PMID: 11909105Mar 23, 2002Paper

Statistical mechanics of secondary structures formed by random RNA sequences

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Ralf Bundschuh, Terence Hwa

Abstract

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA molecule in six-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the external statistics of rare regions can be constructed to show that the low-temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low-temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length s...Continue Reading

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Citations

Mar 8, 2006·The European Physical Journal. E, Soft Matter·R Bundschuh, U Gerland
Aug 14, 2009·The Journal of Chemical Physics·Alexey PolotskyFriederike Schmid
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