Prof. Dr. Peter Stadler

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RNA molecules are quite well represented in terms of their secondary
structure. In this discrete model, which considers only base pair stacking,
ground state energies as well as properties of the equilibrium ensemble can
be computed efficiently by means of exact dynamic programming
algorithms. In addition, it allows a very detailed analysis of the entire
energy landscapes and therefore access to details of the processes of
structural change. To this end, however, the huge space of all secondary
structures needs to be condensed to a coarse grained representation that is
small enough to allow detailed dynamical analyses. Examples are barrier
trees and the more accurate 'base hopping graph'. These condensed graph
structures can be computed exactly for moderate size molecules making use
by enumeration and admit rather effective sampling techniques for larger
RNAs. Kinetic parameters can be estimated with acceptable accuracy in this
manner providing insights into the folding and refolding dynamics of RNAs.
The landscape paradigm can be extended to co-transcriptional folding as
well as a variety of settings in which environmental conditions lead to
small changes in the RNA itself or in underlying parametrization. In this
picture, intricate effects, as they occur e.g. in kinetically controlled
riboswitches can be modelled.

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University of Leipzig
Biocentre, Ground Floor Lecture Hall
Contact: Joachim Krug