BIOPHYSICS

Mean pairwise distances in rouse polymer subject to fast loop extrusion

I. Nikitin^ab, N. Masnev^b, S. Belan<sup>ab

a</sup> Faculty of Physics, HSE University, 101000, Moscow, Russia
^b Landau Institute for Theoretical Physics, Russian Academy of Sciences, 142432, Chernogolovka, Moscow region, Russia

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.

Received: 07.05.2025
Revised: 29.05.2025
Accepted: 03.06.2025

DOI: 10.31857/S0370274X25070103

 English version: Journal of Experimental and Theoretical Physics Letters, 2025, 122:1, 65–70