A review of the nondeterministic waiting time algorithm

  • Authors:

  • John Jack;Andrei Păun;Alfonso Rodríguez-Patón

  • Affiliations:

  • Department of Computer Science, IfM Louisiana Tech University, Ruston, USA 71272;Department of Computer Science, IfM Louisiana Tech University, Ruston, USA 71272 and Facultad de Informática, Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, ...;Facultad de Informática, Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, Boadilla del Monte, Madrid, Spain 28660

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2011

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Abstract

We provide the description for the nondeterministic waiting time (NWT) algorithm, a biochemical modeling approach based on the membrane systems paradigm of computation. The technique provides a unique (different to Gillespie's algorithm or ODE modeling) perspective on the biochemical evolution of the cell. That is, depending on the reactions and molecular multiplicities of a given model, our simulator is capable of producing results comparable to the alternative techniques--continuous and deterministic or discrete and stochastic. Some results for sample models are given, illustrating the differences between the NWT algorithm, the Gillespie algorithm, and the solutions to systems of ordinary differential equations. We have previously used this simulation technique to address issues surrounding Fas-induced apoptosis in cancerous cells and so-called latent HIV-infected cells.