Chapter

Applications of Membrane Computing in Systems and Synthetic Biology

Volume 7 of the series Emergence, Complexity and Computation pp 247-266

Date:

Modelling and Analysis of E. coli Respiratory Chain

  • Adrian ŢurcanuAffiliated withDepartment of Computer Science, University of Piteşti Email author 
  • , Laurenţiu MierlăAffiliated withDepartment of Computer Science, University of Piteşti
  • , Florentin IpateAffiliated withDepartment of Computer Science, University of PiteştiDepartment of Computer Science, University of Bucharest
  • , Alin StefanescuAffiliated withDepartment of Computer Science, University of Piteşti
  • , Hao BaiAffiliated withDepartment of Computer Science, University of Sheffield
  • , Mike HolcombeAffiliated withDepartment of Computer Science, University of Sheffield
  • , Simon CoakleyAffiliated withDepartment of Computer Science, University of Sheffield

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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.