma,
abstract = {Summary On the basis of statistical mechanics, it is shown that the following rules concerning the relative stability of different polymorphic modifications are usually obeyed. (1) The enthalpy of transition of two enantiotropic forms is always positive at temperatures above their transition point, and negative at temperatures below the transition point or between monotropic forms (heat-of-transition rule). (2) Instead of the heat of transition, the difference in the heats of fusion may generally be used (heat-of-fusion rule). (3) If a modification is less dense, it is less stable at absolute zero. (4) For hydrogen-bonded crystals, the modification for which the first absorption band in the infrared spectrum is at higher frequencies has the larger entropy. The possibility of exceptions is discussed.},
author = {Burger, a. and Ramberger, R.},


isbn = {0026-3672},

journal = {Microchimica Acta},

pages = {259--271},
title = {{On the polymorphism of pharmaceuticals and other molecular crystals. I}},

volume = {72},
year = {1979}
}
@article{sene+13jcp,
abstract = {The OH stretching vibrational spectrum of water was measured in a wide range of temperatures across the triple point, 269 K {\textless}T {\textless} 296 K, using Inelastic Neutron Scattering (INS). The hydrogen projected density of states and the proton mean kinetic energy, ⟨E K ⟩ OH , were determined for the first time within the framework of a harmonic description of the proton dynamics. We found that in the liquid the value of ⟨E K ⟩ OH is nearly constant as a function of T, indicating that quantum effects on the OH stretching frequency are weakly dependent on temperature. In the case of ice, ab initio electronic structure calculations, using non-local van der Waals functionals, provided ⟨E K ⟩ OH values in agreement with INS experiments. We also found that the ratio of the stretching (⟨E K ⟩ OH ) to the total (⟨E K ⟩ exp ) kinetic energy, obtained from the present measurements, increases in going from ice, where hydrogen bonding is the strongest, to the liquid at ambient conditions and then to the vapour phase, where hydrogen bonding is the weakest. The same ratio was also derived from the combination of previous deep inelastic neutron scattering data, which does not rely upon the harmonic approximation, and the present measurements. We found that the ratio of stretching to the total kinetic energy shows a minimum in the metastable liquid phase. This finding suggests that the strength of intermolecular interactions increases in the supercooled phase, with respect to that in ice, contrary to the accepted view that supercooled water exhibits weaker hydrogen bonding than ice.},
author = {Senesi, Roberto and Flammini, Davide and Kolesnikov, Alexander I. and Murray, {\'{E}}amonn D. and Galli, Giulia and Andreani, Carla},



journal = {J. Chem. Phys.},

pages = {74504},
pmid = {23968099},
title = {{The quantum nature of the OH stretching mode in ice and water probed by neutron scattering experiments}},

volume = {139},
year = {2013}
}
@article{guid+08jcp,
abstract = {Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.},
author = {Guidon, Manuel and Schiffmann, Florian and Hutter, J{\"{u}}rg and Vandevondele, Joost},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pages = {1--15},
pmid = {18537412},
title = {{Ab initio molecular dynamics using hybrid density functionals}},
volume = {128},
year = {2008}
}
@article{tuck+91jcp,
abstract = {advocating PODS (periodic orbit dividing surfaces)},
author = {Tucker, Susan C. and Tuckerman, Mark E. and Berne, Bruce J. and Pollak, Eli},



journal = {J. Chem. Phys.},



pages = {5809--5826},
title = {{Comparison of rate theories for generalized Langevin dynamics}},

volume = {95},
year = {1991}
}
@article{garc11jmp,
abstract = {The distribution of distance in the sphere is reviewed. The distribution of distance in the ellipsoid is given as an integral which can be done in terms of elementary functions for the spheroid. As an application, Maclaurin‚{\"{A}}{\^{o}}s ratio of the polar to equatorial radius of the Earth due to its rotation is rederived using the distribution found here.},
author = {Garc{\'{i}}a-Pelayo, Ricardo},



journal = {Journal of Mathematical Physics},

title = {{Moments of the distribution of distance}},
volume = {52},
year = {2011}
}
@article{naga+12prl,
author = {Nagata, Yuki and Pool, Ruben E and Backus, Ellen H G and Bonn, Mischa},

journal = {Phys. Rev. Lett.},

pages = {226101},
publisher = {American Physical Society},
title = {{Nuclear Quantum Effects Affect Bond Orientation of Water at the Water-Vapor Interface}},
volume = {109},
year = {2012}
}
@article{kuhn-khal14jacs,
abstract = {The interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the traditional nearly tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen-bond network in water. Here, we present new insights into the nature of local interactions in ice and liquid water obtained using a first-principle energy decomposition method. A comparative analysis shows that the majority of molecules in liquid water in our simulation exhibit hydrogen-bonding energy patterns similar to those in ice and retain the four-fold coordination with only moderately distorted tetrahedral configurations. Although this result indicates that the traditional description of liquid water is fundamentally correct, our study also demonstrates that for a significant fraction of molecules the hydrogen-bonding environments are highly asymmetric with extremely weak and distorted bonds.},
author = {K{\"{u}}hne, Thomas D and Khaliullin, Rustam Z},



journal = {J. Chem. Am. Soc. },


pages = {3395--9},
pmid = {24521433},
title = {{Nature of the asymmetry in the hydrogen-bond networks of hexagonal ice and liquid water.}},

volume = {136},
year = {2014}
}
@article{bloc-parr92prb,
author = {Bl{\"{o}}chl, Peter E. and Parrinello, M.},



journal = {Phys. Rev. B},


pages = {9413--9416},
publisher = {American Physical Society},
title = {{Adiabaticity in first-principles molecular dynamics}},

volume = {45},
year = {1992}
}
@article{lind-broi10prb,
author = {Lindsay, L. and Broido, D. a.},



journal = {Phys. Rev. B},


pages = {205441},
title = {{Optimized Tersoff and Brenner empirical potential parameters for lattice dynamics and phonon thermal transport in carbon nanotubes and graphene}},

volume = {81},
year = {2010}
}
@article{perd-wang92prb,
author = {Perdew, J P and Wang, Y},

journal = {Phys. Rev. B},

pages = {13244--13249},
publisher = {APS},
title = {{Accurate and simple analytic representation of the electron-gas correlation energy}},
volume = {45},
year = {1992}
}
@article{crai-mano04jcp,
author = {Craig, I R and Manolopoulos, D E},

journal = {J. Chem. Phys.},
pages = {3368},
title = {{Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics}},
volume = {121},
year = {2004}
}
@article{cutu07proc,
author = {Cuturi, Marco},

journal = {International Joint Conference on Artificial Intelligence, IJCAI},

pages = {732--737},
title = {{Permanents, transportation polytopes and positive definite kernels on histograms}},

year = {2007}
}
@article{levi60iret,
author = {Levin, Morris J},

journal = {IRE Trans. Inf. Th.},
pages = {545},
title = {{Generation of a Sampled Gaussian Time Series Having a Specified Correlation Function}},
volume = {6},
year = {1960}
}
@article{sing88molp,
author = {Singer, K. and Smith, W.},



journal = {Mol. Phys.},


pages = {1215--1231},
publisher = {Taylor and Francis Ltd},
title = {{Path integral simulations of condensed phase Lennard-Jones systems}},

volume = {64},
year = {1988}
}
@article{tani-woly91pra,
annote = {
        

        

        

        From Duplicate 2 ( 
        

        

        

        
        

        

        

        
          

          

          

          Quantum and classical Fokker-Planck equations for a Gaussian-Markovian noise bath
          

          

          

        
        

        

        

        
        

        

        

         - Tanimura, Y; Wolynes, P G )

          

          

          

        
        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

      },
author = {Tanimura, Y and Wolynes, P G},

journal = {Phys. Rev. A},

pages = {4131--4142},
publisher = {APS},
title = {{Quantum and classical Fokker-Planck equations for a Gaussian-Markovian noise bath}},
volume = {43},
year = {1991}
}
@article{goed-colo94prl,
author = {Goedecker, S and Colombo, L},

journal = {Phys. Rev. Lett.},

pages = {122--125},
publisher = {APS},
title = {{Efficient Linear Scaling Algorithm for Tight-Binding Molecular Dynamics}},
volume = {73},
year = {1994}
}
@article{de+16pccp,
abstract = {Evaluating the (dis)similarity of crystalline, disordered and molecular compounds is a critical step in the development of algorithms to navigate automatically the configuration space of complex materials. For instance, a structural similarity metric is crucial for classifying structures, searching chemical space for better compounds and materials, and to drive the next generation of machine-learning techniques for predicting the stability and properties of molecules and materials. In the last few years several strategies have been designed to compare atomic coordination environments. In particular, the Smooth Overlap of Atomic Positions (SOAP) has emerged as a natural framework to obtain translation, rotation and permutation-invariant descriptors of groups of atoms, driven by the design of various classes of machine-learned inter-atomic potentials. Here we discuss how one can combine such local descriptors using a Regularized Entropy Match (REMatch) approach to describe the similarity of both whole molecular and bulk periodic structures, introducing powerful metrics that allow the navigation of alchemical and structural complexity within a unified framework. Furthermore, using this kernel and a ridge regression method we can also predict atomization energies for a database of small organic molecules with a mean absolute error below 1 kcal/mol, reaching an important milestone in the application of machine-learning techniques to the evaluation of molecular properties.},
archivePrefix = {arXiv},
arxivId = {1601.04077},
author = {De, Sandip and Bart{\'{o}}k, A.P. Albert P. and Cs{\'{a}}nyi, G{\'{a}}bor and Ceriotti, Michele},




journal = {Phys. Chem. Chem. Phys.},


pages = {13754--13769},
publisher = {The Royal Society of Chemistry},
title = {{Comparing molecules and solids across structural and alchemical space}},

volume = {18},
year = {2016}
}
@article{cohe+12cr,
author = {Cohen, Aron J and Mori-S{\'{a}}nchez, Paula and Yang, Weitao},



journal = {Chem. Rev.},


pages = {289--320},
pmid = {22191548},
title = {{Challenges for density functional theory.}},

volume = {112},
year = {2012}
}
@article{rose+98jvsta,
author = {Rosenblad, C and Deller, H R and Dommann, A and Meyer, T and Scroeter, P and von K{\"{a}}nel, H},

journal = {J. Vac. Sci. Technol. A},

pages = {2785},
title = {{Silicon epitaxy by low-energy plasma enhanced chemical vapor deposition}},
volume = {16},
year = {1998}
}
@article{wu+06prl,
author = {Wu, Xifan and Di{\'{e}}guez, Oswaldo and Rabe, Karin and Vanderbilt, David},



journal = {Phys. Rev. Lett.},


pages = {107602},
title = {{Wannier-Based Definition of Layer Polarizations in Perovskite Superlattices}},

volume = {97},
year = {2006}
}
@article{bert+11jacs,
abstract = {Despite the daily use of urea to influence protein folding and stability, the molecular mechanism with which urea acts is still not well understood. Here the use of combined parallel tempering and metadynamics simulation allows us to study the free-energy landscape associated with the folding/unfolding of $\beta$-hairpin GB1 equilibrium in 8 M urea and pure water. The nature of the unfolded state in both solutions has been analyzed: in urea solution the addition of denaturants acts to expand the denatured state, while in pure water solution the unfolded state is noticeably more compact. For what concerns the mechanism by which urea acts as a denaturant, a preferential direct interaction between urea molecules and protein backbone has been found. However, the bias toward urea solvation is largest at intermediate values of the gyration radius.},
author = {Berteotti, Anna and Barducci, Alessandro and Parrinello, Michele},



journal = {J. Chem. Am. Soc. },



pages = {17200--6},
pmid = {21854002},
title = {{Effect of urea on the $\beta$-hairpin conformational ensemble and protein denaturation mechanism.}},

volume = {133},
year = {2011}
}
@article{robe+09ijmtm,
author = {Roberts, I.a. and Wang, C.J. J and Esterlein, R. and Stanford, M. and Mynors, D.J. J},



journal = {International Journal of Machine Tools and Manufacture},

mendeley-tags = {additive manufacturing},


pages = {916--923},
publisher = {Elsevier},
title = {{A three-dimensional finite element analysis of the temperature field during laser melting of metal powders in additive layer manufacturing}},

volume = {49},
year = {2009}
}
@article{vepr+89jvsta,
author = {Veprek, S and Sarrott, F A and Rambert, S and Taglauer, E},

journal = {J. Vac. Sci. Technol. A},

pages = {2614--2624},
publisher = {AVS},
title = {{Surface hydrogen content and passivation of silicon deposited by plasma induced chemical vapor deposition from silane and the implications for the reaction mechanism}},
volume = {7},
year = {1989}
}
@article{han-fritz83jncs,
author = {Han, Daxing and Fritzsche, H},



journal = {Journal of Non-Crystalline Solids},

pages = {397--400},
title = {{Study of light-induced creation of defects in a-Si:H by means of single and dual-beam photoconductivity}},

volume = {59-60},
year = {1983}
}
@article{huan+05jcp,
author = {Huang, Xinchuan and Braams, Bastiaan J and Bowman, Joel M},

journal = {J. Chem. Phys.},

pages = {44308},
publisher = {AIP},
title = {{Ab initio potential energy and dipole moment surfaces for {\$}H{\_}5O{\_}2{\^{}}+{\$}}},
volume = {122},
year = {2005}
}
@article{kris-vanb17iecr,
abstract = {Molecular dynamics (MD) simulations have been performed for binary, ternary, and quaternary liquid mixtures of linear alkanes containing 1?16 carbons. Both the self-diffusivities (Di,self) and the Maxwell?Stefan (M?S) diffusivities (?ij) were determined from the MD simulations for various mixture compositions. The self-diffusivity was determined to be a linear function of the mass fractions ?j of the constituent species in the mixture:? Di,self = ?j where is the self-diffusivity of infinitely dilute species i in species j. The Maxwell?Stefan diffusivity of the binary i?j pair in a multicomponent mixture was determined to be predicted reasonably well by the generalization of the Darken relation:? ?ij = [xi/(xi + xj)]Dj,self + [xj/(xi + xj)]Di,self, where xi is the mole fraction of species i. Molecular dynamics (MD) simulations have been performed for binary, ternary, and quaternary liquid mixtures of linear alkanes containing 1?16 carbons. Both the self-diffusivities (Di,self) and the Maxwell?Stefan (M?S) diffusivities (?ij) were determined from the MD simulations for various mixture compositions. The self-diffusivity was determined to be a linear function of the mass fractions ?j of the constituent species in the mixture:? Di,self = ?j where is the self-diffusivity of infinitely dilute species i in species j. The Maxwell?Stefan diffusivity of the binary i?j pair in a multicomponent mixture was determined to be predicted reasonably well by the generalization of the Darken relation:? ?ij = [xi/(xi + xj)]Dj,self + [xj/(xi + xj)]Di,self, where xi is the mole fraction of species i.},
author = {Krishna, R. and van Baten, J. M.},


isbn = {0888-5885},

journal = {Industrial {\&} Engineering Chemistry Research},


pages = {6939--6947},
title = {{The Darken Relation for Multicomponent Diffusion in Liquid Mixtures of Linear Alkanes: An Investigation Using Molecular Dynamics (MD) Simulations}},

volume = {44},
year = {2005}
}
@article{luts89jap,
abstract = {The general expressions, valid for any potential, for the calculation of elastic constants through computer simulation are given. At zero temperature, the elastic constants are found to be the sum of a generalization of the Born term and a term accounting for internal relaxations that arise when a system with more than one atom in the primitive unit cell is strained. The fluctuation formulae used in finite temperature simulations are found to be straightforward generalizations of those used for pair potentials. The connection between the finite‐temperature and zero‐temperature methods is also made.},
author = {Lutsko, J. F.},



journal = {J. Appl. Phys.},

pages = {2991},
title = {{Generalized expressions for the calculation of elastic constants by computer simulation}},

volume = {65},
year = {1989}
}
@phdthesis{fren02thesis,
author = {Frens, JD D},

school = {Indiana University},
title = {{Matrix factorization using a block-recursive structure and block-recursive algorithms}},

year = {2002}
}
@book{mond76book,
author = {Mondolfo, Lucio F},
publisher = {Butterworths London},
title = {{Aluminum alloys: structure and properties}},
volume = {5},
year = {1976}
}
@article{colo05rnc,
author = {Colombo, L},


journal = {Rivista del Nuovo Cimento},

pages = {1--59},
title = {{Tight-binding molecular dynamics: A primer}},
volume = {28},
year = {2005}
}
@article{bita+90npb,
author = {Bitar, Khalil and Kennedy, A.D. D and Horsley, Roger and Meyer, Steffen and Rossi, Pietro},



journal = {Nucl. Phys. B},


pages = {348--376},
title = {{The QCD finite temperature transition and hybrid Monte Carlo}},

volume = {313},
year = {1989}
}
@article{zhon-vand96prb,
author = {Zhong, W and Vanderbilt, David},



journal = {Phys. Rev. B},


pages = {5047--5050},
pmid = {9984086},
title = {{Effect of quantum fluctuations on structural phase transitions in SrTiO3 and BaTiO3}},

volume = {53},
year = {1996}
}
@article{isay+15cm,
abstract = {As the proliferation of high-throughput approaches in materials science is increasing the wealth of data in the field, the gap between accumulated-information and derived-knowledge widens. We address the issue of scientific discovery in materials databases by introducing novel analytical approaches based on structural and electronic materials fingerprints. The framework is employed to (i) query large databases of materials using similarity concepts, (ii) map the connectivity of materials space (i.e., as a materials cartograms) for rapidly identifying regions with unique organizations/properties, and (iii) develop predictive Quantitative Materials Structure?Property Relationship models for guiding materials design. In this study, we test these fingerprints by seeking target material properties. As a quantitative example, we model the critical temperatures of known superconductors. Our novel materials fingerprinting and materials cartography approaches contribute to the emerging field of materials informatics by enabling effective computational tools to analyze, visualize, model, and design new materials.$\backslash$nAs the proliferation of high-throughput approaches in materials science is increasing the wealth of data in the field, the gap between accumulated-information and derived-knowledge widens. We address the issue of scientific discovery in materials databases by introducing novel analytical approaches based on structural and electronic materials fingerprints. The framework is employed to (i) query large databases of materials using similarity concepts, (ii) map the connectivity of materials space (i.e., as a materials cartograms) for rapidly identifying regions with unique organizations/properties, and (iii) develop predictive Quantitative Materials Structure?Property Relationship models for guiding materials design. In this study, we test these fingerprints by seeking target material properties. As a quantitative example, we model the critical temperatures of known superconductors. Our novel materials fingerprinting and materials cartography approaches contribute to the emerging field of materials informatics by enabling effective computational tools to analyze, visualize, model, and design new materials.},
archivePrefix = {arXiv},
arxivId = {arXiv:1412.4096v3},
author = {Isayev, Olexandr and Fourches, Denis and Muratov, Eugene N. and Oses, Corey and Rasch, Kevin and Tropsha, Alexander and Curtarolo, Stefano},




journal = {Chemistry of Materials},

pages = {735--743},
title = {{Materials cartography: Representing and mining materials space using structural and electronic fingerprints}},
volume = {27},
year = {2015}
}
@article{defo99pre,
author = {de Forcrand, Philippe},



journal = {Phys. Rev. E},


pages = {3698--3701},
title = {{Monte Carlo quasi-heat-bath by approximate inversion}},

volume = {59},
year = {1999}
}
@article{eshe+12prl,
author = {Eshet, Hagai and Khaliullin, Rustam Z. and K{\"{u}}hne, Thomas D. and Behler, J{\"{o}}rg and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {115701},
title = {{Microscopic Origins of the Anomalous Melting Behavior of Sodium under High Pressure}},

volume = {108},
year = {2012}
}
@article{srin+04nmat,
abstract = {Block-copolymer amphiphiles have been observed to assemble into vesicles and other morphologies long known for lipids but with remarkably different properties. Coarse-grain molecular dynamics (CG-MD) is used herein to elaborate the structures and properties of diblock copolymer assemblies in water. By varying the hydrophilic/hydrophobic ratio of the copolymer in line with experiment, bilayer, cylindrical and spherical micelle morphologies spontaneously assemble. Varying the molecular weight (MW) with hydrophilic/hydrophobic ratio appropriate to a bilayer yields a hydrophobic core thickness that scales for large MW as a random coil polymer, in agreement with experiment. The extent of hydrophobic-segment overlap in the core increases nonlinearly with MW, indicative of chain entanglements and consistent with the dramatic decrease reported for lateral mobility in polymer vesicles. Calculated trends with MW as well as hydrophilic/hydrophobic ratio thus agree with experiment, demonstrating that CG-MD simulations provide a rational design tool for diblock copolymer assemblies.},
author = {Srinivas, Goundla and Discher, Dennis E and Klein, Michael L},



journal = {Nature materials},



pages = {638--44},
pmid = {15300242},
title = {{Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics.}},

volume = {3},
year = {2004}
}
@article{braa-mano06jcp,
abstract = {We examine the short-time accuracy of a class of approximate quantum dynamical techniques that includes the centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) methods. Both of these methods are based on the path integral molecular dynamics (PIMD) technique for calculating the exact static equilibrium properties of quantum mechanical systems. For Kubo-transformed real-time correlation functions involving operators that are linear functions of positions or momenta, the RPMD and (adiabatic) CMD approximations differ only in the choice of the artificial mass matrix of the system of ring polymer beads that is employed in PIMD. The obvious ansatz for a general method of this type is therefore to regard the elements of the PIMD (or Parrinello-Rahman) mass matrix as an adjustable set of parameters that can be chosen to improve the accuracy of the resulting approximation. We show here that this ansatz leads uniquely to the RPMD approximation when the criterion that is used to select the mass matrix is the short-time accuracy of the Kubo-transformed correlation function. In particular, we show that the leading error in the RPMD position autocorrelation function is O(t(8)) and the error in the velocity autocorrelation function is O(t(6)), for a general anharmonic potential. The corresponding errors in the CMD approximation are O(t(6)) and O(t(4)), respectively.},
author = {Braams, Bastiaan J and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {124105},
pmid = {17014164},
title = {{On the short-time limit of ring polymer molecular dynamics.}},

volume = {125},
year = {2006}
}
@article{lubc-woly03jcp,
author = {Lubchenko, Vassiliy and Wolynes, Peter G.},



journal = {J. Chem. Phys.},

pages = {9088},
title = {{Barrier softening near the onset of nonactivated transport in supercooled liquids: Implications for establishing detailed connection between thermodynamic and kinetic anomalies in supercooled liquids}},

volume = {119},
year = {2003}
}
@article{geig+79jcp,
author = {Geiger, A. and Stillinger, F. H. and Rahman, A.},



journal = {J. Chem. Phys.},

pages = {4185},
title = {{Aspects of the percolation process for hydrogen-bond networks in water}},

volume = {70},
year = {1979}
}
@article{lang89amc,
author = {Langerholc, John},



journal = {Applied Mathematics and Computation},


pages = {1--18},
publisher = {Elsevier},
title = {{Volumes of diced hyperspheres: resumming the Tam-Zardecki formula}},

volume = {30},
year = {1989}
}
@article{nils-pett11cp,
author = {Nilsson, A. and Pettersson, L.G.M. G M},



journal = {Chemical Physics},


pages = {1--34},
title = {{Perspective on the structure of liquid water}},

volume = {389},
year = {2011}
}
@article{li+15prl,
author = {Li, Zhenwei and Kermode, James R. and {De Vita}, Alessandro},



journal = {Phys. Rev. Lett.},


pages = {096405},
title = {{Molecular Dynamics with On-the-Fly Machine Learning of Quantum-Mechanical Forces}},

volume = {114},
year = {2015}
}
@article{ebbi+07pnas,
abstract = {The focus in protein folding has been very much on the protein backbone and sidechains. However, hydration waters make comparable contributions to the structure and energy of proteins. The coupling between fast hydration dynamics and protein dynamics is considered to play an important role in protein folding. Fundamental questions of protein hydration include, how far out into the solvent does the influence of the biomolecule reach, how is the water affected, and how are the properties of the hydration water influenced by the separation between protein molecules in solution? We show here that Terahertz spectroscopy directly probes such solvation dynamics around proteins, and determines the width of the dynamical hydration layer. We also investigate the dependence of solvation dynamics on protein concentration. We observe an unexpected nonmonotonic trend in the measured terahertz absorbance of the five helix bundle protein lambda(6-85)* as a function of the protein: water molar ratio. The trend can be explained by overlapping solvation layers around the proteins. Molecular dynamics simulations indicate water dynamics in the solvation layer around one protein to be distinct from bulk water out to approximately 10 A. At higher protein concentrations such that solvation layers overlap, the calculated absorption spectrum varies nonmonotonically, qualitatively consistent with the experimental observations. The experimental data suggest an influence on the correlated water network motion beyond 20 A, greater than the pure structural correlation length usually observed.},
author = {Ebbinghaus, Simon and Kim, Seung Joong and Heyden, Matthias and Yu, Xin and Heugen, Udo and Gruebele, Martin and Leitner, David M and Havenith, Martina},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {20749--20752},
pmid = {18093918},
title = {{An extended dynamical hydration shell around proteins.}},

volume = {104},
year = {2007}
}
@article{fabe+18jcp,
abstract = {We introduce a representation of any atom in any chemical environment for the automatized generation of universal kernel ridge regression-based quantum machine learning (QML) models of electronic properties, trained throughout chemical compound space. The representation is based on Gaussian distribution functions, scaled by power laws and explicitly accounting for structural as well as elemental degrees of freedom. The elemental components help us to lower the QML model's learning curve, and, through interpolation across the periodic table, even enable “alchemical extrapolation” to covalent bonding between elements not part of training. This point is demonstrated for the prediction of covalent binding in single, double, and triple bonds among main-group elements as well as for atomization energies in organic molecules. We present numerical evidence that resulting QML energy models, after training on a few thousand random training instances, reach chemical accuracy for out-of-sample compounds. Compound dat...},
archivePrefix = {arXiv},
arxivId = {1712.08417},
author = {Faber, Felix A. and Christensen, Anders S. and Huang, Bing and von Lilienfeld, O. Anatole},




journal = {J. Chem. Phys.},


pages = {241717},
title = {{Alchemical and structural distribution based representation for universal quantum machine learning}},

volume = {148},
year = {2018}
}
@article{rupp+07jcim,
author = {Rupp, Matthias and Proschak, Ewgenij and Schneider, Gisbert},



journal = {Journal of Chemical Information and Modeling},


pages = {2280--2286},
title = {{Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity}},

volume = {47},
year = {2007}
}
@article{kant+10pre,
author = {Kanth, J. Maruthi Pradeep and Vemparala, Satyavani and Anishetty, Ramesh},


journal = {Phys. Rev. E},


pages = {021201},
title = {{Long-distance correlations in molecular orientations of liquid water and shape-dependent hydrophobic force}},

volume = {81},
year = {2010}
}
@article{horn97laa,
author = {Horne, B G},

journal = {Linear Algebra and its Applications},

pages = {261--273},
publisher = {Elsevier Science},
title = {{Lower Bounds for the Spectral Radius of a Matrix}},
volume = {263},
year = {1997}
}
@article{word+07nat,
abstract = {Atmospheric moisture cycling is an important aspect of the Earth's climate system, yet the processes determining atmospheric humidity are poorly understood. For example, direct evaporation of rain contributes significantly to the heat and moisture budgets of clouds, but few observations of these processes are available. Similarly, the relative contributions to atmospheric moisture over land from local evaporation and humidity from oceanic sources are uncertain. Lighter isotopes of water vapour preferentially evaporate whereas heavier isotopes preferentially condense and the isotopic composition of ocean water is known. Here we use this information combined with global measurements of the isotopic composition of tropospheric water vapour from the Tropospheric Emission Spectrometer (TES) aboard the Aura spacecraft, to investigate aspects of the atmospheric hydrological cycle that are not well constrained by observations of precipitation or atmospheric vapour content. Our measurements of the isotopic composition of water vapour near tropical clouds suggest that rainfall evaporation contributes significantly to lower troposphere humidity, with typically 20{\{}{\%}{\}} and up to 50{\{}{\%}{\}} of rainfall evaporating near convective clouds. Over the tropical continents the isotopic signature of tropospheric water vapour differs significantly from that of precipitation, suggesting that convection of vapour from both oceanic sources and evapotranspiration are the dominant moisture sources. Our measurements allow an assessment of the intensity of the present hydrological cycle and will help identify any future changes as they occur.},
author = {Worden, John and Noone, David and Bowman, Kevin},



journal = {Nature},


pages = {528--532},
pmid = {17268467},
title = {{Importance of rain evaporation and continental convection in the tropical water cycle.}},

volume = {445},
year = {2007}
}
@article{AIMS,
abstract = {We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.},
author = {Blum, Volker and Gehrke, Ralf and Hanke, Felix and Havu, Paula and Havu, Ville and Ren, Xinguo and Reuter, Karsten and Scheffler, Matthias},



journal = {Comp. Phys. Comm.},



pages = {2175--2196},
publisher = {Elsevier B.V.},
title = {{Ab initio molecular simulations with numeric atom-centered orbitals}},

volume = {180},
year = {2009}
}
@article{fors-makr98jcp,
author = {Forsythe, Kelsey M. and Makri, Nancy},



journal = {J. Chem. Phys.},

pages = {6819},
title = {{Path integral study of hydrogen and deuterium diffusion in crystalline silicon}},

volume = {108},
year = {1998}
}
@article{dago+01pr,
author = {Dagotto, Elbio and Hotta, Takashi and Moreo, Adriana},

journal = {Phys. Rep.},

pages = {1--153},
title = {{Colossal magnetoresistant materials: the key role of phase separation}},
volume = {344},
year = {2001}
}
@article{voth91pra,
author = {Voth, Gregory A},

journal = {Phys. Rev. A},

pages = {5302--5305},
publisher = {American Physical Society},
title = {{Calculation of equilibrium averages with Feynman-Hibbs effective classical potentials and similar variational approximations}},
volume = {44},
year = {1991}
}
@article{murr98jpe,
author = {Murray, J. L.},



journal = {Journal of Phase Equilibria},


pages = {367--375},
title = {{The Al-Cr (aluminum-chromium) system}},

volume = {19},
year = {1998}
}
@article{holt+13jcp,
abstract = {The thermodynamic properties of the supercooled liquid state of the mW model of water show anomalous behavior. Like in real water, the heat capacity and compressibility sharply increase upon supercooling. One of the possible explanations of these anomalies, the existence of a second (liquid-liquid) critical point, is not supported by simulations for this model. In this work, we reproduce the anomalies of the mW model with two thermodynamic scenarios: one based on a non-ideal "mixture" with two different types of local order of the water molecules, and one based on weak crystallization theory. We show that both descriptions accurately reproduce the model's basic thermodynamic properties. However, the coupling constant required for the power laws implied by weak crystallization theory is too large relative to the regular backgrounds, contradicting assumptions of weak crystallization theory. Fluctuation corrections outside the scope of this work would be necessary to fit the forms predicted by weak crystallization theory. For the two-state approach, the direct computation of the low-density fraction of molecules in the mW model is in agreement with the prediction of the phenomenological equation of state. The non-ideality of the "mixture" of the two states never becomes strong enough to cause liquid-liquid phase separation, also in agreement with simulation results.},
archivePrefix = {arXiv},
arxivId = {1302.5691},
author = {Holten, Vincent and Limmer, David T. and Molinero, Valeria and Anisimov, Mikhail a.},




journal = {J. Chem. Phys.},
pages = {174501},
pmid = {23656138},
title = {{Nature of the anomalies in the supercooled liquid state of the mW model of water}},
volume = {138},
year = {2013}
}
@article{hamm50ams,
abstract = {The use of transformations to stabilize the variance of binomial or Poisson data is familiar(Anscombe 1, Bartlett 2, 3, Curtiss 4, Eisenhart 5). The comparison of transformed binomial or Poisson data with percentage points of the normal distribution to make approximate significance tests or to set approximate confidence intervals is less familiar. Mosteller and Tukey 6 have recently made a graphical application of a transformation related to the square-root transformation for such purposes, where the use of "binomial probability paper" avoids all computation. We report here on an empirical study of a number of approximations, some intended for significance and confidence work and others for variance stabilization. For significance testing and the setting of confidence limits, we should like to use the normal deviate K exceeded with the same probability as the number of successes x from n in a binomial distribution with expectation np, which is defined by frac12pi int{\^{}}K-infty e{\^{}}-frac12t{\^{}}2 dt = operatornameProb x leq k mid operatornamebinomial, n, p. The most useful approximations to K that we can propose here are N (very simple), N{\^{}}+ (accurate near the usual percentage points), and N{\^{}}astast (quite accurate generally), where N = 2 (sqrt(k + 1)q - sqrt(n - k)p). (This is the approximation used with binomial probability paper.) N{\^{}}+ = N + fracN + 2p - 112sqrtE,quad E = textlesser of np textand nq, N{\^{}}ast = N + frac(N - 2)(N + 2)12 big(frac1sqrtnp + 1 - frac1sqrtnq + 1big), N{\^{}}astast = N{\^{}}ast + fracN{\^{}}ast + 2p - 112 sqrtEcdotquad E = textlesser of np textand nq. For variance stabilization, the averaged angular transformation sin{\^{}}-1sqrtfracxn + 1 + sin{\^{}}-1 sqrtfracx + 1n+1 has variance within pm 6{\%} of frac1n + frac12 text(angles in radians), frac821n + frac12 text(angles in degrees), for almost all cases where np geq 1. In the Poisson case, this simplifies to using sqrtx + sqrtx + 1 as having variance 1.},
author = {Hammersley, J. M.},



journal = {The Annals of Mathematical Statistics},


pages = {447--452},
title = {{The Distribution of Distance in a Hypersphere}},

volume = {21},
year = {1950}
}
@article{tobl66aaag,
abstract = {Estimates of the map projection employed for an ancient map is a prerequisite for a variety of other studies. The preliminary evaluation presented here has yielded empirical equations for the Hereford map and illustrated the agreement of a Portolan chart with an oblique Mercator projection.},
author = {Tobler, W. R.},



journal = {Annals of the Association of American Geographers},


pages = {351--360},
publisher = {Taylor {\&} Francis, Ltd. on behalf of the Association of American Geographers},
title = {{Medieval Distortions: the Projections of Ancient Maps}},

volume = {56},
year = {1966}
}
@article{li+11pnas,
author = {Li, X.-Z. and Walker, B and Michaelides, A},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {6369--6373},
publisher = {National Acad Sciences},
title = {{Quantum nature of the hydrogen bond}},

volume = {108},
year = {2011}
}
@article{hass+13pnas,
abstract = {The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.},
author = {Hassanali, Ali and Giberti, Federico and Cuny, J{\'{e}}r{\^{o}}me and K{\"{u}}hne, Thomas D and Parrinello, Michele},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {13723--13728},
pmid = {23868853},
title = {{Proton transfer through the water gossamer.}},

volume = {110},
year = {2013}
}
@article{erre+15prl,
author = {Errea, Ion and Calandra, Matteo and Pickard, Chris J and Nelson, Joseph and Needs, Richard J and Li, Yinwei and Liu, Hanyu and Zhang, Yunwei and Ma, Yanming and Mauri, Francesco},



journal = {Phys. Rev. Lett.},


pages = {157004},
title = {{High-Pressure Hydrogen Sulfide from First Principles: A Strongly Anharmonic Phonon-Mediated Superconductor}},

volume = {114},
year = {2015}
}
@book{hast09book,
address = {New York, NY},
author = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome},

isbn = {978-0-387-84857-0},
publisher = {Springer New York},
series = {Springer Series in Statistics},
title = {{The Elements of Statistical Learning}},

year = {2009}
}
@article{adle81prd,
author = {Adler, SL L},

journal = {Phys. Rev. D},

pages = {2901--2904},
title = {{Over-relaxation method for the Monte Carlo evaluation of the partition function for multiquadratic actions}},

volume = {23},
year = {1981}
}
@article{daw-bask84pb,
abstract = {We develop the embedded-atom method Phys. Rev. Lett. 50 1285 (1983), based on density-functional theory, as a new means of calculating ground-state properties of realistic metal systems. We derive an expression for the total energy of a metal using the embedding energy from which we obtain several ground-state properties, such as the lattice constant, elastic constants, sublimation energy, and vacancy-formation energy. We obtain the embedding energy and accompanying pair potentials semiempirically for Ni and Pd, and use these to treat several problems: surface energy and relaxation of the (100), (110), and (111) faces; properties of H in bulk metal (H migration, binding of H to vacancies, and lattice expansion in the hydride phase); binding site and adsorption energy of hydrogen on (100), (110), and (111) surfaces; and lastly, fracture of Ni and the effects of hydrogen on the fracture. We emphasize problems with hydrogen and with surfaces because none of these can be treated with pair potentials. The agreement with experiment, the applicability to practical problems, and the simplicity of the technique make it an effective tool for atomistic studies of defects in metals.},
author = {Daw, Murray S. and Baskes, M. I.},


isbn = {01631829 (ISSN)},

journal = {Phys. Rev. B},


pages = {6443--6453},
pmid = {21688283},
title = {{Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals}},

volume = {29},
year = {1984}
}
@article{rahm-stil71jcp,
author = {Rahman, Aneesur and Stillinger, F. H.},



journal = {J. Chem. Phys.},

pages = {3336},
title = {{Molecular Dynamics Study of Liquid Water}},

volume = {55},
year = {1971}
}
@article{ceri+16cr,
abstract = {Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water?s properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water?s quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water?s isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research.$\backslash$nNuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water?s properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water?s quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water?s isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research.},
author = {Ceriotti, Michele and Fang, Wei and Kusalik, Peter G. P.G. and McKenzie, R.H. Ross H. and Michaelides, Angelos and Morales, Miguel A. M.A. and Markland, Thomas E. T.E.},



journal = {Chem. Rev.},


pages = {7529--7550},
title = {{Nuclear Quantum Effects in Water and Aqueous Systems: Experiment, Theory, and Current Challenges}},

volume = {116},
year = {2016}
}
@article{brun+07jpcb,
author = {Bruneval, F and Donadio, D and Parrinello, M},

journal = {J. Phys. Chem. B},

pages = {12219},
title = {{Molecular Dynamics Study of the Solvation of Calcium Carbonate in Water}},
volume = {111},
year = {2007}
}
@article{impe+83jpc,
author = {Impey, R. W. and Madden, P. a. and McDonald, I. R.},



journal = {J. Phys. Chem.},


pages = {5071--5083},
title = {{Hydration and mobility of ions in solution}},

volume = {87},
year = {1983}
}
@article{sope09prl,
author = {Soper, A K},



journal = {Phys. Rev. Lett.},


pages = {69801},
publisher = {American Physical Society},
title = {{Comment on “Excess of Proton Mean Kinetic Energy in Supercooled Water”}},

volume = {103},
year = {2009}
}
@article{bart-schl98jcp,
author = {Barth, Eric and Schlick, Tamar},



journal = {J. Chem. Phys.},

pages = {1617},
title = {{Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN}},

volume = {109},
year = {1998}
}
@article{kudo-mise09csr,
abstract = {This critical review shows the basis of photocatalytic water splitting and experimental points, and surveys heterogeneous photocatalyst materials for water splitting into H2 and O2, and H2 or O2 evolution from an aqueous solution containing a sacrificial reagent. Many oxides consisting of metal cations with d0 and d10 configurations, metal (oxy)sulfide and metal (oxy)nitride photocatalysts have been reported, especially during the latest decade. The fruitful photocatalyst library gives important information on factors affecting photocatalytic performances and design of new materials. Photocatalytic water splitting and H2 evolution using abundant compounds as electron donors are expected to contribute to construction of a clean and simple system for solar hydrogen production, and a solution of global energy and environmental issues in the future (361 references).},
author = {Kudo, Akihiko and Miseki, Yugo},



journal = {Chemical Society reviews},


pages = {253--78},
pmid = {19088977},
title = {{Heterogeneous photocatalyst materials for water splitting.}},

volume = {38},
year = {2009}
}
@article{Spaepen1975,
abstract = {A structural model for the solid-liquid interface has been developed by applying the construction rules for the liquid to the boundary condition of a crystal plane. In particular, an interface has been created between a dense random packing of hard spheres and a close packed crystal plane by preferentially forming tetrahedral holes (typical for the liquid) and disallowing octahedral holes (necessary for the crystal). The resulting interface has zero density deficit in agreement with conclusions from positron lifetime studies. The surface tension, of entropic origin, is of the same magnitude as the experimental values. The model can account qualitatively for the ease of step nucleation during crystal growth.},
author = {Spaepen, Frans},



journal = {Scripta Metallurgica},

pages = {xvii},
title = {{A structural model for the solid-liquid interface in monatomic systems}},
volume = {9},
year = {1975}
}
@article{Hwang2000,
author = {Hwang, Gyeong S},


pages = {789--793},
title = {{Surf. Sci. Letters A channel for dimer flipping on the Si ( 001 ) surface}},
volume = {465},
year = {2000}
}
@article{lueh+14jcp,
author = {Luehr, Nathan and Markland, Thomas E. and Mart$\backslash$'$\backslash$inez, Todd J and Mart{\'{i}}nez, Todd J.},



journal = {J. Chem. Phys.},

pages = {84116},
title = {{Multiple time step integrators in ab initio molecular dynamics}},

volume = {140},
year = {2014}
}
@article{zhou+08jmr,
author = {Zhou, X W and Zimmerman, J A and Wong, B M and Hoyt, J J},

journal = {J. Mat. Res.},

pages = {704--718},
publisher = {Pittsburgh, PA: Published for the Materials Research Society by the American Institute of Physics, c1986-},
title = {{An embedded-atom method interatomic potential for Pd-H alloys}},
volume = {23},
year = {2008}
}
@article{zipo+08apl,
author = {Zipoli, F and Cereda, S and Ceriotti, M and Bernasconi, M and Miglio, Leo and Montalenti, F},



journal = {Applied Physics Letters},

pages = {191908},
title = {{First principles study of Ge∕Si exchange mechanisms at the Si(001) surface}},

volume = {92},
year = {2008}
}
@article{mile65bm,
author = {Miles, R. E.},



journal = {Biometrika},


pages = {636},
title = {{On Random Rotations in R 3}},

volume = {52},
year = {1965}
}
@article{rijs+08jac,
author = {Rijssenbeek, J and Gao, Y and Hanson, J and Huang, Q and Jones, C and Toby, B},

journal = {J. Alloys Compd.},

pages = {233--244},
publisher = {Elsevier},
title = {{Crystal structure determination and reaction pathway of amide-hydride mixtures}},
volume = {454},
year = {2008}
}
@article{gasp+18jctc,
abstract = {{\textcopyright} 2018 American Chemical Society. Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs (e.g., H-bonds, coordination polyhedra, and protein secondary structure). Here we demonstrate an algorithm to automatically recognize such patterns, based on the identification of local maxima in the probability distributions observed in atomistic computer simulations, which is robust to the dimensionality and the sparsity of the reference atomistic data. We first discuss its main features, demonstrating some on artificial data sets, and then show how it can be applied to identify coordination environments in Lennard-Jones clusters and to recognize secondary-structure patterns in the simulation of an oligopeptide. To assess the applicability of this algorithm for motifs that involve several interdependent degrees of freedom, we also employ it to identify groups of conformers of the cluster and the polypeptide, considered in their entirety. The motifs identified by analyzing atomistic simulations can be used to interpret and rationalize the stability and behavior of the system at hand, and also as a tool to accelerate sampling, in association with biased molecular dynamics schemes.},
author = {Gasparotto, Piero and Mei{\ss}ner, R.H. Robert Horst and Ceriotti, Michele},



journal = {J. Chem. Theory Comput.},


pages = {486--498},
title = {{Recognizing Local and Global Structural Motifs at the Atomic Scale}},

volume = {14},
year = {2018}
}
@article{behl11jcp,
abstract = {Neural networks offer an unbiased and numerically very accurate approach to represent high-dimensional ab initio potential-energy surfaces. Once constructed, neural network potentials can provide the energies and forces many orders of magnitude faster than electronic structure calculations, and thus enable molecular dynamics simulations of large systems. However, Cartesian coordinates are not a good choice to represent the atomic positions, and a transformation to symmetry functions is required. Using simple benchmark systems, the properties of several types of symmetry functions suitable for the construction of high-dimensional neural network potential-energy surfaces are discussed in detail. The symmetry functions are general and can be applied to all types of systems such as molecules, crystalline and amorphous solids, and liquids.},
author = {Behler, J{\"{o}}rg},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pmid = {21341827},
title = {{Atom-centered symmetry functions for constructing high-dimensional neural network potentials}},
volume = {134},
year = {2011}
}
@article{kuma+07jcp,
author = {Kumar, R and Schmidt, J R and Skinner, J L},

journal = {J. Chem. Phys.},
pages = {204107},
title = {{Hydrogen bonding definitions and dynamics in liquid water}},
volume = {126},
year = {2007}
}
@book{risk96book,
address = {Berlin},
author = {Risken, H},
publisher = {Springer},
title = {{The Fokker-Planck Equation}},
year = {1996}
}
@article{lin+02nm,
abstract = {One of the main bottlenecks to deploying large-scale carbon dioxide capture and storage (CCS) in power plants is the energy required to separate the CO(2) from flue gas. For example, near-term CCS technology applied to coal-fired power plants is projected to reduce the net output of the plant by some 30{\%} and to increase the cost of electricity by 60-80{\%}. Developing capture materials and processes that reduce the parasitic energy imposed by CCS is therefore an important area of research. We have developed a computational approach to rank adsorbents for their performance in CCS. Using this analysis, we have screened hundreds of thousands of zeolite and zeolitic imidazolate framework structures and identified many different structures that have the potential to reduce the parasitic energy of CCS by 30-40{\%} compared with near-term technologies.},
author = {Lin, Li-Chiang and Berger, Adam H and Martin, Richard L and Kim, Jihan and Swisher, Joseph a and Jariwala, Kuldeep and Rycroft, Chris H and Bhown, Abhoyjit S and Deem, Michael W and Haranczyk, Maciej and Smit, Berend},



journal = {Nature materials},



pages = {633--41},
pmid = {22635045},
publisher = {Nature Publishing Group},
title = {{In silico screening of carbon-capture materials.}},

volume = {11},
year = {2012}
}
@article{pere-tuck11jcp,
abstract = {Higher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the Takahashi-Imada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the end-to-end distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.},
author = {P{\'{e}}rez, Alejandro and Tuckerman, Mark E},



journal = {J. Chem. Phys.},


pages = {064104},
pmid = {21842923},
title = {{Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes.}},

volume = {135},
year = {2011}
}
@article{henk-jons99jcp,
author = {Henkelman, G and J{\'{o}}nsson, H},

journal = {J. Chem. Phys.},
pages = {7010},
publisher = {AIP},
title = {{A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives}},
volume = {111},
year = {1999}
}
@article{lain-curi13njp,
abstract = {Nowadays, simulation techniques are routinely used to generate accurate models of the structures of crystalline and amorphous solids, to study surfaces, defects and the properties of complex systems, and to screen possible candidate materials for the most diverse types of technological applications. The screening of novel molecular structures has been so far pursued by calculation of intrinsic properties with first-principle methods. Still, the use of intrinsic properties as scoring functions may not always be optimal for systems of high complexity. In these cases, increasingly detailed and realistic simulations that take into account the interaction with the surrounding molecules are of crucial importance. In this paper, we present an effective way to screen different solvents with respect to their chemical stability versus Li 2 O 2 solid particles. To achieve this, the minimum energy paths for different types of reactions of a series of aprotic solvents (acetonitrile and pivalonitrile, dimethyl sulphoxide, N -methyl-2-pyrrolidone and some of its derivatives, penta ethylene glycol (PEG-5) and a fluorinated derivative) with solid Li 2 O 2 are computed and reported. From these data, we can extract the reaction energy barriers, which compare extremely well with the available experimental data and offer a convenient way for screening and designing suitable solvents for Li–air batteries from first-principle calculations.},
author = {Laino, Teodoro and Curioni, Alessandro},


isbn = {1367-2630},

journal = {New Journal of Physics},


pages = {95009},
title = {{Chemical reactivity of aprotic electrolytes on a solid Li 2 O 2 surface: screening solvents for Li–air batteries}},

volume = {15},
year = {2013}
}
@article{webb-mill14jpca,
abstract = {We combine path-integral Monte Carlo methods with high-quality potential energy surfaces to compute equilibrium isotope effects in a variety of systems relevant to 'clumped' isotope analysis and isotope geochemistry, including CO2, N2O, methane, and propane. Through a systematic study of heavy-atom isotope-exchange reactions, we quantify and analyze errors that arise in the widely used Urey model for predicting equilibrium constants of isotope-exchange reactions using reduced partition function ratios. These results illustrate that the Urey model relies on a nontrivial cancellation of errors that can shift the apparent equilibrium temperature by as much as 35 K for a given distribution of isotopologues. The calculations reported here provide the same level of precision as the best existing analytical instrumentation, resolving the relative enrichment of certain isotopologues to as little as 0.01‰. These findings demonstrate path-integral methods to be a rigorous and viable alternative to more approximate methods for heavy-atom geochemical applications.},
author = {Webb, Michael a and Miller, Thomas F},



journal = {J. Phys. Chem.. A},


pages = {467--74},
pmid = {24372450},
title = {{Position-specific and clumped stable isotope studies: comparison of the Urey and path-integral approaches for carbon dioxide, nitrous oxide, methane, and propane.}},

volume = {118},
year = {2014}
}
@article{henk-jons03prl,
author = {Henkelman, Graeme and J{\'{o}}nsson, Hannes},



journal = {Phys. Rev. Lett.},

mendeley-tags = {aluminum},


pages = {116101},
title = {{Multiple Time Scale Simulations of Metal Crystal Growth Reveal the Importance of Multiatom Surface Processes}},

volume = {90},
year = {2003}
}
@article{car-parr85prl,
author = {Car, R and Parrinello, M},

journal = {Phys. Rev. Lett.},

pages = {2471--2474},
publisher = {APS},
title = {{Unified Approach for Molecular Dynamics and Density-Functional Theory}},
volume = {55},
year = {1985}
}
@article{ford+88pra,
author = {Ford, G W and Lewis, J T and {O' Connell}, R F},

journal = {Phys. Rev. A},

pages = {4419--4428},
publisher = {APS},
title = {{Quantum Langevin equation}},
volume = {37},
year = {1988}
}
@article{delb+15jcp2,
author = {{Del Ben}, Mauro and Hutter, J{\"{u}}rg and VandeVondele, Joost},



journal = {J. Chem. Phys.},

pages = {54506},
title = {{Probing the structural and dynamical properties of liquid water with models including non-local electron correlation}},

volume = {143},
year = {2015}
}
@article{shir-chod08jcp,
abstract = {We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which we call the multistate Bennett acceptance ratio estimator (MBAR) because it reduces to the Bennett acceptance ratio estimator (BAR) when only two states are considered, has significant advantages over multiple histogram reweighting methods for combining data from multiple states. It does not require the sampled energy range to be discretized to produce histograms, eliminating bias due to energy binning and significantly reducing the time complexity of computing a solution to the estimating equations in many cases. Additionally, an estimate of the statistical uncertainty is provided for all estimated quantities. In the large sample limit, MBAR is unbiased and has the lowest variance of any known estimator for making use of equilibrium data collected from multiple states. We illustrate this method by producing a highly precise estimate of the potential of mean force for a DNA hairpin system, combining data from multiple optical tweezer measurements under constant force bias.},
archivePrefix = {arXiv},
arxivId = {0801.1426},
author = {Shirts, Michael R. and Chodera, John D.},



isbn = {0021-9606},

journal = {J. Chem. Phys.},

pages = {124105},
pmid = {19045004},
title = {{Statistically optimal analysis of samples from multiple equilibrium states}},
volume = {129},
year = {2008}
}
@article{fren14nm,
author = {Frenkel, Daan},



journal = {Nature Materials},


pages = {9--12},
publisher = {Nature Publishing Group},
title = {{Order through entropy}},

volume = {14},
year = {2014}
}
@article{yama+02nmat,
abstract = {The mechanical behaviour of nanocrystalline materials (that is, polycrystals with a grain size of less than 100 nm) remains controversial. Although it is commonly accepted that the intrinsic deformation behaviour of these materials arises from the interplay between dislocation and grain-boundary processes, little is known about the specific deformation mechanisms. Here we use large-scale molecular-dynamics simulations to elucidate this intricate interplay during room-temperature plastic deformation of model nanocrystalline Al microstructures. We demonstrate that, in contrast to coarse-grained Al, mechanical twinning may play an important role in the deformation behaviour of nanocrystalline Al. Our results illustrate that this type of simulation has now advanced to a level where it provides a powerful new tool for elucidating and quantifying--in a degree of detail not possible experimentally--the atomic-level mechanisms controlling the complex dislocation and grain-boundary processes in heavily deformed materials with a submicrometre grain size.},
author = {Yamakov, Vesselin and Wolf, Dieter and Phillpot, Simon R and Mukherjee, Amiya K and Gleiter, Herbert},



journal = {Nature materials},

mendeley-tags = {aluminum},


pages = {45--8},
pmid = {12618848},
title = {{Dislocation processes in the deformation of nanocrystalline aluminium by molecular-dynamics simulation.}},

volume = {1},
year = {2002}
}
@article{jacu-omer83jcp,
author = {Jacucci, G and Omerti, E},

journal = {J. Chem. Phys.},

pages = {3051},
title = {{Monte Carlo calculation of the radial distribution function of quantum hard spheres at finite temperatures using path integrals with boundary conditions}},

volume = {79},
year = {1983}
}
@article{hira+16nature,
author = {Hirano, Yu and Takeda, Kazuki and Miki, Kunio},

journal = {Nature},


pages = {281--284},
publisher = {Springer Nature},
title = {{Charge-density analysis of an iron{\{}$\backslash$textendash{\}}sulfur protein at an ultra-high resolution of 0.48{\{}$\backslash$hspace{\{}0.167em{\}}{\}}{\{}{\{}AA{\}}{\}}}},

volume = {534},
year = {2016}
}
@article{Review1988,
author = {Review, Physical},
pages = {3098--3100},
title = {f 2 4/3},
volume = {38},
year = {1988}
}
@article{trib+14cpc,
author = {Tribello, Gareth a. and Bonomi, Massimiliano and Branduardi, Davide and Camilloni, Carlo and Bussi, Giovanni},



journal = {Comp. Phys. Comm.},


pages = {604--613},
publisher = {Elsevier B.V.},
title = {{PLUMED 2: New feathers for an old bird}},

volume = {185},
year = {2014}
}
@article{tiwa-parr14jpcb,
abstract = {Metadynamics is a powerful and well-established enhanced sampling method for exploring and quantifying free energy surfaces of complex systems as a function of appropriately chosen variables. In the limit of long simulation time, metadynamics converges to the exact free energy surface plus a time-dependent constant. In this article, we analyze in detail this time-dependent constant. We show an easy way to calculate it, and by explicitly calculating the time dependence of this constant, we are able to derive a time-independent and locally convergent free energy estimator for metadynamics. We also derive an alternate procedure for obtaining the full unbiased distributions of generic operators from biased metadynamics simulations and explicitly test its usefulness.},
author = {Tiwary, Pratyush and Parrinello, Michele},



journal = {J. Phys. Chem.. B},

pmid = {25046020},
title = {{A Time-Independent Free Energy Estimator for Metadynamics.}},

year = {2014}
}
@article{part-schw97jcp,
author = {Partridge, Harry and Schwenke, David W.},


journal = {J. Chem. Phys.},

pages = {4618},
title = {{The determination of an accurate isotope dependent potential energy surface for water from extensive ab initio calculations and experimental data}},

volume = {106},
year = {1997}
}
@article{bark-newm98pre,
author = {Barkema, G. and Newman, M.},



journal = {Phys. Rev. E},


pages = {1155--1166},
title = {{Monte Carlo simulation of ice models}},

volume = {57},
year = {1998}
}
@article{vand90prb,
author = {Vanderbilt, D},

journal = {Phys. Rev. B},

pages = {7892--7895},
publisher = {APS},
title = {{Soft self-consistent pseudopotentials in a generalized eigenvalue formalism}},
volume = {41},
year = {1990}
}
@article{gall-bern96jcp,
author = {Gallicchio, E. and Berne, B. J.},



journal = {J. Chem. Phys.},

pages = {7064},
title = {{On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral Monte Carlo data}},

volume = {105},
year = {1996}
}
@article{gill-96pre,
author = {Gillespie, Daniel T},

journal = {Phys. Rev. E},

pages = {2084--2091},
publisher = {American Physical Society},
title = {{Exact numerical simulation of the Ornstein-Uhlenbeck process and its integral}},
volume = {54},
year = {1996}
}
@article{magy+06prb,
author = {Magyari-K{\"{o}}pe, B. and Ozoli$\backslash$cn{\v{s}}, V and Wolverton, C. and Ozoliņ{\v{s}}, V.},



journal = {Phys. Rev. B},


pages = {220101},
publisher = {APS},
title = {{Theoretical prediction of low-energy crystal structures and hydrogen storage energetics in Li{\_}2 NH}},

volume = {73},
year = {2006}
}
@article{schr05jn,
author = {Schr{\"{o}}der, Elsebeth},



journal = {Journal of Nanomaterials},
pages = {1--6},
title = {{Methanol Adsorption on Graphene}},

volume = {2013},
year = {2013}
}
@article{rama+99jap,
author = {Ramalingam, Shyam and Maroudas, Dimitrios and Aydil, Eray S},


journal = {J. Appl. Phys.},

pages = {2872--2888},
publisher = {AIP},
title = {{Atomistic simulation study of the interactions of SiH[sub 3] radicals with silicon surfaces}},
volume = {86},
year = {1999}
}
@article{mazz+14nc,
abstract = {The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular dynamics based on the quantum Monte Carlo method, which can describe accurately the electronic correlation and treat a large number of hydrogen atoms, allowing a realistic and reliable prediction of thermodynamic properties. We find that the molecular liquid phase is unexpectedly stable, and the transition towards a fully atomic liquid phase occurs at much higher pressure than previously believed. The old standing problem of low-temperature atomization is, therefore, still far from experimental reach.},
archivePrefix = {arXiv},
arxivId = {1404.5471},
author = {Mazzola, Guglielmo and Yunoki, Seiji and Sorella, Sandro},



isbn = {2041-1723 (Electronic) 2041-1723 (Linking)},

journal = {Nature Comm.},

pages = {3487},
pmid = {24647280},
publisher = {Nature Publishing Group},
title = {{Unexpectedly high pressure for molecular dissociation in liquid hydrogen by electronic simulation}},

volume = {5},
year = {2014}
}
@article{tutt-adam98prb,
author = {Tuttle, Blair and Adams, James},



journal = {Phys. Rev. B},


pages = {12859--12868},
title = {{Energetics of hydrogen in amorphous silicon: An ab initio study}},

volume = {57},
year = {1998}
}
@article{earl-deem05pccp,
abstract = {We review the history of the parallel tempering simulation method. From its origins in data analysis, the parallel tempering method has become a standard workhorse of physicochemical simulations. We discuss the theory behind the method and its various generalizations. We mention a selected set of the many applications that have become possible with the introduction of parallel tempering, and we suggest several promising avenues for future research.},
author = {Earl, David J and Deem, Michael W},



journal = {Physical Chemistry Chemical Physics},



pages = {3910},
pmid = {19810318},
title = {{Parallel tempering: Theory, applications, and new perspectives}},

volume = {7},
year = {2005}
}
@phdthesis{ceri10phd,
author = {Ceriotti, Michele},

school = {ETH Z{\"{u}}rich},
title = {{A novel framework for enhanced molecular dynamics based on the generalized Langevin equation}},
year = {2010}
}
@article{fell+95jcp,
author = {Feller, Scott E and Zhang, Yuhong and Pastor, Richard W and Brooks, Bernard R},

journal = {J. Chem. Phys.},

pages = {4613--4621},
publisher = {AIP},
title = {{Constant pressure molecular dynamics simulation: The Langevin piston method}},
volume = {103},
year = {1995}
}
@article{terr-scot92as,
abstract = {We investigate some of the possibilities for improvement of univariate and multivariate kernel density estimates by varying the window over the domain of estimation, pointwise and globally. Two general approaches are to vary the window width by the point of estimation and by point of the sample observation. The first possibility is shown to be of little efficacy in one variable. In particular, nearest-neighbor estimators in all versions perform poorly in one and two dimensions, but begin to be useful in three or more variables. The second possibility is more promising. We give some general properties and then focus on the popular Abramson estimator. We show that in many practical situations, such as normal data, a nonlocality phenomenon limits the commonly applied version of the Abramson estimator to bias of O([h/logh]2) instead of the hoped for O(h4).},
author = {Terrell, George R. and Scott, David W.},


isbn = {0090-5364},

journal = {The Annals of Statistics},

pages = {1236--1265},
title = {{Variable Kernel Density Estimation}},

volume = {20},
year = {1992}
}
@article{bolh+02arpc,
abstract = {This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.},
author = {Bolhuis, Peter G and Chandler, David and Dellago, Christoph and Geissler, Phillip L},



journal = {Annual review of physical chemistry},


pages = {291--318},
pmid = {11972010},
title = {{Transition path sampling: throwing ropes over rough mountain passes, in the dark.}},

volume = {53},
year = {2002}
}
@article{mice+11prb,
author = {Miceli, Giacomo and Ceriotti, Michele and Bernasconi, Marco and Parrinello, Michele},



journal = {Phys. Rev. B},


pages = {054119},
publisher = {American Physical Society},
title = {{Static disorder and structural correlations in the low-temperature phase of lithium imide}},

volume = {83},
year = {2011}
}
@article{eins05anp,
author = {Einstein, A},

journal = {Ann. Phys.},

pages = {549},
title = {{{\{}{\"{U}}{\}}ber die von der molekularkinetischen Theorie der W{\{}{\"{a}}{\}}rme geforderte Bewegung von in ruhenden Fl{\{}{\"{u}}{\}}ssigkeiten suspendierten Teilchen}},
volume = {322},
year = {1905}
}
@article{day+09acb,
abstract = {We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules.},
author = {Day, Graeme M. and Cooper, Timothy G. and Cruz-Cabeza, Aurora J. and Hejczyk, Katarzyna E. and Ammon, Herman L. and Boerrigter, Stephan X M and Tan, Jeffrey S. and {Della Valle}, Raffaele G. and Venuti, Elisabetta and Jose, Jovan and Gadre, Shridhar R. and Desiraju, Gautam R. and Thakur, Tejender S. and {Van Eijck}, Bouke P. and Facelli, Julio C. and Bazterra, Victor E. and Ferraro, Marta B. and Hofmann, Detlef W M and Neumann, Marcus A. and Leusen, Frank J J and Kendrick, John and Price, Sarah L. and Misquitta, Alston J. and Karamertzanis, Panagiotis G. and Welch, Gareth W A and Scheraga, Harold A. and Arnautova, Yelena A. and Schmidt, Martin U. and {Van De Streek}, Jacco and Wolf, Alexandra K. and Schweizer, Bernd},


isbn = {0108-7681},

journal = {Acta Cryst. B: Structural Science},


pages = {107--125},
pmid = {19299868},
publisher = {International Union of Crystallography},
title = {{Significant progress in predicting the crystal structures of small organic molecules - A report on the fourth blind test}},
volume = {65},
year = {2009}
}
@article{liu+11jcp,
abstract = {The dynamical properties of liquid water play an important role in many processes in nature. In this paper, we focus on the infrared (IR) absorption spectrum of liquid water based on the linearized semiclassical initial value representation (LSC-IVR) with the local Gaussian approximation (LGA) [J. Liu and W. H. Miller, J. Chem. Phys. 131, 074113 (2009)] and an ab initio based, flexible, polarizable Thole-type model (TTM3-F) [G. S. Fanourgakis and S. S. Xantheas, J. Chem. Phys. 128, 074506 (2008)]. Although the LSC-IVR (LGA) gives the exact result for the isolated three-dimensional shifted harmonic stretching model, it yields a blueshifted peak position for the more realistic anharmonic stretching potential. By using the short-time information of the LSC-IVR correlation function; however, it is shown how one can obtain more accurate results for the position of the stretching peak. Due to the physical decay in the condensed phase system, the LSC-IVR (LGA) is a good and practical approximate quantum approach for the IR spectrum of liquid water. The present results offer valuable insight into future attempts to improve the accuracy of the TTM3-F potential or other ab initio-based models in reproducing the IR spectrum of liquid water.},
author = {Liu, Jian and Miller, William H and Fanourgakis, George S and Xantheas, Sotiris S and Imoto, Sho and Saito, Shinji},



journal = {J. Chem. Phys.},


pages = {244503},
pmid = {22225165},
title = {{Insights in quantum dynamical effects in the infrared spectroscopy of liquid water from a semiclassical study with an ab initio-based flexible and polarizable force field.}},

volume = {135},
year = {2011}
}
@article{gris-buch04jcp,
abstract = {Orientational defects in hexagonal ice were investigated using molecular dynamics simulations. Energy relaxation during L- and D-defect migration was shown to be associated with improved alignment of water molecules along the local electric fields. Two new forms of defects, an "L+D complex," and a "5+7 defect," were characterized. These forms appear in ice trajectories close to the melting point, and in the course of L- and D-pair recombination process. Defect pair recombination was shown to be a complex process, involving collective H-bond changes in groups of molecules.},
author = {Grishina, N. and Buch, V.},



journal = {J. Chem. Phys.},

pages = {5217--5225},
pmid = {15267393},
title = {{Structure and dynamics of orientational defects in ice I}},
volume = {120},
year = {2004}
}
@article{brow+16jpcl,
author = {Browning, Nicholas J and Ramakrishnan, Raghunathan and von Lilienfeld, O Anatole and Roethlisberger, Ursula},


journal = {J. Phys. Chem. Letters},


pages = {1351--1359},
title = {{Genetic Optimization of Training Sets for Improved Machine Learning Models of Molecular Properties}},

volume = {8},
year = {2017}
}
@article{neld-mead65cj,
abstract = {A method is described for the minimization of a function of n variables, which depends on the comparison of function values at the (n + 1) vertices of a general simplex, followed by the replacement of the vertex with the highest value by another point. The simplex adapts itself to the local landscape, and contracts on to the final minimum. The method is shown to be effective and computationally compact. A procedure is given for the estimation of the Hessian matrix in the neighbourhood of the minimum, needed in statistical estimation problems.},
author = {Nelder, J A and Mead, R},



journal = {Comp. J.},


pages = {308--313},
title = {{A Simplex Method for Function Minimization}},

volume = {7},
year = {1965}
}
@article{ambr+16science,
abstract = {Recent experiments on noncovalent interactions at the nanoscale have challenged the basic assumptions of commonly used particle- or fragment-based models for describing van der Waals (vdW) or dispersion forces.We demonstrate that a qualitatively correct description of the vdW interactions between polarizable nanostructures over a wide range of finite distances can only be attained by accounting for the wavelike nature of charge density fluctuations. By considering a diverse set of materials and biological systems with markedly different dimensionalities, topologies, and polarizabilities, we find a visible enhancement in the nonlocality of the charge density response in the range of 10 to 20 nanometers. These collective wavelike fluctuations are responsible for the emergence of nontrivial modifications of the power laws that govern noncovalent interactions at the nanoscale.},
author = {Ambrosetti, Alberto and Ferri, Nicola and DiStasio, R. A. and Tkatchenko, Alexandre},



journal = {Science},

pages = {1171--1176},
pmid = {26965622},
title = {{Wavelike charge density fluctuations and van der Waals interactions at the nanoscale}},

volume = {351},
year = {2016}
}
@article{liu+13jpcc,
author = {Liu, Jian and Andino, Richard S. and Miller, Christina M. and Chen, Xin and Wilkins, David M. and Ceriotti, Michele and Manolopoulos, David E.},



journal = {J. Phys. Chem. C},


pages = {2944--2951},
title = {{A Surface-Specific Isotope Effect in Mixtures of Light and Heavy Water}},

volume = {117},
year = {2013}
}
@article{pini+14gca,
author = {Pinilla, Carlos and Blanchard, Marc and Balan, Etienne and Ferlat, Guillaume and Vuilleumier, Rodolphe and Mauri, Francesco},



journal = {Geochimica et Cosmochimica Acta},

pages = {203--216},
publisher = {Elsevier Ltd},
title = {{Equilibrium fractionation of H and O isotopes in water from path integral molecular dynamics}},

volume = {135},
year = {2014}
}
@article{rein+96jcp,
author = {{Rein ten Wolde}, Pieter and Ruiz-Montero, Maria J. and Frenkel, Daan},



journal = {J. Chem. Phys.},

pages = {9932},
title = {{Numerical calculation of the rate of crystal nucleation in a Lennard-Jones system at moderate undercooling}},

volume = {104},
year = {1996}
}
@article{kraj-parr07prb,
author = {Krajewski, F R and Parrinello, M},

journal = {Phys. Rev. B},

pages = {235108},
publisher = {APS},
title = {{Linear scaling electronic structure Monte Carlo method for metals}},
volume = {75},
year = {2007}
}
@article{stei+99prb,
abstract = {The elastic constant tensors for the hcp phases of three transition metals (Co, Re, and Fe) are computed as functions of pressure using the Linearized Augmented Plane Wave method with both the local density and generalized gradient approximations. Spin-polarized states are found to be stable for Co (ferromagnetic) and Fe (antiferromagnetic at low pressure). The elastic constants of Co and Re are compared to experimental measurements near ambient conditions and excellent agreement is found. Recent measurements of the lattice strain in high pressure experiments when interpreted in terms of elastic constants for Re and Fe are inconsistent with the calculated moduli.},
archivePrefix = {arXiv},
arxivId = {cond-mat/9904431},
author = {Steinle-Neumann, G. and Stixrude, L. and Cohen, R. E.},



isbn = {0163-1829},

journal = {Phys. Rev. B},

pages = {10},
primaryClass = {cond-mat},
title = {{First-Principles Elastic Constants for the hcp Transition Metals Fe, Co, and Re at High Pressure}},

volume = {60},
year = {1999}
}
@article{agge+01pnas,
abstract = {A generic statistical mechanical model is presented for the self-assembly of chiral rod-like units, such as beta-sheet-forming peptides, into helical tapes, which with increasing concentration associate into twisted ribbons (double tapes), fibrils (twisted stacks of ribbons), and fibers (entwined fibrils). The finite fibril width and helicity is shown to stem from a competition between the free energy gain from attraction between ribbons and the penalty because of elastic distortion of the intrinsically twisted ribbons on incorporation into a growing fibril. Fibers are stabilized similarly. The behavior of two rationally designed 11-aa residue peptides, P(11)-I and P(11)-II, is illustrative of the proposed scheme. P(11)-I and P(11)-II are designed to adopt the beta-strand conformation and to self-assemble in one dimension to form antiparallel beta-sheet tapes, ribbons, fibrils, and fibers in well-defined solution conditions. The energetic parameters governing self-assembly have been estimated from the experimental data using the model. The 8-nm-wide fibrils consist of eight tapes, are extremely robust (scission energy approximately 200 k(B)T), and sufficiently rigid (persistence length l(fibril) approximately 20-70 microm) to form nematic solutions at peptide concentration c approximately 0.9 mM (volume fraction approximately 0.0009 vol/vol), which convert to self-supporting nematic gels at c {\textgreater} 4 mM. More generally, these observations provide a new insight into the generic self-assembling properties of beta-sheet-forming peptides and shed new light on the factors governing the structures and stability of pathological amyloid fibrils in vivo. The model also provides a prescription of routes to novel macromolecules based on a variety of self-assembling chiral units, and protocols for extraction of the associated energy changes.},
author = {Aggeli, A and Nyrkova, I A and Bell, M and Harding, R and Carrick, L and McLeish, T C and Semenov, A N and Boden, N},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {11857--11862},
pmid = {11592996},
title = {{Hierarchical self-assembly of chiral rod-like molecules as a model for peptide beta -sheet tapes, ribbons, fibrils, and fibers.}},

volume = {98},
year = {2001}
}
@article{CSBT6,
abstract = {The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered {\{}$\backslash$it Z{\}}{\{}{\$}{\^{}}\backslashprime{\$}{\}} = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.},
author = {Reilly, Anthony M and Others},

journal = {Acta Cryst. B},



pages = {439--459},
title = {{Report on the sixth blind test of organic crystal structure prediction methods}},

volume = {72},
year = {2016}
}
@article{lin+09prb,
abstract = {We propose a multipole representation of the Fermi-Dirac function and the Fermi operator, and use this representation to develop algorithms for electronic structure analysis of metallic systems. The new algorithm is quite simple and efficient. Its computational cost scales logarithmically with {\$}\backslashbeta\backslashDelta\backslasheps{\$} where {\$}\backslashbeta{\$} is the inverse temperature, and {\$}\backslashDelta \backslasheps{\$} is the width of the spectrum of the discretized Hamiltonian matrix.},
archivePrefix = {arXiv},
arxivId = {0812.4352},
author = {Lin, Lin and Lu, Jianfeng and Car, Roberto and E, Weinan},




journal = {Phys. Rev. B},


pages = {115133},
publisher = {APS},
title = {{Multipole representation of the Fermi operator with application to the electronic structure analysis of metallic systems}},

volume = {79},
year = {2009}
}
@article{cend+16pccp,
author = {Cendagorta, Joseph R. and Powers, Anna and Hele, Timothy J. H. and Marsalek, Ondrej and Ba{\v{c}}i{\'{c}}, Zlatko and Tuckerman, Mark E.},


journal = {Phys. Chem. Chem. Phys.},

pages = {32169--32177},
title = {{Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates}},

volume = {18},
year = {2016}
}
@article{otto+12jfa,
author = {Ottobre, M. and Pavliotis, G.a. and Pravda-Starov, K.},



journal = {Journal of Functional Analysis},



pages = {4000--4039},
publisher = {Elsevier Inc.},
title = {{Exponential return to equilibrium for hypoelliptic quadratic systems}},

volume = {262},
year = {2012}
}
@article{wolv-ozol01prl,
author = {Wolverton, C. and Ozolins, V.},



journal = {Phys. Rev. Lett.},

mendeley-tags = {aluminum},


pages = {5518--5521},
title = {{Entropically Favored Ordering: The Metallurgy of Al2Cu Revisited}},

volume = {86},
year = {2001}
}
@article{beck93jcp,
abstract = {Despite the remarkable thermochemical accuracy of KohnSham densityfunctional theories with gradient corrections for exchangecorrelation see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992), we believe that further improvements are unlikely unless exactexchange information is considered. Arguments to support this view are presented, and a semiempirical exchangecorrelation functional containing localspindensity, gradient, and exactexchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first and secondrow systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.},
author = {Becke, Axel D},

journal = {J. Chem. Phys.},

pages = {5648},
publisher = {AIP},
title = {{Density-functional thermochemistry. III. The role of exact exchange}},

volume = {98},
year = {1993}
}
@article{vans+04nmat,
abstract = {The search for deformation mechanisms in nanocrystalline metals has profited from the use of molecular dynamics calculations. These simulations have revealed two possible mechanisms; grain boundary accommodation, and intragranular slip involving dislocation emission and absorption at grain boundaries. But the precise nature of the slip mechanism is the subject of considerable debate, and the limitations of the simulation technique need to be taken into consideration. Here we show, using molecular dynamics simulations, that the nature of slip in nanocrystalline metals cannot be described in terms of the absolute value of the stacking fault energy-a correct interpretation requires the generalized stacking fault energy curve, involving both stable and unstable stacking fault energies. The molecular dynamics technique does not at present allow for the determination of rate-limiting processes, so the use of our calculations in the interpretation of experiments has to be undertaken with care.},
author = {{Van Swygenhoven}, H and Derlet, P M and Fr{\o}seth, A G},



journal = {Nature materials},


pages = {399--403},
pmid = {15156199},
title = {{Stacking fault energies and slip in nanocrystalline metals.}},

volume = {3},
year = {2004}
}
@article{ceri+09prl,
author = {Ceriotti, Michele and Bussi, Giovanni and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {020601},
publisher = {APS},
title = {{Langevin Equation with Colored Noise for Constant-Temperature Molecular Dynamics Simulations}},

volume = {102},
year = {2009}
}
@article{croi+14nc,
abstract = {Biomaterials are constructed from limited sets of building blocks but exhibit extraordinary and versatile properties, because hierarchical structure formation lets them employ identical supramolecular motifs for different purposes. Here we exert a similar degree of structural control in synthetic supramolecular elastomers and thus tailor them for a broad range of thermomechanical properties. We show that oligopeptide-terminated polymers selectively self-assemble into small aggregates or nanofibrils, depending on the length of the oligopeptides. This process is self-sorting if differently long oligopeptides are combined so that different nanostructures coexist in bulk mixtures. Blends of polymers with oligopeptides matching in length furnish reinforced elastomers that exhibit shear moduli one order of magnitude higher than the parent polymers. By contrast, novel interpenetrating supramolecular networks that display excellent vibration damping properties are obtained from blends comprising non-matching oligopeptides or unmodified polymers. Hence, blends of oligopeptide-modified polymers constitute a toolbox for tailored elastomers with versatile properties.},
author = {Croisier, Emmanuel and Liang, Su and Schweizer, Thomas and Balog, Sandor and Mioni{\'{c}}, Marijana and Snellings, Ruben and Cugnoni, Jo{\"{e}}l and Michaud, V{\'{e}}ronique and Frauenrath, Holger},



journal = {Nature Comm.},

pages = {4728},
pmid = {25198134},
title = {{A toolbox of oligopeptide-modified polymers for tailored elastomers.}},

volume = {5},
year = {2014}
}
@article{liu-mill09jcp,
abstract = {A simple model is presented for treating local imaginary frequencies that are important in the study of quantum effects in chemical reactions and various dynamical processes in molecular liquids. It significantly extends the range of accuracy of conventional local harmonic approximations (LHAs) used in the linearized semiclassical initial value representation/classical Wigner approximation for real time correlation functions. The key idea is realizing that a local Gaussian approximation (LGA) for the momentum distribution (from the Wigner function involving the Boltzmann operator) can be a good approximation even when a LHA for the potential energy surface fails. The model is applied here to two examples where imaginary frequencies play a significant role: the chemical reaction rate for a linear model of the H+H(2) reaction and an analogous asymmetric barrier--a case where the imaginary frequency of the barrier dominates the process--and for momentum autocorrelation functions in liquid para-hydrogen at two thermal state points (25 and 14 K under nearly zero external pressure). We also generalize the LGA model to the Feynman-Kleinert approximation.},
author = {Liu, Jian and Miller, William H},



journal = {J. Chem. Phys.},


pages = {074113},
pmid = {19708738},
title = {{A simple model for the treatment of imaginary frequencies in chemical reaction rates and molecular liquids.}},

volume = {131},
year = {2009}
}
@article{wang+03prb,
author = {Wang, Neng-Ping and Rohlfing, Michael and Kr{\"{u}}ger, Peter and Pollmann, Johannes},



journal = {Phys. Rev. B},


pages = {115111},
publisher = {American Physical Society},
title = {{Quasiparticle band structure and optical spectrum of LiF(001)}},

volume = {67},
year = {2003}
}
@article{dunk+01jmgm,
author = {Dunker, A.Keith and Lawson, J.David and Brown, Celeste J and Williams, Ryan M and Romero, Pedro and Oh, Jeong S and Oldfield, Christopher J and Campen, Andrew M and Ratliff, Catherine M and Hipps, Kerry W and Ausio, Juan and Nissen, Mark S and Reeves, Raymond and Kang, ChulHee and Kissinger, Charles R and Bailey, Robert W and Griswold, Michael D and Chiu, Wah and Garner, Ethan C and Obradovic, Zoran},



journal = {Journal of Molecular Graphics and Modelling},



pages = {26--59},
title = {{Intrinsically disordered protein}},

volume = {19},
year = {2001}
}
@article{habe-mano09jcp,
author = {Habershon, Scott and Manolopoulos, David E},

journal = {J. Chem. Phys.},

pages = {244518},
publisher = {AIP},
title = {{Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water}},
volume = {131},
year = {2009}
}
@article{marx-parr95jcp,
author = {Marx, Dominik and Parrinello, Michele},



journal = {J. Chem. Phys.},

pages = {4077},
publisher = {AIP},
title = {{Ab initio path integral molecular dynamics: Basic ideas}},

volume = {104},
year = {1996}
}
@article{adel-broo92jpc,
author = {Adelman, SA A. and Brooks, C L},



journal = {J. Phys. Chem.},


pages = {1511--1524},
title = {{Generalized Langevin models and condensed-phase chemical reaction dynamics}},

volume = {4471},
year = {1982}
}
@article{brou-gilm83jcp2,
author = {Broughton, Jeremy Q. and Gilmer, George H.},



journal = {J. Chem. Phys.},

pages = {5105},
title = {{Molecular dynamics investigation of the crystal–fluid interface. II. Structures of the fcc (111), (100), and (110) crystal–vapor systems}},

volume = {79},
year = {1983}
}
@article{wolk92prl,
author = {Wolkow, Robert},



journal = {Phys. Rev. Lett.},


pages = {2636--2639},
title = {{Direct observation of an increase in buckled dimers on Si(001) at low temperature}},

volume = {68},
year = {1992}
}
@article{rupp+12prl,
author = {Rupp, Matthias and Tkatchenko, Alexandre and M{\"{u}}ller, Klaus-Robert and von Lilienfeld, O. Anatole},


journal = {Phys. Rev. Lett.},


pages = {058301},
title = {{Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning}},

volume = {108},
year = {2012}
}
@article{schm+09jpcb,
abstract = {We present herein a comprehensive density functional theory study toward assessing the accuracy of two popular gradient-corrected exchange correlation functionals on the structure and density of liquid water at near ambient conditions in the isobaric-isothermal ensemble. Our results indicate that both PBE and BLYP functionals under predict the density and over structure the liquid. Adding the dispersion correction due to Grimme (1, 2) improves the predicted densities for both BLYP and PBE in a significant manner. Moreover, the addition of the dispersion correction for BLYP yields an oxygen-oxygen radial distribution function in excellent agreement with experiment. Thus, we conclude that one can obtain a very satisfactory model for water using BLYP and a correction for dispersion.},
author = {Schmidt, Jochen and VandeVondele, Joost and Kuo, I-F William and Sebastiani, Daniel and Siepmann, J Ilja and Hutter, J{\"{u}}rg and Mundy, Christopher J},



journal = {J. Phys. Chem.. B},


pages = {11959--64},
pmid = {19663399},
title = {{Isobaric-isothermal molecular dynamics simulations utilizing density functional theory: an assessment of the structure and density of water at near-ambient conditions.}},

volume = {113},
year = {2009}
}
@article{more-nemi10jcp,
abstract = {We calculated the kinetic energies of the H-atom in ice Ih between 5 and 269 K and in water in the range 293-673 K. To do so we used the literature optical vibration frequencies of ice and water of the different phases assuming the harmonic approximation and decoupling between the degrees of freedom of translation, rotation (libration), and internal vibrations. Apart for ice at 269 K, good agreement was obtained with published experimental values for both cases. Similar agreement with experiment was found for the case of water confined in 14 A diameter carbon nanotubes at 268 K. However, serious deviations from measured values were found in nanotube water in the range 5-230 K. Possible reasons for those deviations are discussed.},
author = {Moreh, R and Nemirovsky, D},



journal = {J. Chem. Phys.},


pages = {084506},
pmid = {20815579},
title = {{On the proton kinetic energy in H2O and in nanotube water.}},

volume = {133},
year = {2010}
}
@article{van+12pccp,
abstract = {Classical molecular dynamics is a convenient method for computing anharmonic infrared spectra of polyatomic molecules and condensed phase systems. However it does not perform well for predicting accurate intensities and it lacks nuclear quantization, two deficiencies that are usually accounted for by empirical scaling factors. In this paper we show on the examples of the trans isomer of nitrous acid and naphthalene that both issues can be alleviated by preparing the initial conditions according to semiclassical quantization based on a normal mode representation. The method correctly reproduces fundamental frequencies obtained with quantum mechanical methods. At increasing temperatures, the effective frequencies are found to follow the same trends as path-integral based methods. In the low-temperature limit, the band intensities predicted by the method are also found to agree with quantum mechanical considerations.},
author = {Van-Oanh, Nguyen-Thi and Falvo, Cyril and Calvo, Florent and Lauvergnat, David and Basire, Marie and Gaigeot, Marie-Pierre and Parneix, Pascal},



journal = {PCCP},



pages = {2381--90},
pmid = {22249945},
title = {{Improving anharmonic infrared spectra using semiclassically prepared molecular dynamics simulations.}},

volume = {14},
year = {2012}
}
@article{wilm11met,
author = {Wilm, Alfred},
journal = {Metallurgie: Zeitschrift f{\"{u}}r de gesamte H{\"{u}}ttenkunde},

pages = {225--227},
title = {{Physikalisch-metallurgische Untersuchungen {\{}{\"{u}}{\}}ber magnesiumhaltige Aluminiumlegierungen}},
volume = {8},
year = {1911}
}
@article{schl+98jcp,
author = {Schlick, Tamar and Mandziuk, Margaret and Skeel, Robert D. and Srinivas, K.},



journal = {J. Comp. Phys.},


pages = {1--29},
title = {{Nonlinear Resonance Artifacts in Molecular Dynamics Simulations}},

volume = {140},
year = {1998}
}
@article{maho-drin09pnas,
author = {Mahoney, Michael W. and Drineas, Petros},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {697--702},
title = {{CUR matrix decompositions for improved data analysis}},

volume = {106},
year = {2009}
}
@article{ivan+10jcp,
abstract = {Centroid molecular dynamics (CMD) is a popular method to extract approximate quantum dynamics from path integral simulations. Very recently we have shown that CMD gas phase infrared spectra exhibit significant artificial redshifts of stretching peaks, due to the so-called "curvature problem" imprinted by the effective centroid potential. Here we provide evidence that for condensed phases, and in particular for liquid water, CMD produces pronounced artificial redshifts for high-frequency vibrations such as the OH stretching band. This peculiar behavior intrinsic to the CMD method explains part of the unexpectedly large quantum redshifts of the stretching band of liquid water compared to classical frequencies, which is improved after applying a simple and rough "harmonic curvature correction."},
author = {Ivanov, Sergei D and Witt, Alexander and Shiga, Motoyuki and Marx, Dominik},



journal = {J. Chem. Phys.},


pages = {031101},
pmid = {20095719},
title = {{Communications: On artificial frequency shifts in infrared spectra obtained from centroid molecular dynamics: Quantum liquid water.}},

volume = {132},
year = {2010}
}
@article{wein-dove03rgm,
abstract = {Biomineralization links soft organic tissues, which are compositionally akin to the atmosphere and oceans, with the hard materials of the solid Earth. It provides organisms with skeletons and shells while they are alive, and when they die these are deposited as sediment in environments from river plains to the deep ocean floor. It is also these hard, resistant products of life which are mainly responsible for the Earths fossil record. Consequently, biomineralization involves biologists, chemists, and geologists in interdisciplinary studies at one of the interfaces between Earth and life.},
author = {Weiner, Steve and Dove, Patricia M},


isbn = {1529-6466},

journal = {Reviews in Mineralogy and Geochemistry},


pages = {1--29},
title = {{An Overview of Biomineralization Processes and the Problem of the Vital Effect}},

volume = {54},
year = {2003}
}
@article{baer-head97jcp,
author = {Baer, R and Head-Gordon, M},

journal = {J. Chem. Phys.},
pages = {10003--10013},
title = {{Chebyshev expansion methods for electronic structure calculations on large molecular systems}},
volume = {107},
year = {1997}
}
@article{brou-gilm86jcp,
author = {Broughton, J. Q. and Gilmer, G. H.},



journal = {J. Chem. Phys.},

pages = {5759},
title = {{Molecular dynamics investigation of the crystal–fluid interface. VI. Excess surface free energies of crystal–liquid systems}},

volume = {84},
year = {1986}
}
@article{pena+04jcp,
abstract = {The centroid molecular dynamics (CMD) method is applied to the study of liquid water in the context of the rigid-body approximation. This rigid-body CMD technique, which is significantly more efficient than the standard CMD method, is implemented on the TIP4P model for water and used to examine isotopic effects in the equilibrium and dynamical properties of liquid H(2)O and D(2)O. The results obtained with this approach compare remarkably well with those determined previously with path integrals simulations as well as those obtained from the standard CMD method employing flexible models. In addition, an examination of the impact of quantization on the rotational and librational motion of the water molecule is also reported.},
author = {{Hern{\'{a}}ndez de la Pe{\~{n}}a}, L and Kusalik, P G},



journal = {J. Chem. Phys.},


pages = {5992--6002},
pmid = {15367027},
publisher = {AIP},
title = {{Quantum effects in light and heavy liquid water: A rigid-body centroid molecular dynamics study.}},

volume = {121},
year = {2004}
}
@article{Scott1997,
author = {Cohen, Scott D. and Guibas, Leonidas},

pages = {1--44},
title = {{The earth mover's distance: Lower bounds and invariance under translation}},

year = {1997}
}
@article{loer+11pccp,
abstract = {Many acronyms are used in the literature for describing different kinds of amorphous ice, mainly because many different preparation routes and many different sample histories need to be distinguished. We here introduce these amorphous ices and discuss the question of how many of these forms are of relevance in the context of polyamorphism. We employ the criterion of reversible transitions between amorphous "states" in finite intervals of pressure and temperature to discriminate between independent metastable amorphous "states" and between "substates" of the same amorphous "state". We argue that the experimental evidence suggests we should consider there to be three polyamorphic "states" of ice, namely low-(LDA), high-(HDA) and very high-density amorphous ice (VHDA). In addition to the realization of reversible transitions between them, they differ in terms of their properties, e.g., compressibility, or number of "interstitial" water molecules. Thus they cannot be regarded as structurally relaxed variants of each other and so we suggest considering them as three distinct megabasins in an energy landscape visualization.},
author = {Loerting, Thomas and Winkel, Katrin and Seidl, Markus and Bauer, Marion and Mitterdorfer, Christian and Handle, Philip H and Salzmann, Christoph G and Mayer, Erwin and Finney, John L and Bowron, Daniel T},



journal = {PCCP},

mendeley-tags = {amorphous ice},


pages = {8783--8794},
pmid = {21431195},
title = {{How many amorphous ices are there?}},

volume = {13},
year = {2011}
}
@article{sugi+97apl,
author = {Sugiyama, S and Yang, J and Guha, S},



journal = {Applied Physics Letters},

pages = {378},
title = {{Improved stability against light exposure in amorphous deuterated silicon alloy solar cell}},

volume = {70},
year = {1997}
}
@article{jain-stoc12jctc,
abstract = {Recent molecular dynamics simulations of biopolymers have shown that in many cases the global features of the free energy landscape can be characterized in terms of the metastable conformational states of the system. To identify these states, a conceptionally and computationally simple approach is proposed. It consists of (i) an initial preprocessing via principal component analysis to reduce the dimensionality of the data, followed by k-means clustering to generate up to 104 microstates, (ii) the most probable path algorithm to identify the metastable states of the system, and (iii) boundary corrections of these states via the introduction of cluster cores in order to obtain the correct dynamics. By adopting two well-studied model problems, hepta-alanine and the villin headpiece protein, the potential and the performance of the approach are demonstrated.},
author = {Jain, Abhinav and Stock, Gerhard},


isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},

pages = {3810--3819},
title = {{Identifying metastable states of folding proteins}},
volume = {8},
year = {2012}
}
@article{kerm+08nature,
author = {Kermode, J. R. and Albaret, T. and Sherman, D. and Bernstein, N. and Gumbsch, P. and Payne, M. C. and Cs{\'{a}}nyi, G. and {De Vita}, A.},



journal = {Nature},


pages = {1224--1227},
title = {{Low-speed fracture instabilities in a brittle crystal}},

volume = {455},
year = {2008}
}
@article{tocc+16jpcl,
abstract = {Second-harmonic scattering experiments of water and other bulk molecular liquids have long been assumed to be insensitive to interactions between the molecules. The measured intensity is generally thought to arise from incoherent scattering due to individual molecules. We introduce a method to compute the second-harmonic scattering pattern of molecular liquids directly from atomistic computer simulations, which takes into account the coherent terms. We apply this approach to large-scale molecular dynamics simulations of liquid water, where we show that nanosecond second-harmonic scattering experiments contain a coherent contribution arising from radial and angular correlations on a length scale of ≲1 nm, much shorter than had been recently hypothesized (Shelton, D. P. J. Chem. Phys. 2014, 141). By combining structural correlations from simulations with experimental data (Shelton, D. P. J. Chem. Phys. 2014, 141), we can also extract an effective molecular hyperpolarizability in the liquid phase. This work ...},
author = {Tocci, Gabriele and Liang, Chungwen and Wilkins, D.M. David M. and Roke, Sylvie and Ceriotti, Michele},



journal = {J. Phys. Chem. Letters},

pages = {4311--4316},
title = {{Second-Harmonic Scattering as a Probe of Structural Correlations in Liquids}},
volume = {7},
year = {2016}
}
@article{wang-land01prl,
author = {Wang, Fugao and Landau, D.},



journal = {Phys. Rev. Lett.},


pages = {2050--2053},
title = {{Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States}},

volume = {86},
year = {2001}
}
@article{gerb-hore17pnas,
author = {Gerber, Susanne and Horenko, Illia},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {4863--4868},
title = {{Toward a direct and scalable identification of reduced models for categorical processes}},

volume = {114},
year = {2017}
}
@article{zhon+95prb,
author = {Zhong, W and Vanderbilt, David and Rabe, K M},

journal = {Phys. Rev. B},

pages = {6301--6312},
publisher = {American Physical Society},
title = {{First-principles theory of ferroelectric phase transitions for perovskites: The case of BaTiO{\_}3}},
volume = {52},
year = {1995}
}
@article{suh-12cr,
author = {Suh, Myunghyun Paik and Park, Hye Jeong and Prasad, Thazhe Kootteri and Lim, Dae-Woon},



journal = {Chem. Rev.},



pages = {782--835},
pmid = {22191516},
title = {{Hydrogen storage in metal-organic frameworks.}},

volume = {112},
year = {2012}
}
@article{tama-tana99pre,
author = {Tamai, Yoshinori and Tanaka, Hideki},



journal = {Phys. Rev. E},


pages = {5647--5654},
title = {{Effects of polymer chains on structure and dynamics of supercooled water in poly(vinyl alcohol)}},

volume = {59},
year = {1999}
}
@article{wang+14pnas,
author = {Wang, Lu and Fried, Stephen D and Boxer, Steven G and Markland, Thomas E},


isbn = {1091-6490 (Electronic) 0027-8424 (Linking)},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {18454--18459},
pmid = {25503367},
title = {{Quantum delocalization of protons in the hydrogen bond network of an enzyme active site}},
volume = {111},
year = {2014}
}
@article{tris+15jctc,
author = {Bereau, Tristan and Andrienko, Denis and von Lilienfeld, O Anatole},



journal = {J. Chem. Theory Comput.},


pages = {3225--3233},
title = {{Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules}},

volume = {11},
year = {2015}
}
@article{jorg+96jacs,
author = {Jorgensen, W L and Maxwell, D S and Tirado-Rives, J},

journal = {J. Am. Chem. Soc},

pages = {11225--11236},
title = {{Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids}},
volume = {118},
year = {1996}
}
@article{comi+17jcp,
abstract = {The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover...},
author = {Comitani, Federico and Rossi, Kevin and Ceriotti, Michele and Sanz, M. Eugenia and Molteni, Carla},



journal = {J. Chem. Phys.},


pages = {145102},
title = {{Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution}},

volume = {146},
year = {2017}
}
@article{poho+10jpcb,
author = {Pohorille, A and Jarzynski, C and Chipot, C},

journal = {J. Phys. Chem. B},
publisher = {ACS Publications},
title = {{Good practices in free-energy calculations}},
year = {2010}
}
@article{erre+14prb,
abstract = {Harmonic calculations based on density-functional theory are generally the method of choice for the description of phonon spectra of metals and insulators. The inclusion of anharmonic effects is, however, delicate as it relies on perturbation theory requiring a considerable amount of computer time, fast increasing with the cell size. Furthermore, perturbation theory breaks down when the harmonic solution is dynamically unstable or the anharmonic correction of the phonon energies is larger than the harmonic frequencies themselves. We present here a stochastic implementation of the self-consistent harmonic approximation valid to treat anharmonicity at any temperature in the nonperturbative regime. The method is based on the minimization of the free energy with respect to a trial density matrix described by an arbitrary harmonic Hamiltonian. The minimization is performed with respect to all the free parameters in the trial harmonic Hamiltonian, namely, equilibrium positions, phonon frequencies, and polarization vectors. The gradient of the free energy is calculated following a stochastic procedure. The method can be used to calculate thermodynamic properties, dynamical properties, and even anharmonic corrections to the Eliashberg function of the electron-phonon coupling. The scaling with the system size is greatly improved with respect to perturbation theory. The validity of the method is demonstrated in the strongly anharmonic palladium and platinum hydrides. In both cases, we predict a strong anharmonic correction to the harmonic phonon spectra, far beyond the perturbative limit. In palladium hydrides, we calculate thermodynamic properties beyond the quasiharmonic approximation, while in PtH, we demonstrate that the high superconducting critical temperatures at 100 GPa predicted in previous calculations based on the harmonic approximation are strongly suppressed when anharmonic effects are included.},
archivePrefix = {arXiv},
arxivId = {arXiv:1311.3083v1},
author = {Errea, Ion and Calandra, Matteo and Mauri, Francesco},




journal = {Phys. Rev. B - Condensed Matter and Materials Physics},

pages = {1--16},
title = {{Anharmonic free energies and phonon dispersions from the stochastic self-consistent harmonic approximation: Application to platinum and palladium hydrides}},
volume = {89},
year = {2014}
}
@article{herr-rami09prb,
author = {Herrero, Carlos and Ram{\'{i}}rez, Rafael},



journal = {Phys. Rev. B},


pages = {035207},
title = {{Molecular hydrogen in silicon: A path-integral simulation}},

volume = {80},
year = {2009}
}
@article{bals+95jgr,
author = {Balsiger, H and Altwegg, K and Geiss, J},



journal = {Journal of Geophysical Research},

mendeley-tags = {isotope fractionation},

pages = {5827},
title = {{D/H and 18 O/ 16 O ratio in the hydronium ion and in neutral water from in situ ion measurements in comet Halley}},

volume = {100},
year = {1995}
}
@article{smit-robe93jrssb,
author = {Smith, A F M and Roberts, G O},

journal = {J. Royal Stat. Soc. B},


pages = {3--23},
publisher = {JSTOR},
title = {{Bayesian computation via the Gibbs sampler and related Markov chain Monte Carlo methods}},
volume = {55},
year = {1993}
}
@article{haig66jcp,
author = {Haigh, Paul J. and Forman, R A and Frisch, R C},



journal = {J. Chem. Phys.},

pages = {812},
title = {{Nuclear Magnetic Resonance of 7Li and 1H in Solid Lithium Imide, Lithium Amide, and Lithium Nitride}},

volume = {45},
year = {1966}
}
@article{tang06jcp,
abstract = {The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.},
author = {Tangney, Paul},



journal = {J. Chem. Phys.},


pages = {044111},
pmid = {16460153},
title = {{On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter.}},

volume = {124},
year = {2006}
}
@article{kohn96prl,
author = {Kohn, W},

journal = {Phys. Rev. Lett.},

pages = {3168--3171},
publisher = {APS},
title = {{Density Functional and Density Matrix Method Scaling Linearly with the Number of Atoms}},
volume = {76},
year = {1996}
}
@article{pfro+00jacs,
author = {Pfrommer, Bernd G. and Mauri, Francesco and Louie, Steven G.},



journal = {J. Chem. Am. Soc. },


pages = {123--129},
title = {{NMR Chemical Shifts of Ice and Liquid Water: The Effects of Condensation}},

volume = {122},
year = {2000}
}
@article{bran+07jcp,
abstract = {The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.},
author = {Branduardi, Davide and Gervasio, Francesco Luigi and Parrinello, Michele},



journal = {J. Chem. Phys.},



pages = {054103},
pmid = {17302470},
title = {{From A to B in free energy space.}},

volume = {126},
year = {2007}
}
@article{bono-parr10prl,
author = {Bonomi, M and Parrinello, M},

journal = {Phys. Rev. Lett.},

pages = {190601},
publisher = {APS},
title = {{Enhanced sampling in the well-tempered ensemble}},
volume = {104},
year = {2010}
}
@article{gibe+13jctc,
author = {Giberti, Federico and Tribello, Gareth A. and Parrinello, Michele},



journal = {J. Chem. Theory Comput.},


pages = {2526--2530},
title = {{Transient Polymorphism in NaCl}},

volume = {9},
year = {2013}
}
@article{yang+18cm,
author = {Yang, Jack and De, Sandip and Campbell, Josh E. and Li, Sean and Ceriotti, Michele and Day, Graeme M.},



journal = {Chemistry of Materials},

pages = {4361--4371},
publisher = {American Chemical Society},
title = {{Large-Scale Computational Screening of Molecular Organic Semiconductors Using Crystal Structure Prediction}},
volume = {30},
year = {2018}
}
@article{hayw-reim97jcp,
author = {Hayward, J A and Reimers, J R},

journal = {J. Chem. Phys.},

pages = {1518--1529},
publisher = {AIP},
title = {{Unit cells for the simulation of hexagonal ice}},
volume = {106},
year = {1997}
}
@article{grus+08jac,
author = {Grushko, B. and Przepi{\'{o}}rzynski, B. and Pavlyuchkov, D.},



journal = {J. Alloys Compd.},



pages = {214--220},
title = {{On the constitution of the high-Al region of the Al-Cr alloy system}},

volume = {454},
year = {2008}
}
@article{daw+93msr,
author = {Daw, Murray S. and Foiles, Stephen M. and Baskes, Michael I.},



journal = {Materials Science Reports},

mendeley-tags = {aluminum,eam},


pages = {251--310},
title = {{The embedded-atom method: a review of theory and applications}},

volume = {9},
year = {1993}
}
@article{bart+10prl,
author = {Bart{\'{o}}k, Albert P. and Payne, Mike C. and Kondor, Risi and Cs{\'{a}}nyi, G{\'{a}}bor},



journal = {Phys. Rev. Lett.},


pages = {136403},
title = {{Gaussian Approximation Potentials: The Accuracy of Quantum Mechanics, without the Electrons}},

volume = {104},
year = {2010}
}
@article{VASP,
author = {Kresse, G and Furthm{\"{u}}ller, J},
journal = {Phys. Rev. B},

pages = {11169--11186},
publisher = {APS},
title = {{Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set}},
volume = {54},
year = {1996}
}
@article{chen+17jcp,
abstract = {In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters of a model based on classical nucleation theory can be fit using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the parameters of the macroscopic model are fitted in this way the numerical errors for the final fitted model are smaller and that the extrapolated predictions for large nuclei are thus more reliable.},
archivePrefix = {arXiv},
arxivId = {1703.06062},
author = {Cheng, Bingqing and Tribello, G.A. Gareth A. and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {104707},
title = {{The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit}},

volume = {147},
year = {2017}
}
@article{coli+07prb,
author = {Colizzi, Giuseppe and Filippetti, Alessio and Fiorentini, Vincenzo},

journal = {Phys. Rev. B},

pages = {64428},
publisher = {American Physical Society},
title = {{Magnetism of La{\_}0.625Sr{\_}0.375MnO{\_}3 under high pressure from first principles}},
volume = {76},
year = {2007}
}
@article{liu+09jcp,
abstract = {The important role of liquid water in many areas of science from chemistry, physics, biology, geology to climate research, etc., has motivated numerous theoretical studies of its structure and dynamics. The significance of quantum effects on the properties of water, however, has not yet been fully resolved. In this paper we focus on quantum dynamical effects in liquid water based on the linearized semiclassical initial value representation (LSC-IVR) with a quantum version of the simple point charge/flexible (q-SPC/fw) model [Paesani et al., J. Chem. Phys. 125, 184507 (2006)] for the potential energy function. The infrared (IR) absorption spectrum and the translational diffusion constants have been obtained from the corresponding thermal correlation functions, and the effects of intermolecular and intramolecular correlations have been studied. The LSC-IVR simulation results are compared with those predicted by the centroid molecular dynamics (CMD) approach. Although the LSC-IVR and CMD results agree well for the broadband for hindered motions in liquid water, the intramolecular bending and O-H stretching peaks predicted by the LSC-IVR are blueshifted from those given by CMD; reasons for this are discussed. We also suggest that the broadband in the IR spectrum corresponding to restricted translation and libration gives more information than the diffusion constant on the nature of quantum effects on translational and rotational motions and should thus receive more attention in this regard.},
author = {Liu, Jian and Miller, William H and Paesani, Francesco and Zhang, Wei and Case, David a},



journal = {J. Chem. Phys.},



pages = {164509},
pmid = {19894958},
title = {{Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum.}},

volume = {131},
year = {2009}
}
@article{maro01ace,
author = {Maroudas, Dimitrios},


journal = {Advances in Chemical Engineering},
pages = {251},
title = {{Modeling of radical-surface interactions in the plasma-enhanced chemical vapor deposition of silicon thin films}},

volume = {28},
year = {2001}
}
@article{todo+06jpcb,
abstract = {The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.},
author = {Todorova, Teodora and Seitsonen, Ari P and Hutter, J{\"{u}}rg and Kuo, I-Feng W and Mundy, Christopher J},



journal = {J. Phys. Chem.. B},



pages = {3685--91},
pmid = {16494424},
title = {{Molecular dynamics simulation of liquid water: hybrid density functionals.}},

volume = {110},
year = {2006}
}
@article{wei+97apl,
author = {Wei, Jeng-Hua and Sun, Ming-Shyan and Lee, Si-Chen},



journal = {Applied Physics Letters},

pages = {1498},
title = {{A possible mechanism for improved light-induced degradation in deuterated amorphous-silicon alloy}},

volume = {71},
year = {1997}
}
@article{hoov85pra,
author = {Hoover, W G},

journal = {Phys. Rev. A},

pages = {1695--1697},
publisher = {APS},
title = {{Canonical dynamics: Equilibrium phase-space distributions}},
volume = {31},
year = {1985}
}
@article{perd+96prl,
abstract = {Generalized gradient approximations (GGA's) for the exchange-correlation energy improve upon the local spin density (LSD) description of atoms, molecules, and solids. We present a simple derivation of a simple GGA, in which all parameters (other than those in LSD) are fundamental constants. Only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked. Improvements over PW91 include an accurate description of the linear response of the uniform electron gas, correct behavior under uniform scaling, and a smoother potential.},
author = {Perdew, Jp P and Burke, K and Ernzerhof, M},
chapter = {3865},

journal = {Phys. Rev. Lett.},

pages = {3865},
publisher = {American Physical Society},
series = {Phys. Rev. Lett. (USA)},
title = {{Generalized Gradient Approximation made simple}},

volume = {77},
year = {1996}
}
@article{mant+09am,
author = {Mantina, M. and Wang, Y. and Chen, L.Q. Q and Liu, Z.K. K and Wolverton, C.},



journal = {Acta Materialia},



pages = {4102--4108},
publisher = {Acta Materialia Inc.},
title = {{First principles impurity diffusion coefficients}},

volume = {57},
year = {2009}
}
@article{pete-voth06jpcb,
abstract = {The solvation and transport properties of the sulfonate-hydronium ion pair have been studied in hydrated Nafion through molecular dynamics simulation. Explicit proton and charge delocalization of the excess proton transport, via the Grotthuss hopping mechanism, were treated using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. The nature of the sulfonate-hydronium ion pair was characterized through analysis of free-energy profiles. It was found that, in general, the excess proton is solvated between two water molecules of a Zundel moiety while in the contact ion pair position, but then it transitions to an Eigen-like configuration in the solvent-separated pair position. Furthermore, the positive charge associated with the excess proton passes between the contact and solvent-separated ion pair positions through the Grotthuss mechanism rather than simple vehicular diffusion. The total proton diffusion was decomposed into vehicular and Grotthuss components and were found to be of the same relative magnitude, but with a strong negative correlation resulting in a smaller overall diffusion. Correlated motions between the ion pair were examined through the distinct portion of the van Hove correlation function, and a characteristic time scale of approximately 425 ps was observed. Additionally, the association of the hydrated proton with the hydrophobic polymer backbone suggests its amphiphile-like behavior (see Acc. Chem. Res. 2006, 39, 143; Phys. Rev. 1954, 95, 249; J. Chem. Phys. 2005, 123, 084309).},
author = {Petersen, Matt K and Voth, Gregory a},



journal = {J. Phys. Chem.. B},



pages = {18594--600},
pmid = {16970488},
title = {{Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion.}},

volume = {110},
year = {2006}
}
@article{lee-mcke09ic,
abstract = {The formation of LiNH(2)BH(3) from (LiH)(4) and NH(3)BH(3) and the subsequent dehydrogenation have been studied computationally at the CCSD(T)/6-311++G(3d,2p)//MP2/6-311++G(2d,p) level. A cubic unit of (LiH)(4) is predicted to react readily with NH(3)BH(3) to form LiNH(2)BH(3) plus H(2). The (LiH)(4) tetramer enables dehydrogenation through the exchange of a hydride vertex of (LiH)(4) and NH(2)BH(3)(-) where NH(2)BH(3)(-) is formed when the hydride vertex of (LiH)(4) abstracts a proton from NH(3). The free energy of activation for loss of H(2) is reduced from 37.2 kcal/mol in NH(3)BH(3) to 11.0 kcal/mol in (LiH)(4) + NH(3)BH(3). Further, H(2) elimination from the (LiNH(2)BH(3))(2) dimer is predicted to be much easier than from the monomer which may suggest a cooperative H(2)-loss mechanism is possible in solid LiNH(2)BH(3). While two molecules of H(2) can be lost reversibly from (LiNH(2)BH(3))(2), loss of further H(2) molecules is more difficult but could occur if the lattice energy stabilization accompanying H(2) loss is sufficiently large.},
author = {Lee, Tae Bum and McKee, Michael L},



journal = {Inorganic chemistry},


pages = {7564--75},
pmid = {19591435},
title = {{Mechanistic study of LiNH(2)BH(3) formation from (LiH)(4) + NH(3)BH(3) and subsequent dehydrogenation.}},

volume = {48},
year = {2009}
}
@article{ples-simo01proc,
author = {Pless, R and Simon, I},

institution = {Citeseer},
journal = {Proc. of the International Conference on Imaging Science, Systems, and Technology},
title = {{Embedding images in non-flat spaces}},

year = {2002}
}
@article{kara-vani17jcp,
author = {Karandashev, Konstantin and Van{\'{i}}{\v{c}}ek, Jiř{\'{i}}},



journal = {J. Chem. Phys.},


pages = {184102},
title = {{Accelerating equilibrium isotope effect calculations. I. Stochastic thermodynamic integration with respect to mass}},

volume = {146},
year = {2017}
}
@inproceedings{kazh+03proc,
author = {Kazhdan, Michael and Funkhouser, Thomas and Rusinkiewicz, Szymon},
booktitle = {Proceedings of the 2003 Eurographics/ACM SIGGRAPH Symposium on Geometry Processing},
isbn = {1-58113-687-0},
pages = {156--164},
publisher = {Eurographics Association},
series = {SGP '03},
title = {{Rotation Invariant Spherical Harmonic Representation of 3D Shape Descriptors}},

year = {2003}
}
@book{bade02book,
author = {Bader, Richard FW},

isbn = {0198558651},
publisher = {Clarendon Press},
title = {{Atoms in molecules: A quantum theory}},
year = {1994}
}
@article{love+96prl,
author = {Loveday, J S and Nelmes, R J and Marshall, W G and Besson, J M and Klotz, S and Hamel, G},

journal = {Phys. Rev. Lett.},

pages = {74--77},
publisher = {American Physical Society},
title = {{Structure of Deuterated Ammonia IV}},
volume = {76},
year = {1996}
}
@article{cava+04pcgcm,
author = {Cavallotti, C and {Di Stanislao}, M and Carr{\`{a}}, S},

journal = {Progress in Crystal Growth and Characterization of Materials},
pages = {123},
title = {{Interplay of physical and chemical aspects in the PECVD and etching of thin solid films}},
volume = {48-49},
year = {2004}
}
@article{ceri+08jcp,
abstract = {We present a method to compute the Fermi function of the Hamiltonian for a system of independent fermions based on an exact decomposition of the grand-canonical potential. This scheme does not rely on the localization of the orbitals and is insensitive to ill-conditioned Hamiltonians. It lends itself naturally to linear scaling as soon as the sparsity of the system's density matrix is exploited. By using a combination of polynomial expansion and Newton-like iterative techniques, an arbitrarily large number of terms can be employed in the expansion, overcoming some of the difficulties encountered in previous papers. Moreover, this hybrid approach allows us to obtain a very favorable scaling of the computational cost with increasing inverse temperature, which makes the method competitive with other Fermi operator expansion techniques. After performing an in-depth theoretical analysis of computational cost and accuracy, we test our approach on the density functional theory Hamiltonian for the metallic phase of the LiAl alloy.},
archivePrefix = {arXiv},
arxivId = {0805.2822},
author = {Ceriotti, Michele and K{\"{u}}hne, Thomas D. and Parrinello, Michele},



isbn = {0021-9606},

journal = {J. Chem. Phys.},


pages = {24707},
pmid = {18624552},
title = {{An efficient and accurate decomposition of the Fermi operator}},

volume = {129},
year = {2008}
}
@article{geng15jcp,
author = {Geng, Hua Y.},



journal = {J. Comp. Phys.},

pages = {299--311},
publisher = {Elsevier Inc.},
title = {{Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface}},

volume = {283},
year = {2015}
}
@article{pede+15jcp,
abstract = {An essential parameter for crystal growth is the kinetic coefficient given by the proportionality between supercooling and average growth velocity. Here, we show that this coefficient can be computed in a single equilibrium simulation using the interface pinning method where two-phase configurations are stabilized by adding a spring-like bias field coupling to an order-parameter that discriminates between the two phases. Crystal growth is a Smoluchowski process and the crystal growth rate can, therefore, be computed from the terminal exponential relaxation of the order parameter. The approach is investigated in detail for the Lennard-Jones model. We find that the kinetic coefficient scales as the inverse square-root of temperature along the high temperature part of the melting line. The practical usability of the method is demonstrated by computing the kinetic coefficient of the elements Na and Si from first principles. A generalized version of the method may be used for computing the rates of crystal nucleation or other rare events.},
archivePrefix = {arXiv},
arxivId = {1406.2659},
author = {Pedersen, Ulf R and Hummel, Felix and Dellago, Christoph},




journal = {J. Chem. Phys.},

pages = {44104},
pmid = {25637966},
title = {{Computing the crystal growth rate by the interface pinning method.}},

volume = {142},
year = {2015}
}
@article{yama05jcp,
abstract = {We first show that a simple scaling of fluctuation coordinates defined in terms of a given reference point gives the conventional virial estimator in discretized path integral, where different choices of the reference point lead to different forms of the estimator (e.g., centroid virial). The merit of this procedure is that it allows a finite-difference evaluation of the virial estimator with respect to temperature, which totally avoids the need of higher-order potential derivatives. We apply this procedure to energy and heat-capacity calculations of the (H(2))(22) and Ne(13) clusters at low temperature using the fourth-order Takahashi-Imada [J. Phys. Soc. Jpn. 53, 3765 (1984)] and Suzuki [Phys. Lett. A 201, 425 (1995)] propagators. This type of calculation requires up to third-order potential derivatives if analytical virial estimators are used, but in practice only first-order derivatives suffice by virtue of the finite-difference scheme above. From the application to quantum clusters, we find that the fourth-order propagators do improve upon the primitive approximation, and that the choice of the reference point plays a vital role in reducing the variance of the virial estimator.},
author = {Yamamoto, Takeshi M},



journal = {J. Chem. Phys.},


pages = {104101},
pmid = {16178583},
title = {{Path-integral virial estimator based on the scaling of fluctuation coordinates: Application to quantum clusters with fourth-order propagators}},

volume = {123},
year = {2005}
}
@article{dona-reif85jap,
author = {Donahue, T. J. and Reif, R},



journal = {J. Appl. Phys.},

pages = {2757},
publisher = {AIP},
title = {{Silicon epitaxy at 650–800 °C using low-pressure chemical vapor deposition both with and without plasma enhancement}},

volume = {57},
year = {1985}
}
@article{heye83cp,
author = {Heyes, D M},

journal = {Chem. Phys.},

pages = {285--301},
title = {{Molecular dynamics at constant pressure and temperature}},
volume = {82},
year = {1983}
}
@article{buss+06prl,
author = {Bussi, G and Laio, A and Parrinello, M},

journal = {Phys. Rev. Lett.},

pages = {90601},
publisher = {APS},
title = {{Equilibrium free energies from nonequilibrium metadynamics}},
volume = {96},
year = {2006}
}
@article{rapp+07mp,
abstract = {Modelling reactivity at the nanoscale is a major computational challenge. Both reactive force field and combined QM–MM methodologies have been and are being developed to study reactivity at this boundary between molecules and the solid state. There have been more than 1500 publications since the mid-1990s, on combined QM–MM methodologies. Limitations in current models include the distortional characteristics of force field potential terms, the smooth transit from one potential surface to another, rather than surface hopping, and the blending of electrostatics between QM and MM portions of a QM–MM model. Functional forms, potential surface coupling terms, and parameterization strategies for the Approximate Pair Theory (APT), a next generation reactive force field model, are described. The APT model has been developed to correct a number of limitations in current reactive force field models as well as providing a foundation for a next generation QM–MM model. Chemical bonding concepts are used to develop fully dissociative bond stretch, bend, torsion, and inversion valence terms. Quantum mechanics also provides functional forms for potential surface coupling terms that permit a general description of reactivity from hydrogen bonding, through non-classical carbocations and cracking, to olefin polymerization, oxidation, and metathesis. Van der Waals, electrostatic, and metallic bonding models also derive from quantum mechanical resonance. Finally, Pauli Principle-based orthogonality provides a way to electrostatically couple the QM and MM portions of a QM–MM model that will support arbitrarily large basis sets.},
author = {Rapp{\'{e}}, A. K. and Bormann-Rochotte, L. M. and Wiser, D. C. and Hart, J. R. and Pietsch, M. A. and Casewit, C. J. and Skiff, W. M.},


isbn = {0026-8976},

journal = {Mol. Phys.},

pages = {301--324},
pmid = {24404705},
title = {{APT a next generation QM-based reactive force field model}},
volume = {105},
year = {2007}
}
@article{andr+05advp,
author = {Andreani, C. and Colognesi, D. and Mayers, J. and Reiter, G. F. and Senesi, R.},



journal = {Adv. Phys.},


pages = {377--469},
publisher = {Taylor {\&} Francis},
title = {{Measurement of momentum distribution of light atoms and molecules in condensed matter systems using inelastic neutron scattering}},

volume = {54},
year = {2005}
}
@article{wang+14jcp,
abstract = {{\textcopyright} 2014 AIP Publishing LLC. Isotope substitution is extensively used to investigate the microscopic behavior of hydrogen bonded systems such as liquid water. The changes in structure and stability of these systems upon isotope substitution arise entirely from the quantum mechanical nature of the nuclei. Here, we provide a fully ab initio determination of the isotope exchange free energy and fractionation ratio of hydrogen and deuterium in water treating exactly nuclear quantum effects and explicitly modeling the quantum nature of the electrons. This allows us to assess how quantum effects in water manifest as isotope effects, and unravel how the interplay between electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.},
author = {Wang, L. Lu and Ceriotti, Michele and Markland, Thomas E. T.E.},



journal = {J. Chem. Phys.},


pages = {104502},
title = {{Quantum fluctuations and isotope effects in ab initio descriptions of water}},

volume = {141},
year = {2014}
}
@article{buch-vani13cpl,
author = {Buchowiecki, Marcin and Van{\'{i}}cek, Jir{\'{i}} and Van{\'{i}}{\v{c}}ek, Jiř{\'{i}}},



journal = {Chem. Phys. Lett.},

pages = {11--16},
title = {{Monte Carlo evaluation of the equilibrium isotope effects using the Takahashi-Imada factorization of the Feynman path integral}},

volume = {588},
year = {2013}
}
@article{nowi-vays97ssi,
author = {Nowick, A.S S and Vaysleyb, A.V V},



journal = {Solid State Ionics},



pages = {17--26},
title = {{Isotope effect and proton hopping in high-temperature protonic conductors}},

volume = {97},
year = {1997}
}
@article{gonc+05prl,
author = {Goncharov, Alexander and Goldman, Nir and Fried, Laurence and Crowhurst, Jonathan and Kuo, I-Feng and Mundy, Christopher and Zaug, Joseph},



journal = {Phys. Rev. Lett.},


pages = {125508},
title = {{Dynamic Ionization of Water under Extreme Conditions}},

volume = {94},
year = {2005}
}
@article{bhol+07nimpr,
author = {Bholoa, a. and Kenny, S.D. D and Smith, R.},



journal = {Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms},



pages = {1--7},
title = {{A new approach to potential fitting using neural networks}},

volume = {255},
year = {2007}
}
@article{fox91pra,
author = {Fox, Ronald F},


journal = {Phys. Rev. A},

pages = {2649--2654},
publisher = {American Physical Society},
title = {{Second-order algorithm for the numerical integration of colored-noise problems}},
volume = {43},
year = {1991}
}
@article{hend74pla,
author = {Henderson, R L},

journal = {Phys. Lett. A},

pages = {197--198},
title = {{A uniqueness theorem for fluid pair correlation functions}},
volume = {49},
year = {1974}
}
@article{izag+99jcp,
author = {Izaguirre, Jesús A. and Reich, Sebastian and Skeel, Robert D.},



journal = {J. Chem. Phys.},

pages = {9853},
title = {{Longer time steps for molecular dynamics}},

volume = {110},
year = {1999}
}
@article{seba-parr02cpc,
abstract = {We present a theoretical investigation of the hydrogen nuclear magnetic resonance (NMR) chemical shift and the magnetic susceptibility of normal and supercritical water using a recently developed ab initio approach in the framework of density functional perturbation theory. The results are in very good agreement with experiment. The shifts can be used to determine whether the atomic configurations, taken from a first principles simulation, give a good description of the system on a microscopic scale. In particular, the hydrogen chemical shifts are very sensitive to the character of the hydrogen bond network, which plays a crucial role in the macroscopic properties of liquid water under normal and supercritical conditions.},
author = {Sebastiani, Daniel and Parrinello, Michele},



journal = {ChemPhysChem},



pages = {675--9},
pmid = {12503147},
title = {{Ab-initio study of NMR chemical shifts of water under normal and supercritical conditions.}},

volume = {3},
year = {2002}
}
@article{brom+92prl,
abstract = {An ab initio investigation of the Si(l l l)-(7x7) surface reconstruction is undertaken using the state of the art in massively parallel computation. Calculations of the total energy of an -700 effective-atom supercell are performed to determine (1) the fully relaxed atomic geometry, (2) the scanning tunneling microscope images as a function of bias voltage, and (3) the energy difference between the (7{\&}7) and the (2x I) reconstructions. The (7x7) reconstruction is found to be energetically favorable to the (2{\&} 1) surface by 60 meV per (1 x 1) unit cell.},
annote = {NULL},
author = {Brommer, Karl D. and Needels, M and Larson, B and Joannopoulos, J. D.},



journal = {Phys. Rev. Lett.},


pages = {1355--1358},
title = {{Ab initio theory of the Si(111)-(7×7) surface reconstruction: A challenge for massively parallel computation}},

volume = {68},
year = {1992}
}
@article{rose+77siam,
author = {Rosenkrantz, Daniel J. and Stearns, Richard E. and {Lewis, II}, Philip M.},


journal = {SIAM Journal on Computing},


pages = {563--581},
title = {{An Analysis of Several Heuristics for the Traveling Salesman Problem}},

volume = {6},
year = {1977}
}
@article{guin38nature,
author = {Guinier, Andre},



journal = {Nature},


pages = {569--570},
title = {{Structure of Age-Hardened Aluminium-Copper Alloys}},

volume = {142},
year = {1938}
}
@article{gate+90jvsta,
annote = {
        

        

        

        From Duplicate 2 ( 
        

        

        

        
        

        

        

        
          

          

          

          Surface reactions in Si chemical vapor deposition from silane
          

          

          

        
        

        

        

        
        

        

        

         - Gates, S M; Greenlief, C M; Kulkarni, S K; Sawin, H H )

          

          

          

        
        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

      },
author = {Gates, S M},



journal = {Journal of Vacuum Science {\&} Technology A: Vacuum, Surfaces, and Films},


pages = {2965},
publisher = {AVS},
title = {{Surface reactions in Si chemical vapor deposition from silane}},

volume = {8},
year = {1990}
}
@article{xia+95jcp,
author = {Xia, L Q and Jones, M E and Maity, N and Engstrom, J R},


journal = {J. Chem. Phys.},

pages = {1691--1701},
publisher = {AIP},
title = {{Dissociation and pyrolysis of Si2H6 on Si surfaces: The influence of surface structure and adlayer composition}},
volume = {103},
year = {1995}
}
@article{west61cr,
author = {Westheimer, F H},

journal = {Chem. Rev.},

pages = {265--273},
publisher = {ACS Publications},
title = {{The Magnitude of the Primary Kinetic Isotope Effect for Compounds of Hydrogen and Deuterium.}},
volume = {61},
year = {1961}
}
@article{tuck-parr94jcp,
author = {Tuckerman, M E and Parrinello, M},

journal = {J. Chem. Phys.},

pages = {1302},
publisher = {AIP},
title = {{Integrating the Car{\{}--{\}}Parrinello equations. I. Basic integration techniques}},
volume = {101},
year = {1994}
}
@article{kars+97plb,
abstract = {A new perturbative scheme is proposed for the evaluation of the free energy density of field theories at finite temperature. The screened loop expansion takes into account exactly the phenomenon of screening in thermal propagators.The approach is tested in the N-component scalar field theory at 2-loop level and also at 3-loop in the large N limit. The perturbative series generated by the screened loop expansion shows much better numerical convergence than previous expansions generated in powers of the quartic coupling.},
author = {Karsch, Frithjof and Patk{\'{o}}s, A. and Petreczky, Peter},



journal = {Phys. Lett. B},


pages = {69--73},
title = {{Screened perturbation theory}},

volume = {401},
year = {1997}
}
@book{feyn-hibb65book,
address = {New York},
author = {Feynman, R P and Hibbs, A R},
publisher = {McGraw-Hill},
title = {{Quantum Mechanics and Path Integrals}},
year = {1964}
}
@article{vegg+01prl,
author = {Vegge, Tejs and Sethna, James and Cheong, Siew-Ann and Jacobsen, K. and Myers, Christopher and Ralph, Daniel},



journal = {Phys. Rev. Lett.},


pages = {1546--1549},
title = {{Calculation of Quantum Tunneling for a Spatially Extended Defect: The Dislocation Kink in Copper Has a Low Effective Mass}},

volume = {86},
year = {2001}
}
@article{wang-bowm10cpl,
author = {Wang, Yimin and Bowman, Joel M.},



journal = {Chem. Phys. Lett.},


pages = {1--10},
publisher = {Elsevier B.V.},
title = {{Towards an ab initio flexible potential for water, and post-harmonic quantum vibrational analysis of water clusters}},

volume = {491},
year = {2010}
}
@article{matu+99jcp,
author = {Matubayasi, Nobuyuki and Wakai, Chihiro and Nakahara, Masaru},



journal = {J. Chem. Phys.},

pages = {8000},
title = {{Structural study of supercritical water. II. Computer simulations}},

volume = {110},
year = {1999}
}
@article{paes+07jcp,
abstract = {The importance of quantum effects as well as the accuracy of the ab initio-based polarizable TTM2.1-F force field in describing liquid water are quantitatively assessed by a detailed analysis of the temperature dependence of several thermodynamic and dynamical properties computed using the path-integral molecular dynamics and centroid molecular dynamics methods. The results show that quantum effects are not negligible even at relatively high temperatures, and their inclusion in simulations with the TTM2.1-F water model is necessary to achieve a more accurate description of the liquid properties. Comparison with the results reported in the literature for empirical, nonpolarizable force fields demonstrates that the effects of the nuclear quantization on the dielectric constant are dependent in part on how the electronic polarization is described in the underlying water model, while comparison with other ab initio-based force fields shows that the TTM2.1-F model provides an overall accurate description of liquid water. Analysis of the isotope effect on the dynamical properties does not display significant temperature dependence. This suggests that the contribution of quantum tunneling, which has been proposed as a possible cause for the different orientational dynamics observed for the HDO:H(2)O and HDO:D(2)O systems, appears to be small.},
author = {Paesani, Francesco and Iuchi, Satoru and Voth, Gregory A.},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pages = {074506},
pmid = {17718619},
title = {{Quantum effects in liquid water from an ab initio-based polarizable force field}},

volume = {127},
year = {2007}
}
@article{sokh+15pnas,
author = {Sokhan, Vlad P. and Jones, Andrew P. and Cipcigan, Flaviu S. and Crain, Jason and Martyna, Glenn J.},



journal = {Proc. Natl. Acad. Sci. USA},
pages = {201418982},
title = {{Signature properties of water: Their molecular electronic origins}},

year = {2015}
}
@article{mahd-gahc00jpe,
author = {Mahdouk, Kamal and Gachon, Jean-Claude},



journal = {Journal of Phase Equilibria},


pages = {157--166},
title = {{Thermodynamic investigation of the aluminum-chromium system}},

volume = {21},
year = {2000}
}
@article{sant-tosa06jpa,
author = {Santoro, Giuseppe E and Tosatti, Erio},

journal = {J. Phys. A},

pages = {R393},
title = {{Optimization using quantum mechanics: quantum annealing through adiabatic evolution}},
volume = {39},
year = {2006}
}
@article{erco05unp,
author = {Ercolessi, Furio},


pages = {1--13},
title = {{Lecture notes on Tight-Binding Molecular Dynamics , and Tight-Binding justification of classical potentials The tight-binding formalism}},
year = {2005}
}
@article{wars71jcp,
abstract = {A scheme for the calculation of anharmonicity in crystal vibrations is developed for crystals with one molecule per unit cell. This method is applied to n‐hexane crystal. It is found that the contribution from anharmonicity can be very important in lattice vibrations of molecular crystals. Hence, the use of harmonic crystal vibrations for evaluation of nonbonded potentials without an anharmonicity correction can lead to an inconsistent potential.},
author = {Warshel, A.},



journal = {J. Chem. Phys.},

pages = {5324--5330},
title = {{Anharmonicity in Crystal Vibrations}},

volume = {54},
year = {1971}
}
@article{ross+15jpcl,
author = {Rossi, Mariana and Fang, Wei and Michaelides, Angelos},


journal = {J. Phys. Chem. Letters},


pages = {4233--4238},
title = {{Stability of Complex Biomolecular Structures: van der Waals, Hydrogen Bond Cooperativity, and Nuclear Quantum Effects}},

volume = {6},
year = {2015}
}
@article{piet+09prl,
author = {Pietropaolo, A and Senesi, R and Andreani, C and Botti, A and Ricci, M A and Bruni, F},



journal = {Phys. Rev. Lett.},


pages = {69802},
publisher = {American Physical Society},
title = {{Pietropaolo et al. Reply:}},

volume = {103},
year = {2009}
}
@article{doll+99jpcm,
author = {Doll, K and Harrison, N M and Saunders, V R},

journal = {J. Phys. Cond. Matt.},
pages = {5007},
publisher = {IOP Publishing},
title = {{A density functional study of lithium bulk and surfaces}},
volume = {11},
year = {1999}
}
@article{curt87prl,
abstract = {A density-functional theory for the structure and surface free energy {\$}\gamma{\$} of solid-liquid interfaces is presented which avoids perturbation and square-gradient approximations by the utilization of (i) the weighted-density approximation for the Helmholtz free-energy functional and (ii) a physical, two-parameter density profile of the interfacial region. The hard-sphere [100] fcc-liquid interface is found to be only 4–5 layers wide with {\$}\gamma{\$}=0.66kT/{\$}\sigma{\$}2, consistent with simulations on the similar {\$}\epsilon{\$}(r/{\$}\sigma{\$})-12 interface.},
author = {Curtin, W. a.},



journal = {Phys. Rev. Lett.},


pages = {1228--1231},
title = {{Density-functional theory of the solid-liquid interface}},

volume = {59},
year = {1987}
}
@article{snel06nips,
abstract = {We present a new Gaussian process (GP) regression model whose covariance is parameterized by the the locations of M pseudo-input points, which we learn by a gradient based optimization. We take M N, where N is the number of real data points, and hence obtain a sparse regression method which has O(M2N) training cost and O(M2 ) prediction cost per test case. We also find hyperparameters of the covariance function in the same joint optimization. The method can be viewed as a Bayesian regression model with particular input dependent noise. The method turns out to be closely related to several other sparse GP approaches, and we discuss the relation in detail. We finally demonstrate its performance on some large data sets, and make a direct comparison to other sparse GP methods. We show that our method can match full GP performance with small M, i.e. very sparse solutions, and it significantly outperforms other approaches in this regime.},
author = {Snelson, Edward and Ghahramani, Zoubin},


isbn = {9780262232531},

journal = {Advances in Neural Information Processing Systems},
pages = {1257--1264},
title = {{Sparse Gaussian Processes using Pseudo-inputs}},

volume = {18},
year = {2006}
}
@article{soss+12prb,
author = {Sosso, Gabriele C. and Miceli, Giacomo and Caravati, Sebastiano and Behler, J{\"{o}}rg and Bernasconi, Marco},



journal = {Phys. Rev. B},


pages = {174103},
title = {{Neural network interatomic potential for the phase change material GeTe}},

volume = {85},
year = {2012}
}
@article{mous+17jctc,
abstract = {Four methods for calculation of the classical free energy of crystalline systems are compared with respect to their efficiency and accuracy. Two of the methods involve thermodynamic integration along an unphysical path ($\lambda$ integration, $\lambda$I), and two involve integration in temperature from the low-temperature harmonic limit (T integration, TI). Specifically, the methods considered are (1) Frenkel−Ladd integration from a noninteracting Einstein crystal reference (ECR-$\lambda$I); (2) conventional integration in temperature (Conv- TI); (3) integration from an interacting quasi-harmonic reference (QHR-$\lambda$I); and (4) temperature integration using harmonically mapped averaging to evaluate the integrand (HMA-TI). The latter two methods are “harmonically assisted”, meaning that they exploit the harmonic nature of the crystal to greatly reduce fluctuations in the relevant averages. This feature allows them to deliver a result of much higher precision for a given computational effort, compared to ECR-$\lambda$I and Conv-TI, and with no less accuracy. Regarding the harmonically assisted methods, HMA-TI has several advantages over QHR-$\lambda$I with respect to the simplicity of the integration path (which promotes a more accurate result), ease of implementation, and usefulness of the data recorded along the integration path.},
author = {Moustafa, Sabry G. and Schultz, Andrew J. and Kofke, David A.},



journal = {J. Chem. Theory Comput.},


pages = {825--834},
title = {{Harmonically Assisted Methods for Computing the Free Energy of Classical Crystals by Molecular Simulation: A Comparative Study}},

volume = {13},
year = {2017}
}
@article{brie+16jctc,
author = {Brieuc, Fabien and Dammak, Hichem and Hayoun, Marc},


journal = {J. Chem. Theory Comput.},


pages = {1351--1359},
title = {{Quantum Thermal Bath for Path Integral Molecular Dynamics Simulation}},

volume = {12},
year = {2016}
}
@article{melo+05cpc,
author = {Meloni, S and Rosati, M and Federico, A and Ferraro, L and Mattoni, A and Colombo, L},

journal = {Comput. Phys. Commun.},

pages = {462--466},
publisher = {Elsevier},
title = {{{\{}Computational Materials Science application programming interface (CMSapi): a tool for developing applications for atomistic simulations{\}}}},
volume = {169},
year = {2005}
}
@article{kuhn+07prl,
author = {K{\"{u}}hne, Thomas D and Krack, Matthias and Mohamed, Fawzi R and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {66401},
title = {{Efficient and Accurate Car-Parrinello-like Approach to Born-Oppenheimer Molecular Dynamics}},

volume = {98},
year = {2007}
}
@article{fox87jsp,
author = {Fox, Ronald F},



journal = {J. Stat. Phys.},



pages = {1145--1157},
publisher = {Springer},
title = {{Stochastic calculus in physics}},

volume = {46},
year = {1987}
}
@article{li+14ncomm,
author = {Li, Dianzhong and Chen, Xing-Qiu and Fu, Paixian and Ma, Xiaoping and Liu, Hongwei and Chen, Yun and Cao, Yanfei and Luan, Yikun and Li, Yiyi},



journal = {Nature Comm.},
pages = {5572},
publisher = {Nature Publishing Group},
title = {{Inclusion flotation-driven channel segregation in solidifying steels}},

volume = {5},
year = {2014}
}
@article{ette+90acb,
author = {Etter, M. C. and MacDonald, J. C. and Bernstein, J.},



journal = {Acta Cryst. B Structural Science},

mendeley-tags = {graph theory,hydrogen bonds},


pages = {256--262},
publisher = {International Union of Crystallography},
title = {{Graph-set analysis of hydrogen-bond patterns in organic crystals}},

volume = {46},
year = {1990}
}
@article{limm-chan11jcp,
abstract = {We use numerical simulation to examine the possibility of a reversible liquid-liquid transition in supercooled water and related systems. In particular, for two atomistic models of water, we have computed free energies as functions of multiple order parameters, where one is density and another distinguishes crystal from liquid. For a range of temperatures and pressures, separate free energy basins for liquid and crystal are found, conditions of phase coexistence between these phases are demonstrated, and time scales for equilibration are determined. We find that at no range of temperatures and pressures is there more than a single liquid basin, even at conditions where amorphous behavior is unstable with respect to the crystal. We find a similar result for a related model of silicon. This result excludes the possibility of the proposed liquid-liquid critical point for the models we have studied. Further, we argue that behaviors others have attributed to a liquid-liquid transition in water and related systems are in fact reflections of transitions between liquid and crystal.},
author = {Limmer, David T and Chandler, David},



journal = {J. Chem. Phys.},

mendeley-tags = {amorphous ice,liquid-liquid,water},


pages = {134503},
pmid = {21992320},
title = {{The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water.}},

volume = {135},
year = {2011}
}
@book{rasm06book,
author = {Rasmussen, Carl Edward},

publisher = {MIT Press},
title = {{Gaussian processes for machine learning}},
year = {2006}
}
@article{kuo-mund04science,
abstract = {We present an ab initio molecular dynamics simulation of the aqueous liquid-vapor interface. Having successfully stabilized a region of bulk water in the center of a water slab, we were able to reproduce and further quantify the experimentally observed abundance of surface "acceptor-only"(19{\%}) and "single-donor"(66{\%}) moieties as well as substantial surface relaxation approaching the liquid-vapor interface. Examination of the orientational dynamics points to a faster relaxation in the interfacial region. Furthermore, the average value of the dipole decreases and the average value of the highest occupied molecular orbital for each water molecule increases approaching the liquid-vapor interface. Our results support the idea that the surface contains, on average, far more reactive states than the bulk.},
author = {Kuo, I-Feng F W and Mundy, Christopher J},


institution = {Computational Chemical Biology, Chemistry and Materials Science L-091, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.},

journal = {Science},


pages = {658--660},
pmid = {14752157},
publisher = {American Association for the Advancement of Science},
title = {{An ab initio molecular dynamics study of the aqueous liquid-vapor interface}},

volume = {303},
year = {2004}
}
@article{muel-cede06prb,
author = {Mueller, T and Ceder, G},

journal = {Phys. Rev. B},

pages = {134104},
publisher = {APS},
title = {{Effective interactions between the NH bond orientations in lithium imide and a proposed ground-state structure}},
volume = {74},
year = {2006}
}
@article{khan+02science,
abstract = {Although n-type titanium dioxide (TiO2) is a promising substrate for photogeneration of hydrogen from water, most attempts at doping this material so that it absorbs light in the visible region of the solar spectrum have met with limited success. We synthesized a chemically modified n-type TiO2 by controlled combustion of Ti metal in a natural gas flame. This material, in which carbon substitutes for some of the lattice oxygen atoms, absorbs light at wavelengths below 535 nanometers and has a lower band-gap energy than rutile (2.32 versus 3.00 electron volts). At an applied potential of 0.3 volt, chemically modified n-type TiO2 performs water splitting with a total conversion efficiency of 11{\%} and a maximum photoconversion efficiency of 8.35{\%} when illuminated at 40 milliwatts per square centimeter. The latter value compares favorably with a maximum photoconversion efficiency of 1{\%} for n-type TiO2 biased at 0.6 volt.},
author = {Khan, Shahed U M and Al-Shahry, Mofareh and Ingler, William B},



journal = {Science (New York, N.Y.)},


pages = {2243--5},
pmid = {12351783},
title = {{Efficient photochemical water splitting by a chemically modified n-TiO2.}},

volume = {297},
year = {2002}
}
@article{good-soka89prd,
author = {Goodman, Jonathan and Sokal, Alan},



journal = {Phys. Rev. D},


pages = {2035--2071},
title = {{Multigrid Monte Carlo method. Conceptual foundations}},

volume = {40},
year = {1989}
}
@article{wu+15jcc,
author = {Wu, Xiongwu and Brooks, Bernard R. and Vanden-Eijnden, Eric},



journal = {J. Comp. Chem.},

pages = {n/a----n/a},
title = {{Self-guided Langevin dynamics via generalized Langevin equation}},

year = {2015}
}
@article{lewi+95jcp,
author = {Lewis, Lisa B and Segall, Jeffrey and Janda, Kenneth C},

journal = {J. Chem. Phys.},

pages = {7222--7228},
publisher = {AIP},
title = {{Recombinative desorption of hydrogen from the Ge(100){\{}--{\}}(2 x 1) surface: A laser-induced desorption study}},
volume = {102},
year = {1995}
}
@article{ceri+06prb,
abstract = {Based on density functional perturbation theory, we have studied the vibrational properties of three crystalline phases of tellurium dioxide: paratellurite alpha-TeO2, tellurite beta-TeO2, and the new phase gamma-TeO2, recently identified experimentally. Calculated Raman and IR spectra are in good agreement with available experimental data. The vibrational spectra of alpha- and beta-TeO2 can be interpreted in terms of vibrations of TeO2 molecular units.},
author = {Ceriotti, Michele and Pietrucci, Fabio and Bernasconi, Marco},



journal = {Phys. Rev. B},


pages = {104304},
title = {{Ab initio study of the vibrational properties of crystalline TeO2: The $\alpha$, $\beta$, and $\gamma$ phases}},

volume = {73},
year = {2006}
}
@article{mori65ptp2,
author = {Mori, Hazime},

journal = {Prog. Th. Phys.},

pages = {399},
title = {{A Continued-Fraction Representation of the Time-Correlation Functions}},
volume = {34},
year = {1965}
}
@article{earl-deem04jpcb,
author = {Earl, David J and Deem, Michael W},



journal = {J. Phys. Chem. B},


pages = {6844--6849},
title = {{Optimal Allocation of Replicas to Processors in Parallel Tempering Simulations}},

volume = {108},
year = {2004}
}
@article{bers+66jcp,
abstract = {Double-quantum light scattering by a system of molecules is discussed in this paper. Expressions have been obtained for the scattered light intensity considering both the coherent and incoherent contributions. In that coherent contributions are also considered in this treatment, it goes beyond the scope of previous studies. It is shown that, for molecules of low symmetry, elliptically polarized light must be used in order to determine five independent quadratic forms in the 18 symmetric components (betaijk+betaikj). According to the present results, the apparent discrepancy between the observed value of [fraction one-third] for the depolarization ratio for {\{}CCl4{\}} and the value to be expected from theory may be due to the fact that the coherent contribution had been neglected in previous theoretical considerations. In general, orientational correlation is essential if there is to be appreciable contribution from coherent scattering. For macromolecules, this constitutes a major difference between single- and double-quantum scattering, and additional information may be expected if the latter is investigated experimentally.},
author = {Bersohn, R and Pao, YohHan and Frisch, H L},



journal = {J. Chem. Phys.},

pages = {3184--3198},
title = {{Double-Quantum Light Scattering by Molecules}},

volume = {45},
year = {1966}
}
@article{frit01arms,
author = {Fritzsche, Hellmut},



journal = {Annual Review of Materials Research},



pages = {47--79},
title = {{Development in Understanding and Controlling the Staebler-Wronski Effect in a-Si:H}},

volume = {31},
year = {2001}
}
@article{izum+04surf,
author = {Izumi, S. and Sato, Y. and Hara, S. and Sakai, S.},



journal = {Surf. Sci.},



pages = {1--11},
title = {{Development of a molecular dynamics potential for Si–H systems and its application to CVD reaction processes}},

volume = {560},
year = {2004}
}
@article{maur-moor04cr,
author = {Mauritz, Kenneth a and Moore, Robert B},



journal = {Chem. Rev.},


pages = {4535--4586},
pmid = {15669162},
title = {{State of Understanding of Nafion}},

volume = {104},
year = {2004}
}
@article{boes+97jpcb,
author = {Boese, Roland and Niederpr{\"{u}}m, Norbert and Bl{\"{a}}ser, Dieter and Maulitz, Andreas and Antipin, Mikhael Yu. and Mallinson, Paul R},

journal = {J. Phys. Chem. B},

pages = {5794--5799},
title = {{Single-Crystal Structure and Electron Density Distribution of Ammonia at 160 K on the Basis of X-ray Diffraction Data}},
volume = {101},
year = {1997}
}
@book{zwan+01book,
address = {New York},
author = {Zwanzig, Robert},
publisher = {Oxford University Press},
title = {{Nonequilibrium statistical mechanics}},
year = {2001}
}
@article{srir02nature,
abstract = {Hydrogenated amorphous and nanocrystalline silicon films manufactured by plasma deposition techniques are used widely in electronic and optoelectronic devices. The crystalline fraction and grain size of these films determines electronic and optical properties; the nanocrystal nucleation mechanism, which dictates the final film structure, is governed by the interactions between the hydrogen atoms of the plasma and the solid silicon matrix. Fundamental understanding of these interactions is important for optimizing the film structure and properties. Here we report the mechanism of hydrogen-induced crystallization of hydrogenated amorphous silicon films during post-deposition treatment with an H(2) (or D(2)) plasma. Using molecular-dynamics simulations and infrared spectroscopy, we show that crystallization is mediated by the insertion of H atoms into strained Si-Si bonds as the atoms diffuse through the film. This chemically driven mechanism may be operative in other covalently bonded materials, where the presence of hydrogen leads to disorder-to-order transitions.},
author = {Sriraman, Saravanapriyan and Agarwal, Sumit and Aydil, Eray S and Maroudas, Dimitrios},



journal = {Nature},


pages = {62--5},
pmid = {12097905},
title = {{Mechanism of hydrogen-induced crystallization of amorphous silicon.}},

volume = {418},
year = {2002}
}
@article{majo-gao07jctc,
author = {Major, Dan Thomas and Gao, Jiali},



journal = {J. Chem. Theory Comput.},


pages = {949--960},
title = {{An Integrated Path Integral and Free-Energy Perturbation−Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes}},

volume = {3},
year = {2007}
}
@article{lued-autr10ic,
abstract = {A series of metal amidoboranes LiNH(2)BH(3) (LAB), NaNH(2)BH(3) (SAB), LiNH(Me)BH(3) (LMAB), NaNH(Me)BH(3) (SMAB), KNH(Me)BH(3) (PMAB), and KNH((t)Bu)BH(3) (PBAB) were synthesized by solution phase methods, and the thermal release of H(2) in the solid state was studied. The mechanism of hydrogen release from metal amidoboranes, a metal ion assisted hydride transfer, is very different than the mechanism of hydrogen release from the parent compound ammonia borane (AB). On the basis of the observed trends in reaction rates of H {\textgreater} Me {\textgreater} (t)Bu, K {\textgreater} Na {\textgreater} Li, and the kinetic isotope effect, the mechanism of hydrogen release from MAB compounds was found to proceed through a bimolecular mechanism involving the intermediacy of a MH (M = Li, Na, or K). The non-volatile products formed from MABs are significantly different than the products formed after hydrogen release from AB. The boron containing products resulting from the release of 1 equiv of hydrogen from the metal amidoboranes were characterized by MAS (11)B NMR spectroscopy and found to contain both BH(3) and sp(2) hybridized BH groups, consistent with the general structure MN(R)=BHN(R)MBH(3).},
author = {Luedtke, Avery T and Autrey, Tom},



journal = {Inorganic chemistry},


pages = {3905--10},
pmid = {20232793},
title = {{Hydrogen release studies of alkali metal amidoboranes.}},

volume = {49},
year = {2010}
}
@article{reil+10jcp,
abstract = {Path-integral molecular dynamics have been used to simulate the phase-I crystalline form of ammonia, using an empirical force field. This method allows quantum-mechanical effects on the average geometry and vibrational quantities to be evaluated. When these are used to adjust the output of a high-temperature density functional theory simulation, the results are consistent with those given by the most recent structural refinement based on powder neutron diffraction data. It is clear that the original refinement overestimated thermal motion, and therefore also overestimated the equilibrium N-{\{}H/D{\}} bond length.},
author = {Reilly, Anthony M and Habershon, Scott and Morrison, Carole a and Rankin, David W H},



journal = {J. Chem. Phys.},


pages = {134511},
pmid = {20387945},
title = {{Simulating thermal motion in crystalline phase-I ammonia.}},

volume = {132},
year = {2010}
}
@article{ghos+98fe,
author = {Ghosez, P.Sc. H. S H and Gonze, X. and Michenaud, J. P.},



journal = {Ferroelectrics},


pages = {205--217},
publisher = {Taylor {\&} Francis},
title = {{Ab initio phonon dispersion curves and interatomic force constants of barium titanate}},

volume = {206},
year = {1998}
}
@article{ecke+84jcp,
author = {Eckert, J. and Mills, R. L. and Satija, S. K.},



journal = {J. Chem. Phys.},

pages = {6034--6038},
publisher = {AIP},
title = {{Structure of ND[sub 3] solids I and II at high pressure by neutron diffraction}},

volume = {81},
year = {1984}
}
@article{benj94prl,
author = {Benjamin, Ilan},

journal = {Phys. Rev. Lett.},

pages = {2083--2086},
publisher = {American Physical Society},
title = {{Vibrational Spectrum of Water at the Liquid/Vapor Interface}},
volume = {73},
year = {1994}
}
@article{wang+98jcp,
author = {Wang, Haobin and Sun, Xiong and Miller, William H.},



journal = {J. Chem. Phys.},

pages = {9726},
title = {{Semiclassical approximations for the calculation of thermal rate constants for chemical reactions in complex molecular systems}},

volume = {108},
year = {1998}
}
@article{herr97prb,
author = {Herrero, Carlos P},



journal = {Phys. Rev. B},


pages = {9235--9238},
title = {{Thermally assisted tunneling of hydrogen in silicon: A path-integral Monte Carlo study}},

volume = {55},
year = {1997}
}
@article{stoc09prl,
author = {Stock, Gerhard},

journal = {Phys. Rev. Lett.},

pages = {118301},
title = {{Classical Simulation of Quantum Energy Flow in Biomolecules}},
volume = {102},
year = {2009}
}
@article{stei+83prb,
author = {Steinhardt, Paul J and Nelson, David R and Ronchetti, Marco},

journal = {Phys. Rev. B},

pages = {784--805},
publisher = {American Physical Society},
title = {{Bond-orientational order in liquids and glasses}},
volume = {28},
year = {1983}
}
@article{fuch+10pre,
author = {Fuchs, Sebastian and Pruschke, Thomas and Jarrell, Mark},



journal = {Phys. Rev. E},


pages = {056701},
title = {{Analytic continuation of quantum Monte Carlo data by stochastic analytical inference}},

volume = {81},
year = {2010}
}
@article{droz+15nature,
author = {Drozdov, a P and Eremets, M I and Troyan, I a and Ksenofontov, V and Shylin, S I},


journal = {Nature},
title = {{Conventional superconductivity at 203 kelvin at high pressures in the sulfur hydride system}},
year = {2015}
}
@article{Sciortino1992,
author = {Sciortino, Francesco and Geiger, Alfons and Stanley, H. Eugene},



journal = {J. Chem. Phys.},

pages = {3857},
title = {{Network defects and molecular mobility in liquid water}},

volume = {96},
year = {1992}
}
@article{buss+07jcp,
author = {Bussi, G and Donadio, D and Parrinello, M},

journal = {J. Chem. Phys.},

pages = {14101},
title = {{Canonical sampling through velocity rescaling}},
volume = {126},
year = {2007}
}
@article{hewa-riek79ac,
author = {Hewat, A W and Riekel, C},

journal = {Acta Crystallogr. Sect. A Cryst. Physics, Diffraction, Theor. Gen. Crystallogr.},

pages = {569--571},
publisher = {International Union of Crystallography},
title = {{The crystal structure of deuteroammonia between 2 and 180 K by neutron powder profile refinement}},
volume = {35},
year = {1979}
}
@article{10.1021/acs.jctc.6b00684,
author = {Brieuc, Fabien and Bronstein, Yael and Dammak, Hichem and Depondt, Philippe and Finocchi, Fabio and Hayoun, Marc},



journal = {J. Chem. Theory Comput.},



pages = {5688--5697},
title = {{Zero-Point Energy Leakage in Quantum Thermal Bath Molecular Dynamics Simulations}},

volume = {12},
year = {2016}
}
@article{colo11pbcm,
author = {Colognesi, D.},



journal = {Physica B: Condensed Matter},



pages = {2723--2730},
publisher = {Elsevier},
title = {{Extraction of single-particle mean kinetic energy from macroscopic thermodynamic data}},

volume = {406},
year = {2011}
}
@article{scho38tams,
abstract = {n/a},
author = {Schoenberg, I. J.},



journal = {Transactions of the American Mathematical Society},
pages = {522},
pmid = {17746742},
title = {{Metric spaces and positive definite functions}},
volume = {44},
year = {1938}
}
@article{nini+14am,
author = {Ninive, Per Harald and Strandlie, Are and Gulbrandsen-Dahl, Sverre and Lefebvre, Williams and Marioara, Calin D. and Andersen, Sigmund J. and Friis, Jesper and Holmestad, Randi and L{\o}vvik, Ole Martin},



journal = {Acta Materialia},


pages = {126--134},
publisher = {Acta Materialia Inc.},
title = {{Detailed atomistic insight into the $\beta$″ phase in Al–Mg–Si alloys}},

volume = {69},
year = {2014}
}
@article{rodr+98prb,
author = {Rodr{\$}\backslash{\$}'iguez-Carvajal, J and Hennion, M and Moussa, F and Moudden, A H and Pinsard, L and Revcolevschi, A and Rodr$\backslash$'iguez-Carvajal, J and Hennion, M and Moussa, F and Moudden, A H and Pinsard, L and Revcolevschi, A},

journal = {Phys. Rev. B},

pages = {----3189},
publisher = {American Physical Society},
title = {{Neutron-diffraction study of the Jahn-Teller transition in stoichiometric LaMnO{\{}{\_}{\}}3}},
volume = {57},
year = {1998}
}
@article{darv-poho01jcp,
author = {Darve, Eric and Pohorille, Andrew},



journal = {J. Chem. Phys.},

pages = {9169},
title = {{Calculating free energies using average force}},

volume = {115},
year = {2001}
}
@article{shig-shin05jcp,
abstract = {As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2O at 300 K, 6.9 in the liquid H2O at 300 K, and 4.1 in the ice Ih H2O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10{\%} higher than that of H2O, while it is 13{\%} higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions.},
author = {Shiga, Motoyuki and Shinoda, Wataru},



journal = {J. Chem. Phys.},


pages = {134502},
pmid = {16223309},
publisher = {AIP},
title = {{Calculation of heat capacities of light and heavy water by path-integral molecular dynamics}},

volume = {123},
year = {2005}
}
@article{ceri-mano12prl,
author = {Ceriotti, Michele and Manolopoulos, David E},



journal = {Phys. Rev. Lett.},


pages = {100604},
title = {{Efficient First-Principles Calculation of the Quantum Kinetic Energy and Momentum Distribution of Nuclei}},

volume = {109},
year = {2012}
}
@article{rink+14nl,
author = {Rinke, Gordon and Rauschenbach, Stephan and Harnau, Ludger and Albarghash, Alyazan and Pauly, Matthias and Kern, Klaus},


journal = {Nano Letters},

pages = {5609},
title = {{Active Conformation Control of Unfolded Proteins by Hyperthermal Collision with a Metal Surface}},
volume = {14},
year = {2014}
}
@article{morr+07jcp,
abstract = {Recent neutron Compton scattering experiments have detected the proton momentum distribution in water. The theoretical calculation of this property can be carried out via "open" path integral expressions. In this work, present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize a flexible, single point charge empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.},
author = {Morrone, Joseph A and Srinivasan, Varadharajan and Sebastiani, Daniel and Car, Roberto},



journal = {J. Chem. Phys.},


pages = {234504},
pmid = {17600422},
title = {{Proton momentum distribution in water: an open path integral molecular dynamics study.}},

volume = {126},
year = {2007}
}
@article{hast70bio,
abstract = {A generalization of the sampling method introduced by Metropolis et al. (1953) is presented along with an exposition of the relevant theory, techniques of application and methods and difficulties of assessing the error in Monte Carlo estimates. Examples of the methods, including the generation of random orthogonal matrices and potential applications of the methods to numerical problems arising in statistics, are discussed.},
author = {Hastings, W. K.},



journal = {Biometrika},

pages = {97--109},
publisher = {Biometrika Trust},
title = {{Monte Carlo sampling methods using Markov chains and their applications}},

volume = {57},
year = {1970}
}
@article{spae94msea,
author = {Spaepen, Frans},



journal = {Materials Science and Engineering: A},

pages = {15--18},
title = {{The temperature dependence of the crystal-melt interfacial tension: a simple model}},
volume = {178},
year = {1994}
}
@article{pres+14jcp,
abstract = {In standard nucleation theory, the nucleation process is characterized by computing $\Delta$$\Omega$(V), the reversible work required to form a cluster of volume V of the stable phase inside the metastable mother phase. However, other quantities besides the volume could play a role in the free energy of cluster formation, and this will in turn affect the nucleation barrier and the shape of the nucleus. Here we exploit our recently introduced mesoscopic theory of nucleation to compute the free energy cost of a nearly spherical cluster of volume V and a fluctuating surface area A, whereby the maximum of $\Delta$$\Omega$(V) is replaced by a saddle point in $\Delta$$\Omega$(V, A). Compared to the simpler theory based on volume only, the barrier height of $\Delta$$\Omega$(V, A) at the transition state is systematically larger by a few kBT. More importantly, we show that, depending on the physical situation, the most probable shape of the nucleus may be highly non-spherical, even when the surface tension and stiffness of the model are isotropic. Interestingly, these shape fluctuations do not influence or modify the standard Classical Nucleation Theory manner of extracting the interface tension from the logarithm of the nucleation rate near coexistence.},
archivePrefix = {arXiv},
arxivId = {1402.3934},
author = {Prestipino, Santi and Laio, Alessandro and Tosatti, Erio},



isbn = {doi:10.1063/1.4866971},

journal = {J. Chem. Phys.},


pages = {094501},
pmid = {24606362},
title = {{Shape and area fluctuation effects on nucleation theory}},

volume = {140},
year = {2014}
}
@article{fris-argo95proteins,
abstract = {We have developed an automatic algorithm STRIDE for protein secondary structure assignment from atomic coordinates based on the combined use of hydrogen bond energy and statistically derived backbone torsional angle information. Parameters of the pattern recognition procedure were optimized using designations provided by the crystallographers as a standard-of-truth. Comparison to the currently most widely used technique DSSP by Kabsch and Sander (Biopolymers 22:2577-2637, 1983) shows that STRIDE and DSSP assign secondary structural states in 58 and 31{\{}{\%}{\}} of 226 protein chains in our data sample, respectively, in greater agreement with the specific residue-by-residue definitions provided by the discoverers of the structures while in 11{\{}{\%}{\}} of the chains, the assignments are the same. STRIDE delineates every 11th helix and every 32nd strand more in accord with published assignments.},
author = {Frishman, D and Argos, P},



journal = {Proteins},

mendeley-tags = {proteins,structure},


pages = {566--579},
pmid = {8749853},
title = {{Knowledge-based protein secondary structure assignment.}},

volume = {23},
year = {1995}
}
@article{camp+17jmcc,
abstract = {Crystal structure prediction is used to calculate energy–structure–function maps of the charge mobilities in molecular organic semiconductors.},
author = {Campbell, Josh E. and Yang, Jack and Day, Graeme M.},


journal = {J. Mat. Chem. C},

pages = {7574--7584},
title = {{Predicted energy–structure–function maps for the evaluation of small molecule organic semiconductors}},

volume = {5},
year = {2017}
}
@article{kubo66rpp,
author = {Kubo, R},

journal = {Reports Prog. Phys.},

pages = {255--284},
title = {{The fluctuation-dissipation theorem}},
volume = {29},
year = {1966}
}
@article{cubu+15prl,
abstract = {We use machine-learning methods on local structure to identify flow defects—or particles susceptible to rearrangement—in jammed and glassy systems. We apply this method successfully to two very different systems: a two-dimensional experimental realization of a granular pillar under compression and a Lennard- Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.},
archivePrefix = {arXiv},
arxivId = {1409.6820},
author = {Cubuk, E. D. and Schoenholz, S. S. and Rieser, J. M. and Malone, B. D. and Rottler, J. and Durian, D. J. and Kaxiras, E. and Liu, A. J.},




journal = {Phys. Rev. Lett.},

pages = {108001},
title = {{Identifying Structural Flow Defects in Disordered Solids Using Machine-Learning Methods}},

volume = {114},
year = {2015}
}
@article{taka-imad84jpsj,
author = {Takahashi, M and Imada, M},

journal = {J. Phys. Soc. Jap.},

pages = {3765--3769},
publisher = {**********},
title = {{Monte Carlo calculation of quantum systems. II. Higher order correction}},
volume = {53},
year = {1984}
}
@article{ross+16prl,
abstract = {{\textcopyright} 2016 American Physical Society. Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.},
author = {Rossi, Mariana and Gasparotto, Piero and Ceriotti, Michele},



journal = {Phys. Rev. Lett.},


pages = {115702},
title = {{Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol}},

volume = {117},
year = {2016}
}
@article{sit-marz05jcp,
author = {Sit, P H L and Marzari, N},

journal = {J. Chem. Phys.},
pages = {204510},
publisher = {AIP},
title = {{Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics}},
volume = {122},
year = {2005}
}
@article{keen+10jpcm,
author = {Keen, D A and Dove, M T and Evans, J S O and Goodwin, A L and Peters, L and Tucker, M G},

journal = {J. Phys. Cond. Matt.},
pages = {404202},
publisher = {IOP Publishing},
title = {{The hydrogen-bonding transition and isotope-dependent negative thermal expansion in H3Co (CN) 6}},
volume = {22},
year = {2010}
}
@article{lee+88prb,
abstract = {A correlation-energy formula due to Colle and Salvetti Theor. Chim. Acta 37, 329 (1975), in which the correlation energy density is expressed in terms of the electron density and a Laplacian of the second-order Hartree-Fock density matrix, is restated as a formula involving the density and local kinetic-energy density. On insertion of gradient expansions for the local kinetic-energy density, density-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.},
author = {Lee, Chengteh and Yang, W and Parr, R G},

journal = {Phys. Rev. B},

pages = {785},
publisher = {APS},
title = {{Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density}},

volume = {37},
year = {1988}
}
@article{gonz85tcs,
author = {Gonzalez, Teofilo F.},


journal = {Theoretical Computer Science},
pages = {293--306},
title = {{Clustering to minimize the maximum intercluster distance}},

volume = {38},
year = {1985}
}
@article{bern-fors71arpc,
author = {Berne, B J and Forster, Dieter},



journal = {Annu. Rev. Phys. Chem.},


pages = {563--596},
title = {{Topics in Time-Dependent Statistical Mechanics}},

volume = {22},
year = {1971}
}
@article{laio-parr02pnas,
author = {Laio, A and Parrinello, M},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {12562--12566},
publisher = {National Acad Sciences},
title = {{Escaping free-energy minima}},
volume = {99},
year = {2002}
}
@article{bika+07abb,
abstract = {Knowledge of the relationship between protein's structure and its dynamic behavior is essential for understanding protein function. In this study, the description of a protein three-dimensional structure as a network of hydrogen bonding interactions (HB plot) is introduced as a tool for exploring protein structure and function. HB plot offers a simple way of analyzing protein secondary and tertiary structure. Moreover, hydrogen bonds stabilizing secondary structural elements and those formed between distant amino residues--defined as tertiary hydrogen bonds--can be easily distinguished in HB plot, thus, amino acid residues involved in stabilizing protein structure and function can be easily identified. By analyzing the network of tertiary interactions the possible spread of information within a protein can be investigated as well. The alteration in tertiary hydrogen bonding network during conformational transitions were investigated through case studies; and showed the applicability of HB plot in exploring mechanistic details in proteins.},
author = {Bikadi, Zsolt and Demko, Laszlo and Hazai, Eszter},



journal = {Archives of biochemistry and biophysics},



pages = {225--234},
pmid = {17391641},
title = {{Functional and structural characterization of a protein based on analysis of its hydrogen bonding network by hydrogen bonding plot.}},

volume = {461},
year = {2007}
}
@article{arna69jpc,
author = {{\AA}rnason, Bragi},


journal = {J. Phys. Chem.},

pages = {3491},
title = {{Equilibrium Constant for the Fractionation of Deuterium between Ice and Water}},
volume = {75},
year = {1969}
}
@article{schu+14prb,
author = {Sch{\"{u}}tt, K. T. and Glawe, H. and Brockherde, F. and Sanna, A. and M{\"{u}}ller, K. R. and Gross, E. K. U.},


journal = {Phys. Rev. B},


pages = {205118},
title = {{How to represent crystal structures for machine learning: Towards fast prediction of electronic properties}},

volume = {89},
year = {2014}
}
@article{Irony2004,
author = {Irony, Dror and Shklarski, Gil and Toledo, Sivan},



journal = {Future Generation Computer Systems},



pages = {425--440},
title = {{Parallel and fully recursive multifrontal sparse Cholesky}},

volume = {20},
year = {2004}
}
@article{ceri-mark13jcp,
abstract = {The shift in chemical equilibria due to isotope substitution is frequently exploited to obtain insight into a wide variety of chemical and physical processes. It is a purely quantum mechanical effect, which can be computed exactly using simulations based on the path integral formalism. Here we discuss how these techniques can be made dramatically more efficient, and how they ultimately outperform quasi-harmonic approximations to treat quantum liquids not only in terms of accuracy, but also in terms of computational cost. To achieve this goal we introduce path integral quantum mechanics estimators based on free energy perturbation, which enable the evaluation of isotope effects using only a single path integral molecular dynamics trajectory of the naturally abundant isotope. We use as an example the calculation of the free energy change associated with H/D and (16)O/(18)O substitutions in liquid water, and of the fractionation of those isotopes between the liquid and the vapor phase. In doing so, we demonstrate and discuss quantitatively the relative benefits of each approach, thereby providing a set of guidelines that should facilitate the choice of the most appropriate method in different, commonly encountered scenarios. The efficiency of the estimators we introduce and the analysis that we perform should in particular facilitate accurate ab initio calculation of isotope effects in condensed phase systems.},
author = {Ceriotti, Michele and Markland, Thomas E},



journal = {J. Chem. Phys.},


pages = {014112},
pmid = {23298033},
publisher = {AIP},
title = {{Efficient methods and practical guidelines for simulating isotope effects.}},

volume = {138},
year = {2013}
}
@article{chin06pla,
author = {Chin, S A},

journal = {Phys. Lett. A},

pages = {373--376},
publisher = {Elsevier},
title = {{A fundamental theorem on the structure of symplectic integrators}},
volume = {354},
year = {2006}
}
@article{sodd+03pre,
author = {Soddemann, Thomas and D{\"{u}}nweg, Burkhard and Kremer, Kurt},



journal = {Phys. Rev. E},


pages = {46702},
title = {{Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations}},

volume = {68},
year = {2003}
}
@article{engi+02mcp,
author = {Enginer, Y and Saliho$\backslash$uglu, S and Yurtseven, H},

journal = {Materials Chemistry and Physics},

pages = {57--61},
title = {{T{\{}--{\}}P phase diagram of ammonia solid phases I, II and III}},
volume = {73},
year = {2002}
}
@article{mora+14jctc,
abstract = {The accurate description of the thermodynamic and dynamical properties of liquid water from first-principles is a very important challenge to the theoretical community. This represents not only a critical test of the predictive capabilities of first-principles methods, but it will also shed light into the microscopic properties of such an important substance. Density Functional Theory, the main workhorse in the field of first-principles methods, has been so far unable to properly describe water and its unusual properties in the liquid state. With the recent introduction of exact exchange and an improved description of dispersion interaction, the possibility of an accurate description of the liquid is finally within reach. Unfortunately, there is still no way to systematically improve exchange-correlation functionals, and the number of available functionals is very large. In this article we use highly accurate quantum Monte Carlo calculations to benchmark a selection of exchange-correlation functionals typically used in Density Functional Theory simulations of bulk water. This allows us to test the predictive capabilities of these functionals in water, giving us a way to choose optimal functionals for first-principles simulations. We compare and contrast the importance of different features of functionals, including the hybrid component, the vdW component, and their importance within different aspects of the PES. In addition, in order to correct the inaccuracies in the description of short-range interactions in the liquid, we test a recently introduced scheme that combines Density Functional Theory with Coupled Cluster calculations through a Many-Body expansion of the energy. The accurate description of the thermodynamic and dynamical properties of liquid water from first-principles is a very important challenge to the theoretical community. This represents not only a critical test of the predictive capabilities of first-principles methods, but it will also shed light into the microscopic properties of such an important substance. Density Functional Theory, the main workhorse in the field of first-principles methods, has been so far unable to properly describe water and its unusual properties in the liquid state. With the recent introduction of exact exchange and an improved description of dispersion interaction, the possibility of an accurate description of the liquid is finally within reach. Unfortunately, there is still no way to systematically improve exchange-correlation functionals, and the number of available functionals is very large. In this article we use highly accurate quantum Monte Carlo calculations to benchmark a selection of exchange-correlation functionals typically used in Density Functional Theory simulations of bulk water. This allows us to test the predictive capabilities of these functionals in water, giving us a way to choose optimal functionals for first-principles simulations. We compare and contrast the importance of different features of functionals, including the hybrid component, the vdW component, and their importance within different aspects of the PES. In addition, in order to correct the inaccuracies in the description of short-range interactions in the liquid, we test a recently introduced scheme that combines Density Functional Theory with Coupled Cluster calculations through a Many-Body expansion of the energy.},
author = {Morales, Miguel a. and Gergely, John R. and McMinis, Jeremy and McMahon, Jeffrey M. and Kim, Jeongnim and Ceperley, David M.},



journal = {J. Chem. Theory Comput.},

pages = {2355--2362},
title = {{Quantum Monte Carlo benchmark of exchange-correlation functionals for bulk water}},
volume = {10},
year = {2014}
}
@article{pric09acr,
abstract = {The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.},
author = {Price, Sarah Sally L},



journal = {Acc. Chem. Res.},


pages = {117--126},
pmid = {18925751},
title = {{Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.}},

volume = {42},
year = {2009}
}
@article{Muller2013,
author = {M{\"{u}}ller, Pierre and Sa{\`{u}}l, Andres and Leroy, Fr{\'{e}}d{\'{e}}ric},


journal = {Advances in Natural Sciences: Nanoscience and Nanotechnology},



pages = {013002},
title = {{Simple views on surface stress and surface energy concepts}},

volume = {5},
year = {2013}
}
@article{vide+14jpcl,
author = {Videla, Pablo E. and Rossky, Peter J. and Laria, Daniel},


journal = {J. Phys. Chem. Letters},


pages = {2375--2379},
title = {{Surface Isotope Segregation as a Probe of Temperature in Water Nanoclusters}},

volume = {5},
year = {2014}
}
@article{hele+15jcp2,
author = {Hele, Timothy J. H. and Willatt, Michael J. and Muolo, Andrea and Althorpe, Stuart C.},



journal = {J. Chem. Phys.},

pages = {191101},
title = {{Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics}},

volume = {142},
year = {2015}
}
@article{PLUMED,
author = {Bonomi, Massimiliano and Branduardi, Davide and Bussi, Giovanni and Camilloni, Carlo and Provasi, Davide and Raiteri, Paolo and Donadio, Davide and Marinelli, Fabrizio and Pietrucci, Fabio and Broglia, Ricardo A and Parrinello, Michele},



journal = {Comp. Phys. Comm.},


pages = {1961--1972},
title = {{PLUMED: A portable plugin for free-energy calculations with molecular dynamics}},

volume = {180},
year = {2009}
}
@article{poga+14prl,
author = {Pogatscher, S. and Antrekowitsch, H. and Werinos, M. and Moszner, F. and Gerstl, S. S. A. and Francis, M. F. and Curtin, W. A. and L{\"{o}}ffler, J. F. and Uggowitzer, P. J.},



journal = {Phys. Rev. Lett.},


pages = {225701},
title = {{Diffusion on Demand to Control Precipitation Aging: Application to Al-Mg-Si Alloys}},

volume = {112},
year = {2014}
}
@article{bold+03jtac2,
author = {Boldyreva, E V and Drebushchak, V A and Drebushchak, T N and Paukov, I E and Kovalevskaya, Y A and Shutova, E S},



journal = {Journal of Thermal Analysis and Calorimetry},


pages = {419--428},
publisher = {Kluwer Academic Publishers},
title = {{Polymorphism of glycine, Part II}},
volume = {73},
year = {2003}
}
@article{mori+06jcp,
abstract = {One of the most important challenges in density functional theory (DFT) is the proper description of fractional charge systems relating to the self-interaction error (SIE). Traditionally, the SIE has been formulated as a one-electron problem, which has been addressed in several recent functionals. However, these recent one-electron SIE-free functionals, while greatly improving the description of thermochemistry and reaction barriers in general, still exhibit many of the difficulties associated with SIE. Thus we emphasize the need to surpass this limit and shed light on the many-electron SIE. After identifying the sufficient condition for functionals to be free from SIE, we focus on the symptoms and investigate the performance of most popular functionals. We show that these functionals suffer from many-electron SIE. Finally, we give a SIE classification of density functionals.},
author = {Mori-S{\'{a}}nchez, Paula and Cohen, Aron J and Yang, Weitao},



journal = {J. Chem. Phys.},


pages = {201102},
pmid = {17144681},
title = {{Many-electron self-interaction error in approximate density functionals.}},

volume = {125},
year = {2006}
}
@article{gatti+99nature,
author = {Gatti, F and Fontanelli, F and Galeazzi, M and Swift, A M and Vitale, S},
journal = {Nature},
pages = {137--139},
title = {{Detection of environmental fine structure in the low-energy {\$}\beta{\$}-decay spectrum of 187Re}},
volume = {397},
year = {1999}
}
@article{boom+08pna,
abstract = {Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state. Our method represents a significant theoretical and practical improvement over the widely used fragment assembly technique by avoiding the drawbacks associated with a discrete and nonprobabilistic approach.},
author = {Boomsma, Wouter and Mardia, Kanti V and Taylor, Charles C and Ferkinghoff-Borg, Jesper and Krogh, Anders and Hamelryck, Thomas},


isbn = {0801715105},

journal = {Proc. Natl. Acad. Sci. USA},


pages = {8932--8937},
pmid = {18579771},
title = {{A generative, probabilistic model of local protein structure}},

volume = {105},
year = {2008}
}
@article{li+14prl,
author = {Li, Yujiao and Raabe, Dierk and Herbig, Michael and Choi, Pyuck-Pa and Goto, Shoji and Kostka, Aleksander and Yarita, Hiroshi and Borchers, Christine and Kirchheim, Reiner},



journal = {Phys. Rev. Lett.},


pages = {106104},
title = {{Segregation Stabilizes Nanocrystalline Bulk Steel with Near Theoretical Strength}},

volume = {113},
year = {2014}
}
@article{sope-benm08prl,
abstract = {The structures of heavy and light water at ambient conditions are investigated with the combined techniques of x-ray diffraction, neutron diffraction, and computer simulation. It is found that heavy water is a more structured liquid than light water. We find the OH bond length in H2O is approximately 3{\{}{\%}{\}} longer than the OD bond length in D2O. This is a much larger change than current predictions. Corresponding to this, the hydrogen bond in light water is approximately 4{\{}{\%}{\}} shorter than in heavy water, while the intermolecular HH distance is approximately 2{\{}{\%}{\}} longer.},
author = {Soper, a. K. and Benmore, C. J.},


isbn = {1079-7114},

journal = {Phys. Rev. Lett.},

pages = {1--4},
pmid = {18764471},
title = {{Quantum differences between heavy and light water}},
volume = {101},
year = {2008}
}
@article{chan-woly81jcp,
author = {Chandler, David and Wolynes, Peter G},

journal = {J. Chem. Phys.},

pages = {4078--4095},
publisher = {AIP},
title = {{Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids}},
volume = {74},
year = {1981}
}
@article{agmo12acr,
abstract = {Water deviates from tetrahedral symmetry on different scales, creating "defects" that are important for its dynamics. In this Account, I trace the manifestations of these distortions from the isolated molecule through gas-phase clusters to the liquid phase. Unlike the common depiction, an isolated water molecule has a nonsymmetric charge distribution: although its positive charge is localized at the hydrogens, the negative charge is smeared between the lone-pair sites. This creates a "negativity track" along which a positive charge may slide. Consequently, the most facile motion within the water dimer is a reorientation of the hydrogen-bond (HB) accepting molecule (known as an "acceptor switch"), such that the donor hydrogen switches from one lone pair to the other. Liquid water exhibits asymmetry between donor and acceptor HBs. Molecular dynamics simulations show that the water oxygens accepting HBs from the central molecule are spatially localized, whereas water hydrogens donating HBs to it are distributed along the negativity track. This asymmetry is manifested in a wider acceptor- versus donor-HB distribution. There is a higher probability for a water molecule to accept one (trigonal symmetry) or three HBs than to donate one or three HBs. A simple model can explain semiquantitatively how these distributions evolve by distorting perfectly tetrahedral water. Just two reactions are required: the dissociation of a HB between a double-donor donating to a double-acceptor, D(2){\textperiodcentered}{\textperiodcentered}{\textperiodcentered}A(2), followed by a switching reaction in which a HB donor rotates its hydrogen between two double-acceptor molecules. The preponderance of D(2){\textperiodcentered}{\textperiodcentered}{\textperiodcentered}A(2) dissociation events is in line with HB "anticooperativity", whereas positive cooperativity is exhibited by conditional HB distributions: a molecule with more acceptor bonds tends to have more donor bonds and vice versa. Quantum mechanically, such an effect arises from intermolecular charge transfer, but it is observed even for fixed-charge water models. Possibly, in the liquid state this is partly a collective effect, for example, a more ordered hydration shell that enhances the probability for both acceptor and donor HBs. The activation energy for liquid water self-diffusion is considerably larger than its HB strength, pointing to the involvement of collective dynamics. The remarkable agreement between the temperature dependence of the water self-diffusion coefficient and its Debye relaxation time suggests that both share the same mechanism, likely consisting of coupled rotation and translation with collective rearrangement of the environment. The auto-correlation function of a hydrogen-bonded water molecule pair is depicted quantitatively by the solution of the diffusion equation for reversible geminate recombination, up to long times where the ubiquitous t(-3/2) power law prevails. From the model, one obtains the HB dissociation and formation rate coefficients and their temperature dependence. Both have a similar activation enthalpy, suggesting rapid formation of HBs with alternate partners, perhaps by the HB switching reaction involving the trigonal site. A detailed picture of how small fluctuations evolve into large-scale molecular motions in water remains elusive. Nonetheless, our results demonstrate how the plasticity of water can be traced to its asymmetric charge distribution, with duality between tetrahedral and trigonal ligation states.},
author = {Agmon, Noam},


isbn = {1520-4898 (Electronic){\$}\backslash{\$}n0001-4842 (Linking)},

journal = {Acc. Chem. Res.},

pages = {63--73},
pmid = {21978022},
title = {{Liquid water: From symmetry distortions to diffusive motion}},
volume = {45},
year = {2012}
}
@article{greg-08jmc,
author = {Gregory, D H},

journal = {J. Mat. Chem.},

pages = {2321--2330},
publisher = {Royal Society of Chemistry},
title = {{Lithium nitrides, imides and amides as lightweight, reversible hydrogen stores}},
volume = {18},
year = {2008}
}
@article{jeli+07prb,
author = {Jelinek, B. and Houze, J. and Kim, Seong-Gon Sungho and Horstemeyer, M. and Baskes, M. and Kim, Seong-Gon Sungho},



journal = {Phys. Rev. B},

mendeley-tags = {aluminum magnesium,eam},


pages = {054106},
title = {{Modified embedded-atom method interatomic potentials for the Mg-Al alloy system}},

volume = {75},
year = {2007}
}
@article{nose84jcp,
author = {Nos{\'{e}}, Shuichi},



journal = {J. Chem. Phys.},

pages = {511},
title = {{A unified formulation of the constant temperature molecular dynamics methods}},

volume = {81},
year = {1984}
}
@article{kuo+04jpcb,
abstract = {A series of first principles molecular dynamics and Monte Carlo simulations were carried out for liquid water to investigate the reproducibility of different sampling approaches. These simulations include Car−Parrinello molecular dynamics simulations using the program cpmd with different values of the fictitious electron mass in the microcanonical and canonical ensembles, Born−Oppenheimer molecular dynamics using the programs cpmd and cp2k in the microcanonical ensemble, and Metropolis Monte Carlo using cp2k in the canonical ensemble. With the exception of one simulation for 128 water molecules, all other simulations were carried out for systems consisting of 64 molecules. Although the simulations yield somewhat fortuitous agreement in structural properties, analysis of other properties demonstrate that one should exercise caution when assuming the reproducibility of Car−Parrinello and Born−Oppenheimer molecular dynamics simulations for small system sizes in the microcanonical ensemble. In contrast, the molecular dynamics and Monte Carlo simulations in the canonical ensemble appear to be more reliable. Furthermore, in the case of canonical Car−Parrinello molecular dynamics simulations the application of Nos{\{}{\'{e}}{\}}−Hoover chain thermostats allows the use of larger fictitious electron masses. For the Becke−Lee−Yang−Parr exchange and correlation energy functionals and norm-conserving Troullier−Martins or Goedecker−Teter−Hutter pseudopotentials, these simulations at a fixed density of 1.0 g/cm3 and a temperature close to 315 K point to an overstructured liquid with a height of the first peak in the oxygen−oxygen radial distribution function of about 3.0, an underestimated value of the classical constant-volume heat capacity of about 70 J/(mol K), and an underestimated self-diffusion constant of about 0.04 {\{}{\AA}{\}}2/ps.},
author = {Kuo, I-Feng W and Mundy, Christopher J and McGrath, Matthew J and Siepmann, J Ilja and VandeVondele, Joost and Sprik, Michiel and Hutter, J{\"{u}}rg and Chen, Bin and Klein, Michael L and Mohamed, Fawzi and Krack, Matthias and Parrinello, Michele},


isbn = {1520-6106},

journal = {J. Phys. Chem. B},


pages = {12990--12998},
title = {{Liquid Water from First Principles: Investigation of Different Sampling Approaches}},

volume = {108},
year = {2004}
}
@article{schm-voth98jpcb,
author = {Schmitt, Udo W. and Voth, Gregory a.},



journal = {J. Phys. Chem. B},


pages = {5547--5551},
title = {{Multistate Empirical Valence Bond Model for Proton Transport in Water}},

volume = {102},
year = {1998}
}
@article{chen+03prl,
author = {Chen, Bin and Ivanov, Ivaylo and Klein, Michael L and Parrinello, Michele},

journal = {Phys. Rev. Lett.},

pages = {215503},
publisher = {American Physical Society},
title = {{Hydrogen Bonding in Water}},
volume = {91},
year = {2003}
}
@article{poho+87jcp,
author = {Pohorille, Andrew and Pratt, Lawrence R. and LaViolette, Randall a. and Wilson, Michael a. and MacElroy, Robert D.},



journal = {J. Chem. Phys.},

pages = {6070},
publisher = {AIP},
title = {{Comparison of the structure of harmonic aqueous glasses and liquid water}},

volume = {87},
year = {1987}
}
@article{bert+11jacs,
abstract = {Despite the daily use of urea to influence protein folding and stability, the molecular mechanism with which urea acts is still not well understood. Here the use of combined parallel tempering and metadynamics simulation allows us to study the free-energy landscape associated with the folding/unfolding of {\$}\beta{\$}-hairpin GB1 equilibrium in 8 M urea and pure water. The nature of the unfolded state in both solutions has been analyzed: in urea solution the addition of denaturants acts to expand the denatured state, while in pure water solution the unfolded state is noticeably more compact. For what concerns the mechanism by which urea acts as a denaturant, a preferential direct interaction between urea molecules and protein backbone has been found. However, the bias toward urea solvation is largest at intermediate values of the gyration radius.},
author = {Berteotti, Anna and Barducci, Alessandro and Parrinello, Michele},
journal = {J. Chem. Am. Soc.},
pages = {17200--17206},
pmid = {21854002},
title = {{Effect of urea on the {\$}\beta{\$}-hairpin conformational ensemble and protein denaturation mechanism.}},
volume = {133},
year = {2011}
}
@article{ridu+09ac,
abstract = {Activate and reduce: Carbon dioxide was reduced with silane using a stable N-heterocyclic carbene organocatalyst to provide methanol under very mild conditions. Dry air can serve as the feedstock, and the organocatalyst is much more efficient than transition-metal catalysts for this reaction. This approach offers a very promising protocol for chemical CO(2) activation and fixation.},
author = {Riduan, Siti Nurhanna and Zhang, Yugen and Ying, Jackie Y},



journal = {Angewandte Chemie (International ed. in English)},



pages = {3322--5},
pmid = {19338007},
title = {{Conversion of carbon dioxide into methanol with silanes over N-heterocyclic carbene catalysts.}},

volume = {48},
year = {2009}
}
@article{tuck-marx01prl,
author = {Tuckerman, Mark and Marx, Dominik},



journal = {Phys. Rev. Lett.},


pages = {4946--4949},
title = {{Heavy-Atom Skeleton Quantization and Proton Tunneling in “Intermediate-Barrier” Hydrogen Bonds}},

volume = {86},
year = {2001}
}
@article{bell+07pa,
author = {Bellesia, Giovanni and Fedorov, Maxim V. and Timoshenko, Edward G.},



journal = {Physica A: Statistical Mechanics and its Applications},


pages = {455--476},
title = {{Molecular dynamics study of structural properties of -sheet assemblies formed by synthetic de novo oligopeptides}},

volume = {373},
year = {2007}
}
@article{koji-kawa05jac,
author = {Kojima, Y and Kawai, Y},

journal = {J. Alloys Compd.},

pages = {236--239},
publisher = {Elsevier},
title = {{IR characterizations of lithium imide and amide}},
volume = {395},
year = {2005}
}
@article{vuil-borg97jms,
author = {Vuilleumier, Rodolphe and Borgis, Daniel},



journal = {Journal of Molecular Structure},

pages = {555--565},
title = {{Molecular dynamics of an excess proton in water using a non-additive valence bond force field}},

volume = {436-437},
year = {1997}
}
@article{finn-sinc84pma,
author = {Finnis, M. W. and Sinclair, J. E.},



journal = {Philosophical Magazine A},


pages = {45--55},
title = {{A simple empirical N -body potential for transition metals}},

volume = {50},
year = {1984}
}
@article{lair+09jcp,
abstract = {We calculate the solid-liquid interfacial free energy gamma(sl) for the Lennard-Jones (LJ) system at several points along the pressure-temperature coexistence curve using molecular-dynamics simulation and Gibbs-Cahn integration. This method uses the excess interfacial energy (e) and stress (tau) along the coexistence curve to determine a differential equation for gamma(sl) as a function of temperature. Given the values of gamma(sl) for the (100), (110), and (111) LJ interfaces at the triple-point temperature (T( *)=kT/varepsilon=0.618), previously obtained using the cleaving method by Davidchack and Laird [J. Chem. Phys. 118, 7657 (2003)], this differential equation can be integrated to obtain gamma(sl) for these interfaces at higher coexistence temperatures. Our values for gamma(sl) calculated in this way at T( *)=1.0 and 1.5 are in good agreement with those determined previously by cleaving, but were obtained with significantly less computational effort than required by either the cleaving method or the capillary fluctuation method of Hoyt, Asta, and Karma [Phys. Rev. Lett. 86, 5530 (2001)]. In addition, the orientational anisotropy in the excess interface energy, stress and entropy, calculated using the conventional Gibbs dividing surface, are seen to be significantly larger than the relatively small anisotropies in gamma(sl) itself.},
author = {Laird, Brian B and Davidchack, Ruslan L and Yang, Yang and Asta, Mark},



journal = {J. Chem. Phys.},

mendeley-tags = {solid-liquid interface},


pages = {114110},
pmid = {19778103},
title = {{Determination of the solid-liquid interfacial free energy along a coexistence line by Gibbs-Cahn integration.}},

volume = {131},
year = {2009}
}
@article{krzy-fern11prb,
author = {Krzystyniak, Maciej and Fernandez-Alonso, Felix},

journal = {Phys. Rev. B},

pages = {134305},
publisher = {American Physical Society},
title = {{Ab initio nuclear momentum distributions in lithium hydride: Assessing nonadiabatic effects}},
volume = {83},
year = {2011}
}
@article{schm17c,
abstract = {We perform a large scale benchmark of machine learning methods for the prediction of the thermodynamic stability of solids. We start by constructing a data set that comprises density functional theory calculations of around 250$\backslash$,000 cubic perovskite systems. This includes all possible perovskite and anti-perovskite crystals that can be generated with elements from hydrogen to bismuth, and neglecting rare gases and lanthanides. Incidentally, these calculations already reveal a large number of systems (around 500) that are thermodynamically stable, but that are not present in crystal structure databases. Moreover, some of these phases have unconventional compositions and define completely new families of perovskites. This data set is then used to train and test a series of machine learning algorithms to predict the energy distance to the convex hull of stability. In particular, we study the performance of ridge regression, random forests, extremely randomized trees (including adaptive boosting), and neural ...},
author = {Schmidt, Jonathan and Shi, Jingming and Borlido, Pedro and Chen, Liming and Botti, Silvana and Marques, Miguel A. L.},



journal = {Chemistry of Materials},

pages = {acs.chemmater.7b00156},
title = {{Predicting the Thermodynamic Stability of Solids Combining Density Functional Theory and Machine Learning}},

year = {2017}
}
@article{mont+13njp,
abstract = {The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure–property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine' is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.},
author = {Montavon, Gr{\'{e}}goire and Rupp, Matthias and Gobre, Vivekanand and Vazquez-Mayagoitia, Alvaro and Hansen, Katja and Tkatchenko, Alexandre and M{\"{u}}ller, Klaus Robert and {Anatole Von Lilienfeld}, O.},



journal = {New Journal of Physics},
pages = {095003},
title = {{Machine learning of molecular electronic properties in chemical compound space}},
volume = {15},
year = {2013}
}
@article{piet-mart15jcp,
author = {Pietrucci, Fabio and Martoň{\'{a}}k, Roman},



journal = {J. Chem. Phys.},
pages = {104704},
title = {{Systematic comparison of crystalline and amorphous phases: Charting the landscape of water structures and transformations}},

volume = {142},
year = {2015}
}
@article{fang+00prl,
author = {Fang, Z and Solovyev, I V and Terakura, K},

journal = {Phys. Rev. Lett.},

pages = {3169--3172},
publisher = {American Physical Society},
title = {{Phase Diagram of Tetragonal Manganites}},
volume = {84},
year = {2000}
}
@article{prin+11jcp,
abstract = {Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data.},
author = {Prinz, Jan Hendrik and Wu, Hao and Sarich, Marco and Keller, Bettina and Senne, Martin and Held, Martin and Chodera, John D. and Schtte, Christof and No{\'{e}}, Frank},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

mendeley-tags = {fokker-planck,markov state model},

pages = {0--23},
pmid = {21548671},
title = {{Markov models of molecular kinetics: Generation and validation}},
volume = {134},
year = {2011}
}
@article{ande+98am,
author = {Andersen, S J and Zandbergen, H W and Jansen, J and Tr{\AE}holt, C and Tundal, U and Reiso, O},
journal = {Acta Materialia},
pages = {3283--3298},
title = {{The crystal structure of the {\$}\beta{\$}″ phase in Al–Mg–Si alloys}},
volume = {46},
year = {1998}
}
@article{giro-cald11jrss,
abstract = {The paper proposes Metropolis adjusted Langevin and Hamiltonian Monte Carlo sampling methods defined on the Riemann manifold to resolve the shortcomings of existing Monte Carlo algorithms when sampling from target densities that may be high dimensional and exhibit strong correlations. The methods provide fully automated adaptation mechanisms that circumvent the costly pilot runs that are required to tune proposal densities for Metropolis-Hastings or indeed Hamiltonian Monte Carlo and Metropolis adjusted Langevin algorithms. This allows for highly efficient sampling even in very high dimensions where different scalings may be required for the transient and stationary phases of the Markov chain. The methodology proposed exploits the Riemann geometry of the parameter space of statistical models and thus automatically adapts to the local structure when simulating paths across this manifold, providing highly efficient convergence and exploration of the target density. The performance of these Riemann manifold Monte Carlo methods is rigorously assessed by performing inference on logistic regression models, log-Gaussian Cox point processes, stochastic volatility models and Bayesian estimation of dynamic systems described by non-linear differential equations. Substantial improvements in the time-normalized effective sample size are reported when compared with alternative sampling approaches. MATLAB code that is available from http://www.ucl.ac.uk/statistics/research/rmhmc allows replication of all the results reported.},
archivePrefix = {arXiv},
arxivId = {0907.1100},
author = {Girolami, Mark and Calderhead, Ben},




journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},



pages = {123--214},
title = {{Riemann manifold Langevin and Hamiltonian Monte Carlo methods}},

volume = {73},
year = {2011}
}
@article{mart+96prb,
author = {Martin, Michael C and Shirane, G and Endoh, Y and Hirota, K and Moritomo, Y and Tokura, Y},

journal = {Phys. Rev. B},

pages = {14285--14290},
publisher = {American Physical Society},
title = {{Magnetism and structural distortion in the La{\_}0.7Sr{\_}0.3MnO{\_}3 metallic ferromagnet}},
volume = {53},
year = {1996}
}
@article{frit+14jctc,
author = {Fritsch, Sebastian and Potestio, Raffaello and Donadio, Davide and Kremer, Kurt},



journal = {J. Chem. Theory Comput.},


pages = {816--824},
title = {{Nuclear Quantum Effects in Water: A Multiscale Study}},

volume = {10},
year = {2014}
}
@article{adle89npb,
author = {Adler, S. L.},

journal = {Nucl. Phys. B},
pages = {437--446},
title = {{Algorithms for pure gauge theory}},

volume = {9},
year = {1989}
}
@article{form71jcp,
author = {Forman, R A},

journal = {J. Chem. Phys.},

pages = {1987},
title = {{Order{\{}--{\}}Disorder Transition in Lithium Imide, LiNH}},
volume = {55},
year = {1971}
}
@article{dell+98jcp,
author = {Dellago, Christoph and Bolhuis, Peter G. and Csajka, Félix S. and Chandler, David},



journal = {J. Chem. Phys.},

pages = {1964},
title = {{Transition path sampling and the calculation of rate constants}},

volume = {108},
year = {1998}
}
@article{walc+01cpl,
author = {Walch, S P and Ramalingam, S and Sriraman, S and Aydil, E S and Maroudas, D},

journal = {Chem. Phys. Lett.},

pages = {249--255},
publisher = {Elsevier Science},
title = {{Mechanisms and energetics of SiH3 adsorption on the pristine Si (001)-(2x1) surface}},
volume = {344},
year = {2001}
}
@article{koon91nature,
author = {Koonin, Steven E},
journal = {Nature},
pages = {468--470},
title = {{Environmental fine structure in low-energy {\$}\beta{\$}-particle spectra}},
volume = {354},
year = {1991}
}
@article{zimm-vani09jcp,
abstract = {A general and rigorous methodology to compute the quantum equilibrium isotope effect is described. Unlike standard approaches, ours does not assume separability of rotational and vibrational motions and does not make the harmonic approximation for vibrations or rigid rotor approximation for the rotations. In particular, zero point energy and anharmonicity effects are described correctly quantum mechanically. The approach is based on the thermodynamic integration with respect to the mass of isotopes and on the Feynman path integral representation of the partition function. An efficient estimator for the derivative of free energy is used whose statistical error is independent of the number of imaginary time slices in the path integral, speeding up calculations by a factor of approximately 60 at 500 K and more at room temperature. We describe the implementation of the methodology in the molecular dynamics package AMBER 10. The method is tested on three [1,5] sigmatropic hydrogen shift reactions. Because of the computational expense, we use ab initio potentials to evaluate the equilibrium isotope effects within the harmonic approximation and then the path integral method together with semiempirical potentials to evaluate the anharmonicity corrections. Our calculations show that the anharmonicity effects amount up to 30{\{}{\%}{\}} of the symmetry reduced reaction free energy. The numerical results are compared with recent experiments of Doering et al., [J. Am. Chem. Soc. 128, 9080 (2006); J. Am. Chem. Soc.129, 2488 (2007)] confirming the accuracy of the most recent measurement on 2,4,6,7,9-pentamethyl-5-(5,5-(2)H(2))methylene-11,11a-dihydro-12H-naphthacene as well as concerns about compromised accuracy, due to side reactions, of another measurement on 2-methyl-10-(10,10-(2)H(2))methylenebicyclo[4.4.0]dec-1-ene.},
author = {Zimmermann, Tom{\'{a}}s and Van$\backslash$'$\backslash$icek, Jir$\backslash$'$\backslash$i and Van{\'{i}}cek, Jir{\'{i}}},



journal = {J. Chem. Phys.},


pages = {24111},
pmid = {19603974},
title = {{Path integral evaluation of equilibrium isotope effects.}},

volume = {131},
year = {2009}
}
@article{mara+90aop,
author = {Maradudin, A A and Michel, T and McGurn, A R and M{\'{e}}ndez, E R},

journal = {Ann. Phys.},

pages = {255--307},
title = {{Enhanced backscattering of light from a random grating}},
volume = {203},
year = {1990}
}
@article{matu+97prl,
author = {Matubayasi, Nobuyuki and Wakai, Chihiro and Nakahara, Masaru},



journal = {Phys. Rev. Lett.},


pages = {2573--2576},
title = {{NMR Study of Water Structure in Super- and Subcritical Conditions}},

volume = {78},
year = {1997}
}
@article{rehr-albe00rmp,
author = {Rehr, J. J. and Albers, R.C. C},



journal = {Rev. Mod. Phys.},


pages = {621--654},
title = {{Theoretical approaches to x-ray absorption fine structure}},

volume = {72},
year = {2000}
}
@article{calv+12pccp,
abstract = {We assess the performance of colored-noise thermostats to generate quantum mechanical initial conditions for molecular dynamics simulations, in the context of infrared spectra of large polyatomic molecules. Comparison with centroid molecular dynamics simulations taken as reference shows that the method is accurate in predicting line shifts and band widths in the ionic cluster (NaCl)(32) and in the naphthalene molecule. As illustrated on much larger polycyclic aromatic hydrocarbons, the method also allows fundamental spectra to be evaluated in the limit of T = 0, taking into account anharmonicities and vibrational delocalization.},
author = {Calvo, Florent and Van-Oanh, Nguyen-Thi and Parneix, Pascal and Falvo, Cyril},



journal = {PCCP},


pages = {10503--6},
pmid = {22743582},
title = {{Vibrational spectra of polyatomic molecules assisted by quantum thermal baths.}},

volume = {14},
year = {2012}
}
@article{wend+10jpca,
abstract = {First, different approaches to detect hydrogen bonds and to evaluate their energies are introduced newly or are extended. Supermolecular interaction energies of 256 dimers, each containing one single hydrogen bond, were correlated to various descriptors by a fit function depending both on the donor and acceptor atoms of the hydrogen bond. On the one hand, descriptors were orbital-based parameters as the two-center or three-center shared electron number, products of ionization potentials and shared electron numbers, and the natural bond orbital interaction energy. On the other hand, integral descriptors examined were the acceptor-proton distance, the hydrogen bond angle, and the IR frequency shift of the donor-proton stretching vibration. Whereas an interaction energy dependence on 1/r(3.8) was established, no correlation was found for the angle. Second, the fit functions are applied to hydrogen bonds in polypeptides, amino acid dimers, and water cluster, thus their reliability is demonstrated. Employing the fit functions to assign intramolecular hydrogen bond energies in polypeptides, several side chain CH...O and CH...N hydrogen bonds were detected on the fly. Also, the fit functions describe rather well intermolecular hydrogen bonds in amino acid dimers and the cooperativity of hydrogen bond energies in water clusters.},
author = {Wendler, Katharina and Thar, Jens and Zahn, Stefan and Kirchner, Barbara},



journal = {J. Phys. Chem. A},



pages = {9529--36},
pmid = {20707378},
title = {{Estimating the hydrogen bond energy.}},

volume = {114},
year = {2010}
}
@article{kapi+18jpcb,
abstract = {{\textcopyright} 2018 American Chemical Society. One of the many peculiar properties of water is the pronounced deviation of the proton momentum distribution from Maxwell-Boltzmann behaviour. This deviation from the classical limit is a manifestation of the quantum mechanical nature of protons. Its extent, which can be probed directly by Deep Inelastic Neutron Scattering (DINS) experiments, gives important insight on the potential of mean force felt by H atoms. The determination of the full distribution of particle momenta, however, is a real tour de force for both experiments and theory, which has led to unresolved discrepancies between the two. In this Letter we present comprehensive, fully-converged momentum distributions for water at several thermodynamic state points, focusing on the components that cannot be described in terms of a scalar contribution to the quantum kinetic energy, and providing a benchmark that can serve as a reference for future simulations and experiments. In doing so, we also introduce a number of technical developments that simplify and accelerate greatly the calculation of momentum distributions by means of atomistic simulations.},
author = {Kapil, Venkat and Cuzzocrea, Alice and Ceriotti, Michele},



journal = {J. Phys. Chem. B},


pages = {6048--6054},
title = {{Anisotropy of the Proton Momentum Distribution in Water}},

volume = {122},
year = {2018}
}
@article{agmo+16cr,
author = {Agmon, Noam and Bakker, Huib J and Campen, R Kramer and Henchman, Richard H and Pohl, Peter and Roke, Sylvie and Hassanali, Ali},


title = {{Protons and Hydroxide Ions in Aqueous Systems}},
year = {2015}
}
@article{stel+14prb,
author = {Stella, L. and Lorenz, C. D. and Kantorovich, L.},



journal = {Phys. Rev. B},

mendeley-tags = {GLE,colored noise,open system},


pages = {134303},
title = {{Generalized Langevin equation: An efficient approach to nonequilibrium molecular dynamics of open systems}},

volume = {89},
year = {2014}
}
@article{ross+14jcp2,
abstract = {{\"{i}}¿½ 2014 AIP Publishing LLC. Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here, we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer model and a mixed quantum-classical model as representatives of the first family of methods, and centroid molecular dynamics and thermostatted ring polymer molecular dynamics as examples of the latter. We use as benchmarks D 2 O doped with HOD and pure H 2 O at three distinct thermodynamic state points (ice Ih at 150 K, and the liquid at 300 K and 600 K), modeled with the simple q-TIP4P/F potential energy and dipole moment surfaces. With few exceptions the different techniques yield IR absorption frequencies that are consistent with one another within a few tens of cm -1 . Comparison with classical molecular dynamics demonstrates the importance of nuclear quantum effects up to the highest temperature, and a detailed discussion of the discrepancies between the various methods let us draw some (circumstantial) conclusions about the impact of the very different approximations that underlie them. Such cross validation between radically different approaches could indicate a way forward to further improve the state of the art in simulations of condensed-phase quantum dynamics.},
author = {Rossi, Mariana and Liu, Hanchao and Paesani, Francesco and Bowman, Joel and Ceriotti, Michele},



journal = {J. Chem. Phys.},


pages = {181101},
title = {{Communication: On the consistency of approximate quantum dynamics simulation methods for vibrational spectra in the condensed phase}},

volume = {141},
year = {2014}
}
@article{hugh-harr09njc,
author = {Hughes, Colan E. and Harris, Kenneth D. M.},



journal = {New Journal of Chemistry},

pages = {713},
title = {{The effect of deuteration on polymorphic outcome in the crystallization of glycine from aqueous solution}},

volume = {33},
year = {2009}
}
@article{bald12ijgfs,
abstract = {Sous vide is a method of cooking in vacuumized plastic pouches at precisely controlled temperatures. Precise temperature control gives more choice over doneness and texture than traditional cooking methods. Cooking in heat-stable, vacuumized pouches improves shelf-life and can enhance taste and nutrition. This article reviews the basic techniques, food safety, and science of sous vide cooking.},
author = {Baldwin, Douglas E.},


isbn = {1878-450X},

journal = {International Journal of Gastronomy and Food Science},


pages = {15--30},
publisher = {Elsevier},
title = {{Sous vide cooking: A review}},

volume = {1},
year = {2012}
}
@article{klim-mich12jcp,
abstract = {Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals, and many other systems. However, an accurate description of dispersion is highly challenging, with the most widely used electronic structure technique, density functional theory (DFT), failing to describe them with standard approximations. Therefore, applications of DFT to systems where dispersion is important have traditionally been of questionable accuracy. However, the last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods. Here we discuss, classify, and evaluate some of the promising schemes to emerge in recent years. A brief perspective on the outstanding issues that remain to be resolved and some directions for future research are also provided.},
author = {Klime{\v{s}}, Jir{\'{i}} and Michaelides, Angelos},



journal = {J. Chem. Phys.},



pages = {120901},
pmid = {23020317},
title = {{Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory.}},

volume = {137},
year = {2012}
}
@article{delb+13jctc,
abstract = {The second-order M?ller?Plesset perturbation energy (MP2) and the Random Phase Approximation (RPA) correlation energy are increasingly popular post-Kohn?Sham correlation methods. Here, a novel algorithm based on a hybrid Gaussian and Plane Waves (GPW) approach with the resolution-of-identity (RI) approximation is developed for MP2, scaled opposite-spin MP2 (SOS-MP2), and direct-RPA (dRPA) correlation energies of finite and extended system. The key feature of the method is that the three center electron repulsion integrals (??|P) necessary for the RI approximation are computed by direct integration between the products of Gaussian basis functions ?? and the electrostatic potential arising from the RI fitting densities P. The electrostatic potential is obtained in a plane waves basis set after solving the Poisson equation in Fourier space. This scheme is highly efficient for condensed phase systems and offers a particularly easy way for parallel implementation. The RI approximation allows to speed up the MP2 energy calculations by a factor 10 to 15 compared to the canonical implementation but still requires O(N5) operations. On the other hand, the combination of RI with a Laplace approach in SOS-MP2 and an imaginary frequency integration in dRPA reduces the computational effort to O(N4) in both cases. In addition to that, our implementations have low memory requirements and display excellent parallel scalability up to tens of thousands of processes. Furthermore, exploiting graphics processing units (GPU), a further speedup by a factor ?2 is observed compared to the standard only CPU implementations. In this way, RI-MP2, RI-SOS-MP2, and RI-dRPA calculations for condensed phase systems containing hundreds of atoms and thousands of basis functions can be performed within minutes employing a few hundred hybrid nodes. In order to validate the presented methods, various molecular crystals have been employed as benchmark systems to assess the performance, while solid LiH has been used to study the convergence with respect to the basis set and system size in the case of RI-MP2 and RI-dRPA. The second-order M?ller?Plesset perturbation energy (MP2) and the Random Phase Approximation (RPA) correlation energy are increasingly popular post-Kohn?Sham correlation methods. Here, a novel algorithm based on a hybrid Gaussian and Plane Waves (GPW) approach with the resolution-of-identity (RI) approximation is developed for MP2, scaled opposite-spin MP2 (SOS-MP2), and direct-RPA (dRPA) correlation energies of finite and extended system. The key feature of the method is that the three center electron repulsion integrals (??|P) necessary for the RI approximation are computed by direct integration between the products of Gaussian basis functions ?? and the electrostatic potential arising from the RI fitting densities P. The electrostatic potential is obtained in a plane waves basis set after solving the Poisson equation in Fourier space. This scheme is highly efficient for condensed phase systems and offers a particularly easy way for parallel implementation. The RI approximation allows to speed up the MP2 energy calculations by a factor 10 to 15 compared to the canonical implementation but still requires O(N5) operations. On the other hand, the combination of RI with a Laplace approach in SOS-MP2 and an imaginary frequency integration in dRPA reduces the computational effort to O(N4) in both cases. In addition to that, our implementations have low memory requirements and display excellent parallel scalability up to tens of thousands of processes. Furthermore, exploiting graphics processing units (GPU), a further speedup by a factor ?2 is observed compared to the standard only CPU implementations. In this way, RI-MP2, RI-SOS-MP2, and RI-dRPA calculations for condensed phase systems containing hundreds of atoms and thousands of basis functions can be performed within minutes employing a few hundred hybrid nodes. In order to validate the presented methods, various molecular crystals have been employed as benchmark systems to assess the performance, while solid LiH has been used to study the convergence with respect to the basis set and system size in the case of RI-MP2 and RI-dRPA.},
author = {{Del Ben}, Mauro and Hutter, J{\"{u}}rg and VandeVondele, Joost},


isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},


pages = {2654--2671},
title = {{Electron Correlation in the Condensed Phase from a Resolution of Identity Approach Based on the Gaussian and Plane Waves Scheme}},

volume = {9},
year = {2013}
}
@article{raus01surfr,
author = {Rauscher, Hubert},



journal = {Surf. Sci. Reports},


pages = {207--328},
title = {{The interaction of silanes with silicon single crystal surfaces: microscopic processes and structures}},

volume = {42},
year = {2001}
}
@article{ceri+10jcp,
abstract = {The path integral molecular dynamics (PIMD) method provides a convenient way to compute the quantum mechanical structural and thermodynamic properties of condensed phase systems at the expense of introducing an additional set of high frequency normal modes on top of the physical vibrations of the system. Efficiently sampling such a wide range of frequencies provides a considerable thermostatting challenge. Here we introduce a simple stochastic path integral Langevin equation (PILE) thermostat which exploits an analytic knowledge of the free path integral normal mode frequencies. We also apply a recently developed colored noise thermostat based on a generalized Langevin equation (GLE), which automatically achieves a similar, frequency-optimized sampling. The sampling efficiencies of these thermostats are compared with that of the more conventional Nos{\'{e}}-Hoover chain (NHC) thermostat for a number of physically relevant properties of the liquid water and hydrogen-in-palladium systems. In nearly every case, the new PILE thermostat is found to perform just as well as the NHC thermostat while allowing for a computationally more efficient implementation. The GLE thermostat also proves to be very robust delivering a near-optimum sampling efficiency in all of the cases considered. We suspect that these simple stochastic thermostats will therefore find useful application in many future PIMD simulations.},
author = {Ceriotti, Michele and Parrinello, Michele and Markland, Thomas E and Manolopoulos, David E},



journal = {J. Chem. Phys.},



pages = {124104},
pmid = {20886921},
publisher = {AIP},
title = {{Efficient stochastic thermostatting of path integral molecular dynamics.}},

volume = {133},
year = {2010}
}
@article{laag-hyne06science,
abstract = {Despite long study, a molecular picture of the mechanism of water reorientation is still lacking. Using numerical simulations, we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor. The H-bond cleavage and the molecular reorientation occur concertedly and not successively as usually considered. This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive.},
author = {Laage, Damien and Hynes, James T},



journal = {Science (New York, N.Y.)},


pages = {832--5},
pmid = {16439623},
title = {{A molecular jump mechanism of water reorientation.}},

volume = {311},
year = {2006}
}
@article{de+16jci,
abstract = {High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from compu-tational searches, as well as the agglomeration of data of heterogeneous provenance leads to considerable challenges when it comes to navigating the database, representing its structure at a glance, understanding structure-property relations, eliminat-ing duplicates and identifying inconsistencies. Here we present a case study, based on a data set of conformers of amino acids and dipeptides, of how machine-learning techniques can help addressing these issues. We will exploit a recently-developed strategy to define a metric between structures, and use it as the basis of both clustering and dimensionality reduction tech-niques – showing how these can help reveal structure-property relations, identify outliers and inconsistent structures, and rationalise how perturbations (e.g. binding of ions to the molecule) affect the stability of different conformers.},
archivePrefix = {arXiv},
arxivId = {1611.06246},
author = {De, Sandip and Musil, Felix and Ingram, Teresa and Baldauf, Carsten and Ceriotti, Michele},




journal = {Journal of Cheminformatics},



pages = {6},
publisher = {Springer International Publishing},
title = {{Mapping and classifying molecules from a high-throughput structural database}},

volume = {9},
year = {2017}
}
@incollection{henk+02book,
abstract = {The problem of finding minimum energy paths and, in particular, saddle points on high dimensional potential energy surfaces is discussed. Several different methods are reviewed and their efficiency compared on a test problem involving conformational transitions in an island of adatoms on a crystal surface. The focus is entirely on methods that only require the potential energy and its first derivative with respect to the atom coordinates. Such methods can be applied, for example, in plane wave based Density Functional Theory calculations, and the computational effort typically scales well with system size. When the final state of the transition is known, both the initial and final coordinates of the atoms can be used as boundary conditions in the search. Methods of this type include the Nudged Elastic Band, Ridge, Conjugate Peak Refinement, Drag method and the method of Dewar, Healy and Stewart. When only the initial state is known, the problem is more challenging and the search for the saddle point represents also a search for the optimal transition mechanism. We discuss a recently proposed method that can be used in such cases, the Dimer method.},
author = {Henkelman, Graeme and J{\'{o}}hannesson, G$\backslash$'$\backslash$isli G{\'{i}}sli and J{\'{o}}nsson, Hannes},
booktitle = {Theoretical Methods in Condensed Phase Chemistry - Progress in Theoretical Chemistry and Physics - Volume 5},


isbn = {978-0-306-46949-7},

pages = {269--302},
title = {{Theoretical Methods in Condensed Phase Chemistry}},

volume = {5},
year = {2002}
}
@article{wang-zung94jcp,
author = {Wang, Lin-Wang and Zunger, Alex},

journal = {J. Chem. Phys.},

pages = {2394--2397},
publisher = {AIP},
title = {{Solving Schr{\{}{\"{o}}{\}}dinger{\{}'{\}}s equation around a desired energy: Application to silicon quantum dots}},
volume = {100},
year = {1994}
}
@article{deli-atun11jns,
abstract = {The estimation of multivariate densities using the kernel method has wide applicability. However, this problem has received less attention than the univariate case. This is mainly due to the increasing difficulty in estimating the optimal smoothing matrix, especially when the components are correlated. To overcome this difficulty, we propose in this work a Bayesian method to estimate the optimal smoothing matrix H. A loss function is defined and the estimator of H is the matrix minimising the loss function. We carried out simulations with a mixture of multivariate densities with correlation and the results were highly satisfactory.$\backslash$nThe estimation of multivariate densities using the kernel method has wide applicability. However, this problem has received less attention than the univariate case. This is mainly due to the increasing difficulty in estimating the optimal smoothing matrix, especially when the components are correlated. To overcome this difficulty, we propose in this work a Bayesian method to estimate the optimal smoothing matrix H. A loss function is defined and the estimator of H is the matrix minimising the loss function. We carried out simulations with a mixture of multivariate densities with correlation and the results were highly satisfactory.},
author = {de Lima, Max Sousa and Atuncar, Gregorio Saravia},



journal = {Journal of Nonparametric Statistics},


pages = {137--148},
title = {{A Bayesian method to estimate the optimal bandwidth for multivariate kernel estimator}},

volume = {23},
year = {2011}
}
@article{peng-chen08ees,
author = {Peng, Bo and Chen, Jun},



journal = {Energy {\&} Environmental Science},
pages = {479--483},
title = {{Ammonia borane as an efficient and lightweight hydrogen storage medium}},

year = {2008}
}
@article{uhl+16jcp,
author = {Uhl, Felix and Marx, Dominik and Ceriotti, Michele},



journal = {J. Chem. Phys.},


pages = {054101},
title = {{Accelerated path integral methods for atomistic simulations at ultra-low temperatures}},

volume = {145},
year = {2016}
}
@article{deng+12nl,
abstract = {Imaging of individual protein molecules at the single amino acid level has so far not been possible due to the incompatibility of proteins with the vacuum environment necessary for high-resolution scanning probe microscopy. Here we demonstrate electrospray ion beam deposition of selectively folded and unfolded cytochrome c protein ions on atomically defined solid surfaces in ultrahigh vacuum (10(-10) mbar) and achieve unprecedented resolution with scanning tunneling microscopy. On the surface folded proteins are found to retain their three-dimensional structure. Unfolded proteins are observed as extended polymer strands displaying submolecular features with resolution at the amino acid level. On weakly interacting surfaces, unfolded proteins refold into flat, irregular patches composed of individual molecules. This suggests the possibility of two-dimensionally confined folding of peptides of an appropriate sequence into regular two-dimensional structures as a new approach toward functional molecular surface coatings.},
author = {Deng, Zhitao and Thontasen, Nicha and Malinowski, Nikola and Rinke, Gordon and Harnau, Ludger and Rauschenbach, Stephan and Kern, Klaus},



journal = {Nano letters},



pages = {2452--2458},
pmid = {22530980},
title = {{A close look at proteins: submolecular resolution of two- and three-dimensionally folded cytochrome c at surfaces.}},

volume = {12},
year = {2012}
}
@article{hans-yang08jcp,
abstract = {The statistical properties of the autocorrelation function from a time series composed of independently and identically distributed stochastic variables has been studied. Analytical expressions for the autocorrelation function's variance have been derived. It has been found that two common ways of calculating the autocorrelation, moving-average and Fourier transform, exhibit different uncertainty characteristics. For periodic time series, the Fourier transform method is preferred because it gives smaller uncertainties that are uniform through all time lags. Based on these analytical results, a statistically robust method has been proposed to test the existence of correlations in a time series. The statistical test is verified by computer simulations and an application to single-molecule fluorescence spectroscopy is discussed.},
author = {Hanson, Jeffery a and Yang, Haw},



journal = {J. Chem. Phys.},



pages = {214101},
pmid = {18537409},
publisher = {AIP},
title = {{A general statistical test for correlations in a finite-length time series}},

volume = {128},
year = {2008}
}
@article{rowe-saul00science,
abstract = {Many areas of science depend on exploratory data analysis and visualization. The need to analyze large amounts of multivariate data raises the fundamental problem of dimensionality reduction: how to discover compact representations of high-dimensional data. Here, we introduce locally linear embedding (LLE), an unsupervised learning algorithm that computes low-dimensional, neighborhood-preserving embeddings of high-dimensional inputs. Unlike clustering methods for local dimensionality reduction, LLE maps its inputs into a single global coordinate system of lower dimensionality, and its optimizations do not involve local minima. By exploiting the local symmetries of linear reconstructions, LLE is able to learn the global structure of nonlinear manifolds, such as those generated by images of faces or documents of text.},
author = {Roweis, S T and Saul, L K},



journal = {Science},



pages = {2323--6},
pmid = {11125150},
title = {{Nonlinear dimensionality reduction by locally linear embedding.}},

volume = {290},
year = {2000}
}
@article{ono-hiro99prl,
abstract = {We present a simple and efficient technique in ab initio electronic-structure calculation utilizing real-space double grid with a high density of grid points in the vicinity of nuclei. This technique promises to greatly reduce the overhead for performing the integrals that involve nonlocal parts of pseudopotentials, while keeping a high degree of accuracy. our procedure gives rise to no Pulay forces, unlike other real-space methods using adaptive coordinates. Moreover; we demonstrate the potential power of the method by calculating several properties of atoms and molecules.},
archivePrefix = {arXiv},
arxivId = {cond-mat/9904111},
author = {Ono, T and Hirose, K},




journal = {Phys. Rev. Lett.},


pages = {5016--5019},
primaryClass = {cond-mat},
title = {{Timesaving double-grid method for real-space electronic-structure calculations}},

volume = {82},
year = {1999}
}
@article{barr+05cp,
annote = {Combining Simulations and Neutron Scattering Experiments: from Models to Systems of Biological and Technological Interest},
author = {Barrera, G D and Colognesi, D and Mitchell, P C H and Ramirez-Cuesta, A J},

journal = {Chemical Physics},

pages = {119--129},
title = {{LDA or GGA?: A combined experimental inelastic neutron scattering and ab initio lattice dynamics study of alkali metal hydrides}},
volume = {317},
year = {2005}
}
@article{snyd+12prl,
author = {Snyder, John C. and Rupp, Matthias and Hansen, Katja and M{\"{u}}ller, Klaus-Robert and Burke, Kieron},


journal = {Phys. Rev. Lett.},


pages = {253002},
title = {{Finding Density Functionals with Machine Learning}},

volume = {108},
year = {2012}
}
@article{kapi+16jcp,
abstract = {The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modelling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator, or generalized Langevin equation thermostats.},
archivePrefix = {arXiv},
arxivId = {1512.00176},
author = {Kapil, Venkat and VandeVondele, Joost and Ceriotti, Michele},




journal = {J. Chem. Phys.},



pages = {054111},
title = {{Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods}},

volume = {144},
year = {2016}
}
@article{lowe99el,
author = {Lowe, C P},
journal = {Europhys. Lett.},

pages = {145--151},
title = {{An alternative approach to dissipative particle dynamics}},
volume = {47},
year = {1999}
}
@article{hoov86pra,
author = {Hoover, William},



journal = {Phys. Rev. A},


pages = {2499--2500},
title = {{Constant-pressure equations of motion}},

volume = {34},
year = {1986}
}
@article{hage+07jpcb,
abstract = {Parallel tempering (or the replica exchange method (REM)) is a powerful method for speeding up the sampling of conformational states of systems with rough energy landscapes, like proteins, where stable conformational states can be separated by large energy barriers. The usual implementation of the REM is performed on local computer clusters (or parallel processors) where the different replicas must be run synchronously. Here, we present serial replica exchange (SREM), a method that is equivalent to the standard REM in terms of efficiency yet runs asynchronously on a distributed network of computers. A second advantage is the method's greatly enhanced fault tolerance, which enables the study of biological systems on worldwide distributed computing environments, such as Folding@Home. For proof of concept, we apply the SREM to a single alanine dipeptide molecule in explicit water. We show that the SREM reproduces the thermodynamic and structural properties determined by the REM.},
author = {Hagen, Morten and Kim, Byungchan and Liu, Pu and Friesner, Richard a and Berne, B J},



journal = {J. Phys. Chem. B},



pages = {1416--23},
pmid = {17249714},
title = {{Serial replica exchange.}},

volume = {111},
year = {2007}
}
@article{vote+02armr,
author = {Voter, Arthur F. and Montalenti, Francesco and Germann, Timothy C.},



journal = {Annual Review of Materials Research},



pages = {321--346},
title = {{Extending the Time Scale In Atomistic Simulation Of Materials}},

volume = {32},
year = {2002}
}
@article{tria02unpub,
author = {Triantafyllopoulos, Kostas},

journal = {Department of Mathematics, {\ldots}},

pages = {1--8},
title = {{Moments and cumulants of the multivariate real and complex Gaussian distributions}},

year = {2002}
}
@article{zeid+12jpcm,
abstract = {The ordered (1 x 2) monolayer of Bi on the InAs(110) surface is studied by means of angle-resolved high-resolution ultra-violet photoemission at room temperature. Four bands of Bi;induced surface states are singled out and their dispersion is mapped along the high-symmetry directions of the surface Brillouin zone. The highest occupied state S' lies inside the InAs(110) energy gap at 0.2 eV binding energy and spreads across the Fermi level, determining the semimetallic character of the system. The second-highest occupied state Sn is located at 0.83 eV binding energy (at {\textless}(Gamma)over bar{\textgreater}), while states Sm and SN are located near the internal gap edge at 2.57 eV and 3.3 eV binding energy, and present band dispersions along {\textless}(Gamma)over bar{\textgreater}(X) over bar of similar to 340 meV and 300 meV, respectively. The Pi-induced bands of the (1 x 2) phase are shifted in energy relative to the corresponding bands of the (1 x 1)-Bi/InAs(110) phase and their width is reduced. These differences are discussed in the light of the geometric structure of the two phases.},
author = {Zeidler, Anita and Salmon, Philip S and Fischer, Henry E and Neuefeind, J{\"{o}}rg C and {Mike Simonson}, J and Markland, Thomas E},



journal = {J. Phys. Cond. Matt.},



pages = {284126},
title = {{Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics}},

volume = {24},
year = {2012}
}
@article{henk+00jcp,
author = {Henkelman, G and Uberuaga, B P and J{\'{o}}nsson, H},

journal = {J. Chem. Phys.},

pages = {9901},
publisher = {AIP},
title = {{A climbing image nudged elastic band method for finding saddle points and minimum energy paths}},
volume = {113},
year = {2000}
}
@article{baro-gian92epl,
author = {Baroni, S and Giannozzi, P},

journal = {Europhysics Letters},
pages = {547},
title = {{Towards very large-scale electronic-structure calculations}},
volume = {17},
year = {1992}
}
@article{kats+05acb,
author = {Katsaounis, A. and Balomenou, S. and Tsiplakides, D. and Brosda, S. and Neophytides, S. and Vayenas, C.G. G},



journal = {Applied Catalysis B: Environmental},



pages = {251--258},
title = {{Proton tunneling-induced bistability, oscillations and enhanced performance of PEM fuel cells}},

volume = {56},
year = {2005}
}
@article{amsl-goed10jcp,
abstract = {A structure prediction method is presented based on the minima hopping method. To escape local minima, moves on the configurational enthalpy surface are performed by variable cell shape molecular dynamics. To optimize the escape steps the initial atomic and cell velocities are aligned to low curvature directions of the current local minimum. The method is applied to both silicon crystals and well-studied binary Lennard-Jones mixtures. For the latter new putative ground state structures are presented. It is shown that a high success rate is achieved and a reliable prediction of unknown ground state structures is possible.},
author = {Amsler, Maximilian and Goedecker, Stefan},



journal = {J. Chem. Phys.},



pages = {224104},
pmid = {21171680},
title = {{Crystal structure prediction using the minima hopping method.}},

volume = {133},
year = {2010}
}
@article{roac+05jacs,
abstract = {Protein adhesion plays a major role in determining the biocompatibility of materials. The first stage of implant integration is the adhesion of protein followed by cell attachment. Surface modification of implants (surface chemistry and topography) to induce and control protein and cell adhesion is currently of great interest. This communication presents data on protein adsorption (bovine serum albumin and fibrinogen) onto model hydrophobic (CH(3)) and hydrophilic (OH) surfaces, investigated using a quartz crystal microbalance (QCM) and grazing angle infrared spectroscopy. Our data suggest that albumin undergoes adsorption via a single step whereas fibrinogen adsorption is a more complex, multistage process. Albumin has a stronger affinity toward the CH(3) compared to OH terminated surface. In contrast, fibrinogen adheres more rapidly to both surfaces, having a slightly higher affinity toward the hydrophobic surface. Conformational assessment of the adsorbed proteins by grazing angle infrared spectroscopy (GA-FTIR) shows that after an initial 1 h incubation few further time-dependent changes are observed. Both proteins exhibited a less organized secondary structure upon adsorption onto a hydrophobic surface than onto a hydrophilic surface, with the effect observed greatest for albumin. This study demonstrates the ability of simple tailor-made monochemical surfaces to influence binding rates and conformation of bound proteins through protein-surface interactions. Current interest in biocompatible materials has focused on surface modifications to induce rapid healing, both of implants and for wound care products. This effect may also be of significance at the next stage of implant integration, as cell adhesion occurs through the surface protein layer.},
author = {Roach, Paul and Farrar, David and Perry, Carole C},



journal = {J. Chem. Am. Soc.},



pages = {8168--8173},
pmid = {15926845},
title = {{Interpretation of protein adsorption: surface-induced conformational changes.}},

volume = {127},
year = {2005}
}
@article{brou-gilm86jcp4,
author = {Broughton, J. Q. and Gilmer, G. H.},



journal = {J. Chem. Phys.},


pages = {5741},
title = {{Molecular dynamics investigation of the crystal–fluid interface. IV. Free energies of crystal–vapor systems}},

volume = {84},
year = {1986}
}
@article{brow-woch87prl,
author = {Brown, Frank and Woch, Thomas},



journal = {Phys. Rev. Lett.},


pages = {2394--2396},
title = {{Overrelaxed heat-bath and Metropolis algorithms for accelerating pure gauge Monte Carlo calculations}},

volume = {58},
year = {1987}
}
@article{ande83jcp,
author = {Andersen, Hans C},



journal = {J. Comp. Phys.},


pages = {24--34},
publisher = {Elsevier},
title = {{Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations}},

volume = {52},
year = {1983}
}
@article{cahn-hill58jcp,
author = {Cahn, John W. and Hilliard, John E.},



journal = {J. Chem. Phys.},

pages = {258},
title = {{Free Energy of a Nonuniform System. I. Interfacial Free Energy}},

volume = {28},
year = {1958}
}
@article{gast+17cs,
abstract = {Artificial neural networks are combined with molecular dynamics to simulate molecular infrared spectra including anharmonicities and temperature effects.},
author = {Gastegger, Michael and Behler, J{\"{o}}rg and Marquetand, Philipp},


journal = {Chemical Science},

pages = {6924--6935},
title = {{Machine learning molecular dynamics for the simulation of infrared spectra}},

volume = {8},
year = {2017}
}
@article{born-opp27adp,
author = {Born, M. and Oppenheimer, R.},



journal = {Ann. Phys.},

pages = {457--484},
title = {{Zur Quantentheorie der Molekeln}},

volume = {389},
year = {1927}
}
@article{pore+95prb,
abstract = {We present a density-functional-based scheme for determining the necessary parameters of com-mon nonorthogonal tight-binding (TB) models within the framework of the linear-combination-of-atomic-orbitals formalism using the local-density approximation (LDA). By only considering two-center integrals the Hamiltonian and overlap matrix elements are calculated out of suitable input densities and potentials rather than 6tted to experimental data. We can derive analytical functions for the C-C, C-H, and H-H Hamiltonian and overlap matrix elements. The usual short-range repul-sive potential appearing in most TB models is fitted to self-consistent calculations performed within the LDA. The calculation of forces is easy and allow's an application of the method to molecular-dynamics simulations. Despite its extreme simplicity, the method is transferable to complex carbon and hydrocarbon systems. The determination of equilibrium geometries, total energies, and vibra-tional modes of carbon clusters, hydrocarbon molecules, and solid-state modifications of carbon yield results showing an overall good agreement with more sophisticated methods.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Porezag, D. and Frauenheim, Th and K{\"{o}}hler, Th and Seifert, G. and Kaschner, R.},



isbn = {0163-1829},

journal = {Phys. Rev. B},


pages = {12947--12957},
pmid = {9978089},
title = {{Construction of tight-binding-like potentials on the basis of density-functional theory: Application to carbon}},

volume = {51},
year = {1995}
}
@article{nini+14mmta,
author = {Ninive, Per Harald and L{\o}vvik, Ole Martin and Strandlie, Are},



journal = {Metallurgical and Materials Transactions A},


pages = {2916--2924},
title = {{Density Functional Study of the $\beta$″ Phase in Al-Mg-Si Alloys}},

volume = {45},
year = {2014}
}
@article{fors+11natp,
author = {F{\"{o}}rst, M and Manzoni, C and Kaiser, S and Tomioka, Y and Tokura, Y and Merlin, R and Cavalleri, A},

journal = {Nature Physics},
publisher = {Nature Publishing Group},
title = {{Nonlinear phononics as an ultrafast route to lattice control}},
year = {2011}
}
@article{uver+08arbp,
abstract = {Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structures under physiological conditions in vitro. They are highly abundant in nature and their functional repertoire complements the functions of ordered proteins. IDPs are involved in regulation, signaling, and control, where binding to multiple partners and high-specificity/low-affinity interactions play a crucial role. Functions of IDPs are tuned via alternative splicing and posttranslational modifications. Intrinsic disorder is a unique structural feature that enables IDPs to participate in both one-to-many and many-to-one signaling. Numerous IDPs are associated with human diseases, including cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, and diabetes. Overall, intriguing interconnections among intrinsic disorder, cell signaling, and human diseases suggest that protein conformational diseases may result not only from protein misfolding, but also from misidentification, missignaling, and unnatural or nonnative folding. IDPs, such as alpha-synuclein, tau protein, p53, and BRCA1, are attractive targets for drugs modulating protein-protein interactions. From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept.},
author = {Uversky, Vladimir N and Oldfield, Christopher J and Dunker, a Keith},


isbn = {10.1146/annurev.biophys.37.032807.125924},

journal = {Annual review of biophysics},

pages = {215--246},
pmid = {18573080},
title = {{Intrinsically disordered proteins in human diseases: introducing the D2 concept.}},
volume = {37},
year = {2008}
}
@article{zoug+14csda,
abstract = {Bandwidth selection in multivariate kernel density estimation has received considerable attention. In addition to classical methods of bandwidth selection, such as plug-in and cross-validation methods, Bayesian approaches have also been previously investigated. Bayesian estimation of adaptive bandwidth matrices in multivariate kernel density estimation is investigated, when the quadratic and entropy loss functions are used. Under the quadratic loss function, the proposed method is evaluated through a simulation study and two real data sets, which were already discussed in the literature. For these real-data applications, very interesting advantages of the proposed method are pointed out. ?? 2014 Elsevier B.V. All rights reserved.},
author = {Zougab, Nabil and Adjabi, Smail and Kokonendji, C{\'{e}}lestin C.},



journal = {Computational Statistics {\&} Data Analysis},


pages = {28--38},
publisher = {Elsevier B.V.},
title = {{Bayesian estimation of adaptive bandwidth matrices in multivariate kernel density estimation}},

volume = {75},
year = {2014}
}
@article{uran-inou76jcp,
abstract = {The static dielectric constant of a simple anisotropic dielectric model, which consists of anisotropically polarizable molecules, is calculated with the aid of the extended Fr{\"{o}}hlich formula, and a molecular Clausius-Mossotti type formula is obtained. The macroscopic Clausius-Mossotti formula for anisotropic dielectrics is also derived. In these calculations the inside field and the reaction field in anisotropic dielectrics have been used, the derivation of which is given in detail. Copyright {\textcopyright} 1977 American Institute of Physics.},
author = {Urano, Kaoru and Inoue, Masayoshi},


isbn = {9788578110796},

journal = {J. Chem. Phys.},


pages = {791--794},
title = {{Clausius-Mossotti formula for anisotropic dielectrics}},

volume = {71},
year = {1976}
}
@article{fano+06jcp,
abstract = {We report converged quantum statistical mechanical simulations of liquid water with the Thole-type Model (version 2.1), Flexible, polarizable (TTM2.1-F) interaction potential for water. Simulations of total length of 600 ps with a 0.05 fs time step for a periodic unit cell of 256 molecules with up to 32 replicas per atom suggest that the quantum effects contribute 1.01+/-0.02 kcal/mol to the liquid enthalpy of formation at 298.15 K. They furthermore demonstrate for the first time a quantitative agreement with experiment for the heights and broadening of the intramolecular OH and HH peaks in the radial distribution functions.},
author = {Fanourgakis, G.S. and Schenter, G.K. and Xantheas, S.S.},



journal = {J. Chem. Phys.},

pages = {141102},
pmid = {17042571},
title = {{A quantitative account of quantum effects in liquid water.}},

volume = {125},
year = {2006}
}
@article{jung-tobi02jpcb,
author = {Jungwirth, Pavel and Tobias, Douglas J.},



journal = {J. Phys. Chem. B},


pages = {6361--6373},
title = {{Ions at the Air/Water Interface}},

volume = {106},
year = {2002}
}
@article{ifti-tuck05jcp,
abstract = {The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.},
author = {Iftimie, Radu and Tuckerman, Mark E},



journal = {J. Chem. Phys.},


pages = {214508},
pmid = {15974755},
title = {{Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals.}},

volume = {122},
year = {2005}
}
@article{mara-vand06cpl,
author = {Maragliano, Luca and Vanden-Eijnden, Eric},


journal = {Chem. Phys. Lett.},

pages = {168--175},
title = {{A temperature accelerated method for sampling free energy and determining reaction pathways in rare events simulations}},
volume = {426},
year = {2006}
}
@article{wang+94surf,
author = {Wang, Y and Bronikowski, M J and Hamers, R J},

journal = {Surf. Sci.},
pages = {64},
title = {{An atomically resolved scanning tunneling microscopy study of the thermal decomposition of disilane on Si(001)}},
volume = {311},
year = {1994}
}
@article{kola04jcc,
abstract = {An improved method for classic molecular dynamics of polarizable molecules is proposed. The method uses a predictor, one evaluation of the electrostatic field per integration step, and relaxation (damping). The self-consistent solution is approximated with error of the second order (with respect to the timestep). The time reversibility (long-time energy conservation) error is of the (2n - 1)th order, where n is the predictor length. The method is easy to implement, efficient, accurate, and suitable for any model of polarizability.},
author = {Kolafa, Jir{\'{i}}},



journal = {J. Comp. Chem.},



pages = {335--42},
pmid = {14696069},
title = {{Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules.}},

volume = {25},
year = {2004}
}
@article{rott+94acryb,
author = {R{\"{o}}ttger, K. and Endriss, a. and Ihringer, J. and Doyle, S. and Kuhs, W. F.},



journal = {Acta Cryst. B},


pages = {644--648},
publisher = {International Union of Crystallography},
title = {{Lattice constants and thermal expansion of H$\backslash$sb 2O and D$\backslash$sb 2O ice Ih between 10 and 265 K}},

volume = {50},
year = {1994}
}
@article{gres+80ssc,
author = {Grest, G S and Nagel, S R and Rahman, A},

journal = {Sol. St. Comm.},

pages = {875--879},
title = {{Quench echoes in molecular dynamics - A new phonon spectroscopy}},
volume = {36},
year = {1980}
}
@article{tsuc11jcp,
abstract = {Mass tensor molecular dynamics method was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy.},
author = {Tsuchida, Eiji},



journal = {J. Chem. Phys.},


pages = {44112},
pmid = {21280692},
title = {{Ab initio mass tensor molecular dynamics.}},

volume = {134},
year = {2011}
}
@article{good+08pnas,
abstract = {Silver(I) hexacyanocobaltate(III), Ag3[Co(CN)6], shows a large negative linear compressibility (NLC, linear expansion under hydrostatic pressure) at ambient temperature at all pressures up to our experimental limit of 7.65(2) GPa. This behavior is qualitatively unaffected by a transition at 0.19 GPa to a new phase Ag3[Co(CN)6]-II, whose structure is reported here. The high-pressure phase also shows anisotropic thermal expansion with large uniaxial negative thermal expansion (NTE, expansion on cooling). In both phases, the NLC/NTE effect arises as the rapid compression/contraction of layers of silver atoms{\{}---{\}}weakly bound via argentophilic interactions{\{}---{\}}is translated via flexing of the covalent network lattice into an expansion along a perpendicular direction. It is proposed that framework materials that contract along a specific direction on heating while expanding macroscopically will, in general, also expand along the same direction under hydrostatic pressure while contracting macroscopically.},
author = {Goodwin, Andrew L and Keen, David A and Tucker, Matthew G},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {18708--18713},
title = {{Large negative linear compressibility of Ag3[Co(CN)6]}},
volume = {105},
year = {2008}
}
@article{dong+01sp,
author = {Dongarra, J and Eijkhout, V and Luszczek, P},

journal = {Scientific Programming},

pages = {51--60},
title = {{Recursive approach in sparse matrix LU factorization}},

volume = {9},
year = {2001}
}
@article{trou-mart91prb,
annote = {
        

        From Duplicate 2 ( 
        

        
          

          Efficient pseudopotentials for plane-wave calculations
          

        
        

         - Troullier, N; Martins, J L )

          

        
        

        

        

        

        

        

        

      },
author = {Troullier, N. and Martins, Jos{\'{e}} Luriaas},



journal = {Phys. Rev. B},


pages = {1993--2006},
publisher = {APS},
title = {{Efficient pseudopotentials for plane-wave calculations}},

volume = {43},
year = {1991}
}
@article{ceri+07pre,
author = {Ceriotti, Michele and Bussi, Giovanni and Parrinello, Michele},



journal = {Phys. Rev. E},


pages = {26707},
title = {{Conjugate gradient heat bath for ill-conditioned actions}},

volume = {76},
year = {2007}
}
@article{ters89prb,
author = {Tersoff, J},
journal = {Phys. Rev. B},

pages = {5566--5568},
publisher = {American Physical Society},
title = {{Modeling solid-state chemistry: Interatomic potentials for multicomponent systems}},
volume = {39},
year = {1989}
}
@article{ette90acr,
author = {Etter, Margaret C.},



journal = {Acc. Chem. Res.},

mendeley-tags = {graph theory,hydrogen bond},


pages = {120--126},
title = {{Encoding and decoding hydrogen-bond patterns of organic compounds}},

volume = {23},
year = {1990}
}
@article{neyt+12jctc,
abstract = {Uniform acceptance force biased Monte Carlo (UFMC) simulations have previously been shown to be a powerful tool to simulate atomic scale processes, enabling one to follow the dynamical path during the simulation. In this contribution, we present a simple proof to demonstrate that this uniform acceptance still complies with the condition of detailed balance, on the condition that the characteristic parameter ? = 1/2 and that the maximum allowed step size is chosen to be sufficiently small. Furthermore, the relation to Metropolis Monte Carlo (MMC) is also established, and it is shown that UFMC reduces to MMC by choosing the characteristic parameter ? = 0 [Rao, M. et al. Mol. Phys.1979, 37, 1773]. Finally, a simple example compares the UFMC and MMC methods.},
author = {Neyts, E. C. and Thijsse, B. J. and Mees, M. J. and Bal, K. M. and Pourtois, G.},


isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},
pages = {1865--1869},
title = {{Establishing uniform acceptance in force biased Monte Carlo simulations}},
volume = {8},
year = {2012}
}
@article{lim+06prb,
author = {Lim, F C H and Tok, E S and Kang, H C},

journal = {Phys. Rev. B},

pages = {205333},
publisher = {APS},
title = {{Decomposition of SiH3 to SiH2 on Si (100)-(2{\{}$\backslash$times{\}}1)}},
volume = {74},
year = {2006}
}
@article{schm+05jcp,
abstract = {In the context of vibrational spectroscopy in liquids, non-Condon effects refer to the dependence of the vibrational transition dipole moment of a particular molecule on the rotational and translational coordinates of all the molecules in the liquid. For strongly hydrogen-bonded systems, such as liquid water, non-Condon effects are large. That is, the bond dipole derivative of an OH stretch depends strongly on its hydrogen-bonding environment. Previous calculations of nonlinear vibrational spectroscopy in liquids have not included these non-Condon effects. We find that for water, inclusion of these effects is important for an accurate calculation of, for example, homodyned and heterodyned three-pulse echoes. Such echo experiments have been "inverted" to obtain the OH stretch frequency time-correlation function, but by necessity the Condon and other approximations are made in this inversion procedure. Our conclusion is that for water, primarily because of strong non-Condon effects, this inversion may not lead to the correct frequency time-correlation function. Nevertheless, one can still make comparison between theory and experiment by calculating the experimental echo observables themselves.},
author = {Schmidt, J R and Corcelli, S a and Skinner, J L},



journal = {J. Chem. Phys.},



pages = {044513},
pmid = {16095375},
title = {{Pronounced non-Condon effects in the ultrafast infrared spectroscopy of water.}},

volume = {123},
year = {2005}
}
@article{pric+99prb,
author = {Price, R W and Tok, E S and Zhang, J},

journal = {Phys. Rev. B},

pages = {5292--5295},
publisher = {APS},
title = {{Probing the disilane adsorption kinetics: An alternative approach}},
volume = {59},
year = {1999}
}
@article{nava+14pre,
author = {Nava, Marco and Ceriotti, Michele and Dryzun, Chaim and Parrinello, Michele},



journal = {Phys. Rev. E},


pages = {023302},
title = {{Evaluating functions of positive-definite matrices using colored-noise thermostats}},

volume = {89},
year = {2014}
}
@article{hube+94jcamd,
abstract = {The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.},
author = {Huber, T and Torda, a E and van Gunsteren, W F},


journal = {Journal of computer-aided molecular design},



pages = {695--708},
pmid = {7738605},
title = {{Local elevation: a method for improving the searching properties of molecular dynamics simulation.}},

volume = {8},
year = {1994}
}
@article{kaji+17sr,
author = {Kajita, Seiji and Ohba, Nobuko and Jinnouchi, Ryosuke and Asahi, Ryoji},



journal = {Scientific Reports},

pages = {1--9},
publisher = {Springer US},
title = {{A Universal 3D Voxel Descriptor for Solid-State Material Informatics with Deep Convolutional Neural Networks}},

volume = {7},
year = {2017}
}
@article{skin97jcp,
author = {Skinner, J. L.},



journal = {J. Chem. Phys.},

pages = {8717},
title = {{Semiclassical approximations to golden rule rate constants}},

volume = {107},
year = {1997}
}
@article{zwan61pr,
author = {Zwanzig, Robert},



journal = {Phys. Rev.},


pages = {983--992},
publisher = {APS},
title = {{Memory Effects in Irreversible Thermodynamics}},

volume = {124},
year = {1961}
}
@article{henc-irud10jpcb,
abstract = {A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of liquid water. We demonstrate the robustness of this hydrogen-bond definition versus the many other definitions which use fixed, arbitrary parameters, do not account for variable molecular environments, and cannot effectively resolve transition states. Our topology definition unambiguously shows that most water molecules are double acceptors but sizable proportions are single or triple acceptors. Almost all hydrogens are found to take part in hydrogen bonds. Broken hydrogen bonds only form when two molecules try to form two hydrogen bonds between them. The double acceptors have tetrahedral geometry, lower potential energy, entropy, and density, and slower dynamics. The single and triple acceptors have trigonal and trigonal bipyramidal geometry and when considered together have higher density, potential energy, and entropy, faster dynamics, and a tendency to cluster. These calculations use an extended theory for the entropy of liquid water that takes into account the variable number of hydrogen bonds. Hydrogen-bond switching is shown to depend explicitly on the variable number of hydrogen bonds accepted and the presence of interstitial water molecules. Transition state theory indicates that the switching of hydrogen bonds is a mildly activated process, requiring only a moderate distortion of hydrogen bonds. Three main types of switching events are observed depending on whether the donor and acceptor are already sharing a hydrogen bond. The switch may proceed with no intermediate or via a bifurcated-oxygen or cyclic dimer, both of which have a broken hydrogen bond and symmetric and asymmetric forms. Switching is found to be strongly coupled to whole-molecule vibration, particularly for the more mobile single and triple acceptors. Our analysis suggests that even though water is heterogeneous in terms of the number of hydrogen bonds, the coupling between neighbors on various length and time scales brings about greater continuity in its properties.},
author = {Henchman, Richard H. and Irudayam, Sheeba Jem},


isbn = {1520-5207},

journal = {J. Phys. Chem. B},

pages = {16792--16810},
pmid = {21114302},
title = {{Topological hydrogen-bond definition to characterize the structure and dynamics of liquid water}},
volume = {114},
year = {2010}
}
@article{berg+07prb,
author = {Bergmann, U. and Nordlund, D. and Wernet, Ph and Odelius, M. and Pettersson, L. G M and Nilsson, A.},


isbn = {1098-0121},

journal = {Phys. Rev. B},


pages = {024202},
title = {{Isotope effects in liquid water probed by x-ray Raman spectroscopy}},

volume = {76},
year = {2007}
}
@article{pals-mano98prb,
author = {Palser, A H R and Manolopoulos, D E},

journal = {Phys. Rev. B},

pages = {12704--12711},
publisher = {APS},
title = {{Canonical purification of the density matrix in electronic-structure theory}},
volume = {58},
year = {1998}
}
@article{duan+87plb,
author = {Duane, Simon and Kennedy, AD D and Pendleton, Brian J. and Roweth, Duncan},



journal = {Phys. Lett. B},


pages = {216--222},
title = {{Hybrid Monte Carlo}},

volume = {195},
year = {1987}
}
@article{schm-voth99jcp,
author = {Schmitt, Udo W. and Voth, Gregory A.},



journal = {J. Chem. Phys.},

pages = {9361},
title = {{The computer simulation of proton transport in water}},

volume = {111},
year = {1999}
}
@article{FamilyName1-AbbrevJournalName-year,
author = {FamilyName1, FirstName1 and FamilyName2, FirstName2 and FamilyName3, FirstName3},
pages = {first page},
title = {{Title of article}},
volume = {volume}
}
@book{schu96book,
author = {Schulman, L S},
isbn = {9780471166108},
publisher = {John Wiley},
series = {Wiley classics library},
title = {{Techniques and applications of path integration}},
year = {1996}
}
@article{mats04jjap,
author = {Matsuda, Akihisa},



journal = {Jpn. J. Appl. Phys.},



pages = {7909},
title = {{Thin-Film Silicon - Growth Process and Solar Cell Application}},

volume = {43},
year = {2004}
}
@article{sort+13jpcc,
author = {Sorte, Eric G and Bowman, Robert C and Majzoub, Eric H and Verkuijlen, Margriet H W and Udovic, Terrence J and Conradi, Mark S},



journal = {J. Phys. Chem. C},


pages = {8105--8113},
title = {{Mobile Species in NaAlH 4}},

volume = {117},
year = {2013}
}
@article{jerr+04jacm,
abstract = {We present a polynomial-time randomized algorithm for estimating the permanent of an arbitrary n x n matrix with nonnegative entries. This algorithm--technically a "fully-polynomial randomized approximation scheme"--computes an approximation that is, with high probability, within arbitrarily small specified relative error of the true value of the permanent.ABSTRACT FROM AUTHOR},
archivePrefix = {arXiv},
arxivId = {arXiv:1210.6463},
author = {Jerrum, Mark and Sinclair, Alistair and Vigoda, Eric},



isbn = {0219477507},

journal = {Journal of the ACM},

pages = {671--697},
title = {{A polynomial-time approximation algorithm for the permanent of a matrix with nonnegative entries}},
volume = {51},
year = {2004}
}
@misc{parr-rahm82book,
annote = {M. Parrinello and A. Rahman, in Monte Carlo Methods in Quantum Problems, edited by M. H. Kalos (Reidel, Dordrecht, 1984), page 105.},
title = {{No Title}}
}
@article{reit+06prl,
author = {Reiter, G. and Burnham, C. and Homouz, D. and Platzman, P. and Mayers, J. and Abdul-Redah, T. and Moravsky, A. and Li, J. and Loong, C.-K. and Kolesnikov, A.},



journal = {Phys. Rev. Lett.},


pages = {247801},
title = {{Anomalous Behavior of Proton Zero Point Motion in Water Confined in Carbon Nanotubes}},

volume = {97},
year = {2006}
}
@article{hoan+12prb,
author = {Hoang, Khang and Janotti, Anderson and {Van de Walle}, Chris G.},



journal = {Phys. Rev. B},


pages = {064115},
title = {{Mechanisms for the decomposition and dehydrogenation of Li amide/imide}},

volume = {85},
year = {2012}
}
@article{guid+09jctc,
author = {Guidon, Manuel and Hutter, Jürg and VandeVondele, Joost},



journal = {J. Chem. Theory Comput.},


pages = {3010--3021},
title = {{Robust Periodic Hartree−Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets}},

volume = {5},
year = {2009}
}
@article{kuhn55nrlq,
author = {Kuhn, H. W.},


journal = {Naval Research Logistics Quarterly},


pages = {83--97},
title = {{The Hungarian method for the assignment problem}},

volume = {2},
year = {1955}
}
@article{delb+13jpcl,
abstract = {MP2 provides a good description of hydrogen bonding in water clusters and includes long-range dispersion interactions without the need to introduce empirical elements in the description of the interatomic potential. To assess its performance for bulk liquid water under ambient conditions, an isobaric?isothermal (NpT) Monte Carlo simulation at the second-order M?ller?Plesset perturbation theory level (MP2) has been performed. The obtained value of the water density is excellent (1.02 g/mL), and the calculated radial distribution functions are in fair agreement with experimental data. The MP2 results are compared to a few density functional approximations, including semilocal functionals, hybrid functionals, and functionals including empirical dispersion corrections. These results demonstrate the feasibility of directly sampling the potential energy surface of condensed-phase systems using correlated wave function theory, and their quality paves the way for further applications.},
author = {{Del Ben}, Mauro and Sch{\"{o}}nherr, Mandes and Hutter, J{\"{u}}rg and Vandevondele, Joost},



journal = {J. Phys. Chem. Letters},


pages = {3753--3759},
title = {{Bulk liquid water at ambient temperature and pressure from mp2 theory}},

volume = {4},
year = {2013}
}
@article{dese-holm98jcp,
abstract = {Standard Ewald sums, which calculate, e.g., the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the fast Fourier transformation (FFT). In this article we investigate three algorithms for the FFT-accelerated Ewald sum, which have attracted widespread attention, namely, the so-called particle–particle–particle mesh (P3M), particle mesh Ewald (PME), and smooth PME method. We present a unified view of the underlying techniques and the various ingredients which comprise those routines. Additionally, we offer detailed accuracy measurements, which shed some light on the influence of several tuning parameters and also show that the existing methods — although similar in spirit — exhibit remarkable differences in accuracy. We propose a set of combinations of the individual components, mostly relying on the P3M approach, that we regard to be the most flexible. The issue of estimating the errors connected with particle mesh routines is reserved to paper II},
archivePrefix = {arXiv},
arxivId = {cond-mat/9807099},
author = {Deserno, Markus and Holm, Christian},



isbn = {doi:10.1063/1.477415},

journal = {J. Chem. Phys.},

pages = {7678},
primaryClass = {cond-mat},
title = {{How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines}},

volume = {109},
year = {1998}
}
@article{kuhn+09jctc,
abstract = {Using the recently developed Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics (Kuhne, T. D.; et al. Phys. Rev. Lett. 2007, 98, 066401.), we assess the accuracy of ab initio molecular dynamics at the semilocal density functional level of theory to describe structural and dynamic properties of liquid water at ambient conditions. We have performed a series of large-scale simulations using a number of parameter-free exchange and correlation functionals, to minimize and investigate the influence of finite size effects as well as statistical errors. We find that finite size effects in structural properties are rather small and, given an extensive sampling, reproducible. On the other hand, the influence of finite size effects on dynamical properties are much larger than generally appreciated. So much so that the infinite size limit is practically out of reach. However, using a finite size scaling procedure, thanks to the greater effectiveness of our new method we can estimate both the thermodynamic value of the diffusion coefficient and the shear viscosity. The hydrogen bond network structure and its kinetics are consistent with the conventional view of tetrahedrally coordinated water.},
author = {K{\"{u}}hne, Thomas D. and Krack, Matthias and Parrinello, Michele},


isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},
pages = {235--241},
title = {{Static and dynamical properties of liquid water from first principles by a novel car-parrinello-like approach}},

volume = {5},
year = {2009}
}
@article{prod-kohn05pnas,
author = {Prodan, E and Kohn, W},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {11635--11638},
title = {{Nearsightedness of electronic matter}},

volume = {102},
year = {2005}
}
@article{derz-pfef65jstor,
author = {Url, Stable and Society, American Mathematical and Archive, The Jstor and Derzko, N A and Pfeffer, A M},

journal = {Math. Comput.},

pages = {62--67},
publisher = {JSTOR},
title = {{Bounds for the Spectral Radius of a Matrix}},
volume = {19},
year = {1965}
}
@article{piet-mart15jcp,
abstract = {Systematically resolving different crystalline phases starting from the atomic positions, a mandatory step in algorithms for the prediction of structures or for the simulation of phase transitions, can be a non-trivial task. Extending to amorphous phases and liquids which lack the discrete symmetries, the problem becomes even more difficult, involving subtle topological differences at medium range that, however, are crucial to the physico-chemical and spectroscopic properties of the corresponding materials. Typically, system-tailored order parameters are devised, like global or local symmetry indicators, ring populations, etc. We show that a recently introduced metric provides a simple and general solution to this intricate problem. In particular, we demonstrate that a map can be traced displaying distances among water phases, including crystalline as well as amorphous states and the liquid, consistently with experimental knowledge in terms of phase diagram, structural features, and preparation routes.},
author = {Pietrucci, Fabio and Martoň{\'{a}}k, Roman},



journal = {J. Chem. Phys.},

pmid = {25770554},
title = {{Systematic comparison of crystalline and amorphous phases: Charting the landscape of water structures and transformations}},
volume = {142},
year = {2015}
}
@article{tuck+93jcp,
annote = {From Duplicate 2 ( 




















Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals




















- Tuckerman, Mark E; Berne, Bruce J; Martyna, Glenn J; Klein, Michael L )







},
author = {Tuckerman, Mark E. and Berne, Bruce J. and Martyna, Glenn J. and Klein, Michael L.},



journal = {J. Chem. Phys.},

pages = {2796},
publisher = {AIP},
title = {{Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals}},

volume = {99},
year = {1993}
}
@article{ross+14jcp,
abstract = {Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual differences, practical implementations of these methods differ in just two respects: the choice of the Parrinello-Rahman mass matrix and whether or not a thermostat is applied to the internal modes of the ring polymer during the dynamics. Here, we explore a method which is halfway between the two approximations: we keep the path integral bead masses equal to the physical particle masses but attach a Langevin thermostat to the internal modes of the ring polymer during the dynamics. We justify this by showing analytically that the inclusion of an internal mode thermostat does not affect any of the established features of RPMD: thermostatted RPMD is equally valid with respect to everything that has actually been proven about the method as RPMD itself. In particular, because of the choice of bead masses, the resulting method is still optimum in the short-time limit, and the transition state approximation to its reaction rate theory remains closely related to the semiclassical instanton approximation in the deep quantum tunneling regime. In effect, there is a continuous family of methods with these properties, parameterised by the strength of the Langevin friction. Here, we explore numerically how the approximation to quantum dynamics depends on this friction, with a particular emphasis on vibrational spectroscopy. We find that a broad range of frictions approaching optimal damping give similar results, and that these results are immune to both the resonance problem of RPMD and the curvature problem of CMD.},
author = {Rossi, Mariana and Ceriotti, Michele and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {234116},
pmid = {24952532},
title = {{How to remove the spurious resonances from ring polymer molecular dynamics.}},

volume = {140},
year = {2014}
}
@article{tobi+93jpc,
author = {Tobias, D J and Martyna, G J and Klein, M L},

journal = {J. Phys. Chem.},

pages = {12959--12966},
publisher = {American Chemical Society},
title = {{Molecular dynamics simulations of a protein in the canonical ensemble}},
volume = {97},
year = {1993}
}
@article{shel15jcp,
abstract = {Strong short-range intermolecular interactions result in position and orientation correlations between nearest neighbour molecules in isotropic liquids, and it is generally assumed that such correlations extend at most a few molecular diameters. This assumption is contradicted by results from second harmonic light scattering experiments presented here, which reveal long-range orientation correlations in several isotropic liquids including water. These experiments measure the polarization dependence of the scattered light, and the observations are interpreted in terms of transverse and longitudinal polar collective modes, as well as simple explicit models. The results revise our understanding of the structure of molecular liquids and provide a test of computational simulations.},
author = {Shelton, David P.},



journal = {J. Chem. Phys.},


pages = {134503},
pmid = {22299887},
title = {{Long-range orientation correlation in dipolar liquids probed by hyper-Rayleigh scattering}},

volume = {143},
year = {2015}
}
@article{fisc+06natm,
abstract = {Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.},
author = {Fischer, Christopher C and Tibbetts, Kevin J and Morgan, Dane and Ceder, Gerbrand},



journal = {Nature materials},


pages = {641--6},
pmid = {16845417},
title = {{Predicting crystal structure by merging data mining with quantum mechanics.}},

volume = {5},
year = {2006}
}
@article{lech+11pr,
abstract = {For the homogeneous crystal nucleation process in a soft-core colloid model, we identify optimal reaction coordinates from a set of novel order parameters based on the local structure within the nucleus, by employing transition path sampling techniques combined with a likelihood maximization of the committor function. We find that nucleation is governed by solid clusters that consist of an hcp core embedded within a cloud of surface particles that are highly correlated with their nearest neighbors but not ordered in a high-symmetry crystal structure. The results shed new light on the interpretation of the surface and volume terms in classical nucleation theory.},
author = {Lechner, Wolfgang and Dellago, Christoph and Bolhuis, Peter G.},


isbn = {1079-7114 (Electronic){\$}\backslash{\$}r0031-9007 (Linking)},

journal = {Phys. Rev. Lett.},

pages = {1--4},
pmid = {21405585},
title = {{Role of the prestructured surface cloud in crystal nucleation}},
volume = {106},
year = {2011}
}
@book{cox-cox10boox,
author = {Cox, Trevor F and Cox, Michael A A},
publisher = {CRC Press},
title = {{Multidimensional scaling}},
year = {2010}
}
@article{ghir+15prl,
author = {Ghiringhelli, Luca M. and Vybiral, Jan and Levchenko, Sergey V. and Draxl, Claudia and Scheffler, Matthias},


journal = {Phys. Rev. Lett.},


pages = {105503},
title = {{Big Data of Materials Science: Critical Role of the Descriptor}},

volume = {114},
year = {2015}
}
@article{hart+11nature,
abstract = {For decades, the source of Earth's volatiles, especially water with a deuterium-to-hydrogen ratio (D/H) of (1.558 ± 0.001) × 10(-4), has been a subject of debate. The similarity of Earth's bulk composition to that of meteorites known as enstatite chondrites suggests a dry proto-Earth with subsequent delivery of volatiles by local accretion or impacts of asteroids or comets. Previous measurements in six comets from the Oort cloud yielded a mean D/H ratio of (2.96 ± 0.25) × 10(-4). The D/H value in carbonaceous chondrites, (1.4 ± 0.1) × 10(-4), together with dynamical simulations, led to models in which asteroids were the main source of Earth's water, with ≤10 per cent being delivered by comets. Here we report that the D/H ratio in the Jupiter-family comet 103P/Hartley 2, which originated in the Kuiper belt, is (1.61 ± 0.24) × 10(-4). This result substantially expands the reservoir of Earth ocean-like water to include some comets, and is consistent with the emerging picture of a complex dynamical evolution of the early Solar System.},
author = {Hartogh, Paul and Lis, Dariusz C and Bockel{\'{e}}e-Morvan, Dominique and de Val-Borro, Miguel and Biver, Nicolas and K{\"{u}}ppers, Michael and Emprechtinger, Martin and Bergin, Edwin a and Crovisier, Jacques and Rengel, Miriam and Moreno, Raphael and Szutowicz, Slawomira and Blake, Geoffrey a},



journal = {Nature},

mendeley-tags = {isotope fractionation},


pages = {218--220},
pmid = {21976024},
title = {{Ocean-like water in the Jupiter-family comet 103P/Hartley 2.}},

volume = {478},
year = {2011}
}
@article{gill+13jcp,
abstract = {Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for cluster, solid, and liquid forms of water. Recent work has stressed the importance of DFT errors in describing dispersion, but we note that errors in other parts of the energy may also contribute. We obtain information about the nature of DFT errors by using a many-body separation of the total energy into its 1-body, 2-body, and beyond-2-body components to analyze the deficiencies of the popular PBE and BLYP approximations for the energetics of water clusters and ice structures. The errors of these approximations are computed by using accurate benchmark energies from the coupled-cluster technique of molecular quantum chemistry and from quantum Monte Carlo calculations. The systems studied are isomers of the water hexamer cluster, the crystal structures Ih, II, XV, and VIII of ice, and two clusters extracted from ice VIII. For the binding energies of these systems, we use the machine-learning technique of Gaussian Approximation Potentials to correct successively for 1-body and 2-body errors of the DFT approximations. We find that even after correction for these errors, substantial beyond-2-body errors remain. The characteristics of the 2-body and beyond-2-body errors of PBE are completely different from those of BLYP, but the errors of both approximations disfavor the close approach of non-hydrogen-bonded monomers. We note the possible relevance of our findings to the understanding of liquid water.},
archivePrefix = {arXiv},
arxivId = {arXiv:1303.0751v1},
author = {Gillan, M. J. and Alf{\`{e}}, D. and Bart{\'{o}}k, a. P. and Cs{\'{a}}nyi, G.},



isbn = {0021-9606},

journal = {J. Chem. Phys.},


pages = {244504},
pmid = {24387379},
title = {{First-principles energetics of water clusters and ice: A many-body analysis}},

volume = {139},
year = {2013}
}
@article{zhu+16jcp,
author = {Zhu, Li and Amsler, Maximilian and Fuhrer, Tobias and Schaefer, Bastian and Faraji, Somayeh and Rostami, Samare and Ghasemi, S Alireza and Sadeghi, Ali and Grauzinyte, Migle and Wolverton, Chris and Goedecker, Stefan},


journal = {J. Chem. Phys.},


pages = {034203},
title = {{A fingerprint based metric for measuring similarities of crystalline structures}},

volume = {144},
year = {2016}
}
@article{ani13aa,
author = {Anick, David J.},



journal = {AIP Advances},

mendeley-tags = {ice amorphous},

pages = {42119},
title = {{Atypical water lattices and their possible relevance to the amorphous ices: A density functional study}},

volume = {3},
year = {2013}
}
@article{habe+13arpc,
abstract = {This article reviews the ring-polymer molecular dynamics model for condensed-phase quantum dynamics. This model, which involves classical evolution in an extended ring-polymer phase space, provides a practical approach to approximating the effects of quantum fluctuations on the dynamics of condensed-phase systems. The review covers the theory, implementation, applications, and limitations of the approximation.},
author = {Habershon, Scott and Manolopoulos, David E and Markland, Thomas E and Miller, Thomas F},


isbn = {0404121101},

journal = {Annual review of physical chemistry},


pages = {387--413},
pmid = {23298242},
title = {{Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space.}},

volume = {64},
year = {2013}
}
@inproceedings{marx-hutt00proc,
address = {J{\{}{\"{u}}{\}}lich, Germany},
author = {Marx, D and Hutter, J},
booktitle = {Modern Methods and Algorithms of Quantum Chemistry},
editor = {Grotendorst, J},

pages = {301--449},
publisher = {NIC Series},
title = {{Ab initio molecular dynamics: theory and implementation}},
volume = {1},
year = {2000}
}
@article{nong+17prb,
author = {Artrith, Nongnuch and Urban, Alexander and Ceder, Gerbrand},


journal = {Phys. Rev. B},


pages = {014112},
title = {{Efficient and accurate machine-learning interpolation of atomic energies in compositions with many species}},

volume = {96},
year = {2017}
}
@article{mark-bern12pnas,
author = {Markland, T E and Berne, B J},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {7988--7991},
publisher = {National Acad Sciences},
title = {{Unraveling quantum mechanical effects in water using isotopic fractionation}},
volume = {109},
year = {2012}
}
@article{darv+09pnas,
abstract = {The Mori{\{}--{\}}Zwanzig formalism is an effective tool to derive differential equations describing the evolution of a small number of resolved variables. In this paper we present its application to the derivation of generalized Langevin equations and generalized non-Markovian Fokker{\{}--{\}}Planck equations. We show how long time scales rates and metastable basins can be extracted from these equations. Numerical algorithms are proposed to discretize these equations. An important aspect is the numerical solution of the orthogonal dynamics equation which is a partial differential equation in a high dimensional space. We propose efficient numerical methods to solve this orthogonal dynamics equation. In addition, we present a projection formalism of the Mori{\{}--{\}}Zwanzig type that is applicable to discrete maps. Numerical applications are presented from the field of Hamiltonian systems. },
author = {Darve, Eric and Solomon, Jose and Kia, Amirali},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {10884--10889},
title = {{Computing generalized Langevin equations and generalized Fokker{\{}--{\}}Planck equations}},
volume = {106},
year = {2009}
}
@article{vanl79ieee,
author = {{Van Loan}, Charles},

journal = {IEEE Trans. Autom. Contr.},

pages = {320--321},
title = {{A Note on the Evaluation of Matrix Polynomials}},
volume = {24},
year = {1979}
}
@article{andr+16jpcl,
author = {Andreani, Carla and Romanelli, Giovanni and Senesi, Roberto},



journal = {J. Phys. Chem. Letters},

pages = {2216--2220},
title = {{Direct Measurements of Quantum Kinetic Energy Tensor in Stable and Metastable Water near the Triple Point: An Experimental Benchmark}},
volume = {7},
year = {2016}
}
@article{kata+12langmuir,
abstract = {The systematic control over surface chemistry is a long-standing challenge in biomedical and nanotechnological applications for graphitic materials. As a novel approach, we utilize graphite-binding dodecapeptides that self-assemble into dense domains to form monolayer-thick long-range-ordered films on graphite. Specifically, the peptides are rationally designed through their amino acid sequences to predictably display hydrophilic and hydrophobic characteristics while maintaining their self-assembly capabilities on the solid substrate. The peptides are observed to maintain a high tolerance for sequence modification, allowing control over surface chemistry via their amino acid sequence. Furthermore, through a single-step coassembly of two differently designed peptides, we predictably and precisely tune the wettability of the resulting functionalized graphite surfaces from 44° to 83°. The modular molecular structures and predictable behavior of short peptides demonstrated here give rise to a novel platform for functionalizing graphitic materials that offers numerous advantages, including noninvasive modification of the substrate, biocompatible processing in an aqueous environment, and simple fusion with other functional biological molecules.},
author = {Khatayevich, Dmitriy and So, Christopher R and Hayamizu, Yuhei and Gresswell, Carolyn and Sarikaya, Mehmet},



journal = {Langmuir : the ACS Journal of surfaces and colloids},



pages = {8589--93},
pmid = {22428620},
title = {{Controlling the surface chemistry of graphite by engineered self-assembled peptides.}},

volume = {28},
year = {2012}
}
@article{paes13jpcc,
author = {Paesani, Francesco},



journal = {J. Phys. Chem. C},


pages = {130827131917004},
title = {{Molecular Mechanisms of Water-Mediated Proton Transport in MIL-53 Metal-Organic Frameworks}},

volume = {3},
year = {2013}
}
@article{gupt+88prb,
author = {Gupta, P and Colvin, V L and George, S M},


journal = {Phys. Rev. B},

pages = {8234--8243},
publisher = {American Physical Society},
title = {{Hydrogen desorption kinetics from monohydride and dihydride species on silicon surfaces}},
volume = {37},
year = {1988}
}
@article{flan-oate91arms,
author = {Flanagan, T B and Oates, W A},



journal = {Annual Review of Materials Science},


pages = {269--304},
publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA},
title = {{The Palladium-Hydrogen System}},

volume = {21},
year = {1991}
}
@article{scho+98nc,
abstract = {A new method for performing a nonlinear form of principal component analysis is proposed. By the use of integral operator kernel functions, one can efficiently compute principal components in high-dimensional feature spaces, related to input space by some nonlinear map—for instance, the space of all possible five-pixel products in 16 × 16 images. We give the derivation of the method and present experimental results on polynomial feature extraction for pattern recognition.},
author = {Sch{\"{o}}lkopf, Bernhard and Smola, Alexander and M{\"{u}}ller, Klaus-Robert},


isbn = {08997667 (ISSN)},

journal = {Neural Computation},

pages = {1299--1319},
pmid = {21939901},
title = {{Nonlinear Component Analysis as a Kernel Eigenvalue Problem}},
volume = {10},
year = {1998}
}
@incollection{thur12siam,
address = {Philadelphia, PA},
author = {Thurau, Christian and Kersting, Kristian and Bauckhage, Christian},
booktitle = {Proceedings of the 2012 SIAM International Conference on Data Mining},



pages = {684--695},
publisher = {Society for Industrial and Applied Mathematics},
title = {{Deterministic CUR for Improved Large-Scale Data Analysis: An Empirical Study}},

year = {2012}
}
@article{huan-wang07laa,
author = {Huang, T and Wang, L},

journal = {Linear Algebra and its Applications},
pages = {841--854},
title = {{Improving bounds for eigenvalues of complex matrices using traces}},
volume = {426},
year = {2007}
}
@article{brow-dore98jcp,
author = {{Robinson Brown}, A and Doren, D J and Brown, A Robinson},

journal = {J. Chem. Phys.},

pages = {2442},
publisher = {AIP},
title = {{Energetics of silicon hydrides on the Si (100)-(2$\backslash$times 1) surface}},
volume = {109},
year = {1998}
}
@article{pren95prb,
author = {Prencipe, M and Zupan, A and Dovesi, R and Apr{\`{a}}, E. and Saunders, VR R},



journal = {Phys. Rev. B},


pages = {3391--3396},
publisher = {American Physical Society},
title = {{Ab initio study of the structural properties of LiF, NaF, KF, LiCl, NaCl, and KCl}},

volume = {51},
year = {1995}
}
@article{raus+09jctc,
author = {Rauscher, Sarah and Neale, Chris and Pomès, Régis},



journal = {J. Chem. Theory Comput.},


pages = {2640--2662},
title = {{Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling}},

volume = {5},
year = {2009}
}
@article{ceri+09proc,
abstract = {In a recent paper we have suggested that the finite temperature density matrix can be computed efficiently by a combination of polynomial expansion and iterative inversion techniques. We present here significant improvements over this scheme. The original complex-valued formalism is turned into a purely real one. In addition, we use Chebyshev polynomials expansion and fast summation techniques. This drastically reduces the scaling of the algorithm with the width of the Hamiltonian spectrum, which is now of the order of the cubic root of such parameter. This makes our method very competitive for applications to ab-initio simulations, when high energy resolution is required. {\textcopyright} 2009 American Institute of Physics.},
author = {Ceriotti, Michele and K{\"{u}}hne, Thomas D T.D. and Parrinello, Michele and Kiihne, Thomas D},

editor = {Maroulis, George and Simos, Theodore E},

isbn = {9780735406858},

journal = {AIP Conference Proceedings},


pages = {658--661},
publisher = {AIP},
title = {{A Hybrid Approach to Fermi Operator Expansion}},
volume = {1148},
year = {2009}
}
@article{gree+06nm,
abstract = {The pace of materials discovery for heterogeneous catalysts and electrocatalysts could, in principle, be accelerated by the development of efficient computational screening methods. This would require an integrated approach, where the catalytic activity and stability of new materials are evaluated and where predictions are benchmarked by careful synthesis and experimental tests. In this contribution, we present a density functional theory-based, high-throughput screening scheme that successfully uses these strategies to identify a new electrocatalyst for the hydrogen evolution reaction (HER). The activity of over 700 binary surface alloys is evaluated theoretically; the stability of each alloy in electrochemical environments is also estimated. BiPt is found to have a predicted activity comparable to, or even better than, pure Pt, the archetypical HER catalyst. This alloy is synthesized and tested experimentally and shows improved HER performance compared with pure Pt, in agreement with the computational screening results.},
author = {Greeley, Jeff and Jaramillo, Thomas F and Bonde, Jacob and Chorkendorff, I B and N{\o}rskov, Jens K},



journal = {Nature materials},


pages = {909--13},
pmid = {17041585},
title = {{Computational high-throughput screening of electrocatalytic materials for hydrogen evolution.}},

volume = {5},
year = {2006}
}
@article{hans+15jpcl,
author = {Hansen, Katja and Biegler, Franziska and Ramakrishnan, Raghunathan and Pronobis, Wiktor and von Lilienfeld, O. Anatole and M{\"{u}}ller, Klaus-Robert and Tkatchenko, Alexandre},



journal = {J. Phys. Chem. Letters},


pages = {2326--2331},
title = {{Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space}},

volume = {6},
year = {2015}
}
@article{trib+12pnas,
abstract = {When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.},
author = {Tribello, Gareth A and Ceriotti, Michele and Parrinello, Michele},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {5196--201},
pmid = {22427357},
title = {{Using sketch-map coordinates to analyze and bias molecular dynamics simulations.}},

volume = {109},
year = {2012}
}
@article{DLPOLY,
author = {Smith, W and Forester, T R and Todorov, I T and Leslie, M},
journal = {CCLRC Daresbury Lab. Daresbury, Warrington, UK},
title = {{{\{}{\{}{\}}DL-POLY{\{}{\}}{\}}}},
year = {2006}
}
@article{glie+18prb,
abstract = {We provide a definition and explicit expressions for {\$}n{\$}-body Gaussian Process (GP) kernels which can learn any interatomic interaction occurring in a physical system, up to {\$}n{\$}-body contributions, for any value of {\$}n{\$}. The series is complete, as it can be shown that the "universal approximator" squared exponential kernel can be written as a sum of {\$}n{\$}-body kernels. These recipes enable the choice of optimally efficient force models for each target system, as confirmed by extensive testing on various materials. We furthermore describe how the {\$}n{\$}-body kernels can be "mapped" on equivalent representations that provide database-size-independent predictions and are thus crucially more efficient. We explicitly carry out this mapping procedure for the first non-trivial (3-body) kernel of the series, and show that this reproduces the GP-predicted forces with {\$}\backslashtext{\{}meV/\backslashAA{\}}{\$} accuracy while being orders of magnitude faster. These results open the way to using novel force models ("M-FFs") that are computationally as fast as their corresponding standard parametrised {\$}n{\$}-body force fields, while retaining the non-parametric character, the ease of training and validation, and the accuracy of the best recently proposed machine learning potentials.},
archivePrefix = {arXiv},
arxivId = {1801.04823},
author = {Glielmo, Aldo and Zeni, Claudio and {De Vita}, Alessandro},




journal = {Phys. Rev. B},



pages = {184307},
publisher = {American Physical Society},
title = {{Efficient nonparametric {\textless}math{\textgreater} {\textless}mi{\textgreater}n{\textless}/mi{\textgreater} {\textless}/math{\textgreater} -body force fields from machine learning}},

volume = {97},
year = {2018}
}
@article{jang-voth01jcp,
author = {Jang, Seogjoo Soonmin and Voth, Gregory A},

journal = {J. Chem. Phys.},

pages = {7832--7842},
publisher = {AIP},
title = {{Applications of higher order composite factorization schemes in imaginary time path integral simulations}},
volume = {115},
year = {2001}
}
@article{shen+11prb,
author = {Sheng, H. W. and Kramer, M. J. and Cadien, A. and Fujita, T. and Chen, M. W.},



journal = {Phys. Rev. B},


pages = {134118},
title = {{Highly optimized embedded-atom-method potentials for fourteen fcc metals}},

volume = {83},
year = {2011}
}
@article{mora+13prl,
abstract = {Using first-principles molecular dynamics, we study the influence of nuclear quantum effects (NQEs) and nonlocal exchange-correlation density functionals (DFs) near molecular dissociation in liquid hydrogen. NQEs strongly influence intramolecular properties, such as bond stability, and are thus an essential part of the dissociation process. Moreover, by including DFs that account for either the self-interaction error or dispersion interactions, we find a much better description of molecular dissociation and metallization than previous studies based on classical protons and/or local or semilocal DFs. We obtain excellent agreement with experimentally measured optical properties along Hugoniot curves for precompressed states, and while we still find a first-order liquid-liquid transition at low temperatures, transition pressures are increased by more than 100 GPa.},
archivePrefix = {arXiv},
arxivId = {arXiv:1303.6671v1},
author = {Morales, Miguel A. and McMahon, Jeffrey M. and Pierleoni, Carlo and Ceperley, David M.},




journal = {Phys. Rev. Lett.},


pages = {065702},
pmid = {23432276},
title = {{Nuclear Quantum Effects and Nonlocal Exchange-Correlation Functionals Applied to Liquid Hydrogen at High Pressure}},

volume = {110},
year = {2013}
}
@article{lomm+00acb,
abstract = {A collaborative workshop was held in May 1999 at the Cambridge Crystallographic Data Centre to test how well currently available methods of crystal structure prediction perform when given only the atomic connectivity for an organic compound. A blind test was conducted on a selection of four compounds and a wide range of methodologies representing the principal computer programs currently available were used. There were 11 participants who were allowed to propose at most three structures for each compound. No program gave consistently reliable results. However, seven proposed structures were close to an experimental one and were classified as `correct'. One compound occurred in two polymorphs, but only one form was predicted correctly among the calculated structures. The basic problem with lattice energy based methods of crystal structure prediction is that many structures are found within a few kJ mol-1 of the global minimum. The fine detail of the force-field methodology and parametrization influences the energy ranking within each method. Nevertheless, present methods may be useful in providing a set of structures as possible polymorphs for a given molecular structure.},
author = {Lommerse, Jos P. M. and Motherwell, W. D. Sam and Ammon, Herman L. and Dunitz, Jack D. and Gavezzotti, Angelo and Hofmann, Detlef W. M. and Leusen, Frank J. J. and Mooij, Wijnand T. M. and Price, Sarah L. and Schweizer, Bernd and Schmidt, Martin U. and van Eijck, Bouke P. and Verwer, Paul and Williams, Donald E.},



journal = {Acta Cryst. B Structural Science},


pages = {697--714},
publisher = {International Union of Crystallography},
title = {{A test of crystal structure prediction of small organic molecules}},

volume = {56},
year = {2000}
}
@article{guil-guis98jcp,
author = {Guillot, Bertrand and Guissani, Yves},

journal = {J. Chem. Phys.},

pages = {10162--10174},
publisher = {AIP},
title = {{Quantum effects in simulated water by the Feynman{\{}--{\}}Hibbs approach}},
volume = {108},
year = {1998}
}
@article{chma+03prb,
author = {Chmaissem, O and Dabrowski, B and Kolesnik, S and Mais, J and Jorgensen, J D and Short, S},

journal = {Phys. Rev. B},

pages = {94431},
publisher = {American Physical Society},
title = {{Structural and magnetic phase diagrams of La{\_}1-xSr{\_}xMnO{\_}3 and Pr{\_}1-ySr{\_}yMnO{\_}3 }},
volume = {67},
year = {2003}
}
@article{Teilvolumen,
author = {Teilvolumen, Im},
title = {{Uber d4e von der rnolekuZarh{\%}net4schem Theorie der WUrme geforderte Bewegumg vow in ruhenden P Z ikss4ykeitem}}
}
@article{ross+16jpcl,
abstract = {The diffusion of protons and hydroxide ions along water wires provides an efficient mechanism for charge transport that is exploited by biological membrane channels and shows promise for technological applications such as fuel cells. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we focus on two aspects of this process that are often disregarded because of their high computational cost: the use of first-principles potential energy surfaces and the treatment of the nuclei as quantum particles. We consider proton and hydroxide ions in finite water wires using density functional theory augmented with an apolar cylindrical confining potential. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition that takes explicitly into account the delocalization of the charge in the Grotthus-like mechanism. We include nuclear quantum effects (NQEs) thr...},
author = {Rossi, Mariana and Ceriotti, Michele and Manolopoulos, David E.},



journal = {J. Phys. Chem. Letters},

pages = {3001--3007},
pmid = {27440483},
title = {{Nuclear Quantum Effects in H+ and OH- Diffusion along Confined Water Wires}},
volume = {7},
year = {2016}
}
@article{colu-frenk05cpc,
author = {Coluzza, Ivan and Frenkel, Daan},



journal = {Chemphyschem : a European J. Chem. Phys. and physical chemistry},


pages = {1779--83},
pmid = {16110517},
title = {{Virtual-move parallel tempering.}},

volume = {6},
year = {2005}
}
@article{beck-karp97jcp,
author = {Becker, Oren M. and Karplus, Martin},



journal = {J. Chem. Phys.},

pages = {1495},
title = {{The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics}},

volume = {106},
year = {1997}
}
@article{russ-eker96surf,
author = {Russell, N M and Ekerdt, J G},

journal = {Surf. Sci.},

pages = {51--68},
title = {{Kinetics of hydrogen desorption from germanium-covered Si(100)}},
volume = {369},
year = {1996}
}
@article{hash+03ass,
author = {Hashizume, T and Kajiyama, H and Suwa, Y and Heike, S and Matsuura, S and Nara, J and Ohno, T},

journal = {Applied Surf. Sci.},

pages = {15--18},
publisher = {Elsevier},
title = {{Adsorption of Si atom on H-terminated Si (001)-2$\backslash$times 1 surface}},
volume = {216},
year = {2003}
}
@article{coli+08prb,
author = {Colizzi, Giuseppe and Filippetti, Alessio and Cossu, Fabrizio and Fiorentini, Vincenzo},

journal = {Phys. Rev. B},

pages = {235122},
publisher = {American Physical Society},
title = {{Interplay of strain and magnetism in La{\_}1-xSr{\_}xMnO{\_}3 from first principles}},
volume = {78},
year = {2008}
}
@article{buck+05jcp,
abstract = {An algorithm is proposed for the structural optimization of periodic systems in internal (chemical) coordinates. Internal coordinates may include in addition to the usual bond lengths, bond angles, out-of-plane and dihedral angles, various "lattice internal coordinates" such as cell edge lengths, cell angles, cell volume, etc. The coordinate transformations between Cartesian (or fractional) and internal coordinates are performed by a generalized Wilson B-matrix, which in contrast to the previous formulation by Kudin et al. [J. Chem. Phys. 114, 2919 (2001)] includes the explicit dependence of the lattice parameters on the positions of all unit cell atoms. The performance of the method, including constrained optimizations, is demonstrated on several examples, such as layered and microporous materials (gibbsite and chabazite) as well as the urea molecular crystal. The calculations used energies and forces from the ab initio density functional theory plane wave method in the projector-augmented wave formalism.},
author = {Bučko, Tomáš and Hafner, Jürgen and Ángyán, János G.},


isbn = {0021-9606 (Print)$\backslash$r0021-9606 (Linking)},

journal = {J. Chem. Phys.},

pages = {124508},
pmid = {15836398},
title = {{Geometry optimization of periodic systems using internal coordinates}},

volume = {122},
year = {2005}
}
@article{souz+97prb,
author = {Souza, Ivo and Martins, Jos{\'{e}}Lu{\'{i}}s},



journal = {Phys. Rev. B},


pages = {8733--8742},
title = {{Metric tensor as the dynamical variable for variable-cell-shape molecular dynamics}},

volume = {55},
year = {1997}
}
@article{wein80arma,
author = {Weinert, Ulrich},



journal = {Archive for Rational Mechanics and Analysis},


pages = {165--196},
title = {{Spherical tensor representation}},

volume = {74},
year = {1980}
}
@article{cepe95rmp,
author = {Ceperley, D M},

journal = {Rev. Mod. Phys.},

pages = {279--355},
publisher = {American Physical Society},
title = {{Path integrals in the theory of condensed helium}},
volume = {67},
year = {1995}
}
@article{khal+10prb,
author = {Khaliullin, Rustam Z and Eshet, Hagai and K{\"{u}}hne, Thomas D and Behler, J{\"{o}}rg and Parrinello, Michele},

journal = {Phys. Rev. B},

pages = {100103},
publisher = {American Physical Society},
title = {{Graphite-diamond phase coexistence study employing a neural-network mapping of the ab initio potential energy surface}},
volume = {81},
year = {2010}
}
@article{khom+11prl,
author = {Khomyakov, P. a. and Andreoni, Wanda and Afify, N. D. and Curioni, Alessandro},



journal = {Phys. Rev. Lett.},


pages = {255502},
title = {{Large-Scale Simulations of a-Si:H: The Origin of Midgap States Revisited}},

volume = {107},
year = {2011}
}
@article{basi+17jcp,
author = {Basire, Marie and Mouhat, F{\'{e}}lix and Fraux, Guillaume and Bordage, Am{\'{e}}lie and Hazemann, Jean-Louis and Louvel, Marion and Spezia, Riccardo and Bonella, Sara and Vuilleumier, Rodolphe},



journal = {J. Chem. Phys.},


pages = {134102},
title = {{Fermi resonance in CO 2 : Mode assignment and quantum nuclear effects from first principles molecular dynamics}},

volume = {146},
year = {2017}
}
@article{tese+14jpcb,
abstract = {Poly(vinyl alcohol) (PVA) is an amphiphilic macromolecule with surfactant activity. The peculiar behavior of this polymer at the water-air interface is at the basis of its use as material for hydrated microdevices, films, and nanofibers. This work aims to investigate the behavior of PVA and water within the surface domain of highly diluted aqueous solutions by means of atomistic molecular dynamics simulations. Monodisperse atactic oligomers of 30 residues were distributed within water slabs in a vacuum box and allowed to diffuse toward the surface. After equilibration, structural features and dynamical properties of polymer chains and water in the interfacial domains were analyzed as a function of PVA surface concentration at 293 K. Surface pressure values obtained from simulations are in agreement with experimental values at corresponding polymer specific surface areas. In the explored concentration range of 6-34 {\$}\mu{\$}mol of residues/m(2), the chains display a transition between two states. At lower surface concentrations, elongated, quite rigid structures are adsorbed on the surface, whereas partially submerged globular aggregates, locally covered by thin water layers, are formed at higher surface concentrations. At PVA concentrations higher than about 20 {\$}\mu{\$}mol of residues/m(2), the percolation of chain aggregates over the interface plane produces a surface-confined polymer network with stable pores filled by water molecules. A substantial slowing of polymer and water dynamics in the interfacial domains is highlighted by the mean squared displacement time behavior of terminal residues and the interaction time of PVA-water hydrogen bonding. The diffusion coefficient of water and lifetime of hydrogen bonds between solvent molecules are halved and doubled, respectively, at the interface with the highest polymer concentration. The attenuation of water and polymer mobility concur to stabilize PVA hydrated networks in contact with air.},
author = {Tesei, Giulio and Paradossi, Gaio and Chiessi, Ester},



journal = {J. Phys. Chem.. B},


pages = {6946--6955},
pmid = {24877893},
title = {{Influence of surface concentration on poly(vinyl alcohol) behavior at the water-vacuum interface: a molecular dynamics simulation study.}},

volume = {118},
year = {2014}
}
@article{majz+05prb,
author = {Majzoub, E. and McCarty, K. and Ozoliņ{\v{s}}, V.},



journal = {Phys. Rev. B},


pages = {024118},
title = {{Lattice dynamics of NaAlH4 from high-temperature single-crystal Raman scattering and ab initio calculations: Evidence of highly stable AlH4− anions}},

volume = {71},
year = {2005}
}
@misc{EPAPS-sih3deco,
annote = {See EPAPS Document No. ----- for a movie of metadynamics trajectory, and a discussion of Brillouin-zone sampling issues.},
title = {{No Title}}
}
@article{vazq+95jced,
abstract = {The surface tension of aqueous solutions of methanol, ethanol, 1-propanol, and 2-propanol was measured over the entire concentration range at temperatures of 20-50 "C. The experimental values were correlated with temperature and with mole fraction. The maximum deviation was in both cases always less than 3{\%}.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Vazquez, Gonzalo and Alvarez, Estrella and Navaza, Jose M},



isbn = {0021-9568},

journal = {Journal of Chemical {\&} Engineering Data},


pages = {611--614},
pmid = {25246403},
title = {{Surface Tension of Alcohol Water + Water from 20 to 50 .degree.C}},

volume = {40},
year = {1995}
}
@article{wike+11pccp,
abstract = {In the supercooled regime at elevated pressure two forms of liquid water, high-density (HDL) and low-density (LDL), have been proposed to be separated by a coexistence line ending at a critical point, but a connection to water at ambient conditions has been lacking. Here we perform large-scale molecular dynamics simulations and demonstrate that the underlying potential energy surface gives a strictly bimodal characterization of the molecules at all temperatures and pressures, including the biologically and technologically important ambient regime, as spatially inhomogeneous either LDL- or HDL-like with a 3 : 1 predominance for HDL under ambient conditions. The Widom line in the supercooled regime, where maximal structural fluctuations take place, coincides with a 1 : 1 distribution. Although our results are based on molecular dynamics force-field simulations the close agreement with recent analyses of experimental X-ray spectroscopy and scattering data indicates a unified description also of real liquid water covering supercooled to ambient conditions.},
author = {Wikfeldt, K T and Nilsson, A and Pettersson, L G M},



journal = {PCCP},


pages = {19918--24},
pmid = {21915406},
title = {{Spatially inhomogeneous bimodal inherent structure of simulated liquid water.}},

volume = {13},
year = {2011}
}
@article{boet+02armr,
author = {Boettinger, W. J. and Warren, J. a. and Beckermann, C. and Karma, A.},



journal = {Annual Review of Materials Research},



pages = {163--194},
title = {{Phase-field simulation of solidification}},

volume = {32},
year = {2002}
}
@article{ford-kac87jsp,
annote = {NULL},
author = {Ford, G W and Kac, M},

journal = {J. Stat. Phys.},

pages = {803},
title = {{On the quantum langevin equation}},
volume = {46},
year = {1987}
}
@article{trib+10pnas,
abstract = {A new self-learning algorithm for accelerated dynamics, reconnaissance metadynamics, is proposed that is able to work with a very large number of collective coordinates. Acceleration of the dynamics is achieved by constructing a bias potential in terms of a patchwork of one-dimensional, locally valid collective coordinates. These collective coordinates are obtained from trajectory analyses so that they adapt to any new features encountered during the simulation. We show how this methodology can be used to enhance sampling in real chemical systems citing examples both from the physics of clusters and from the biological sciences.},
author = {Tribello, Gareth A and Ceriotti, Michele and Parrinello, Michele},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {17509--14},
pmid = {20876135},
title = {{A self-learning algorithm for biased molecular dynamics.}},

volume = {107},
year = {2010}
}
@article{binn+83prl,
abstract = {The 7 × 7 reconstruction on Si(111) was observed in real space by scanning tunneling microscopy. The experiment strongly favors a modified adatom model with 12 adatoms per unit cell and an inhomogeneously relaxed underlying top layer.},
annote = {NULL},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Binnig, G. and Rohrer, H. and Gerber, Ch and Weibel, E.},



isbn = {0031-9007},

journal = {Phys. Rev. Lett.},

pages = {120--123},
pmid = {25246403},
title = {{7 ?? 7 Reconstruction on Si(111) Resolved in Real Space}},
volume = {50},
year = {1983}
}
@article{palm+14nature,
abstract = {Liquid water's isothermal compressibility and isobaric heat capacity, and the magnitude of its thermal expansion coefficient, increase sharply on cooling below the equilibrium freezing point. Many experimental, theoretical and computational studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions. Some experimental evidence is consistent with this hypothesis, but no definitive proof of a liquid-liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently. Computer simulations are therefore crucial for exploring water's structure and behaviour in this regime, and have shown that some water models exhibit liquid-liquid transitions and others do not. However, recent work has argued that the liquid-liquid transition has been mistakenly interpreted, and is in fact a liquid-crystal transition in all atomistic models of water. Here we show, by studying the liquid-liquid transition in the ST2 model of water with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition. We follow the rearrangement of water's coordination shell and topological ring structure along a thermodynamically reversible path from the low-density liquid to cubic ice. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid-liquid transition in the ST2 model of water, and point to the separation of time scales between crystallization and relaxation as being crucial for enabling it.},
author = {Palmer, Jeremy C and Martelli, Fausto and Liu, Yang and Car, Roberto and Panagiotopoulos, Athanassios Z and Debenedetti, Pablo G},



journal = {Nature},



pages = {385--8},
pmid = {24943954},
publisher = {Nature Publishing Group},
title = {{Metastable liquid-liquid transition in a molecular model of water.}},

volume = {510},
year = {2014}
}
@article{haye+11jpca,
author = {Hayes, Robin L. and Paddison, Stephen J. and Tuckerman, Mark E.},


journal = {J. Phys. Chem. A},


pages = {6112--6124},
title = {{Proton Transport in Triflic Acid Pentahydrate Studied via Ab Initio Path Integral Molecular Dynamics}},

volume = {115},
year = {2011}
}
@article{seel+12jpcm,
abstract = {We present momentum widths and mean kinetic energies of lithium and fluorine in (7)LiF, as determined simultaneously from deep inelastic neutron scattering (DINS) measurements. Experimental data across a temperature range from 4 to 300 K are presented, and these results compared to those calculated using a quasi-harmonic density-functional approach. In all cases, measured momentum widths are seen to be within approximately 5{\%} of those calculated, despite the very low scattering cross sections of both (7)Li and (19)F. This is the first determination and comparison with theory of such simultaneous measurements for nuclei of mass {\textgreater} 4 amu, and demonstrates the implementation of the DINS method in its current form as a mass-selective neutron spectroscopy.},
author = {Seel, A G and Ceriotti, M and Edwards, P P and Mayers, J},



journal = {J. Phys. Cond. Matt. },


pages = {365401},
pmid = {22906949},
publisher = {IOP Publishing},
title = {{Simultaneous measurement of lithium and fluorine momentum in 7LiF.}},

volume = {24},
year = {2012}
}
@article{kreu+04cr,
author = {Kreuer, Klaus-Dieter and Paddison, Stephen J and Spohr, Eckhard and Schuster, Michael},


journal = {Chem. Rev.},


pages = {4637--78},
pmid = {15669165},
title = {{Transport in proton conductors for fuel-cell applications: simulations, elementary reactions, and phenomenology.}},

volume = {104},
year = {2004}
}
@article{laas+93jcp,
author = {Laasonen, K. and Sprik, M. and Parrinello, M. and Car, R.},



journal = {J. Chem. Phys.},

pages = {9080},
title = {{‘‘Ab initio'' liquid water}},

volume = {99},
year = {1993}
}
@article{ifti-scho01jcp,
abstract = {In this article, the classical potential based importance Monte Carlo sampling method of Iftimie et al. [J. Chem. Phys. 113, 4852, (2000)] is applied to an ab initio simulation of the proton transfer tautomerization reaction of malonaldehyde in an aprotic, nonpolar solvent. It is demonstrated that ad hoc bond-energy bond-order relations derived from bond evolution theory combined with Pauling's valence bond ideas can be used to construct a molecular mechanics guidance potential for the simulation of the proton transfer reaction which improves the statistics of the calculation by three orders of magnitude. The sampling method is extended to simulations in which quantum effects are treated using the imaginary time path-integral representation. A new algorithm based on multiple Markov chain theory is introduced by which it is possible to obtain very short integrated correlation lengths in calculations of quantum static correlation functions.},
author = {Iftimie, R. and Schofield, J.},


isbn = {0021-9606},

journal = {J. Chem. Phys.},

pages = {6763--6773},
title = {{Efficient ab initio sampling methods in rate constant calculations for proton-transfer reactions}},
volume = {114},
year = {2001}
}
@article{pant87prb,
author = {Pantelides, Sokrates},



journal = {Phys. Rev. B},


pages = {3479--3482},
title = {{Defect dynamics and the Staebler-Wronski effect in hydrogenated amorphous silicon}},

volume = {36},
year = {1987}
}
@article{herm-bern82jcp,
author = {Herman, M. F. and Bruskin, E J and Berne, B J},



journal = {J. Chem. Phys.},

pages = {5150},
title = {{On path integral Monte Carlo simulations}},

volume = {76},
year = {1982}
}
@article{pres38prsa,
author = {Preston, G. D.},



journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},


pages = {526--538},
title = {{The Diffraction of X-Rays by Age-Hardening Aluminium Copper Alloys}},

volume = {167},
year = {1938}
}
@article{mars-mark17jpcl,
abstract = {Understanding the reactivity and spectroscopy of aqueous solutions at the atomistic level is crucial for the elucidation and design of chemical processes. However, the simulation of these systems requires addressing the formidable challenges of treating the quantum nature of both the electrons and nuclei. Exploiting our recently developed methods that provide acceleration by up to two orders of magnitude, we combine path integral simulations with on-the-fly evaluation of the electronic structure at the hybrid density functional theory level to capture the interplay between nuclear quantum effects and the electronic surface. Here we show that this combination provides accurate structure and dynamics, including the full infra-red and Raman spectra of liquid water. This allows us to demonstrate and explain the failings of lower-level density functionals for dynamics and vibrational spectroscopy when the nuclei are treated quantum mechanically. These insights thus provide a foundation for the reliable investigation of spectroscopy and reactivity in aqueous environments.},
archivePrefix = {arXiv},
arxivId = {1702.07797},
author = {Marsalek, Ondrej and Markland, Thomas E.},




journal = {J. Phys. Chem. Letters},


pages = {1545--1551},
title = {{Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects}},

volume = {8},
year = {2017}
}
@article{Sim2012,
abstract = {We develop a unique algorithm implemented in the program MOSAICS (Methodologies for Optimization and Sampling in Computational Studies) that is capable of nanoscale modeling without compromising the resolution of interest. This is achieved by modeling with customizable hierarchical degrees of freedom, thereby circumventing major limitations of conventional molecular modeling. With the emergence of RNA-based nanotechnology, large RNAs in all-atom representation are used here to benchmark our algorithm. Our method locates all favorable structural states of a model RNA of significant complexity while improving sampling accuracy and increasing speed many fold over existing all-atom RNA modeling methods. We also modeled the effects of sequence mutations on the structural building blocks of tRNA-based nanotechnology. With its flexibility in choosing arbitrary degrees of freedom as well as in allowing different all-atom energy functions, MOSAICS is an ideal tool to model and design biomolecules of the nanoscale.},
author = {Sim, a. Y. L. and Levitt, M. and Minary, P.},


isbn = {1091-6490 (Electronic){\$}\backslash{\$}n0027-8424 (Linking)},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {2890--2895},
pmid = {22308445},
title = {{From the Cover: Modeling and design by hierarchical natural moves}},
volume = {109},
year = {2012}
}
@article{mish-stan98nature,
author = {Mishima, Osamu and Stanley, HE E},


journal = {Nature},
pages = {329--335},
title = {{The relationship between liquid, supercooled and glassy water}},

volume = {396},
year = {1998}
}
@article{smit+17cs,
abstract = {We demonstrate how a deep neural network (NN) trained on a data set of quantum mechanical (QM) DFT calculated energies can learn an accurate and transferable atomistic potential for organic molecules containing H, C, N, and O atoms.},
author = {Smith, J S and Isayev, O and Roitberg, A E},


journal = {Chemical Science},

pages = {3192--3203},
publisher = {Royal Society of Chemistry ({\{}RSC{\}})},
title = {{ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost}},

volume = {8},
year = {2017}
}
@article{paes+06jcp,
abstract = {The path-integral molecular dynamics and centroid molecular dynamics methods have been applied to investigate the behavior of liquid water at ambient conditions starting from a recently developed simple point charge/flexible (SPC/Fw) model. Several quantum structural, thermodynamic, and dynamical properties have been computed and compared to the corresponding classical values, as well as to the available experimental data. The path-integral molecular dynamics simulations show that the inclusion of quantum effects results in a less structured liquid with a reduced amount of hydrogen bonding in comparison to its classical analog. The nuclear quantization also leads to a smaller dielectric constant and a larger diffusion coefficient relative to the corresponding classical values. Collective and single molecule time correlation functions show a faster decay than their classical counterparts. Good agreement with the experimental measurements in the low-frequency region is obtained for the quantum infrared spectrum, which also shows a higher intensity and a redshift relative to its classical analog. A modification of the original parametrization of the SPC/Fw model is suggested and tested in order to construct an accurate quantum model, called q-SPC/Fw, for liquid water. The quantum results for several thermodynamic and dynamical properties computed with the new model are shown to be in a significantly better agreement with the experimental data. Finally, a force-matching approach was applied to the q-SPC/Fw model to derive an effective quantum force field for liquid water in which the effects due to the nuclear quantization are explicitly distinguished from those due to the underlying molecular interactions. Thermodynamic and dynamical properties computed using standard classical simulations with this effective quantum potential are found in excellent agreement with those obtained from significantly more computationally demanding full centroid molecular dynamics simulations. The present results suggest that the inclusion of nuclear quantum effects into an empirical model for water enhances the ability of such model to faithfully represent experimental data, presumably through an increased ability of the model itself to capture realistic physical effects.},
author = {Paesani, Francesco and Zhang, Wei and Case, David a and Cheatham, Thomas E and Voth, Gregory a},



journal = {J. Chem. Phys.},



pages = {184507},
pmid = {17115765},
title = {{An accurate and simple quantum model for liquid water.}},

volume = {125},
year = {2006}
}
@article{alim+92jcp,
author = {Alimi, R and Garc$\backslash$'ia-Vela, A and Gerber, R B},

journal = {J. Chem. Phys.},
pages = {2034},
publisher = {AIP},
title = {{A remedy for zero-point energy problems in classical trajectories: A combined semiclassical/classical molecular dynamics algorithm}},
volume = {96},
year = {1992}
}
@article{sump+94arpc,
author = {Sumpter, B G and Getino, Coral and Noid, D W},



journal = {Annual Review of Physical Chemistry},


pages = {439--481},
title = {{Theory and Applications of Neural Computing in Chemical Science}},

volume = {45},
year = {1994}
}
@article{bowl-gori96surf,
author = {Bowler, D R and Goringe, C M},

journal = {Surf. Sci.},

pages = {L489--L494},
publisher = {Elsevier Science},
title = {{An ab initio study of SiH2 fragments on the Si(001) surface}},
volume = {360},
year = {1996}
}
@article{xion+08nmat,
abstract = {The safe and efficient storage of hydrogen is widely recognized as one of the key technological challenges in the transition towards a hydrogen-based energy economy. Whereas hydrogen for transportation applications is currently stored using cryogenics or high pressure, there is substantial research and development activity in the use of novel condensed-phase hydride materials. However, the multiple-target criteria accepted as necessary for the successful implementation of such stores have not yet been met by any single material. Ammonia borane, NH3BH3, is one of a number of condensed-phase compounds that have received significant attention because of its reported release of approximately 12 wt{\%} hydrogen at moderate temperatures (approximately 150 degrees C). However, the hydrogen purity suffers from the release of trace quantities of borazine. Here, we report that the related alkali-metal amidoboranes, LiNH2BH3 and NaNH2BH3, release approximately 10.9 wt{\%} and approximately 7.5 wt{\%} hydrogen, respectively, at significantly lower temperatures (approximately 90 degrees C) with no borazine emission. The low-temperature release of a large amount of hydrogen is significant and provides the potential to fulfil many of the principal criteria required for an on-board hydrogen store.},
author = {Xiong, Zhitao and Yong, Chaw Keong and Wu, Guotao and Chen, Ping and Shaw, Wendy and Karkamkar, Abhi and Autrey, Thomas and Jones, Martin Owen and Johnson, Simon R and Edwards, Peter P and David, William I F},



journal = {Nature materials},


pages = {138--41},
pmid = {18157135},
title = {{High-capacity hydrogen storage in lithium and sodium amidoboranes.}},

volume = {7},
year = {2008}
}
@article{ford+65jmp,
author = {Ford, G W and Kac, M and Mazur, P},

journal = {Journal of Mathematical Physics},
pages = {504--515},
title = {{Statistical mechanics of ensembles of coupled oscillators}},
volume = {6},
year = {1965}
}
@article{rohr+arpc13,
abstract = {The long-timescale dynamics of macromolecular systems can be oftentimes viewed as a reaction connecting metastable states of the system. In the past decade, various approaches have been developed to discover the collective motions associated with this dynamics. The corresponding collective variables are used in many applications, e.g., to understand the reaction mechanism, to quantify the system's free energy landscape, to enhance the sampling of the reaction path, and to determine the reaction rate. In this review we focus on a number of key developments in this field, providing an overview of several methods along with their relative regimes of applicability.},
author = {Rohrdanz, Mary A and Zheng, Wenwei and Clementi, Cecilia},



journal = {Annual review of physical chemistry},


pages = {295--316},
pmid = {23298245},
title = {{Discovering mountain passes via torchlight: methods for the definition of reaction coordinates and pathways in complex macromolecular reactions.}},

volume = {64},
year = {2013}
}
@article{andr+94jcp,
author = {Andresen, Peter and Ondrey, G. S. and Titze, B. and Rothe, Erhard W.},



journal = {J. Chem. Phys.},

pages = {2548},
title = {{Nuclear and electron dynamics in the photodissociation of water}},

volume = {80},
year = {1984}
}
@article{wood+13jacs,
abstract = {We investigate the structure, topology, and dynamics of liquid water at the interface with natively hydroxylated (001) surfaces of InP and GaP photoelectrodes. Using ab initio molecular dynamics simulations, we show that contact with the semiconductor surface enhances the water hydrogen-bond strength at the interface. This leads to the formation of an ice-like structure, within which dynamically driven water dissociation and local proton hopping are amplified. Nevertheless, the structurally similar and isovalent InP and GaP surfaces generate qualitatively different interfacial water dynamics. This can be traced to slightly more covalent-like character in the binding of surface adsorbates to GaP, which results in a more rigid hydrogen-bond network that limits the explored topological phase space. As a consequence, local proton hopping can give rise to long-range surface proton transport on InP, whereas the process is kinetically limited on GaP. This allows for spatial separation of individual stages of hydrogen-evolving, multistep reactions on InP(001). Possible implications for the mechanisms of cathodic water splitting and photocorrosion on the two surfaces are considered in light of available experimental evidence.},
author = {Wood, Brandon C and Schwegler, Eric and Choi, Woon Ih and Ogitsu, Tadashi},



journal = {J. Chem. Am. Soc. },


pages = {15774--83},
pmid = {24053479},
title = {{Hydrogen-Bond Dynamics of Water at the Interface with InP/GaP(001) and the Implications for Photoelectrochemistry.}},

volume = {135},
year = {2013}
}
@article{auer+07pnas,
abstract = {We present improvements on our previous approaches for calculating vibrational spectroscopy observables for the OH stretch region of dilute HOD in liquid D2O. These revised approaches are implemented to calculate IR and isotropic Raman spectra, using the SPC/E simulation model, and the results are in good agreement with experiment. We also calculate observables associated with three-pulse IR echoes: the peak shift and 2D-IR spectrum. The agreement with experiment for the former is improved over our previous calculations, but discrepancies between theory and experiment still exist. Using our proposed definition for hydrogen bonding in liquid water, we decompose the distribution of frequencies in the OH stretch region in terms of subensembles of HOD molecules with different local hydrogen-bonding environments. Such a decomposition allows us to make the connection with experiments and calculations on water clusters and more generally to understand the extent of the relationship between transition frequency and local structure in the liquid.},
author = {Auer, B and Kumar, R and Schmidt, J R and Skinner, J L},


isbn = {0027-8424},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {14215--14220},
pmid = {17576923},
title = {{Hydrogen bonding and Raman, IR, and 2D-IR spectroscopy of dilute HOD in liquid D2O.}},
volume = {104},
year = {2007}
}
@article{apos-mish11prb,
author = {Apostol, F. and Mishin, Y.},



journal = {Phys. Rev. B},

mendeley-tags = {aluminum},


pages = {054116},
title = {{Interatomic potential for the Al-Cu system}},

volume = {83},
year = {2011}
}
@article{ceri+12jpcm,
abstract = {By means of first-principles calculations we studied the decomposition pathways of SiH₃ on Ge(100) and of GeH₃ on Si(100), of interest for the growth of crystalline SiGe alloys and Si/Ge heterostructures by plasma-enhanced chemical vapor deposition. We also investigated H desorption via reaction of two adsorbed SiH₂/GeH₂ species ({\$}\beta{\$}₂ reaction) or via Eley-Rideal abstraction of surface H atoms from the impinging SiH₃ and GeH₃ species. The calculated activation energies for the different processes suggest that the rate-limiting step for the growth of Si/Ge systems is still the {\$}\beta{\$}₂ reaction of two SiH₂ as in the growth of crystalline Si.},
author = {Ceriotti, M and Montalenti, F and Bernasconi, M},



journal = {J. Phys. Cond. Matt.},


pages = {104002},
pmid = {22354872},
title = {{Density functional study of the decomposition pathways of SiH₃ and GeH₃ at the Si(100) and Ge(100) surfaces.}},

volume = {24},
year = {2012}
}
@article{Williams2002,
author = {Williams, CKI K I},


journal = {Machine Learning},

pages = {11--19},
title = {{On a connection between kernel PCA and metric multidimensional scaling}},

year = {2002}
}
@article{reit+10prl,
author = {Reiter, G. F. and Senesi, R. and Mayers, J.},



journal = {Phys. Rev. Lett.},


pages = {148101},
title = {{Changes in the Zero-Point Energy of the Protons as the Source of the Binding Energy of Water to A-Phase DNA}},

volume = {105},
year = {2010}
}
@article{yang+11apa,
author = {Yang, Lingqi and Gan, Yong and Zhang, Yuwen and Chen, J. K.},



journal = {Applied Physics A},

mendeley-tags = {additive manufacturing},


pages = {725--735},
title = {{Molecular dynamics simulation of neck growth in laser sintering of different-sized gold nanoparticles under different heating rates}},

volume = {106},
year = {2011}
}
@article{lian+17prb,
author = {Liang, Chungwen and Tocci, Gabriele and Wilkins, David M. and Grisafi, Andrea and Roke, Sylvie and Ceriotti, Michele},



journal = {Phys. Rev. B},


pages = {041407},
title = {{Solvent fluctuations and nuclear quantum effects modulate the molecular hyperpolarizability of water}},

volume = {96},
year = {2017}
}
@article{poli-roma94aos,
author = {Politis, Dimitris N. and Romano, Joseph P.},



journal = {The Annals of Statistics},


pages = {2031--2050},
title = {{Large Sample Confidence Regions Based on Subsamples under Minimal Assumptions}},

volume = {22},
year = {1994}
}
@article{bono+09jcc,
author = {Bonomi, M and Barducci, A and Parrinello, M},

journal = {J. Comp. Chem.},

pages = {1615--1621},
publisher = {Wiley Online Library},
title = {{Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics}},
volume = {30},
year = {2009}
}
@article{cao-bern89jcp,
author = {Cao, Jianshu and Berne, Bruce J.},



journal = {J. Chem. Phys.},

pages = {6359},
title = {{On energy estimators in path integral Monte Carlo simulations: Dependence of accuracy on algorithm}},

volume = {91},
year = {1989}
}
@article{nikl-tymc06prl,
author = {Niklasson, A M N and Tymczak, C J and Challacombe, M},

journal = {Phys. Rev. Lett.},
pages = {123001},
title = {{Time-Reversible Born-Oppenheimer Molecular Dynamics}},
volume = {97},
year = {2006}
}
@article{webb+16gca,
author = {Webb, Michael A. and Wang, Yimin and Braams, Bastiaan J. and Bowman, Joel M. and {Miller III}, Thomas F.},



journal = {Geochimica et Cosmochimica Acta},

title = {{Equilibrium Clumped-Isotope Effects in Doubly Substituted Isotopologues of Ethane}},

year = {2016}
}
@article{ghas+15prb,
author = {Ghasemi, S. Alireza and Hofstetter, Albert and Saha, Santanu and Goedecker, Stefan},


journal = {Phys. Rev. B},


pages = {045131},
title = {{Interatomic potentials for ionic systems with density functional accuracy based on charge densities obtained by a neural network}},

volume = {92},
year = {2015}
}
@article{sene+13cp,
abstract = {By means of Deep Inelastic Neutron Scattering we determined the temperature dependence of the proton kinetic energy in polycrystalline ice Ih between 5 K and 271 K. We compare our results with predictions form Path Integral quantum simulations and semiclassical quasi-harmonic models with phase-dependent frequencies. The latter show the best agreement with the experiment if the librational contribution is properly taken into account. The kinetic energy increase with temperature in ice is also found to be approximately a factor ??? 5 smaller than in the case of liquid water above room temperature, highlighting the role played by anharmonic quantum fluctuations in the two phases. ?? 2013 Elsevier B.V.},
author = {Senesi, R. and Romanelli, G. and Adams, M. A. and Andreani, C.},



journal = {Chemical Physics},

pages = {111--116},
publisher = {Elsevier B.V.},
title = {{Temperature dependence of the zero point kinetic energy in ice and water above room temperature}},

volume = {427},
year = {2013}
}
@article{hirn+15arxiv,
author = {Hirn, Matthew and Poilvert, Nicolas and Mallat, Stephane},
journal = {arXiv preprint arXiv:1502.02077},
title = {{Quantum Energy Regression using Scattering Transforms}},
year = {2015}
}
@article{ceri+12prsa,
abstract = {Computing averages over a target probability density by statistical re-weighting of a set of samples with a different distribution is a strategy which is commonly adopted in fields as diverse as atomistic simulation and finance. Here we present a very general analysis of the accuracy and efficiency of this approach, highlighting some of its weaknesses. We then give an example of how our results can be used, specifically to assess the feasibility of high-order path integral methods. We demonstrate that the most promising of these techniques -- which is based on re-weighted sampling -- is bound to fail as the size of the system is increased, because of the exponential growth of the statistical uncertainty in the re-weighted average.},
archivePrefix = {arXiv},
arxivId = {1107.1908},
author = {Ceriotti, Michele and Brain, Guy A. R. and Riordan, Oliver and Manolopoulos, David E.},




journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},


pages = {2--17},
publisher = {The Royal Society},
title = {{The inefficiency of re-weighted sampling and the curse of system size in high order path integration}},

volume = {468},
year = {2011}
}
@article{read-shoc50pr,
author = {Read, WT T and Shockley, W},



journal = {Phys. Rev.},


pages = {275--289},
title = {{Dislocation Models of Crystal Grain Boundaries}},

volume = {78},
year = {1950}
}
@article{eick+17nips,
author = {Eickenberg, Michael and Hirn, Matthew},


title = {{Solid Harmonic Wavelet Scattering : Predicting Quantum Molecular Energy from Invariant Descriptors of 3D Electronic Densities}}
}
@misc{EPAPS-sih3deco,
annote = {See EPAPS Document No. ----- for a movie of metadynamics trajectory, and a discussion of Brillouin-zone sampling issues.},
title = {{No Title}}
}
@article{mars-mark16jcp,
abstract = {Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, our implementation is as fast as a typical classical ab initio molecular dynamics simulation and 35{\$}\backslashtimes{\$} faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.},
archivePrefix = {arXiv},
arxivId = {1512.00473},
author = {Marsalek, Ondrej and Markland, Thomas E.},




journal = {J. Chem. Phys.},

pmid = {26851913},
title = {{Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory}},

volume = {144},
year = {2016}
}
@article{mari+16jctc,
author = {Marianski, Mateusz and Supady, Adriana and Ingram, Teresa and Schneider, Markus and Baldauf, Carsten},



journal = {J. Chem. Theory Comput.},


pages = {6157--6168},
title = {{Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and $\alpha$-Maltose}},

volume = {12},
year = {2016}
}
@article{zhan+08prl,
author = {Zhang, Qianfan and Wahnstr{\"{o}}m, G{\"{o}}ran and Bj{\"{o}}rketun, M{\aa}rten and Gao, Shiwu and Wang, Enge},



journal = {Phys. Rev. Lett.},


pages = {215902},
title = {{Path Integral Treatment of Proton Transport Processes in BaZrO3}},

volume = {101},
year = {2008}
}
@article{mill05pnas,
abstract = {This Perspective presents a broad overview of the present status of theoretical capabilities for describing quantum dynamics in molecular systems with many degrees of freedom, e.g., chemical reactions in solution, clusters, solids, or biomolecular environments. },
author = {Miller, William H},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {6660--6664},
title = {{Quantum dynamics of complex molecular systems}},
volume = {102},
year = {2005}
}
@article{neum-perr09cec,
abstract = {The results of an extensive in silico polymorph screen with the program GRACE of paracetamol in all 230 space groups with one and two molecules in the asymmetric unit are presented. The three experimentally known forms I, II and III are found in the list of predicted crystal structures in the correct stability order with rank 1, 3 and 6, respectively. Structures with ranks 3 to 8 exhibit the same motif of 2-D hydrogen-bonded sheets. The hydrogen-bonding scheme of the rank 2 structure is markedly different from the known forms, consisting of two interpenetrating 3-D hydrogen-bonded networks. The excellent agreement with experiment and the prediction of one and only one new packing motif within the lattice energy window delimited by the known forms confirms the fitness for crystal structure prediction of the employed methodology. Analysis of the structure at rank 2 is used to propose experimental strategies that may lead to a new form IV of paracetamol.},
author = {Neumann, Marcus Aurelius and Perrin, Marc-Antoine},


isbn = {1466-8033},

journal = {CrystEngComm},

pages = {2475},
title = {{Can crystal structure prediction guide experimentalists to a new polymorph of paracetamol?}},

volume = {11},
year = {2009}
}
@article{pier+04prl,
author = {Pierleoni, Carlo and Ceperley, David M. and Holzmann, Markus},


journal = {Phys. Rev. Lett.},


pages = {146402},
title = {{Coupled Electron-Ion Monte Carlo Calculations of Dense Metallic Hydrogen}},

volume = {93},
year = {2004}
}
@article{laag-hyne08jpcb,
abstract = {We detail and considerably extend the analysis recently presented in Science 2006, 311, 832- 835 of the molecular mechanism of water reorientation based on molecular dynamics simulations and the analytic framework of the extended jump model (EJM). The water reorientation is shown to occur through large-amplitude angular jumps due to the exchange of hydrogen (H)-bond acceptors, with a minor contribution from the diffusive H-bond frame reorientation between these exchanges. The robust character of this mechanism with respect to different water models is discussed. We fully characterize these jump events, including the distributions of trajectories around the average path. The average path values and the distributions of the jump time and the jump amplitude, the two key parameters in the Ivanov jump model component of the EJM, are determined. We also discuss the possibility of selectively exciting water molecules close to the jump event, of interest for ultrafast infrared experiments. In addition to a comparison of predicted reorientation times with experimental results, the reorientation time temperature dependence is discussed. A detailed description of the pathway free energetics for the water reorientation is presented; this is used to identify the jump rate-limiting step as the translational motion in which the initial H-bond of the reorientating water is elongated and the new H-bond acceptor water approaches.},
author = {Laage, Damien and Hynes, James T},



journal = {J. Phys. Chem.. B},


pages = {14230--42},
pmid = {18942871},
title = {{On the molecular mechanism of water reorientation.}},

volume = {112},
year = {2008}
}
@article{guid+10jctc,
author = {Guidon, Manuel and Hutter, Jürg and VandeVondele, Joost},



journal = {J. Chem. Theory Comput.},


pages = {2348--2364},
title = {{Auxiliary Density Matrix Methods for Hartree−Fock Exchange Calculations}},

volume = {6},
year = {2010}
}
@article{ceri+11pnas,
abstract = {A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.},
author = {Comitani, F. and Rossi, K. and Ceriotti, Michele and Sanz, M.E. and Molteni, C. and Tribello, Gareth A and Parrinello, Michele},


isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)},

journal = {Proc. Natl. Acad. Sci. USA},


pages = {13023--13028},
pmid = {21730167},
title = {{Simplifying the representation of complex free-energy landscapes using sketch-map.}},

volume = {108},
year = {2011}
}
@article{oki+97prb,
author = {Okimoto, Y and Katsufuji, T and Ishikawa, T and Arima, T and Tokura, Y},

journal = {Phys. Rev. B},

pages = {4206--4214},
publisher = {American Physical Society},
title = {{Variation of electronic structure in $\backslash$mathrmLa{\_}1$\backslash$mathrm-$\backslash$mathrmx$\backslash$mathrmSr{\_}$\backslash$mathrmx$\backslash$mathrmMnO{\_}3f(0$\backslash$leqslantx$\backslash$leqslant0.3) as investigated by optical conductivity spectra}},
volume = {55},
year = {1997}
}
@article{endr-schi03ieee,
author = {Endres, D M and Schindelin, J E},

journal = {IEEE Trans. Inf. Th.},

pages = {1858--1860},
title = {{A new metric for probability distributions}},
volume = {49},
year = {2003}
}
@article{boer+00prl,
author = {Boero, Mauro and Terakura, Kiyoyuki and Ikeshoji, Tamio and Liew, Chee Chin and Parrinello, Michele},

journal = {Phys. Rev. Lett.},

pages = {3245--3248},
publisher = {American Physical Society},
title = {{Hydrogen Bonding and Dipole Moment of Water at Supercritical Conditions: A First-Principles Molecular Dynamics Study}},
volume = {85},
year = {2000}
}
@article{Wise1990,
author = {Wise, S and Francot, John},

pages = {282--296},
title = {{Costs of Quadtree Representation of Nondense Matrices}},
year = {1990}
}
@article{rick+94jcp,
author = {Rick, Steven W and Stuart, Steven J and Berne, B J},


journal = {J. Chem. Phys.},

pages = {6141--6156},
publisher = {AIP},
title = {{Dynamical fluctuating charge force fields: Application to liquid water}},
volume = {101},
year = {1994}
}
@article{rose+98tsf,
author = {Rosenblad, C and Graf, T and Stangl, J and Zhuang, Y and Bauer, G and Schulze, J and von K{\"{a}}nel, H},

journal = {Thin Solid Films},
pages = {89},
title = {{Epitaxial growth at high rates with LEPECVD}},
volume = {336},
year = {1998}
}
@article{muno+04prb,
author = {Mu{\~{n}}oz, D and Harrison, N M and Illas, F},

journal = {Phys. Rev. B},

pages = {85115},
publisher = {American Physical Society},
title = {{Electronic and magnetic structure of LaMnO{\_}3 from hybrid periodic density-functional theory}},
volume = {69},
year = {2004}
}
@article{chen-ceri14jcp,
abstract = {Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.},
author = {Cheng, Bingqing and Ceriotti, Michele},



journal = {J. Chem. Phys.},


pages = {244112},
pmid = {25554138},
title = {{Direct path integral estimators for isotope fractionation ratios.}},

volume = {141},
year = {2014}
}
@article{andr+01jcp,
author = {Andreani, C and Degiorgi, E and Senesi, R and Cilloco, F and Colognesi, D and Mayers, J and Nardone, M and Pace, E},

journal = {J. Chem. Phys.},

pages = {387--398},
publisher = {AIP},
title = {{Single particle dynamics in fluid and solid hydrogen sulphide: An inelastic neutron scattering study}},
volume = {114},
year = {2001}
}
@article{sope00cp,
author = {a.K. Soper and a.K. Soper},



journal = {Chemical Physics},


pages = {121--137},
title = {{The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa}},

volume = {258},
year = {2000}
}
@article{chan+79jcp,
abstract = {The nature of solvent structure around ions is considered using a model of hard spheres with embedded point charges in a solvent of hard spheres with embedded point dipoles. The statistical mechanics of this model is treated in the mean spherical approximation which is a natural extension of the Debye–H{\"{u}}ckel theory of electrolytes to include discrete charges and dipoles of finite size. Our results include (i) a modified expression for the Born energy which had been used empirically to fit solubility data, (ii) explicit forms for the polarization density about an ion from which we can deduce the orientation order of the dipolar solvents and the validity or otherwise of the concept of a ''local'' dielectric constant near charged bodies, and (iii) the form of the interaction free energy (potential of mean force) between ions at separations comparable to the solvent size. In presenting these results which are given in detail in Section IV only a familiarity with the general description of this model given in Section II is assumed; it will not be necessary to refer to the mathematical detail in Section III.},
author = {Chan, Derek Y. C. and Mitchell, D. John and Ninham, Barry W.},



journal = {J. Chem. Phys.},

pages = {2946--2957},
title = {{A model of solvent structure around ions}},

volume = {70},
year = {1979}
}
@book{Grotendorst,
author = {Grotendorst, Johannes},
isbn = {3000136185},
title = {{High Performance Computing in Chemistry}}
}
@article{hoyt+01prl,
author = {Hoyt, J. and Asta, Mark and Karma, Alain},



journal = {Phys. Rev. Lett.},


pages = {5530--5533},
title = {{Method for Computing the Anisotropy of the Solid-Liquid Interfacial Free Energy}},

volume = {86},
year = {2001}
}
@article{mars+14jctc,
author = {Marsalek, Ondrej and Chen, Pei-Yang and Dupuis, Romain and Benoit, Magali and M{\'{e}}heut, Merlin and Ba{\v{c}}i{\'{c}}, Zlatko and Tuckerman, Mark E.},



journal = {J. Chem. Theory Comput.},


pages = {1440--1453},
title = {{Efficient Calculation of Free Energy Differences Associated with Isotopic Substitution Using Path-Integral Molecular Dynamics}},

volume = {10},
year = {2014}
}
@article{morri-park87ajp,
abstract = {To lay a foundation for the study and use of rotation operators in graduate quantum mechanics and in research, a thorough discussion is presented of rotations in Euclidean three space (R3 ) and of their effect on kets in the Hilbert space of a single particle. The Wigner D-matrices are obtained and used to rotate spherical harmonics. An extensive ready-reference appendix of the properties of these matrices, expressed in a consistent notation, is provided. Careful attention is paid throughout to various conventions (e.g. active versus passive viewpoints) that are used in the literature.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {{A Morrison}, Michael and {A Parker}, Gregory},



isbn = {9788578110796},

journal = {Australian Journal of Physics},

pages = {465},
pmid = {25246403},
title = {{A Guide to Rotations in Quantum Mechanics}},

volume = {40},
year = {1987}
}
@article{ross+18jcp,
abstract = {{\textcopyright} 2018 Author(s). Generalized Langevin Equation (GLE) thermostats have been used very effectively as a tool to manipulate and optimize the sampling of thermodynamic ensembles and the associated static properties. Here we show that a similar, exquisite level of control can be achieved for the dynamical properties computed from thermostatted trajectories. We develop quantitative measures of the disturbance induced by the GLE to the Hamiltonian dynamics of a harmonic oscillator, and show that these analytical results accurately predict the behavior of strongly anharmonic systems. We also show that it is possible to correct, to a significant extent, the effects of the GLE term onto the corresponding microcanonical dynamics, which puts on more solid grounds the use of non-equilibrium Langevin dynamics to approximate quantum nuclear effects and could help improve the prediction of dynamical quantities from techniques that use a Langevin term to stabilize dynamics. Finally we address the use of thermostats in the context of approximate path-integral-based models of quantum nuclear dynamics. We demonstrate that a custom-tailored GLE can alleviate some of the artifacts associated with these techniques, improving the quality of results for the modeling of vibrational dynamics of molecules, liquids, and solids.},
archivePrefix = {arXiv},
arxivId = {arXiv:1704.05099v1},
author = {Rossi, Mariana and Kapil, Venkat and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {102301},
title = {{Fine tuning classical and quantum molecular dynamics using a generalized Langevin equation}},

volume = {148},
year = {2018}
}
@article{yan+17am,
abstract = {{\textcopyright} 2017 WILEY-VCH Verlag GmbH  {\&}  Co. KGaA, Weinheim The recent ability to integrate semiconductor-based optoelectronic functionalities within thin fibers is opening intriguing opportunities for flexible electronics and advanced textiles. The scalable integration of high-quality semiconducting devices within functional fibers however remains a challenge. It is difficult with current strategies to combine high light absorption, good microstructure and efficient electrical contact. The growth of semiconducting nanowires is a great tool to control crystal orientation and ensure a combination of light absorption and charge extraction for efficient photodetection. Thus far, however, leveraging the attributes of nanowires has remained seemingly incompatible with fiber materials, geometry, and processing approaches. Here, the integration of semiconducting nanowire-based devices at the tip and along the length of polymer fibers is demonstrated for the first time. The scalable thermal drawing process is combined with a simple sonochemical treatment to grow nanowires out of electrically addressed amorphous selenium domains. First principles density-functional theory calculations show that this approach enables to tailor the surface energy of crystal facets and favors nanowire growth along a preferred orientation, resulting in fiber-integrated devices of unprecedented performance. This novel platform is exploited to demonstrate an all-fiber-integrated fluorescence imaging system, highlighting novel opportunities in sensing, advanced optical probes, and smart textiles.},
author = {Yan, Wei and Qu, Yunpeng and Gupta, Tapajyoti Das T.D. and Darga, Arouna and Nguy{\^{e}}n, Dang T{\`{u}}ng D.T. and Page, Alexis G{\'{e}}rald A.G. and Rossi, Mariana and Ceriotti, Michele and Sorin, Fabien},



journal = {Advanced Materials},



pages = {1700681},
title = {{Semiconducting Nanowire-Based Optoelectronic Fibers}},

volume = {1700681},
year = {2017}
}
@misc{gle4md,
author = {Ceriotti, M.},
howpublished = {http://gle4md.org},
title = {{GLE4MD}},

year = {2010}
}
@article{yang91prl,
author = {Yang, W},

journal = {Phys. Rev. Lett.},

pages = {1438--1441},
publisher = {APS},
title = {{Direct calculation of electron density in density-functional theory}},
volume = {66},
year = {1991}
}
@article{voit+16ncomm,
abstract = {{\textcopyright} The Author(s) 2016. At the interface with solids, the mobility of liquid molecules tends to be reduced compared with bulk, often resulting in increased local order due to interactions with the surface of the solid. At room temperature, liquids such as water and methanol can form solvation structures, but the molecules remain highly mobile, thus preventing the formation of long-lived supramolecular assemblies. Here we show that mixtures of water with methanol can form a novel type of interfaces with hydrophobic solids. Combining in situ atomic force microscopy and multiscale molecular dynamics simulations, we identify solid-like two-dimensional interfacial structures that nucleate thermally, and are held together by an extended network of hydrogen bonds. On graphite, nucleation occurs above ∼ 35 °C, resulting in robust, multilayered nanoscopic patterns. Our findings could have an impact on many fields where water-alcohol mixtures play an important role such as fuel cells, chemical synthesis, self-assembly, catalysis and surface treatments.},
author = {Vo{\"{i}}tchovsky, Kislon and Giofr{\`{e}}, Daniele and {Jos{\'{e}} Segura}, Juan and Stellacci, Francesco and Ceriotti, Michele},



journal = {Nature Comm.},

pages = {13064},
title = {{Thermally-nucleated self-assembly of water and alcohol into stable structures at hydrophobic interfaces}},

volume = {7},
year = {2016}
}
@article{damm+12jpcm,
abstract = {Molecular dynamics (MD) simulations have been carried out to study isotope effects in lithium hydride and lithium deuteride crystals. Quantum effects on nuclear motion have been included through a quantum thermal bath (QTB). The interatomic forces were described either within the density functional theory (DFT) in the generalized gradient approximation (GGA) or by the phenomenological approach using the shell model. For both models, the isotopic shift in the lattice parameter can be successfully predicted by QTB-MD simulations. The slope of the experimental isotopic shift in pressure is satisfactorily reproduced by QTB-MD within DFT-GGA, in contrast to both density functional perturbation theory and QTB-MD with the shell model. We have analyzed the reasons for these discrepancies through the vibrational densities of states and the isotopic shifts in bulk modulus. The results illustrate the importance of anharmonic contributions to vibrations and to the isotopic pressure shift between LiH and LiD.},
author = {Dammak, Hichem and Antoshchenkova, Ekaterina and Hayoun, Marc and Finocchi, Fabio},



journal = {J. Phys. Cond. Matt. },



pages = {435402},
pmid = {23034812},
title = {{Isotope effects in lithium hydride and lithium deuteride crystals by molecular dynamics simulations.}},

volume = {24},
year = {2012}
}
@article{belk-niyo03nc,
author = {Belkin, Mikhail and Niyogi, Partha},



journal = {Neural Computation},


pages = {1373--1396},
title = {{Laplacian Eigenmaps for Dimensionality Reduction and Data Representation}},

volume = {15},
year = {2003}
}
@article{zile+18nc,
author = {Ziletti, Angelo and Kumar, Devinder and Scheffler, Matthias and Ghiringhelli, Luca M.},


journal = {Nature Comm.},


pages = {2775},
title = {{Insightful classification of crystal structures using deep learning}},

volume = {9},
year = {2018}
}
@article{artr+11prb,
author = {Artrith, Nongnuch and Morawietz, Tobias and Behler, J{\"{o}}rg},



journal = {Phys. Rev. B},


pages = {153101},
title = {{High-dimensional neural-network potentials for multicomponent systems: Applications to zinc oxide}},

volume = {83},
year = {2011}
}
@article{Goedecker2004,
author = {Goedecker, S},

journal = {J. Chem. Phys.},


pages = {9911--9917},
title = {{{\{}M{\}}inima hopping: {\{}A{\}}n efficient search method for the global minimum of the potential energy surface of complex molecular systems}},
volume = {120},
year = {2004}
}
@article{sun+16sa,
abstract = {The space of metastable materials offers promising new design opportunities for next-generation technological materials such as complex oxides, semiconductors, pharmaceuticals, steels, and beyond. Although metastable phases are ubiquitous in both nature and technology, only a heuristic understanding of their underlying ther- modynamics exists. We report a large-scale data-mining study of the Materials Project, a high-throughput database of density functional theory–calculated energetics of Inorganic Crystal Structure Database structures, to explicitly quantify the thermodynamic scale of metastability for 29,902 observed inorganic crystalline phases. We reveal the influence of chemistry and composition on the accessible thermodynamic range of crystalline meta- stability for polymorphic and phase-separating compounds, yielding new physical insights that can guide the design of novel metastable materials. We further assert that not all low-energy metastable compounds can necessarily be synthesized, and propose a principle of ‘remnant metastability'—that observable metastable crystalline phases are generally remnants of thermodynamic conditions where they were once the lowest free-energy phase.},
author = {Sun, W. and Dacek, S. T. and Ong, S. P. and Hautier, G. and Jain, A. and Richards, W. D. and Gamst, A. C. and Persson, K. A. and Ceder, G.},



journal = {Science Advances},

pages = {e1600225--e1600225},
title = {{The thermodynamic scale of inorganic crystalline metastability}},

volume = {2},
year = {2016}
}
@article{goed+96prb,
author = {Goedecker, S and Teter, M and Hutter, J},

journal = {Phys. Rev. B},

pages = {1703--1710},
publisher = {APS},
title = {{Separable dual-space Gaussian pseudopotentials}},
volume = {54},
year = {1996}
}
@article{sing+11sm,
author = {Singh, C.V. V and Mateos, A.J. J and Warner, D.H. H},



journal = {Scripta Materialia},

mendeley-tags = {aluminum},


pages = {398--401},
publisher = {Acta Materialia Inc.},
title = {{Atomistic simulations of dislocation–precipitate interactions emphasize importance of cross-slip}},

volume = {64},
year = {2011}
}
@article{yama-reif94jap,
author = {Yamauchi, Noriyoshi and Reif, Rafael},



journal = {J. Appl. Phys.},

pages = {3235--3257},
publisher = {AIP},
title = {{Polycrystalline silicon thin films processed with silicon ion implantation and subsequent solid-phase crystallization: Theory, experiments, and thin-film transistor applications}},

volume = {75},
year = {1994}
}
@article{mitc-nell82jcp,
author = {Mitchell, A. C. and Nellis, W. J.},



journal = {J. Chem. Phys.},

pages = {6273},
title = {{Equation of state and electrical conductivity of water and ammonia shocked to the 100 GPa (1 Mbar) pressure range}},

volume = {76},
year = {1982}
}
@misc{murt68or,
abstract = {The Hungarian method gives an efficient algorithm for finding the minimal cost assignment. However, in some cases it may be useful to determine the second minimal assignment (i.e., the best assignment after excluding the minimal cost assignment) and in general the kth minimal assignment for k = 1, 2, {\{}{\ldots}{\}}. These things can easily be determined if all the assignments can be arranged as a sequence in increasing order of cost. This paper describes an efficient algorithm for such a ranking of all the assignments. The maximum computational effort required to generate an additional assignment in the sequence is that of solving at most (n − 1) different assignment problems, one each of sizes 2, 3, {\{}{\ldots}{\}}, n.},
author = {Murty, K. G.},
booktitle = {Operations Research},




pages = {682--687},
title = {{Letter to the Editor--An Algorithm for Ranking all the Assignments in Order of Increasing Cost}},
volume = {16},
year = {1968}
}
@article{ramo+11fd,
author = {Ramos-Cordoba, Eloy and Lambrecht, Daniel S. and Head-Gordon, Martin},



journal = {Faraday Discussions},
pages = {345},
title = {{Charge-transfer and the hydrogen bond: Spectroscopic and structural implications from electronic structure calculations}},

volume = {150},
year = {2011}
}
@article{bowm+09jcp,
abstract = {Markov state models (MSMs) are a powerful tool for modeling both the thermodynamics and kinetics of molecular systems. In addition, they provide a rigorous means to combine information from multiple sources into a single model and to direct future simulations/experiments to minimize uncertainties in the model. However, constructing MSMs is challenging because doing so requires decomposing the extremely high dimensional and rugged free energy landscape of a molecular system into long-lived states, also called metastable states. Thus, their application has generally required significant chemical intuition and hand-tuning. To address this limitation we have developed a toolkit for automating the construction of MSMs called MSMBUILDER (available at https://simtk.org/home/msmbuilder). In this work we demonstrate the application of MSMBUILDER to the villin headpiece (HP-35 NleNle), one of the smallest and fastest folding proteins. We show that the resulting MSM captures both the thermodynamics and kinetics of the original molecular dynamics of the system. As a first step toward experimental validation of our methodology we show that our model provides accurate structure prediction and that the longest timescale events correspond to folding.},
author = {Bowman, Gregory R. and Beauchamp, Kyle a. and Boxer, George and Pande, Vijay S.},


isbn = {doi:10.1063/1.3216567},

journal = {J. Chem. Phys.},
pages = {124101},
pmid = {19791846},
title = {{Progress and challenges in the automated construction of Markov state models for full protein systems}},
volume = {131},
year = {2009}
}
@article{vilc+12nchem,
abstract = {Neat liquid phosphoric acid (H(3)PO(4)) has the highest intrinsic proton conductivity of any known substance and is a useful model for understanding proton transport in other phosphate-based systems in biology and clean energy technologies. Here, we present an ab initio molecular dynamics study that reveals, for the first time, the microscopic mechanism of this high proton conductivity. Anomalously fast proton transport in hydrogen-bonded systems involves a structural diffusion mechanism in which intramolecular proton transfer is driven by specific hydrogen bond rearrangements in the surrounding environment. Aqueous media transport excess charge defects through local hydrogen bond rearrangements that drive individual proton transfer reactions. In contrast, strong, polarizable hydrogen bonds in phosphoric acid produce coupled proton motion and a pronounced protic dielectric response of the medium, leading to the formation of extended, polarized hydrogen-bonded chains. The interplay between these chains and a frustrated hydrogen-bond network gives rise to the high proton conductivity.},
author = {Vil{\v{c}}iauskas, Linas and Tuckerman, Mark E and Bester, Gabriel and Paddison, Stephen J and Kreuer, Klaus-dieter},



journal = {Nature chemistry},



pages = {461--6},
pmid = {22614380},
title = {{The mechanism of proton conduction in phosphoric acid.}},

volume = {4},
year = {2012}
}
@article{pris+12prl,
abstract = {We reconsider the applicability of classical nucleation theory (CNT) to the calculation of the free energy of solid cluster formation in a liquid and its use to the evaluation of interface free energies from nucleation barriers. Using two different freezing transitions (hard spheres and NaCl) as test cases, we first observe that the interface-free-energy estimates based on CNT are generally in error. As successive refinements of nucleation-barrier theory, we consider corrections due to a nonsharp solid-liquid interface and to a nonspherical cluster shape. Extensive calculations for the Ising model show that corrections due to a nonsharp and thermally fluctuating interface account for the barrier shape with excellent accuracy. The experimental solid nucleation rates that are measured in colloids are better accounted for by these non-CNT terms, whose effect appears to be crucial in the interpretation of data and in the extraction of the interface tension from them.},
archivePrefix = {arXiv},
arxivId = {arXiv:1206.3849v1},
author = {Prestipino, Santi and Laio, Alessandro and Tosatti, Erio},



isbn = {0031-9007 1079-7114},

journal = {Phys. Rev. Lett.},

pages = {1--5},
title = {{Systematic improvement of classical nucleation theory}},
volume = {108},
year = {2012}
}
@article{puli+17nature,
author = {Pulido, Angeles and Chen, Linjiang and Kaczorowski, Tomasz and Holden, Daniel and Little, Marc A. and Chong, Samantha Y. and Slater, Benjamin J. and McMahon, David P. and Bonillo, Baltasar and Stackhouse, Chloe J. and Stephenson, Andrew and Kane, Christopher M. and Clowes, Rob and Hasell, Tom and Cooper, Andrew I. and Day, Graeme M.},



journal = {Nature},


pages = {657--664},
publisher = {Nature Publishing Group},
title = {{Functional materials discovery using energy–structure–function maps}},

volume = {543},
year = {2017}
}
@article{marc09cr,
abstract = {The Hofmeister series, first noted in 1888, ranks the relative influence of ions on the physical behavior of a wide variety of aqueous processes ranging from colloidal assembly to protein folding. Originally, it was thought that an ion's influence on macromolecular properties was caused at least in part by 'making' or 'breaking' bulk water structure. Recent time-resolved and thermodynamic studies of water molecules in salt solutions, however, demonstrate that bulk water structure is not central to the Hofmeister effect. Instead, models are being developed that depend upon direct ion-macromolecule interactions as well as interactions with water molecules in the first hydration shell of the macromolecule.},
author = {Marcus, Yizhak},


isbn = {0009-2665},

journal = {Chem. Rev.},

pages = {1346--1370},
pmid = {19236019},
title = {{Effect of ions on the structure of water: Structure making and breaking}},
volume = {109},
year = {2009}
}
@article{ande80jcp,
author = {Andersen, Hans C},

journal = {J. Chem. Phys.},

pages = {2384--2393},
title = {{Molecular dynamics simulations at constant pressure and/or temperature}},
volume = {72},
year = {1980}
}
@article{gian+09jpcm,
author = {Giannozzi, Paolo and Baroni, Stefano and Bonini, Nicola and Calandra, Matteo and Car, Roberto and Cavazzoni, Carlo and Ceresoli, Davide and Chiarotti, Guido L and Cococcioni, Matteo and Dabo, Ismaila and Corso, Andrea Dal and de Gironcoli, Stefano and Fabris, Stefano and Fratesi, Guido and Gebauer, Ralph and Gerstmann, Uwe and Gougoussis, Christos and Kokalj, Anton and Lazzeri, Michele and Martin-Samos, Layla and Marzari, Nicola and Mauri, Francesco and Mazzarello, Riccardo and Paolini, Stefano and Pasquarello, Alfredo and Paulatto, Lorenzo and Sbraccia, Carlo and Scandolo, Sandro and Sclauzero, Gabriele and Seitsonen, Ari P and Smogunov, Alexander and Umari, Paolo and Wentzcovitch, Renata M},
journal = {J. Phys. Cond. Matt.},

pages = {395502--395519},
title = {{QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials}},
volume = {21},
year = {2009}
}
@article{smit+95jcp,
author = {Smith, A P and Wiggs, J K and J{\'{o}}nsson, H and Yan, H and Corrales, L R and Nachtigall, P and Jordan, K D},

journal = {J. Chem. Phys.},

pages = {1044},
title = {{Si adatom binding and diffusion on the Si (100) surface: Comparison of ab initio, semiempirical and empirical potential results}},
volume = {102},
year = {1995}
}
@article{cahn59jcp,
author = {Cahn, John W.},



journal = {J. Chem. Phys.},

pages = {1121},
title = {{Free Energy of a Nonuniform System. II. Thermodynamic Basis}},

volume = {30},
year = {1959}
}
@article{mcke12cpl,
author = {McKenzie, Ross H.},



journal = {Chem. Phys. Lett.},

pages = {196--200},
publisher = {Elsevier B.V.},
title = {{A diabatic state model for donor-hydrogen vibrational frequency shifts in hydrogen bonded complexes}},

volume = {535},
year = {2012}
}
@article{cort+jcp85,
author = {Cortés, Emilio and West, Bruce J. and Lindenberg, Katja},



journal = {J. Chem. Phys.},

pages = {2708},
publisher = {AIP},
title = {{On the generalized Langevin equation: Classical and quantum mechanicala)}},

volume = {82},
year = {1985}
}
@article{habe+09jcp,
abstract = {Numerous studies have identified large quantum mechanical effects in the dynamics of liquid water. In this paper, we suggest that these effects may have been overestimated due to the use of rigid water models and flexible models in which the intramolecular interactions were described using simple harmonic functions. To demonstrate this, we introduce a new simple point charge model for liquid water, q-TIP4P/F, in which the O-H stretches are described by Morse-type functions. We have parametrized this model to give the correct liquid structure, diffusion coefficient, and infrared absorption frequencies in quantum (path integral-based) simulations. The model also reproduces the experimental temperature variation of the liquid density and affords reasonable agreement with the experimental melting temperature of hexagonal ice at atmospheric pressure. By comparing classical and quantum simulations of the liquid, we find that quantum mechanical fluctuations increase the rates of translational diffusion and orientational relaxation in our model by a factor of around 1.15. This effect is much smaller than that observed in all previous simulations of empirical water models, which have found a quantum effect of at least 1.4 regardless of the quantum simulation method or the water model employed. The small quantum effect in our model is a result of two competing phenomena. Intermolecular zero point energy and tunneling effects destabilize the hydrogen-bonding network, leading to a less viscous liquid with a larger diffusion coefficient. However, this is offset by intramolecular zero point motion, which changes the average water monomer geometry resulting in a larger dipole moment, stronger intermolecular interactions, and a slower diffusion. We end by suggesting, on the basis of simulations of other potential energy models, that the small quantum effect we find in the diffusion coefficient is associated with the ability of our model to produce a single broad O-H stretching band in the infrared absorption spectrum.},
author = {Habershon, Scott and Markland, Thomas E and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {24501},
pmid = {19603998},
title = {{Competing quantum effects in the dynamics of a flexible water model.}},

volume = {131},
year = {2009}
}
@article{knig-ruiz13jna,
abstract = {As long as a square non-negative matrix A has total support then it can be balanced, that is, we can find a diagonal scaling of A that has row and column sums equal to one. A number of algorithms have been proposed to achieve the balancing, the most well known of these being Sinkhorn-Knopp. In this paper, we derive new algorithms based on inner-outer iteration schemes. We show that Sinkhorn-Knopp belongs to this family, but other members can converge much more quickly. In particular, we show that while stationary iterative methods offer little or no improvement in many cases, a scheme using a preconditioned conjugate gradient method as the inner iteration converges at much lower cost (in terms of matrix-vector products) for a broad range of matrices; and succeeds in cases where the Sinkhorn-Knopp algorithm fails.},
author = {Knight, Philip a. and Ruiz, Daniel},



journal = {IMA Journal of Numerical Analysis},


pages = {1029--1047},
title = {{A fast algorithm for matrix balancing}},
volume = {33},
year = {2013}
}
@article{angi11jpcm,
author = {Angioletti-Uberti, S},



journal = {J. Phys. Cond. Matt.},


pages = {435008},
title = {{The solid-liquid interface free-energy of Pb: comparison of theory and experiments}},

volume = {23},
year = {2011}
}
@article{izra+97bj,
author = {Izrailev, S and Stepaniants, S and Balsera, M and Oono, Y and Schulten, K},

journal = {Biophys. J.},

pages = {1568--1581},
publisher = {Elsevier},
title = {{Molecular dynamics study of unbinding of the avidin-biotin complex}},
volume = {72},
year = {1997}
}
@article{Luscher1994,
author = {L{\"{u}}scher, Martin},



journal = {Nucl. Phys. B},


pages = {637--648},
title = {{A new approach to the problem of dynamical quarks in numerical simulations of lattice QCD}},

volume = {418},
year = {1994}
}
@article{bart+13prb,
author = {Bart{\'{o}}k, Albert P. and Kondor, Risi and Cs{\'{a}}nyi, G{\'{a}}bor},



journal = {Phys. Rev. B},


pages = {184115},
title = {{On representing chemical environments}},

volume = {87},
year = {2013}
}
@article{jack-mant91bba,
author = {Jackson, Michael and Mantsch, Henry H.},



journal = {Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology},


pages = {231--235},
title = {{Beware of proteins in DMSO}},

volume = {1078},
year = {1991}
}
@article{bisw-pan98apl,
author = {Biswas, R and Pan, B C},



journal = {Applied Physics Letters},

pages = {371},
title = {{Microscopic nature of Staebler-Wronski defect formation in amorphous silicon}},

volume = {72},
year = {1998}
}
@article{mali00ieee,
author = {Malik, J.},



journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},

pages = {888--905},
title = {{Normalized cuts and image segmentation}},

volume = {22},
year = {2000}
}
@article{behl+08prl,
author = {Behler, J{\"{o}}rg and Marton{\'{a}}k, Roman and Donadio, Davide and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {185501},
title = {{Metadynamics Simulations of the High-Pressure Phases of Silicon Employing a High-Dimensional Neural Network Potential}},

volume = {100},
year = {2008}
}
@article{risk72zpa,
author = {Risken, H},

journal = {Zeitschrift f{\{}{\"{u}}{\}}r Physik A},

pages = {231--243},
publisher = {Springer},
title = {{Solutions of the Fokker-Planck equation in detailed balance}},
volume = {251},
year = {1972}
}
@article{burk12jcp,
abstract = {Density functional theory (DFT) is an incredible success story. The low computational cost, combined with useful (but not yet chemical) accuracy, has made DFT a standard technique in most branches of chemistry and materials science. Electronic structure problems in a dazzling variety of fields are currently being tackled. However, DFT has many limitations in its present form: too many approximations, failures for strongly correlated systems, too slow for liquids, etc. This perspective reviews some recent progress and ongoing challenges.},
author = {Burke, Kieron},



journal = {J. Chem. Phys.},


pages = {150901},
pmid = {22519306},
title = {{Perspective on density functional theory.}},

volume = {136},
year = {2012}
}
@article{will-chan10jpcb,
author = {Willard, A P and Chandler, D},

journal = {J. Phys. Chem. B},

pages = {1954--1958},
publisher = {ACS Publications},
title = {{Instantaneous liquid interfaces}},
volume = {114},
year = {2010}
}
@misc{parr-rahm82book,
annote = {M. Parrinello and A. Rahman, in Monte Carlo Methods in Quantum Problems, edited by M. H. Kalos (Reidel, Dordrecht, 1984), page 105.},
title = {{No Title}}
}
@article{olms+04msmse,
abstract = {Diffusion of vacancies and impurities in metals is important in many processes occurring in structural materials. This diffusion often takes place in the presence of spatially rapidly varying stresses. Diffusion under stress is frequently modelled by local approximations to the vacancy formation and diffusion activation enthalpies which are linear in the stress, in order to account for its dependence on the local stress state and its gradient. Here, more accurate local approximations to the vacancy formation and diffusion activation enthalpies, and the simulation methods needed to implement them, are introduced. The accuracy of both these approximations and the linear approximations are assessed via comparison to full atomistic studies for the problem of vacancies around a Lomer dislocation in Aluminium. Results show that the local and linear approximations for the vacancy formation enthalpy and diffusion activation enthalpy are accurate to within 0.05 eV outside a radius of about 13 Angstrom (local) and 17 Angstrom (linear) from the centre of the dislocation core or, more generally, for a strain gradient of roughly up to 6 x 10(6) m(-1) and 3 x 10(6) m(-1), respectively. These results provide a basis for the development of multiscale models of diffusion under highly non-uniform stress.},
author = {Olmsted, D.L. and Philips, R. and Curtin, W. A.},


isbn = {0965-0393},

journal = {Modelling and Simulation in Materials Science and Engineering},

pages = {159--161},
title = {{Modelling diffusion in crystals under high internal stress gradients}},

volume = {13},
year = {2004}
}
@article{boyk+16science,
author = {Boyken, S. E. and Chen, Z and Groves, B and Langan, R. A. and Oberdorfer, G and Ford, A and Gilmore, J. M. and Xu, C and DiMaio, F and Pereira, J. H. and Sankaran, B and Seelig, G and Zwart, P. H. and Baker, D},



journal = {Science},


pages = {680--687},
pmid = {27151862},
title = {{De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity}},

volume = {352},
year = {2016}
}
@article{kent82jrss,
author = {Kent, JT T},


journal = {Journal of the Royal Statistical Society. Series BSeries B},


pages = {71--80},
title = {{The Fisher-Bingham distribution on the sphere}},

volume = {44},
year = {1982}
}
@article{klon+08nl,
abstract = {A combination of quantum and classical calculations have been performed in order to investigate hydrogen storage in metal-organic frameworks (MOFs) modified by lithium alkoxide groups. Ab initio calculations showed that the interaction energies between the hydrogen molecules and this functional group are up to three times larger compared with unmodified MOF. This trend was verified by grand canonical Monte Carlo (GCMC) simulations in various thermodynamic conditions. The gravimetric capacity of the Li-modified MOFs reached the value of 10 wt {\%} at 77 K and 100 bar, while our results are very promising at room temperature, too, with 4.5 wt {\%}.},
author = {Klontzas, Emmanouel and Mavrandonakis, Andreas and Tylianakis, Emmanuel and Froudakis, George E},



journal = {Nano letters},



pages = {1572--6},
pmid = {18494530},
title = {{Improving hydrogen storage capacity of MOF by functionalization of the organic linker with lithium atoms.}},

volume = {8},
year = {2008}
}
@article{tan-yang08apl,
author = {Tan, X and Yang, G W},


journal = {Applied Physics Letters},

pages = {61902},
publisher = {AIP},
title = {{Physical mechanisms of hydrogen-enhanced onset of epitaxial growth of silicon by plasma-enhanced chemical vapor deposition}},
volume = {93},
year = {2008}
}
@article{orim+07cr,
author = {Orimo, S and Nakamori, Y and Eliseo, J R and Zuttel, A and Jensen, C M},

journal = {Chem. Rev},

pages = {4111--4132},
title = {{Complex hydrides for hydrogen storage}},
volume = {107},
year = {2007}
}
@article{hors+01tafm,
author = {Horstemeyer, M.F. F and Baskes, M.I. I and Plimpton, S.J. J},



journal = {Theoretical and Applied Fracture Mechanics},

mendeley-tags = {aluminum},


pages = {49--98},
title = {{Computational nanoscale plasticity simulations using embedded atom potentials}},

volume = {37},
year = {2001}
}
@article{du+93prl,
author = {Du, Q. and Superfine, R. and Freysz, E. and Shen, Y. R},



journal = {Phys. Rev. Lett.},


pages = {2313--2316},
publisher = {American Physical Society},
title = {{Vibrational spectroscopy of water at the vapor/water interface}},

volume = {70},
year = {1993}
}
@article{medd+14jctc,
author = {Medders, Gregory R. and Babin, Volodymyr and Paesani, Francesco},



journal = {J. Chem. Theory Comput.},


pages = {2906--2910},
title = {{Development of a "First-Principles" Water Potential with Flexible Monomers. III. Liquid Phase Properties}},

volume = {10},
year = {2014}
}
@article{sit+07prb,
abstract = {A direct measure of hydrogen bonding in water under conditions ranging from the normal state to the supercritical regime is derived from the Compton scattering of inelastically-scattered X-rays. First, we show that a measure of the number of electrons {\{}{\$}{\}}n{\{}{\_}{\}}e{\{}{\$}{\}} involved in hydrogen bonding at varying thermodynamic conditions can be directly obtained from Compton profile differences. Then, we use first-principles simulations to provide a connection between {\{}{\$}{\}}n{\{}{\_}{\}}e{\{}{\$}{\}} and the number of hydrogen bonds {\{}{\$}{\}}n{\{}{\_}{\}}{\{}{\{}{\}}HB{\{}{\}}{\}}{\{}{\$}{\}}. Our study shows that over the broad range studied the relationship between {\{}{\$}{\}}n{\{}{\_}{\}}e{\{}{\$}{\}} and {\{}{\$}{\}}n{\{}{\_}{\}}{\{}{\{}{\}}HB{\{}{\}}{\}}{\{}{\$}{\}} is linear, allowing for a direct experimental measure of bonding and coordination in water. In particular, the transition to supercritical state is characterized by a sharp increase in the number of water monomers, but also displays a significant number of residual dimers and trimers.},
archivePrefix = {arXiv},
arxivId = {cond-mat/0702617},
author = {Sit, Patrick H L and Bellin, Christophe and Barbiellini, Bernardo and Testemale, D. and Hazemann, J. L. and Buslaps, T. and Marzari, Nicola and Shukla, Abhay},



isbn = {1098-0121},

journal = {Phys. Rev. B - Condensed Matter and Materials Physics},

mendeley-tags = {electron compton scattering,hydrogen bond},
pages = {1--7},
pmid = {251986600094},
primaryClass = {cond-mat},
title = {{Hydrogen bonding and coordination in normal and supercritical water from x-ray inelastic scattering}},
volume = {76},
year = {2007}
}
@article{li+10jpcc,
author = {Li, Wen and Scheicher, Ralph H and Ara{\'{u}}jo, C. Moys{\'{e}}s and Wu, Guotao and Blomqvist, Andreas and Wu, Chenzhang and Ahuja, Rajeev and Feng, Yuan Ping and Chen, Ping},



journal = {J. Phys. Chem. C},


pages = {19089--19095},
title = {{Understanding from First-Principles Why LiNH 2 BH 3 {\textperiodcentered}NH 3 BH 3 Shows Improved Dehydrogenation over LiNH 2 BH 3 and NH 3 BH 3}},

volume = {114},
year = {2010}
}
@article{brod+77prb,
author = {Brodsky, M. and Cardona, Manuel and Cuomo, J.},



journal = {Phys. Rev. B},


pages = {3556--3571},
title = {{Infrared and Raman spectra of the silicon-hydrogen bonds in amorphous silicon prepared by glow discharge and sputtering}},

volume = {16},
year = {1977}
}
@article{lin+11jsp,
author = {Lin, Lin and Morrone, Joseph A. and Car, Roberto},



journal = {J. Stat. Phys.},



pages = {365--384},
title = {{Correlated Tunneling in Hydrogen Bonds}},

volume = {145},
year = {2011}
}
@article{adam-baro99jcp,
abstract = {We present an analysis of the performances of a parameter free density functional model (PBE0) obtained combining the so called PBE generalized gradient functional with a predefined amount of exact exchange. The results obtained for structural, thermodynamic, kinetic and spectroscopic (magnetic, infrared and electronic) properties are satisfactory and not far from those delivered by the most reliable functionals including heavy parameterization. The way in which the functional is derived and the lack of empirical parameters fitted to specific properties make the PBE0 model a widely applicable method for both quantum chemistry and condensed matter physics.},
author = {Adamo, Carlo and Barone, Vincenzo},



journal = {J. Chem. Phys.},

pages = {6158},
publisher = {Aip},
title = {{Toward reliable density functional methods without adjustable parameters: The PBE0 model}},

volume = {110},
year = {1999}
}
@article{habe+07jcp,
abstract = {The maximum entropy analytic continuation (MEAC) and ring polymer molecular dynamics (RPMD) methods provide complementary approaches to the calculation of real time quantum correlation functions. RPMD becomes exact in the high temperature limit, where the thermal time betavariant Planck's over 2pi tends to zero and the ring polymer collapses to a single classical bead. MEAC becomes most reliable at low temperatures, where betavariant Planck's over 2pi exceeds the correlation time of interest and the numerical imaginary time correlation function contains essentially all of the information that is needed to recover the real time dynamics. We show here that this situation can be exploited by combining the two methods to give an improved approximation that is better than either of its parts. In particular, the MEAC method provides an ideal way to impose exact moment (or sum rule) constraints on a prior RPMD spectrum. The resulting scheme is shown to provide a practical solution to the "nonlinear operator problem" of RPMD, and to give good agreement with recent exact results for the short-time velocity autocorrelation function of liquid parahydrogen. Moreover these improvements are obtained with little extra effort, because the imaginary time correlation function that is used in the MEAC procedure can be computed at the same time as the RPMD approximation to the real time correlation function. However, there are still some problems involving long-time dynamics for which the RPMD+MEAC combination is inadequate, as we illustrate with an example application to the collective density fluctuations in liquid orthodeuterium.},
author = {Habershon, Scott and Braams, Bastiaan J and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {174108},
pmid = {17994808},
title = {{Quantum mechanical correlation functions, maximum entropy analytic continuation, and ring polymer molecular dynamics}},

volume = {127},
year = {2007}
}
@article{koon91nature,
author = {Koonin, Steven E.},



journal = {Nature},


pages = {468--470},
title = {{Environmental fine structure in low-energy $\beta$-particle spectra}},

volume = {354},
year = {1991}
}
@article{mazz+10prl,
author = {Mazzarello, Riccardo and Caravati, Sebastiano and Angioletti-Uberti, Stefano and Bernasconi, Marco and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {85503},
title = {{Signature of Tetrahedral Ge in the Raman Spectrum of Amorphous Phase-Change Materials}},

volume = {104},
year = {2010}
}
@article{math-pava04jcp,
author = {Mathias, Gerald and Tavan, Paul},


journal = {J. Chem. Phys.},


pages = {4393--4403},
title = {{Angular resolution and range of dipole?dipole correlations in water}},

volume = {120},
year = {2004}
}
@article{mora+13prb,
abstract = {We examine the influence of the main approximations employed in density-functional theory de- scriptions of the solid phase of molecular hydrogen near dissociation. We consider the importance of nuclear quantum effects on equilibrium properties and find that they strongly influence intramolec- ular properties, such as bond fluctuations and stability. We demonstrate that the combination of both thermal and quantum effects make a drastic change to the predicted optical properties of the molecular solid, suggesting a limited value to dynamical, e.g., finite-temperature, predictions based on classical ions and static crystals. We also consider the influence of the chosen exchange– correlation density functional on the predicted properties of hydrogen, in particular, the pressure dependence of the band gap and the zero-point energy. Finally, we use our simulations to make an assessment of the accuracy of typically employed approximations to the calculation of the Gibbs free energy of the solid, namely the quasi-harmonic approximation for solids. We find that, while the approximation is capable of producing free energies with an accuracy of ≈ 10 meV, this is not enough to make reliable predictions of the phase diagram of hydrogen from first-principles due to the small free energy differences seen between several potential structures for the solid; direct free energy calculations for quantum protons are required in order to make definite predictions.},
archivePrefix = {arXiv},
arxivId = {arXiv:1303.6673v1},
author = {Morales, Miguel a. and McMahon, Jeffrey M. and Pierleoni, Carlo and Ceperley, David M.},




journal = {Phys. Rev. B - Condensed Matter and Materials Physics},

pages = {1--9},
title = {{Towards a predictive first-principles description of solid molecular hydrogen with density functional theory}},
volume = {87},
year = {2013}
}
@article{wang07prl,
author = {Wang, Jian-Sheng},

journal = {Phys. Rev. Lett.},

pages = {160601},
title = {{Quantum Thermal Transport from Classical Molecular Dynamics}},
volume = {99},
year = {2007}
}
@article{poma+12pccp,
abstract = {The path integral single sweep method is used to assess quantum effects on the free energy barrier for hydrogen vacancy diffusion in a defective Na(3)AlH(6) crystal. This process has been investigated via experiments and simulations due to its potential relevance in the H release mechanism in sodium alanates, prototypical materials for solid state hydrogen storage. Previous computational studies, which used density functional methods for the electronic structure, were restricted to a classical treatment of the nuclear degrees of freedom. We show that, although they do not change the qualitative picture of the process, nuclear quantum effects reduce the free energy barrier height by about 18{\%} with respect to the classical calculation improving agreement with available neutron scattering data.},
author = {Poma, Adolfo and Monteferrante, Michele and Bonella, Sara and Ciccotti, Giovanni},



journal = {PCCP},


pages = {15458--63},
pmid = {23064527},
title = {{The quantum free energy barrier for hydrogen vacancy diffusion in Na3AlH6.}},

volume = {14},
year = {2012}
}
@article{medd+15jcp,
author = {Medders, Gregory R. and G{\"{o}}tz, Andreas W. and Morales, Miguel A. and Bajaj, Pushp and Paesani, Francesco},



journal = {J. Chem. Phys.},


pages = {104102},
title = {{On the representation of many-body interactions in water}},

volume = {143},
year = {2015}
}
@article{grau05ieee,
abstract = {Discriminative learning is challenging when examples are sets of features, and the sets vary in cardinality and lack any sort of meaningful ordering. Kernel-based classification methods can learn complex decision boundaries, but a kernel over unordered set inputs must somehow solve for correspondences epsivnerally a computationally expensive task that becomes impractical for large set sizes. We present a new fast kernel function which maps unordered feature sets to multi-resolution histograms and computes a weighted histogram intersection in this space. This "pyramid match" computation is linear in the number of features, and it implicitly finds correspondences based on the finest resolution histogram cell where a matched pair first appears. Since the kernel does not penalize the presence of extra features, it is robust to clutter. We show the kernel function is positive-definite, making it valid for use in learning algorithms whose optimal solutions are guaranteed only for Mercer kernels. We demonstrate our algorithm on object recognition tasks and show it to be accurate and dramatically faster than current approaches},
author = {Grauman, Kristen and Darrell, Trevor},


isbn = {076952334X},

journal = {Proceedings of the IEEE International Conference on Computer Vision},

pages = {1458--1465},
title = {{The pyramid match kernel: Discriminative classification with sets of image features}},
volume = {II},
year = {2005}
}
@article{chen-zhu08mt,
author = {Chen, Ping and Zhu, Min},



journal = {Materials Today},


pages = {36--43},
publisher = {Elsevier},
title = {{Recent progress in hydrogen storage}},

volume = {11},
year = {2008}
}
@article{metr+53jcp,
annote = {
        

        

        

        From Duplicate 2 ( 
        

        

        

        
        

        

        

        
          

          

          

          Equation of State Calculations by Fast Computing Machines
          

          

          

        
        

        

        

        
        

        

        

         - Metropolis, Nicholas; Rosenbluth, Arianna W; Rosenbluth, Marshall N; Teller, Augusta H; Teller, Edward )

          

          

          

        
        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

      },
author = {Metropolis, Nicholas and Rosenbluth, Arianna W and Rosenbluth, Marshall N and Teller, Augusta H and Teller, Edward},

journal = {J. Chem. Phys.},


pages = {1087--1092},
publisher = {AIP},
title = {{Equation of State Calculations by Fast Computing Machines}},
volume = {21},
year = {1953}
}
@article{plim95jcp,
author = {Plimpton, Steve},



journal = {J. Comp. Phys.},


pages = {1--19},
title = {{Fast Parallel Algorithms for Short-Range Molecular Dynamics}},

volume = {117},
year = {1995}
}
@article{chen+15prb,
abstract = {{\textcopyright} 2015 American Physical Society. The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill defined. Here we draw a connection between the atomistic description of a diffuse solid-liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.},
author = {Cheng, Bingqing and Tribello, G.A. Gareth A. and Ceriotti, Michele},



journal = {Phys. Rev. B},


pages = {180102},
title = {{Solid-liquid interfacial free energy out of equilibrium}},

volume = {92},
year = {2015}
}
@article{gude+72jcp,
author = {G{\"{u}}del, H U and Ludi, A and Fischer, P},

journal = {J. Chem. Phys.},

pages = {674--675},
publisher = {AIP},
title = {{Hydrogen Bond in D[sub 3]Co(CN)[sub 6]. A Low Temperature Neutron Diffraction Study}},
volume = {56},
year = {1972}
}
@article{alav-frenk92jcp,
author = {Alavi, A and Frenkel, D},

journal = {J. Chem. Phys.},
pages = {9249},
title = {{Grand-canonical simulations of solvated ideal fermions. Evidence for phase separation}},
volume = {97},
year = {1992}
}
@article{litm+17jcp,
abstract = {Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQE) influence properties of these systems. In this work, we explore the impact of NQE on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account conformational entropy and anharmonicities at finite temperatures. We propose that when when adsorption is weak and NQE on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We calculate the contribution of NQE to the free energies, including anharmonic terms. We find that they result in an increase of up to 20{\%} of the quantum contribution to the dissociation free energy compared to harmonic estimates. We also find that the dissociation has a negligible contribution from tunneling, but is dominated by ZPE, which can enhance the rate by three orders of magnitude. Finally we highlight how both temperature and NQE indirectly impact dipoles and the redistribution of electron density, causing work function to changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces.},
archivePrefix = {arXiv},
arxivId = {1710.04876},
author = {Litman, Yair and Donadio, Davide and Ceriotti, Michele and Rossi, Mariana},




journal = {J. Chem. Phys.},


pages = {102320},
title = {{Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature}},

volume = {148},
year = {2018}
}
@article{morr+11jcp,
abstract = {Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.},
archivePrefix = {arXiv},
arxivId = {arXiv:1008.5377v1},
author = {Morrone, Joseph A. and Markland, Thomas E. and Ceriotti, Michele and Berne, B. J.},



institution = {Department of Chemistry, Columbia University, New York, New York 10027, USA.},

journal = {J. Chem. Phys.},



pages = {14103},
pmid = {21218993},
publisher = {AIP},
title = {{Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances}},

volume = {134},
year = {2011}
}
@article{bedo+14prb,
author = {Bedoya-Mart{\'{i}}nez, O. N. and Barrat, Jean-Louis and Rodney, David and Bedoya-Mart$\backslash$'$\backslash$inez, O N and Barrat, Jean-Louis and Rodney, David},



journal = {Phys. Rev. B},


pages = {14303},
title = {{Computation of the thermal conductivity using methods based on classical and quantum molecular dynamics}},

volume = {89},
year = {2014}
}
@article{giof+17am,
abstract = {Age hardening induced by the formation of (semi)-coherent precipitate phases is crucial for the processing and final properties of the widely used Al-6000 alloys. Early stages of precipitation are particularly important from the fundamental and technological side, but are still far from being fully understood. Here, an analysis of the energetics of nanometric precipitates of the meta-stable $\beta$″ phases is performed, identifying the bulk, elastic strain and interface energies that contribute to the stability of a nucleating cluster. Results show that needle-shape precipitates are unstable to growth even at the smallest size $\beta$″ formula unit, i.e. there is no energy barrier to growth. The small differences between different compositions points toward the need for the study of possible precipitate/matrix interface reconstruction. A classical semi-quantitative nucleation theory approach including elastic strain energy captures the trends in precipitate energy versus size and composition. This validates the use of mesoscale models to assess stability and interactions of precipitates. Studies of smaller 3D clusters also show stability relative to the solid solution state, indicating that the early stages of precipitation may be diffusion-limited. Overall, these results demonstrate the important interplay among composition-dependent bulk, interface, and elastic strain energies in determining nanoscale precipitate stability and growth.},
author = {Giofr{\'{e}}, Daniele and Junge, Till and Curtin, W.A. A. and Ceriotti, Michele},



journal = {Acta Materialia},

pages = {240--249},
title = {{Ab initio modelling of the early stages of precipitation in Al-6000 alloys}},
volume = {140},
year = {2017}
}
@article{marx06cpc,
abstract = {In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.},
author = {Marx, Dominik},



journal = {Chemphyschem : a European J. Chem. Phys. and physical chemistry},


pages = {1848--70},
pmid = {16929553},
title = {{Proton transfer 200 years after von Grotthuss: insights from ab initio simulations.}},

volume = {7},
year = {2006}
}
@article{yang+11prl,
abstract = {Nonequilibrium kinetic properties of alloy crystal-melt interfaces are calculated by molecular-dynamics simulations. The relationships between the interface velocity, thermodynamic driving force, and solute partition coefficient are computed and analyzed within the framework of kinetic theories accounting for solute trapping and solute drag. The results show a transition to complete solute trapping at high growth velocities, establish appreciable solute drag at low growth velocities, and provide insights into the nature of crystalline anisotropies and solute effects on interface mobilities.},
author = {Yang, Yang and Humadi, Harith and Buta, Dorel and Laird, Brian B. and Sun, Deyan and Hoyt, Jeffrey J. and Asta, Mark},



journal = {Phys. Rev. Lett.},

pages = {8--11},
pmid = {21797620},
title = {{Atomistic simulations of nonequilibrium crystal-growth kinetics from alloy melts}},
volume = {107},
year = {2011}
}
@article{harri-wool79jcs,
author = {Harris, Kenneth R. and Woolf, Lawrence A.},



journal = {Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases},
pages = {377},
title = {{Pressure and temperature dependence of the self diffusion coefficient of water and oxygen-18 water}},

volume = {76},
year = {1980}
}
@article{zhan+11jctc,
abstract = {We show that first principles hybrid functional (PBE0) simulations of the infrared spectrum of liquid water yields a much better agreement with experimental results than a semilocal functional description; in particular, the quantitative accord with measured stretching and bending bands is very good. Such an improved description stems from two effects: a more accurate account, at the PBE0 level of theory, of the vibrational properties of the monomer and dimer and an underlying structural model for the liquid with a smaller number of hydrogen bonds and oxygen coordination than those obtained with semilocal functionals. The average electronic gap of the liquid is increased by 60{\%} with respect to the PBE value, when computed at the PBE0 level of theory, and is in fair agreement with experimental results.},
author = {Zhang, Cui and Donadio, Davide and Galli, Giulia and Gygi, François},



journal = {J. Chem. Theory Comput.},

pages = {1443--1449},
title = {{First Principles Simulations of the Infrared Spectrum of Liquid Water Using Hybrid Density Functionals}},

volume = {7},
year = {2011}
}
@article{wolv+04prb,
author = {Wolverton, C. and Ozoliņ{\v{s}}, V. and Asta, M.},



journal = {Phys. Rev. B},

mendeley-tags = {aluminum,diffusion,hydrogen in metals},


pages = {144109},
title = {{Hydrogen in aluminum: First-principles calculations of structure and thermodynamics}},

volume = {69},
year = {2004}
}
@article{behl-parr07prl,
author = {Behler, J{\"{o}}rg and Parrinello, Michele},



journal = {Phys. Rev. Lett.},


pages = {146401},
title = {{Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces}},

volume = {98},
year = {2007}
}
@article{pred+04jcp,
abstract = {We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the ratio of the temperatures. The law, called the incomplete beta function law, is valid in the limit that the two temperatures involved in swaps are close to one another. An empirical version of the law, which involves the heat capacity of the system, is developed and tested on a Lennard-Jones cluster. We argue that the best initial guess for the distribution of intermediate temperatures for parallel tempering is a geometric progression and we also propose a technique for the computation of optimal temperature schedules. Finally, we demonstrate that the swap efficiency of the parallel tempering method for condensed-phase systems decreases naturally to zero at least as fast as the inverse square root of the dimensionality of the physical system.},
author = {Predescu, Cristian and Predescu, Mihaela and Ciobanu, Cristian V},



journal = {J. Chem. Phys.},


pages = {4119--28},
pmid = {15268578},
title = {{The incomplete beta function law for parallel tempering sampling of classical canonical systems.}},

volume = {120},
year = {2004}
}
@article{lucz05chaos,
abstract = {We survey classical non-Markovian processes driven by thermal equilibrium or nonequilibrium (nonthermal) colored noise. Examples of colored noise are presented. For processes driven by thermal equilibrium noise, the fluctuation-dissipation relation holds. In consequence, the system has to be described by a generalized (integro-differential) Langevin equation with a restriction on the damping integral kernel: Its form depends on the correlation function of noise. For processes driven by nonequilibrium noise, there is no such a restriction: They are considered to be described by stochastic differential (Ito- or Langevin-type) equations with an independent noise term. For the latter, we review methods of analysis of one-dimensional systems driven by Ornstein-Uhlenbeck noise.},
author = {Luczka, J},



journal = {Chaos},



pages = {26107},
pmid = {16035909},
title = {{Non-Markovian stochastic processes: Colored noise}},

volume = {15},
year = {2005}
}
@article{jang+14jcp,
author = {Jang, Seogjoo and Sinitskiy, Anton V. and Voth, Gregory a.},



journal = {J. Chem. Phys.},


pages = {154103},
title = {{Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?}},

volume = {140},
year = {2014}
}
@article{ceri-parr10pcs,
annote = {ICCS 2010},
author = {Ceriotti, Michele and Parrinello, Michele},



journal = {Procedia Computer Science},


pages = {1607--1614},
title = {{The $\delta$-thermostat: selective normal-modes excitation by colored-noise Langevin dynamics}},

volume = {1},
year = {2010}
}
@article{coll+08jcp,
abstract = {We have used the ring polymer molecular dynamics method to study the Azzouz-Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A-H distance is used as the reaction coordinate, the ring polymer trajectories are found to exhibit multiple recrossings of the transition state dividing surface and to give a rate coefficient that is smaller than the quantum transition state theory value by an order of magnitude. This is to be expected on kinematic grounds for a heavy-light-heavy reaction when the light atom transfer coordinate is used as the reaction coordinate, and it clearly precludes the use of transition state theory with this reaction coordinate. As has been shown previously for this problem, a solvent polarization coordinate defined in terms of the expectation value of the proton transfer distance in the ground adiabatic quantum state provides a better reaction coordinate with less recrossing. These results are discussed in light of the wide body of earlier theoretical work on the Azzouz-Borgis model and the considerable range of previously reported values for its proton and deuteron transfer rate coefficients.},
author = {Collepardo-Guevara, Rosana and Craig, Ian R and Manolopoulos, David E},



journal = {J. Chem. Phys.},


pages = {144502},
pmid = {18412454},
title = {{Proton transfer in a polar solvent from ring polymer reaction rate theory.}},

volume = {128},
year = {2008}
}
@article{scha+93jltp,
author = {Scharf, Daphna and Martyna, Glenn J and Klein, Michael L},

journal = {J. Low Temp. Phys.},

pages = {364--367},
publisher = {AIP},
title = {{Structure and energetics of fluid para-hydrogen}},
volume = {19},
year = {1993}
}
@article{kang-musg01prb,
author = {{Ku Kang}, Jeung and Musgrave, Charles B},



journal = {Phys. Rev. B},


pages = {245330},
title = {{Theoretical study of the chemical vapor deposition of (100) silicon from silane}},

volume = {64},
year = {2001}
}
@article{Publishing2011,
author = {Publishing, Blackwell},

pages = {3--23},
title = {{No Title}},
volume = {55},
year = {2011}
}
@inproceedings{pan-reif85proc,
address = {New York, NY, USA},
author = {Pan, V and Reif, J},
booktitle = {STOC85: Proceedings of the seventeenth annual ACM symposium on Theory of computing},


isbn = {0-89791-151-2},
pages = {143},
publisher = {ACM Press},
title = {{Efficient parallel solution of linear systems}},
year = {1985}
}
@article{ceri+09prl2,
abstract = {We present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasiharmonic system. By properly fitting the correlation function of the noise, one can vary the fluctuations in positions and momenta as a function of the vibrational frequency, and fit them so as to reproduce the quantum-mechanical behavior, with minimal a priori knowledge of the details of the system. We discuss the application of the thermostat to diamond and to ice Ih. We find that results in agreement with path-integral methods can be obtained using only a fraction of the computational effort.},
author = {Ceriotti, Michele and Bussi, Giovanni and Parrinello, Michele},


institution = {Computational Science, Department of Chemistry and Applied Biosciences, ETH Z{\"{u}}rich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland. michele.ceriotti@phys.chem.ethz.ch},

journal = {Phys. Rev. Lett.},


pages = {30603},
publisher = {APS},
title = {{Nuclear Quantum Effects in Solids Using a Colored-Noise Thermostat}},

volume = {103},
year = {2009}
}
@article{liu+99prb,
author = {Liu, Amy Y and Quong, Andrew A and Jones, Emily C and Freericks, J K and Nicol, E J},

journal = {Phys. Rev. B},

pages = {4028--4035},
publisher = {American Physical Society},
title = {{Structural phase stability and electron-phonon coupling in lithium}},
volume = {59},
year = {1999}
}
@article{frol-mish09prb,
author = {Frolov, T. and Mishin, Y.},



journal = {Phys. Rev. B},


pages = {045430},
title = {{Temperature dependence of the surface free energy and surface stress: An atomistic calculation for Cu(110)}},

volume = {79},
year = {2009}
}
@article{vann+18jctc,
abstract = {{\textcopyright} 2018 American Chemical Society. The Density Overlap Region Indicator (DORI) is a density-based scalar field that reveals covalent bonding patterns and noncovalent interactions in the same value range. This work goes beyond the traditional static quantum chemistry use of scalar fields and illustrates the suitability of DORI for analyzing geometrical and electronic signatures in highly fluxional molecular systems. Examples include a dithiocyclophane, which possesses multiple local minima with differing extents of $\pi$-stacking interactions and a temperature dependent rotation of a molecular rotor, where the descriptor is employed to capture fingerprints of CH-$\pi$ and $\pi$- $\pi$ interactions. Finally, DORI serves to examine the fluctuating $\pi$-conjugation pathway of a photochromic torsional switch (PTS). Attention is also placed on postprocessing the large amount of generated data and juxtaposing DORI with a data-driven low-dimensional representation of the structural landscape.},
author = {Vannay, Laurent and Meyer, Benjamin and Petraglia, Riccardo and Sforazzini, Giuseppe and Ceriotti, Michele and Corminboeuf, Cl{\'{e}}mence},



journal = {J. Chem. Theory Comput.},


pages = {2370--2379},
title = {{Analyzing Fluxional Molecules Using DORI}},

volume = {14},
year = {2018}
}
@article{delb+15cpc,
abstract = {The Random Phase Approximation (RPA), which represents the fifth rung of accuracy in Density Functional Theory (DFT), is made practical for large systems. Energies of condensed phase systems containing thousands of explicitly correlated electrons and 1500 atoms can now be computed in minutes and less than 1 h, respectively. GPU acceleration is employed for dense and sparse linear algebra, while communication is minimized by a judicious data layout. The performance of the algorithms, implemented in the widely used CP2K simulation package, has been investigated on hybrid Cray XC30 and XK7 architectures, up to 16,384 nodes. Our results emphasize the importance of good network performance, in addition to the availability of GPUs and generous on node memory. A new level of predictivity has thus become available for routine application in Monte Carlo and molecular dynamics simulations.},
author = {{Del Ben}, Mauro and Sch{\"{u}}tt, Ole and Wentz, Tim and Messmer, Peter and Hutter, J{\"{u}}rg and VandeVondele, Joost},



journal = {Comp. Phys. Comm.},

pages = {120--129},
publisher = {Elsevier B.V.},
title = {{Enabling simulation at the fifth rung of DFT: Large scale RPA calculations with excellent time to solution}},

volume = {187},
year = {2015}
}
@article{salv+12jacs,
author = {Salvalaglio, Matteo and Vetter, Thomas and Giberti, Federico and Mazzotti, Marco and Parrinello, Michele},



journal = {J. Chem. Am. Soc.},


pages = {17221--17233},
title = {{Uncovering Molecular Details of Urea Crystal Growth in the Presence of Additives}},

volume = {134},
year = {2012}
}
@article{broc+17nc,
abstract = {Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of density functional theory to solve electronic structure problems in a wide variety of scientific fields, ranging from materials science to biochemistry to astrophysics. Machine learning holds the promise of learning the kinetic energy functional via examples, by-passing the need to solve the Kohn-Sham equations. This should yield substantial savings in computer time, allowing either larger systems or longer time-scales to be tackled, but attempts to machine-learn this functional have been limited by the need to find its derivative. The present work overcomes this difficulty by directly learning the density-potential and energy-density maps for test systems and various molecules. Both improved accuracy and lower computational cost with this method are demonstrated by reproducing DFT energies for a range of molecular geometries generated during molecular dynamics simulations. Moreover, the methodology could be applied directly to quantum chemical calculations, allowing construction of density functionals of quantum-chemical accuracy.},
archivePrefix = {arXiv},
arxivId = {1609.02815},
author = {Brockherde, Felix and Vogt, Leslie and Li, Li and Tuckerman, Mark E. and Burke, Kieron and M{\"{u}}ller, Klaus-Robert},




journal = {Nature Comm.},


pages = {872},
pmid = {29021555},
title = {{Bypassing the Kohn-Sham equations with machine learning}},

volume = {8},
year = {2017}
}
@article{menz+11jcp,
abstract = {The use of ring polymer molecular dynamics (RPMD) for the direct simulation of electron transfer (ET) reaction dynamics is analyzed in the context of Marcus theory, semiclassical instanton theory, and exact quantum dynamics approaches. For both fully atomistic and system-bath representations of condensed-phase ET, we demonstrate that RPMD accurately predicts both ET reaction rates and mechanisms throughout the normal and activationless regimes of the thermodynamic driving force. Analysis of the ensemble of reactive RPMD trajectories reveals the solvent reorganization mechanism for ET that is anticipated in the Marcus rate theory, and the accuracy of the RPMD rate calculation is understood in terms of its exact description of statistical fluctuations and its formal connection to semiclassical instanton theory for deep-tunneling processes. In the inverted regime of the thermodynamic driving force, neither RPMD nor a related formulation of semiclassical instanton theory capture the characteristic turnover in the reaction rate; comparison with exact quantum dynamics simulations reveals that these methods provide inadequate quantization of the real-time electronic-state dynamics in the inverted regime.},
archivePrefix = {arXiv},
arxivId = {1107.5091},
author = {Menzeleev, Artur R. and Ananth, Nandini and Miller, Thomas F.},



isbn = {doi:10.1063/1.3624766},

journal = {J. Chem. Phys.},

pages = {1--17},
pmid = {21861555},
title = {{Direct simulation of electron transfer using ring polymer molecular dynamics: Comparison with semiclassical instanton theory and exact quantum methods}},
volume = {135},
year = {2011}
}
@article{gane+13prb,
abstract = {Molecules like water have vibrational modes with a zero-point energy well above room temperature. As a consequence, classical molecular dynamics simulations of their liquids largely underestimate the energy of modes with a higher zero-point temperature, which translates into an underestimation of covalent interatomic distances due to anharmonic effects. Zero-point effects can be recovered using path integral molecular dynamics simulations, but these are computationally expensive, making their combination with ab initio molecular dynamics simulations a challenge. As an alternative to path integral methods, from a computationally simple perspective, one would envision the design of a thermostat capable of equilibrating and maintaining the different vibrational modes at their corresponding zero-point temperatures. Recently, Ceriotti et al. [ Phys. Rev. Lett. 102 020601 (2009)] introduced a framework to use a custom-tailored Langevin equation with correlated noise that can be used to include quantum fluctuations in classical molecular dynamics simulations. Here we show that it is possible to use the generalized Langevin equation with suppressed noise in combination with Nose-Hoover thermostats to efficiently impose a zero-point temperature on independent modes in liquid water. Using our simple and inexpensive method, we achieve excellent agreement for all atomic pair correlation functions compared to the path integral molecular dynamics simulation.},
archivePrefix = {arXiv},
arxivId = {1208.1928},
author = {Ganeshan, Sriram and Ram{\'{i}}rez, R. and Fern{\'{a}}ndez-Serra, M. V.},




journal = {Phys. Rev. B},


pages = {134207},
title = {{Simulation of quantum zero-point effects in water using a frequency-dependent thermostat}},

volume = {87},
year = {2013}
}
@article{tkat-sche09prl,
author = {Tkatchenko, Alexandre and Scheffler, Matthias},



journal = {Phys. Rev. Lett.},


pages = {073005},
title = {{Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data}},

volume = {102},
year = {2009}
}
@article{nusk+14jctc,
abstract = {The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer operator) contain the essential information about the molecular thermodynamics and kinetics. This includes the stationary distribution, the metastable states, and state-to-state transition rates. Here, we present a variational approach for computing these dominant eigenvalues and eigenvectors. This approach is analogous to the variational approach used for computing stationary states in quantum mechanics. A corresponding method of linear variation is formulated. It is shown that the matrices needed for the linear variation method are correlation matrices that can be estimated from simple MD simulations for a given basis set. The method proposed here is thus to first define a basis set able to capture the relevant conformational transitions, then compute the respective correlation matrices, and then to compute their dominant eigenvalues and eigenvectors, thus obtaining the key ingredients of the slow kinetics.},
author = {N{\"{u}}ske, Feliks and Keller, Bettina G and Pe, Guillermo and Mey, Antonia S J S and Noe, Frank},



journal = {J. Chem. Theory Comput.},
pages = {1739--1752},
title = {{Variational Approach to Molecular Kinetics}},
volume = {10},
year = {2014}
}
@article{szla+14prb,
author = {Szlachta, Wojciech J. and Bart{\'{o}}k, Albert P. and Cs{\'{a}}nyi, G{\'{a}}bor},


journal = {Phys. Rev. B},


pages = {104108},
title = {{Accuracy and transferability of Gaussian approximation potential models for tungsten}},

volume = {90},
year = {2014}
}
@article{habe-mano11pccp,
abstract = {In this work, we consider the problem of calculating the classical free energies of liquids and solids for molecular models with intramolecular flexibility. We show that thermodynamic integration from the fully-interacting solid of interest to a Debye crystal reference state, with anisotropic harmonic interactions derived from the Hessian of the original crystal, provides a straightforward route to calculating the Gibbs free energy of the solid. To calculate the molecular liquid free energy, it is essential to correctly account for contributions from both intermolecular and intramolecular motion; we employ thermodynamic integration to a Lennard-Jones reference fluid, coupled with direct evaluation of the molecular ro-vibrational partition function. These approaches are used to study the low-pressure classical phase diagram of the flexible q-TIP4P/F water model. We find that, while the experimental ice-I/liquid and ice-III/liquid coexistence lines are described reasonably well by this model, the ice-II phase is predicted to be metastable. In light of this finding, we go on to examine how the coupling between intramolecular flexibility and intermolecular interactions influences the computed phase diagram by comparing our results with those of the underlying rigid-body water model.},
author = {Habershon, Scott and Manolopoulos, David E},



journal = {Physical Chemistry Chemical Physics},

pages = {19714},
pmid = {21887423},
title = {{Free energy calculations for a flexible water model}},

volume = {13},
year = {2011}
}
@article{Barbara1986,
author = {Barbara, Santa and Jolla, La and Diego, San and Physik, Fachbereich and Kaiserslautern, Universitrit},

pages = {133--160},
title = {{Program for Efficient Monte Carlo Computations of Quenched W ( 3 ) Lattice Gauge Theory Using the Quasi- heatbath Method on a CDC CYBER 205 Computer}},
volume = {160},
year = {1986}
}
@article{reil-tkat14prl,
abstract = {Aspirin has been used and studied for over a century but has only recently been shown to have an additional polymorphic form, known as form II. Since the two observed solid forms of aspirin are degenerate in terms of lattice energy, kinetic effects have been suggested to determine the metastability of the less abundant form II. Here, first-principles calculations provide an alternative explanation based on free-energy differences at room temperature. The explicit consideration of many-body van der Waals interactions in the free energy demonstrates that the stability of the most abundant form of aspirin is due to a subtle coupling between collective electronic fluctuations and quantized lattice vibrations. In addition, a systematic analysis of the elastic properties of the two forms of aspirin rules out mechanical instability of form II as making it metastable.},
annote = {NULL},
author = {Reilly, Anthony M. and Tkatchenko, Alexandre},


isbn = {0031-9007},

journal = {Phys. Rev. Lett.},


pages = {055701},
pmid = {25126928},
publisher = {American Physical Society},
title = {{Role of Dispersion Interactions in the Polymorphism and Entropic Stabilization of the Aspirin Crystal}},

volume = {113},
year = {2014}
}
@article{cava+99science,
abstract = {The phase diagrams of water and ammonia were determined by constant pressure ab initio molecular dynamic simulations at pressures (30 to 300 gigapascal) and temperatures (300 to 7000 kelvin) of relevance for the middle ice layers of the giant planets Neptune and Uranus. Along the planetary isentrope water and ammonia behave as fully dissociated ionic, electronically insulating fluid phases, which turn metallic at temperatures exceeding 7000 kelvin for water and 5500 kelvin for ammonia. At lower temperatures, the phase diagrams of water and ammonia exhibit a superionic solid phase between the solid and the ionic liquid. These simulations improve our understanding of the properties of the middle ice layers of Neptune and Uranus.},
author = {Cavazzoni, C and Chiarotti, G L and Scandolo, S and Tosatti, E and Bernasconi, M and Parrinello, M},



journal = {Science (New York, N.Y.)},

pages = {44--46},
pmid = {9872734},
title = {{Superionic and metallic states of water and ammonia at giant planet conditions.}},
volume = {283},
year = {1999}
}
@article{bo-smin09cc,
abstract = {To determine the breeding system of Lycium cestroides, several treatments were performed: self-, cross-, and geitonogamous pollinations, autonomous self-pollination, and a control (flowers exposed to natural pollinators). Production and quality of fruits and seeds as well as pollen tube growth were evaluated for each treatment. Experimental pollinations indicate that L. cestroides is self-incompatible since fruits were obtained only under cross-, and open-pollination treatments. However, in self- and geitonogamous hand pollinations, as well as in autonomous self-pollination, pollen tubes developed successfully and reached the ovules. The speed of pollen tube growth did not differ significantly among the different hand-pollinated flowers (cross-, self-, and geitonogamous). These facts indicate the presence of an ovarian self-incompatibility system. Significant differences were observed in fruit set, fruit size, and seed number per fruit between cross-pollinated flowers and open pollination (control). These results could be explained in terms of quantity and quality of pollination in each case},
author = {Bo, Liefeng and Sminchisescu, Cristian},


isbn = {9781615679119},

journal = {Computational Complexity},

pages = {1--9},
pmid = {9256856},
title = {{Efficient Match Kernels between Sets of Features for Visual Recognition}},

volume = {2},
year = {2009}
}
@article{gasp-ceri14jcp,
abstract = {{\textcopyright} 2014 AIP Publishing LLC. The concept of chemical bonding can ultimately be seen as a rationalization of the recurring structural patterns observed in molecules and solids. Chemical intuition is nothing but the ability to recognize and predict such patterns, and how they transform into one another. Here, we discuss how to use a computer to identify atomic patterns automatically, so as to provide an algorithmic definition of a bond based solely on structural information. We concentrate in particular on hydrogen bonding - a central concept to our understanding of the physical chemistry of water, biological systems, and many technologically important materials. Since the hydrogen bond is a somewhat fuzzy entity that covers a broad range of energies and distances, many different criteria have been proposed and used over the years, based either on sophisticate electronic structure calculations followed by an energy decomposition analysis, or on somewhat arbitrary choices of a range of structural parameters that is deemed to correspond to a hydrogen-bonded configuration. We introduce here a definition that is univocal, unbiased, and adaptive, based on our machine-learning analysis of an atomistic simulation. The strategy we propose could be easily adapted to similar scenarios, where one has to recognize or classify structural patterns in a material or chemical compound.},
author = {Gasparotto, Piero and Ceriotti, Michele},



journal = {J. Chem. Phys.},


pages = {174110},
title = {{Recognizing molecular patterns by machine learning: An agnostic structural definition of the hydrogen bond}},

volume = {141},
year = {2014}
}
@article{morr-car08prl,
author = {Morrone, Joseph A and Car, Roberto},

journal = {Phys. Rev. Lett.},

pages = {17801},
title = {{Nuclear Quantum Effects in Water}},
volume = {101},
year = {2008}
}
@article{coma-meer02ieee,
author = {Comaniciu, Dorin and Meer, Peter},



journal = {IEEE Trans. Pattern Anal. Mach. Intell.},


pages = {603--619},
title = {{Mean shift: a robust approach toward feature space analysis}},

volume = {24},
year = {2002}
}
@article{kimi+11prb,
author = {Kimizuka, Hajime and Mori, Hideki and Ogata, Shigenobu},



journal = {Phys. Rev. B},


pages = {094110},
title = {{Effect of temperature on fast hydrogen diffusion in iron: A path-integral quantum dynamics approach}},

volume = {83},
year = {2011}
}
@article{buyu+08pre,
author = {Buyukdagli, Sahin and Savin, Alexander V and Hu, Bambi},

journal = {Phys. Rev. E},

pages = {66702},
publisher = {APS},
title = {{Computation of the temperature dependence of the heat capacity of complex molecular systems using random color noise}},
volume = {78},
year = {2008}
}
@article{upma+99am,
author = {Upmanyu, M. and Srolovitz, D.J. J and Shvindlerman, L.S. S and Gottstein, G.},



journal = {Acta Materialia},



pages = {3901--3914},
title = {{Misorientation dependence of intrinsic grain boundary mobility: simulation and experiment}},

volume = {47},
year = {1999}
}
@article{dama+14prl,
author = {Dama, James F and Parrinello, Michele and Voth, Gregory A},



journal = {Phys. Rev. Lett.},


pages = {240602},
title = {{Well-Tempered Metadynamics Converges Asymptotically}},

volume = {112},
year = {2014}
}
@article{maro91jcp,
author = {Maroulis, George},



journal = {J. Chem. Phys.},


pages = {1182--1190},
title = {{Hyperpolarizability of H 2 O}},

volume = {94},
year = {1991}
}
@article{vand-roth02jpcb,
author = {VandeVondele, J and Rothlisberger, U},
journal = {J. Phys. Chem. B},
pages = {203--208},
title = {{Canonical Adiabatic Free Energy Sampling (CAFES): A Novel Method for the Exploration of Free Energy Surfaces }},
volume = {106},
year = {2002}
}
@article{artr-behl12prb,
author = {Artrith, Nongnuch and Behler, J{\"{o}}rg},



journal = {Phys. Rev. B},


pages = {045439},
title = {{High-dimensional neural network potentials for metal surfaces: A prototype study for copper}},

volume = {85},
year = {2012}
}
@article{wilk+17jcp,
abstract = {Long-range ion induced water-water correlations were recently observed in femtosecond elastic second harmonic scattering experiments of electrolyte solutions. To further the qualitative understanding of these correlations, we derive an analytical expression that quantifies ion induced dipole-dipole correlations in a non-interacting gas of dipoles. This model is a logical extension of Debye-H$\backslash$"uckel theory that can be used to qualitatively understand how the combined electric field of the ions induces correlations in the orientational distributions of the water molecules in an aqueous solution. The model agrees with results from molecular dynamics simulations and provides an important starting point for further theoretical work.},
archivePrefix = {arXiv},
arxivId = {1703.09288},
author = {Wilkins, D.M. David M. and Manolopoulos, D.E. David E. and Roke, Sylvie and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {181103},
title = {{Communication: Mean-field theory of water-water correlations in electrolyte solutions}},

volume = {146},
year = {2017}
}
@article{herb+14prl,
author = {Herbig, M. and Raabe, D. and Li, Y. J. and Choi, P. and Zaefferer, S. and Goto, S.},



journal = {Phys. Rev. Lett.},


pages = {126103},
title = {{Atomic-Scale Quantification of Grain Boundary Segregation in Nanocrystalline Material}},

volume = {112},
year = {2014}
}
@article{klei-shab95pra,
author = {Kleinert, H and Shabanov, S V},

journal = {Phys. Lett. A},

pages = {224--232},
publisher = {Elsevier},
title = {{Quantum Langevin equation from forward-backward path integral}},
volume = {200},
year = {1995}
}
@book{berg84book,
address = {New York, NY},
author = {Berg, Christian and Christensen, Jens Peter Reus and Ressel, Paul},

isbn = {978-1-4612-7017-1},
publisher = {Springer New York},
series = {Graduate Texts in Mathematics},
title = {{Harmonic Analysis on Semigroups}},

volume = {100},
year = {1984}
}
@article{mice+11jpcc,
author = {Miceli, Giacomo and Ceriotti, Michele and Angioletti-Uberti, Stefano and Bernasconi, Marco and Parrinello, Michele},



journal = {J. Phys. Chem. C},


pages = {7076--7080},
title = {{First-Principles Study of the High-Temperature Phase of Li 2 NH}},

volume = {115},
year = {2011}
}
@article{fodo-katz02plb,
author = {Fodor, Z and Katz, S D},

journal = {Phys. Lett. B},

pages = {87--92},
publisher = {Elsevier},
title = {{A New method to study lattice QCD at finite temperature and chemical potential}},
volume = {534},
year = {2002}
}
@article{sun+15ncomm,
author = {Sun, Jiming and Clark, Bryan K. and Torquato, Salvatore and Car, Roberto},



journal = {Nature Comm.},

pages = {8156},
publisher = {Nature Publishing Group},
title = {{The phase diagram of high-pressure superionic ice}},

volume = {6},
year = {2015}
}
@article{dupl+05cpl,
author = {Duplan, Jean C and Mahi, L and Brunet, Jean L},

journal = {Chem. Phys. Lett.},

pages = {400--403},
title = {{NMR determination of the equilibrium constant for the liquid H2O{\{}--{\}}D2O mixture}},
volume = {413},
year = {2005}
}
@misc{EPAPS-sih3deco,
annote = {See EPAPS Document No. ----- for a movie of metadynamics trajectory, and a discussion of Brillouin-zone sampling issues.},
title = {{No Title}}
}
@article{upma+02am,
author = {Upmanyu, M and Srolovitz, D.J J and Shvindlerman, L.S S and Gottstein, G},



journal = {Acta Materialia},



pages = {1405--1420},
title = {{Molecular dynamics simulation of triple junction migration}},

volume = {50},
year = {2002}
}
@article{bits+87pra,
author = {Bitsanis, I. and Tirrell, M. and Davis, H.},



journal = {Phys. Rev. A},


pages = {958--961},
title = {{Statistics of correlation functions from molecular dynamics}},

volume = {36},
year = {1987}
}
@article{lian+03jcp,
author = {Liang, W Z and Saravanan, C and Shao, Y and Baer, R and Bell, A T and Head-Gordon, M},

journal = {J. Chem. Phys.},

pages = {4117},
title = {{Improved Fermi operator expansion methods for fast electronic structure calculations}},
volume = {119},
year = {2003}
}
@article{kinu+97jcp,
author = {Kinugawa, Kenichi and Moore, Preston B. and Klein, Michael L.},



journal = {J. Chem. Phys.},

pages = {1154},
title = {{Centroid path integral molecular dynamics simulation of lithium para-hydrogen clusters}},

volume = {106},
year = {1997}
}
@article{witt+09jcp,
abstract = {Centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD) are two conceptually distinct extensions of path integral molecular dynamics that are able to generate approximate quantum dynamics of complex molecular systems. Both methods can be used to compute quasiclassical time correlation functions which have direct application in molecular spectroscopy; in particular, to infrared spectroscopy via dipole autocorrelation functions. The performance of both methods for computing vibrational spectra of several simple but representative molecular model systems is investigated systematically as a function of temperature and isotopic substitution. In this context both CMD and RPMD feature intrinsic problems which are quantified and investigated in detail. Based on the obtained results guidelines for using CMD and RPMD to compute infrared spectra of molecular systems are provided.},
author = {Witt, Alexander and Ivanov, Sergei D and Shiga, Motoyuki and Forbert, Harald and Marx, Dominik},



journal = {J. Chem. Phys.},


pages = {194510},
pmid = {19466846},
title = {{On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy.}},

volume = {130},
year = {2009}
}
@article{cutu12arxiv,
address = {2},
archivePrefix = {arXiv},
arxivId = {arXiv:1209.2655v1},
author = {Cuturi, Marco},


pages = {1--13},
title = {{A Positive Definite Formulation for Optimal Transport}},
year = {2015}
}
@article{kim+09chem,
abstract = {Alkali-metal amidoboranes have been recently highlighted as materials that satisfy many of the criteria required to make hydrogen-storage media. It is, therefore, crucial for us to understand the dehydrogenation mechanism of these materials for further development towards making successful hydrogen-storage media. In the present study, we attempt to shed light on the mechanisms involved in the loss of one molar equivalent of H(2) from solid lithium amidoboranes by using high-level ab initio calculations of monomeric and dimeric compounds in the gas phase. In the lithium amidoborane dimer, H(2) is released by the formation of LiH, which is followed by a redox reaction of the dihydrogen bond formed between the strongly basic H(-) in LiH and H(delta+) bonded to N. In the dehydrogenation process, the Li cation catalyzes the intermolecular N-B bond formation; this could lead to new pathways for N-B polymerization. After the release of the first molecule of H(2), a Li cation binds to a nitrogen atom, resulting in a lowering of the energy barrier for the second dehydrogenation process per dimer. These results will be useful for the design of future hydrogen-storage media.},
author = {Kim, Dong Young and Singh, N Jiten and Lee, Han Myoung and Kim, Kwang S},



journal = {Chemistry},



pages = {5598--604},
pmid = {19370741},
title = {{Hydrogen-release mechanisms in lithium amidoboranes.}},

volume = {15},
year = {2009}
}
@article{eike+05fcr,
author = {Eikerling, M and Kornyshev, A and Kulikovsky, A},

journal = {Fuel Cell Review},
title = {{Can theory help to improve fuel cells}},

year = {2005}
}
@article{lin+10prl,
author = {Lin, Lin and Morrone, Joseph A and Car, Roberto and Parrinello, Michele},

journal = {Phys. Rev. Lett.},

pages = {110602},
publisher = {American Physical Society},
title = {{Displaced Path Integral Formulation for the Momentum Distribution of Quantum Particles}},
volume = {105},
year = {2010}
}
@misc{hele+15jcp,
abstract = {We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or “classical Wigner approximation”) results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e., a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads N → ∞, such that the lowest normal-mode frequencies take their “Matsubara” values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of ħ2 at ħ0 (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting “Matsubara” dynamics is inherently classical (since all terms O ( ħ 2 ) disappear from the Matsubara Liouvillian in the limit N → ∞) and conserves the quantum Boltzmann distribution because the Matsubara Hamiltonian is symmetric with respect to imaginary-time translation. Numerical tests show that the Matsubara approximation to the quantum time-correlation function converges with respect to the number of modes and gives better agreement than LSC-IVR with the exact quantum result. Matsubara dynamics is too computationally expensive to be applied to complex systems, but its further approximation may lead to practical methods.},
author = {Hele, Timothy J. H. and Willatt, Michael J. and Muolo, Andrea and Althorpe, Stuart C.},
booktitle = {J. Chem. Phys.},




pages = {134103},
title = {{Boltzmann-conserving classical dynamics in quantum time-correlation functions: “Matsubara dynamics”}},

volume = {142},
year = {2015}
}
@article{ston75mp,
author = {Stone, A.J.},



journal = {Mol. Phys.},


pages = {1461--1471},
title = {{Transformation between cartesian and spherical tensors}},

volume = {29},
year = {1975}
}
@article{kuhn-khal13ncomm,
abstract = {Interpretation of the X-ray spectra of water as evidence for its asymmetric structure has challenged the conventional symmetric nearly tetrahedral model and initiated an intense debate about the order and symmetry of the hydrogen-bond network in water. Here we present new insights into the nature of local interactions in water obtained using a novel energy-decomposition method. Our simulations reveal that although a water molecule forms, on average, two strong donor and two strong acceptor bonds, there is a significant asymmetry in the energy of these contacts. We demonstrate that this asymmetry is a result of small instantaneous distortions of hydrogen bonds, which appear as fluctuations on a time scale of hundreds of femtoseconds around the average symmetric structure. Furthermore, we show that the distinct features of the X-ray absorption spectra originate from molecules with high instantaneous asymmetry. Our findings have important implications as they help reconcile the symmetric and asymmetric views on the structure of water.},
author = {K{\"{u}}hne, Thomas D and Khaliullin, Rustam Z},



journal = {Nature Comm.},

pages = {1450},
pmid = {23385594},
title = {{Electronic signature of the instantaneous asymmetry in the first coordination shell of liquid water.}},

volume = {4},
year = {2013}
}
@article{mcgi17jcp,
abstract = {Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materi-als science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essen-tial role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest com-putational cost, second-order M{\o}ller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when model-ing van der Waals interactions and $\pi$-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interac-tion energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol 1 (root-mean-square error 0.09 kcal mol 1), a 6-to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory-and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Further-more, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction},
author = {McGibbon, Robert T. and Taube, Andrew G. and Donchev, Alexander G. and Siva, Karthik and Hern{\'{a}}ndez, Felipe and Hargus, Cory and Law, Ka-Hei and Klepeis, John L. and Shaw, David E.},



journal = {J. Chem. Phys.},

pages = {161725},
title = {{Improving the accuracy of M{\o}ller-Plesset perturbation theory with neural networks}},

volume = {147},
year = {2017}
}
@article{giul+11prl,
author = {Giuliani, A and Bruni, F and Ricci, M A and Adams, M A},

journal = {Phys. Rev. Lett.},

pages = {255502},
publisher = {American Physical Society},
title = {{Isotope Quantum Effects on the Water Proton Mean Kinetic Energy}},
volume = {106},
year = {2011}
}
@article{padd03armr,
author = {Paddison, S.J. J},



journal = {Annual Review of Materials Research},



pages = {289--319},
title = {{Proton Conduction Mechanisms at Low Degrees of Hydration in Sulfonic-acid-based Polymer Electrolyte Membranes}},

volume = {33},
year = {2003}
}
@article{2,
author = {Romanelli, Giovanni and Ceriotti, Michele and Manolopoulos, David E and Pantalei, Claudia and Senesi, Roberto and Andreani, Carla},



journal = {J. Phys. Chem. Letters},


pages = {3251--3256},
title = {{Direct Measurement of Competing Quantum Effects on the Kinetic Energy of Heavy Water upon Melting}},

volume = {4},
year = {2013}
}
@article{bono+08jacs,
author = {Bonomi, Massimiliano and Branduardi, Davide and Gervasio, Francesco L. and Parrinello, Michele},


journal = {J. Chem. Am. Soc. },


pages = {13938--13944},
title = {{The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 $\beta$-Hairpin}},

volume = {130},
year = {2008}
}
@article{rami-herr11prb,
author = {Ram{\'{i}}rez, R. and Herrero, C. P.},



journal = {Phys. Rev. B},


pages = {064130},
title = {{Kinetic energy of protons in ice Ih and water: A path integral study}},

volume = {84},
year = {2011}
}
@article{pian-laio07jpcb,
abstract = {By suitably extending a recent approach [Bussi, G.; et al. J. Am. Chem. Soc. 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at the same temperature are performed, biasing each replica with a time-dependent potential constructed in a different set of collective variables. Exchanges between the bias potentials in the different variables are periodically allowed according to a replica exchange scheme. Due to the efficaciously multidimensional nature of the bias the method allows exploring complex free energy landscapes with high efficiency. The usefulness of the method is demonstrated by performing an atomistic simulation in explicit solvent of the folding of a Triptophane cage miniprotein. It is shown that the folding free energy landscape can be fully characterized starting from an extended conformation with use of only 40 ns of simulation on 8 replicas.},
author = {Piana, Stefano and Laio, Alessandro},



journal = {J. Phys. Chem.. B},



pages = {4553--4559},
pmid = {17419610},
title = {{A bias-exchange approach to protein folding.}},

volume = {111},
year = {2007}
}
@article{silv-parr99jcp,
author = {Silvestrelli, Pier Luigi and Parrinello, Michele},



journal = {J. Chem. Phys.},

pages = {3572},
title = {{Structural, electronic, and bonding properties of liquid water from first principles}},

volume = {111},
year = {1999}
}
@book{grot04book,
author = {Grotendorst, Johannes},

isbn = {3-00-013618-5},
publisher = {NIC Series},
title = {{High performance computing in chemistry and massively parallel computers: A simple transition?}},
year = {2004}
}
@article{abe+96prep,
author = {Abe, Y and Ayikb, S and Reinhard, P G and Suraudd, E and Quantique, De and Sabatier, Universitk Paul and Narbonne, I Route De and Oxford, N E W York and Surauddql, E and Ayik, S and Reinhard, P G and Suraud, E},

journal = {Physics Reports},

pages = {49--196},
title = {{On stochastic approaches of nuclear dynamics}},
volume = {275},
year = {1996}
}
@article{pant+08prl,
author = {Pantalei, C and Pietropaolo, A and Senesi, R and Imberti, S and Andreani, C and Mayers, J and Burnham, C and Reiter, G},

journal = {Phys. Rev. Lett.},

pages = {177801},
publisher = {APS},
title = {{Proton momentum distribution of liquid water from room temperature to the supercritical phase}},
volume = {100},
year = {2008}
}
@article{baer+14jpcb,
abstract = {For strong acids, like hydrochloric acid, the complete dissociation into an excess proton and conjugated base as well as the formation of independent solvated charged fragments is assumed. The existence of chloride-hydronium (Cl(-){\textperiodcentered}{\textperiodcentered}{\textperiodcentered}H3O(+)) contact ion pairs even in moderate concentration hydrochloric acid (2.5 m) demonstrates that the counterions do not behave merely as spectators. Through comparison of recent extended X-ray absorption fine structure (EXAFS) measurements to state-of-the-art density functional theory (DFT) simulations, we are able to obtain a unique view into the molecular structure of medium-to-high concentrated electrolytes. Here we report that the Cl(-){\textperiodcentered}{\textperiodcentered}{\textperiodcentered}H3O(+) contact ion pair structure persists throughout the entire concentration range studied and that these structures differ significantly from moieties studied in microsolvated hydrochloric acid gas phase clusters. Characterizing distinct populations of these ion pairs gives rise to a novel molecular level description of how to view the reaction network for acid dissociation and how it relates to our picture of acid-base equilibria.},
author = {Baer, Marcel D and Fulton, John L and Balasubramanian, Mahalingam and Schenter, Gregory K and Mundy, Christopher J},



journal = {J. Phys. Chem.. B},


pages = {7211--7220},
pmid = {24837190},
title = {{Persistent ion pairing in aqueous hydrochloric acid.}},

volume = {118},
year = {2014}
}
@article{abra+99prb,
author = {Abrashev, M V and Litvinchuk, A P and Iliev, M N and Meng, R L and Popov, V N and Ivanov, V G and Chakalov, R A and Thomsen, C},

journal = {Phys. Rev. B},

pages = {4146--4153},
publisher = {APS},
title = {{Comparative study of optical phonons in the rhombohedrally distorted perovskites LaAlO{\_} 3 and LaMnO{\_} 3}},
volume = {59},
year = {1999}
}
@article{pere+09jcp,
abstract = {The problems of ergodicity and internal consistency in the centroid and ring-polymer molecular dynamics methods are addressed in the context of a comparative study of the two methods. Enhanced sampling in ring-polymer molecular dynamics (RPMD) is achieved by first performing an equilibrium path integral calculation and then launching RPMD trajectories from selected, stochastically independent equilibrium configurations. It is shown that this approach converges more rapidly than periodic resampling of velocities from a single long RPMD run. Dynamical quantities obtained from RPMD and centroid molecular dynamics (CMD) are compared to exact results for a variety of model systems. Fully converged results for correlations functions are presented for several one dimensional systems and para-hydrogen near its triple point using an improved sampling technique. Our results indicate that CMD shows very similar performance to RPMD. The quality of each method is further assessed via a new chi(2) descriptor constructed by transforming approximate real-time correlation functions from CMD and RPMD trajectories to imaginary time and comparing these to numerically exact imaginary time correlation functions. For para-hydrogen near its triple point, it is found that adiabatic CMD and RPMD both have similar chi(2) error.},
author = {P{\'{e}}rez, Alejandro and Tuckerman, Mark E and M{\"{u}}ser, Martin H},



journal = {J. Chem. Phys.},


pages = {184105},
pmid = {19449906},
title = {{A comparative study of the centroid and ring-polymer molecular dynamics methods for approximating quantum time correlation functions from path integrals.}},

volume = {130},
year = {2009}
}
@article{pete+17pccp,
abstract = {Machine-learning regression can precisely emulate the potential energy and forces of more expensive electronic-structure calculations, but to make useful predictions an assessment must be made of the prediction's credibility.},
author = {Peterson, Andrew A and Christensen, Rune and Khorshidi, Alireza},



journal = {Physical Chemistry Chemical Physics},

pages = {10978--10985},
publisher = {Royal Society of Chemistry},
title = {{Addressing uncertainty in atomistic machine learning}},

volume = {19},
year = {2017}
}
@article{jahn+08am,
author = {Jahnke, E. and Severin, N. and Kreutzkamp, P. and Rabe, J. P. and Frauenrath, H.},


isbn = {2000211135},

journal = {Advanced Materials},


pages = {409--414},
title = {{Molecular Level Control over Hierarchical Structure Formation and Polymerization of Oligopeptide-Polymer Conjugates}},

volume = {20},
year = {2008}
}
@article{cohe+08science,
abstract = {Density functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, for many predicted properties, there are spectacular failures that can be traced to the delocalization error and static correlation error of commonly used approximations. These errors can be characterized and understood through the perspective of fractional charges and fractional spins introduced recently. Reducing these errors will open new frontiers for applications of density functional theory.},
author = {Cohen, Aron J and Mori-S{\'{a}}nchez, Paula and Yang, Weitao},



journal = {Science},


pages = {792--4},
pmid = {18687952},
title = {{Insights into current limitations of density functional theory.}},

volume = {321},
year = {2008}
}
@unpublished{biblio-car-parrinello,
title = {{No Title}}
}
@article{calv05jcp,
author = {Calvo, F.},



journal = {J. Chem. Phys.},

pages = {124106},
title = {{All-exchanges parallel tempering}},

volume = {123},
year = {2005}
}
@article{pena+05jcp,
abstract = {Quantum and classical simulations are carried out on ice Ih over a range of temperatures utilizing the TIP4P water model. The rigid-body centroid molecular dynamics method employed allows for the investigation of equilibrium and dynamical properties of the quantum system. The impact of quantization on the local structure, as measured by the radial and spatial distribution functions, as well as the energy is presented. The effects of quantization on the lattice vibrations, associated with the molecular translations and librations, are also reported. Comparison of quantum and classical simulation results indicates that shifts in the average potential energy are equivalent to rising the temperature about 80 K and are therefore non-negligible. The energy shifts due to quantization and the quantum mechanical uncertainties observed in ice are smaller than the values previously reported for liquid water. Additionally, we carry out a comparative study of melting in our classical and quantum simulations and show that there are significant differences between classical and quantum ice.},
author = {{Hern{\'{a}}ndez de la Pe{\~{n}}a}, L and {Gulam Razul}, M S and Kusalik, P G and Pe{\~{n}}a, L Hern{\'{a}}ndez De and Razul, M S Gulam and de la Pe{\~{n}}a, L Hern{\'{a}}ndez},



journal = {J. Chem. Phys.},


pages = {144506},
pmid = {16238406},
publisher = {AIP},
title = {{Quantum effects in ice Ih.}},

volume = {123},
year = {2005}
}
@article{marz-vand97prb,
author = {Marzari, Nicola and Vanderbilt, David},



journal = {Phys. Rev. B},


pages = {12847--12865},
title = {{Maximally localized generalized Wannier functions for composite energy bands}},

volume = {56},
year = {1997}
}
@article{hene72jpa,
author = {Henery, RJ J},



journal = {J. Phys. A: General Physics},


pages = {1312--1319},
publisher = {Institute of Physics Publishing},
title = {{The generalized Langevin equation}},

volume = {5},
year = {1972}
}
@book{frenk-smit02book,
address = {London},
author = {Frenkel, Daan and Smit, Berend},
edition = {Second},
publisher = {Academic Press},
title = {{Understanding Molecular Simulation}},
year = {2002}
}
@article{barb+96acm,
abstract = {The convex hull of a set of points is the smallest convex set that contains the points. This article presents a practical convex hull algorithm that combines the two-dimensional Quick- hull Algorithm with the general-dimension Beneath-Beyond Algorithm. It is similar to the randomized, incremental algorithms for convex hull and Delaunay triangulation. We provide empirical evidence that the algorithm runs faster when the input contains nonextreme points and that it uses less memory. Computational geometry algorithms have traditionally assumed that input sets are well behaved. When an algorithm is implemented with floating-point arithmetic, this assumption can lead to serious errors. We briefly describe a solution to this problem when computing the convex hull in two, three, or four dimensions. The output is a set of “thick” facets that contain all possible exact convex hulls of the input. A variation is effective in five or more dimensions.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.1669v3},
author = {Barber, C. Bradford and Dobkin, David P. and Huhdanpaa, Hannu},



isbn = {0098-3500},

journal = {ACM Transactions on Mathematical Software},


pages = {469--483},
pmid = {25246403},
title = {{The quickhull algorithm for convex hulls}},

volume = {22},
year = {1996}
}
@article{rami-herr10jcp,
abstract = {The isotope effect in the melting temperature of ice Ih has been studied by free energy calculations within the path integral formulation of statistical mechanics. Free energy differences between isotopes are related to the dependence of their kinetic energy on the isotope mass. The water simulations were performed by using the q-TIP4P/F model, a point charge empirical potential that includes molecular flexibility and anharmonicity in the OH stretch of the water molecule. The reported melting temperature at ambient pressure of this model (T=251 K) increases by 6.5±0.5 and 8.2±0.5 K upon isotopic substitution of hydrogen by deuterium and tritium, respectively. These temperature shifts are larger than the experimental ones (3.8 and 4.5 K, respectively). In the classical limit, the melting temperature is nearly the same as that for tritiated ice. This unexpected behavior is rationalized by the coupling between intermolecular interactions and molecular flexibility. This coupling makes the kinetic energy of the OH stretching modes larger in the liquid than in the solid phase. However, the opposite behavior is found for intramolecular modes, which display larger kinetic energy in ice than in liquid water.},
author = {Ram{\'{i}}rez, R and Herrero, C P},



journal = {J. Chem. Phys.},


pages = {144511},
pmid = {20950021},
title = {{Quantum path integral simulation of isotope effects in the melting temperature of ice Ih}},

volume = {133},
year = {2010}
}
@article{arau+prb09,
author = {Ara{\'{u}}jo, C M and Blomqvist, A and Scheicher, R H and Chen, P and Ahuja, R},

journal = {Phys. Rev. B},

pages = {172101},
publisher = {APS},
title = {{Superionicity in the hydrogen storage material Li{\_}2 NH: Molecular dynamics simulations}},
volume = {79},
year = {2009}
}
@article{tene+00science,
abstract = {Scientists working with large volumes of high-dimensional data, such as global climate patterns, stellar spectra, or human gene distributions, regularly confront the problem of dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. The human brain confronts the same problem in everyday perception, extracting from its high-dimensional sensory inputs-30,000 auditory nerve fibers or 10(6) optic nerve fibers-a manageably small number of perceptually relevant features. Here we describe an approach to solving dimensionality reduction problems that uses easily measured local metric information to learn the underlying global geometry of a data set. Unlike classical techniques such as principal component analysis (PCA) and multidimensional scaling (MDS), our approach is capable of discovering the nonlinear degrees of freedom that underlie complex natural observations, such as human handwriting or images of a face under different viewing conditions. In contrast to previous algorithms for nonlinear dimensionality reduction, ours efficiently computes a globally optimal solution, and, for an important class of data manifolds, is guaranteed to converge asymptotically to the true structure.},
author = {Tenenbaum, J B and de Silva, V and Langford, J C},



journal = {Science},



pages = {2319--2323},
pmid = {11125149},
publisher = {AAAS},
title = {{A global geometric framework for nonlinear dimensionality reduction.}},

volume = {290},
year = {2000}
}
@article{sutt+88jphc,
author = {Suttont, A P and Sutton, A P and Finnis, M W and Pettifor, D G and Ohta, Y},

journal = {Journal of Physics C: Solid State Physics},
pages = {35--66},
publisher = {Institute of Physics Publishing},
title = {{The tight-binding bond model}},
volume = {21},
year = {1988}
}
@article{fang-wang00prb,
abstract = {The core structure of an edge dislocation in aluminum is studied by molecular dynamics simulation with the glue potential. The edge dislocation of the 1/2[1¯10](111) type is observed to dissociate into two partials separating from each other by a distance of 9 {\AA}. The half width of the two partial dislocations is deduced to be 6.5 {\AA}, giving a half width of the whole dislocation of 12 {\AA}. Dislocation mobility is studied by applying a shear stress on the crystal and by observing the corresponding shift of the Burgers vector density. After considering the mirror force on the dislocation exerted by the fixed boundaries, a Peierls stress of 0.75×10-4$\mu$ ($\mu$ is the shear modulus) for the motion of the whole dislocation is obtained. Atomic diffusion in the core region of the edge dislocation is simulated by hyper molecular dynamics method and the migration energy for vacancy diffusing in the dislocation core is calculated to approximate 0.5 eV.},
author = {Fang, Q. F. and Wang, R.},


isbn = {0163-1829},

journal = {Phys. Rev. B - Condensed Matter and Materials Physics},


pages = {9317--9324},
title = {{Atomistic simulation of the atomic structure and diffusion within the core region of an edge dislocation in aluminum}},

volume = {62},
year = {2000}
}
@article{ensi+07jctc,
author = {Ensing, B and Nielsen, S O and Moore, P B and Klein, M L and Parrinello, M},
journal = {J. Chem. Theory Comput.},

pages = {1100--1105},
title = {{Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics}},
volume = {3},
year = {2007}
}
@article{pisa+14jctc,
author = {Pisani, Pasquale and Piro, Paolo and Decherchi, Sergio and Bottegoni, Giovanni and Sona, Diego and Murino, Vittorio and Rocchia, Walter and Cavalli, Andrea},



journal = {J. Chem. Theory Comput.},


pages = {2557--2568},
title = {{Describing the Conformational Landscape of Small Organic Molecules through Gaussian Mixtures in Dihedral Space}},

volume = {10},
year = {2014}
}
@article{lubb+18jcp,
author = {Lubbers, Nicholas and Smith, Justin S. and Barros, Kipton},


journal = {J. Chem. Phys.},


pages = {241715},
title = {{Hierarchical modeling of molecular energies using a deep neural network}},

volume = {148},
year = {2018}
}
@article{ceri+06nano,
abstract = {Low-energy atomic impacts on the Ag(110) surface are investigated by molecular dynamics simulations based on reliable many-body semiempirical potentials. Trajectory deflections (steering) caused by the atom-surface interaction are observed, together with impact-following, transient-mobility effects. Such processes are quantitatively analysed and their dependence on the initial kinetic energy and on the impinging direction is discussed. A clear influence of the surface anisotropy on both steering and transient mobility effects is revealed by our simulations for the simple isolated-atom case and in the submonolayer-growth regime. For the latter case, we illustrate how steering and transient mobility affect the film morphology at the nanoscale.},
author = {Ceriotti, Michele and Ferrando, Riccardo and Montalenti, Francesco},


institution = {Dipartimento di Scienza dei Materiali della Universit{\`{a}} degli Studi di Milano-Bicocca, Via Cozzi 53, I-20125 Milano, Italy.},

journal = {Nanotechnology},


pages = {3556--62},
pmid = {19661604},
title = {{Impact-driven effects in thin-film growth: steering and transient mobility at the Ag(110) surface.}},

volume = {17},
year = {2006}
}
@article{fabe+15ijqc,
author = {Faber, Felix and Lindmaa, Alexander and von Lilienfeld, O. Anatole and Armiento, Rickard},



journal = {International Journal of Quantum Chemistry},
pages = {n/a----n/a},
title = {{Crystal structure representations for machine learning models of formation energies}},

year = {2015}
}
@article{ceri14jpcs,
abstract = {{\textcopyright} Published under licence by IOP Publishing Ltd. Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.},
author = {Ceriotti, M.},



journal = {Journal of Physics: Conference Series},


pages = {12011},
title = {{Ab initio simulation of particle momentum distributions in high-pressure water}},

volume = {571},
year = {2014}
}
@incollection{hama74book,
author = {Hamann, S. D.},
booktitle = {Modern aspects of electrochemistry},

pages = {47--158},
publisher = {Springer},
title = {{Electrolyte solutions at high pressure}},
year = {1974}
}
@article{katz+13prb,
author = {Katzarov, Ivaylo H. and Pashov, Dimitar L. and Paxton, Anthony T.},



journal = {Phys. Rev. B},


pages = {54107},
title = {{Fully quantum mechanical calculation of the diffusivity of hydrogen in iron using the tight-binding approximation and path integral theory}},

volume = {88},
year = {2013}
}
@article{coif+05pnas,
abstract = {We provide a framework for structural multiscale geometric organization of graphs and subsets of R(n). We use diffusion semigroups to generate multiscale geometries in order to organize and represent complex structures. We show that appropriately selected eigenfunctions or scaling functions of Markov matrices, which describe local transitions, lead to macroscopic descriptions at different scales. The process of iterating or diffusing the Markov matrix is seen as a generalization of some aspects of the Newtonian paradigm, in which local infinitesimal transitions of a system lead to global macroscopic descriptions by integration. We provide a unified view of ideas from data analysis, machine learning, and numerical analysis.},
author = {Coifman, R R and Lafon, S and Lee, a B and Maggioni, M and Nadler, B and Warner, F and Zucker, S W},


isbn = {0500334102},

journal = {Proc. Natl. Acad. Sci. USA},

pages = {7426--7431},
pmid = {15899970},
title = {{Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps.}},

volume = {102},
year = {2005}
}
@article{gran+98prb,
author = {Granado, E and Moreno, N O and Garcia, A and Sanjurjo, J A and Rettori, C and Torriani, I and Oseroff, S B and Neumeier, J J and McClellan, K J and Cheong, S W and Others},
journal = {Phys. Rev. B},

pages = {11435--11440},
publisher = {APS},
title = {{Phonon Raman scattering in R{\_} 1-x A{\_} x MnO{\_} 3+ {\{}$\delta${\}}(R= La, Pr; A= Ca, Sr)}},
volume = {58},
year = {1998}
}
@article{lutt+02surf,
author = {Lutterloh, C and Wickleinb, M and Dingerb, A and Bienera, J and K{\"{u}}ppers, J},

journal = {Surf. Sci.},

pages = {123},
title = {{Thermal stability and hydrogen induced abstraction of silyl groups on Si(100) surfaces}},
volume = {498},
year = {2002}
}
@article{elda+97ieee,
abstract = {A new method of farthest point strategy (FPS) for progressive image acquisition-an acquisition process that enables an approximation of the whole image at each sampling stage-is presented. Its main advantage is in retaining its uniformity with the increased density, providing efficient means for sparse image sampling and display. In contrast to previously presented stochastic approaches, the FPS guarantees the uniformity in a deterministic min-max sense. Within this uniformity criterion, the sampling points are irregularly spaced, exhibiting anti-aliasing properties comparable to those characteristic of the best available method (Poisson disk). A straightforward modification of the FPS yields an image-dependent adaptive sampling scheme. An efficient O(N log N) algorithm for both versions is introduced, and several applications of the FPS are discussed.},
author = {Eldar, Y and Lindenbaum, M and Porat, M and Zeevi, Y Y},


journal = {IEEE transactions on image processing : a publication of the IEEE Signal Processing Society},


pages = {1305--15},
pmid = {18283019},
title = {{The farthest point strategy for progressive image sampling.}},

volume = {6},
year = {1997}
}
@article{raug-klei03jacs,
author = {Raugei, Simone and Klein, Michael L},


isbn = {0002-7863},

journal = {J. Chem. Am. Soc. },



pages = {8992--8993},
title = {{Nuclear Quantum Effects and Hydrogen Bonding in Liquids}},

volume = {125},
year = {2003}
}
@article{bard+08prl,
author = {Barducci, Alessandro and Bussi, Giovanni and Parrinello, Michele},

journal = {Phys. Rev. Lett.},

pages = {20603},
publisher = {APS},
title = {{Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method}},
volume = {100},
year = {2008}
}
@unpublished{biblio-car-parrinello,
title = {{No Title}}
}
@article{bald+17jpcm,
abstract = {{\textcopyright} 2017 IOP Publishing Ltd. Interfaces between different materials and phases play a crucial role in many physical and chemical phenomena. When performing simulations of matter at the atomic scale, however, it is often not trivial to characterize these interfaces, particularly when they are rough or diffuse. Here we discuss a generalization of a construction, due to Willard and Chandler, that allows one to obtain a smooth dividing surface that follows the irregular, ever changing shape of these fluctuating interfaces. We show how this construction can be used to study the surface that separates a solid material from its melt and how analyses of the Fourier modes for the capillary fluctuations of this instantaneous dividing surface can be performed. This particular analysis is useful as one can compute the specific free energy excess of the interface, and its dependence on orientation relative to the bulk phases, from the average amplitude of the Fourier modes. We therefore discuss the efficiency of this approach, both in terms of system size and statistical sampling.},
author = {Baldi, Edoardo and Ceriotti, Michele and Tribello, Gareth A G.A.},



journal = {J. Phys. Cond. Matt.},


pages = {445001},
publisher = {IOP Publishing},
title = {{Extracting the interfacial free energy and anisotropy from a smooth fluctuating dividing surface}},

volume = {29},
year = {2017}
}
@article{lamo+06cpl,
author = {Lamoureux, G and Harder, E and Vorobyov, I V and Roux, B and MacKerell, A D},

journal = {Chem. Phys. Lett.},

pages = {245--249},
publisher = {Elsevier},
title = {{A polarizable model of water for molecular dynamics simulations of biomolecules}},
volume = {418},
year = {2006}
}
@article{daub-mueh86ieee,
author = {Daube-Witherspoon, Margaret E. and Muehllehner, Gerd},


journal = {IEEE Transactions on Medical Imaging},


pages = {61--66},
title = {{An Iterative Image Space Reconstruction Algorthm Suitable for Volume ECT}},

volume = {5},
year = {1986}
}
@article{tuck+01jcp,
author = {Tuckerman, Mark E. and Liu, Yi and Ciccotti, Giovanni and Martyna, Glenn J.},



journal = {J. Chem. Phys.},

pages = {1678},
title = {{Non-Hamiltonian molecular dynamics: Generalizing Hamiltonian phase space principles to non-Hamiltonian systems}},

volume = {115},
year = {2001}
}
@article{pere-vonl11jctc,
author = {Pérez, Alejandro and von Lilienfeld, Anatole O.},



journal = {J. Chem. Theory Comput.},


pages = {2358--2369},
title = {{Path Integral Computation of Quantum Free Energy Differences Due to Alchemical Transformations Involving Mass and Potential}},

volume = {7},
year = {2011}
}
@article{good90jpcm,
author = {Goodwin, Leif},

journal = {J. Phys.: Condens. Matter},

pages = {3869--3878},
title = {{A new tight binding parametrization for carbon}},
volume = {3},
year = {1991}
}
@article{bao-zhuo03prl,
author = {Bao, Jing-Dong and Zhuo, Yi-Zhong},

journal = {Phys. Rev. Lett.},

pages = {138104},
publisher = {American Physical Society},
title = {{Ballistic Diffusion Induced by a Thermal Broadband Noise}},
volume = {91},
year = {2003}
}
@article{roke09cpc,
abstract = {Soft matter consists of complex molecules that can undergo drastic structural transformations under mild changes of chemical and physical conditions. Since a wide variety of chemical, physical and biological processes occur at soft matter interfaces, they can exhibit complex behavior. This is even more so for interfaces of colloidal soft matter since the relative amount of interface material increases by orders of magnitude. Herein, we focus on new developments that enable us to obtain detailed molecular structural changes in the topmost molecular layers of soft matter interfaces composed of complex bio-molecules. In particular, the possibilities to probe interfaces of colloidal soft matter systems are discussed.},
author = {Roke, Sylvie},



journal = {Chemphyschem : a European J. Chem. Phys. and physical chemistry},



pages = {1380--1388},
pmid = {19472266},
title = {{Nonlinear optical spectroscopy of soft matter interfaces.}},

volume = {10},
year = {2009}
}
@article{tuck+92jcp,
author = {Tuckerman, M. and Berne, B. J. and Martyna, G. J.},



journal = {J. Chem. Phys.},

pages = {1990},
title = {{Reversible multiple time scale molecular dynamics}},

volume = {97},
year = {1992}
}
@article{yate-pant62pps,
abstract = {The linear thermal expansions of LiF, NaCl, KCl, KBr and KI single crystals have been measured by a Fizeau interferometric method in the temperature range 20{\{}{\^{}}$\backslash$circ{\}} to 270 {\{}{\^{}}$\backslash$circ{\}}K with an accuracy to 0.04 {\{}$\backslash$times{\}} 10 -5 deg -1 . The apparatus is described, and the expansion coefficients as a function of temperature are shown graphically together with those of previous workers. Smoothed values of the volume expansion coefficients {\{}$\beta${\}}, and values of the Gr{\{}{\"{u}}{\}}neisen parameter {\{}$\gamma${\}}, calculated from {\{}$\beta${\}} using recent experimental elasticity and specific heat data, are tabulated. For all except LiF, the values of {\{}$\gamma${\}} show a marked decrease towards low temperatures in qualitative agreement with simple point-charge ion models. For LiF, however, {\{}$\gamma${\}} appears to be constant (= 1.60) to within 3{\%} over the whole temperature range.},
author = {Yates, B. and Panter, C.H.},

journal = {Proceedings of the Physical Society},

pages = {373},
title = {{Thermal Expansion of Alkali Halides at Low Temperatures}},

volume = {80},
year = {1962}
}
@article{mill01jpca,
author = {Miller, William H.},



journal = {J. Phys. Chem. A},


pages = {2942--2955},
title = {{The Semiclassical Initial Value Representation: A Potentially Practical Way for Adding Quantum Effects to Classical Molecular Dynamics Simulations}},

volume = {105},
year = {2001}
}
@article{dett+17jctc,
annote = {NULL},
author = {Dettori, Riccardo and Ceriotti, Michele and Hunger, Johannes and Melis, Claudio and Colombo, Luciano and Donadio, Davide},



journal = {J. Chem. Theory Comput.},


pages = {1284--1292},
title = {{Simulating Energy Relaxation in Pump–Probe Vibrational Spectroscopy of Hydrogen-Bonded Liquids}},

volume = {13},
year = {2017}
}
@article{DLPOLY,
author = {Smith, W and Forester, T R and Todorov, I T and Leslie, M},
journal = {CCLRC Daresbury Lab. Daresbury, Warrington, UK},
title = {{{\{}DL-POLY{\}}}},
year = {2006}
}
@article{lewi-noce06pnas,
abstract = {Global energy consumption is projected to increase, even in the face of substantial declines in energy intensity, at least 2-fold by midcentury relative to the present because of population and economic growth. This demand could be met, in principle, from fossil energy resources, particularly coal. However, the cumulative nature of CO(2) emissions in the atmosphere demands that holding atmospheric CO(2) levels to even twice their preanthropogenic values by midcentury will require invention, development, and deployment of schemes for carbon-neutral energy production on a scale commensurate with, or larger than, the entire present-day energy supply from all sources combined. Among renewable energy resources, solar energy is by far the largest exploitable resource, providing more energy in 1 hour to the earth than all of the energy consumed by humans in an entire year. In view of the intermittency of insolation, if solar energy is to be a major primary energy source, it must be stored and dispatched on demand to the end user. An especially attractive approach is to store solar-converted energy in the form of chemical bonds, i.e., in a photosynthetic process at a year-round average efficiency significantly higher than current plants or algae, to reduce land-area requirements. Scientific challenges involved with this process include schemes to capture and convert solar energy and then store the energy in the form of chemical bonds, producing oxygen from water and a reduced fuel such as hydrogen, methane, methanol, or other hydrocarbon species.},
author = {Lewis, Nathan S and Nocera, Daniel G},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {15729--35},
pmid = {17043226},
title = {{Powering the planet: chemical challenges in solar energy utilization.}},

volume = {103},
year = {2006}
}
@article{guis+12apl,
author = {Guisbiers, G. and Arscott, S. and Snyders, R.},



journal = {Applied Physics Letters},

pages = {231606},
title = {{An accurate determination of the surface energy of solid selenium}},

volume = {101},
year = {2012}
}
@book{frie-onei77book,
author = {Friedman, I and O'Neil, J R},
publisher = {USGPO},
title = {{Compilation of stable isotope fractionation factors of geochemical interest}},
volume = {440},
year = {1977}
}
@article{beng-kac81prl,
abstract = {The macroscopic description of a quantum particle with passive dissipation and moving in an arbitrary external potential is formulated in termos of the generelized Langevin equation. The coupling with the heat bath corresponds to two terms: a mean force characterized by a memory function {\$}\backslashmu{\$}(t) and an operator-valued random force. The random force is never Markovian. It is shown that {\$}\backslash{\~{}}mu{\$}(z), the fourier transform of the memory function, must be a positive real function, analytic in the upper half plane and with Re[{\$}\backslash{\~{}}mu{\$}($\backslash$omega+i0{\^{}}+)] a positive distribution on the real axis. This form is then derived for the independent-oscillator model of a heat bath. It is shown that the most general quantum langevin equation can be realized by this simple model. A critical comparison is made with a number of other models that have appeared in the literature.},
author = {Benguria, Rafael and Kac, Mark},



journal = {Phys. Rev. Lett.},


pages = {1--4},
pmid = {9899572},
publisher = {APS},
title = {{Quantum Langevin Equation}},

volume = {46},
year = {1981}
}
@article{mart+92jcp,
annote = {From Duplicate 1 (Nos{\{}{\'{e}}{\}}-Hoover chains: The canonical ensemble via continuous dynamics - Martyna, G J; Tuckerman, M E; Klein, M L)

From Duplicate 2 ( Nos{\{}{\'{e}}{\}}-Hoover chains: The canonical ensemble via continuous dynamics - Martyna, G J; Tuckerman, M E; Klein, M L )





From Duplicate 2 ( 








Nos{\{}{\'{e}}{\}}-Hoover chains: The canonical ensemble via continuous dynamics








- Martyna, G J; Tuckerman, M E; Klein, M L )



},
author = {Martyna, G J and Tuckerman, M E and Klein, M L},



journal = {J. Chem. Phys.},

pages = {2635},
title = {{Nos{\{}{\'{e}}{\}}-Hoover chains: The canonical ensemble via continuous dynamics}},

volume = {97},
year = {1992}
}
@article{post+93nature,
author = {Postorino, P. and Tromp, R. H. and Ricci, M-A. and Soper, A. K. and Neilson, G. W.},



journal = {Nature},


pages = {668--670},
title = {{The interatomic structure of water at supercritical temperatures}},

volume = {366},
year = {1993}
}
@article{vonl+15ijqc,
author = {von Lilienfeld, O. Anatole and Ramakrishnan, Raghunathan and Rupp, Matthias and Knoll, Aaron},


journal = {International Journal of Quantum Chemistry},


pages = {1084--1093},
title = {{Fourier series of atomic radial distribution functions: A molecular fingerprint for machine learning models of quantum chemical properties}},

volume = {115},
year = {2015}
}
@article{chen+15pnas,
author = {Chen, Ming and Yu, Tang-Qing and Tuckerman, Mark E.},



journal = {Proc. Natl. Acad. Sci. USA},


pages = {3235--3240},
title = {{Locating landmarks on high-dimensional free energy surfaces}},

volume = {112},
year = {2015}
}
@article{mora+16pnas,
abstract = {While the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing e.g. a pronounced contraction of the second solvation shell upon cooling that induces the density maximum.},
archivePrefix = {arXiv},
arxivId = {1606.07775},
author = {Morawietz, Tobias and Singraber, Andreas and Dellago, Christoph and Behler, J{\"{o}}rg},




journal = {Proc. Natl. Acad. Sci. USA},


pages = {8368--8373},
pmid = {27402761},
title = {{How van der Waals interactions determine the unique properties of water}},

volume = {113},
year = {2016}
}
@article{hori-weso94gca,
abstract = {The equilibrium fractionation factors of oxygen and hydrogenisotopes{\$}\backslash{\$}nbetween liquid water and water vapor have been precisely determined{\$}\backslash{\$}nfrom 25 to 350°C on the VSMOW-SLAP scale, using three different types{\$}\backslash{\$}nof apparatus with static or dynamic techniques for the sampling of{\$}\backslash{\$}nwater vapor. Our results for both oxygen and hydrogenisotope fractionation{\$}\backslash{\$}nfactors between 25 and 100°C are in excellent agreement with the{\$}\backslash{\$}nliterature (e.g., Majoube, 1971). Our results for the hydrogenisotope{\$}\backslash{\$}nfractionation factor above 100°C also agree quantitatively with the{\$}\backslash{\$}nliterature values of Merlivat et al. (1963) and Bottinga (1968).{\$}\backslash{\$}nThe results for the hydrogenisotope fractionation factor obtained{\$}\backslash{\$}nin this study and from most of the literature were regressed to the{\$}\backslash{\$}nequation, ) −1620.1 () + 794.84() −161.04 + 2.9992(), from 0°C to{\$}\backslash{\$}nthe critical temperature of water (374.1°C) within ± 1.2(1{\$}\sigma{\$}) (n ={\$}\backslash{\$}n157); T(K). The cross- over temperature is 229 ± 13°C (1{\$}\sigma{\$}).{\$}\backslash{\$}n{\$}\backslash{\$}nOur values for the oxygen isotope fractionation factor between liquid{\$}\backslash{\$}nwater and water vapor are, however, at notable variance with the{\$}\backslash{\$}nonly dataset available above 100°C in the literature (Bottinga, 1968),{\$}\backslash{\$}nwhich is systematically higher (av. + 0.15 in 103 In {\$}\alpha{\$}1−v(18O)) with{\$}\backslash{\$}nlarge errors (± 0.23 in 1{\$}\sigma{\$}). Our results and most of the literature{\$}\backslash{\$}ndata below 100°C were regressed to the equation, 103 In {\$}\alpha{\$}1−v(18O){\$}\backslash{\$}n= −7.685 + 6.7123() − 1.6664() + 0.35041 (), from 0 to 374.1°C within{\$}\backslash{\$}n± 0.11 (1{\$}\sigma{\$})(n = 112); T(K).{\$}\backslash{\$}n{\$}\backslash{\$}nA third water-steam isotope geothermometer, using the ratio of {\$}\Delta{\$}{\$}\delta{\$}D/{\$}\Delta{\$}{\$}\delta{\$}18O{\$}\backslash{\$}ngiven by water and steam samples, is readily obtained from the above{\$}\backslash{\$}nequations. This geothermometer is less affected by incomplete separation{\$}\backslash{\$}nof water and steam, and partial condensation of steam than those{\$}\backslash{\$}nemploying the oxygen and hydrogen isotopic compositions alone.},
author = {Horita, Juske and Wesolowski, David J.},


isbn = {0016-7037},

journal = {Geochimica et Cosmochimica Acta},

pages = {3425--3437},
title = {{Liquid-vapor fractionation of oxygen and hydrogen isotopes of water from the freezing to the critical temperature}},
volume = {58},
year = {1994}
}
@article{Shewchuk1994,
author = {Shewchuk, JR R},



title = {{An introduction to the conjugate gradient method without the agonizing pain}},

year = {1994}
}
@article{irud-henc12jcp,
abstract = {There is a considerable disagreement about the extent to which solutes perturb water structure. On the one hand, studies that analyse structure directly only show local structuring in a solute's first and possibly second hydration shells. On the other hand, thermodynamic and kinetic data imply indirectly that structuring occurs much further away. Here, the hydrogen-bond structure of water around halide anions, alkali cations, noble-gas solutes, and at the vapor-water interface is examined using molecular dynamics simulations. In addition to the expected perturbation in the first hydration shell, deviations from bulk behavior are observed at longer range in the rest of the simulation box. In particular, at the longer range, there is an excess of acceptors around halide anions, an excess of donors around alkali cations, weakly enhanced tetrahedrality and an oscillating excess and deficiency of donors and acceptors around noble-gas solutes, and enhanced tetrahedrality at the vapor-water interface. The structuring compensates for the short-range perturbation in water-water hydrogen bonds induced by the solute. Rather than being confined close to the solute, it is spread over as many water molecules as possible, presumably to minimize the perturbation to each water molecule.},
author = {Irudayam, Sheeba Jem and Henchman, Richard H.},



journal = {J. Chem. Phys.},
pages = {034508},
pmid = {22830712},
title = {{Long-range hydrogen-bond structure in aqueous solutions and the vapor-water interface}},
volume = {137},
year = {2012}
}
@article{uhle-orns30pr,
author = {Uhlenbeck, G E and Ornstein, L S},

journal = {Phys. Rev.},

pages = {823--841},
publisher = {American Physical Society},
title = {{On the Theory of the Brownian Motion}},
volume = {36},
year = {1930}
}
@article{arde+15jctc,
abstract = {This work examines the conformational ensemble involved in ?-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.},
author = {Ardevol, Albert and Tribello, G.A. Gareth A. and Ceriotti, Michele and Parrinello, Michele},



journal = {J. Chem. Theory Comput.},


pages = {1086--1093},
pmid = {26579758},
title = {{Probing the Unfolded Configurations of a $\beta$-Hairpin Using Sketch-Map}},

volume = {11},
year = {2015}
}
@article{hect-herb08jpcm,
author = {{Hector Jr}, L G and Herbst, J F},



journal = {J. Phys. Cond. Matt.},


pages = {64229},
publisher = {Institute of Physics Publishing},
title = {{Density functional theory for hydrogen storage materials: successes and opportunities}},

volume = {20},
year = {2008}
}
@article{brow+13jcp,
abstract = {The self-consistent phonons (SCP) method provides a consistent way to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate the system's properties, such as its free energy or its vibrational spectrum. The numerical bottleneck of the method is the evaluation of Gaussian averages of the potential energy and its derivatives. Several algorithmic ideas/tricks are introduced to reduce the cost of such integration by orders of magnitude, e.g., relative to that of the previous implementation of the SCP approach by Calvo et al. [J. Chem. Phys. 133, 074303 (2010)]. One such algorithmic improvement is the replacement of standard Monte Carlo integration by quasi-Monte Carlo integration utilizing low-discrepancy sequences. The performance of the method is demonstrated on the calculation of vibrational frequencies of pyrene. It is then applied to compute the free energies of five isomers of water hexamer using the WHBB potential of Bowman and co-workers [J. Chem. Phys. 134, 094509 (2011)]. The present results predict the hexamer prism being thermodynamically most stable, with the free energy of the hexamer cage being about 0.2 kcal mol(-1) higher at all temperatures below T = 200 K.},
author = {Brown, Sandra E and Georgescu, Ionuţ and Mandelshtam, Vladimir a},



journal = {J. Chem. Phys.},


pages = {044317},
pmid = {23387594},
title = {{Self-consistent phonons revisited. II. A general and efficient method for computing free energies and vibrational spectra of molecules and clusters.}},

volume = {138},
year = {2013}
}
@article{kasa+18nm,
abstract = {L ayered van der Waals (vdW) materials have unique properties, and these two-dimensional solids are central to current research in solid-state science. Although graphite is probably the most widely known layered material, nowadays transition metal dichal-cogenides (TMDs) are attracting much attention due to a range of exciting applications, including electrode materials for ion batter-ies 1 , thermoelectrics 2 , catalysis 3 , topological insulators 4 , supercon-ductors 5 , and charge-density-wave materials 6 . In addition, single layers of TMDs are available due to the weak interlayer interaction 7 . Mono-and few-layer TMDs have unique properties which cannot appear in the bulk 8 , and heterostructures built layer by layer using different materials have entirely new properties 9 . In all the numer-ous fundamental and applied investigations of vdW materials, the weak interlayer interactions play a central role in the formation, intercalation, exfoliation and layer-by-layer building of the materi-als as well as being decisive for their unique properties. Here we provide the experimental quantification of interlayer interactions in the archetypal vdW material TiS 2 through modelling of structure factors extracted from accurate single-crystal synchrotron X-ray diffraction measurements. In TMDs, a transition metal atom (M) layer is sandwiched by two chalcogen atom (X) layers. It is commonly assumed that the MX 2 slabs are stacked by vdW interactions, whereas the intralayer M–X interactions are covalent. The interlayer part of the structure is typically referred to as the vdW gap. In the condensed-matter field, the vdW term is used typically for London dispersion forces, which are caused by instantaneously induced dipoles 10},
author = {Kasai, Hidetaka and Tolborg, Kasper and Sist, Mattia and Zhang, Jiawei and Hathwar, Venkatesha R. and Fils{\o}, Mette and Cenedese, Simone and Sugimoto, Kunihisa and Overgaard, Jacob and Nishibori, Eiji and Iversen, Bo B.},



journal = {Nature Materials},

pages = {1--4},
publisher = {Springer US},
title = {{X-ray electron density investigation of chemical bonding in van der Waals materials}},

volume = {17},
year = {2018}
}
@article{ceri+09prb,
abstract = {Diffusion and decomposition of SiHx species adsorbed on the clean Si(100) surface are processes of relevance for the growth of crystalline silicon by plasma-enhanced chemical vapor deposition. In this work, we report an extensive search of diffusion and decomposition pathways for SiH3, SiH2, and SiH by means of combined ab initio metadynamics simulations and optimization of minimum-energy reactions paths. We find that on the clean surface SiH3 undergoes stepwise decompositions into Si and H adatoms according to SiH3 → SiH2 +H→SiH+2H→Si+3H with an overall reaction barrier of the order of 0.8 eV, consistent with the scenario inferred from secondary ion mass spectroscopy data. The lifetime of SiH3 at room temperature calculated within transition state theory in the harmonic approximation is in agreement with experiments. The lifetime of SiH2 turns out to be similar to that of SiH3. Possible trap states for SiH2 are proposed, based on energetics and by comparing calculated scanning tunneling microscope images with experimental data. {\textcopyright} 2009 The American Physical Society.},
author = {Ceriotti, Michele and Cereda, Silvia and Montalenti, Francesco and Miglio, Leo and Bernasconi, Marco},



journal = {Phys. Rev. B},


pages = {165437},
publisher = {APS},
title = {{Ab initio study of the diffusion and decomposition pathways of SiHx species on Si(100)}},

volume = {79},
year = {2009}
}
@article{finn+02prl,
abstract = {The detailed structure of a new dense amorphous ice, VHDA, is determined by isotope substitution neutron diffraction. Its structure is characterized by a doubled occupancy of the stabilizing interstitial location that was found in high density amorphous ice, HDA. As would be expected for a thermally activated unlocking of the stabilizing "interstitial," the transition from VHDA to LDA (low-density amorphous ice) is very sharp. Although its higher density makes VHDA a better candidate than HDA for a physical manifestation of the second putative liquid phase of water, as for the HDA case, the VHDA to LDA transition also appears to be kinetically controlled.},
author = {Finney, J L and Bowron, D T and Soper, a K and Loerting, T and Mayer, E and Hallbrucker, A},


isbn = {1079-7114},

journal = {Phys. Rev. Lett.},


pages = {205503},
pmid = {12443486},
title = {{Structure of a New Dense Amorphous Ice}},

volume = {89},
year = {2002}
}
@article{hass+11pnas,
abstract = {The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.},
author = {Hassanali, Ali and Prakash, Meher K and Eshet, Hagai and Parrinello, Michele},



journal = {Proc. Natl. Acad. Sci. USA},



pages = {20410--5},
pmid = {22143756},
publisher = {National Acad Sciences},
title = {{On the recombination of hydronium and hydroxide ions in water.}},

volume = {108},
year = {2011}
}
@article{wang+02ass,
abstract = {Tapping mode atomic force microscopy (AFM) was applied to study the adsorption behavior of methanol on mica, highly oriented pyrolytic graphite (HOPG) and indium-tin oxide (ITO) coated glass substrates. On mica and HOPG substrates surfaces, the thin films of methanol with bilayer and multilayer were observed, respectively. The formation of irregular islands of methanol was also found on HOPG surface. On ITO surface only aggregates and clusters of methanol molecules were formed. The influence of sample preparation on the adsorption was discussed. ?? 2002 Elsevier Science B.V. All rights reserved.},
author = {Wang, Li and Song, Yonghai and Wu, Aiguo and Li, Zhuang and Zhang, Bailin and Wang, Erkang},



journal = {Applied Surf. Sci.},



pages = {67--73},
title = {{Study of methanol adsorption on mica, graphite and ITO glass by using tapping mode atomic force microscopy}},

volume = {199},
year = {2002}
}
@article{mara+09jpcb,
abstract = {We introduce the Gaussian-mixture umbrella sampling method (GAMUS) , a biased molecular dynamics technique based on adaptive umbrella sampling that efficiently escapes free energy minima in multidimensional problems. The prior simulation data are reweighted with a maximum likelihood formulation, and the new approximate probability density is fit to a Gaussian-mixture model, augmented by information about the unsampled areas. The method can be used to identify free energy minima in multidimensional reaction coordinates. To illustrate GAMUS , we apply it to the alanine dipeptide (2D reaction coordinate) and tripeptide (4D reaction coordinate).},
author = {Maragakis, Paul and van der Vaart, Arjan and Karplus, Martin},



journal = {J. Phys. Chem.. B},



pages = {4664--4673},
pmid = {19284746},
title = {{Gaussian-mixture umbrella sampling.}},

volume = {113},
year = {2009}
}
@article{chen-ceri18jcp,
abstract = {The curvature dependence of interfacial free energy, which is crucial in quantitatively predicting nucleation kinetics and the stability of bubbles and droplets, can be described in terms of the Tolman length {\{}$\backslash$delta{\}}. For solid-liquid interfaces, however,{\{}$\backslash$delta{\}} has never been computed directly due to various theoretical and practical challenges. Here we present a general method that enables the direct evaluation of the Tolman length from atomistic simulations of a solid-liquid planar interface in out-of-equilibrium conditions. This method works by first measuring the surface tension from the amplitude of thermal capillary fluctuations of a localized version of Gibbs dividing surface, and bythen computing the free energy difference between the surface of tension and the equimolar dividing surface. For benchmark purposes, we computed {\{}$\backslash$delta{\}}for a model potential, and compared the results to less rigorous indirect approaches.},
archivePrefix = {arXiv},
arxivId = {1803.09140},
author = {Cheng, Bingqing and Ceriotti, Michele},




journal = {J. Chem. Phys.},


pages = {231102},
title = {{Computing the Tolman length for solid-liquid interfaces}},

volume = {148},
year = {2018}
}
@article{Manousiouthakis1999,
author = {Manousiouthakis, Vasilios I. and Deem, Michael W.},



journal = {J. Chem. Phys.},

pages = {2753},
title = {{Strict detailed balance is unnecessary in Monte Carlo simulation}},

volume = {110},
year = {1999}
}
@article{yu+10cpc,
author = {Yu, R. and Zhu, J. and Ye, H.Q. Q},



journal = {Comp. Phys. Comm.},

pages = {671--675},
publisher = {Elsevier B.V.},
title = {{Calculations of single-crystal elastic constants made simple}},

volume = {181},
year = {2010}
}
@article{marx+99nat,
author = {Marx, D and Tuckerman, M E and Hutter, J and Parrinello, M},

journal = {Nature},

pages = {601--604},
title = {{The nature of the hydrated excess proton in water}},
volume = {397},
year = {1999}
}
@article{petr+15jcc,
abstract = {{\textcopyright} 2015 Wiley Periodicals, Inc. Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.},
author = {Petraglia, Riccardo and Nicola{\"{i}}, Adrien and Wodrich, M.D. Matthew D. and Ceriotti, Michele and Corminboeuf, C.},



journal = {J. Comp. Chem.},



pages = {83--92},
title = {{Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry}},

volume = {37},
year = {2016}
}
@article{jinn-asah17jpcl,
author = {Jinnouchi, Ryosuke and Asahi, Ryoji},



journal = {J. Phys. Chem. Letters},


pages = {4279--4283},
title = {{Predicting Catalytic Activity of Nanoparticles by a DFT-Aided Machine-Learning Algorithm}},

volume = {8},
year = {2017}
}
@article{tana+05jacs,
abstract = {H(2) and D(2) adsorption on single-wall carbon nanohorns (SWNHs) have been measured at 77 K, and the experimental data were compared with grand canonical Monte Carlo simulations for adsorption of these hydrogen isotopes on a model SWNH. Quantum effects were included in the simulations through the Feynman-Hibbs effective potential. The simulation predictions show good agreement with the experimental results and suggest that the hydrogen isotope adsorption at 77 K can be successfully explained with the use of the effective potential. According to the simulations, the hydrogen isotopes are preferentially adsorbed in the cone part of the SWNH with a strong potential field, and quantum effects cause the density of adsorbed H(2) inside the SWNH to be 8-26{\%} smaller than that of D(2). The difference between H(2) and D(2) adsorption increases as pressure decreases because the quantum spreading of H(2), which is wider than that of D(2), is fairly effective at the narrow conical part of the SWNH model. These facts indicate that quantum effects on hydrogen adsorption depend on pore structures and are very important even at 77 K.},
author = {Tanaka, Hideki and Kanoh, Hirofumi and Yudasaka, Masako and Iijima, Sumio and Kaneko, Katsumi},



journal = {J. Chem. Am. Soc. },


pages = {7511--6},
pmid = {15898801},
title = {{Quantum effects on hydrogen isotope adsorption on single-wall carbon nanohorns.}},

volume = {127},
year = {2005}
}
@article{stil-web83jpc,
author = {Stillinger, Frank H. and Weber, Thomas A},



journal = {J. Phys. Chem.},


pages = {2833--2840},
title = {{Inherent structure in water}},

volume = {87},
year = {1983}
}
@article{parr-rahm84jcp,
author = {Parrinello, M and Rahman, A},

journal = {J. Chem. Phys.},
pages = {860},
publisher = {AIP},
title = {{Study of an F center in molten KCl}},
volume = {80},
year = {1984}
}
@article{koba+17prm,
author = {Kobayashi, Ryo and Giofr{\'{e}}, Daniele and Junge, Till and Ceriotti, Michele and Curtin, William A.},



journal = {Phys. Rev. Materials},

pages = {053604},
title = {{Neural network potential for Al-Mg-Si alloys}},

volume = {1},
year = {2017}
}
@article{hele-alth13jcp,
abstract = {Surprisingly, there exists a quantum flux-side time-correlation function which has a non-zero t → 0+ limit and thus yields a rigorous quantum generalization of classical transition-state theory (TST). In this Part I of two articles, we introduce the new time-correlation function and derive its t → 0+ limit. The new ingredient is a generalized Kubo transform which allows the flux and side dividing surfaces to be the same function of path-integral space. Choosing this function to be a single point gives a t → 0+ limit which is identical to an expression introduced on heuristic grounds by Wigner in 1932; however, this expression does not give positive-definite quantum statistics, causing it to fail while still in the shallow-tunnelling regime. Positive-definite quantum statistics is obtained only if the dividing surface is invariant to imaginary-time translation, in which case the t → 0+ limit is identical to ring-polymer molecular dynamics (RPMD) TST. The RPMD-TST rate is not a strict upper bound to the exact quantum rate, but is a good approximation to one if real-time coherence effects are small. Part II will show that the RPMD-TST rate is equal to the exact quantum rate in the absence of recrossing.},
author = {Hele, Timothy J H and Althorpe, Stuart C},



journal = {J. Chem. Phys.},


pages = {084108},
pmid = {23464141},
title = {{Derivation of a true (t-{\textgreater}0+) quantum transition-state theory. I. Uniqueness and equivalence to ring-polymer molecular dynamics transition-state-theory.}},

volume = {138},
year = {2013}
}
@article{pizz+16cms,
author = {Pizzi, Giovanni and Cepellotti, Andrea and Sabatini, Riccardo and Marzari, Nicola and Kozinsky, Boris},


journal = {Computational Materials Science},

pages = {218--230},
title = {{AiiDA: automated interactive infrastructure and database for computational science}},

volume = {111},
year = {2016}
}
@article{cao-voth94jcp,
annote = {From Duplicate 2 ( 




















The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics




















- Cao, Jianshu; Voth, Gregory A )







},
author = {Cao, Jianshu and Voth, Gregory A},

journal = {J. Chem. Phys.},


pages = {6168--6183},
publisher = {AIP},
title = {{The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics}},
volume = {101},
year = {1994}
}
@article{schm82jltp,
author = {Schmid, Albert},



journal = {J. Low Temp. Phys.},


pages = {609--626},
title = {{On a quasiclassical Langevin equation}},

volume = {49},
year = {1982}
}
@article{fate-stee15jctc,
author = {Fatehi, Shervin and Steele, Ryan P.},



journal = {J. Chem. Theory Comput.},

pages = {884--898},
title = {{Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening}},

volume = {11},
year = {2015}
}
@article{wang-bowm11jcp,
abstract = {We employ recent flexible ab initio potential energy and dipole surfaces [Y. Wang, X. Huang, B. C. Shepler, B. J. Braams, and J. M. Bowman, J. Chem. Phys. 134, 094509 (2011)] to the calculation of IR spectra of the intramolecular modes of water clusters. We use a quantum approach that begins with a partitioned normal-mode analysis of perturbed monomers, and then obtains solutions of the corresponding Schrödinger equations for the fully coupled intramolecular modes of each perturbed monomer. For water clusters, these modes are the two stretches and the bend. This approach is tested against benchmark calculations for the water dimer and trimer and then applied to the water clusters (H(2)O)(n) for n = 6-10 and n = 20. Comparisons of the spectra are made with previous ab initio harmonic and empirical potential calculations and available experiments.},
author = {Wang, Yimin and Bowman, Joel M},



journal = {J. Chem. Phys.},


pages = {154510},
pmid = {21513398},
title = {{Ab initio potential and dipole moment surfaces for water. II. Local-monomer calculations of the infrared spectra of water clusters.}},

volume = {134},
year = {2011}
}
@article{maib08prl,
abstract = {Successful theories of phase transformation processes include classical nucleation theory, which envisions a local equilibrium between coexisting phases, and nonequilibrium kinetic cluster theories. Using computer simulations of the magnetization reversal of the Ising model in three different ensembles we make quantitative connections between these physical pictures. We show that the critical nucleus size of classical nucleation theory is strongly correlated with a dynamical measure of metastability, and that the metastable phase persists to thermodynamic conditions previously thought of as unstable.},
author = {Maibaum, Lutz},


isbn = {0031-9007 (Print)$\backslash$r0031-9007 (Linking)},

journal = {Phys. Rev. Lett.},


pages = {256102},
pmid = {19113727},
title = {{Phase Transformation near the Classical Limit of Stability}},

volume = {101},
year = {2008}
}
@article{okad-toku84jap,
author = {Okada, Yasumasa and Tokumaru, Yozo},

journal = {J. Appl. Phys.},

pages = {314--320},
publisher = {AIP},
title = {{Precise determination of lattice parameter and thermal expansion coefficient of silicon between 300 and 1500 K}},
volume = {56},
year = {1984}
}
@article{bran+12jctc,
author = {Branduardi, Davide and Bussi, Giovanni and Parrinello, Michele},



journal = {J. Chem. Theory Comput.},


pages = {2247--2254},
title = {{Metadynamics with Adaptive Gaussians}},

volume = {8},
year = {2012}
}
@article{sant+02science,
abstract = {Probing the lowest energy configuration of a complex system by quantum annealing was recently found to be more effective than its classical, thermal counterpart. By comparing classical and quantum Monte Carlo annealing protocols on the two-dimensional random Ising model (a prototype spin glass), we confirm the superiority of quantum annealing relative to classical annealing. We also propose a theory of quantum annealing based on a cascade of Landau-Zener tunneling events. For both classical and quantum annealing, the residual energy after annealing is inversely proportional to a power of the logarithm of the annealing time, but the quantum case has a larger power that makes it faster.},
author = {Santoro, Giuseppe E and Marton{\'{a}}k, Roman and Tosatti, Erio and Car, Roberto},



journal = {Science},


pages = {2427--2430},
pmid = {11923532},
publisher = {American Association for the Advancement of Science},
series = {New Series},
title = {{Theory of Quantum Annealing of an Ising Spin Glass}},

volume = {295},
year = {2002}
}
@article{chan78jcp,
author = {Chandler, David},



journal = {J. Chem. Phys.},

pages = {2959},
title = {{Statistical mechanics of isomerization dynamics in liquids and the transition state approximation}},

volume = {68},
year = {1978}
}
@article{fan+09jpcb,
author = {Fan, Y and Chen, X and Yang, L and Cremer, P S and Gao, Y Q},

journal = {J. Phys. Chem. B},

pages = {11672--11679},
publisher = {ACS Publications},
title = {{On the structure of water at the aqueous/air interface}},
volume = {113},
year = {2009}
}
@article{tu+06jpcb,
abstract = {Electric field induced second harmonic generation (EFISH) is an important experimental technique in extracting the first hyperpolarizability of an organic chromophore molecule. Such experiments are carried out in solutions with chromophore molecules dissolved in some common solvents. A known fact is that the first hyperpolarizabilities extracted from EFISH experiments are subject to the use of local field factors. In this work, we apply simulations to study the EFISH properties of chromophore solutions. By combining quantum chemistry calculations with the results derived from molecular dynamics simulations, we show how macroscopic EFISH properties can be modeled, using 4-(dimethylamino)-4'-nitroazobenzene dissolved in chloroform as a demonstration case. The focus of the study is on deriving accurate local field factors. We find that the local field approach applies very well to dipolar solutions, such as the one studied here, but that the local field factors derived are much smaller than the commonly used Onsager or Lorentz local field factors. Our study indicates that many of the reported first hyperpolarizabilities for dipolar molecules from EFISH experiments are most probably underestimated because the Onsager/Lorentz approach, commonly used in extracting the molecular first hyperpolarizability, neglects the effects of the shapes of dipolar chromophore molecules on the local field factors.},
author = {Tu, Yaoquan and Luo, Yi and Agren, Hans},



journal = {J. Phys. Chem.. B},

mendeley-tags = {SHS,ions,local field factor,second harmonic},
pages = {8971--8977},
pmid = {16671703},
title = {{Molecular dynamics simulations applied to electric field induced second harmonic generation in dipolar chromophore solutions.}},
volume = {110},
year = {2006}
}
@article{Cheng2018,
abstract = {We investigate the thermodynamics and kinetics of a hydrogen interstitial in magnetic {\{}$\backslash$alpha{\}}-iron, taking account of the quantum fluctuations of the proton as well as the anharmonicities of lattice vibrations and hydrogen hopping. We show that the diffusivity of hydrogen in the lattice of BCC iron deviates strongly from an Arrhenius behavior at and below room temperature. We compare a quantum transition state theory to explicit ring polymer molecular dynamics in the calculation of diffusivity and we find that the role of phonons is to inhibit, not to enhance, diffusivity at intermediate temperatures in constrast to the usual polaron picture of hopping. We then address the trapping of hydrogen by a vacancy as a prototype lattice defect. By a sequence of steps in a thought experiment, each involving a thermodynamic integration, we are able to separate out the binding free energy of a proton to a defect into harmonic and anharmonic, and classical and quantum contributions. We find that about 30{\%} of a typical binding free energy of hydrogen to a lattice defect in iron is accounted for by finite temperature effects and about half of these arise from quantum proton fluctuations. This has huge implications for the comparison between thermal desorption and permeation experiments and standard electronic structure theory. The implications are even greater for the interpretation of muon spin resonance experiments.},
archivePrefix = {arXiv},
arxivId = {1803.00600},
author = {Cheng, Bingqing and Paxton, Anthony T. and Ceriotti, Michele},




journal = {Phys. Rev. Lett.},



pages = {225901},
publisher = {American Physical Society},
title = {{Hydrogen Diffusion and Trapping in $\alpha$-Iron: The Role of Quantum and Anharmonic Fluctuations}},

volume = {120},
year = {2018}
}
@article{mart+94jcp,
author = {Martyna, Glenn J. and Tobias, Douglas J. and Klein, Michael L.},



journal = {J. Chem. Phys.},

pages = {4177},
title = {{Constant pressure molecular dynamics algorithms}},

volume = {101},
year = {1994}
}
@article{goed99rmp,
author = {Goedecker, S},

journal = {Rev. Mod. Phys.},

pages = {1085--1123},
publisher = {APS},
title = {{Linear scaling electronic structure methods}},
volume = {71},
year = {1999}
}
@article{saki+07ijhe,
author = {Sakintuna, B and Lamaridarkrim, F and Hirscher, M},



journal = {International Journal of Hydrogen Energy},



pages = {1121--1140},
title = {{Metal hydride materials for solid hydrogen storage: A review☆}},

volume = {32},
year = {2007}
}
@article{shel+01jpcb,
author = {Shelley, John C. and Shelley, Mee Y. and Reeder, Robert C. and Bandyopadhyay, Sanjoy and Klein, Michael L.},



journal = {J. Phys. Chem. B},


pages = {4464--4470},
title = {{A Coarse Grain Model for Phospholipid Simulations}},

volume = {105},
year = {2001}
}
@article{rama+14sd,
author = {Ramakrishnan, Raghunathan and Dral, Pavlo O and Rupp, Matthias and von Lilienfeld, O. Anatole},



journal = {Scientific Data},

pages = {1--7},
title = {{Quantum chemistry structures and properties of 134 kilo molecules}},

volume = {1},
year = {2014}
}
@article{lude+10cpc,
author = {Ludue{\~{n}}a, G A and Wegner, M and Bj{\aa}lie, L and Sebastiani, D},
journal = {ChemPhysChem},
publisher = {John Wiley {\&} Sons},
title = {{Local Disorder in Hydrogen Storage Compounds: The Case of Lithium Amide/Imide}},
volume = {EARLYVIEW}
}
@article{bote+10as,
abstract = {We present a new adaptive kernel density estimator based on linear diffusion processes. The proposed estimator builds on existing ideas for adaptive smoothing by incorporating information from a pilot density estimate. In addition, we propose a new plug-in bandwidth selection method that is free from the arbitrary normal reference rules used by existing methods. We present simulation examples in which the proposed approach outperforms existing methods in terms of accuracy and reliability.},
archivePrefix = {arXiv},
arxivId = {arXiv:1011.2602v1},
author = {Botev, Z. I. and Grotowski, J. F. and Kroese, D. P.},



isbn = {0090-5364},

journal = {The Annals of Statistics},



pages = {2916--2957},
title = {{Kernel density estimation via diffusion}},

volume = {38},
year = {2010}
}
@article{iann+03prl,
author = {Iannuzzi, M and Laio, A and Parrinello, M},

journal = {Phys. Rev. Lett.},

pages = {238302},
publisher = {APS},
title = {{Efficient Exploration of Reactive Potential Energy Surfaces Using Car-Parrinello Molecular Dynamics}},
volume = {90},
year = {2003}
}
@article{monk-pack76prb,
author = {Monkhorst, H J and Pack, J D},

journal = {Phys. Rev. B},

pages = {5188--5192},
publisher = {APS},
title = {{Special points for Brillouin-zone integrations}},
volume = {13},
year = {1976}
}
@article{libn+95as,
author = {Libnau, F O and Christy, A A and Kvalheim, O M},
journal = {Applied spectroscopy},

pages = {1431--1437},
publisher = {Society for Applied Spectroscopy},
title = {{Determination of the equilibrium constant and resolution of the HOD spectrum by alternating least-squares and infrared analysis}},
volume = {49},
year = {1995}
}
@article{tsap+14mp,
abstract = {This study focuses on the interplay of molecular flexibility and hydrogen bonding manifested in the monoclinic (form I) and orthorhombic (form II) polymorphs of paracetamol. By means of incoherent inelastic neutron scattering and density functional theory calculations, the relaxation processes related to the methyl side-group reorientation were analyzed in detail. Our computational study demonstrates the importance of considering quantum effects to explain how methyl reorientations and subtle conformational changes of the molecule are intertwined. Indeed, by analyzing the quasi elastic signal of the neutron data, we were able to show a unique and complex motional flexibility in form II, reflected by a coupling between the methyl and the phenyl reorientation. This is associated with a higher energy barrier of the methyl rotation and a lower Gibbs free energy when compared to form I. We put forward the idea that correlating solubility and molecular flexibility, through the relation between pKa and methyl rotation activation energy, might bring new insights to understanding and predicting drug bioavailability.},
author = {Tsapatsaris, Nikolaos and Kolesov, Boris a. and Fischer, Jennifer and Boldyreva, Elena V. and Daemen, Luke and Eckert, Juergen and Bordallo, Heloisa N.},



journal = {Molecular Pharmaceutics},

pages = {1032--1041},
pmid = {24506163},
title = {{Polymorphism of paracetamol: A new understanding of molecular flexibility through local methyl dynamics}},
volume = {11},
year = {2014}
}
@misc{TheMendeleySupportTeam2011,
abstract = {A quick introduction to Mendeley. Learn how Mendeley creates your personal digital library, how to organize and annotate documents, how to collaborate and share with colleagues, and how to generate citations and bibliographies.},
address = {London},
author = {{The Mendeley Support Team}},
booktitle = {Mendeley Desktop},


pages = {1--16},
publisher = {Mendeley Ltd.},
title = {{Getting Started with Mendeley}},

year = {2011}
}
@article{dell+03prl,
author = {Dellago, Christoph and Naor, Mor and Hummer, Gerhard},



journal = {Phys. Rev. Lett.},


pages = {105902},
title = {{Proton Transport through Water-Filled Carbon Nanotubes}},

volume = {90},
year = {2003}
}
@article{gurt-voor96am,
abstract = {We develop a general thermodynamical description of an evolving interface appropriate to situations far from equilibrium. The theory represents a broad departure from theories based on classical nonequilibrium thermodynamics, as we do not assume a linear relationship between fluxes and forces, and we do not limit our theory to small departures from equilibrium. Further, we allow for diffusion in the bulk material; we allow the composition of material transferred across the interface to differ from the compositions of either phase, with solute drag included as a special case; and we allow for heat flow in both phases. As an application of the general theory, we develop linearized interface conditions for an evolving interface.},
author = {Gurtin, M. E. and Voorhees, P. W.},



journal = {Acta Materialia},

pages = {235--247},
title = {{The thermodynamics of evolving interfaces far from equilibrium}},
volume = {44},
year = {1996}
}
@book{rasm05book,
author = {Rasmussen, Carl Edward and Williams, Christopher K I},
isbn = {026218253X},
publisher = {The MIT Press},
title = {{Gaussian Processes for Machine Learning (Adaptive Computation and Machine Learning)}},
year = {2005}
}
@article{liu+16jcp,
author = {Liu, Jian and Li, Dezhang and Liu, Xinzijian},



journal = {J. Chem. Phys.},

pages = {024103},
title = {{A simple and accurate algorithm for path integral molecular dynamics with the Langevin thermostat}},

volume = {145},
year = {2016}
}
@article{luza-chan96nature,
author = {Luzar, Alenka and Chandler, David},



journal = {Nature},


pages = {55--57},
title = {{Hydrogen-bond kinetics in liquid water}},

volume = {379},
year = {1996}
}
@article{bowl-gill99cpc,
author = {Bowler, D R and Gillan, M J},

journal = {Comput. Phys. Commun.},

pages = {95--108},
publisher = {Elsevier},
title = {{Density matrices in O (N) electronic structure calculations: theory and applications}},
volume = {120},
year = {1999}
}
@article{2,
author = {Schwegler, Eric and Galli, Giulia and Gygi, Fran{\c{c}}ois and Hood, Randolph},



journal = {Phys. Rev. Lett.},


pages = {265501},
publisher = {American Physical Society},
title = {{Dissociation of Water under Pressure}},

volume = {87},
year = {2001}
}
@article{musi+18cs,
abstract = {Polymorphism is common in molecular crystals, whose energy landscapes usually contain many structures with similar stability, but very different physical–chemical properties. Machine-learning techniques can accelerate the evaluation of energy and properties by side-stepping accurate but demanding electronic-structure calculations, and provide a data-driven classification of the most important molecular packing motifs.},
author = {Musil, F{\'{e}}lix and De, Sandip and Yang, Jack and Campbell, Joshua E. J.E. and Day, G.M. Graeme Matthew and Ceriotti, Michele},



journal = {Chemical Science},

pages = {1289--1300},
title = {{Machine learning for the structure-energy-property landscapes of molecular crystals}},

volume = {9},
year = {2018}
}
@article{ludu-seba10jcpl,
author = {Ludue{\~{n}}a, Guillermo a. and Sebastiani, Daniel},



journal = {J. Phys. Chem. Letters},


pages = {3214--3218},
title = {{Possibility of Coherent Delocalized Nuclear Quantum States of Protons in Li 2 NH}},

volume = {1},
year = {2010}
}
@misc{Cuturi2010,
author = {Cuturi, Marco},


title = {{Positive Definite Kernels in Machine Learning}},
year = {2010}
}
@article{zhan03nb,
abstract = {Two complementary strategies can be used in the fabrication of molecular biomaterials. In the 'top-down' approach, biomaterials are generated by stripping down a complex entity into its component parts (for example, paring a virus particle down to its capsid to form a viral cage). This contrasts with the 'bottom-up' approach, in which materials are assembled molecule by molecule (and in some cases even atom by atom) to produce novel supramolecular architectures. The latter approach is likely to become an integral part of nanomaterials manufacture and requires a deep understanding of individual molecular building blocks and their structures, assembly properties and dynamic behaviors. Two key elements in molecular fabrication are chemical complementarity and structural compatibility, both of which confer the weak and noncovalent interactions that bind building blocks together during self-assembly. Using natural processes as a guide, substantial advances have been achieved at the interface of nanomaterials and biology, including the fabrication of nanofiber materials for three-dimensional cell culture and tissue engineering, the assembly of peptide or protein nanotubes and helical ribbons, the creation of living microlenses, the synthesis of metal nanowires on DNA templates, the fabrication of peptide, protein and lipid scaffolds, the assembly of electronic materials by bacterial phage selection, and the use of radiofrequency to regulate molecular behaviors.},
author = {Zhang, Shuguang},



journal = {Nature biotechnology},



pages = {1171--1178},
pmid = {14520402},
title = {{Fabrication of novel biomaterials through molecular self-assembly.}},

volume = {21},
year = {2003}
}
@article{oost+04jcc,
abstract = {Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.},
author = {Oostenbrink, Chris and Villa, Alessandra and Mark, Alan E and van Gunsteren, Wilfred F},



journal = {J. Comp. Chem.},



pages = {1656--1676},
pmid = {15264259},
title = {{A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.}},

volume = {25},
year = {2004}
}
@article{ferr+15jctc,
abstract = {Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a bottleneck in molecular dynamics simulations. An algorithm to treat smooth biasing forces within a multiple time step framework is here discussed. The implementation is simple and allows a speed up when expensive collective variables are employed. The gain can be substantial when using massively parallel or GPU-based molecular dynamics software. Moreover, a theoretical framework to assess the sampling accuracy is introduced, which can be used to assess the choice of the integration time step in both single and multiple time step biased simulations.{\$}\backslash{\$}nMany recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a bottleneck in molecular dynamics simulations. An algorithm to treat smooth biasing forces within a multiple time step framework is here discussed. The implementation is simple and allows a speed up when expensive collective variables are employed. The gain can be substantial when using massively parallel or GPU-based molecular dynamics software. Moreover, a theoretical framework to assess the sampling accuracy is introduced, which can be used to assess the choice of the integration time step in both single and multiple time step biased simulations.},
archivePrefix = {arXiv},
arxivId = {1412.3916},
author = {Ferrarotti, Marco Jacopo and Bottaro, Sandro and P{\'{e}}rez-Villa, Andrea and Bussi, Giovanni},



isbn = {1549-9618},

journal = {J. Chem. Theory Comput.},

pages = {139--146},
title = {{Accurate Multiple Time Step in Biased Molecular Simulations}},

volume = {11},
year = {2015}
}
@article{flam+12jcp,
abstract = {The spherical momentum distribution of the protons in ice is extracted from a high resolution deep inelastic neutron scattering experiment. Following a recent path integral Car-Parrinello molecular dynamics study, data were successfully interpreted in terms of an anisotropic Gaussian model, with a statistical accuracy comparable to that of the model independent scheme used previously, but providing more detailed information on the three dimensional potential energy surface experienced by the proton. A recently proposed theoretical concept is also employed to directly calculate the mean force from the experimental neutron Compton profile, and to evaluate the accuracy required to unambiguously resolve and extract the effective proton potential from the experimental data.},
author = {Flammini, D. and Pietropaolo, A. and Senesi, R. and Andreani, C. and McBride, F. and Hodgson, A. and Adams, M. a. and Lin, L. and Car, R.},



journal = {J. Chem. Phys.},



pages = {024504},
pmid = {22260600},
title = {{Spherical momentum distribution of the protons in hexagonal ice from modeling of inelastic neutron scattering data.}},

volume = {136},
year = {2012}
}
@article{blan+95jcp,
author = {Blank, Thomas B. and Brown, Steven D. and Calhoun, August W. and Doren, Douglas J.},



journal = {J. Chem. Phys.},

pages = {4129},
title = {{Neural network models of potential energy surfaces}},

volume = {103},
year = {1995}
}
@article{berg02cpc,
author = {Berg, Bernd A},



journal = {Comput. Phys. Commun.},



pages = {52--57},
title = {{Generalized ensemble simulations for complex systems}},

volume = {147},
year = {2002}
}
@article{woot+85prl,
author = {Wooten, F and Winer, K. and Weaire, D.},



journal = {Phys. Rev. Lett.},


pages = {1392--1395},
title = {{Computer Generation of Structural Models of Amorphous Si and Ge}},

volume = {54},
year = {1985}
}
@article{lin+12jctc,
abstract = {We investigate the accuracy provided by different treatments of the exchange and correlation effects, in particular the London dispersion forces, on the properties of liquid water using ab initio molecular dynamics simulations with density functional theory. The lack of London dispersion forces in generalized gradient approximations (GGAs) is remedied by means of dispersion-corrected atom-centered potentials (DCACPs) or damped atom-pairwise dispersion corrections of the C6R?6 form. We compare results from simulations using GGA density functionals (BLYP, PBE, and revPBE) with data from their van der Waals (vdW) corrected counterparts. As pointed out previously, all vdW-corrected BLYP simulations give rise to highly mobile water whose softened structure is closer to experimental data than the one predicted by the bare BLYP functional. Including vdW interactions in the PBE functional, on the other hand, has little influence on both structural and dynamical properties of water. Augmenting the revPBE functional with either damped atom-pairwise dispersion corrections or DCACP evokes opposite behaviors. The former further softens the already under-structured revPBE water, whereas the latter makes it more glassy. These results demonstrate the delicacy needed in describing weak interactions in molecular liquids.},
author = {Lin, I-Chun and Seitsonen, Ari P. and Tavernelli, Ivano and Rothlisberger, Ursula},



journal = {J. Chem. Theory Comput.},
pages = {3902--3910},
title = {{Structure and dynamics of liquid water from ab initio molecular dynamics-comparison of BLYP, PBE, and revPBE density functionals with and without van der Waals corrections}},
volume = {8},
year = {2012}
}
@article{pavo-baro94ssc,
author = {Pavone, Pasquale and Baroni, Stefano},



journal = {Sol. St. Comm.},


pages = {295--297},
publisher = {Elsevier},
title = {{Dependence of the crystal lattice constant on isotopic composition: Theory and ab initio calculations for C, Si, and Ge}},

volume = {90},
year = {1994}
}
@article{paes+09jpcb,
abstract = {A molecular-level description of the unique properties of hydrogen-bond networks is critical for understanding many fundamental physicochemical processes in aqueous environments. In this Article, a novel simulation approach, combining an ab initio-based force field for water with a quantum treatment of the nuclear motion, is applied to investigate hydrogen-bond dynamics in liquid water with a specific focus on the relationship of these dynamics to vibrational spectroscopy. Linear and nonlinear infrared (IR) spectra are calculated for liquid water, HOD in D(2)O and HOD in H(2)O, and discussed in the context of the results obtained using other approaches that have been employed in studies of water dynamics. A comparison between the calculated spectra and the available experimental data yields an overall good agreement, indicating the accuracy of the present simulation approach in describing the properties of liquid water under ambient conditions. Possible improvements on the representation of the underlying water interactions as well as the treatment of the molecular motion at the quantum-mechanical level are also discussed.},
author = {Paesani, Francesco and Xantheas, Sotiris S and Voth, Gregory a},



journal = {J. Phys. Chem. B},



pages = {13118--30},
pmid = {19722542},
title = {{Infrared spectroscopy and hydrogen-bond dynamics of liquid water from centroid molecular dynamics with an ab initio-based force field.}},

volume = {113},
year = {2009}
}
@article{mart+88jafc,
author = {Martin, Gerard J. and Guillou, Claude and Martin, Maryvonne L. and Cabanis, Marie Therese and Tep, Yutthay and Aerny, Jacques},



journal = {Journal of Agricultural and Food Chemistry},


pages = {316--322},
title = {{Natural factors of isotope fractionation and the characterization of wines}},

volume = {36},
year = {1988}
}
@article{brou-gilm83jcp3,
author = {Broughton, Jeremy Q. and Gilmer, George H.},



journal = {J. Chem. Phys.},

pages = {5119},
title = {{Molecular dynamics investigation of the crystal–fluid interface. III. Dynamical properties of fcc crystal–vapor systems}},

volume = {79},
year = {1983}
}
@article{lian+04jcomp,
author = {Liang, W Z and Baer, R and Saravanan, C and Shao, Y and Bell, A T and Head-Gordon, M},

journal = {J. Comp. Phys.},

pages = {575--587},
publisher = {Elsevier},
title = {{Fast methods for resumming matrix polynomials and Chebyshev matrix polynomials}},
volume = {194},
year = {2004}
}
@article{rest94rmp,
author = {Resta, Raffaele},



journal = {Rev. Mod. Phys.},


pages = {899--915},
title = {{Macroscopic polarization in crystalline dielectrics: the geometric phase approach}},

volume = {66},
year = {1994}
}
@article{zhan+18prl,
author = {Zhang, Linfeng and Han, Jiequn and Wang, Han and Car, Roberto and E, Weinan},


journal = {Phys. Rev. Lett.},


pages = {143001},
title = {{Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics}},

volume = {120},
year = {2018}
}
@article{xie-bowm06jpca,
abstract = {A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.},
author = {Xie, Zhen and Bowman, Joel M},



journal = {J. Phys. Chem.. A},


pages = {5446--9},
pmid = {16623473},
title = {{Zero-point energy constraint in quasi-classical trajectory calculations.}},

volume = {110},
year = {2006}
}
@article{wu+06jcp,
abstract = {In order to introduce flexibility into the simple point-charge (SPC) water model, the impact of the intramolecular degrees of freedom on liquid properties was systematically studied in this work as a function of many possible parameter sets. It was found that the diffusion constant is extremely sensitive to the equilibrium bond length and that this effect is mainly due to the strength of intermolecular hydrogen bonds. The static dielectric constant was found to be very sensitive to the equilibrium bond angle via the distribution of intermolecular angles in the liquid: A larger bond angle will increase the angle formed by two molecular dipoles, which is particularly significant for the first solvation shell. This result is in agreement with the work of Hochtl et al. [J. Chem. Phys. 109, 4927 (1998)]. A new flexible simple point-charge water model was derived by optimizing bulk diffusion and dielectric constants to the experimental values via the equilibrium bond length and angle. Due to the large sensitivities, the parametrization only slightly perturbs the molecular geometry of the base SPC model. Extensive comparisons of thermodynamic, structural, and kinetic properties indicate that the new model is much improved over the standard SPC model and its overall performance is comparable to or even better than the extended SPC model.},
author = {Wu, Yujie and Tepper, Harald L and Voth, Gregory a},



journal = {J. Chem. Phys.},



pages = {024503},
pmid = {16422607},
title = {{Flexible simple point-charge water model with improved liquid-state properties.}},

volume = {124},
year = {2006}
}
@article{zhon+94prl,
author = {Zhong, W and Vanderbilt, David and Rabe, K M},

journal = {Phys. Rev. Lett.},

pages = {1861--1864},
publisher = {American Physical Society},
title = {{Phase Transitions in BaTiO{\_}3 from First Principles}},
volume = {73},
year = {1994}
}
@article{kraj-parr06prb-2,
author = {Krajewski, F R and Parrinello, M},

journal = {Phys. Rev. B},
pages = {125107},
title = {{Linear scaling for quasi-one-dimensional systems}},
volume = {74},
year = {2006}
}
@article{chen+16prl,
abstract = {Self-consistent GW calculations with efficient vertex corrections are employed to determine the electronic structure of liquid water. Nuclear quantum effects are taken into account through ab initio path-integral molecular dynamics simulations. We reveal a sizable band-gap renormalization of up to 0.7 eV due to hydrogen-bond quantum fluctuations. Our calculations lead to a band gap of 8.9 eV, in accord with the experimental estimate. We further resolve the ambiguities in the band-edge positions of liquid water. The valence-band maximum and the conduction-band minimum are found at −9.4 and −0.5 eV with respect to the vacuum level, respectively.},
author = {Chen, Wei and Ambrosio, Francesco and Miceli, Giacomo and Pasquarello, Alfredo},



journal = {Phys. Rev. Lett.},


pages = {186401},
title = {{Ab initio Electronic Structure of Liquid Water}},

volume = {117},
year = {2016}
}
@article{silv-gold78jcp,
author = {Silvera, Isaac F. and Goldman, Victor V.},



journal = {J. Chem. Phys.},

pages = {4209},
title = {{The isotropic intermolecular potential for H2 and D2 in the solid and gas phases}},

volume = {69},
year = {1978}
}
@article{sell+14nature,
abstract = {Water has a number of anomalous physical properties, and some of these become drastically enhanced on supercooling below the freezing point. Particular interest has focused on thermodynamic response functions that can be described using a normal component and an anomalous component that seems to diverge at about 228 kelvin (refs 1-3). This has prompted debate about conflicting theories that aim to explain many of the anomalous thermodynamic properties of water. One popular theory attributes the divergence to a phase transition between two forms of liquid water occurring in the 'no man's land' that lies below the homogeneous ice nucleation temperature (TH) at approximately 232 kelvin and above about 160 kelvin, and where rapid ice crystallization has prevented any measurements of the bulk liquid phase. In fact, the reliable determination of the structure of liquid water typically requires temperatures above about 250 kelvin. Water crystallization has been inhibited by using nanoconfinement, nanodroplets and association with biomolecules to give liquid samples at temperatures below TH, but such measurements rely on nanoscopic volumes of water where the interaction with the confining surfaces makes the relevance to bulk water unclear. Here we demonstrate that femtosecond X-ray laser pulses can be used to probe the structure of liquid water in micrometre-sized droplets that have been evaporatively cooled below TH. We find experimental evidence for the existence of metastable bulk liquid water down to temperatures of 227(-1)(+2) kelvin in the previously largely unexplored no man's land. We observe a continuous and accelerating increase in structural ordering on supercooling to approximately 229 kelvin, where the number of droplets containing ice crystals increases rapidly. But a few droplets remain liquid for about a millisecond even at this temperature. The hope now is that these observations and our detailed structural data will help identify those theories that best describe and explain the behaviour of water.},
author = {Sellberg, J a and Huang, C and McQueen, T a and Loh, N D and Laksmono, H and Schlesinger, D and Sierra, R G and Nordlund, D and Hampton, C Y and Starodub, D and DePonte, D P and Beye, M and Chen, C and Martin, a V and Barty, A and Wikfeldt, K T and Weiss, T M and Caronna, C and Feldkamp, J and Skinner, L B and Seibert, M M and Messerschmidt, M and Williams, G J and Boutet, S and Pettersson, L G M and Bogan, M J and Nilsson, A},



journal = {Nature},


pages = {381--384},
pmid = {24943953},
publisher = {Nature Publishing Group},
title = {{Ultrafast X-ray probing of water structure below the homogeneous ice nucleation temperature.}},

volume = {509},
year = {2014}
}
@article{kats+05ea,
author = {Katsaounis, A. and Balomenou, S.P. P and Tsiplakides, D. and Tsampas, M. and Vayenas, C.G. G},



journal = {Electrochimica Acta},



pages = {5132--5143},
title = {{The role of potential-dependent electrolyte resistance in the performance, steady-state multiplicities and oscillations of PEM fuel cells: Experimental investigation and macroscopic modelling}},

volume = {50},
year = {2005}
}
@article{gran+98prb,
author = {Granado, E. and Moreno, N. O. and Garcia, A. and Sanjurjo, J A and Rettori, C and Torriani, I},

journal = {Phys. Rev. B},

pages = {435--440},
title = {{Phonon Raman scattering in RAMnO3}},
volume = {58},
year = {1998}
}
@misc{PWSCF,
author = {Baroni, S and {Dal Corso}, A and de Gironcoli, S and Giannozzi, P and Cavazzoni, C and Ballabio, G and Scandolo, S and Chiarotti, G and Focher, P and Pasquarello, A and Laasonen, K and Trave, A and Car, R and Marzari, N and Kokalj, A},
title = {{PWSCF}}
}
@article{lowd50jcp,
author = {L{\"{o}}wdin, P-O},

journal = {J. Chem. Phys.},
pages = {365--375},
title = {{On the Non-Orthogonality Problem Connected with the Use of Atomic Wave Functions in the Theory of Molecules and Crystals}},
volume = {18},
year = {1950}
}
@article{habe+08jcp,
author = {Habershon, S and Fanourgakis, G S and Manolopoulos, D E},

journal = {J. Chem. Phys.},
pages = {74501},
title = {{Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water}},
volume = {129},
year = {2008}
}
@article{bade-bern94jcp,
author = {Bader, Joel S. and Berne, B. J.},



journal = {J. Chem. Phys.},

pages = {8359},
title = {{Quantum and classical relaxation rates from classical simulations}},

volume = {100},
year = {1994}
}
@article{vara76iecprd,
author = {Varagnat, Jean},



journal = {Industrial {\&} Engineering Chemistry Product Research and Development},


pages = {212--215},
title = {{Hydroquinone and Pyrocatechol Production by Direct Oxidation of Phenol}},

volume = {15},
year = {1976}
}
@article{chen+16jpcl,
abstract = {{\textcopyright} 2016 American Chemical Society. One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell-Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.},
author = {Cheng, Bingqing and Behler, J{\"{o}}rg and Ceriotti, Michele},


isbn = {1948-7185 (Electronic) 1948-7185 (Linking)},

journal = {J. Phys. Chem. Letters},


pages = {2210--2215},
pmid = {27203358},
title = {{Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link Between Experiments}},

volume = {7},
year = {2016}
}
@article{will+18jcp,
abstract = {{\textcopyright} 2018 Author(s). Matsubara dynamics is the quantum-Boltzmann-conserving classical dynamics which remains when real-time coherences are taken out of the exact quantum Liouvillian [T. J. H. Hele et al., J. Chem. Phys. 142, 134103 (2015)]; because of a phase-term, it cannot be used as a practical method without further approximation. Recently, Smith et al. [J. Chem. Phys. 142, 244112 (2015)]  developed a "planetary" model dynamics which conserves the Feynman-Kleinert (FK) approximation to the quantum-Boltzmann distribution. Here, we show that for moderately anharmonic potentials, the planetary dynamics gives a good approximation to Matsubara trajectories on the FK potential surface by decoupling the centroid trajectory from the locally harmonic Matsubara fluctuations, which reduce to a single phase-less fluctuation particle (the "planet"). We also show that the FK effective frequency can be approximated by a direct integral over these fluctuations, obviating the need to solve iterative equations. This modification, together with use of thermostatted ring-polymer molecular dynamics, allows us to test the planetary model on water (gas-phase, liquid, and ice) using the q-TIP4P/F potential surface. The "planetary" fluctuations give a poor approximation to the rotational/librational bands in the infrared spectrum, but a good approximation to the bend and stretch bands, where the fluctuation lineshape is found to be motionally narrowed by the vibrations of the centroid.},
author = {Willatt, Michael J M.J. and Ceriotti, Michele and Althorpe, S.C. Stuart C},



journal = {J. Chem. Phys.},


pages = {102336},
title = {{Approximating Matsubara dynamics using the planetary model: Tests on liquid water and ice}},

volume = {148},
year = {2018}
}
@article{polt-tkat16cs,
abstract = {Here we combine perturbation theory with the Feynman–Kac imaginary-time path integral approach to quantum mechanics for modeling quantum nuclear effects.},
annote = {NULL},
author = {Poltavsky, Igor and Tkatchenko, Alexandre},


journal = {Chemical Science},

pages = {1368--1372},
title = {{Modeling quantum nuclei with perturbed path integral molecular dynamics}},

volume = {7},
year = {2016}
}
@article{sedl+11jacs,
abstract = {We use large-scale classical simulations employing different force fields to study spatial correlations between local density and structural order for water in the liquid temperature range. All force fields investigated reproduce the main features of the experimental SAXS structure factor S(q), including the minimum at small q, and the recent TIP4P/2005 parametrization yields almost quantitative agreement. As local structural order parameters we consider the tetrahedrality and the number of hydrogen bonds and calculate all pure and mixed spatial two-point correlation functions. Except for the density-density correlation function, there are only weak features present in all other correlation functions, showing that the tendency to form structural clusters is much weaker than the well-known tendency of water to form density clusters (i.e., spatially correlated regions where the density deviates from the mean). In particular, there are only small spatial correlations between local density and structural fluctuations, suggesting that features in density-density correlations (such as measured by the structure factor) are not straightforwardly related to spatial correlations of structure in liquid water.},
author = {Sedlmeier, Felix and Horinek, Dominik and Netz, Roland R.},


isbn = {0002-7863},

journal = {J. Chem. Am. Soc. },

pages = {1391--1398},
pmid = {21235232},
title = {{Spatial correlations of density and structural fluctuations in liquid water: A comparative simulation study}},
volume = {133},
year = {2011}
}
@article{lee-bern00jpca,
author = {Lee, Yong-Han and Berne, B J},

journal = {J. Phys. Chem. A},

pages = {86},
title = {{Global Optimization:{\{}{\~{}}{\}} Quantum Thermal Annealing with Path Integral Monte Carlo}},
volume = {104},
year = {2000}
}
@article{fitz-nguy08prl,
author = {Fitzgerald, S. and Nguyen-Manh, D.},



journal = {Phys. Rev. Lett.},


pages = {115504},
title = {{Peierls Potential for Crowdions in the bcc Transition Metals}},

volume = {101},
year = {2008}
}
@article{tuck+96jcp,
author = {Tuckerman, Mark E and Marx, Dominik and Klein, Michael L and Parrinello, Michele},

journal = {J. Chem. Phys.},

pages = {5579--5588},
publisher = {AIP},
title = {{Efficient and general algorithms for path integral Car-Parrinello molecular dynamics}},
volume = {104},
year = {1996}
}
@article{hegd-bowe17sr,
author = {Hegde, Ganesh and Bowen, R. Chris},


journal = {Scientific Reports},

pages = {42669},
title = {{Machine-learned approximations to Density Functional Theory Hamiltonians}},

volume = {7},
year = {2017}
}
@article{wang-john99jcp,
author = {Wang, Qinyu and Johnson, J. Karl},



journal = {J. Chem. Phys.},

pages = {577},
title = {{Molecular simulation of hydrogen adsorption in single-walled carbon nanotubes and idealized carbon slit pores}},

volume = {110},
year = {1999}
}
@book{press07book,
author = {Press, William H},
booktitle = {Cambridge University Press},
publisher = {Cambridge University Press},
title = {{Numerical Recipes: The art of scientific computing}},
year = {2007}
}
@article{brow+17am,
abstract = {Using molecular dynamics simulations and the capillary fluctuation method, we have calculated the anisotropic crystal-melt interfacial free energy and stiffness of aluminum in a rapid solidification system where a temperature gradient is applied to enforce thermal non-equilibrium. To calculate these material properties, the standard capillary fluctuation method typically used for systems in equilibrium has been modified to incorporate a second-order Taylor expansion of the interfacial free energy term. The result is a robust method for calculating interfacial energy, stiffness and anisotropy as a function of temperature gradient using the fluctuations in the defined interface height. This work includes the calculation of interface characteristics for temperature gradients ranging from 11 to 34??K/nm. The captured results are compared to a thermal equilibrium case using the same model and simulation technique with a zero gradient definition. We define the temperature gradient as the change in temperature over height perpendicular to the crystal-melt interface. The gradients are applied in MD simulations using defined thermostat regions on a stable solid-liquid interface initially in thermal equilibrium. The results of this work show that the interfacial stiffness and free energy for aluminum are dependent on the magnitude of the temperature gradient, however the anisotropic parameters remain independent of the non-equilibrium conditions applied in this analysis. The relationships of the interfacial free energy/stiffness are determined to be linearly related to the thermal gradient, and can be interpolated to find material characteristics at additional temperature gradients.},
author = {Brown, Nicholas T. and Martinez, Enrique and Qu, Jianmin},



journal = {Acta Materialia},


pages = {83--90},
publisher = {Elsevier Ltd},
title = {{Interfacial free energy and stiffness of aluminum during rapid solidification}},

volume = {129},
year = {2017}
}
@article{paxt-elsa10prb,
abstract = {An application of the tight binding approximation is presented for the description of electronic structure and interatomic force in magnetic iron, both pure and containing hydrogen impurities. We assess the simple canonical d-band description in comparison to a non orthogonal model including s and d bands. The transferability of our models is tested against known properties including the segregation energies of hydrogen to vacancies and to surfaces of iron. In many cases agreement is remarkably good, opening up the way to quantum mechanical atomistic simulation of the effects of hydrogen on mechanical properties.},
archivePrefix = {arXiv},
arxivId = {1008.1499},
author = {Paxton, A. T. and Els{\"{a}}sser, C.},



isbn = {10980121 (ISSN)},

journal = {Phys. Rev. B - Condensed Matter and Materials Physics},

pages = {13--15},
title = {{Electronic structure and total energy of interstitial hydrogen in iron: Tight-binding models}},
volume = {82},
year = {2010}
}
@misc{CP2K,
howpublished = {http://www.cp2k.org},
title = {{CP2K}}
}
@article{wu+04prb,
author = {Wu, Z and Cohen, R E and Singh, D J},

journal = {Phys. Rev. B},

pages = {104112},
publisher = {APS},
title = {{Comparing the weighted density approximation with the LDA and GGA for ground-state properties of ferroelectric perovskites}},
volume = {70},
year = {2004}
}
@article{mori65ptp,
author = {Mori, Hazime},

journal = {Prog. Th. Phys.},

pages = {423},
title = {{Transport, Collective Motion, and Brownian Motion}},
volume = {33},
year = {1965}
}
@incollection{ronn-mazz15book,
author = {Ronneberger, Ider and Mazzarello, Riccardo},
booktitle = {Molecular Dynamics Simulations of Disordered Materials},

editor = {Massobrio, Carlo and Du, Jincheng and Bernasconi, Marco and Salmon, Philip S.},

isbn = {978-3-319-15674-3},
pages = {57--85},
publisher = {Springer International Publishing},
title = {{Metadynamics Simulations of Nucleation}},

volume = {215},
year = {2015}
}
@article{verl67pr,
author = {Verlet, Loup},



journal = {Phys. Rev.},


pages = {98--103},
title = {{Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules}},

volume = {159},
year = {1967}
}
@article{reit+04bjp,
author = {Reiter, G and Li, J C and Mayers, J and Abdul-Redah, T and Platzman, P},

journal = {Braz. J. Phys.},
pages = {142--147},
publisher = {SciELO Brasil},
title = {{The proton momentum distribution in water and ice}},
volume = {34},
year = {2004}
}
@article{dona+12jacs,
abstract = {Water-metal interfaces are ubiquitous and play a key role in many chemical processes, from catalysis to corrosion. Whereas water adlayers on atomically flat transition metal surfaces have been investigated in depth, little is known about the chemistry of water on stepped surfaces, commonly occurring in realistic situations. Using first-principles simulations, we study the adsorption of water on a stepped platinum surface. We find that water adsorbs preferentially at the step edge, forming linear clusters or chains, stabilized by the cooperative effect of chemical bonds with the substrate and hydrogen bonds. In contrast with their behavior on flat Pt, at steps water molecules dissociate, forming mixed hydroxyl/water structures, through an autocatalytic mechanism promoted by H-bonding. Nuclear quantum effects contribute to stabilize partially dissociated cluster and chains. Together with the recently demonstrated behavior of water chains adsorbed on stepped Pt surfaces to transfer protons via thermally activated hopping, these findings make these systems viable candidates for proton wires.},
author = {Donadio, Davide and Ghiringhelli, Luca M and {Delle Site}, Luigi},



journal = {J. Chem. Am. Soc. },


pages = {19217--22},
pmid = {23098232},
title = {{Autocatalytic and cooperatively stabilized dissociation of water on a stepped platinum surface.}},

volume = {134},
year = {2012}
}
@article{brou-gilm83jcp1,
abstract = {Properties of the crystal and liquid phases have been measured for a system of particles interacting through a modified Lennard‐Jones potential. Through constant pressuremolecular dynamics, we have evaluated the density and internal energy of these phases at a pressure that approximates that of the vapor phase. The free energy of the crystal is obtained with the Einstein crystal as a reference state, and the liquidfree energy is measured relative to the ideal gas. The triple point temperature is obtained. Compressibilities and Gruneisen parameters are obtained at zero temperature and the triple point. Dynamic properties of the supercooled liquid state are also calculated. These results are applied in forthcoming publications which calculate surface excess quantities and dynamic properties of the fcc (111), (100), and (110) faces.},
author = {Broughton, Jeremy Q. and Gilmer, George H.},


isbn = {00219606},

journal = {J. Chem. Phys.},

pages = {5095},
title = {{Molecular dynamics investigation of the crystal–fluid interface. I. Bulk properties}},

volume = {79},
year = {1983}
}
@article{wan-gall15,
abstract = {We present a first-principles framework to compute sum-frequency generation (SFG) vibrational spectra of semiconductors and insulators. The method is based on density functional theory and the use of maximally localized Wannier functions to compute the response to electric fields, and it includes the effect of electric field gradients at surfaces. In addition, it includes quadrupole contributions to SFG spectra, thus enabling the verification of the dipole approximation, whose validity determines the surface specificity of SFG spectroscopy. We compute the SFG spectra of ice I{\_}{\{}h{\}} basal surfaces and identify which spectra components are affected by bulk contributions. Our results are in good agreement with experiments at low temperature.},
author = {Wan, Quan and Galli, Giulia},



journal = {Phys. Rev. Lett.},


pages = {246404},
pmid = {26705645},
title = {{First-Principles Framework to Compute Sum-Frequency Generation Vibrational Spectra of Semiconductors and Insulators}},

volume = {115},
year = {2015}
}
@article{mort+02jcp,
author = {Mortenson, P N and Evans, D A and Wales, D J},

journal = {J. Chem. Phys.},
pages = {1363},
title = {{Energy landscapes of model polyalanines}},
volume = {117},
year = {2002}
}
@article{bere+84jcp,
author = {Berendsen, H J C and Postma, J P M and {Van Gunsteren}, W F and DiNola, A and Haak, J R},

journal = {J. Chem. Phys.},

pages = {3684},
title = {{Molecular dynamics with coupling to an external bath}},
volume = {81},
year = {1984}
}
@article{shel14jcp,
abstract = {Strong short-range intermolecular interactions result in position and orientation correlations between nearetst neighbour molecules in isotropic liquids, and it is generally assumed that such correlations extend at most a few molecular diameters. This assumption is contradicted by results from second harmonic light scattering experiments presented here, which reveal long-range orientation correlations in several isotropic liquids including water. These experiments measure the polarization dependence of the scattered light, and the observations are interpreted in terms of transverse and longitudinal polar collective modes, as well as simple explicit models. The results revise our understanding of the structure of molecular liquids and provide a test of computational simulations.},
author = {Shelton, David P.},



journal = {J. Chem. Phys.},


pages = {224506},
pmid = {22299887},
title = {{Long-range orientation correlation in water}},

volume = {141},
year = {2014}
}
@article{good+89epl,
author = {Goodwin, L and Skinner, A J and Pettifor, D G},

journal = {Europhys. Lett.},
pages = {701--706},
title = {{Generating transferable tight-binding parameters: application to silicon}},
volume = {9},
year = {1989}
}
@article{herb-hect05prb,
author = {Herbst, J F and {Hector Jr}, L G},

journal = {Phys. Rev. B},

pages = {125120},
publisher = {APS},
title = {{Energetics of the Li amide/Li imide hydrogen storage reaction}},
volume = {72},
year = {2005}
}
@article{ahlb+99jcp,
author = {Ahlborn, Heather and Ji, Xingdong and Space, Brian and Moore, Preston B.},



journal = {J. Chem. Phys.},

pages = {10622},
title = {{A combined instantaneous normal mode and time correlation function description of the infrared vibrational spectrum of ambient water}},

volume = {111},
year = {1999}
}

@article{lverlet67pr,

	author = {Verlet, L.},
	title = {{Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules}},
	journal = {{Phys. Rev.}},
	volume = {{159}},
	pages = {98},
   number = {{1}},
	year = {{1967}},

}
