Background With limited agricultural land and increasing human population, it is essential to enhance overall photosynthesis, and thus, productivity. Oxygenic photosynthesis begins with light absorption, followed by excitation energy transfer to the reaction centers, primary photochemistry, electron and proton transport, ATP synthesis, and then CO2 fixation (Calvin-Benson cycle, as well as Hatch-Slack cycle). We mention here some of the discoveries related to this process, such as the existence of two light reactions and two photosystems connected by an electron transport ‘chain’ (the Z-scheme), chemiosmotic hypothesis for ATP synthesis, water oxidation clock for oxygen evolution, steps for carbon fixation, and finally the diverse mechanisms of regulatory processes, such as “state transitions” and “non-photochemical quenching” of the excited state of chlorophyll a. Scope In this review, we emphasize that mathematical modeling is a highly valuable tool in understanding and making predictions on photosynthesis. Different mathematical models have been used to examine current theories on diverse photosynthetic processes; these have been validated through simulation(s) of available experimental data, such as chlorophyll a fluorescence induction, measured with fluorometers using continuous (or modulated) exciting light, and absorbance changes at 820 nm (ΔA820 ) related to redox changes in P700, the reaction center of Photosystem I. Conclusions We show in this review the important role of modeling in deciphering and untangling complex photosynthesis processes taking place simultaneously, as well as in predicting possible ways to obtain higher biomass and productivity in plants, algae and cyanobacteria.

In the photosynthesis process, part of the absorbed photon energy in photosystem II (PSII) may be reemitted as chlorophyll a fluorescence (ChlF). Environmental and plant physiological changes affect the emission of ChlF, which makes ChlF a potentially useful tool to sense these changes. Volumes of research on ChlF are published each year and some published work has been controversial. To facilitate the application of ChlF, it is important to have a holistic picture of the field. This review summarizes ChlF applications published in the last 10 years.

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