Large Deviations for Random Trees and the Branching of RNA Secondary Structures

Abstract

We give a Large Deviation Principle (LDP) with explicit rate function for the distribution of vertex degrees in plane trees, a combinatorial model of RNA secondary structures. We calculate the typical degree distributions based on nearest neighbor free energies, and compare our results with the branching configurations found in two sets of large RNA secondary structures. We find substantial agreement overall, with some interesting deviations which merit further study.

23 pages, 3 figures, 13 tables in the appendix