相关论文: Enhanced solvation force extrapolation for speedin…

We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…

This paper presents the implementation of the eXtended Finite Element Method (XFEM) in the general-purpose commercial software package COMSOL Multiphysics for multi-field thermo-hydro-mechanical problems in discontinuous porous media. To…

A novel description of kinetic theory dynamics is proposed in terms of resummed moments that embed information of both hydrodynamic and non-hydrodynamic modes. The resulting expansion can be used to extend hydrodynamics to higher orders in…

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…

We develop a nonlinear force-free field (NLFFF) extrapolation code based on the magnetohydrodynamic (MHD) relaxation method. We extend the classical MHD relaxation method in two important ways. First, we introduce an algorithm initially…

We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure theory and requires…

We present a 2D parallel implementation of the modified Cahn-Hilliard equation for the simulation of a biofilm in an aqueous enviroment. Biofilms are attached microbial communities made of many different components and can have both…

We introduce a simple and efficient algorithm for diffusion in smoothed particle hydrodynamics (SPH) simulations and apply it to the problem of chemical mixing. Based on the concept of turbulent diffusion, we link the diffusivity of a…

In this work, we study the application the classical Richardson extrapolation (RE) technique to accelerate the convergence of sequences resulting from linear multistep methods (LMMs) for solving initial-value problems of systems of ordinary…

A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this…

Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…

The breakdown of dynamical scaling for a dilute polymer solution in 2D has been suggested by Shannon and Choy [Phys. Rev. Lett. {\bf 79}, 1455 (1997)]. However, we show here both numerically and analytically that dynamical scaling holds…

A second order extrapolation method is presented for shell model calculations, where shell model energies of truncated spaces are well described as a function of energy variance by quadratic curves and exact shell model energies can be…

We introduce an event-driven simulation scheme for overdamped dynamics of frictionless hard spheres subjected to external forces, neglecting hydrodynamic interactions. Our event-driven approach is based on an exact equation of motion which…

We have given theoretical expressions for the forces exerted on a quasi-2D flat and smooth solid plate immersed into a liquid pool of a simple liquid. All forces given by the theory, the local forces on the top, the contact line and the…

This article is the second of a three-part series that derives a self-consistent theoretical framework of the electromechanics of arbitrarily curved lipid membranes. Existing continuum theories commonly treat lipid membranes as strictly…

In this work, we develop an accelerated sharp-interface method based on (Hu et al., JCP, 2006) and (Luo et al., JCP, 2015) for multiphase flows simulations. Traditional multiphase simulation methods use the minimum time step of all fluids…

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…

We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…

Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…