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Feedbacks and Oscillations in the Virtual Cell VICE

  • D. Chiarugi
  • M. Chinellato
  • P. Degano
  • G. Lo Brutto
  • R. Marangoni
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4210)

Abstract

We analyse an enhanced specification of VICE, a hypothetical prokaryote with a genome as basic as possible. Besides the most common metabolic pathways of prokaryotes in interphase, VICE also posseses a regulatory feedback circuit based on the enzyme phosphofructokinase. We use as formal description language a fragment of the stochastic π-calculus. Simulations are run on BEAST, an abstract machine specially tailored to run in silico experimentations. Two kinds of virtual experiments have been carried out, depending on the way nutrients are supplied to VICE. The result of our experimentations in silico confirm that our virtual cell “survives” in an optimal environment, as it exhibits the homeostatic property similary to real living cells. Additionally, oscillatory patterns in the concentration of fructose-6-phosphate and fructose-1,6-bisphosphate show up, similar to the real ones.

Keywords

Metabolic Network Flux Balance Analysis Oscillatory Pattern Abstract Machine Virtual Experiment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • D. Chiarugi
    • 1
  • M. Chinellato
    • 2
  • P. Degano
    • 2
    • 3
  • G. Lo Brutto
    • 2
  • R. Marangoni
    • 2
  1. 1.Dipartimento di Scienze Matematiche e InformaticheUniversit‘a di Siena 
  2. 2.Dipartimento di InformaticaUniversit‘a di Pisa 
  3. 3.The Microsoft Research – University of Trento Centre for Computational and Systems Biology 

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