Spaces of RNA secondary structures

DOI10.1006/AIMA.1993.1039MaRDI QIDQ1312845zbMATH OpenOpenAlexFDO

Authors Michael S. Waterman, Robert Penner

Publication date 10 February 1994

Published in Advances in Mathematics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1006/aima.1993.1039

zbMATH Keywords

bond picturesclasses of rooted treesgeometric realizationsisomorphisms of posetslinear macromoleculespartially ordered sets of macromoleculesposetssecondary structure of RNAsimplicial decomposition of a topological spacesphericityTeichmüller theorytopological spherestrain tracks

Mathematics Subject Classification ID

Partial orders, general (06A06) Teichmüller theory for Riemann surfaces (30F60) General topology of complexes (57Q05) Biochemistry, molecular biology (92C40) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10)

Review text

The primary goal of the authors is to contribute to investigations of the secondary structure of RNA. The starting point are bond pictures that give rise to partially ordered sets of macromolecules. For such posets corresponding to classes of ``arbitrary and ``binary macromolecules (the latter being motivated by the study of secondary structures of RNA) geometric realizations are derived utilizing isomorphisms of posets and certain classes of rooted trees. A geometrical realization is a construction which associates a simplicial decomposition of a topological space to a given poset. The main result of the paper is that the geometrical realization of both the posets of arbitrary and of binary macromolecules are topological spheres. The proof uses techniques from Teichmüller theory and the theory of train tracks.

Recommendations

• Posets and spaces of \(k\)-noncrossing RNA structures
• RNA secondary structures: an approach through pseudoknots and fatgraphs
• Moduli spaces and macromolecules
• Loop homology of bi-secondary structures. II
• Topological classification and enumeration of RNA structures by genus

Cited in

(33)

• Combinatorial design of pseudoknot RNA
• On the decomposition of \(k\)-noncrossing RNA structures
• Modeling RNA secondary structures. II: The geometric structural solution for tRNA
• Combinatorics of RNA secondary structures
• A type-B associahedron.
• Kontsevich-Witten model from \(2+1\) gravity: new exact combinatorial solution
• The rainbow spectrum of RNA secondary structures
• Loop homology of bi-secondary structures
• Loop homology of bi-secondary structures. II
• The block spectrum of RNA pseudoknot structures
• On RNA-RNA interaction structures of fixed topological genus
• Statistics of topological RNA structures
• Irreducibility in RNA structures
• Combinatorics of RNA structures with pseudoknots
• Generation of RNA pseudoknot structures with topological genus filtration
• General combinatorics of RNA secondary structure
• Moduli spaces and macromolecules
• Pretopological spaces as a classification tool for RNAs represented as a succession
• Topological language for RNA
• Fatgraph models of proteins
• Topological classification and enumeration of RNA structures by genus
• scientific article; zbMATH DE number 1086865 (Why is no real title available?)
• A bijection for tricellular maps
• Efficient pattern matching for RNA secondary structures
• Posets and spaces of \(k\)-noncrossing RNA structures
• Fatgraph models of RNA structure
• Reidys' and Stadler's metrics for RNA contact structures
• Convex polytopes and enumeration
• Local connectivity of neutral networks
• RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
• Shapes of topological RNA structures
• Enumeration of chord diagrams on many intervals and their non-orientable analogs
• Asymptotic enumeration of RNA structures with pseudoknots

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