Related papers: Improved Ab Initio Molecular Dynamics by Minimal B…
Bayesian inference with stochastic models is often difficult because their likelihood functions involve high-dimensional integrals. Approximate Bayesian Computation (ABC) avoids evaluating the likelihood function and instead infers model…
The water/electrode interface under an applied bias potential is a challenging out-of-equilibrium phenomenon, which is difficult to accurately model at the atomic scale. In this study, we employ a combined approach of Density Functional…
We describe a method, that we call data projection onto parameter space (DPPS), to optimize an energy functional of the electron density, so that it reproduces a dataset of experimental magnitudes. Our scheme, based on Bayes theorem,…
We review recent results of molecular dynamics simulations of two models of liquid water, the extended simple point charge (SPC/E) and the Mahoney-Jorgensen transferable intermolecular potential with five points (TIP5P), which is closer to…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Finite temperature calculations, based on ab initio molecular dynamics (AIMD) simulations, are a powerful tool able to predict material properties that cannot be deduced from ground state calculations. However, the high computational cost…
The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…
We present a new interatomic potential for water captured in a charge-transfer embedded atom method (EAM) framework. The potential accounts for explicit, dynamical charge transfer in atoms as a function of the local chemical environment. As…
Comparison of free energies between different phases and different compositions underlies the prediction of alloy phase diagrams. To allow direct comparison, consistent reference points for the energies or enthalpies are required, and the…
Water is a unique solvent with many remarkable properties. An example is its exceptionally high heat capacity, which plays an important role in storing and transporting thermal energy, with implications for many processes from regulating…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
The spectral features of water clusters provide important information on their structure and dynamics and can assist in deciphering the nature of the local environment of aqueous solutions in a variety of different conditions. Accurately…
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics…
We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable…
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular…
Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a…
An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD) [J. Chem.…
Accurate simulation of the non-adiabatic dynamics of molecules in excited electronic states is key to understanding molecular photo-physical processes. Here we present a novel method, based on a semiclassical approximation, that is as…
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…
Using simulations or experiments performed at some set of temperatures to learn about the physics or chemistry at some other arbitrary temperature is a problem of immense practical and theoretical relevance. Here we develop a framework…