title: 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.
authors.affiliation: Department of Physics and Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK. m.s.turner@warwick.ac.uk.
authors.forename: Davide
authors.initials: D
authors.lastname: Michieletto
authors.forename: Marco
authors.initials: M
authors.lastname: Baiesi
authors.forename: Enzo
authors.initials: E
authors.lastname: Orlandini
authors.forename: Matthew S
authors.initials: MS
authors.lastname: Turner
mesh_terms: D004586:Electrophoresis; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011108:Polymers / Q000737:chemistry*
chemical_list: D011108:Polymers