Abstract
This paper presents a general framework for modelling with membrane systems that is based on a computational paradigm where rules have associated a finite set of attributes and a corresponding function. Attributes and functions are meant to provide those extra features that allow to define different strategies to run a P system. Such a strategy relying on a bounded parallelism is presented using an operational approach and applying it for a case study presenting the basic model of quorum sensing for Vibrio fischeri bacteria.
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References
Bernardini, F., Gheorghe, M.: Population P Systems. J. UCS 10(5), 509–539 (2004)
Bianco, L., Fontana, F., Manca, V.: P Systems with Reaction Maps. International Journal of Foundations of Computer Science 17(1), 27–48 (2006)
Calder, M., Vyshemirsky, V., Gilbert, D., Orton, R.: Analysis of Signalling Pathways using Continuous Time Markov Chains. Transactions on Computational Systems Biology (to appear, 2006)
Cardelli, L., Philips, A.: A Correct Abstract Machine for the Stochastic Pi-calculus. Electronical Notes in Theoretical Computer Science (to appear, 2004)
Andrei, O., Ciobanu, G., Lucanu, D.: Structural Operational Semantics of P Systems. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 31–48. Springer, Heidelberg (2006)
Collado-Vides, J.: Grammatical Models of the Regulation of Gene Expression. Proc. of National Academy of Science 89, 9405–9409 (1992)
Dang, Z., Ibarra, O.H., Li, C., Gaoyan, X.: Decidability of Model-Checking P Systems. Journal of Automata, Languages and Combinatorics (to appear, 2006)
Dang, Z., Ibarra, O.H.: On One-membrane P systems Operating in Sequential Mode. Int. J. Found. Comput. Sci. 16(5), 867–881 (2005)
Duan, Z., Holcombe, M., Bell, A.: A Logic for Biological System. Biosystems 53, 93–155 (2000)
Freund, R.: Asynchronous P Systems and P Systems Working in the Sequential Mode. In: Mauri, G., Păun, G., Jesús Pérez-Jímenez, M., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 36–62. Springer, Heidelberg (2005)
Gillespie, D.T.: A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions. J. Comput. Physics 22, 403–434 (1976)
Gillespie, D.T.: Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry 81(25), 2340–2361 (1977)
Hardie, K.R., Williams, P., Winzer, K.: Bacterial cell-to-cell communication: sorry, can’t talk now, gone to lunch. Current Opinion in Microbiology 5, 216–222 (2002)
Fargerströn, T., James, G., James, S., Kjelleberg, S., Nilsson, P.: Luminescence Control in the Marine Bacterium Vibrio fischeri: An Analysis of the Dynamics of lux Regulation. J. Mol. Biol. 296, 1127–1137 (2000)
Kam, N., Cohen, I.R., Harel, D.: The Immune System as a Reactive Systems: Modelling T Cell Activation with Statecharts, The Weizmann Institute of Science, Israel (2001)
Matsuno, H., Doi, A., Nagasaki, M., Miyano, S., Hybrid: Petri Net Representation of Gene Regulatory Network. In: Pacific Symposium on Biocompting, pp. 338–349. World Scientific, Singapore (2000)
Meng, T.C., Somani, S., Dhar, P.: Modelling and Simulation of Biological Systems with Stochasticity. Silico Biology 4(0024), 137–158 (2004)
Nealson, K.H., Hastings, J.W.: Bacterial Bioluminescence: Its Control and Ecological Significance. Microbiology Review 43, 496–518 (1979)
Păun, G.: Computing with Membranes. Journal of Computer and System Sciences 61(1), 108–143 (2000)
Păun, G.: Membrane Computing. An Introduction. Springer, Berlin (2002)
Jesús Pérez-Jímenez, M., Romero-Campero, F.J.: P Systems, a New Computational Modelling Tool for Systems Biology. In: Priami, C., Plotkin, G. (eds.) Transactions on Computational Systems Biology VI. LNCS (LNBI), vol. 4220, pp. 176–197. Springer, Heidelberg (2006)
Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic P systems. International Journal of Foundations of Computer Science 17(1), 183–195 (2006)
Priami, C., Regev, A., Shapiro, E., Silverman, W.: Application of a Stochastic Name-Passing Calculus to Representation and Simulation of Molecular Processes. Information Processing Letters 80, 25–31 (2001)
Regev, A., Shapiro, E.: The π-calculus as an abstraction for biomolecular systems. In: Ciobanu, G., Rozenberg, G. (eds.) Modelling in Molecular Biology, pp. 219–266. Springer, Heidelberg (2004)
Segel, I.H.: Biochemical Calculations: How to Solve Mathematical Problems in General Biochemistry, 2nd edn. John Wiley and Sons, Chichester (1976)
Till, J.E., McCulloch, F., Siminovitch, L.: A Stochastic Model of Stem Cell Proliferation based on the Growth of Spleen Colony-Forming Cells. Proc. National Academy of Science USA 51, 117–128 (1964)
Walker, D., Holcombe, M., Southgate, J., McNeil, S., Smalwood, R.: The Epitheliome: Agent-Based Modelling of The Social Behaviour of Cells. Biosystems 76(1-3), 89–100 (2004)
Waters, C.M., Bassler, B.L.: Quorum Sensing: Cell-to-Cell Communication in Bacteria. Annu. Rev. Cell. Dev. Biol. 21, 319–346 (2005)
The P Systems: http://psystems.disco.unimib.it
Nottingham Quorum Sensing Web Site, http://www.nottingham.ac.uk/quorum/
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Bernardini, F., Romero-Campero, F.J., Gheorghe, M., Pérez-Jiménez, M.J. (2006). A Modeling Approach Based on P Systems with Bounded Parallelism. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds) Membrane Computing. WMC 2006. Lecture Notes in Computer Science, vol 4361. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11963516_4
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DOI: https://doi.org/10.1007/11963516_4
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