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Model checking temporal properties of reaction systems

Artur Męski, Wojciech Penczek, Grzegorz Rozenberg: Model checking temporal properties of reaction systems. Information Sciences 313: 22-42 (2015)

Abstract. This paper defines a temporal logic for reaction systems (rsCTL). The logic is interpreted over the models for the context restricted reaction systems that generalise standard reaction systems by controlling context sequences. Moreover, a translation from the context restricted reaction systems into boolean functions is defined in order to be used for a symbolic model checking for rsCTL over these systems. The model checking for rsCTL is proved to be pspace-complete. The proposed approach to model checking was implemented and experimentally evaluated using four benchmarks.

Towards Quantitative Verification of Reaction Systems

Artur Męski, Maciej Koutny, Wojciech Penczek: Towards Quantitative Verification of Reaction Systems. UCNC 2016: 142-154

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.