Related papers: Conformational statistics of non-equilibrium polym…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
We study the out-of-equilibrium large time dynamics of a gaussian polymer chain in a quenched random potential. The dynamics studied is a simple Langevin dynamics commonly referred to as the Rouse model. The equations for the two-time…
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 report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the scaling behavior of the global relaxation…
We study dynamics of a Rouse polymer chain, which diffuses in a three-dimensional space under the constraint that one of its ends, referred to as the slip-link, may move only along a one-dimensional line containing randomly placed,…
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual…
We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3,…
A number of recent experiments have provided detailed observations of the configurations of long DNA strands under nano-to-micrometer sized confinement. We therefore revisit the problem of an excluded volume polymer chain confined between…
The predictions of the polymer mode coupling theory for the finite size corrections to the transport coefficients of entangled polymeric systems are tested in comparisons with various experimental data. It is found that quantitative…
Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…
We report the results of extensive Dynamic Monte Carlo simulations of systems of self-assembled Equilibrium Polymers without rings in good solvent. Confirming recent theoretical predictions, the mean-chain length is found to scale as $\Lav…
This study deals with polymer looping, an important process in many chemical and biological systems. We investigate basic questions on the looping dynamics of a polymer under tension using the freely-jointed chain (FJC) model. Previous…
Understanding looping probabilities, including the particular case of ring-closure or cyclization, of fluctuating polymers (eg DNA) is important in many applications in molecular biology and chemistry. In a continuum limit the configuration…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…
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…
We show the presence of both a minimum and clear oscillations in the frequency dependence of the translocation time of a polymer described as a unidimensional Rouse chain driven by a spatially localized oscillating linear potential. The…
While stretching of a polymer along a flat surface is hardly different from the classical Pincus problem of pulling chain ends in free space, the role of curved geometry in conformational statistics of the stretched chain is an exciting…
We study the diffusion of a linear polymer in the presence of permeable membranes without excluded volume interactions, using scaling theory and Monte Carlo simulations. We find that the average time it takes for a chain with polymerization…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
We consider how active forces modeled as non-thermal random noise affect the average dynamical properties of a Rouse polymer. As the power spectrum of the noise is not known we keep the analytical treatment as generic as possible and then…