RNA folding and large N matrix theory

DOI10.1016/S0550-3213(01)00522-3MaRDI QIDQ5951465zbMATH OpenFDO

Authors Henri Orland, Anthony Zee

Publication date 6 January 2002

Published in Nuclear Physics B (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/cond-mat/0106359

zbMATH Keywords

1/N-square correctionsHartree recursion relationpartition function

Mathematics Subject Classification ID

Basic linear algebra (15A99) Biochemistry, molecular biology (92C40)

Abstract: We formulate the RNA folding problem as an $NimesN$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit $Noinfty$ yields the so-called secondary structure (Hartree theory). Tertiary structure and pseudo-knots are obtained by calculating the $1/N^2$ corrections to the partition function. We propose a generalization of the Hartree recursion relation to generate the tertiary structure.

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Cites work

• scientific article; zbMATH DE number 433099 (Why is no real title available?)
• Meanders and the Temperley-Lieb algebra
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• Planar diagrams
• Rapid dynamic programming algorithms for RNA secondary structure
• Renormalization and renormalization group: From the discovery of UV divergences to the concept of effective field theories
• Universal relation between Green functions in random matrix theory

Cited in

(29)

• A continuous analogue for RNA folding
• Structure combinatorics and thermodynamics of a matrix model with Penner interaction inspired by interacting RNA
• Narayana number, Chebyshev polynomial and Motzkin path on RNA abstract shapes
• 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
• A topological framework for signed permutations
• On a uniformly random chord diagram and its intersection graph
• Statistical mechanics of a simplified bipartite matching problem: An analytical treatment
• Generation of RNA pseudoknot structures with topological genus filtration
• Moduli spaces and macromolecules
• Algebraic dynamic programming for multiple context-free grammars
• Random matrix theory and ribonucleic acid (RNA) folding
• Topological language for RNA
• Topological classification and enumeration of RNA structures by genus
• Loop entropy assists tertiary order: loopy stabilization of stacking motifs
• Information generation and the loss of conformational entropy during RNA folding
• Unified approach to partition functions of RNA secondary structures
• Fatgraph models of RNA structure
• Large-N random matrices for RNA folding
• Random matrix theory and RNA folding
• Crossover ensembles of random matrices and skew-orthogonal polynomials
• The Dyck bound in the concave 1-dimensional random assignment model
• Time-convergent random matrices from mean-field pinned interacting eigenvalues
• Topology in soft and biological matter
• Shapes of topological RNA structures
• Enumeration of chord diagrams on many intervals and their non-orientable analogs

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