MP Systems Approaches to Biochemical Dynamics: Biological Rhythms and Oscillations

  • Vincenzo Manca
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4361)


Metabolic P systems are a special class of P systems which seem to be adequate for expressing biological phenomena related to metabolism and signaling transduction in biological systems. We give the basic motivation for their introduction and some ideas about their applicability to some basic biological oscillators.


Microbial Fuel Cell Input Gate Cdc2 Kinase Output Gate Membrane Computing 
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.


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  1. 1.
    Alberts, B., Raff, M.: Essential Cell Biology. An Introduction to the Molecular Biology of the Cell. Garland Science, New York (1997)Google Scholar
  2. 2.
    Bernardini, F., Gheorghe, M.: Cell communication in tissue P systems: universality results. Soft Computing 9(9), 640–649 (2005)MATHCrossRefGoogle Scholar
  3. 3.
    Bernardini, F., Manca, V.: P systems with boundary rules. In: Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 107–118. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  4. 4.
    Besozzi, D., Ciobanu, G.: A P system description of the sodium-potassium pump. In: Mauri, G., Păun, G., Jesús Pérez-Jímenez, M., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 210–223. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  5. 5.
    Bianco, L.: Membrane Models of Biological Systems, PhD Thesis, University of Verona (in preparation)Google Scholar
  6. 6.
    Bianco, L., Fontana, F., Franco, G., Manca, V.: P systems for biological dynamics. In: [9], pp. 81–126 (2006)Google Scholar
  7. 7.
    Bianco, L., Fontana, F., Manca, V.: Reaction-driven membrane systems. In: Wang, L., Chen, K., Ong, Y.-S. (eds.) ICNC 2005. LNCS, vol. 3611, pp. 1155–1158. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  8. 8.
    Bianco, L., Fontana, F., Manca, V.: P systems with reaction maps. International Journal of Foundations of Computer Science 17(1), 27–48 (2006)MATHCrossRefMathSciNetGoogle Scholar
  9. 9.
    Ciobanu, G., Pău, G., Pérez-Jiménez, M.J. (eds.): Applications of Membrane Computing. Springer, Berlin (2006)Google Scholar
  10. 10.
    Clark, B.L.: Stability of complex reaction networks. Adv. Chem. Phys. 43, 1–216 (1983)CrossRefGoogle Scholar
  11. 11.
    Fell, D.A.: Metabolic control analysis: a survey of its theoretical and experimental development. Biochemistry J. 286, 313–330 (1992)Google Scholar
  12. 12.
    Fontana, F., Bianco, L., Manca, V.: P systems and the modeling 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
  13. 13.
    Fontana, F., Manca, V.: Predator-prey dynamics in P systems ruled by metabolic algorithm (submitted)Google Scholar
  14. 14.
    Fontana, F., Manca, V.: Discrete solutions of differential equations by metabolic P systems. Theoretical Computer Science (to appear)Google Scholar
  15. 15.
    Franco, G., Manca, V.: A membrane system for the leukocyte selective recruitment. In: Martín-Vide, C., Mauri, G., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2003. LNCS, vol. 2933, pp. 181–190. Springer, Heidelberg (2004)CrossRefGoogle Scholar
  16. 16.
    Freund, R.: Energy-controlled P systems. In: Păun, G., Rozenberg, G., Salomaa, A., Zandron, C. (eds.) WMC 2002. LNCS, vol. 2597, pp. 247–260. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  17. 17.
    Goldbeter, A.: A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. PNAS 88(20), 9107–9111 (1991)CrossRefGoogle Scholar
  18. 18.
    Goldbeter, A.: Computational approaches to cellular rhythms. Nature 420, 238–245 (2002)CrossRefGoogle Scholar
  19. 19.
    Goldbeter, A.: Biochemical Oscillations and Cellular Rhythms. Cambridge University Press, New York (2004)Google Scholar
  20. 20.
    Kitano, H.: Computational systems biology. Nature 420, 206–210 (2002)CrossRefGoogle Scholar
  21. 21.
    Leloup, J.C., Goldbeter, A.: A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. Journal of Biological Rhythms 13, 70–87 (1998)CrossRefGoogle Scholar
  22. 22.
    Maeda, M., Lu, S., Shaulsky, G., Miyazaki, Y., Kuwayama, H., Tanaka, Y., Kuspa, A., Loomis, W.: Periodic signaling controlled by an oscillatory circuit that includes protein Kinases ERK2 and PK. Science 304, 304–875 (2004)CrossRefGoogle Scholar
  23. 23.
    Manca, V.: Rewriting and metabolism: A logical perspective. In: Păun, G. (ed.) Computing with Bio-Molecules. Springer, Heidelberg (1998)Google Scholar
  24. 24.
    Manca, V., Martino, D.M.: From string rewriting to logical metabolic systems. In: Păun, G., Salomaa, A. (eds.) Grammatical Models of Multi-Agent Systems. Gordon and Breach Science Publishers (1999)Google Scholar
  25. 25.
    Manca, V., Bianco, L., Fontana, F.: Evolution and oscillation in P systems: Applications to biological phenomena. In: Mauri, G., Păun, G., Jesús Pérez-Jímenez, M., Rozenberg, G., Salomaa, A. (eds.) WMC 2004. LNCS, vol. 3365, pp. 63–84. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  26. 26.
    Manca, V., Franco, G., Scollo, G.: State transition dynamics: basic concepts and molecular computing perspectives. In: Gheorghe, M. (ed.) Molecular Computational Models: Unconventional Approachers, Ch. 2, pp. 32–55. Idea Group Inc., UK (2005)Google Scholar
  27. 27.
    Manca, V.: Topics and problems in metabolic P systems. In: Păun, G., Pérez-Jiménez, M.J. (eds.) Proc. of the Fourth Brainstorming Week on Membrane Computing (BWMC4), Sevilla, Spain, Fenix Editora (2006)Google Scholar
  28. 28.
    Manca, V., Bianco, L.: Biological networks in metabolic P systems (submitted)Google Scholar
  29. 29.
    Martin-Vide, C., Păun, G., Rozenberg, G.: Membrane systems with carriers. Theoretical Computer Science 270, 779–796 (2002)MATHCrossRefMathSciNetGoogle Scholar
  30. 30.
    Păun, A., Păun, G.: The power of communication: P systems with symport/antiport. New Generation Computing 20(3), 295–306 (2002)MATHCrossRefGoogle Scholar
  31. 31.
    Păun, G.: Computing with membranes. J. Comput. System Sci. 61(1), 108–143 (2000)MATHCrossRefMathSciNetGoogle Scholar
  32. 32.
    Păun, G.: Membrane Computing. An Introduction. Springer, Berlin (2002)MATHGoogle Scholar
  33. 33.
    Păun, G., Suzuki, Y., Tanaka, H.: P systems with energy accounting. Int. J. Computer Math. 78(3), 343–364 (2001)MATHGoogle Scholar
  34. 34.
    Suzuki, Y., Fujiwara, Y., Takabayashi, J., Tanaka, H.: Artificial life applications of a class of P systems: Abstract rewriting systems on multisets. In: Calude, C.S., Pun, G., Rozenberg, G., Salomaa, A. (eds.) Multiset Processing. LNCS, vol. 2235, pp. 299–346. Springer, Heidelberg (2001)CrossRefGoogle Scholar
  35. 35.
    Suzuki, Y., Tanaka, H.: A symbolic chemical system based on an abstract rewriting system and its behavior pattern. J. of Artificial Life and Robotics 6, 129–132 (2002)CrossRefGoogle Scholar
  36. 36.
    Suzuki, Y., Tanaka, H.: Modelling p53 signaling pathways by using multiset processing. In: Ciobanu, G., Pérez-Jiménez, M.J., Păun, G. (eds.) Applications of Membrane Computing, pp. 203–214. Springer, Berlin (2006)Google Scholar
  37. 37.
    Segel, L.A., Cohen, I.R. (eds.): Design Principles for the Immune System and Other Distributed Autonomous Systems. Oxford University Press, Oxford (2000)Google Scholar
  38. 38.
    Voit, E.O.: Computational Analysis of Biochemical Systems. Cambridge University Press, Cambridge (2000)Google Scholar
  39. 39.
    The P Systems Web Page,

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© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Vincenzo Manca
    • 1
  1. 1.Department of Computer ScienceUniversity of VeronaVeronaItaly

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