Microalgae culture for energy production has emerged as an interesting alternative to fossil fuel and biofuel from terrestrial plants. In this paper, we propose a dynamical model of microalgae growth in photobioreactor in order to further optimize productivity. We consider light and nitrogen effects on microalgae growth and on the intracellular carbon flows between a functional compartment (proteins, nucleic acids, membranes) and two storage pools (carbohydrates and neutral lipids). In a second step, we take into account the photoacclimation dynamics. We also compute the light distribution inside the photobioreactor using a Beer-Lambert law. The proposed model has been assessed with experimental data of Isochrysis affinis galbana under day/night cycles. Finally, the model is used to predict carbohydrate, neutral lipid, and biomass productivities and to identify optimal operating conditions (dilution rate and influent nitrogen concentration).