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

Biochemistry, molecular biology (92C40) 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)

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Cites work

• scientific article; zbMATH DE number 42752 (Why is no real title available?)
• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• A simple population protocol for fast robust approximate majority
• Efficient Turing-universal computation with DNA polymers
• 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)

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

Describes a project that uses

Uses Software

• Visual DSD

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