Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn


Speaker: Manoel Manghi, Université Paul Sabatier, Toulouse, France

Title: The role of torsion in the closure and nucleation dynamics of DNA denaturation bubbles * Colloquium on Complex and Biological Systems

Time: Fri, Jul 11, 2014, 10:15am

Place: bldg 28, room 0.108

The issue of the nucleation and slow closure mechanisms of denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring freely rotating strands with a prescribed torsional modulus in the duplex state. We demonstrate that timescales for the nucleation (resp. closure) of an approximately 10 base-pairs bubble, in agreement with experiments, are associated to the crossing of a free-energy barrier of 22 kBT (resp. 13 kBT) at room temperature T. MetaDynamics allows us to reconstruct accurately the free-energy landscape, to show that the free-energy barriers come from the difference in torsional energy between the bubble and duplex states, to highlight the limiting step, a collective twisting, that controls the nucleation/closure mechanism, and to access opening time scales on the millisecond range.
arXiv:1405.3867 [cond-mat.soft]

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