Entropic organization of topologically modified ring polymers in spherical confinement

TL;DR

This study explores how topological modifications in ring polymers influence their spatial organization within spherical confinement, revealing entropy-driven segregation patterns relevant to nuclear chromosome organization.

Contribution

It introduces asymmetric topological modifications to ring polymers and demonstrates their impact on spatial organization in spherical confinement, a novel approach to studying entropy-driven polymer behavior.

Findings

Single modified polymer's larger loop prefers the periphery.

Multiple polymers' small loops tend to be near the sphere walls.

Increasing small loops enhances radial localization.

Abstract

It has been shown that under high cylindrical confinement, two ring polymers with excluded volume interactions between monomers, segregate to two halves of the cylinder to maximize their entropy. In contrast, two ring polymers remain mixed within a sphere, as there is no symmetry breaking direction [Nat Rev Microbiol, 8, 600-607 (2010)]. Therefore, in order to observe emergent organization of ring polymers in a sphere, we can introduce an asymmetric topological modification to the polymer architecture by creating a small loop and a big loop within the ring polymer. We consider the bead-spring model of polymers where there are only repulsive excluded volume interactions between the monomers ensuring that the organization we observe is purely entropy-driven. We find that for a single topologically modified polymer within a sphere, the monomers of the bigger loop are statistically more probable to be found closer to the periphery. However, the situation is reversed when we have multiple such topologically modified polymers in a sphere. The monomers of the small loops are found closer to the walls of the sphere. We can increase this localization and radial organization of polymer segments by increasing the number of small loops in each ring polymer. We study how these loops interact with each other within a polymer, as well as with loops of other polymers in spherical confinement. We compare contact maps of multiple such topologically modified polymers in a sphere. Finally, we discuss the plausible relevance of our studies to eukaryotic chromosomes that are confined within a spherical nucleus.