Related papers: Molecular dynamics simulation of polymer helix for…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
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…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We present Molecular Dynamics simulations of the thermal glass transition in a dense model polymer liquid. We performed a comparative study of both constant volume and constant pressure cooling of the polymer melt. Great emphasis was laid…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The breakage of a polymer chain of segments, coupled by anharmonic bonds with applied constant external tensile force is studied by means of Molecular Dynamics simulation. We show that the mean life time of the chain becomes progressively…
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,…