NWA a discrete stochastic simulation technique: a review

November 17, 2014

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Article Title:	NWA a discrete stochastic simulation technique: a review
Authors:	Tusa I., Roata G., Paun P. A.
Affiliation:	Department of Bioinformatics, National Institute for Research and Development for Biological Sciences, Bucharest, Romania
Abstract:	We give the description for the Nondeterministic Waiting Time (NWT) algorithm, a biochemical modeling approach based on the Membrane Systems paradigm of computation. This simulation technique provides a unique perspective on the biochemical evolution of the cell different from Gillespie’s algorithm and different from ODE-based simulations. 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 a few models are given, illustrating the differences between the NWT algorithm, the Gillespie algorithm, and the solutions to systems of ordinary differential equations. We are able to show that in some cases the NWT technique yields results closer to Gillespie, while for other models the results of the NWT simulator are much closer to the results of the ODE simulator.
Keywords:	Discrete simulation, Gillespie’s algorithm, cellular pathways, deterministic simulation, nondeterministic waiting time simulation with memory
References:
*Correspondence:	Paun Andrei, National Institute for Research and Development for Biological Sciences, Department of Bioinformatics, No. 296, Splaiul Independentei, Sector 6, postal code: 060031, Bucharest, Romania, Tel. +40-(21)-2207780, Fax. +40-(21)-2207695, email: apaun@dbio.ro

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