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.
Borri, A., Carravetta, F., Mavelli, G., Palumbo, P. (2013). Chemical Master Equations A Mathematical Scheme for the Multi-site Phosphorylation Case. In Proceedings of 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH13), Reykjavik, Islanda, 29-31 July 2013 (pp.681-688).
Chemical Master Equations A Mathematical Scheme for the Multi-site Phosphorylation Case
Palumbo, P
2013
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.File | Dimensione | Formato | |
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