Knots are Generic Stable Phases in Semiflexible Polymers

TL;DR

This study uses extensive simulations to demonstrate that stable knots are common and robust phases in semiflexible polymers, depending on specific bond length ratios and stiffness, shedding light on their potential biological relevance.

Contribution

The paper reveals that stable knotted phases are prevalent in semiflexible polymers when the bond length ratio is outside a narrow window, a novel insight into polymer phase behavior.

Findings

Stable knots occur in polymers depending on bond length ratios.

Knotted phases are stable across a range of bending stiffnesses.

Knots are shown to be generic stable phases in semiflexible polymers.

Abstract

Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible polymers has not been explored much. Here, via extensive replica exchange Monte Carlo simulation we investigate the same for a bead-stick and a bead-spring homopolymer model that covers the whole range from flexible to stiff. We establish the fact that the presence of stable knotted phases in the phase diagram is dependent on the ratio $r_b/r_{\rm{min}}$ where $r_b$ is the equilibrium bond length and $r_{\rm{min}}$ is the distance for the strongest nonbonded contacts. Our results provide evidence for both models that if the ratio $r_b/r_{\rm{min}}$ is outside a small window around unity then depending on the bending stiffness one always encounters stable knotted phases along with the usual frozen and bent-like structures at low temperatures. These findings prompt us to conclude that knots are generic stable phases in semiflexible polymers.