Topology of pseudoknotted homopolymers

Graziano Vernizzi, Paolo Ribeca, Henri Orland, and A. Zee
Phys. Rev. E 73, 031902 – Published 3 March 2006

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.

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  • Received 11 September 2005

DOI:https://doi.org/10.1103/PhysRevE.73.031902

©2006 American Physical Society

Authors & Affiliations

Graziano Vernizzi1, Paolo Ribeca2, Henri Orland1, and A. Zee3,4

  • 1Service de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
  • 2Humboldt Universität, Newtonstr. 15, 12489 Berlin, Germany
  • 3Department of Physics, University of California, Santa Barbara, California 93106 USA
  • 4Institute for Theoretical Physics, University of California, Santa Barbara, California 93106 USA

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Vol. 73, Iss. 3 — March 2006

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