The double phosphorylation/dephosphorylation cycle consists of a symmetric network of biochemical reactions of paramount importance in many intracellular mechanisms. From a network perspective, they consist of four enzymatic reactions interconnected in a specular way. The general approach to model enzymatic reactions in a deterministic fashion is by means of stiff Ordinary Differential Equations (ODEs) that are usually hard to integrate according to biologically meaningful parameter settings. Indeed, the quest for model simplification started more than one century ago with the seminal works by Michaelis and Menten, and their Quasi Steady-State Approximation methods are still matter of investigation nowadays. This work proposes an effective algorithm based on Taylor series methods that manages to overcome the problems arising in the integration of stiff ODEs, without settling for model approximations. The double phosphorylation/dephosphorylation cycle is exploited as a benchmark to validate the methodology from a numerical viewpoint.

Borri, A., Carravetta, F., Palumbo, P. (2021). The double phospho/dephosphorylation cycle as a benchmark to validate an effective taylor series method to integrate ordinary differential equations. SYMMETRY, 13(9) [10.3390/sym13091684].

The double phospho/dephosphorylation cycle as a benchmark to validate an effective taylor series method to integrate ordinary differential equations

Palumbo P.
2021

Abstract

The double phosphorylation/dephosphorylation cycle consists of a symmetric network of biochemical reactions of paramount importance in many intracellular mechanisms. From a network perspective, they consist of four enzymatic reactions interconnected in a specular way. The general approach to model enzymatic reactions in a deterministic fashion is by means of stiff Ordinary Differential Equations (ODEs) that are usually hard to integrate according to biologically meaningful parameter settings. Indeed, the quest for model simplification started more than one century ago with the seminal works by Michaelis and Menten, and their Quasi Steady-State Approximation methods are still matter of investigation nowadays. This work proposes an effective algorithm based on Taylor series methods that manages to overcome the problems arising in the integration of stiff ODEs, without settling for model approximations. The double phosphorylation/dephosphorylation cycle is exploited as a benchmark to validate the methodology from a numerical viewpoint.
Articolo in rivista - Articolo scientifico
Enzymatic reactions; ODE integration; Quadratization; Systems biology;
English
Borri, A., Carravetta, F., Palumbo, P. (2021). The double phospho/dephosphorylation cycle as a benchmark to validate an effective taylor series method to integrate ordinary differential equations. SYMMETRY, 13(9) [10.3390/sym13091684].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/356591
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