Feedbacks and oscillations in the virtual cell VICE

  • Authors:

  • D. Chiarugi;M. Chinellato;P. Degano;G. Lo Brutto;R. Marangoni

  • Affiliations:

  • Dipartimento di Scienze Matematiche e Informatiche, Universit‘a di Siena;Dipartimento di Informatica, Universit‘a di Pisa;Dipartimento di Informatica, Universit‘a di Pisa;Dipartimento di Informatica, Universit‘a di Pisa;Dipartimento di Informatica, Universit‘a di Pisa

  • Venue:
  • CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
  • Year:
  • 2006

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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.