Related papers: A protrusion can "eclipse" looping of a long self-…
We study the conformations of a self-avoiding polymer confined to a channel by computing the cross-sectional distributions of the positions of its monomers. By means of Monte-Carlo simulations for a self-avoiding, freely-jointed chain we…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
In this work an approximated path integral model describing the dynamics of a inextensible chain is presented. To this purpose, the nonlinear constraints which enforce the property of inextensibility of the chain are relaxed and are just…
We present a study of connectivity percolation in suspensions of hard spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. We focus attention on polydispersity in the length, the diameter and the…
We analyze the dynamics of random walks with long-term memory (binary chains with long-range correlations) in the presence of an absorbing boundary. An analytically solvable model is presented, in which a dynamical phase-transition occurs…
We perform extensive molecular dynamics simulations of a charged polymer in a good solvent in the regime where the chain is collapsed. We analyze the dependence of the gyration radius $R_g $ on the reduced Bjerrum length $\ell_B$ and find…
We consider the problem of extinction processes on random networks with a given structure. For sufficiently large well-mixed populations, the process of extinction of one or more state variable components occurs in the tail of the…
We develop a strong stretching approximation for a polymer brush made of self-avoiding polymer chains. The density profile of the brush and the distribution of the end monomer positions in stretching direction are computed and compared with…
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…
We discuss a Monte Carlo Markov Chain (MCMC) procedure for the random sampling of some one-dimensional lattice paths with constraints, for various constraints. We show that an approach inspired by optimal transport allows us to bound…
We calculate the survival probability of a stationary target in one dimension surrounded by diffusive or subdiffusive traps of time-dependent density. The survival probability of a target in the presence of traps of constant density is…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
Autocorrelations in MCMC chains increase the variance of the estimators they produce. We propose the occlusion process to mitigate this problem. It is a process that sits upon an existing MCMC sampler, and occasionally replaces its samples…
We have studied the conformational properties of a flexible end-grafted chain (length $N$) with a rigid side chain (length $S$) by means of Monte Carlo simulations. Depending on the lengths $N$ and $S$ and the branching site, $b$, we…
We present Monte Carlo simulations of semidilute solutions of long self-attracting chain polymers near their Ising type critical point. The polymers are modeled as monodisperse self-avoiding walks on the simple cubic lattice with attraction…
We perform simulations for long hard-sphere polymer chains using a recently developed binary-tree based Monte Carlo method. Systems in two to five dimensions with free and periodic boundary conditions and up to $10^7$ repeat units are…
The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the…
For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous…
Genome wide comparisons between enteric bacteria yield large sets of conserved putative regulatory sites on a gene by gene basis that need to be clustered into regulons. Using the assumption that regulatory sites can be represented as…
The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…