Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady-state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it should be supported by a correct implementation of thermodynamic constraints. In this chapter, we review the latter aspect, highlighting its computational challenges and physical insights. The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis, but leads to possibly non-convex feasible flux spaces whose exploration needs efficient algorithms. We briefly review the implementation of thermodynamics through variational principles in constraint-based models of metabolic networks.

The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges / De Martino, A.; De Martino, D.; Marinari, E. - In: Chemical Kinetics-Beyond the Textbook / Lindenberg K., Metzler R.. - [s.l] : World Scientific, 2019. - ISBN 978-1-78634-700-8. - pp. 455-471 [10.1142/9781786347015_0018]

The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges

De Martino, A.;
2019

Abstract

Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady-state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it should be supported by a correct implementation of thermodynamic constraints. In this chapter, we review the latter aspect, highlighting its computational challenges and physical insights. The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis, but leads to possibly non-convex feasible flux spaces whose exploration needs efficient algorithms. We briefly review the implementation of thermodynamics through variational principles in constraint-based models of metabolic networks.
2019
978-1-78634-700-8
978-1-78634-701-5
Chemical Kinetics-Beyond the Textbook
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11583/2976787