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Open Access Methodology article

Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models

Carlos Pozo1, Alberto Marín-Sanguino2, Rui Alves3, Gonzalo Guillén-Gosálbez1, Laureano Jiménez1 and Albert Sorribas3*

Author Affiliations

1 Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007-Tarragona, Spain

2 Technische Universität München. Fachgebiet für Systembiotechnologie, Boltzmannstr. 15 85748 Garching, Germany

3 Departament de Ciències Mèdiques Bàsiques, Institut de Recerca Biomèdica de Lleida (IRBLLEIDA), Universitat de Lleida, Montserrat Roig 2, 25008 Lleida, Spain

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BMC Systems Biology 2011, 5:137  doi:10.1186/1752-0509-5-137

Published: 25 August 2011

Abstract

Background

Design of newly engineered microbial strains for biotechnological purposes would greatly benefit from the development of realistic mathematical models for the processes to be optimized. Such models can then be analyzed and, with the development and application of appropriate optimization techniques, one could identify the modifications that need to be made to the organism in order to achieve the desired biotechnological goal. As appropriate models to perform such an analysis are necessarily non-linear and typically non-convex, finding their global optimum is a challenging task. Canonical modeling techniques, such as Generalized Mass Action (GMA) models based on the power-law formalism, offer a possible solution to this problem because they have a mathematical structure that enables the development of specific algorithms for global optimization.

Results

Based on the GMA canonical representation, we have developed in previous works a highly efficient optimization algorithm and a set of related strategies for understanding the evolution of adaptive responses in cellular metabolism. Here, we explore the possibility of recasting kinetic non-linear models into an equivalent GMA model, so that global optimization on the recast GMA model can be performed. With this technique, optimization is greatly facilitated and the results are transposable to the original non-linear problem. This procedure is straightforward for a particular class of non-linear models known as Saturable and Cooperative (SC) models that extend the power-law formalism to deal with saturation and cooperativity.

Conclusions

Our results show that recasting non-linear kinetic models into GMA models is indeed an appropriate strategy that helps overcoming some of the numerical difficulties that arise during the global optimization task.