Thermodynamic Analysis of Interacting Nucleic Acid Strands

DOI10.1137/060651100zbMath1112.82002OpenAlexW2053783019WikidataQ54152612 ScholiaQ54152612MaRDI QIDQ3427770

Niles A. Pierce, Robert M. Dirks, Erik Winfree, Joseph M. Schaeffer, 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 programmingconvexitypartition functiondilute solutionequilibriumDNAredundancyRNAsecondary structurebase pairmultiple strandsovercounting

Mathematics Subject Classification ID

Convex programming (90C25) Exact enumeration problems, generating functions (05A15) Optimality conditions and duality in mathematical programming (90C46) Dynamic programming (90C39) 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)

Related Items (15)

Using temperature effects to predict the interactions between two RNAs ⋮ Enumeration approach to computing chemical equilibria ⋮ Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands ⋮ The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics ⋮ Computing with chemical reaction networks: a tutorial ⋮ Combinatorial analysis of interacting RNA molecules ⋮ Symmetric circular matchings and RNA folding ⋮ Predicting RNA secondary structures with pseudoknots by MCMC sampling ⋮ Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts. ⋮ Strand algebras for DNA computing ⋮ A heuristic approach to RNA-RNA interaction prediction ⋮ On the local form and transitions of pre-symmetry sets ⋮ Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges ⋮ Localized Hybridization Circuits ⋮ Gibbs/MCMC Sampling for Multiple RNA Interaction with Sub-optimal Solutions

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