Related papers: A Random Loop Model for Long Polymers
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
Random Matrix Theory (RMT) is capable of making predictions for the spectral fluctuations of a physical system only after removing the influence of the level density by unfolding the spectra. When the level density is known, unfolding is…
We study the translocation of a flexible polymer through extended patterned pores using molecular dynamics (MD) simulations. We consider cylindrical and conical pore geometries that can be controlled by the angle of the pore apex $\alpha$.…
The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state - accessibility and the amount of gene expression - of the chromatin. Recent advances in chromosome…
Several methods for preparing well equilibrated melts of long chains polymers are studied. We show that the standard method in which one starts with an ensemble of chains with the correct end-to-end distance arranged randomly in the…
Distribution of loops in a one-dimensional random walk (RW), or, equivalently, neutral segments in a sequence of positive and negative charges is important for understanding the low energy states of randomly charged polymers. We investigate…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
We propose that the degree of sweeling of the 30nm chromatin fiber (a "measure" of its transcriptional activity) is mainly determined by the short-ranged electrostatical interaction between different sections of the "folded" DNA chain.…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
We present results of molecular dynamics simulations of very long model polymer chains analyzed by various experimentally relevant techniques. The segment motion of the chains is found to be in very good agreement with the repatation model.…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
A general method is presented for modeling high entropy alloys as ensembles of randomly sampled, ordered configurations on a given lattice. Statistical mechanics is applied post hoc to derive the ensemble properties as a function of…
Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which interact via the binding of multivalent complexes of…
Active polymeric systems exhibit a rich spectrum of non-equilibrium phenomena arising from stochastic forces that explicitly break detailed balance. Despite the rapid growth of experimental and numerical studies, analytical progress remains…
We study random copolymers consisted of two kinds of monomers with attraction between similar kinds. The mean field analysis of this system indicates a continuous phase transition into a phase with periodic microdomain structure. It is…
Randomly branching polymers with {\em annealed} connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
This paper considers an undirected polymer chain on $\mathbb{Z}^d$, $d \geq 2$, with i.i.d.\ random charges attached to its constituent monomers. Each self-intersection of the polymer chain contributes an energy to the interaction…
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…