The Chemical Master Equation (CME) provides an accurate stochastic description of complex biochemical processes in terms of probability distribution of the underlying chemical population. By reason of that, CMEs are usually considered {it stochastic} methods for the analysis of biochemical reactions, in contrast to {it deterministic} methods, handling biochemical processes by means of Ordinary Differential Equations (ODE) expressing the evolution of the concentration for each involved species. In this deterministic framework, a common practice is to exploit Quasi-Steady State Approximations (QSSAs) to reduce the dimensionality of the system and fasten numerical simulations. In the present paper, we investigate the applicability of QSSAs from a stochastic viewpoint, by making use of the CMEs in the specific case of the double phosphorylation-dephosphorylation reaction. To this end, the stochastic approach is applied to the non-approximated original chemical network, as well as to the extit{standard} and extit{total} QSSAs, confirming by simulations the effectiveness and superiority of the latter with respect to the former.

Quasi-steady-state approximations of the chemical master equation in enzyme kinetics - application to the double phosphorylation/dephosphorylation cycle / Bersani, Alberto Maria; Borri, A.; Carravetta, F.; Mavelli, G.; Palumbo, P.. - CD-ROM. - 15:February(2014), pp. 3053-3058. (Intervento presentato al convegno IEEE 53rd Annual conference on decision and control (CDC 2014) tenutosi a Los Angeles, California, USA nel 15-17 Dicembre 2014) [10.1109/CDC.2014.7039859].

Quasi-steady-state approximations of the chemical master equation in enzyme kinetics - application to the double phosphorylation/dephosphorylation cycle

BERSANI, Alberto Maria;
2014

Abstract

The Chemical Master Equation (CME) provides an accurate stochastic description of complex biochemical processes in terms of probability distribution of the underlying chemical population. By reason of that, CMEs are usually considered {it stochastic} methods for the analysis of biochemical reactions, in contrast to {it deterministic} methods, handling biochemical processes by means of Ordinary Differential Equations (ODE) expressing the evolution of the concentration for each involved species. In this deterministic framework, a common practice is to exploit Quasi-Steady State Approximations (QSSAs) to reduce the dimensionality of the system and fasten numerical simulations. In the present paper, we investigate the applicability of QSSAs from a stochastic viewpoint, by making use of the CMEs in the specific case of the double phosphorylation-dephosphorylation reaction. To this end, the stochastic approach is applied to the non-approximated original chemical network, as well as to the extit{standard} and extit{total} QSSAs, confirming by simulations the effectiveness and superiority of the latter with respect to the former.
2014
IEEE 53rd Annual conference on decision and control (CDC 2014)
Michaelis-Menten kinetics; quasi-steady-state approximation; deterministic and stochastic processes; phosphorylation; Chemical Master Equation; Markov processes
04 Pubblicazione in atti di convegno::04b Atto di convegno in volume
Quasi-steady-state approximations of the chemical master equation in enzyme kinetics - application to the double phosphorylation/dephosphorylation cycle / Bersani, Alberto Maria; Borri, A.; Carravetta, F.; Mavelli, G.; Palumbo, P.. - CD-ROM. - 15:February(2014), pp. 3053-3058. (Intervento presentato al convegno IEEE 53rd Annual conference on decision and control (CDC 2014) tenutosi a Los Angeles, California, USA nel 15-17 Dicembre 2014) [10.1109/CDC.2014.7039859].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/955573
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