In this work we address dynamic optimization of ethanol production by Dynamic Flux Balance Analysis in an engineered cyanobacterium with autotrophic growth (i.e., using CO2 as substrate). The photobioreactor optimization model is integrated to the metabolic network one by replacing the inner problem by its first order optimality conditions. Complementarity constraints that arise associated to the optimality conditions are efficiently handled with a penalty function formulation. Numerical results suggest the possibility to activate the ethanol production pathway after 20h in the batch run to enhance ethanol production. © 2014 Elsevier B.V.

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