Thermodynamic Analysis of Interacting Nucleic Acid Strands

DOI10.1137/060651100MaRDI QIDQ3427770zbMATH OpenOpenAlexWikidataFDO

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

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