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We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
The properties of a semiflexible polymer with fixed ends exposed to oscillatory shear flow are investigated by simulations. The two-dimensionally confined polymer is modeled as a linear bead-spring chain, and the interaction with the fluid…
We analyze the freezing and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer models in…
Kinetically-constrained models are lattice-gas models that are used for describing glassy systems. By construction, their equilibrium state is trivial and there are no equal-time correlations between the occupancy of different sites. We…
We explore the impact of hydrodynamic interactions on the conformational and dynamical properties of wet tangentially-driven active polymers using multiparticle collision dynamics simulations. By analyzing active filaments with varying…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
We present a novel and rigorous approach to the Langevin dynamics of ideal polymer chains subject to internal distance constraints. The permanent constraints are modelled by harmonic potentials in the limit when the strength of the…
Mixtures of polymers of varying topologies and stiffnesses display complex emergent rheological properties that often cannot be predicted from their single-component counterparts. For example, entangled blends of ring and linear polymers…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
We investigate modifications of a stochastic polymer picture through a shift in the boundary between the system and an external environment. A conventional bead-and-spring model serving as the coarse-graining model is given by the Langevin…
We investigate a model for colloidal network formation using Brownian Dynamics computer simulations. Hysteretic springs establish transient bonds between particles with repulsive core. If a bonded pair is separated by a cutoff distance, the…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
We perform equilibrium Langevin dynamics simulations to understand the structure-viscoelasticity relationship of a dually crosslinked reversible polymer network. The cross-linking is achieved by introducing orthogonal crosslinkers (A and B)…
Polymer thin films exhibit pronounced interfacial mobility gradients that modify chain relaxation, yet how these gradients govern chain-scale dynamics across depth remains incompletely understood. Using molecular dynamics simulations of…
Using numerical simulations, we examine a simple model of two or more coupled one-dimensional channels of driven particles with repulsive interactions in the presence of quenched disorder. We find that this model exhibits a remarkably rich…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
In this work, we investigate the dynamics of interacting particle systems subjected to repulsive forces, such as lattices of magnetized particles. To this end, we first develop a general model capable of capturing the complete dynamical…