The Nondeterministic Waiting Time Algorithm: A Review

John Jack
(Louisiana Tech University)
Andrei Păun
(Louisiana Tech University, INCDSB, UPM)

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells.

In Jürgen Dassow, Giovanni Pighizzini and Bianca Truthe: Proceedings Eleventh International Workshop on Descriptional Complexity of Formal Systems (DCFS 2009), Magdeburg, Germany, July 6-9, 2009, Electronic Proceedings in Theoretical Computer Science 3, pp. 29–46.
Published: 30th July 2009.

ArXived at: http://dx.doi.org/10.4204/EPTCS.3.3 bibtex PDF

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