Abstract
Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of the living cell, and from the way cells cooperate in tissues, organs, or other populations of cells. This research area developed very fast, both at the theoretical level and in what concerns the applications. After a very short description of the domain, we mention here the main areas where membrane computing was used as a framework for devising models (biology and bio-medicine, linguistics, economics, computer science, etc.), then we discuss in a certain detail the possibility of using membrane computing as a high level computational modeling framework for addressing structural and dynamical aspects of cellular systems. We close with a comprehensive bibliography of membrane computing applications.
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References
Andrei, O., Ciobanu, G., Lucanu, D.: Executable specification of P systems. In: Mauri, G., et al. (eds.) WMC 2004. LNCS, vol. 3365, pp. 126–145. Springer, Heidelberg (2005)
Ardelean, I.I., Cavaliere, M.: Modelling biological processes by using a probabilistic P system software. Natural Computing 2(2), 173–197 (2003)
Besozzi, D., Ciobanu, G.: A P systems description of the sodium-potassium pump. In: Mauri, G., et al. (eds.) WMC 2004. LNCS, vol. 3365, pp. 210–223. Springer, Heidelberg (2005)
Bianco, L., Fontana, F., Manca, V.: P systems with reaction maps. International Journal of Foundations of Computer Science 17(1), 27–48 (2006)
Cardelli, L.: Brane calculi: Interactions of biological membranes. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol. 3082, pp. 257–278. Springer, Heidelberg (2005)
Cheruku, S., Paun, A., Romero-Campero, F.J., Pérez-Jiménez, M.J., Ibarra, O.H.: Simulating fas-induced apoptosis by using P systems. Progress in Natural Science 17(4), 424–431 (2007)
Ciobanu, G., Pan, L., Păun, G.: P systems with minimal parallelism. Theoretical Computer Science 378(1), 117–130 (2007)
Fontana, F., Bianco, L., Manca, V.: P systems and the modelling of biochemical oscillations. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 199–208. Springer, Heidelberg (2006)
Fontana, F., Manca, V.: Discrete solutions to differential equations by metabolic P systems. Theoretical Computer Science 372(2-3), 165–182 (2007)
Freund, R.: P systems working in the sequential mode on arrays and strings. International Journal of Foundations of Computer Science 16(4), 663–682 (2005)
Gillespie, D.T.: Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35–55 (2007)
Goss, P.J., Peccoud, J.: Quantitative modelling of stochastic system in molecular biology by using stochastic petri nets. Proc. Natl. Acad. Sci. USA 95, 6750–6755 (1998)
Heath, J., Kwiatkowska, M.Z., Norman, G., Parker, D., Tymchyshyn, O.: Probabilistic model checking of complex biological pathways. Theoretical Computer Science 391(3), 239–257 (2008)
Kwiatkowska, M., Norman, G., Parker, D.: Stochastic model checking. In: Bernardo, M., Hillston, J. (eds.) SFM 2007. LNCS, vol. 4486, pp. 220–270. Springer, Heidelberg (2007)
Li, C., Dang, Z., Ibarra, O.H., Yen, H.-C.: Signaling p systems and verification problems. In: Caires, L., Italiano, G.F., Monteiro, L., Palamidessi, C., Yung, M. (eds.) ICALP 2005. LNCS, vol. 3580, pp. 1462–1473. Springer, Heidelberg (2005)
Milner, R.: Communication and Mobile Systems: The π-calculus. Cambridge University Press, Cambridge (1999)
Pérez-Jiménez, M.J., Romero-Campero, F.J.: P systems, a new computational modelling tool for systems biology. In: Transactions on Computational Systems Biology VI, pp. 176–197 (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)
Ptashne, M., Gann, A.: Genes and Signals. Cold Spring Harbor Laboratory Press (2002)
Reddy, V., Liebman, M., Maverovouniotis, M.: Qualitative analysis of biochemical reaction systems. Computers in Biology and Medicine 26(1), 9–24 (1996)
Regev, A., Panina, E., Silvermann, W., Cardelli, L., Shapiro, E.: Bioambients: an abstraction for biological compartments. Theoretical Computer Science 325, 141–167 (2004)
Regev, A., Shapiro, E.: The π-calculus as an abstraction for biomolecular systems. In: Modelling in Molecular Biology, pp. 1–50. Springer, Berlin (2004)
Romero-Campero, F.J., Pérez-Jiménez, M.J.: A model of the quorum sensing system in vibrio fischeri using P systems. Artificial Life 14(1), 95–109 (2008)
Romero-Campero, F.J., Pérez-Jiménez, M.J.: Modelling gene expression control using P systems: The lac operon, a case study. BioSystems 91(3), 438–457 (2008)
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Păun, G., Romero-Campero, F.J. (2008). Membrane Computing as a Modeling Framework. Cellular Systems Case Studies. In: Bernardo, M., Degano, P., Zavattaro, G. (eds) Formal Methods for Computational Systems Biology. SFM 2008. Lecture Notes in Computer Science, vol 5016. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68894-5_6
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DOI: https://doi.org/10.1007/978-3-540-68894-5_6
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