Genus Distributions For Extended Matrix Models Of RNA

Details Genus Distributions For Extended Matrix Models Of RNA Genus Distributions For Extended Matrix Models Of RNA

2008-02-18

arxiv.org/abs/0802.2440v2

Physics

Condensed Matter

Statistical Mechanics

15 pages, 4 figures, 3 tables

Scientific paper

We construct and study an extended random matrix model of RNA (polymer) folding. A perturbation which acts on all the nucleotides in the chain is added to the action of the RNA partition function. The effect of this perturbation on the partition function and the Genus Distributions is studied. This perturbation distinguishes between the paired and unpaired bases. For example, for $\alpha = 1$ (where $\alpha$ is the ratio of the strengths of the original and perturbed term in the action) the partition function and genus distribution for odd lengths vanish completely. This partition function and the genus distribution is non-zero for even lengths where structures with fully paired bases only remain. This implies that (i). the genus distributions are different and (ii). there is a ``structural transition'' (from an ``unpaired-paired base phase'' to a ``completely paired base phase'') as $\alpha$ approaches 1 in the extended matrix models. We compare the results of the extended RNA model with the results of G. Vernizzi, H. Orland and A. Zee in PRL 94, 168103(2005).

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