title: Topology of pseudoknotted homopolymers.
abstract: We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The genus has been recently proposed for classifying pseudoknots (and their topological complexity) in the context of RNA folding. We compare our results on the distribution of the genus of pseudoknots, with the theoretical predictions of an existing combinatorial model for an infinitely flexible and stretchable homopolymer. We thus obtain that steric and geometric constraints considerably limit the topological complexity of pseudoknotted configurations, as it occurs for instance in real RNA molecules. We also analyze the scaling properties at large homopolymer length, and the genus distributions above and below the critical temperature between the swollen phase and the compact-globule phase, both in two and three dimensions.
authors.affiliation: Service de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.
authors.forename: Graziano
authors.initials: G
authors.lastname: Vernizzi
authors.forename: Paolo
authors.initials: P
authors.lastname: Ribeca
authors.forename: Henri
authors.initials: H
authors.lastname: Orland
authors.forename: A
authors.initials: A
authors.lastname: Zee
mesh_terms: D001665:Binding Sites; D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D044367:Phase Transition; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D013696:Temperature; D044366:Transition Temperature
chemical_list: D001704:Biopolymers; D012313:RNA