Related papers: Surface molecular dynamics simulation with two ort…
Stokesian Dynamics (SD) is a numerical framework used for simulating hydrodynamic interactions in particle suspensions at low Reynolds number. It combines far-field approximations with near-field lubrication corrections, offering a balance…
In this paper we develop a stochastic boundary conditions (SBC) for event-driven molecular dynamics simulations of a finite volume embedded within an infinite environment. In this method, we first collect the statistics of…
Cellular scale decision making is modulated by the dynamics of signalling molecules and their diffusive trajectories from a source to small absorbing sites on the cellular surface. Diffusive capture problems are computationally challenging…
We review a molecular dynamics method for nucleon many-body systems called the quantum molecular dynamics (QMD) and our studies using this method. These studies address the structure and the dynamics of nuclear matter relevant to the…
Solids facing a plasma are a common situation in many astrophysical systems and laboratory setups. Moreover, many plasma technology applications rely on the control of the plasma-surface interaction. However, presently often a fundamental…
The crystal nucleation from liquid in most cases is too rare to be accessed within the limited timescales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal…
We investigate by Molecular Dynamics simulation a system of $N$ particles moving on the surface of a two-dimensional sphere and interacting by a Lennard-Jones potential. We detail the way to account for the changes brought by a nonzero…
We show that a novel rectification phenomena is possible for overdamped particles interacting with a 2D periodic substrate and driven with a longitudinal DC drive and a circular AC drive. As a function of DC amplitude, the longitudinal…
We introduce a modified molecular dynamics algorithm that allows one to freeze the dynamics of parts of a physical system, and thus concentrate the simulation effort on selected, central degrees of freedom. This freezing, in contrast to…
Multi-particle collision dynamics (MPCD) is a mesoscopic simulation method to simulate fluid particle-like flows. MPCD has been widely used to simulate various problems in condensed matter. In this study, hydrostatic behavior of gas in the…
Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for…
The Smoothed Particle Hydrodynamics (SPH) is a particle-based, Lagrangian method for fluid-flow simulations. In this work, fundamental concepts of this method are first briefly recalled. Then, the ability to accurately model granular…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Droplet motion over a surface with wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics. GROMACS and Visual Molecular Dynamics (VMD) were used for simulation and intermittent…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…
In this paper, we explore osmotic transport by means of molecular dynamics (MD) simulations. We first consider osmosis through a membrane, and investigate the reflection coefficient of an imperfectly semi-permeable membrane, in the dilute…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
Dissipative particle dynamics (DPD) and multi-particle collision (MPC) dynamics are powerful tools to study mesoscale hydrodynamic phenomena accompanied by thermal fluctuations. To understand the advantages of these types of mesoscale…