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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ehrenfeucht, A., Rozenberg, G.: Reaction Systems. Fundam. Inform. 75(1-4), 263–280 (2007)
Brijder, R., Ehrenfeucht, A., Main, M.G., Rozenberg, G.: A Tour of reaction Systems. Int. J. Found. Comput. Sci. 22(7), 1499–1517 (2011)
Păun, G.: Membrane Computing: An Introduction. Natural Computing Series. Springer, GmbH (2002)
Ehrenfeucht, A., Rozenberg, G.: Introducing time in reaction systems. Theor. Comput. Sci. 410(4-5), 310–322 (2009)
Brijder, R., Ehrenfeucht, A., Rozenberg, G.: Reaction Systems with Duration. In: Kelemen, J., Kelemenová, A. (eds.) Pǎun Festschrift. LNCS, vol. 6610, pp. 191–202. Springer, Heidelberg (2011)
Ehrenfeucht, A., Rozenberg, G.: Events and modules in reaction systems. Theor. Comput. Sci. 376(1-2), 3–16 (2007)
Ehrenfeucht, A., Main, M.G., Rozenberg, G.: Functions Defined by Reaction Systems. Int. J. Found. Comput. Sci. 22(1), 167–178 (2011)
Brijder, R., Ehrenfeucht, A., Rozenberg, G.: Representing reaction systems by trees. In: Dinneen, M.J., Khoussainov, B., Nies, A. (eds.) WTCS 2012 (Calude Festschrift). LNCS, vol. 7160, pp. 330–342. Springer, Heidelberg (2012)
Ehrenfeucht, A., Main, M.G., Rozenberg, G., Brown, A.T.: Stability and Chaos in reaction Systems. Int. J. Found. Comput. Sci. 23(5), 1173–1184 (2012)
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S.: Compositional semantics and behavioral equivalences for P Systems. Theor. Comput. Sci. 395(1), 77–100 (2008)
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S.: Compositional semantics of spiking neural P systems. J. Log. Algebr. Program. 79(6), 304–316 (2010)
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S.: An Overview on Operational Semantics in Membrane Computing. Int. J. Found. Comput. Sci. 22(1), 119–131 (2011)
Barbuti, R., Maggiolo-Schettini, A., Milazzo, P., Tini, S.: A P Systems Flat Form Preserving Step-by-step Behaviour. Fundam. Inform. 87(1), 1–34 (2008)
van Glabbeek, R.: The Linear Time–Branching Time Spectrum I; The Semantics of Concrete, Sequential Processes. In: Handbook of Process Algebra, pp. 3–99. Elsevier (2001)
Pǎun, G., Pérez-Jiménez, M.J.: Towards bridging two cell-inspired models: P systems and R systems. Theor. Comput. Sci. 429(0), 258–264 (2012)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
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
Download citation
DOI: https://doi.org/10.1007/978-3-642-39053-1_39
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-39052-4
Online ISBN: 978-3-642-39053-1
eBook Packages: Computer ScienceComputer Science (R0)