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An important determinant of crop yields is the regulation of photosystem II(PSII) light harvesting by energy-dependent quenching (qE). However, themolecular details of excitation quenching have not been quantitativelyconnected to the PSII yield, which only emerges on the 100 nm scale of thegrana membrane and determines flux to downstream metabolism. Here, weincorporate excitation dissipation by qE into a pigment-scale model ofexcitation transfer and trapping for a 200 nm x 200 nm patch of the granamembrane. We demonstrate that single molecule measurements of qE are consistentwith a weak-quenching regime. Consequently, excitation transport can berigorously coarse-grained to a 2D random walk with an excitation diffusionlength determined by the extent of quenching. A diffusion-corrected lake modelsubstantially improves the PSII yield determined from variable chlorophyllfluorescence measurements and offers an improved model of PSII forphotosynthetic metabolism.

Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting