Saadat 2021 model
The Saadat 2021 model describes linear electron flow through photosystem I (PSI) in the chloroplast. Electrons pass from plastocyanin through P700 and the iron–sulfur cluster FA to ferredoxin and on to NADPH, driven by light (PPFD) and governed by Nernst equilibrium potentials.
The model also includes the Mehler reaction, in which O₂ is reduced at PSI, providing a focused, redox-resolved view of the PSI segment of the photosynthetic electron transport chain.
tune
Simulation parameters
analytics
Analyses
Simulation
Loading chart...
PAM Fluorescence
Loading chart...
Add analysis
Model Details
Review and edit model structure, biological variables, and kinetic parameters.
| Name | Tex name | Initial value | Actions |
|---|---|---|---|
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
Edit Options
preview
Generated LaTeX Code
\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{SBP}{ki\_rubisco\_carboxylase\_SBP} + \frac{3PGA}{ki\_rubisco\_carboxylase\_3PGA} + \frac{nadph}{ki\_rubisco\_carboxylase\_nadph} + \frac{pi}{ki\_rubisco\_carboxylase\_pi}))} \\
& - kre\_phosphoglycerate\_kinase \cdot (3PGA \cdot atp - \frac{BPGA \cdot adp}{keq\_phosphoglycerate\_kinase}) \\
& - \frac{3PGA \cdot vmax\_ex\_pga}{N\_translocator \cdot km\_ex\_pga} \\
\frac{d BPGA}{dt} &= kre\_phosphoglycerate\_kinase \cdot (3PGA \cdot atp - \frac{BPGA \cdot adp}{keq\_phosphoglycerate\_kinase}) \\
& - kre\_gadph \cdot (BPGA \cdot nadph \cdot protons - \frac{GAP \cdot nadp \cdot pi}{keq\_gadph}) \\
\frac{d GAP}{dt} &= kre\_gadph \cdot (BPGA \cdot nadph \cdot protons - \frac{GAP \cdot nadp \cdot pi}{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{pi}{ki\_fbpase\_pi})} \\
\frac{d F6P}{dt} &= \frac{FBP \cdot vmax\_fbpase}{FBP + km\_fbpase\_s \cdot (1 + \frac{F6P}{ki\_fbpase\_F6P} + \frac{pi}{ki\_fbpase\_pi})} \\
& - 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{G1P \cdot atp \cdot vmax\_ex\_g1p}{(G1P + km\_ex\_g1p\_G1P) \cdot ((1 + \frac{adp}{ki\_ex\_g1p}) \cdot (atp + km\_ex\_g1p\_atp) + \frac{km\_ex\_g1p\_atp \cdot pi}{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{pi}{ki\_SBPase\_pi})} \\
\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{pi}{ki\_SBPase\_pi})} \\
\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{SBP}{ki\_rubisco\_carboxylase\_SBP} + \frac{3PGA}{ki\_rubisco\_carboxylase\_3PGA} + \frac{nadph}{ki\_rubisco\_carboxylase\_nadph} + \frac{pi}{ki\_rubisco\_carboxylase\_pi}))} \\
& + \frac{RU5P \cdot atp \cdot vmax\_phosphoribulokinase}{(RU5P + km\_phosphoribulokinase\_RU5P \cdot (1 + \frac{RUBP}{ki\_phosphoribulokinase\_RUBP} + \frac{3PGA}{ki\_phosphoribulokinase\_3PGA} + \frac{pi}{ki\_phosphoribulokinase\_pi})) \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{RU5P \cdot atp \cdot vmax\_phosphoribulokinase}{(RU5P + km\_phosphoribulokinase\_RU5P \cdot (1 + \frac{RUBP}{ki\_phosphoribulokinase\_RUBP} + \frac{3PGA}{ki\_phosphoribulokinase\_3PGA} + \frac{pi}{ki\_phosphoribulokinase\_pi})) \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 kf\_atp\_synthase \cdot (\frac{adp}{convf} - \frac{atp}{convf \cdot keq\_atp\_synthase}) \\
& - kre\_phosphoglycerate\_kinase \cdot (3PGA \cdot atp - \frac{BPGA \cdot adp}{keq\_phosphoglycerate\_kinase}) \\
& - \frac{RU5P \cdot atp \cdot vmax\_phosphoribulokinase}{(RU5P + km\_phosphoribulokinase\_RU5P \cdot (1 + \frac{RUBP}{ki\_phosphoribulokinase\_RUBP} + \frac{3PGA}{ki\_phosphoribulokinase\_3PGA} + \frac{pi}{ki\_phosphoribulokinase\_pi})) \cdot (atp \cdot (1 + \frac{adp}{ki\_phosphoribulokinase\_4}) + km\_phosphoribulokinase\_atp \cdot (1 + \frac{adp}{ki\_phosphoribulokinase\_5}))} \\
& - \frac{G1P \cdot atp \cdot vmax\_ex\_g1p}{(G1P + km\_ex\_g1p\_G1P) \cdot ((1 + \frac{adp}{ki\_ex\_g1p}) \cdot (atp + km\_ex\_g1p\_atp) + \frac{km\_ex\_g1p\_atp \cdot pi}{F6P \cdot ki\_ex\_g1p\_F6P + FBP \cdot ki\_ex\_g1p\_FBP + 3PGA \cdot ki\_ex\_g1p\_3PGA})} \\
& - atp \cdot kf\_ex\_atp \\
\frac{d fd\_ox}{dt} &= fd\_red \cdot kf\_ferredoxin\_thioredoxin\_reductase \cdot tr\_ox \\
& + 2 \cdot kf\_cyclic\_electron\_flow \cdot pq\_ox \cdot {fd\_red}^{2} \\
& + 2 \cdot \frac{vmax\_fnr \cdot (\frac{nadp \cdot {\frac{fd\_red}{km\_fnr\_fd\_red}}^{2}}{convf \cdot km\_fnr\_nadp} - \frac{nadph \cdot {\frac{fd\_ox}{km\_fnr\_fd\_red}}^{2}}{convf \cdot keq\_fnr \cdot km\_fnr\_nadp})}{-1 + (1 + \frac{nadp}{convf \cdot km\_fnr\_nadp}) \cdot (1 + {\frac{fd\_red}{km\_fnr\_fd\_red}}^{2} + \frac{fd\_red}{km\_fnr\_fd\_red}) + (1 + \frac{nadph}{convf \cdot km\_fnr\_nadp}) \cdot (1 + {\frac{fd\_ox}{km\_fnr\_fd\_red}}^{2} + \frac{fd\_ox}{km\_fnr\_fd\_red})} \\
& - ps1states \cdot fd\_ox \cdot vmax\_ferredoxin\_reductase - \frac{ps1states \cdot fd\_red \cdot vmax\_ferredoxin\_reductase}{keq\_ferredoxin\_reductase} \\
\frac{d protons\_lumen}{dt} &= - \frac{HPR}{bH} \cdot kf\_atp\_synthase \cdot (\frac{adp}{convf} - \frac{atp}{convf \cdot keq\_atp\_synthase}) \\
& + \frac{4}{bH} \cdot \max(- kcat\_b6f, kcat\_b6f \cdot (pq\_red \cdot {pc\_ox}^{2} - \frac{pq\_ox \cdot {pc\_red}^{2}}{keq\_b6f})) \\
& + \frac{2}{bH} \cdot 0.5 \cdot ps2states \cdot k2 \\
& - \frac{1}{bH} \cdot kf\_proton\_leak \cdot (protons\_lumen - 4000 \cdot {10}^{- pH}) \\
\frac{d lhc}{dt} &= - \frac{1 \cdot kStt7 \cdot lhc}{1 + {\frac{pq\_ox}{PQ\_tot \cdot km\_lhc\_state\_transition\_12}}^{n\_ST}} \\
& + kPph1 \cdot lhc\_prot \\
\frac{d nadph}{dt} &= convf \cdot \frac{vmax\_fnr \cdot (\frac{nadp \cdot {\frac{fd\_red}{km\_fnr\_fd\_red}}^{2}}{convf \cdot km\_fnr\_nadp} - \frac{nadph \cdot {\frac{fd\_ox}{km\_fnr\_fd\_red}}^{2}}{convf \cdot keq\_fnr \cdot km\_fnr\_nadp})}{-1 + (1 + \frac{nadp}{convf \cdot km\_fnr\_nadp}) \cdot (1 + {\frac{fd\_red}{km\_fnr\_fd\_red}}^{2} + \frac{fd\_red}{km\_fnr\_fd\_red}) + (1 + \frac{nadph}{convf \cdot km\_fnr\_nadp}) \cdot (1 + {\frac{fd\_ox}{km\_fnr\_fd\_red}}^{2} + \frac{fd\_ox}{km\_fnr\_fd\_red})} \\
& - kre\_gadph \cdot (BPGA \cdot nadph \cdot protons - \frac{GAP \cdot nadp \cdot pi}{keq\_gadph}) \\
& - \frac{MDA \cdot nadph \cdot vmax\_mda\_reductase\_2}{MDA \cdot km\_mda\_reductase\_2\_nadph + MDA \cdot nadph + km\_mda\_reductase\_2\_MDA \cdot km\_mda\_reductase\_2\_nadph + km\_mda\_reductase\_2\_MDA \cdot nadph} \\
& - \frac{GSSG \cdot nadph \cdot vmax\_glutathion\_reductase}{GSSG \cdot km\_glutathion\_reductase\_nadph + GSSG \cdot nadph + km\_glutathion\_reductase\_GSSG \cdot km\_glutathion\_reductase\_nadph + km\_glutathion\_reductase\_GSSG \cdot nadph} \\
& - kf\_ex\_nadph \cdot nadph \\
\frac{d pc\_ox}{dt} &= - 2 \cdot \max(- kcat\_b6f, kcat\_b6f \cdot (pq\_red \cdot {pc\_ox}^{2} - \frac{pq\_ox \cdot {pc\_red}^{2}}{keq\_b6f})) \\
& + ps1states \cdot PPFD \cdot (1 - PSII\_cross\_section) \\
\frac{d pq\_ox}{dt} &= \max(- kcat\_b6f, kcat\_b6f \cdot (pq\_red \cdot {pc\_ox}^{2} - \frac{pq\_ox \cdot {pc\_red}^{2}}{keq\_b6f})) \\
& - kf\_cyclic\_electron\_flow \cdot pq\_ox \cdot {fd\_red}^{2} \\
& - kf\_ndh \cdot pq\_ox - 0.5 \cdot ps2states \cdot k2 \\
& + O2\_lumen \cdot kPTOX \cdot pq\_red \\
\frac{d psbs\_de}{dt} &= - \frac{kf\_lhc\_protonation \cdot psbs\_de \cdot {protons\_lumen}^{kh\_lhc\_protonation}}{{protons\_lumen}^{kh\_lhc\_protonation} + {4000 \cdot {10}^{- ksat\_lhc\_protonation}}^{kh\_lhc\_protonation}} \\
& + kf\_lhc\_deprotonation \cdot psbs\_pr \\
\frac{d vx}{dt} &= - \frac{kf\_violaxanthin\_deepoxidase \cdot vx \cdot {protons\_lumen}^{kh\_violaxanthin\_deepoxidase}}{{protons\_lumen}^{kh\_violaxanthin\_deepoxidase} + {4000 \cdot {10}^{- ksat\_violaxanthin\_deepoxidase}}^{kh\_violaxanthin\_deepoxidase}} \\
& + kf\_zeaxanthin\_epoxidase \cdot zx \\
\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 km\_mda\_reductase\_2\_nadph + MDA \cdot nadph + km\_mda\_reductase\_2\_MDA \cdot km\_mda\_reductase\_2\_nadph + km\_mda\_reductase\_2\_MDA \cdot 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} &= convf \cdot ps1states \cdot O2\_lumen \cdot kMehler \\
& - \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 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 km\_glutathion\_reductase\_nadph + GSSG \cdot nadph + km\_glutathion\_reductase\_GSSG \cdot km\_glutathion\_reductase\_nadph + km\_glutathion\_reductase\_GSSG \cdot 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 tr\_ox}{dt} &= - fd\_red \cdot kf\_ferredoxin\_thioredoxin\_reductase \cdot tr\_ox \\
& + 5 \cdot E\_inactive \cdot kf\_tr\_activation \cdot tr\_red \\
\frac{d E\_inactive}{dt} &= - 5 \cdot E\_inactive \cdot kf\_tr\_activation \cdot tr\_red \\
& + 5 \cdot E\_active \cdot kf\_tr\_inactivation
\end{align*}Fit to data
Fit settings
| Setting | Value |
|---|---|
| Fit backend | |
| Function evaluations per progress update | |
| Maximum total function evaluations | |
| Stop once residual norm reaches |
Curriculum learning (advanced)
Every bar shares one fixed step budget. Drag a divider to move a cutoff, drag a bar's top edge (or focus it and use the arrow keys) to change its share — the final stage isn't draggable, it always gets whatever's left. Double-click a bar or use its + to split it, use a divider's × (or Delete/Backspace while it's focused) to remove it.
Split into equal stages:
min viable
t=0 t=100
| Stage | Data cutoff | Iteration budget |
|---|---|---|
| 1 (final) | full data | 1000 iterations (runs to convergence within this) |
Data
Plot options
| Parameter | Fit | Log-space | Initial guess / fixed value | Fitted value |
|---|---|---|---|---|
| PPFD | — | |||
| CO2__dissolved_ | — | |||
| O2_lumen | — | |||
| pH | — | |||
| protons | — | |||
| bH | — | |||
| F | — | |||
| E_0_PC | — | |||
| E_0_P700 | — | |||
| E_0_FA | — | |||
| E_0_Fd | — | |||
| E_0_NADP | — | |||
| convf | — | |||
| R | — | |||
| T | — | |||
| Carotenoids_tot | — | |||
| Fd_ | — | |||
| PC_tot | — | |||
| PSBS_tot | — | |||
| LHC_tot | — | |||
| gamma0 | — | |||
| gamma1 | — | |||
| gamma2 | — | |||
| gamma3 | — | |||
| kZSat | — | |||
| E_0_QA | — | |||
| E_0_PQ | — | |||
| PQ_tot | — | |||
| staticAntII | — | |||
| staticAntI | — | |||
| Thioredoxin_tot | — | |||
| E_total | — | |||
| NADP_ | — | |||
| A_P | — | |||
| Pi_tot | — | |||
| kf_ferredoxin_thioredoxin_reductase | — | |||
| kf_tr_activation | — | |||
| kf_tr_inactivation | — | |||
| ASC_tot_ | — | |||
| Glutathion_tot | — | |||
| kf_atp_synthase | — | |||
| HPR | — | |||
| Pi_mol | — | |||
| DeltaG0_ATP | — | |||
| kcat_b6f | — | |||
| kh_lhc_protonation | — | |||
| kf_lhc_protonation | — | |||
| ksat_lhc_protonation | — | |||
| kf_lhc_deprotonation | — | |||
| kf_cyclic_electron_flow | — | |||
| kf_violaxanthin_deepoxidase | — | |||
| kh_violaxanthin_deepoxidase | — | |||
| ksat_violaxanthin_deepoxidase | — | |||
| kf_zeaxanthin_epoxidase | — | |||
| km_fnr_fd_red | — | |||
| km_fnr_nadp | — | |||
| E0_fnr | — | |||
| kcat_fnr | — | |||
| kf_ndh | — | |||
| PSII_total | — | |||
| PSI_total | — | |||
| kH0 | — | |||
| kPQred | — | |||
| kPCox | — | |||
| kFdred | — | |||
| k2 | — | |||
| kH | — | |||
| kF | — | |||
| kMehler | — | |||
| E0_ferredoxin_reductase | — | |||
| kcat_ferredoxin_reductase | — | |||
| kf_proton_leak | — | |||
| kPTOX | — | |||
| kStt7 | — | |||
| km_lhc_state_transition_12 | — | |||
| n_ST | — | |||
| kPph1 | — | |||
| E0_rubisco | — | |||
| kcat_rubisco_carboxylase | — | |||
| km_rubisco_carboxylase_RUBP | — | |||
| km_rubisco_carboxylase_CO2__dissolved_ | — | |||
| ki_rubisco_carboxylase_3PGA | — | |||
| ki_rubisco_carboxylase_FBP | — | |||
| ki_rubisco_carboxylase_SBP | — | |||
| ki_rubisco_carboxylase_pi | — | |||
| ki_rubisco_carboxylase_nadph | — | |||
| kre_phosphoglycerate_kinase | — | |||
| keq_phosphoglycerate_kinase | — | |||
| kre_gadph | — | |||
| keq_gadph | — | |||
| kre_triose_phosphate_isomerase | — | |||
| keq_triose_phosphate_isomerase | — | |||
| kre_aldolase_dhap_gap | — | |||
| keq_aldolase_dhap_gap | — | |||
| kre_aldolase_dhap_e4p | — | |||
| keq_aldolase_dhap_e4p | — | |||
| E0_fbpase | — | |||
| kcat_fbpase | — | |||
| km_fbpase_s | — | |||
| ki_fbpase_F6P | — | |||
| ki_fbpase_pi | — | |||
| kre_transketolase_gap_f6p | — | |||
| keq_transketolase_gap_f6p | — | |||
| kre_transketolase_gap_s7p | — | |||
| keq_transketolase_gap_s7p | — | |||
| E0_SBPase | — | |||
| kcat_SBPase | — | |||
| km_SBPase_s | — | |||
| ki_SBPase_pi | — | |||
| kre_ribose_phosphate_isomerase | — | |||
| keq_ribose_phosphate_isomerase | — | |||
| kre_ribulose_phosphate_epimerase | — | |||
| keq_ribulose_phosphate_epimerase | — | |||
| E0_phosphoribulokinase | — | |||
| kcat_phosphoribulokinase | — | |||
| km_phosphoribulokinase_RU5P | — | |||
| km_phosphoribulokinase_atp | — | |||
| ki_phosphoribulokinase_3PGA | — | |||
| ki_phosphoribulokinase_RUBP | — | |||
| ki_phosphoribulokinase_pi | — | |||
| ki_phosphoribulokinase_4 | — | |||
| ki_phosphoribulokinase_5 | — | |||
| kre_g6pi | — | |||
| keq_g6pi | — | |||
| kre_phosphoglucomutase | — | |||
| keq_phosphoglucomutase | — | |||
| pi_ext | — | |||
| km_ex_pga | — | |||
| km_ex_gap | — | |||
| km_ex_dhap | — | |||
| km_N_translocator_pi_ext | — | |||
| km_N_translocator_pi | — | |||
| kcat_N_translocator | — | |||
| E0_N_translocator | — | |||
| E0_ex_g1p | — | |||
| km_ex_g1p_G1P | — | |||
| km_ex_g1p_atp | — | |||
| ki_ex_g1p | — | |||
| ki_ex_g1p_3PGA | — | |||
| ki_ex_g1p_F6P | — | |||
| ki_ex_g1p_FBP | — | |||
| kcat_ex_g1p | — | |||
| kf_mda_reductase_1 | — | |||
| E0_mda_reductase_2 | — | |||
| kcat_mda_reductase_2 | — | |||
| km_mda_reductase_2_nadph | — | |||
| km_mda_reductase_2_MDA | — | |||
| kf1 | — | |||
| kr1 | — | |||
| kf2 | — | |||
| kr2 | — | |||
| kf3 | — | |||
| kf4 | — | |||
| kr4 | — | |||
| kf5 | — | |||
| XT | — | |||
| E0_glutathion_reductase | — | |||
| kcat_glutathion_reductase | — | |||
| km_glutathion_reductase_nadph | — | |||
| km_glutathion_reductase_GSSG | — | |||
| km_dehydroascorbate_reductase_DHA | — | |||
| km_dehydroascorbate_reductase_GSH | — | |||
| K | — | |||
| E0_dehydroascorbate_reductase | — | |||
| kcat_dehydroascorbate_reductase | — | |||
| kf_ex_atp | — | |||
| kf_ex_nadph | — |
Edit analysis
Plot options
Variable selection
Show Normalize
Edit PAM analysis
Protocol phases
Group 1 - repeat times
PFD Duration (s) Label
Group 2 - repeat times
PFD Duration (s) Label
Group 3 - repeat times
PFD Duration (s) Label
Variable selection
Show Normalize