Related papers: Polymer reptation and nucleosome repositioning
Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We…
The interaction of amphiphilic polymers with small colloids, capable to reversibly stick onto the chains, is studied. Adhesive small colloids in solution are able to dynamically bind two polymer segments. This association leads to…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
We showed in our previous studies that just $3\%$ cross-links, at special points along the contour of the bacterial DNA help the DNA-polymer to get organized at micron length scales \cite{jpcm,epl}. In this work, we investigate how does the…
We consider the magnetophoresis problem within the Rubinstein-Duke model, i.e. a reptating polymer pulled by a constant field applied to a single repton at the edge of a chain. Extensive density matrix renormalization calculations are…
Dense rubbery networks are highly entangled polymer systems, with significant topological restrictions for the mobility of neighbouring chains and crosslinks preventing the reptation constraint release. In a mean field approach,…
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…
The competition between reptation and Rouse Dynamics is incorporated in the Rubinstein-Duke model for polymer motion by extending it with sideways motions, which cross barriers and create or annihilate hernias. Using the Density-Matrix…
Common experience tells us that a knot significantly weakens the polymer strand in which it is tied, which in turn leads to more facile chain rupture under tensile loading. Using first-principles molecular dynamics calculations we describe…
We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these…