algae/phytoplankton_physiology/downregulation.htm
Almost quoted from Walker (1987)
No wone know precisely how this works, but cation exchange processes (both protons and Mg++ ions) bring about changes in the thylakoid ustrastructure which switches excitation energy dissipation from fluoresecence into thermal channels. This means that energy is lost as heat rather than fluorescence and looks like a quenching of the energy loss through fluorescence qE.
If CO2 is being rapidly fixed, ATP consumption will be high and there will be plenty of ADP to use up the proton gradient. If CO2 supply is limited, the ATP will build up, ADP will be limiting and the proton gradient will increase. When proton gradient is high, qE is high and energy loss through fluorescence will be quenched.
Walker, D. (1987) The use of the oxygen electrode and fluorescence probes in simple measurements of photosynthesis.Oxygraphics Limited.
Cross reference to:
Miyake et al 1999 - only AsA peroxidase containing cyanobacteria quenched fluorescence
Fujita - fluorescence quenching is part of short term response with deltapH