Related papers: Randomly cross-linked polymer models
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
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…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
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…
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
A polymer folding model on the square lattice is constructed with attractive contact interactions of strength 1/c^2, 0<c<1. The corresponding model on a dynamical random lattice, with freely fluctuating co-ordination number at each vertex,…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
We examine entanglements using monomer contacts between pairs of chains in a Brownian-dynamics simulation of a polymer melt. A map of contact positions with respect to the contacting monomer numbers (i,j) shows clustering in small regions…
Collapse of the polymer chain upon the sharp decrease of solvent quality is studied. During collapse, any pair of polymer units appearing in a sufficiently close vicinity in space has the possibility with a certain probability to form an…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Random heteropolymers are a minimal description of biopolymers and can provide a theoretical framework to the investigate the formation of loops in biophysical experiments. A two--state model provides a consistent and robust way to study…
The calculation of Euclidean distance between points is generalized to one-dimensional objects such as strings or polymers. Necessary and sufficient conditions for the minimal transformation between two polymer configurations are derived.…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability $P(s)$ as a scale-dependent order parameter depending on the chemical distance $s$, our…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…