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/

Recommendations

• Stochastic simulation of the kinetics of multiple interacting nucleic acid strands
• Unified approach to partition functions of RNA secondary structures
• scientific article; zbMATH DE number 4116367
• Combinatorial analysis of interacting RNA molecules
• Strand design for biomolecular computation.

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 (22)

• Enumeration approach to computing chemical equilibria
• 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
• Title not available (Why is that?)
• Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions
• 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
• 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
• Using temperature effects to predict the interactions between two RNAs
• Symmetric circular matchings and RNA folding
• Energy and structural analysis of double nucleic acid triplets
• A heuristic approach to RNA-RNA interaction prediction

This page was built for publication: Thermodynamic Analysis of Interacting Nucleic Acid Strands

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q3427770)