RNAlike polymer model: exact calculation on the Bethe lattice
arXiv:cond-mat/0601705 · doi:10.1103/PhysRevE.74.051803
Abstract
We consider a lattice polymer model (random walk), in which the walk is allowed to visit lattice bonds at most twice. Such a model might have some relevance to describe statistical properties of RNA molecules. In order to mimic base pairing, we assign an attractive energy term to each doubly-visited bond, and a further contribution to each pair of consecutive doubly-visited bonds. The latter term is expected to mimic the stacking effect, whereas no effect of sequence, that is, of chemical specificity, is taken into account. The phase diagram is worked out exactly on a Bethe lattice, in a grand-canonical formulation. In the dilute solution (single molecule) limit, the system undergoes two different phase transitions, upon decreasing temperature: a Thetalike collapse from a swollen "coil" state to a "molten" state, with a low fraction of doubly-visited bonds, and subsequently to a "paired" state, with empty or doubly-visited bonds only. The stacking effect drives the latter transition from second to first order.
10 pages, 6 figures, 1 table. Minor changes to the text, added references
References in corpus (10)
- Statistical mechanics of secondary structures formed by random RNA sequences
- Statistical Physics of RNA-folding
- Zero Temperature Properties of RNA Secondary Structures
- Statistical mechanics of RNA folding: a lattice approach
- RNA denaturation: excluded volume, pseudoknots and transition scenarios
- Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?
- The Phase Diagram of Random Heteropolymers
- Statistical mechanics of RNA folding: importance of alphabet size
- Dependence of RNA secondary structure on the energy model
- Glassy phases in Random Heteropolymers with correlated sequences