Large deviations for random trees and the branching of RNA secondary structures

Yuri Bakhtin, Christine E. Heitsch

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)84-106
Number of pages23
JournalBulletin of Mathematical Biology
Volume71
Issue number1
DOIs
StatePublished - Jan 1 2009

Keywords

  • Branching loops
  • Gibbs distributions
  • Large deviations
  • Picornavirus
  • RNA secondary structure
  • Random trees
  • Ribosome
  • Vertex degree

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology
  • Mathematics(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)
  • Pharmacology
  • Agricultural and Biological Sciences(all)
  • Computational Theory and Mathematics

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