Modeling reaction noise with a desired accuracy by using the X level approach reaction noise estimator (XARNES) method

Journal of Theoretical Biology
Zoran Konkoli

Abstract

A novel computational method for modeling reaction noise characteristics has been suggested. The method can be classified as a moment closure method. The approach is based on the concept of correlation forms which are used for describing spatially extended many body problems where particle numbers change in space and time. In here, it was shown how the formalism of spatially extended correlation forms can be adapted to study well mixed reaction systems. Stochastic fluctuations in particle numbers are described by selectively capturing correlation effects up to the desired order, ξ. The method is referred to as the ξ-level Approximation Reaction Noise Estimator method (XARNES). For example, the ξ=1 description is equivalent to the mean field theory (first-order effects), the ξ=2 case corresponds to the previously developed PARNES method (pair effects), etc. The main idea is that inclusion of higher order correlation effects should lead to better (more accurate) results. Several models were used to test the method, two versions of a simple complex formation model, the Michaelis-Menten model of enzymatic kinetics, the smallest bistable reaction network, a gene expression network with negative feedback, and a random large network. ...Continue Reading

References

Aug 17, 2002·Science·Nina Fedoroff, Walter Fontana
Feb 28, 2003·Proceedings of the National Academy of Sciences of the United States of America·Masaki Sasai, Peter G Wolynes
Sep 2, 2003·Theoretical Population Biology·Ingemar Nåsell
Jan 30, 2004·Nature·Johan Paulsson
May 11, 2005·Nature Reviews. Genetics·Mads KaernJames J Collins
Sep 24, 2005·Science·Jonathan M Raser, Erin K O'Shea
Apr 20, 2007·Bulletin of Mathematical Biology·Abhyudai Singh, João Pedro Hespanha
Jul 16, 2008·Scientific American·Melinda Wenner
Jan 22, 2009·IET Systems Biology·C S Gillespie
Apr 10, 2009·The Journal of Chemical Physics·Chang Hyeong LeePilwon Kim
Sep 10, 2009·BMC Systems Biology·Thomas Wilhelm
Jul 1, 2010·BMC Systems Biology·William J Bosl, Rong Li
Dec 7, 2010·Journal of Theoretical Biology·Zoran Konkoli
Jul 13, 2011·Journal of Theoretical Biology·Zoran Konkoli

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Citations

Mar 19, 2013·Theoretical Biology & Medical Modelling·Zoran Konkoli, Aldo Jesorka

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