Rings in Random Environments: Sensing Disorder Through Topology

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

arXiv comment8 pages,6 figures Accepted for publication in Soft Matter

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Cited by in corpus (6)

• Negative differential response in chemical reactions
• Role of trapping and crowding as sources of negative differential mobility
• Topological Patterns in Two-dimensional Gel Electrophoresis of DNA Knots
• Rate dependence of current and fluctuations in jump models with negative differential mobility
• Topological Sieving of Rings According to their Rigidity
• Macroscopic charge segregation in driven polyelectrolyte solutions