Henri Orland (ITP, Saclay)
Prediction of RNA structures with pseudoknots
After reviewing some elementary properties of RNA, we discuss how
statistical mechanics can be used to determine the secondary structure of RNA.
One has first to parametrize as precisely as possible the free energy of secondary
structures. Given such a parametrization, we review some methods used to predict
secondary structures without pseudoknots. To include pseudoknots, we propose a
classification of RNA structures in terms of their topological genii. This topological
classification stems from a matrix field-theory representation of the RNA folding
problem. The free energy is parametrized so as to include a penalty proportional to
the genus of the RNA structure. We show how this can be used to efficiently predict
RNA structures with pseudoknots.
Dec 6 at 3pm in Braunstein Room 300
(Joint Astro/Particle and Condensed Matter Seminar)