Verifying chemical reaction network implementations: a bisimulation approach

DOI10.1007/978-3-319-43994-5_8MaRDI QIDQ2835707zbMATH OpenOpenAlexFDO

Authors Robert F. Johnson, Qing Dong, Erik Winfree

Publication date 30 November 2016

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

Full work available at URL https://resolver.caltech.edu/CaltechAUTHORS:20190617-104717955

Mathematics Subject Classification ID

Analysis of algorithms and problem complexity (68Q25) Specification and verification (program logics, model checking, etc.) (68Q60) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Biochemistry, molecular biology (92C40)

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Cites work

• A simple population protocol for fast robust approximate majority
• Efficient Turing-universal computation with DNA polymers
• scientific article; zbMATH DE number 42752 (Why is no real title available?)
• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• Modular verification of chemical reaction network encodings via serializability analysis
• Relationships between nondeterministic and deterministic tape complexities
• The covering and boundedness problems for vector addition systems
• Two-domain DNA strand displacement

Cited in

(11)

• A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities
• Verifying polymer reaction networks using bisimulation
• Verifying chemical reaction network implementations: a bisimulation approach
• Verifying chemical reaction network implementations: a pathway decomposition approach
• Runtime verification for biochemical programs
• Modular verification of chemical reaction network encodings via serializability analysis
• Syntactic Markovian bisimulation for chemical reaction networks
• Forward and backward bisimulations for chemical reaction networks
• Population-induced phase transitions and the verification of chemical reaction networks
• Computing with chemical reaction networks: a tutorial
• Testing binomiality of chemical reaction networks using comprehensive Gröbner systems

Describes a project that uses

Uses Software

• Visual DSD

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