Related papers: Conformations, Dynamics, and Looping Kinetics of P…
The non-equilibrium structural and dynamical properties of a semiflexible polymer confined in a cylindrical microchannel and exposed to a Poiseuille flow is studied by mesoscale hydrodynamic simulations. For a polymer with a length half of…
To understand the dynamical and conformational properties of deformable active agents in porous media, we computationally investigate the dynamics of linear chains and rings made of active Brownian monomers. In porous media, flexible linear…
Thermodynamic behavior of polymer chains out of equilibrium is a fundamental problem in both polymer physics and biological physics. By using molecular dynamics simulation, we discover a general non-equilibrium mechanism that controls the…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
We develop a scaling theory to describe dynamic fluctuations of a semiflexible polymer and find several distinct regimes. We performed simulations to characterize the longitudinal and transverse dynamics; using ensemble averaging for a…
Many researchers have been encouraged to describe the dynamics of chromosomal loci in chromatin using the classical Rouse model of polymer dynamics by the agreement between the measured mean square displacement (MSD) versus time of…
We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [Nat. Chem. 4, 268 (2012)] that showed that the distribution of the polymer…
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
Motivated by chromosomes enclosed in nucleus and the recently discovered active topological glass, we study a spherically confined melt of long nonconcatenated active polymer rings. Without activity, the rings exhibit the same average…
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…
Star polymers can exhibit a heterogeneous dynamical behavior due to their internal structure. In this work we employ atomistic molecular dynamics simulations to study translational motion in non-entangled polystyrene and poly(ethylene…
We show the presence of both a minimum and clear oscillations in the frequency dependence of the translocation time of a polymer described as a unidimensional Rouse chain driven by a spatially localized oscillating linear potential. The…
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as…
The local dynamical features of a PEO melt studied by MD simulations are compared to two model chain systems, namely the well-known Rouse model as well as the semiflexible chain model (SFCM) that additionally incorporates chain stiffness.…
Dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an…
The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
In the presented work we study, by means of numerical simulations, the behaviour of a suspension of active ring polymers in the bulk and under lateral confinement. When changing the separation between the confining planes and the polymers'…