Related papers: Molecular Dynamics Simulations of Binary Sphere Mi…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
We present a numerical method to deal efficiently with large numbers of particles in incompressible fluids. The interactions between particles and fluid are taken into account by a physically motivated ansatz based on locally defined drag…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T=3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to…
Discrete particle simulations are used to model segregation in granular mixtures of three different particle species in a horizontal rotating drum. Axial band formation is observed, with medium-size particles tending to be located between…
The dynamics of sheared inelastic-hard-sphere systems are studied using non-equilibrium molecular dynamics simulations and direct simulation Monte Carlo. In the molecular dynamics simulations Lees-Edwards boundary conditions are used to…
The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles,…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
We investigate the dynamics of an ensemble of inelastic hard spheres confined between two horizontal plates separated a distance smaller than twice the diameter of the particles, in such a way that the system is quasi-two-dimensional. The…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
In this paper, we perform molecular dynamics (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from $1.0 \, \mu m$ to $7.0 \, \mu m$. The system was allowed to…
We study by molecular dynamics computer simulation a binary soft-sphere mixture that shows a pronounced decoupling of the species' long-time dynamics. Anomalous, power-law-like diffusion of small particles arises, that can be understood as…
An efficient technique to simulate turbulent particle-laden flow at high mass loadings within the four-way coupled simulation regime is presented. The technique implements large eddy simulation, discrete phase simulation, a deterministic…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
The dynamic behavior of a hard-sphere colloidal suspension was studied by X-ray Photon Correlation Spectroscopy and Small Angle X-ray Scattering over a wide range of particle volume fractions. The short-time mobility of the particles was…
We have carried out molecular dynamics simulations of the crystallization of hard spheres modelling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of…
We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
We study numerically the crystallization of a hard-sphere mixture with 8\% polydispersity. Although often used as a model glass former, for small system sizes we observe crystallization in molecular dynamics simulations. This opens the…
Hard spheres are a central and important model reference system for both homogeneous and inhomogeneous fluid systems. In this paper we present new high-precision molecular-dynamics computer simulations for a hard sphere fluid at a planar…