Related papers: Thermodynamically Stable Knots in Semiflexible Pol…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…
A {\it new} formula for the force vs extension relation is derived from the discrete version of the so called {\it worm like chain} model. This formula correctly fits some recent experimental data on polymer stretching and some numerical…
Systematic microcanonical inflection-point analysis of precise numerical results obtained in extensive generalized-ensemble Monte Carlo simulations reveals a bifurcation of the coil-globule transition line for polymers with a bending…
We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…
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…
Bead spring models for polymers in solution are nonlinear if either the finite extensibility of the polymer, excluded volume effects or hydrodynamic interactions between polymer segments are taken into account. For such models we use a…
We study by Monte Carlo simulations a model of knotted polymer ring adsorbing onto an impenetrable, attractive wall. The polymer is described by a self-avoiding polygon (SAP) on the cubic lattice. We find that the adsorption transition…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
The role of the topology and its relation with the geometry of biopolymers under different physical conditions is a nontrivial and interesting problem. Aiming at understanding this issue for a related simpler system, we use Monte Carlo…
We derive the Frank elastic constants for nematic solutions of semiflexible polymers. We plot these results as a function of the coarse-grained Maier-Saupe quadrupole aligning strength and polymer stiffness ranging from rigid to highly…
Knots are familiar entities that appear at a captivating nexus of art, technology, mathematics, and science. As topologically stable objects within field theories, they have been speculatively proposed as explanations for diverse persistent…
Motivated by recent advances in single molecule manipulation techniques that enabled several groups to tie knots in individual polymer strands and to monitor their dynamics, we have used computer simulations to study "friction knots"…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
We develop a simple coarse-grained bead-spring polymer model exhibiting competing crystallization and glass transitions. For quench rates slower than the critical nucleation rate $|\dot{T}|_{crit}$, systems exhibit a first-order…
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 present using simple scaling arguments and one step replica symmetry breaking a theory for the localization of semiflexible polymers in a quenched random environment. In contrast to completely flexible polymers, localization of…
We present a methodology to simulate the mechanics of knots in elastic rods using geometrically nonlinear, full three-dimensional (3D) finite element analysis. We focus on the mechanical behavior of knots in tight configurations, for which…
A {\it stuck knot} is a knot diagram containing designated crossings, called {\it stuck crossings}, whose incident strands are required to remain locally non-separable. These rigidity constraints restrict the allowable ambient isotopies and…
Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a…