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Quantitative studies of cell metabolism are often based on large chemicalreaction network models. A steady state approach is suited to analyze phenomenaon the timescale of cell growth and circumvents the problem of incompleteexperimental knowledge on kinetic laws and parameters, but it shall besupported by a correct implementation of thermodynamic constraints. In thisarticle we review the latter aspect highlighting its computational challengesand physical insights. The simple introduction of Gibbs inequalities avoids thepresence of unfeasible loops allowing for correct timescale analysis but leadsto possibly non-convex feasible flux spaces, whose exploration needs efficientalgorithms. We shorty review on the implementation of thermodynamics throughvariational principles in constraints based models of metabolic networks.

The Essential Role of Thermodynamics in metabolic network modeling: physical insights and computational challenges