Discrete Nondeterministic Modeling of the Fas Pathway

Jack, John and Rodríguez-Patón Aradas, Alfonso and Ibarra, Oscar H. and Paun, Andrei Paul (2008). Discrete Nondeterministic Modeling of the Fas Pathway. "International Journal of Foundations of Computer Science", v. 19 (n. 5); pp. 1147-1162. ISSN 0129-0541.


Title: Discrete Nondeterministic Modeling of the Fas Pathway
  • Jack, John
  • Rodríguez-Patón Aradas, Alfonso
  • Ibarra, Oscar H.
  • Paun, Andrei Paul
Item Type: Article
Título de Revista/Publicación: International Journal of Foundations of Computer Science
Date: October 2008
Volume: 19
Faculty: Facultad de Informática (UPM)
Department: Inteligencia Artificial
Creative Commons Licenses: Recognition - No derivative works - Non commercial

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Official URL: http://dx.doi.org/10.1142/S0129054108006194


Abstract: Computer modeling of molecular signaling cascades can provide useful insight into the underlying complexities of biological systems. We present a refined approach for the discrete modeling of protein interactions within the environment of a single cell. The technique we offer utilizes the Membrane Systems paradigm which, due to its hierarchical structure, lends itself readily to mimic the behavior of cells. Since our approach is nondeterministic and discrete, it provides an interesting contrast to the standard deterministic ordinary differential equations techniques. We argue that our approach may outperform ordinary differential equations when modeling systems with relatively low numbers of molecules – a frequent occurrence in cellular signaling cascades. Refinements over our previous modeling efforts include the addition of nondeterminism for handling reaction competition over limited reactants, increased efficiency in the storing and sorting of reaction waiting times, and modifications of the model reactions. Results of our discrete simulation of the type I and type II Fas-mediated apoptotic signaling cascade are illustrated and compared with two approaches: one based on ordinary differential equations and another based on the well-known Gillespie algorithm.

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Item ID: 2261
DC Identifier: http://oa.upm.es/2261/
OAI Identifier: oai:oa.upm.es:2261
Deposited by: Memoria Investigacion
Deposited on: 12 Feb 2010 12:31
Last Modified: 20 Apr 2016 12:01
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