Thermodynamic Analysis of Interacting Nucleic Acid Strands

DOI10.1137/060651100zbMATH Open1112.82002OpenAlexW2053783019WikidataQ54152612 ScholiaQ54152612MaRDI QIDQ3427770FDOQ3427770

Authors Robert M. Dirks, Justin S. Bois, J. Schäeffer, Erik Winfree, Niles A. Pierce

Publication date 27 March 2007

Published in SIAM Review (Search for Journal in Brave)

Full work available at URL https://authors.library.caltech.edu/7706/

zbMATH Keywords

symmetrydynamic programmingconvexityDNAequilibriumpartition functionredundancyRNAsecondary structuredilute solutionbase pairmultiple strandsovercounting

Mathematics Subject Classification ID

Convex programming (90C25) Optimality conditions and duality in mathematical programming (90C46) Dynamic programming (90C39) Exact enumeration problems, generating functions (05A15) Classical equilibrium statistical mechanics (general) (82B05) Molecular structure (graph-theoretic methods, methods of differential topology, etc.) (92E10) Chemistry (general) in thermodynamics and heat transfer (80A50)

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Cited in

(22)

• Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
• Characterization of alpha helices interacting with nucleic acids
• Enumeration approach to computing chemical equilibria
• Strand algebras for DNA computing
• Intramolecular interactions in aminoacyl cyclic-3',5'-nucleotides
• Localized hybridization circuits
• A heuristic approach to RNA-RNA interaction prediction
• Energy and structural analysis of double nucleic acid triplets
• On the local form and transitions of pre-symmetry sets
• The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics
• scientific article; zbMATH DE number 1342094 (Why is no real title available?)
• DNA Computing
• Using temperature effects to predict the interactions between two RNAs
• Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts.
• Stochastic simulation of the kinetics of multiple interacting nucleic acid strands
• Predicting RNA secondary structures with pseudoknots by MCMC sampling
• Symmetric circular matchings and RNA folding
• Computing with chemical reaction networks: a tutorial
• Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions
• Computing properties of thermodynamic binding networks: an integer programming approach
• Predicting minimum free energy structures of multi-stranded nucleic acid complexes is APX-hard
• Combinatorial analysis of interacting RNA molecules

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