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

An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the fraction of excitations converted to chemical energy by PSII reaction centers (PSII yield), which determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 × 200-nm patch of the grana membrane. We show that excitation transport can be rigorously coarse grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. We present an alternative method for analyzing pulse amplitude-modulated chlorophyll fluorescence measurements that incorporates the effects of a variable excitation diffusion length during qE activation.