Stochastic simulation of the kinetics of multiple interacting nucleic acid strands

DOI10.1007/978-3-319-21999-8_13MaRDI QIDQ2948418zbMATH OpenOpenAlexFDO

Authors J. Schäeffer, Chris Thachuk, Erik Winfree

Publication date 30 September 2015

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://thesis.library.caltech.edu/7460/1/JosephSchaeffer_PhD_Thesis_Complete.pdf

Mathematics Subject Classification ID

Applications of continuous-time Markov processes on discrete state spaces (60J28) Protein sequences, DNA sequences (92D20) Data structures (68P05)

Recommendations

• Thermodynamic Analysis of Interacting Nucleic Acid Strands
• A strand graph semantics for DNA-based computation
• DNA Computing
• A Framework for Modeling DNA Based Molecular Systems
• Unconventional Computation

Cites work

• Equation of state calculations by fast computing machines
• Handbook of statistical systems biology.
• Thermodynamic Analysis of Interacting Nucleic Acid Strands

Cited in

(9)

• A Framework for Modeling DNA Based Molecular Systems
• The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics
• Verifying chemical reaction network implementations: a pathway decomposition approach
• Abstract modelling of tethered DNA circuits
• Thermodynamic Analysis of Interacting Nucleic Acid Strands
• Pseudo-Marginal Inference for CTMCs on Infinite Spaces via Monotonic Likelihood Approximations
• Inferring parameters for an elementary step model of DNA structure kinetics with locally context-dependent Arrhenius rates
• Numerical simulation of biological base pairs considering geometric and energetic criteria
• Design of nucleic acid strands with long low-barrier folding pathways

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