dorsal/arxiv
View SchemaThe Topology of Pseudoknotted Homopolymers
| Authors | G. Vernizzi, P. Ribeca, H. Orland, A. Zee |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0508042 |
| URL | https://arxiv.org/abs/q-bio/0508042 |
| DOI | 10.1103/PhysRevE.73.031902 |
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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"abstract": "We consider the folding of a self-avoiding homopolymer on a lattice, with\nsaturating hydrogen bond interactions. Our goal is to numerically evaluate the\nstatistical distribution of the topological genus of pseudoknotted\nconfigurations. The genus has been recently proposed for classifying\npseudoknots (and their topological complexity) in the context of RNA folding.\nWe compare our results on the distribution of the genus of pseudoknots, with\nthe theoretical predictions of an existing combinatorial model for an\ninfinitely flexible and stretchable homopolymer. We thus obtain that steric and\ngeometric constraints considerably limit the topological complexity of\npseudoknotted configurations, as it occurs for instance in real RNA molecules.\nWe also analyze the scaling properties at large homopolymer length, and the\ngenus distributions above and below the critical temperature between the\nswollen phase and the compact-globule phase, both in two and three dimensions.",
"arxiv_id": "q-bio/0508042",
"authors": [
"G. Vernizzi",
"P. Ribeca",
"H. Orland",
"A. Zee"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"doi": "10.1103/PhysRevE.73.031902",
"title": "The Topology of Pseudoknotted Homopolymers",
"url": "https://arxiv.org/abs/q-bio/0508042"
},
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