Spontaneous helicity of a polymer with side-loops confined to a cylinder

TL;DR

This study demonstrates that a bottle brush polymer with side loops spontaneously forms a helical structure when confined in a small cylinder, influenced by chain stiffness and packing effects, with implications for bacterial chromosome organization.

Contribution

It reveals the spontaneous helical organization of side-loop polymers under confinement, modeling bacterial chromosomes and highlighting the effects of chain stiffness and packing.

Findings

Polymer adopts a helical structure under confinement.

Helicity persists over various cylinder sizes and aspect ratios.

Circular backbone forms two parallel helices connected at poles.

Abstract

Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect-ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze this results in terms of the interplay between the effective stiffness and actual intra-chain packing effects caused by the side-loops in response to the confinement. For the case of a circular backbone, mimicking e.g. the E. coli chromosome, the polymer adopts a linearized configuration of two parallel helices connected at the cylinder poles.