Related papers: Entropic competition between knots and slip-links
The number of allowed configurations of a polymer is reduced by the presence of a repulsive surface resulting in an entropic force between them. We develop a method to calculate the entropic force, and detailed pressure distribution, for…
The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…
We consider self-avoiding polymers attached to the tip of an impenetrable probe. The scaling exponents $\gamma_1$ and $\gamma_2$, characterizing the number of configurations for the attachment of the polymer by one end, or at its midpoint,…
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…
Under high cylindrical confinement, segments of ring polymers can be localized along the long axis of the cylinder by introducing internal loops within the ring polymer. The emergent organization of the polymer segments occurs because of…
In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot…
Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
Bridging algorithms are global Monte Carlo moves which allow for an efficient sampling of single polymer chains. In this manuscript we discuss the adaptation of three bridging algorithms from lattice to continuum models, and give details on…
The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
We give two different, statistically consistent definitions of the length l of a prime knot tied into a polymer ring. In the good solvent regime the polymer is modelled by a self avoiding polygon of N steps on cubic lattice and l is the…
We present the results of Monte Carlo simulation for a Kondo lattice model in which itinerant electrons interact with Ising spins with spin-ice type easy-axis anisotropy on a pyrochlore lattice. We demonstrate the efficiency of the…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
Exact results for the scaling properties of compact polymers on the square lattice are obtained from an effective field theory. The entropic exponent \gamma=117/112 is calculated, and a line of fixed points associated with interacting…
We study several related models of self-avoiding polygons in a tubular subgraph of the simple cubic lattice, with a particular interest in the asymptotics of the knotting statistics. Polygons in a tube can be characterised by a finite…
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…