Confinement and Viscoelastic effects on Chain Closure Dynamics

TL;DR

This paper investigates how confinement and viscoelastic effects influence the chain closure time in polymer reactions, revealing scaling laws under different cellular-like conditions using the Rouse model and Wilemski-Fixman approximation.

Contribution

It derives new scaling relationships for polymer chain closure times considering confinement and viscoelasticity effects, extending the Rouse model analysis.

Findings

Closure time scales as ND^2 under confinement when D is small.

Closure time scales as N^{2/(2-2H)} in viscoelastic media, with H around 0.7 leading to N^{3.4}.

Viscoelastic effects significantly slow down chain relaxation and reaction dynamics.

Abstract

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 cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t_{c} of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius D, and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when D is much smaller than the size of the chain, t_{c}\simND^{2}, and that in case (b), t_{c}\simN^{2/(2-2H)}, H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known \`a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t_{c}\simN^3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium.