TABLE 1.

Definitions for Scheme 2

Value	Description
L	All light harvesting antennas in PSII.
P	P680.
I	Pheophytin.
A	QA.
B	QB.
PQ	Oxidized plastoquinone molecules in the PQ pool.
PQH2	Reduced and protonated PQ molecules in the PQ pool.
	Reduced/oxidized state of tyrosine 161-D1.
	Reduced/oxidized state of tyrosine 160-D2.
Sn (n = 0, 1, 2, 3)	The S-states of OEC.
[]	(n = 0, 1, 2, 3) and the intermediate S-states of OEC.
e.d.	In Part A, electron donation to P680+ by YZ as it is described by part D.
*	Excited state.
Scheme sections
Part A	Includes:
	1. Formation of excited states, which is defined by rate constant kL and in our case simulate δ-flashes.
	2. Reactions of primary photochemistry: charge separation, stabilization, electron transfer to QB, and charge recombination.
Part B	Incorporates exchange of double-reduced QB by free plastoquinone molecule from the PQ pool.
Part C	Includes the loss of excited state by:
	1. Heat dissipation in the light harvesting antennas.
	2. Heat dissipation by P680+.
	3. Heat dissipation by oxidized PQ pool.
	4. Energy transfer between closed and open reaction centers of PSII.
	5. Chlorophyll fluorescence emission.
Part D	Mainstream of the electron transfer at the donor side of PSII is represented in part D, which connects Kok cycle of the S-states advancement and electron transport through PSII with the help of newly introduced intermediate S-states.
Part E	Describes charge recombination between the S2-state of OEC and
Part F	Shows slow electron transfer at the donor side of PSII; specifically, redox reaction between YD and OEC.
Rate constants
kL	Rate of excited states formation.
ki	Symbolic rate constant representing all processes of the excited state utilization except for the primary photochemistry as described in part C.
	Overall nonradiative loss of excited states in light harvesting antennas in PSII.
	Nonradiative heat dissipation of excited states by P680+ (the fluorescence quenching by P680+).
	Nonradiative heat dissipation of excited states by PQ molecules (the fluorescence quenching by PQ molecules).
kUU	Excited states transfer between reaction centers of PSII.
kF	Fluorescence.
	Overall electron transfer from P680 to Pheo (the charge separation) in the open (closed) reaction centers of PSII.
	Backward electron transfer from Pheo− to P680+ (the charge recombination) in open (closed) reaction centers of PSII leading to formation of an excited state.
	Electron transfer from Pheo− to QA (the charge stabilization) in open reaction centers of PSII.
	Backward electron transfer from Pheo− to P680+ (nonradiative charge recombination) in closed reaction centers of PSII leading to the ground state of P680 and Pheo.
kAB1(2)	Electron transfer from ).
kBA1(2)	Backward electron transfer from
k(B/PQ)ex	Exchange of double-reduced QB () with an oxidized PQ molecule from the PQ pool.
k(PQ/B)ex	Backward exchange of reduced and protonated PQ molecule (PQH2) from the PQ pool with QB.
kPQox	Overall oxidation of reduced PQ molecules (PQH2) from the PQ pool.
kPQred	Overall reduction of oxidized PQ molecules from the PQ pool.
k(P/A)rec	Charge recombination between P680+ and leading to the formation of a particular excited state.
kiS0, kiS1, kiS2, kiS3	Proposed kinetics of the intermediate S-states.
k01, k12, k23, k30	Electron donation from OEC to during the S0 → S1, S1 → S2, S2 → S3, and S3 → S0 transitions (Kok cycle), respectively.
	P680+ reduction by YZ in the S0 and S1 states of OEC.
and	P680+ reduction (both rates contribute each by 50% to overall rate) by YZ in the S2 and S3 states of OEC.
	Backward electron transfers from P680 to in previous reactions.
kS2QA	Charge recombination of the state.
kDox1/kDox2	YD oxidation by S3/S2 state of OEC.
kDred	reduction by S0 state of OEC.

Values of the newly considered rate constants from parts D, E, and F, and rate constants from part A changed for description of cyanobacterial samples, are listed in Table 2; the rest of the rate constants already used in our previous model (16) are listed in Table 3.