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- Title
A review of the nondeterministic waiting time algorithm.
- Authors
Jack, John; Păun, Andrei; Rodríguez-Patón, Alfonso
- 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.
- Subjects
ALGORITHMS; SYSTEMS biology; CIRCADIAN rhythms; BIOCOMPUTERS; NUMERICAL solutions to differential equations; NUMERICAL analysis software; STOCHASTIC analysis
- Publication
Natural Computing, 2011, Vol 10, Issue 1, p139
- ISSN
1567-7818
- Publication type
Article
- DOI
10.1007/s11047-010-9195-z