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

DOI10.1007/S11538-008-9353-YzbMATH Open1169.92018arXiv0803.3990OpenAlexW1968104166WikidataQ39485077 ScholiaQ39485077MaRDI QIDQ841783FDOQ841783

Authors: Christine E. Heitsch, Yuri Bakhtin 

Publication date: 18 September 2009

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

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.

Full work available at URL: https://arxiv.org/abs/0803.3990

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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)

Cites Work

• Investigation of the Bernoulli model for RNA secondary structures
• Title not available (Why is that?)
• Moments of the Boltzmann distribution for RNA secondary structures
• Entropy, large deviations, and statistical mechanics.
• Combinatorics of RNA secondary structures
• Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov--Jacobson energy model
• Large deviations for random trees

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

Uses Software

• Mfold

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