Abstract
Reaction systems are an abstract model of interactions among biochemical reactions, developed around two opposite mechanisms: facilitation and inhibition. The evolution of a Reaction System is driven by the external objects which are sent into the system by the environment at each step. In this paper, we propose the Reaction Algebra, a calculus resembling reaction systems extended with a restriction operator. Restriction increases the expressiveness of the calculus by allowing the modeling of hidden entities, such as those contained in membranes.
We define a compositional semantics and a behavioral equivalence for the Reaction Algebra, in order to enable the modular description of biological systems.
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Pardini, G., Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S. (2013). A Compositional Semantics of Reaction Systems with Restriction. In: Bonizzoni, P., Brattka, V., Löwe, B. (eds) The Nature of Computation. Logic, Algorithms, Applications. CiE 2013. Lecture Notes in Computer Science, vol 7921. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39053-1_39
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DOI: https://doi.org/10.1007/978-3-642-39053-1_39
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