Related papers: Kinetics of Interior Loop Formation in Semiflexibl…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…
The linear viscoelastic response of single semiflexible polymer chains in the infinite-dilution limit is studied using Brownian dynamics simulations of coarse-grained bead-spring chains. The springs obey the FENE-Fraenkel force law, a…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and…
We use lattice-Boltzmann molecular dynamics (LBMD) simulations to study the compression of a confined polymer immersed in a fluid and pushed by a large spherical colloid with a diameter comparable to the channel width. We examined the…
We study the effects of intrinsic sequence-dependent curvature for a two dimensional semiflexible biopolymer with short-range correlation in intrinsic curvatures. We show exactly that when not subjected to any external force, such a system…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
We consider an inextensible, semiflexible polymer or worm-like chain which is confined in the transverse direction by a parabolic potential and subject to a longitudinal force at the ends, so that the polymer is stretched out and…
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and…
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion…
We describe a simple meanfield variational approach to study a number of properties of intrinsically stiff chains which are appropriate models for a large class of biopolymers. We present the calculation of the distribution of end-to-end…
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…
Aiming at the mechanical properties of cross-linked biopolymers, we set up and analyze a model of two weakly bending wormlike chains subjected to a tensile force, with regularly spaced inter-chain bonds (cross-links) represented by harmonic…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
We develop a segment-scale, force-based theory for the breakdown of the unentangled Rouse model and subsequent emergence of isotropic mesoscopic localization and entropic elasticity in chain polymer liquids in the absence of…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
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…