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arXiv · 1410.5980

Rings in Random Environments: Sensing Disorder Through Topology

Davide Michieletto·Marco Baiesi·Enzo Orlandini·Matthew S. Turner
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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

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Davide Michieletto, Marco Baiesi, Enzo Orlandini, Matthew S. Turner. 2014-10-22. Rings in Random Environments: Sensing Disorder Through Topology. https://doi.org/10.1039/c4sm02324b

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