Advertisement

Membrane Computing as a Modeling Framework. Cellular Systems Case Studies

  • Gheorghe Păun
  • Francisco José Romero-Campero
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5016)

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.

Keywords

Model Check Cellular System Membrane Computing Invite Paper Gillespie Algorithm 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    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)Google Scholar
  2. 2.
    Ardelean, I.I., Cavaliere, M.: Modelling biological processes by using a probabilistic P system software. Natural Computing 2(2), 173–197 (2003)zbMATHCrossRefGoogle Scholar
  3. 3.
    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)Google Scholar
  4. 4.
    Bianco, L., Fontana, F., Manca, V.: P systems with reaction maps. International Journal of Foundations of Computer Science 17(1), 27–48 (2006)zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    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)Google Scholar
  6. 6.
    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)CrossRefMathSciNetGoogle Scholar
  7. 7.
    Ciobanu, G., Pan, L., Păun, G.: P systems with minimal parallelism. Theoretical Computer Science 378(1), 117–130 (2007)zbMATHCrossRefMathSciNetGoogle Scholar
  8. 8.
    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)CrossRefGoogle Scholar
  9. 9.
    Fontana, F., Manca, V.: Discrete solutions to differential equations by metabolic P systems. Theoretical Computer Science 372(2-3), 165–182 (2007)zbMATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    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)zbMATHCrossRefMathSciNetGoogle Scholar
  11. 11.
    Gillespie, D.T.: Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35–55 (2007)CrossRefGoogle Scholar
  12. 12.
    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)CrossRefGoogle Scholar
  13. 13.
    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)zbMATHCrossRefMathSciNetGoogle Scholar
  14. 14.
    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)CrossRefGoogle Scholar
  15. 15.
    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)Google Scholar
  16. 16.
    Milner, R.: Communication and Mobile Systems: The π-calculus. Cambridge University Press, Cambridge (1999)Google Scholar
  17. 17.
    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)Google Scholar
  18. 18.
    Pescini, D., Besozzi, D., Mauri, G., Zandron, C.: Dynamical probabilistic p systems. International Journal of Foundations of Computer Science 17(1), 183–195 (2006)zbMATHCrossRefMathSciNetGoogle Scholar
  19. 19.
    Ptashne, M., Gann, A.: Genes and Signals. Cold Spring Harbor Laboratory Press (2002)Google Scholar
  20. 20.
    Reddy, V., Liebman, M., Maverovouniotis, M.: Qualitative analysis of biochemical reaction systems. Computers in Biology and Medicine 26(1), 9–24 (1996)CrossRefGoogle Scholar
  21. 21.
    Regev, A., Panina, E., Silvermann, W., Cardelli, L., Shapiro, E.: Bioambients: an abstraction for biological compartments. Theoretical Computer Science 325, 141–167 (2004)zbMATHCrossRefMathSciNetGoogle Scholar
  22. 22.
    Regev, A., Shapiro, E.: The π-calculus as an abstraction for biomolecular systems. In: Modelling in Molecular Biology, pp. 1–50. Springer, Berlin (2004)Google Scholar
  23. 23.
    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)CrossRefGoogle Scholar
  24. 24.
    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)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Gheorghe Păun
    • 1
  • Francisco José Romero-Campero
    • 2
  1. 1.Institute of Mathematics of the Romanian AcademyBucureştiRomania
  2. 2.Automated Scheduling, Optimisation and Planning Research Group School of Computer Science and Information TechnologyUniversity of NottinghamNottinghamUK

Personalised recommendations