Related papers: Molecular dynamics study of T=3 capsid assembly
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…
Molecular dynamics simulations are performed for a finite non-relativistic system of particles with Lennard-Jones potential. We study the effect of liquid-gas mixed phase on particle number fluctuations in coordinate subspace. A metastable…
Using a realistic flexible molecule model of the fragile glass former orthoterphenyl, we calculate via molecular dynamics simulation the collective dynamic structure factor, recently measured in this system by Inelastic X-ray Scattering.…
We investigate the behavior of colloidal suspensions with different volume fractions confined between parallel walls under a range of steady shears. We model the particles using molecular dynamics (MD) with full hydrodynamic interactions…
Recently, we have shown how current cosmological N-body codes already follow the fine grained phase-space information of the dark matter fluid. Using a tetrahedral tesselation of the three-dimensional manifold that describes perfectly cold…
We present molecular dynamics (MD) simulations results for dense fluids of ultrasoft, fully-penetrable particles. These are a binary mixture and a polydisperse system of particles interacting via the generalized exponential model, which is…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
The formation of novel dynamical states for a collection of dust particles in two dimensions has been shown with the help of Molecular Dynamics (MD) simulation. The charged dust particles interact with each other with Yukawa pair potential…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Molecular dynamics simulations of 3C-SiC have been performed as a function of pressure and temperature. These simulations treat both electrons and atomic nuclei by quantum mechanical methods. While the electronic structure of the solid is…
In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Depending on the pH value and salt concentration of Al2O3 suspensions different microstructures can form. Especially the clustered one is of major interest for industrial purposes as found in the production of ceramics. In this paper we…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
Robust empirical constitutive laws for granular materials in air or in a viscous fluid have been expressed in terms of timescales based on the dynamics of a single particle. However, some behaviours such as viscosity bifurcation or shear…
Synchrotron X-ray diffraction measurements have been conducted on liquid phosphorus trichloride, tribromide and triiodide. Molecular Dynamics simulations for these molecular liquids were performed with a dual purpose: (1) to establish…
Confinement can have a considerable effect on the behavior of particle systems, and is therefore an effective way to discover new phenomena. A notable example is a system of identical bosons at low temperature under an external field…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…