Related papers: Molecular dynamics study of T=3 capsid assembly
A particle-based model for mesoscopic fluid dynamics is used to simulate steady and unsteady flows around a circular and a square cylinder in a two-dimensional channel for a range of Reynolds number between 10 and 130. Numerical results for…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
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…
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…
We use particle-in-magnetohydrodynamics-cells to model particle acceleration and magnetic field amplification in a high Mach, parallel shock in three dimensions and compare the result to 2-D models. This allows us to determine whether 2-D…
We perform numerical simulations of athermal repulsive frictionless disks and spheres in two and three spatial dimensions undergoing cyclic quasi-static simple shear to investigate particle-scale reversible motion. We identify three classes…
The dynamics of a tagged particle immersed in a fluid of particles of the same size but different mass is studied when the system is confined between two hard parallel plates separated a distance smaller than twice the diameter of the…
We present a new approach to studies of bubble dynamics in fluids. Relying on particle-based simulations, this method is general and suitable for cases where the commonly used perfect fluid description fails. We study expanding true vacuum…
We study dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this purpose we have adopted a hybrid simulation method, consisting of molecular dynamics and multi-particle collision…
We study the settling of solid particles within a viscous incompressible fluid contained in a two-dimensional channel, where the mass density of the particles is slightly greater than that of the fluid. The fluid-structure interaction…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or…
Using both computational and experimental methods, the capacity of four different surfactant molecules to inhibit the agglomeration of sII hydrate particles was assessed. The computational simulations were carried out using both steered and…
All-atom and coarse-grained molecular dynamics are two widely used computational tools to study the conformational states of proteins. Yet, these two simulation methods suffer from the fact that without access to supercomputing resources,…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
Three-dimensional, time-dependent numerical simulations of the dynamics of magnetic flux ropes are presented. The simulations are targeted towards an experiment previously conducted at CalTech (Bellan, P. M. and J. F. Hansen, Phys. Plasmas,…
We perform numerical simulations of purely repulsive soft colloidal particles interacting via a generalized elastic potential and constrained to a two-dimensional plane and to the surface of a spherical shell. For the planar case, we…
Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters…
The structure and mechanical properties of a simple two-dimensional model of a cohesive powder are investigated by molecular dynamics simulations. Micromechanical ingredients involve elasticity, friction, a short range attraction and,…
We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural…
Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral…