Related papers: How to derive and parameterize effective potential…
The impact of impenetrable obstacles on the energetics and equilibrium structure of strongly repulsive directed polymers is investigated. As a result of the strong interactions, regions of severe polymer depletion and excess are found in…
The polymer systems are discussed in the framework of the Landau-Ginzburg model. The model is derived from the mesoscopic Edwards hamiltonian via the conditional partition function. We discuss flexible, semiflexible and rigid polymers. The…
We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters we…
We treat the accurate simulation of the calcination reaction in particles, where the particles are large and, thus, the inner-particle processes must be resolved. Because these processes need to be described with coupled partial…
The effective quasistatic conductivity of composite polymeric electrolytes is studied in terms of a hard-core--penetrable-layer model. Used to incorporate the interface phenomena (such as amorphization of the polymer matrix around filler…
We study the conformational properties of complex polymer macromolecules, consisting in general of $n$ subsequently connected chains (blocks) of different lengths and distinct chemical structure. Depending on the solvent conditions, the…
The insertion of solvent particles in molecular dynamics simulations of complex fluids is required in many situations involving open systems, but this challenging task has been scarcely explored in the literature. We propose a simple and…
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…
Interaction of particles of many systems can be effectively approximated by multiscale interaction potentials. Such potentials are widely used for investigation of colloidal systems and colloid-polymer mixtures, complex liquids (for…
We propose an efficient Monte Carlo algorithm for the off-lattice simulation of dense hard sphere polymer melts using cluster moves, called event chains, which allow for a rejection-free treatment of the excluded volume. Event chains also…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
We report an approach to obtain effective pair potentials which describe the structure of two-dimensional systems of active Brownian particles. The pair potential is found by an inverse method, which matches the radial distribution function…
Given the ubiquity of depletion effects in biological and other soft matter systems, it is desirable to have coarse-grained Molecular Dynamics simulation approaches appropriate for the study of complex systems. This paper examines the use…
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned…
Coupled length and time scales determine the dynamic behavior of polymers and underlie their unique viscoelastic properties. To resolve the long-time dynamics it is imperative to determine which time and length scales must be correctly…
The number of allowed configurations of a polymer is reduced by the presence of a repulsive surface resulting in an entropic force between them. We develop a method to calculate the entropic force, and detailed pressure distribution, for…
Packing spheres efficiently in large dimension $d$ is a particularly difficult optimization problem. In this paper we add an isotropic interaction potential to the pure hard-core repulsion, and show that one can tune it in order to maximize…
The accuracy of atomistic simulations depends on the precision of force fields. Traditional numerical methods often struggle to optimize the empirical force field parameters for reproducing target properties. Recent approaches rely on…
Polymer self-consistent field theory techniques are used to find radial electron densities and total binding energies for isolated atoms. Quantum particles are modelled as Gaussian threads with ring-polymer architecture in a four…
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…