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New Alphabet-Dependent Morphological Transition in Random RNA Alignment

O. V. Valba, M. V. Tamm, and S. K. Nechaev
Phys. Rev. Lett. 109, 018102 – Published 5 July 2012

Abstract

We study the fraction f of nucleotides involved in the formation of a cactuslike secondary structure of random heteropolymer RNA-like molecules. In the low-temperature limit, we study this fraction as a function of the number c of different nucleotide species. We show, that with changing c, the secondary structures of random RNAs undergo a morphological transition: f(c)1 for cccr as the chain length n goes to infinity, signaling the formation of a virtually perfect gapless secondary structure; while f(c)<1 for c>ccr, which means that a nonperfect structure with gaps is formed. The strict upper and lower bounds 2ccr4 are proven, and the numerical evidence for ccr is presented. The relevance of the transition from the evolutional point of view is discussed.

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  • Received 24 December 2011

DOI:https://doi.org/10.1103/PhysRevLett.109.018102

© 2012 American Physical Society

Authors & Affiliations

O. V. Valba1,3, M. V. Tamm2, and S. K. Nechaev3,4

  • 1Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
  • 2Physics Department, Moscow State University, 119992, Moscow, Russia
  • 3LPTMS, Université Paris Sud, 91405 Orsay Cedex, France
  • 4P.N. Lebedev Physical Institute of the Russian Academy of Sciences, 119991, Moscow, Russia

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Vol. 109, Iss. 1 — 6 July 2012

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