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Authors: Alessandro Borri ; Francesco Carravetta ; Gabriella Mavelli and Pasquale Palumbo

Affiliation: Istituto di Analisi dei Sistemi ed Informatica “A. Ruberti”, Italy

Keyword(s): Systems Biology, Chemical Master Equation, Markov Processes, Enzymatic Reactions.

Abstract: The Chemical Master Equation (CME) provides a fruitful approach for the stochastic description of complex biochemical processes, because it is able to cope with random fluctuations of the chemical agents and to fit the experimental behavior in a more accurate way than deterministic concentration equations. In this work, our attention is focused on modeling and simulation of multisite phosphorylation/dephosphorylation cycles, by using the quasi-steady state approximation of enzymatic kinetics. The CME dynamics is written from the coefficients of the deterministic reaction-rate equations and the stationary distribution is computed explicitly, according to a recently developed realization scheme. Simulations are included to provide a comparison with Monte Carlo methods in terms of computational complexity.

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Paper citation in several formats:
Borri, A.; Carravetta, F.; Mavelli, G. and Palumbo, P. (2013). Chemical Master Equations - A Mathematical Scheme for the Multi-site Phosphorylation Case. In Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2013) - BIOMED; ISBN 978-989-8565-69-3; ISSN 2184-2841, SciTePress, pages 681-688. DOI: 10.5220/0004632306810688

@conference{biomed13,
author={Alessandro Borri. and Francesco Carravetta. and Gabriella Mavelli. and Pasquale Palumbo.},
title={Chemical Master Equations - A Mathematical Scheme for the Multi-site Phosphorylation Case},
booktitle={Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2013) - BIOMED},
year={2013},
pages={681-688},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004632306810688},
isbn={978-989-8565-69-3},
issn={2184-2841},
}

TY - CONF

JO - Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2013) - BIOMED
TI - Chemical Master Equations - A Mathematical Scheme for the Multi-site Phosphorylation Case
SN - 978-989-8565-69-3
IS - 2184-2841
AU - Borri, A.
AU - Carravetta, F.
AU - Mavelli, G.
AU - Palumbo, P.
PY - 2013
SP - 681
EP - 688
DO - 10.5220/0004632306810688
PB - SciTePress

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