Verifying chemical reaction network implementations: a bisimulation approach

DOI10.1016/J.TCS.2018.01.002MaRDI QIDQ2422008zbMATH OpenOpenAlexFDO

Authors Robert F. Johnson, Qing Dong, Erik Winfree

Publication date 18 June 2019

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

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.1016/j.tcs.2018.01.002

zbMATH Keywords

bisimulationchemical reaction networkscomplexity theoryformal verification

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)

Recommendations

• Verifying chemical reaction network implementations: a bisimulation approach
• Verifying polymer reaction networks using bisimulation
• Verifying chemical reaction network implementations: a pathway decomposition approach
• Modular verification of chemical reaction network encodings via serializability analysis
• Forward and backward bisimulations for chemical reaction networks

Cites work

• A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities
• A simple population protocol for fast robust approximate majority
• Advances in artificial life. Third European conference on artificial life, Granada, Spain, June 4-6, 1995. Proceedings
• An efficient incremental algorithm for solving systems of linear diophantine equations
• An implementation of an efficient algorithm for bisimulation equivalence
• Comparing Chemical Reaction Networks
• Complexity of some problems in Petri nets
• Computation with finite stochastic chemical reaction networks
• Deterministic function computation with chemical reaction networks
• Efficient syntax-driven lumping of differential equations
• Efficient Turing-universal computation with DNA polymers
• Forward and backward bisimulations for chemical reaction networks
• scientific article; zbMATH DE number 42752 (Why is no real title available?)
• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• Leaderless deterministic chemical reaction networks
• Minimal solutions of linear diophantine systems : bounds and algorithms
• Modular verification of chemical reaction network encodings via serializability analysis
• Rate-independent computation in continuous chemical reaction networks
• Relationships between nondeterministic and deterministic tape complexities
• Space and energy efficient computation with DNA strand displacement systems
• Stably computable predicates are semilinear
• Syntactic Markovian bisimulation for chemical reaction networks
• Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice
• The covering and boundedness problems for vector addition systems
• Two-domain DNA strand displacement
• Undecidability of bisimilarity for Petri nets and some related problems
• Verifying chemical reaction network implementations: a bisimulation approach

Cited in

(14)

• A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities
• Verifying polymer reaction networks using bisimulation
• Comparing chemical reaction networks: a categorical and algorithmic perspective
• Verifying chemical reaction network implementations: a pathway decomposition approach
• Runtime verification for biochemical programs
• Verifying chemical reaction network implementations: a bisimulation approach
• Modular verification of chemical reaction network encodings via serializability analysis
• Space and energy efficient computation with DNA strand displacement systems
• Syntactic Markovian bisimulation for chemical reaction networks
• Forward and backward bisimulations for chemical reaction networks
• Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks
• Population-induced phase transitions and the verification of chemical reaction networks
• Polynomial equivalence of extended chemical reaction models
• Testing binomiality of chemical reaction networks using comprehensive Gröbner systems

Describes a project that uses

Uses Software

• ERODE
• Visual DSD

This page was built for publication: Verifying chemical reaction network implementations: a bisimulation approach

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2422008)