Spontaneous Unknotting of a Polymer Confined in a Nanochannel

TL;DR

This study investigates how knots in confined semiflexible polymers spontaneously unknot through combined simulation and modeling, revealing that external forces accelerate the unknotting process and that knots grow large before disappearing.

Contribution

It introduces a combined simulation and stochastic model to analyze knot dynamics in confined polymers, highlighting the role of external forces in speeding up unknotting.

Findings

Knots grow to macroscopic size before unknotting.

External forces accelerate the unknotting process.

Spontaneous unknotting involves coupled size variation and diffusion.

Abstract

We study the dynamics of a knot in a semiflexible polymer confined to a narrow channel of width comparable to the polymers' persistence length. Using a combination of Brownian dynamics simulations and a coarse-grained stochastic model, we characterize the coupled dynamics of knot size variation and knot diffusion along the polymer, which ultimately leads to spontaneous unknotting. We find that the knot grows to macroscopic size before disappearing. Interestingly, an external force applied to the ends of the confined polymer speeds up spontaneous unknotting.