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We study active agents embedded in bulk or in confinement explicitly considering hydrodynamics and simulating the swimmers via an implementation inspired by the squirmer model. We develop a Dissipative Particle Dynamics scheme for the…
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…
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a…
The conformational properties of flexible and semiflexible polymers exposed to active noise are studied theoretically. The noise may originate from the interaction of the polymer with surround- ing active (Brownian) particles or from the…
Using Brownian Dynamics, we study the dynamical behavior of a polymer grafted onto an adhesive surface close to the mechanically induced adsorption-stretching transition. Even though the transition is first order, (in the infinite chain…
Worm-like filaments that are propelled homogeneously along their tangent vector are studied by Brownian dynamics simulations. Systems in two dimensions are investigated, corresponding to filaments adsorbed to interfaces or surfaces. A large…
The statistical theory of polymers tethered around the inner surface of a cylindrical channel has traditionally employed the assumption that the equilibrium density of the polymers is independent of the azimuthal coordinate. However,…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
We study the over-damped dynamics of individual one-dimensional elastic filaments subjected to a chiral active force which propels each point of the filament at a fixed angle relative to the tangent vector of the filament at that point.…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
Whereas it is experimentally known that the inclusion of nanoparticles in hydrogels can lead to a mechanical reinforcement, a detailed molecular understanding of the adhesion mechanism is still lacking. Here we use coarse-grained molecular…
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.…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
We investigate the motion of active semiflexible filament with shape kinematics and hydrodynamic interaction including. Three types of filament motion are found: Translation, snaking and rotation. Change of flexibility will induce…
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…
We analyze the conformational dynamics and statistical properties of an active polymer model. The polymer is described as a freely-jointed bead-rod chain subject to stochastic active force dipoles that act on the suspending solvent where…
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from…
We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical…
We report extensive numerical simulations of different models of 2D polymer rings with internal elasticity. We monitor the dynamical behavior of the rings as a function of the packing fraction, to address the effects of particle deformation…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…