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

DOI10.1007/S11538-008-9353-YMaRDI QIDQ841783zbMATH OpenOpenAlexWikidataFDO

Authors Christine E. Heitsch, Yuri Bakhtin

Publication date 18 September 2009

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0803.3990, https://europepmc.org/articles/pmc2834537

zbMATH Keywords

vertex degreeGibbs distributionsbranching loopspicornavirusribosome

Mathematics Subject Classification ID

Applications of graph theory (05C90) Large deviations (60F10) Biochemistry, molecular biology (92C40) Random graphs (graph-theoretic aspects) (05C80)

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.

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Cites work

• scientific article; zbMATH DE number 1158743 (Why is no real title available?)
• Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov--Jacobson energy model
• Combinatorics of RNA secondary structures
• Entropy, large deviations, and statistical mechanics.
• Investigation of the Bernoulli model for RNA secondary structures
• Large deviations for random trees
• Moments of the Boltzmann distribution for RNA secondary structures

Cited in

(5)

• Parametric analysis of RNA branching configurations
• Large deviations for random trees
• Thermodynamic limit for large random trees
• Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding
• Algebraic methods in mathematical biology

Describes a project that uses

Uses Software

• Mfold

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