Abstract
Complex reaction systems in molecular biology are often composed of partially independent subsystems associated with the activity of external or internal triggers. Occurring as random events or dedicated physical signals, triggers effect transitions from one subsystem to another which might result in substantial changes of detectable behavior. From a modeling point of view, those subsystems typically differ in their reaction rules or principle of operation. We propose a formulation of trigger-based switching between models from a class of P systems with progression in time employing discretized mass-action kinetics. Two examples inspired by biological phenomena illustrate the consecutive interplay of P systems towards structural plasticity in reaction rules: evolutionary construction of reaction networks and artificial chemistries with self-reproducible subunits.
Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Similar content being viewed by others
Keywords
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.
References
Alon, U.: An Introduction to Systems Biology. Chapman & Hall, Boca Raton (2006)
Belousov, B.P.: A periodic reaction and its mechanism. Compilation of Abstracts in Radiation Medicine 147, 145 (1959)
Blankenship, R.E.: Molecular Mechanisms of Photosynthesis. Blackwell Science, Malden (2002)
Brody, H.M., et al.: Phenotypic Plasticity. Oxford University Press, Oxford (2003)
Connors, K.A.: Chemical Kinetics. VCH Publishers, Weinheim (1990)
Debanne, D.: Brain plasticity and ion channels. Journal of Physiology 97, 403–414 (2003)
Dittrich, P., et al.: Artificial chemistries. A review. Artificial Life 7, 225–275 (2001)
Fontana, F., et al.: Discrete solutions to differential equations by metabolic P systems. Theor. Comput. Sci. 372, 165–182 (2007)
Funahashi, A., et al.: CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 1, 159–162 (2003), www.celldesigner.org
Hinze, T., Hayat, S., Lenser, T., Matsumaru, N., Dittrich, P.: Hill kinetics meets P systems: A case study on gene regulatory networks as computing agents in silico and in vivo. In: Eleftherakis, G., Kefalas, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2007. LNCS, vol. 4860, pp. 320–335. Springer, Heidelberg (2007)
Hucka, M., et al.: The systems biology markup language SBML: A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524–531 (2003)
Lenser, T., Hinze, T., Ibrahim, B., Dittrich, P.: Towards evolutionary network reconstruction tools for systems biology. In: Marchiori, E., Moore, J.H., Rajapakse, J.C. (eds.) EvoBIO 2007. LNCS, vol. 4447, pp. 132–142. Springer, Heidelberg (2007)
Magnasco, M.O.: Chemical kinetics is Turing universal. Physical Review Letters 78, 1190–1193 (1997)
Manca, V.: Metabolic P systems for biomolecular dynamics. Progress in Natural Sciences 17, 384–391 (2006)
Nepomuceno, I., et al.: A tool for using the SBML format to represent P systems which model biological reaction networks. In: Proc. 3rd Brainstorming Week on Membrane Computing, Fenix Editora, Sevilla, pp. 219–228 (2005)
Păun, G.: Computing with membranes. J. Comp. Syst. Sci. 61, 108–143 (2000)
Păun, G.: Membrane Computing: An Introduction. Springer, Heidelberg (2002)
Pescini, D., et al.: Investigating local evolutions in dynamical probabilistic P systems. In: Ciobanu, G., et al. (eds.) Proc. First Intern. Workshop on Theory and Application of P Systems, pp. 275–288 (2005)
Rozenberg, G., Salomaa, A. (eds.): Handbook of Formal Languages. Springer, Heidelberg (1997)
Suzuki, Y., Tanaka, H.: Symbolic chemical system based on abstract rewriting system and its behavior pattern. Artificial Life and Robotics 1, 211–219 (1997)
Zhabotinsky, A.M.: Periodic processes of malonic acid oxidation in a liquid phase. Biofizika 9, 306–311 (1964)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hinze, T., Faßler, R., Lenser, T., Matsumaru, N., Dittrich, P. (2009). Event-Driven Metamorphoses of P Systems. In: Corne, D.W., Frisco, P., Păun, G., Rozenberg, G., Salomaa, A. (eds) Membrane Computing. WMC 2008. Lecture Notes in Computer Science, vol 5391. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-95885-7_17
Download citation
DOI: https://doi.org/10.1007/978-3-540-95885-7_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-95884-0
Online ISBN: 978-3-540-95885-7
eBook Packages: Computer ScienceComputer Science (R0)