Topological classification and enumeration of RNA structures by genus (Q378306): Difference between revisions

The authors study the association between RNA pseudoknot structures and topological surfaces, and the classification of the former by the genus of the latter. On the basis of earlier work [\textit{J. Harer} and \textit{D. Zagier}, Invent. Math. 85, 457--485 (1986; Zbl 0616.14017)], they calculate the generating function for the number of structures with a fixed genus and number of nucleotides, and given minimum stack size so that no two consecutive nucleotides are base-paired. In particular, they show that the generating function is algebraic, and they prove that for stack size at least two, the genus of the surface only enters sub-exponentially; hence, they argue that, for any genus, the resulting slow growth rates with respect to RNA molecule numbers imply the existence of neutral networks [\textit{C. Reidys} et al., Bull. Math. Biol. 59, No. 2, 339--397 (1997; Zbl 0925.92006)]. Specific structures known as shapes are shown to be in a one-to-one correspondence with cells in the Penner-Strebel decomposition [\textit{R.C. Penner}, Commun. Math. Phys. 113, 299--339 (1987; Zbl 0642.32012)] of Riemann's moduli space of a surface with a given genus and one boundary component.