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 language | English (US) |
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Pages (from-to) | 84-106 |
Number of pages | 23 |
Journal | Bulletin of Mathematical Biology |
Volume | 71 |
Issue number | 1 |
DOIs | |
State | Published - Jan 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