Facilitation in reaction systems

Journal of Membrane Computing, vol. 2, pp. 149–161

Abstract

Abstract Reaction systems is a formal model of computation which originated as a model of interactions between biochemical reactions in the living cell. These interactions are based on two mechanisms, facilitation and inhibition, and this is well reflected in the formulation of reaction systems. In this paper, we investigate the facilitation aspect of reaction systems, where the products of a reaction may facilitate other reactions by providing some of their reactants. This aspect is formalized through positive dependency graphs which depict explicitly such facilitating interactions. The focus of the paper is on demonstrating how structural properties of reaction systems defined through the properties of their positive dependency graphs influence the behavioural properties of (suitable subclasses of) reaction systems, which, as usual, are defined through their transition graphs.

Authors 3

1. Luca Manzoni corresponding

   University of Trieste

   Affiliation as printed

   Dipartimento di Matematica e Geoscienze, Università degli Studi di Trieste, Via Valerio 12/1, 34127, Trieste, Italy

2. Antonio E. Porreca
   Affiliation as printed

   Université publique, Marseille, France

3. Grzegorz Rozenberg Aachen Leiden Institute of Advanced Computer Science

   Leiden University · University of Colorado Boulder

   Affiliation as printed

   Department of Computer Science, University of Colorado, Boulder, CO, 80309-0347, USA

   Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333 CA, Leiden, The Netherlands