A strand graph semantics for DNA-based computation

DOI10.1016/J.TCS.2015.07.041MaRDI QIDQ288814zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Rasmus L. Petersen, Matthew R. Lakin, Andrew Phillips

Publication date 27 May 2016

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2015.07.041

zbMATH Keywords

DNA computingprogramming languagemolecular programmingbiological computationprocess calculussite graphstrand graph

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20) Modes of computation (nondeterministic, parallel, interactive, probabilistic, etc.) (68Q10) Semantics in the theory of computing (68Q55) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

Recommendations

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• Unconventional Computation

Cites work

• scientific article; zbMATH DE number 1296290 (Why is no real title available?)
• scientific article; zbMATH DE number 1738644 (Why is no real title available?)
• A Grammatical Approach to Self-Organizing Robotic Systems
• A calculus of mobile processes. I
• Abstract Interpretation of Cellular Signalling Networks
• Abstract modelling of tethered DNA circuits
• Efficient Turing-universal computation with DNA polymers
• Formal molecular biology
• Functional analysis of large-scale DNA strand displacement circuits
• Localized hybridization circuits
• Modelling, simulating and verifying Turing-powerful strand displacement systems
• Parallel and scalable computation and spatial dynamics with DNA-based chemical reaction networks on a surface
• Stochastic simulation of multiple process calculi for biology

Cited in

(4)

• Stochastic simulation of the kinetics of multiple interacting nucleic acid strands
• Implementation of Turing machine using DNA strand displacement
• Automated analysis of tethered DNA nanostructures using constraint solving
• Edge-outer graph embedding and the complexity of the DNA reporter strand problem

Describes a project that uses

Uses Software

• Visual DSD
• PRISM

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