Ebeling 2026 model

\begin{align*}
  \frac{d 3PGA}{dt} &= 2 \cdot \frac{CO2 (dissolved) \cdot RUBP \cdot vmax\_rubisco\_carboxylase}{(CO2 (dissolved) + km\_rubisco\_carboxylase\_CO2 (dissolved)) \cdot (RUBP + km\_rubisco\_carboxylase\_RUBP \cdot (1 + \frac{FBP}{ki\_rubisco\_carboxylase\_FBP} + \frac{NADPH}{ki\_rubisco\_carboxylase\_NADPH} + \frac{Orthophosphate}{ki\_rubisco\_carboxylase\_Orthophosphate} + \frac{SBP}{ki\_rubisco\_carboxylase\_SBP} + \frac{3PGA}{ki\_rubisco\_carboxylase\_3PGA}))} \\
  & - kre\_phosphoglycerate\_kinase \cdot (ATP \cdot 3PGA - \frac{ADP \cdot BPGA}{keq\_phosphoglycerate\_kinase}) \\
  & - \frac{3PGA \cdot vmax\_ex\_pga}{N\_translocator \cdot km\_ex\_pga} \\ 
  \frac{d BPGA}{dt} &= kre\_phosphoglycerate\_kinase \cdot (ATP \cdot 3PGA - \frac{ADP \cdot BPGA}{keq\_phosphoglycerate\_kinase}) \\
  & - kre\_gadph \cdot (BPGA \cdot NADPH \cdot protons - \frac{GAP \cdot NADP \cdot Orthophosphate}{keq\_gadph}) \\ 
  \frac{d GAP}{dt} &= kre\_gadph \cdot (BPGA \cdot NADPH \cdot protons - \frac{GAP \cdot NADP \cdot Orthophosphate}{keq\_gadph}) \\
  & - kre\_triose\_phosphate\_isomerase \cdot (GAP - \frac{DHAP}{keq\_triose\_phosphate\_isomerase}) \\
  & - kre\_aldolase\_dhap\_gap \cdot (DHAP \cdot GAP - \frac{FBP}{keq\_aldolase\_dhap\_gap}) \\
  & - kre\_transketolase\_gap\_f6p \cdot (F6P \cdot GAP - \frac{E4P \cdot X5P}{keq\_transketolase\_gap\_f6p}) \\
  & - kre\_transketolase\_gap\_s7p \cdot (GAP \cdot S7P - \frac{R5P \cdot X5P}{keq\_transketolase\_gap\_s7p}) \\
  & - \frac{GAP \cdot vmax\_ex\_pga}{N\_translocator \cdot km\_ex\_gap} \\ 
  \frac{d DHAP}{dt} &= kre\_triose\_phosphate\_isomerase \cdot (GAP - \frac{DHAP}{keq\_triose\_phosphate\_isomerase}) \\
  & - kre\_aldolase\_dhap\_gap \cdot (DHAP \cdot GAP - \frac{FBP}{keq\_aldolase\_dhap\_gap}) \\
  & - kre\_aldolase\_dhap\_e4p \cdot (DHAP \cdot E4P - \frac{SBP}{keq\_aldolase\_dhap\_e4p}) \\
  & - \frac{DHAP \cdot vmax\_ex\_pga}{N\_translocator \cdot km\_ex\_dhap} \\ 
  \frac{d FBP}{dt} &= kre\_aldolase\_dhap\_gap \cdot (DHAP \cdot GAP - \frac{FBP}{keq\_aldolase\_dhap\_gap}) \\
  & - \frac{FBP \cdot vmax\_fbpase}{FBP + km\_fbpase\_s \cdot (1 + \frac{F6P}{ki\_fbpase\_F6P} + \frac{Orthophosphate}{ki\_fbpase\_Orthophosphate})} \\ 
  \frac{d F6P}{dt} &= \frac{FBP \cdot vmax\_fbpase}{FBP + km\_fbpase\_s \cdot (1 + \frac{F6P}{ki\_fbpase\_F6P} + \frac{Orthophosphate}{ki\_fbpase\_Orthophosphate})} \\
  & - kre\_transketolase\_gap\_f6p \cdot (F6P \cdot GAP - \frac{E4P \cdot X5P}{keq\_transketolase\_gap\_f6p}) \\
  & - kre\_g6pi \cdot (F6P - \frac{G6P}{keq\_g6pi}) \\ 
  \frac{d G6P}{dt} &= kre\_g6pi \cdot (F6P - \frac{G6P}{keq\_g6pi}) \\
  & - kre\_phosphoglucomutase \cdot (G6P - \frac{G1P}{keq\_phosphoglucomutase}) \\ 
  \frac{d G1P}{dt} &= kre\_phosphoglucomutase \cdot (G6P - \frac{G1P}{keq\_phosphoglucomutase}) \\
  & - \frac{ATP \cdot G1P \cdot vmax\_ex\_g1p}{(G1P + km\_ex\_g1p\_G1P) \cdot ((1 + \frac{ADP}{ki\_ex\_g1p}) \cdot (ATP + km\_ex\_g1p\_ATP) + \frac{Orthophosphate \cdot km\_ex\_g1p\_ATP}{F6P \cdot ki\_ex\_g1p\_F6P + FBP \cdot ki\_ex\_g1p\_FBP + 3PGA \cdot ki\_ex\_g1p\_3PGA})} \\ 
  \frac{d SBP}{dt} &= kre\_aldolase\_dhap\_e4p \cdot (DHAP \cdot E4P - \frac{SBP}{keq\_aldolase\_dhap\_e4p}) \\
  & - \frac{SBP \cdot vmax\_SBPase}{SBP + km\_SBPase\_s \cdot (1 + \frac{Orthophosphate}{ki\_SBPase\_Orthophosphate})} \\ 
  \frac{d S7P}{dt} &= - kre\_transketolase\_gap\_s7p \cdot (GAP \cdot S7P - \frac{R5P \cdot X5P}{keq\_transketolase\_gap\_s7p}) \\
  & + \frac{SBP \cdot vmax\_SBPase}{SBP + km\_SBPase\_s \cdot (1 + \frac{Orthophosphate}{ki\_SBPase\_Orthophosphate})} \\ 
  \frac{d E4P}{dt} &= - kre\_aldolase\_dhap\_e4p \cdot (DHAP \cdot E4P - \frac{SBP}{keq\_aldolase\_dhap\_e4p}) \\
  & + kre\_transketolase\_gap\_f6p \cdot (F6P \cdot GAP - \frac{E4P \cdot X5P}{keq\_transketolase\_gap\_f6p}) \\ 
  \frac{d X5P}{dt} &= kre\_transketolase\_gap\_f6p \cdot (F6P \cdot GAP - \frac{E4P \cdot X5P}{keq\_transketolase\_gap\_f6p}) \\
  & + kre\_transketolase\_gap\_s7p \cdot (GAP \cdot S7P - \frac{R5P \cdot X5P}{keq\_transketolase\_gap\_s7p}) \\
  & - kre\_ribulose\_phosphate\_epimerase \cdot (X5P - \frac{RU5P}{keq\_ribulose\_phosphate\_epimerase}) \\ 
  \frac{d R5P}{dt} &= kre\_transketolase\_gap\_s7p \cdot (GAP \cdot S7P - \frac{R5P \cdot X5P}{keq\_transketolase\_gap\_s7p}) \\
  & - kre\_ribose\_phosphate\_isomerase \cdot (R5P - \frac{RU5P}{keq\_ribose\_phosphate\_isomerase}) \\ 
  \frac{d RUBP}{dt} &= - \frac{CO2 (dissolved) \cdot RUBP \cdot vmax\_rubisco\_carboxylase}{(CO2 (dissolved) + km\_rubisco\_carboxylase\_CO2 (dissolved)) \cdot (RUBP + km\_rubisco\_carboxylase\_RUBP \cdot (1 + \frac{FBP}{ki\_rubisco\_carboxylase\_FBP} + \frac{NADPH}{ki\_rubisco\_carboxylase\_NADPH} + \frac{Orthophosphate}{ki\_rubisco\_carboxylase\_Orthophosphate} + \frac{SBP}{ki\_rubisco\_carboxylase\_SBP} + \frac{3PGA}{ki\_rubisco\_carboxylase\_3PGA}))} \\
  & + \frac{ATP \cdot RU5P \cdot vmax\_phosphoribulokinase}{(RU5P + km\_phosphoribulokinase\_RU5P \cdot (1 + \frac{Orthophosphate}{ki\_phosphoribulokinase\_Orthophosphate} + \frac{RUBP}{ki\_phosphoribulokinase\_RUBP} + \frac{3PGA}{ki\_phosphoribulokinase\_3PGA})) \cdot (ATP \cdot (1 + \frac{ADP}{ki\_phosphoribulokinase\_4}) + km\_phosphoribulokinase\_ATP \cdot (1 + \frac{ADP}{ki\_phosphoribulokinase\_5}))} \\ 
  \frac{d RU5P}{dt} &= kre\_ribose\_phosphate\_isomerase \cdot (R5P - \frac{RU5P}{keq\_ribose\_phosphate\_isomerase}) \\
  & + kre\_ribulose\_phosphate\_epimerase \cdot (X5P - \frac{RU5P}{keq\_ribulose\_phosphate\_epimerase}) \\
  & - \frac{ATP \cdot RU5P \cdot vmax\_phosphoribulokinase}{(RU5P + km\_phosphoribulokinase\_RU5P \cdot (1 + \frac{Orthophosphate}{ki\_phosphoribulokinase\_Orthophosphate} + \frac{RUBP}{ki\_phosphoribulokinase\_RUBP} + \frac{3PGA}{ki\_phosphoribulokinase\_3PGA})) \cdot (ATP \cdot (1 + \frac{ADP}{ki\_phosphoribulokinase\_4}) + km\_phosphoribulokinase\_ATP \cdot (1 + \frac{ADP}{ki\_phosphoribulokinase\_5}))} \\ 
  \frac{d ATP}{dt} &= convf \cdot ATP\_pmf\_activity \cdot ATPactivity \cdot k\_ATPsynthase \cdot (\frac{ADP}{convf} - \frac{ATP}{convf \cdot kf\_atp\_synthase}) \\
  & - kre\_phosphoglycerate\_kinase \cdot (ATP \cdot 3PGA - \frac{ADP \cdot BPGA}{keq\_phosphoglycerate\_kinase}) \\
  & - \frac{ATP \cdot RU5P \cdot vmax\_phosphoribulokinase}{(RU5P + km\_phosphoribulokinase\_RU5P \cdot (1 + \frac{Orthophosphate}{ki\_phosphoribulokinase\_Orthophosphate} + \frac{RUBP}{ki\_phosphoribulokinase\_RUBP} + \frac{3PGA}{ki\_phosphoribulokinase\_3PGA})) \cdot (ATP \cdot (1 + \frac{ADP}{ki\_phosphoribulokinase\_4}) + km\_phosphoribulokinase\_ATP \cdot (1 + \frac{ADP}{ki\_phosphoribulokinase\_5}))} \\
  & - \frac{ATP \cdot G1P \cdot vmax\_ex\_g1p}{(G1P + km\_ex\_g1p\_G1P) \cdot ((1 + \frac{ADP}{ki\_ex\_g1p}) \cdot (ATP + km\_ex\_g1p\_ATP) + \frac{Orthophosphate \cdot km\_ex\_g1p\_ATP}{F6P \cdot ki\_ex\_g1p\_F6P + FBP \cdot ki\_ex\_g1p\_FBP + 3PGA \cdot ki\_ex\_g1p\_3PGA})} \\
  & + ADP \cdot k\_import\_ATP - ATP \cdot kf\_ex\_atp \\ 
  \frac{d Ferredoxine (oxidised)}{dt} &= Ferredoxine (reduced) \cdot Thioredoxin (oxidised) \cdot kf\_ferredoxin\_thioredoxin\_reductase \\
  & + 2 \cdot Plastoquinone (oxidised) \cdot kf\_cyclic\_electron\_flow \cdot {Ferredoxine (reduced)}^{2} \\
  & + 2 \cdot \frac{vmax\_fnr \cdot (\frac{NADP \cdot {\frac{Ferredoxine (reduced)}{km\_fnr\_Ferredoxine (reduced)}}^{2}}{convf \cdot km\_fnr\_NADP} - \frac{NADPH \cdot {\frac{Ferredoxine (oxidised)}{km\_fnr\_Ferredoxine (reduced)}}^{2}}{convf \cdot keq\_fnr \cdot km\_fnr\_NADP})}{-1 + (1 + \frac{NADP}{convf \cdot km\_fnr\_NADP}) \cdot (1 + {\frac{Ferredoxine (reduced)}{km\_fnr\_Ferredoxine (reduced)}}^{2} + \frac{Ferredoxine (reduced)}{km\_fnr\_Ferredoxine (reduced)}) + (1 + \frac{NADPH}{convf \cdot km\_fnr\_NADP}) \cdot (1 + {\frac{Ferredoxine (oxidised)}{km\_fnr\_Ferredoxine (reduced)}}^{2} + \frac{Ferredoxine (oxidised)}{km\_fnr\_Ferredoxine (reduced)})} \\
  & - Ferredoxine (oxidised) \cdot P700FA- \cdot kFdred - \frac{Ferredoxine (reduced) \cdot P700FA \cdot kFdred}{keq\_FAFd} \\
  & - Ferredoxine (oxidised) \cdot P700+FA- \cdot kFdred - \frac{Ferredoxine (reduced) \cdot P700+FA \cdot kFdred}{keq\_FAFd} \\
  & + 2 \cdot \frac{0.9 \cdot Plastoquinone (oxidised) \cdot k\_NDH1 \cdot {10}^{-6.5 + pH\_lumen} \cdot {Ferredoxine (reduced)}^{2}}{(0.5 + {10}^{-6.5 + pH\_lumen}) \cdot (1 + 7.38905609893065 \cdot e^{- 100 \cdot P700+FA-})} \\ 
  \frac{d Light-harvesting complex}{dt} &= - \frac{1 \cdot Light-harvesting complex \cdot kStt7}{1 + {\frac{Plastoquinone (oxidised)}{PQ\_tot \cdot km\_lhc\_state\_transition\_12}}^{n\_ST}} \\
  & + Light-harvesting complex (protonated) \cdot kPph1 \\ 
  \frac{d NADPH}{dt} &= convf \cdot \frac{vmax\_fnr \cdot (\frac{NADP \cdot {\frac{Ferredoxine (reduced)}{km\_fnr\_Ferredoxine (reduced)}}^{2}}{convf \cdot km\_fnr\_NADP} - \frac{NADPH \cdot {\frac{Ferredoxine (oxidised)}{km\_fnr\_Ferredoxine (reduced)}}^{2}}{convf \cdot keq\_fnr \cdot km\_fnr\_NADP})}{-1 + (1 + \frac{NADP}{convf \cdot km\_fnr\_NADP}) \cdot (1 + {\frac{Ferredoxine (reduced)}{km\_fnr\_Ferredoxine (reduced)}}^{2} + \frac{Ferredoxine (reduced)}{km\_fnr\_Ferredoxine (reduced)}) + (1 + \frac{NADPH}{convf \cdot km\_fnr\_NADP}) \cdot (1 + {\frac{Ferredoxine (oxidised)}{km\_fnr\_Ferredoxine (reduced)}}^{2} + \frac{Ferredoxine (oxidised)}{km\_fnr\_Ferredoxine (reduced)})} \\
  & - kre\_gadph \cdot (BPGA \cdot NADPH \cdot protons - \frac{GAP \cdot NADP \cdot Orthophosphate}{keq\_gadph}) \\
  & - \frac{MDA \cdot NADPH \cdot vmax\_mda\_reductase\_2}{MDA \cdot NADPH + MDA \cdot km\_mda\_reductase\_2\_NADPH + NADPH \cdot km\_mda\_reductase\_2\_MDA + km\_mda\_reductase\_2\_MDA \cdot km\_mda\_reductase\_2\_NADPH} \\
  & - \frac{GSSG \cdot NADPH \cdot vmax\_glutathion\_reductase}{GSSG \cdot NADPH + GSSG \cdot km\_glutathion\_reductase\_NADPH + NADPH \cdot km\_glutathion\_reductase\_GSSG + km\_glutathion\_reductase\_GSSG \cdot km\_glutathion\_reductase\_NADPH} \\
  & + NADP \cdot k\_import\_NADPH - NADPH \cdot kf\_ex\_nadph \\ 
  \frac{d Plastocyanine (oxidised)}{dt} &= P700+FA- \cdot Plastocyanine (reduced) \cdot kPCox - \frac{P700FA- \cdot Plastocyanine (oxidised) \cdot kPCox}{keq\_PCP700} \\
  & + P700+FA \cdot Plastocyanine (reduced) \cdot kPCox - \frac{P700FA \cdot Plastocyanine (oxidised) \cdot kPCox}{keq\_PCP700} \\
  & - 2 \cdot \frac{Plastocyanine (oxidised) \cdot Plastoquinone (reduced) \cdot keq\_b6f\_dyn}{Plastoquinone (oxidised) + Plastoquinone (reduced)} - \frac{Plastocyanine (reduced) \cdot keq\_b6f\_dyn \cdot (1 - \frac{Plastoquinone (reduced)}{Plastoquinone (oxidised) + Plastoquinone (reduced)})}{keq\_b6f} \\ 
  \frac{d Plastoquinone (oxidised)}{dt} &= - Plastoquinone (oxidised) \cdot kf\_cyclic\_electron\_flow \cdot {Ferredoxine (reduced)}^{2} \\
  & - Plastoquinone (oxidised) \cdot kf\_ndh \\
  & + O2 (dissolved)\_lumen \cdot Plastoquinone (reduced) \cdot kPTOX \\
  & - 0.5 \cdot B2 \cdot Plastoquinone (oxidised) \cdot kPQred - \frac{B0 \cdot Plastoquinone (reduced) \cdot kPQred}{keq\_Plastoquinone (reduced)} \\
  & + \frac{Plastocyanine (oxidised) \cdot Plastoquinone (reduced) \cdot keq\_b6f\_dyn}{Plastoquinone (oxidised) + Plastoquinone (reduced)} - \frac{Plastocyanine (reduced) \cdot keq\_b6f\_dyn \cdot (1 - \frac{Plastoquinone (reduced)}{Plastoquinone (oxidised) + Plastoquinone (reduced)})}{keq\_b6f} \\
  & - \frac{0.9 \cdot Plastoquinone (oxidised) \cdot k\_NDH1 \cdot {10}^{-6.5 + pH\_lumen} \cdot {Ferredoxine (reduced)}^{2}}{(0.5 + {10}^{-6.5 + pH\_lumen}) \cdot (1 + 7.38905609893065 \cdot e^{- 100 \cdot P700+FA-})} \\ 
  \frac{d PsbS (de-protonated)}{dt} &= - \frac{PsbS (de-protonated) \cdot kf\_lhc\_protonation \cdot {protons\_lumen}^{kh\_lhc\_protonation}}{{protons\_lumen}^{kh\_lhc\_protonation} + {4000 \cdot {10}^{- ksat\_lhc\_protonation}}^{kh\_lhc\_protonation}} \\
  & + PsbS (protonated) \cdot kf\_lhc\_deprotonation \\ 
  \frac{d Violaxanthin}{dt} &= - \frac{Violaxanthin \cdot kf\_violaxanthin\_deepoxidase \cdot {protons\_lumen}^{kh\_violaxanthin\_deepoxidase}}{{protons\_lumen}^{kh\_violaxanthin\_deepoxidase} + {4000 \cdot {10}^{- ksat\_violaxanthin\_deepoxidase}}^{kh\_violaxanthin\_deepoxidase}} \\
  & + Zeaxanthin \cdot kf\_zeaxanthin\_epoxidase \\ 
  \frac{d MDA}{dt} &= - 2 \cdot kf\_mda\_reductase\_1 \cdot {MDA}^{2} \\
  & - 2 \cdot \frac{MDA \cdot NADPH \cdot vmax\_mda\_reductase\_2}{MDA \cdot NADPH + MDA \cdot km\_mda\_reductase\_2\_NADPH + NADPH \cdot km\_mda\_reductase\_2\_MDA + km\_mda\_reductase\_2\_MDA \cdot km\_mda\_reductase\_2\_NADPH} \\
  & + 2 \cdot \frac{H2O2 \cdot XT \cdot ascorbate}{\frac{H2O2}{kf2} + \frac{H2O2}{kf4} + \frac{ascorbate}{kf1} + H2O2 \cdot ascorbate \cdot (\frac{1}{kf3} + \frac{1}{kf5}) + \frac{kr1}{kf1 \cdot kf2} + \frac{H2O2 \cdot kr2}{kf2 \cdot kf3} + \frac{H2O2 \cdot kr4}{kf4 \cdot kf5} + \frac{kr1 \cdot kr2}{kf1 \cdot kf2 \cdot kf3}} \\ 
  \frac{d H2O2}{dt} &= - \frac{H2O2 \cdot XT \cdot ascorbate}{\frac{H2O2}{kf2} + \frac{H2O2}{kf4} + \frac{ascorbate}{kf1} + H2O2 \cdot ascorbate \cdot (\frac{1}{kf3} + \frac{1}{kf5}) + \frac{kr1}{kf1 \cdot kf2} + \frac{H2O2 \cdot kr2}{kf2 \cdot kf3} + \frac{H2O2 \cdot kr4}{kf4 \cdot kf5} + \frac{kr1 \cdot kr2}{kf1 \cdot kf2 \cdot kf3}} \\
  & + convf \cdot O2 (dissolved)\_lumen \cdot P700FA- \cdot kMehler \\
  & + convf \cdot O2 (dissolved)\_lumen \cdot P700+FA- \cdot kMehler \\ 
  \frac{d DHA}{dt} &= kf\_mda\_reductase\_1 \cdot {MDA}^{2} \\
  & - \frac{DHA \cdot GSH \cdot vmax\_dehydroascorbate\_reductase}{K + DHA \cdot GSH + DHA \cdot km\_dehydroascorbate\_reductase\_GSH + GSH \cdot km\_dehydroascorbate\_reductase\_DHA} \\ 
  \frac{d GSSG}{dt} &= - \frac{GSSG \cdot NADPH \cdot vmax\_glutathion\_reductase}{GSSG \cdot NADPH + GSSG \cdot km\_glutathion\_reductase\_NADPH + NADPH \cdot km\_glutathion\_reductase\_GSSG + km\_glutathion\_reductase\_GSSG \cdot km\_glutathion\_reductase\_NADPH} \\
  & + \frac{DHA \cdot GSH \cdot vmax\_dehydroascorbate\_reductase}{K + DHA \cdot GSH + DHA \cdot km\_dehydroascorbate\_reductase\_GSH + GSH \cdot km\_dehydroascorbate\_reductase\_DHA} \\ 
  \frac{d Thioredoxin (oxidised)}{dt} &= - Ferredoxine (reduced) \cdot Thioredoxin (oxidised) \cdot kf\_ferredoxin\_thioredoxin\_reductase \\
  & + 5 \cdot E\_inactive \cdot Thioredoxin (reduced) \cdot kf\_tr\_activation \\ 
  \frac{d E\_inactive}{dt} &= - 5 \cdot E\_inactive \cdot Thioredoxin (reduced) \cdot kf\_tr\_activation \\
  & + 5 \cdot E\_active \cdot kf\_tr\_inactivation \\ 
  \frac{d P700FA}{dt} &= Ferredoxine (oxidised) \cdot P700FA- \cdot kFdred - \frac{Ferredoxine (reduced) \cdot P700FA \cdot kFdred}{keq\_FAFd} \\
  & + P700+FA \cdot Plastocyanine (reduced) \cdot kPCox - \frac{P700FA \cdot Plastocyanine (oxidised) \cdot kPCox}{keq\_PCP700} \\
  & - P700FA \cdot PPFD \cdot (1 - PSII\_cross\_section) \\
  & + 2 \cdot O2 (dissolved)\_lumen \cdot P700FA- \cdot kMehler \\ 
  \frac{d P700+FA-}{dt} &= - P700+FA- \cdot Plastocyanine (reduced) \cdot kPCox - \frac{P700FA- \cdot Plastocyanine (oxidised) \cdot kPCox}{keq\_PCP700} \\
  & - Ferredoxine (oxidised) \cdot P700+FA- \cdot kFdred - \frac{Ferredoxine (reduced) \cdot P700+FA \cdot kFdred}{keq\_FAFd} \\
  & + P700FA \cdot PPFD \cdot (1 - PSII\_cross\_section) \\
  & - 2 \cdot O2 (dissolved)\_lumen \cdot P700+FA- \cdot kMehler \\ 
  \frac{d P700FA-}{dt} &= P700+FA- \cdot Plastocyanine (reduced) \cdot kPCox - \frac{P700FA- \cdot Plastocyanine (oxidised) \cdot kPCox}{keq\_PCP700} \\
  & - Ferredoxine (oxidised) \cdot P700FA- \cdot kFdred - \frac{Ferredoxine (reduced) \cdot P700FA \cdot kFdred}{keq\_FAFd} \\
  & - 2 \cdot O2 (dissolved)\_lumen \cdot P700FA- \cdot kMehler \\ 
  \frac{d B0}{dt} &= - B0 \cdot PPFD \cdot PSII\_cross\_section \\
  & + B1 \cdot (kH0 + Q \cdot kH\_Qslope) + B1 \cdot kF \\
  & + B2 \cdot Plastoquinone (oxidised) \cdot kPQred - \frac{B0 \cdot Plastoquinone (reduced) \cdot kPQred}{keq\_Plastoquinone (reduced)} \\ 
  \frac{d B1}{dt} &= B0 \cdot PPFD \cdot PSII\_cross\_section \\
  & - B1 \cdot (kH0 + Q \cdot kH\_Qslope) - B1 \cdot kF \\
  & - B1 \cdot k2 \\ 
  \frac{d B2}{dt} &= B1 \cdot k2 \\
  & - B2 \cdot Plastoquinone (oxidised) \cdot kPQred - \frac{B0 \cdot Plastoquinone (reduced) \cdot kPQred}{keq\_Plastoquinone (reduced)} \\
  & - B2 \cdot PPFD \cdot PSII\_cross\_section + B3 \cdot kF \\
  & + B3 \cdot (kH0 + Q \cdot kH\_Qslope) \\ 
  \frac{d pH\_lumen}{dt} &= 0.04666666666666667 \cdot ATP\_pmf\_activity \cdot ATPactivity \cdot k\_ATPsynthase \cdot (\frac{ADP}{convf} - \frac{ATP}{convf \cdot kf\_atp\_synthase}) \\
  & + 0.01 \cdot kf\_proton\_leak \cdot (protons\_lumen - 4000 \cdot {10}^{- pH}) \\
  & - 0.01 \cdot B1 \cdot k2 \\
  & - 0.04 \cdot \frac{Plastocyanine (oxidised) \cdot Plastoquinone (reduced) \cdot keq\_b6f\_dyn}{Plastoquinone (oxidised) + Plastoquinone (reduced)} - \frac{Plastocyanine (reduced) \cdot keq\_b6f\_dyn \cdot (1 - \frac{Plastoquinone (reduced)}{Plastoquinone (oxidised) + Plastoquinone (reduced)})}{keq\_b6f} \\
  & + 0.01 \cdot \max(0, KEA3\_reg \cdot k\_KEA \cdot (K\_stroma \cdot protons\_lumen - K\_lumen \cdot protons)) \\
  & - 0.04 \cdot \frac{0.9 \cdot Plastoquinone (oxidised) \cdot k\_NDH1 \cdot {10}^{-6.5 + pH\_lumen} \cdot {Ferredoxine (reduced)}^{2}}{(0.5 + {10}^{-6.5 + pH\_lumen}) \cdot (1 + 7.38905609893065 \cdot e^{- 100 \cdot P700+FA-})} \\ 
  \frac{d pH}{dt} &= - 0.011666666666666667 \cdot ATP\_pmf\_activity \cdot ATPactivity \cdot k\_ATPsynthase \cdot (\frac{ADP}{convf} - \frac{ATP}{convf \cdot kf\_atp\_synthase}) \\
  & - 0.0025 \cdot kf\_proton\_leak \cdot (protons\_lumen - 4000 \cdot {10}^{- pH}) \\
  & + 0.0025 \cdot B2 \cdot Plastoquinone (oxidised) \cdot kPQred - \frac{B0 \cdot Plastoquinone (reduced) \cdot kPQred}{keq\_Plastoquinone (reduced)} \\
  & + 0.01 \cdot \frac{Plastocyanine (oxidised) \cdot Plastoquinone (reduced) \cdot keq\_b6f\_dyn}{Plastoquinone (oxidised) + Plastoquinone (reduced)} - \frac{Plastocyanine (reduced) \cdot keq\_b6f\_dyn \cdot (1 - \frac{Plastoquinone (reduced)}{Plastoquinone (oxidised) + Plastoquinone (reduced)})}{keq\_b6f} \\
  & - 0.0025 \cdot \max(0, KEA3\_reg \cdot k\_KEA \cdot (K\_stroma \cdot protons\_lumen - K\_lumen \cdot protons)) \\
  & + 0.01 \cdot \frac{0.9 \cdot Plastoquinone (oxidised) \cdot k\_NDH1 \cdot {10}^{-6.5 + pH\_lumen} \cdot {Ferredoxine (reduced)}^{2}}{(0.5 + {10}^{-6.5 + pH\_lumen}) \cdot (1 + 7.38905609893065 \cdot e^{- 100 \cdot P700+FA-})} \\ 
  \frac{d ATPactivity}{dt} &= \begin{cases}kActATPase \cdot (1 - ATPactivity) & PPFD > 0 \\ - ATPactivity \cdot kDeactATPase & \text{else}\end{cases} \\ 
  \frac{d delta\_psi}{dt} &= - HPR \cdot volts\_per\_charge \cdot ATP\_pmf\_activity \cdot ATPactivity \cdot k\_ATPsynthase \cdot (\frac{ADP}{convf} - \frac{ATP}{convf \cdot kf\_atp\_synthase}) \\
  & - 1 \cdot volts\_per\_charge \cdot kf\_proton\_leak \cdot (protons\_lumen - 4000 \cdot {10}^{- pH}) \\
  & + volts\_per\_charge \cdot B1 \cdot k2 \\
  & + 4 \cdot volts\_per\_charge \cdot \frac{Plastocyanine (oxidised) \cdot Plastoquinone (reduced) \cdot keq\_b6f\_dyn}{Plastoquinone (oxidised) + Plastoquinone (reduced)} - \frac{Plastocyanine (reduced) \cdot keq\_b6f\_dyn \cdot (1 - \frac{Plastoquinone (reduced)}{Plastoquinone (oxidised) + Plastoquinone (reduced)})}{keq\_b6f} \\
  & - 1 \cdot volts\_per\_charge \cdot \frac{0.9 \cdot K\_lumen \cdot dG\_K\_ions \cdot perm\_K}{K\_stroma \cdot (1 + e^{1000 \cdot K\_delta\_psi\_treshold - 1000 \cdot delta\_psi})} \\
  & - 1 \cdot volts\_per\_charge \cdot \frac{0.9 \cdot Cl\_driving\_force \cdot Cl\_stroma \cdot k\_VCCN1}{Cl\_lumen \cdot (1 + e^{1000 \cdot VCCN\_delta\_psi\_treshold - 1000 \cdot delta\_psi})} \\
  & + volts\_per\_charge \cdot \frac{0.9 \cdot k\_Cl\_leak \cdot {Cl\_lumen - Cl\_stroma}^{2}}{total\_Cl\_2 \cdot (1 + e^{10 \cdot Cl\_leak\_PQ - 10 \cdot Plastoquinone (oxidised)})} \\
  & + 4 \cdot volts\_per\_charge \cdot \frac{0.9 \cdot Plastoquinone (oxidised) \cdot k\_NDH1 \cdot {10}^{-6.5 + pH\_lumen} \cdot {Ferredoxine (reduced)}^{2}}{(0.5 + {10}^{-6.5 + pH\_lumen}) \cdot (1 + 7.38905609893065 \cdot e^{- 100 \cdot P700+FA-})} \\ 
  \frac{d K\_stroma}{dt} &= - \max(0, KEA3\_reg \cdot k\_KEA \cdot (K\_stroma \cdot protons\_lumen - K\_lumen \cdot protons)) \\
  & + \frac{0.9 \cdot K\_lumen \cdot dG\_K\_ions \cdot perm\_K}{K\_stroma \cdot (1 + e^{1000 \cdot K\_delta\_psi\_treshold - 1000 \cdot delta\_psi})} \\ 
  \frac{d Cl\_stroma}{dt} &= - \frac{0.9 \cdot Cl\_driving\_force \cdot Cl\_stroma \cdot k\_VCCN1}{Cl\_lumen \cdot (1 + e^{1000 \cdot VCCN\_delta\_psi\_treshold - 1000 \cdot delta\_psi})} \\
  & + \frac{0.9 \cdot k\_Cl\_leak \cdot {Cl\_lumen - Cl\_stroma}^{2}}{total\_Cl\_2 \cdot (1 + e^{10 \cdot Cl\_leak\_PQ - 10 \cdot Plastoquinone (oxidised)})} \\
  & - ClCe\_activation \cdot k\_ClCe \cdot (Cl\_stroma - Cl\_lumen)
\end{align*}