A model of photosynthesis and photo‐protection based on reaction center damage and repair

<jats:p>Phytoplankton photosynthesis under the rapidly fluctuating irradiance which results from turbulent mixing through the vertical light gradient is poorly understood. Ship‐based measurements often apply the fast repetition rate fluorescence (FRRF) technique in situ or in vivo to gauge the physiological state of the phytoplankton community and infer some of the physical properties of the water column (such as mixing time scales). We describe the development and validation of a model of photosynthetic electron turnover at photosystemII with consideration of downstream limitation, based on the redox state of photosystem II. We also include empirical formulations for slower processes such as photo‐protection (from nonphotochemical quenching) and photo‐inhibition. By confronting the simple model with laboratory data for <jats:italic>Dunaliella tertiolecta</jats:italic>, we were able to refine the model so that it faithfully produced rates of photosynthetic electron transfer determined by FRR fluorescence. Further, we were able to validate the model estimates of linear photosynthetic electron transfer rates against completely independent measurements obtained using 14C‐bicarbonate assimilation in photosynthesis‐light curves.</jats:p>