Rings in Random Environments: Sensing Disorder Through Topology

TL;DR

This study demonstrates that ring polymers can be used as a non-invasive topological sensor to detect microscopic disorder in gel environments, with results supported by simulations and analytical modeling.

Contribution

The paper introduces a novel approach using ring polymers to sense microscopic disorder in gels through topology, validated by simulations and theory.

Findings

Ring polymers' mobility is sensitive to gel disorder.

Linear polymers are insensitive to microscopic changes.

Simulation results agree with analytical models.

Abstract

In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby generating a disordered environment. Changes in the microscopic structure of the gel are captured by measuring the electrophoretic mobility of ring polymers moving through the medium, while their linear counterparts provide a control system as we show they are insensitive to these changes. We show that ring polymers provide a novel non-invasive way of exploiting topology to sense microscopic disorder. Finally, we compare the results from the simulations with an analytical model for the non-equilibrium differential mobility, and find a striking agreement between simulation and theory