  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 PSII yield, which only emerges on the 100 nm scale of the
grana membrane and 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 nm x 200 nm patch of the grana
membrane. We demonstrate that single molecule measurements of qE are consistent
with a weak-quenching regime. Consequently, excitation transport can be
rigorously coarse-grained to a 2D random walk with an excitation diffusion
length determined by the extent of quenching. A diffusion-corrected lake model
substantially improves the PSII yield determined from variable chlorophyll
fluorescence measurements and offers an improved model of PSII for
photosynthetic metabolism.
