Mean pairwise distances in Rouse polymer subject to fast loop extrusion

TL;DR

This paper models a Rouse polymer with active loop extrusion, developing a semi-analytical method to compute mean pairwise distances, revealing how loop dynamics influence polymer structure.

Contribution

It introduces a novel semi-analytical approach to analyze mean distances in a Rouse polymer with active loop extrusion, extending previous models.

Findings

Mean square distances depend on loop extrusion rate and sparsity.

Logarithmic derivative of mean distance varies with contour separation.

Comparison shows differences between dynamic and frozen loop disorder.

Abstract

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 sufficiently sparse. Within the one-loop approximation of diagrammatic calculations, a semi-analytical method for determining the mean square physical distance between a pair of chain beads as a function of the contour distance between them is developed. 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 sufficiently sparse. Within the framework of the one-loop approximation of diagrammatic calculations, a semi-analytical method for determining the mean square of the physical distance between a pair of chain sections as a function of the contour distance between them is developed. The mean square of the physical distance and its logarithmic derivative as functions of the contour separation are plotted for different values of the equilibrium degree. The results are compared with the case of frozen disorder of sparse loops.