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Moulton, Vincent 
ORCID: https://orcid.org/0000-0001-9371-6435 and Wu, Taoyang ORCID: https://orcid.org/0000-0002-2663-2001
(2022)
Posets and spaces of k-noncrossing RNA structures.
SIAM Journal on Discrete Mathematics, 36 (3).
pp. 1586-1611.
ISSN 0895-4801
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Abstract
RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modeled combinatorially in terms of a certain type of graph called an RNA diagram. In this paper we introduce a new poset of RNA diagrams ${\mathcal B}^r_{f,k}$, $r\ge 0$, $k \ge 1$, and $f \ge 3$, which we call the Penner--Waterman poset, and, using results from the theory of multitriangulations, we show that this is a pure poset of rank $k(2f-2k+1)+r-f-1$, whose geometric realization is the join of a simplicial sphere of dimension $k(f-2k)-1$ and an $\left((f+1)(k-1)-1\right)$-simplex in case $r=0$. As a corollary for the special case $k=1$, we obtain a result due to Penner and Waterman concerning the topology of the space of RNA secondary structures. These results could eventually lead to new ways to study landscapes of RNA $k$-noncrossing structures.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | rna structures,k-noncrossing pseudoknots,multitriangulations,poset topology,mathematics(all) ,/dk/atira/pure/subjectarea/asjc/2600 |
| Faculty \ School: | Faculty of Science > School of Computing Sciences |
| UEA Research Groups: | Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre Faculty of Science > Research Centres > Centre for Ecology, Evolution and Conservation |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 13 Apr 2022 10:30 |
| Last Modified: | 09 Oct 2024 13:38 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/84621 |
| DOI: | 10.1137/21M1413316 |
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