English

New alphabet-dependent morphological transition in a random RNA alignment

Genomics 2013-05-30 v3 Statistical Mechanics

Abstract

We study the fraction ff of nucleotides involved in the formation of a cactus--like secondary structure of random heteropolymer RNA--like molecules. In the low--temperature limit we study this fraction as a function of the number cc of different nucleotide species. We show, that with changing cc, the secondary structures of random RNAs undergo a morphological transition: f(c)1f(c)\to 1 for cccrc \le c_{\rm cr} as the chain length nn goes to infinity, signaling the formation of a virtually "perfect" gapless secondary structure; while f(c)<1f(c)<1 for c>ccrc>c_{\rm cr}, what means that a non-perfect structure with gaps is formed. The strict upper and lower bounds 2ccr42 \le c_{\rm cr} \le 4 are proven, and the numerical evidence for ccrc_{\rm cr} is presented. The relevance of the transition from the evolutional point of view is discussed.

Keywords

Cite

@article{arxiv.1109.5410,
  title  = {New alphabet-dependent morphological transition in a random RNA alignment},
  author = {O. V. Valba and M. V. Tamm and S. K. Nechaev},
  journal= {arXiv preprint arXiv:1109.5410},
  year   = {2013}
}

Comments

4 pages, 3 figures (title is changed, text is essentially reworked), accepted in PRL

R2 v1 2026-06-21T19:10:00.768Z