Processes of membrane systems with promoters and inhibitors

  • Authors:

  • Jetty Kleijn;Maciej Koutny

  • Affiliations:

  • LIACS, Leiden University, P.O.Box 9512, NL-2300 RA Leiden, The Netherlands;School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2008

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Abstract

Membrane systems (with promoters and inhibitors) are a computational model inspired by the way living cells are divided by membranes into compartments where chemical reactions may take place. We consider synchrony and asynchrony between executed reactions in the computations of such systems using Petri nets and their processes as a formal behavioural model. We first discuss different definitions of individual computational steps, and show how they can be rendered within the Petri net domain by assigning all transitions localities corresponding to the compartments, and using activator and inhibitor arcs. The non-sequential semantics of the resulting nets is formalised through processes based on occurrence nets augmented with additional information about localities and activator/inhibitor arcs. Such processes provide a convenient tool for analysing synchrony and asynchrony in the executions of membrane systems and shed light on the causal relationships between the reactions taking place.