Thermodynamic Analysis of Interacting Nucleic Acid Strands

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

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

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)

Cited In (18)

• Enumeration approach to computing chemical equilibria
• Predicting RNA secondary structures with pseudoknots by MCMC sampling
• Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts.
• Combinatorial analysis of interacting RNA molecules
• Strand algebras for DNA computing
• Title not available (Why is that?)
• Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands
• Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
• Characterization of alpha helices interacting with nucleic acids
• The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics
• Gibbs/MCMC Sampling for Multiple RNA Interaction with Sub-optimal Solutions
• 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
• Using temperature effects to predict the interactions between two RNAs
• Symmetric circular matchings and RNA folding
• Localized Hybridization Circuits
• A heuristic approach to RNA-RNA interaction prediction

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