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Issue 6, 2015
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Rings in random environments: sensing disorder through topology

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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.

Graphical abstract: Rings in random environments: sensing disorder through topology

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Article information


Submitted
22 Oct 2014
Accepted
10 Dec 2014
First published
12 Dec 2014

Soft Matter, 2015,11, 1100-1106
Article type
Paper
Author version available

Rings in random environments: sensing disorder through topology

D. Michieletto, M. Baiesi, E. Orlandini and M. S. Turner, Soft Matter, 2015, 11, 1100
DOI: 10.1039/C4SM02324B

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