Effect of simple shear on knotted polymer coils and globules

TL;DR

This study uses molecular dynamics simulations to investigate how simple shear flow affects knotted polymer chains, revealing knot tightening, tumbling behavior, and structural transformations in globules.

Contribution

It introduces a detailed simulation analysis of shear effects on knotted polymers, highlighting knot dynamics and structural changes not previously characterized.

Findings

Knots tighten beyond a shear rate threshold.

Polymer globules unwind into pearl-necklace structures.

Knot types change over time during shear.

Abstract

We explore the effect of Couette flow on knotted linear polymer chains with extensive Molecular Dynamics (MD) simulations. Hydrodynamic interactions are accounted for by means of Multi-Particle Collision Dynamics (MPCD). The polymer chain, containing originally a simple trefoil knot at rest, is described by a coarse-grained bead-spring model in a coil or globular state. We demonstrate that under shear existing loosely localized knots in polymer coils typically tighten to several segments beyond a certain shear rate threshold. At large shear rates the polymer undergoes a tumbling-like motion during which knot sizes can fluctuate. In contrast, sheared knotted globules unwind into a convoluted pearl-necklace structure of sub-globules that folds back onto itself and in which knot types change over time.