Abstract
The processes in biological systems evolve in discrete and non-deterministic ways. Simulation of conventional models such as ordinary differential equations with continuous and deterministic evolution strategy has disregarded those behaviors in biological systems. Membrane computing which has been applied in a nondeterministic and maximally parallel way to capture the structure and behaviors of biological systems could be used to address the limitations in ordinary differential equations. The stochastic simulation strategy based on Gillespie’s algorithm has been used to simulate membrane computing model. This study was carried out to demonstrate the capability of membrane computing model in characterizing the structure and behaviors of biological systems in comparison to the model of ordinary differential equations. The results demonstrated that the simulation of membrane computing model preserves the structure and non-deterministic behaviors of biological systems that ignored in the ordinary differential equations model.
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References
Jong, H.D.: Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. Journal of Computational Biology 9(1), 67–103 (2002)
Jaynes, E.T., Bretthorst, G.L.: Probability Theory: The Logic of Science. Cambridge University Press, London (2003)
Wilkinson, D.J.: Stochastic Modeling for Systems Biology. CRC Press, London (2006)
Modchang, C., Nadkarni, S., Bartol, T.M., Triampo, W., Sejnowski, T.J., Levine, H., Rappel, W.: A Comparison of Deterministic and Stochastic Simulations of Neuronal Vesicle Release Models. Phys. Biol. 7(2), 26008 (2010)
Hattne, J., Fange, D., Elf, J.: Stochastic Reaction-diffusion Simulation with MesoRD. Bioinformatics 21, 2923–2924 (2005)
Andrews, S.S., Bray, D.: Stochastic Simulation of Chemical Reactions with Spatial Resolution and Single Molecule Detail. Phys. Biol. 1(3), 137–151 (2004)
Kerr, R.A., Bartol, T.M., Kaminsky, B., Dittrich, M., Chang, J.J., Baden, S.B., Sejnowski, T.J., Stiles, J.R.: Fast Monte Carlo Simulation Methods for Biological Reaction-diffusion Systems in Solution and on Surfaces. SIAM J. Sci. Comput. 30, 3126 (2008)
Paun, G.: Computing with Membranes. Journal of Computer and System Sciences 61(1), 108–143 (1998)
Muniyandi, R., Mohd.Zin, A.: Modeling A Multi Compartments Biological System with Membrane Computing. J. Comput. Sci. 6, 1148–1155 (2010)
Muniyandi, R., Mohd.Zin, A.: Experimenting the Simulation Strategy of Membrane Computing with Gillespie Algorithm by Using Two Biological Case Studies. J. Comput. Sci. 6, 525–535 (2010)
Gillespie, D.T.: Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems. Journal of Chemical Physics 115(4), 1716–1733 (2001)
Villar, J.M., Jansen, R., Sander, C.: Signal Processing in the TGF-β Superfamily Ligand-Receptor Network. PLoS Comput. Biol. 2(1), e3 (2006)
Muniyandi, R., Mohd.Zin, A.: Modeling of Biological Processes by Using Membrane Computing Formalism. Am. J. Applied Sci. 6, 1961–1969 (2009)
Bezem, M., Klop, J.W., Vrijer, R.D.: Term rewriting systems. Cambridge University Press, London (2003)
Romero-Campero, F., Gheorghe, M., Auld, J.: Multicompartment Gillespie Simulator in C (2004), http://www.dcs.shef.ac.uk/~marian/PSimulatorWeb/PSystemMF.htm
Muniyandi, R., Mohd.Zin, A., Shukor, Z.: Model checking the biological model of membrane computing with probabilistic symbolic model checker by using two biological systems. J. Comput. Sci. 6, 669–678 (2010)
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Chandren, M.R., Abdullah, M.Z. (2011). Simulation Strategy of Membrane Computing to Characterize the Structure and Non-deterministic Behavior of Biological Systems: A Case Study with Ligand-Receptor Network of Protein TGF-β . In: Badioze Zaman, H., et al. Visual Informatics: Sustaining Research and Innovations. IVIC 2011. Lecture Notes in Computer Science, vol 7066. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25191-7_7
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DOI: https://doi.org/10.1007/978-3-642-25191-7_7
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