Ebenhöh 2014, Philos Trans.

The Ebenhöh 2014 model is a kinetic model of the photosynthetic electron transport chain (PETC), built to study how a photosynthetic organism acclimates to changing light on short timescales. It comprises seven coupled ordinary differential equations and represents the main components of the PETC — photosystem II (PSII), the plastoquinone pool, the cytochrome b6f complex, plastocyanin, photosystem I (PSI), ferredoxin, ferredoxin-NADP+ reductase and the ATP synthase — together with both linear and cyclic electron flow. PSII is described under a quasi-steady-state assumption using a four-state reaction-center model. In addition, the model captures the relocation of light-harvesting complexes between PSII and PSI (state transitions), thereby changing the antenna cross sections of the two photosystems.

Because the model was developed to describe short-term acclimation of the PETC to different light regimes, it was validated against PAM fluorescence data from Chlamydomonas reinhardtii, showing both light-induced and anoxia-induced state transitions. The light-induced state transition reported in the publication is reproduced exactly by this implementation; the anoxia-induced state transition and figure 3, however, show some discrepancies from the original publication while still agreeing with the overall dynamics. Beyond serving as a base model for short-term PETC acclimation, it provided the foundation for Matuszynska 2016 and Matuszynska 2019. For that reason, it is included in GreenSloth as a starting point for understanding how the light reactions of photosynthesis are modeled.

Model definition

Variables

Symbol	ID	Initial value	Unit
	Plastoquinone_oxidised	17.5
	Plastocyanine_oxidised	0.0202
	Ferredoxine_oxidised	5
	ATP	0
	NADPH	0
	protons_lumen	0.00025238293779207717
	Light_minus_harvesting_complex	0.9

Parameters

Symbol	ID	Value	Unit
	pH	7.8
	PPFD	100
	cPPFD	0.3333333333333333
	PSII_total	2.5
	PSI_total	2.5
	PQ_tot	17.5
	PC_tot	4
	Fd_star	5
	NADP_star	25
	A_star_P	60
	LHC_tot	1
	F	96.485
	R	0.0083
	T	298
	bH	100
	E0_QA	-0.14
	E0_PQ	0.354
	E0_PC	0.38
	E0_P700	0.48
	E0_FA	-0.55
	E0_Fd	-0.43
	E0_NADP	-0.113
	kH0	500000000
	kH	0
	kF	62500000
	k2	1200000000
	Q	0
	staticAntI	0.2
	staticAntII	0
	kf_atp_synthase	20
	kf_atp_consumption	10
	Pi_mol	0.01
	DeltaG0_ATP	30.6
	HPR	4.666666666666667
	kf_nadph_consumption	15
	kf_proton_leak	0.01
	kPQred	250
	kcat_b6f	2.5
	kPTOX	0.01
	kPCox	2500
	kFdred	250000
	kcat_fnr	500
	E0_fnr	3
	km_fnr_Ferredoxine_reduced	1.56
	km_fnr_NADP	0.22
	kf_cyclic_electron_flow	1
	O2_dissolved_lumen	8
	kf_ndh	0.004
	kStt7	0.0035
	kPph1	0.0013
	km_lhc_state_transition_12	0.2
	n_ST	2

Derived quantities

Symbol	ID	Equation	Unit
	RT
	dG_pH
	pH_lumen
	Plastoquinone_reduced
	Plastocyanine_reduced
	Ferredoxine_reduced
	ADP
	NADP
	Light_minus_harvesting_complex_protonated
	PSII_cross_section
	keq_Plastoquinone_reduced
	keq_atp_synthase
	keq_b6f
	keq_fnr
	vmax_fnr
	keq_PCP700
	keq_ferredoxin_reductase
	A1
	B0
	B1
	B2
	B3
	PQ_red_div_tot
	Fd_red_div_tot
	PC_red_div_tot
	NADPH_div_tot
	ATP_div_tot
	Fluo

Reactions

Symbol	ID	Rate	Stoichiometry	Unit
	PSII
	PSI
	PTOX
	ndh
	b6f
	cyclic_electron_flow
	fnr
	proton_leak
	lhc_state_transition_12
	lhc_state_transition_21
	atp_synthase
	atp_consumption
	nadph_consumption