Berlin 2005 – scientific programme
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DY: Dynamik und Statistische Physik
DY 21: Statistical Physics in Biological Systems
DY 21.4: Talk
Saturday, March 5, 2005, 09:15–09:30, TU H2032
Comparison of RNA secondary structures with and without pseudoknots — •Alejandro Morales Gallardo, Bernd Burghardt, and Alexander K. Hartmann — Institut für Theoretische Physik, Universität Göttingen
RNA plays an important role in the biochemistry of all living systems. It does not only transmit pure genetic information, but, e.g. works as a catalyst. While for the former the primary structure, i.e. the sequence of the bases, is relevant, for the later the kind of higher order structures, i.e. secondary and tertiary structures, are relevant. While most studies concentrate on plain secondary structures without pseudo knots, we allow some special kinds of pseudo knots, which makes the computational problem more demanding, e.g. the effort for finding the ground state energy increases from O(L3) without pseudo knots to O(L6) the sequence length L. We have done numerical studies on statistical quantities, where we used algorithms that are able to calculate the ground-state energy exactly in polynomial time. We concentrate on the difference between models with and without pseudo knots.