Related papers: Molecular dynamics study of T=3 capsid assembly
In particle-in-cell simulations, excessive or even unfeasible computational demands can be caused by the growth of the number of particles in the course of prolific ionization or cascaded pair production due to the effects of quantum…
We present results from large-scale molecular dynamics (MD) simulations of homogeneous vapor-to-liquid nucleation. The simulations contain between one and eight billion Lennard-Jones (LJ) atoms, covering up to 1.2 {\mu}s (56 million…
In this study some properties of the methanol-water mixture such as diffusivity, density, viscosity, and hydrogen bonding were calculated at different temperatures and atmospheric pressure using molecular dynamics simulations (MDS). The…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Two-dimensional Molecular Dynamics simulations are used to model the free surface flow of spheres falling down an inclined chute. The interaction between the particles in our model is assumed to be subjected to the Hertzian contact force…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Results of quasi-classical molecular dynamics simulations of the quantum electron gas are reported. Quantum effects corresponding to the Pauli and the Heisenberg principle are modeled by an effective momentum-dependent Hamiltonian. The…
We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…
We present a realistic model of the fragile glass former orthoterphenyl and the results of extensive molecular dynamics simulations in which we investigated its basic static and dynamic properties. In this model the internal molecular…
Using molecular dynamics simulations, we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity…
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 develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
The dynamics of a system composed of inelastic hard spheres or disks that are confined between two parallel vertically vibrating walls is studied (the vertical direction is defined as the direction perpendicular to the walls). The distance…
The polymer dynamics of homogeneous C$_{60}$-polystyrene mixtures in the molten state are studied via molecular simulations using two interconnected levels of representation for polystyrene nanocomposites: (a) A coarse-grained…
Vulcanian explosive eruption, which is a nonlinear and nonequilibrium abrupt dynamics of magma-gas mixture, is modeled by a two-component Lennard-Jones particle system. Molecular-dynamics simulation of a shock-tube experiment gives…
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…