Toward an MP Model of Non-Photochemical Quenching

  • Vincenzo Manca
  • Roberto Pagliarini
  • Simone Zorzan
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5391)


In this paper we apply the formalism of metabolic P systems for modeling an important phenomenon of photochemical organisms, which determines the plants accommodation to the environmental light. By using some experimental data of this phenomenon, we determine an MP system which discovers, in a specific simplified case, the regulation mechanism underling the non photochemical quenching phenomenon and reproduces, with a good approximation, the observed behavior of the natural system.


Light Harvest Complex Photochemical Quenching Chlorophyll Molecule Membrane Computing Excited Chlorophyll 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Ahn, T.K., Avenson, T.J., Ballottari, M., Cheng, Y.C., Niyogi, K.K., Bassi, R., Fleming, G.R.: Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein. Science 320(5877), 794–797 (2008)CrossRefGoogle Scholar
  2. 2.
    Alder, N.N., Theg, S.M.: Energetics of protein transport across biological membranes: a study of the thylakoid ΔpH-dependent/cptat pathway. Cell 112, 231–242 (2003)CrossRefGoogle Scholar
  3. 3.
    Benson, A., Calvin, M.: Carbon dioxide fixation by green plants. Annual Review of Plant Physiology and Plant Molecular Biology 1, 25–42 (1950)CrossRefGoogle Scholar
  4. 4.
    von Bertalanffy, L.: General Systems Theory: Foundations, Developments, Applications. George Braziller Inc., New York (1967)Google Scholar
  5. 5.
    Bianco, L., Fontana, F., Franco, G., Manca, V.: P systems for biological dynamics. In: [8], pp. 81–126Google Scholar
  6. 6.
    Bianco, L., Fontana, G., Manca, V.: P systems with reaction maps. Intern. J. Foundations of Computer Sci. 17, 27–48 (2006)MathSciNetCrossRefzbMATHGoogle Scholar
  7. 7.
    Castellini, A., Franco, G., Manca, V.: Toward a representation of Hybrid Functional Petri Nets by MP systems. In: Proc. 2nd International Workshop on Natural Computing, IWNC 2007, Nagoya University, Japan. Springer, Heidelberg (2007)Google Scholar
  8. 8.
    Ciobanu, G., Păun, G., Pérez-Jiménez, M.J. (eds.): Applications of Membrane Computing. Springer, Heidelberg (2006)zbMATHGoogle Scholar
  9. 9.
    Evron, Y., McCarty, R.E.: Simultaneous measurement of deltapH and electron transport in chloroplast thylakoids by 9-aminoacridine fluorescence. Plant Physiol. 124, 407–414 (2000)CrossRefGoogle Scholar
  10. 10.
    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
  11. 11.
    Fontana, F., Manca, V.: Discrete solution to differential equations by metabolic P systems. Theoretical Computer Sci. 372, 165–182 (2007)MathSciNetCrossRefzbMATHGoogle Scholar
  12. 12.
    Gisselsson, A., Szilagyi, A., Akerlund, H.: Role of histidines in the binding of violaxanthin de-epoxidase to the thylakoid membrane as studied by site-directed mutagenesis. Physiol. Plant. 122, 337–343 (2004)CrossRefGoogle Scholar
  13. 13.
    Holzwarth, A.R.: Applications of ultrafast laser spectroscopy for the study of biological systems. Q. Rev. Biophys. 22, 239–295 (1989)CrossRefGoogle Scholar
  14. 14.
    Kanazawa, A., Kramer, D.M.: In vivo modulation of nonphotochemical exciton quenching (NPQ) by regulation of the chloroplast atp synthase. PNAS 99, 12789–12794 (2002)CrossRefGoogle Scholar
  15. 15.
    Manca, V.: Log-gain principles for metabolic P systems (submitted, 2008)Google Scholar
  16. 16.
    Manca, V.: Topics and problems in metabolic P systems. In: Proc. Fourth Braintorming Week on Membrane Computing, Fenix Editora, Sevilla (2006)Google Scholar
  17. 17.
    Manca, V.: Metabolic P systems for biochemical dynamics. Progress in Natural Science 17, 384–391 (2007)MathSciNetCrossRefzbMATHGoogle Scholar
  18. 18.
    Manca, V.: MP systems approaches to biochemical dynamics: Biological rhythms and oscillations. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 86–99. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  19. 19.
    Manca, V.: Discrete simulations of biochemical dynamics. In: Garzon, M.H., Yan, H. (eds.) DNA 2007. LNCS, vol. 4848, pp. 231–235. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  20. 20.
    Manca, V.: The metabolic algorithm for P systems: Principles and applications. Theoretical Computer Sci. 404, 142–157 (2008)MathSciNetCrossRefzbMATHGoogle Scholar
  21. 21.
    Manca, V., Bianco, L.: Biological networks in metabolic P systems. BioSystems 91, 489–498 (2008)CrossRefGoogle Scholar
  22. 22.
    Manca, V., Bianco, L., Fontana, F.: Evolution and oscillation in P systems: Applications to biological phenomena. In: Mauri, G., et al. (eds.) WMC 2004. LNCS, vol. 3365, pp. 63–84. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  23. 23.
    Maxwell, K., Johnson, G.N.: Chlorophyll fluorescence - a practical guide. Journal of Experimental Botany 51, 659–668 (2000)CrossRefGoogle Scholar
  24. 24.
    Nelson, N., Ben-Shem, A.: The complex architecture of oxygenic photosynthesis. Nature Reviews Molecular Cell Biology 5, 971–982 (2006)CrossRefGoogle Scholar
  25. 25.
    Nelson, N., Yocum, C.: Structure and function of photosystems I and II. The Annual Review of Plant Biology 57, 521–565 (2006)CrossRefGoogle Scholar
  26. 26.
    Păun, G.: Computing with membranes. J. Computer and System Sci. 61, 108–143 (2000)MathSciNetCrossRefzbMATHGoogle Scholar
  27. 27.
    Păun, G.: Membrane Computing. An Introduction. Springer, Heidelberg (2002)CrossRefzbMATHGoogle Scholar
  28. 28.
    Trubitsin, B.V., Tikhonov, A.N.: Determination of a transmembrane pH difference in chloroplasts with a spin label tempamine. Journal of Magnetic Resonance 163, 257–269 (2003)CrossRefGoogle Scholar
  29. 29.
    Voit, E.O.: Computational Analysis of Biochemical Systems. Cambridge University Press, Cambridge (2000)Google Scholar
  30. 30.
    Web Pages of polynomial coefficients associated to flux regulation maps of NPQ phenomenon,

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Vincenzo Manca
    • 1
  • Roberto Pagliarini
    • 1
  • Simone Zorzan
    • 2
  1. 1.Computer Science DepartmentVerona UniversityVeronaItaly
  2. 2.Biotechnological DepartmentVerona UniversityVeronaItaly

Personalised recommendations