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)