Related papers: Nonequilibrium free-energy calculation of solids u…
Vibrational properties of solids are key to determining stability, response and functionality. However, they are challenging to computationally predict at Ab-Initio accuracy, even for elemental systems. Ab-Initio methods for modeling atomic…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
Alternative approach for description of the non-equilibrium phenomena arising in solids at a severe external loading is analyzed. The approach is based on the new form of kinetic equations in terms of the internal and modified free energy.…
Jarzynski's equality provides an elegant and powerful tool to directly compute differences in free energy in Monte Carlo simulations and it can be readily extended to lattice gauge theories to compute a large set of physically interesting…
A methodology for calculating the contribution of charged defects to the configurational free energy of an ionic crystal is introduced. The temperature-independent Wang-Landau Monte Carlo technique is applied to a simple model of a solid…
We develop analytic approximations of thermodynamic functions of fully ionized nonideal electron-ion plasma mixtures. In the regime of strong Coulomb coupling, we use our previously developed analytic approximations for the free energy of…
It has recently been shown that the Helmholtz free energy difference between two equilibrium configurations of a system may be obtained from an ensemble of finite-time (nonequilibrium) measurements of the work performed in switching an…
The Jarzynski equality (JE), which relates works of non-equilibrium trajectories to the free energy difference of the initial and final states of the non-equilibrium process, provides an efficient way to calculate free energies of systems…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The interpolation is defined at the sample distribution level, and…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
We propose a method to compute free-energy differences from nonadiabatic alchemical transformations using flow-based generative models. The method, nonadiabatic force matching, hinges on estimating the dissipation along an alchemical…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic…
Recent years have witnessed major advances in our understanding of nonequilibrium processes. The Jarzynski equality, for example, provides a link between equilibrium free energy differences and finite-time, nonequilibrium dynamics. We…
Despite the strength of Molecular Dynamics simulations in providing insights into the microscopic details of phenomenon in many fields in materials science, physics and biology, the biggest barrier is its limited timescale which is several…