Related papers: Spanning trees for the geometry and dynamics of co…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
The non-linear stress-strain relation for crosslinked polymer networks is studied using molecular dynamics simulations. Previously we demonstrated the importance of trapped entanglements in determining the elastic and relaxational…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…
The thermal properties of coarse grained knotted polymers containing two kinds of monomers $A$ and $B$ fluctuating in a solution are investigated on a simple cubic lattice using the Wang-Landau MC algorithm. These knots have a more complex…
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…
Motivated by renewed interest in the physics of branched polymers, we present here a complete characterization of the connectivity and spatial properties of $2$ and $3$-dimensional single-chain conformations of randomly branching polymers…
We consider the force on the end of a polymer chain being pulled through a network at velocity $v$, using computer simulations. We develop algorithms for measuring the force on the end of the chain using lattice models of polymers. Our…
A directed polymer is allowed to branch, with configurations determined by global energy optimization and disorder. A finite size scaling analysis in 2D shows that, if disorder makes branching more and more favorable, a critical transition…
A new master equation to mimic the dynamics of a collection of interacting random walkers in an open system is proposed and solved numerically.In this model, the random walkers interact through excluded volume interaction (single-file…
The conformations of topologically constrained double-folded ring polymers can be described as wrappings of randomly branched primitive trees. We extend previous work on the tree statistics under different (solvent) conditions to explore…
We investigate the dynamical response of glass-forming systems composed of topologically constrained ring polymers subjected to an instantaneous thermal quench, employing large-scale molecular dynamics simulations. We demonstrate that the…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
In this study, one-dimensional systems of masses connected by springs, i.e., spring-chain systems, are investigated numerically. The average kinetic energy of chain-end particles of these systems is larger than that of other particles,…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
We consider the energy of a randomly charged polymer. We assume that only charges on the same site interact pairwise. We study the lower tails of the energy, when averaged over both randomness, in dimension three or more. As a corollary, we…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…