相关论文: Automated Prediction of Thermodynamic Properties v…
Computational studies of the thermodynamic properties of materials at the mesoscopic and macroscopic scales -- involving lengths and times of at least $\mu$m and $\mu$s, respectively -- rely on a coarse-graining approximation such that only…
We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive…
Machine-learning potentials are usually trained on the ground-state, Born-Oppenheimer energy surface, which depends exclusively on the atomic positions and not on the simulation temperature. This disregards the effect of thermally-excited…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
While traditional trial-and-error methods for designing amorphous alloys are costly and inefficient, machine learning approaches based solely on composition lack critical atomic structural information. Machine learning interatomic…
The paper discusses the reconstruction of potentials for quantum systems at finite temperatures from observational data. A nonparametric approach is developed, based on the framework of Bayesian statistics, to solve such inverse problems.…
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab…
Due to one of the most representative contributions to the energy in diatomic molecules being the vibrational, we consider the generalized Morse potential (GMP) as one of the typical potential of interaction for one-dimensional microscopic…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
We numerically study thermodynamic and structural properties of the one-component Gaussian core model (GCM) at very high densities. The solid-fluid phase boundary is carefully determined. We find that the density dependence of both the…
Molecular Density Functional Theory (MDFT) offers an efficient implicit- solvent method to estimate molecule solvation free-energies whereas conserving a fully molecular representation of the solvent. Even within a second order ap-…
We develop a method to fit high-temperature Gibbs free energy data for the development of interatomic potentials for atomic systems. The approach is based on Hamiltonian thermodynamic integration, enabling the identification of suitable…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Computational modeling is an integral part of catalysis research. With it, new methodologies are being developed and implemented to improve the accuracy of simulations while reducing the computational cost. In particular, specific…
Key to being able to accurately model the properties of realistic materials is being able to predict their properties in the thermodynamic limit. Nevertheless, because most many-body electronic structure methods scale as a high-order…
We present a new method to evaluate vibrational free energies of atomic systems without a priori specification of an interatomic potential. Our model-agnostic approach leverages descriptors, high-dimensional feature vectors of atomic…
The anharmonicity resulted from the intrinsic phonon interaction is neglected by quasiharmonic approximation. Although the intensive researches about anharmonicity have been done, up to now the free energy contributed by the anharmonicity…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…