Immersing reaction system specifications in evaluating environments

Abstract

<p>We propose an extension to the framework of reaction systems such that the environment not only plays the role of contributing entities to the successor state, but also influences the actual generation of products. In particular, we consider that an environment can assign <em>valences</em> to entities, be they used as reactants or inhibitors in a reaction, as well as <em>select</em> the entities which can appear in the successor state as product of a reaction. This provides a framework for <em>immersing</em> reaction system specifications into different contexts. We also derive a notion of <em>polarised reaction systems</em>, where entities can appear only as reactants or inhibitors in any given reaction. We compare the expressive power of the models, also showing some equivalences between them, and test them on three case studies derived from physiology, ecology, and chemistry.<br></p>