Entropic alignment of topologically modified ring polymers in cylindrical confinement

TL;DR

This study demonstrates how entropic interactions in topologically modified ring polymers under cylindrical confinement lead to specific spatial and orientational organization, with potential implications for chromosome structure.

Contribution

It introduces a novel approach to manipulate polymer topology to induce effective orientational interactions driven purely by entropy.

Findings

Polymers with internal loops organize along the cylinder axis.

Entropic repulsion causes polymers to occupy separate halves of the cylinder.

Effective orientational interactions emerge without enthalpy involvement.

Abstract

Under high cylindrical confinement, segments of ring polymers can be localized along the long axis of the cylinder by introducing internal loops within the ring polymer. The emergent organization of the polymer segments occurs because of the entropic repulsion between internal loops. These principles were used to identify the underlying mechanism of bacterial chromosome organization. Here, we outline functional principles associated with entropic interactions, leading to specific orientations of the ring polymers relative to their neighbors in the cylindrical confinement. We achieve this by modifying the ring polymer topology by creating internal loops of two different sizes within the polymer, and thus create an asymmetry. This allows us to strategically manipulate polymer topology such that segments of a polymer face certain other segments of a neighboring polymer. The polymers therefore behave as if they are subjected to an `effective' entropic interaction reminiscent of interactions between Ising spins. But this emergent spatial and orientational organization is not enthalpy-driven. We consider a bead spring model of flexible polymers with only repulsive excluded volume interactions between the monomers. The polymers entropically repel each other and occupy different halves of the cylinder, and moreover, the adjacent polymers preferentially re-orient themselves along the axis of the cylinder. We further substantiate our observations by free energy calculations. To the best of our knowledge, this is the first study of the emergence of effective orientational interactions by harnessing entropic interactions in flexible polymers. The principles elucidated here could be relevant to understand the interactions between different sized loops within a large chromosome.