Modelling and Analysis of E. coli Respiratory Chain

  • Adrian Ţurcanu
  • Laurenţiu Mierlă
  • Florentin Ipate
  • Alin Stefanescu
  • Hao Bai
  • Mike Holcombe
  • Simon Coakley
Chapter
Part of the Emergence, Complexity and Computation book series (ECC, volume 7)

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.

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Adrian Ţurcanu
    • 1
  • Laurenţiu Mierlă
    • 1
  • Florentin Ipate
    • 1
    • 2
  • Alin Stefanescu
    • 1
  • Hao Bai
    • 3
  • Mike Holcombe
    • 3
  • Simon Coakley
    • 3
  1. 1.Department of Computer ScienceUniversity of PiteştiPiteştiRomania
  2. 2.Department of Computer ScienceUniversity of BucharestBucharestRomania
  3. 3.Department of Computer ScienceUniversity of SheffieldSheffieldUK

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