Related papers: Molecular dynamics simulation of polymer helix for…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…
Molecular dynamics simulation has been used to model pattern formation in three-dimensional Rayleigh--Benard convection at the discrete-particle level. Two examples are considered, one in which an almost perfect array of hexagonally-shaped…
We present a molecular simulation study of the structure of linear dendronized polymers. We use excluded volume interactions in the context of a generic coarse-grained molecular model whose geometrical parameters are tuned to represent a…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
Model chains are studied via Monte Carlo simulations which are deposited with a fixed flux on a substrate. They may represent, e.g., stiff lipophilic chains with an head group and tail groups mimicking the alkyl chain. After some subsequent…
Vitrimers are a special class of polymers that undergo dynamic cross-linking under thermal stimuli. Their ability to exchange covalent bonds can be harnessed to mitigate damage in a composite or to achieve recyclable aerospace composites.…
We have studied the breakup and subsequent fluid flow in very thin films of partially wetting liquid on solid substrates, using molecular dynamics simulations. The liquid is made of short chain molecules interacting with Lennard-Jones…
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple…
Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motions. Model-free types…
Molecular dynamics is a powerful method for studying the behaviour of materials at high temperature. In practice, however, its effectiveness in representing real systems is limited by the accuracy of the forces, finite size effects,…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Structure and dynamics of an active polymer on a smooth cylindrical surface are studied by Brownian dynamics simulations. The effect of active force on the polymer adsorption behavior and the combined effect of chain mobility, length N,…
Monte Carlo simulations of proteins are hindered by the system's high density which often makes local moves ineffective. Here we devise and test a set of long range moves that work well even when all sites of a lattice simulation are…
Iron, cobalt and nickel nanoparticles, grown in the gas phase, are known to arrange in chains and bracelet-like rings due to the long-range dipolar interaction between the ferromagnetic (or super-paramagnetic) particles. We investigate the…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute which has a concentration gradient, and…