Related papers: Kinetics of Loop Formation in Polymer Chains
Loop formation between monomers in the interior of semiflexible chains describes elementary events in biomolecular folding and DNA bending. We calculate analytically the interior distance distribution function for semiflexible chains using…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
We investigate the conformational and dynamical properties of a partially active Rouse chain, where activity is localized within a specific segment, positioned at various locations along the chain and spanning any given length. Through…
We theoretically investigate the looping dynamics of a linear polymer immersed in a viscoelastic fluid. The dynamics of the chain is governed by a Rouse model with a fractional memory kernel recently proposed by Weber et al. (S. C. Weber,…
We consider a model of a Rouse polymer extended by the mechanism of active loop extrusion. The model is based on a kinetic equation that is valid provided that the extrusion rate is high enough and the resulting loop ensemble is…
We present a theoretical model for understanding the kinetics of a long polymer in solution. A Smoluchowski-like equation has been used to model the problem of polymer looping with a Dirac delta function sink of finite strength. The results…
The Rouse model can be regarded as the standard model to describe the dynamics of a short polymer chain under melt conditions. In this contribution, we explicitly check one of the fundamental assumptions of this model, namely that of a…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
We present exact and analytically accurate results for the problem of a flexible polymer chain in shear flow. Under such a flow the polymer tumbles, and the probability distribution of the tumbling times $\tau$ of the polymer decays…
We show that Kramers rate theory gives a straightforward, accurate estimate of the closing time $\tau_c$ of a semiflexible polymer that is valid in cases of physical interest. The calculation also reveals how the time scales of chain…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
The localization kinetics of a regular block-copolymer of total length $N$ and block size $M$ at a selective liquid-liquid interface is studied in the limit of strong segregation between hydrophobic and polar segments in the chain. We…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
We present large-scale molecular dynamics simulations for a coarse-grained model of polymer melts in equilibrium. From detailed Rouse mode analysis we show that the time-dependent relaxation of the autocorrelation function (ACF) of modes…
The static and dynamic properties of a cyclic Rouse chain modified by the introduction of an effective, spherically symmetric, attracting potential of entropic nature is studied. It is shown that a relatively weak potential can lead to a…
The dynamics of ring polymer melts are studied via molecular dynamics simulations of the Kremer-Grest bead-spring model. Rouse mode analysis is performed in comparison with linear polymers by changing the chain length. Rouse-like behavior…
The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional…
Polymer melts with chains undergoing reversible crosslinking have distinctively favorable dynamic properties, e.g., self healing and reprocessability. In these situations there are two relevant elementary time scales: the segmental and the…
We present results of Monte Carlo simulations measuring the coherent structure function of a chain moving through an ordered lattice of fixed topological obstacles. Our computer experiments use chains up to 320 beads and cover a large range…
A key assumption of polymer physics is that the random chains polymers extend in flow. Recent experimental evidence has shown that polymer chains compress in Couette flow in a manner counter to expectation. Here, scaling arguments developed…