Abstract
Modeling and simulation of biological reaction networks is an essential task in systems biology aiming at formalization, understanding, and prediction of processes in living organisms. Currently, a variety of modeling approaches for specific purposes coexists. P systems form such an approach which owing to its algebraic nature opens growing fields of application. Here, emulating the dynamical system behavior based on reaction kinetics is of particular interest to explore network functions. We demonstrate a transformation of Hill kinetics for gene regulatory networks (GRNs) into the P systems framework. Examples address the switching dynamics of GRNs acting as NAND gate and RS flip-flop. An adapted study in vivo experimentally verifies both practicability for computational units and validity of the system model.
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References
Alon, U.: An Introduction to Systems Biology. Chapman & Hall, Sydney, Australia (2006)
Barbacari, N., et al.: Gene Regulatory Network Modelling by Membrane Systems. In: Freund, R., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2005. LNCS, vol. 3850, pp. 162–178. Springer, Heidelberg (2006)
Bernardini, F., et al.: Quorum Sensing P Systems. Theor. Comp. Sci. 371, 20–33 (2007)
Busi, N., et al.: Computing with Genetic Gates, Proteins, and Membranes. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 233–249. Springer, Heidelberg (2006)
Fontana, F., et al.: Discrete Solutions to Differential Equations by Metabolic P Systems. Theor. Comput. Sci. 372(1), 165–182 (2007)
Gardner, T.S., et al.: Construction of a Genetic Toggle Switch in Escherichia coli. Nature 403, 339–342 (2000)
Hastings, J., et al.: Bacterial Bioluminescence. Annu. Rev. Microbiol. 31, 549–595 (1977)
Hayat, S., et al.: Towards in vivo Computing: Quantitative Analysis of an Artificial Gene Regulatory Network Behaving as a RS Flip-Flop. In: Proc. Bionetics (2006)
Hinze, T., et al.: A Protein Substructure Based P System for Description and Analysis of Cell Signalling Networks. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 409–423. Springer, Heidelberg (2006)
Hoops, S., et al.: Copasi: a COmplex PAthway SImulator. Bioinf. 22, 3067–3074 (2006)
Manca, V.: Metabolic P Systems for Biomolecular Dynamics. Progress in Natural Sciences 17(4), 384–391 (2006)
Mestl, T., et al.: A Mathematical Framework for Describing and Analysing Gene Regulatory Networks. J. Theor. Biol. 176, 291–300 (1995)
Miller, M., et al.: Quorum Sensing in Bacteria. Annu. Rev. Microbiol. 55, 165–199 (2001)
Păun, A., et al.: Modeling Signal Transduction Using P Systems. In: Hoogeboom, H.J., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 100–122. Springer, Heidelberg (2006)
Păun, G.: Computing with Membranes. J. Comp. Syst. Sci. 61(1), 108–143 (2000)
Păun, G.: Membrane Computing: An Introduction. Springer, Berlin (2002)
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Hinze, T., Hayat, S., Lenser, T., Matsumaru, N., Dittrich, P. (2007). 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) Membrane Computing. WMC 2007. Lecture Notes in Computer Science, vol 4860. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77312-2_20
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DOI: https://doi.org/10.1007/978-3-540-77312-2_20
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