In this chapter we present an application of membrane systems to the study of intracellular diffusive processes. In particular, a class of membrane systems, called tau-DPP, is used for the modeling, simulation and analysis of bacterial chemotaxis. Two different models of this signal transduction pathway are presented. The first is a single volume model used to investigate the properties of bacterial chemotaxis and to analyze the effects of different perturbations (deletion of chemotactic proteins, addition of distinct amounts of external ligand, effect of different methylation states of the receptors) on the system dynamics. The second model represents a multivolume extension of the former, and it is exploited for the analysis of the diffusive processes that give rise to the formation of concentration gradients throughout the bacterial cytoplasm. The outcome of stochastic simulations of both models are exploited to analyze the process of synchronization of flagella, in order to evaluate the running and tumbling time intervals of bacterial cells

Cazzaniga, P., Besozzi, D., Pescini, D., Mauri, G. (2014). Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis. In M. Gheorghe, P. Frisco, M. Pérez-Jiménez (a cura di), Applications of Membrane Computing in Systems and Synthetic Biology (pp. 65-96). Springer [10.1007/978-3-319-03191-0_3].

Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis

BESOZZI, DANIELA;PESCINI, DARIO;MAURI, GIANCARLO
2014

Abstract

In this chapter we present an application of membrane systems to the study of intracellular diffusive processes. In particular, a class of membrane systems, called tau-DPP, is used for the modeling, simulation and analysis of bacterial chemotaxis. Two different models of this signal transduction pathway are presented. The first is a single volume model used to investigate the properties of bacterial chemotaxis and to analyze the effects of different perturbations (deletion of chemotactic proteins, addition of distinct amounts of external ligand, effect of different methylation states of the receptors) on the system dynamics. The second model represents a multivolume extension of the former, and it is exploited for the analysis of the diffusive processes that give rise to the formation of concentration gradients throughout the bacterial cytoplasm. The outcome of stochastic simulations of both models are exploited to analyze the process of synchronization of flagella, in order to evaluate the running and tumbling time intervals of bacterial cells
Capitolo o saggio
membrane systems; simulation; bacterial chemotaxis
English
Applications of Membrane Computing in Systems and Synthetic Biology
Gheorghe, M; Frisco, P; Pérez-Jiménez, M
2014
978-3-319-03190-3
7
Springer
65
96
Cazzaniga, P., Besozzi, D., Pescini, D., Mauri, G. (2014). Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis. In M. Gheorghe, P. Frisco, M. Pérez-Jiménez (a cura di), Applications of Membrane Computing in Systems and Synthetic Biology (pp. 65-96). Springer [10.1007/978-3-319-03191-0_3].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/50695
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