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DY: Fachverband Dynamik und Statistische Physik

DY 12: Statistical physics (general)

DY 12.4: Vortrag

Dienstag, 27. März 2007, 10:45–11:00, H3

The density of states in complex systems: the case of RNA secondary structures — •Stefan Wolfsheimer, Bernd Burghardt, and Alexander Hartmann — Institut für theoretische Physik, Friedrich-Hund-Platz 1, 37077 Göttingen

Models for RNA secondary structures (the topology of folded RNA) without pseudo knots have interesting properties: On one side they are complex systems with an ultrametric-like state-space structure, leading to high entropic barriers. Due to this fact Monte Carlo methods to obtain ground-state properties (energy, degeneracy etc.) and density of states become stuck very quickly. On the other side, in contrast to many complex systems, the ground states and the density of states can by computed in polynomial time exactly. Hence, RNA secondary structures provide an ideal benchmark system for new Monte Carlo methods. Recently the ParQ algorithm, a transition matrix approach, was introduced by Heilmann et.al. (Euro.Phys.Lett.70(2): 155-161,2005) In this study we investigate the impact of the ParQ annealing schedule on the performance of the algorithm. We als characterize the ground-state structure using the overlap distribution and the degree of ultrametricity, which turns out to be directly related to tunneling times and performance of the algorithm.