Related papers: Molecular dynamics simulation of polymer helix for…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
Using Langevin simulations, we find that simple 'generic' bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The…
Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and…
Molecular dynamics simulations, with full Coulomb interaction and self-consistent field emission, are used to examine mutual space-charge interactions between beams originating from several emitter areas, in a planar infinite diode. The…
The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…
We present a new reduced-order computational method for the molecular dynamics simulation of entangled polymer systems. The polymer chains are modeled as continuous Gaussian chains. Our algorithm is based on the application of the molecular…
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…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
Herein, we describe new methods to produce colloidal particle chains of three stiffness regimes that can be observed on a single-particle level, that is, on the level of the monomers that make up the chain; the chains can even be observed…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
The structural and dynamic properties of silica melts under high pressure are studied using molecular dynamics (MD) computer simulation. The interactions between the ions are modeled by a pairwise-additive potential, the so-called CHIK…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
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…
We use molecular dynamics simulations to study the dynamics of Janus particles, micro- or nanoparticles which are not spherically symmetric, in the uniform flow of a simple liquid. In particular we consider spheres with an asymmetry in the…
Molecular Dynamic (MD) approach is applied to study the converging cylindrical shock waves in a dense Lennard-Jones (LJ) fluid. MD method is based on tracking of the atom motions and hence it has an fundamental advantages over hydrodynamic…
We use molecular dynamics simulations to test integral equation theory predictions for the structure of fluids of spherical particles with eight different piecewise-constant pair interaction forms comprising a hard core and a combination of…