Regensburg 2007 – scientific programme

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BP: Fachverband Biologische Physik

BP 10: DNA: supercoils, knots and melting

BP 10.3: Talk

Tuesday, March 27, 2007, 14:45–15:00, H43

Dynamics of Knotted Polymers in Nanochannels — •Wolfram Möbius¹, Erwin Frey¹, and Ulrich Gerland² — ¹Arnold-Sommerfeld-Zentrum für theoretische Physik, LMU München — ²Institut für theoretische Physik, Universität zu Köln

We study the dynamics of knotted linear polymers in narrow channels with widths comparable to the polymer’s persistence length. We use a combination of extensive Brownian dynamics simulations and simplified stochastic models to determine the modes of knot motion. In particular, we focus on the dynamics of knot motion along the polymer and the modes of changes in the knot’s configuration. Both aspects of the dynamics can be understood within a coarse-grained stochastic model. The coarse-grained model describes our simulations quantitatively without any free parameters. Furthermore, we determine the modes of knot disassembly and the scaling behavior of the mean unknotting time as a function of the total polymer length for initially small knots.