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Towards Quantitative Verification of Reaction Systems

  • Artur Męski
  • Maciej Koutny
  • Wojciech Penczek
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9726)

Abstract

Reaction systems are a formal model for computational processes inspired by the functioning of the living cell. The key feature of this model is that its behaviour is determined by the interactions of biochemical reactions of the living cell, and these interactions are based on the mechanisms of facilitation and inhibition. The formal treatment of reaction systems is qualitative as there is no direct representation of the number of molecules involved in biochemical reactions.

This paper introduces reaction systems with discrete concentrations which are an extension of reaction systems allowing for quantitative modelling. We demonstrate that although reaction systems with discrete concentrations are semantically equivalent to the original qualitative reaction systems, they provide much more succinct representations in terms of the number of molecules being used. We then define the problem of reachability for reaction systems with discrete concentrations, and provide its suitable encoding in smt, together with a verification method (bounded model checking) for reachability properties. Experimental results show that verifying reaction systems with discrete concentrations instead of the corresponding reaction systems is more efficient.

Notes

Acknowledgements

The study is cofounded by the European Union from resources of the European Social Fund. Project PO KL “Information technologies: Research and their interdisciplinary applications”, Agreement UDA-POKL.04.01.01-00-051/10-00.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Artur Męski
    • 1
  • Maciej Koutny
    • 2
  • Wojciech Penczek
    • 1
    • 3
  1. 1.Institute of Computer Science, PASWarsawPoland
  2. 2.School of Computing ScienceNewcastle UniversityNewcastle upon TyneUK
  3. 3.University of Natural Sciences and Humanities, ICSSiedlcePoland

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