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Microbial electrolysis cells (MECs) are breakthrough technology of cheap hydrogen production with high efficiency. In this paper differential-algebraic equation (DAE) model of a MEC with an algebraic constraint on current was studied, simulated and validated by implementing the model on continuous-flow MECs. Then sensitivity analysis for the system was effectuated. Parameters which have the predominating influence on the current density and hydrogen production rate were defined. This sensitivity analysis was utilized in modeling and validation of the batch-cycle of MEC. After that parameters which have less influence on MEC were eliminated and simplified reduced model was obtained and validated. Finally, MEC energy productivity was maximized by optimization of operating conditions.