Quantitative extensions of reaction systems based on SOS semantics

Abstract

Reaction systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reaction and are produced by reactions or provided by the environment. In this paper, we define two quantitative variants of RSs: the first one is along the time dimension, to specify delays for making available reactions products and durations to protract their permanency, while the second deals with the possibility to specify different concentration levels of a substance in order to enable or inhibit a reaction. Technically, both extensions are obtained by modifying in a modular way the Structural Operational Semantics (SOS) for RSs that was already defined in the literature. Our approach maintains several advantages of the original semantics definition that were: (1) providing a formal specification of the RS dynamics that enables the reuse of many formal analysis techniques and favours the implementation of tools, and (2) making the RS framework extensible, by adding or changing some of the SOS rules in a compositional way. We provide a prototype logic programming implementation and apply our tool to three different case studies: the tumour growth, the Th cell differentiation in the immune system and neural communication.