相关论文: Discretization errors in molecular dynamics simula…

We present a new algorithm for isothermal-isobaric molecular-dynamics simulation. The method uses an extended Hamiltonian with an Andersen piston combined with the Nos'e-Poincar'e thermostat, recently developed by Bond, Leimkuhler and Laird…

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…

This article proposes a novel thermostat applicable to any particle-based dynamic simulation. Each pair of particles is thermostated either (with probability P) with a pairwise Lowe-Andersen thermostat, or (with probability 1-P) with a…

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…

In this work, the univariant two-phase coexistence line of the hydrate of tetrahydrofuran (THF) is determined from 100 to 1000 bar by molecular dynamics simulations. The study is carried out by putting in contact a THF hydrate phase with a…

Diffusion distillation provides an effective approach for learning lightweight and few-steps diffusion models with efficient generation. However, evaluating their generalization remains challenging: theoretical metrics are often impractical…

Properties of water have been well elucidated for temperatures above $\sim$230 K and yet mysteries remain in the deeply supercooled region. By performing extensive molecular dynamics simulations on this supercooled region, we find that…

The randomized midpoint method, proposed by [SL19], has emerged as an optimal discretization procedure for simulating the continuous time Langevin diffusions. Focusing on the case of strong-convex and smooth potentials, in this paper, we…

We propose a novel structure preserving discretization for viscous and resistive magnetohydrodynamics. We follow the recent line of work on discrete least action principle for fluid and plasma equation, incorporating the recent advances to…

In this paper, we analyze the discrete inf-sup condition and related error estimates for a modified Hilbert transformation as used in the space-time discretization of time-dependent partial differential equations. It turns out that the…

Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…

Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using…

We report the combined results of molecular dynamics simulations and theoretical calculations concerning various dynamical arrest transitions in a model system representing a dipolar fluid, namely, N (softcore) rigid spheres interacting…

We propose a new sampling method, the thermostat-assisted continuously-tempered Hamiltonian Monte Carlo, for Bayesian learning on large datasets and multimodal distributions. It simulates the Nos\'e-Hoover dynamics of a…

Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…

We develop a formulation for molecular dynamics, Langevin, and hybrid Monte Carlo algorithms in the recently proposed generalized ensemble that is based on a physically motivated realisation of Tsallis weights. The effectiveness of the…

We consider fully discrete numerical schemes for a downscaling data assimilation algorithm aimed at approximating the velocity field of the 2D Navier-Stokes equations corresponding to given coarse mesh observational measurements. The time…

The Inverse Problem for the estimation of a point-wise approximation error occurring at the discretization and solving of the system of partial differential equations is addressed. The set of the differences between the numerical solutions…

Thermostats are dynamical equations used to model thermodynamic variables such as temperature and pressure in molecular simulations. For computationally intensive problems such as the simulation of biomolecules, we propose to average over…

Fluctuations of dynamical quantities are fundamental and inevitable. For the booming research in nanotechnology, huge relative fluctuation comes with the reduction of system size, leading to large uncertainty for the estimates of dynamical…