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Applications of Membrane Computing in Systems and Synthetic BiologyModelling and Analysis of E. coli Respiratory Chain

Applications of Membrane Computing in Systems and Synthetic Biology: Modelling and Analysis of E.... [In this chapter we present some results obtained in the study of the bacterium E. coli related to its behavior at different level of oxygen in the environment. The biological model is expressed in terms of different molecules and their reactions. First, an agent-based model of E. coli is implemented in the FLAME framework for multi-agents and some simulation results are given. Each agent is represented by an X-machine and the model corresponds to communicating X-machines. Then this model is transformed into a kernel P system. This kernel P system is implemented in the Rodin platform and in Spin and some properties are verified using the associated model checkers. Formulated using the LTL formalism, the verified properties refer to the variation of the number of different molecules as a result of the occurring reactions. Our main contribution is a simplified model of E. coli that preserves the main properties of the initial model, and can be formally verified using a model checker.] http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png

Applications of Membrane Computing in Systems and Synthetic BiologyModelling and Analysis of E. coli Respiratory Chain

Part of the Emergence, Complexity and Computation Book Series (volume 7)
Editors: Frisco, Pierluigi; Gheorghe, Marian; Pérez-Jiménez, Mario J.
Ţurcanu, Adrian; Mierlă, Laurenţiu; Ipate, Florentin; Stefanescu, Alin; Bai, Hao; Holcombe, Mike; Coakley, Simon
Applications of Membrane Computing in Systems and Synthetic Biology — Dec 18, 2013
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Publisher
Springer International Publishing
Copyright
© Springer International Publishing Switzerland 2014
ISBN
978-3-319-03190-3
Pages
247 –266
DOI
10.1007/978-3-319-03191-0_8
Publisher site
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Abstract

[In this chapter we present some results obtained in the study of the bacterium E. coli related to its behavior at different level of oxygen in the environment. The biological model is expressed in terms of different molecules and their reactions. First, an agent-based model of E. coli is implemented in the FLAME framework for multi-agents and some simulation results are given. Each agent is represented by an X-machine and the model corresponds to communicating X-machines. Then this model is transformed into a kernel P system. This kernel P system is implemented in the Rodin platform and in Spin and some properties are verified using the associated model checkers. Formulated using the LTL formalism, the verified properties refer to the variation of the number of different molecules as a result of the occurring reactions. Our main contribution is a simplified model of E. coli that preserves the main properties of the initial model, and can be formally verified using a model checker.]

Published: Dec 18, 2013

Keywords: Model Checker; Oxygen Molecule; Linear Temporal Logic; Formal Verification; Execution Step

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