Hahn 1987 model
The Hahn 1987 model is a comprehensive description of C3 leaf carbon metabolism that combines the Calvin cycle with the glycolate and glycerate pathways of photorespiration, formulated as a large system of non-linear differential equations. It extends Hahn's earlier Calvin-cycle models by adding the competitive inhibition of ribulose-bisphosphate carboxylase by oxygen.
The model settles to an effectively stable steady state and responds realistically to changes in external CO₂ and O₂: photosynthesis is inhibited by higher oxygen levels, while photorespiration is suppressed by higher carbon dioxide levels.
Initial conditions
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Model Details
Review and edit model structure, biological variables, and kinetic parameters.
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Generated LaTeX Code
\begin{align*}
\frac{d RuBP}{dt} &= - CO2 \cdot RuBP \cdot k1 + ATP \cdot Ru5P \cdot k9 \\
& - O2 \cdot RuBP \cdot k16 \\
\frac{d PGA}{dt} &= 2 \cdot CO2 \cdot RuBP \cdot k1 - ATP \cdot PGA \cdot k3 \\
& + O2 \cdot RuBP \cdot k16 + ATP \cdot GA \cdot k21 \\
\frac{d ADP}{dt} &= - ADP \cdot Pi \cdot k2 + ATP \cdot PGA \cdot k3 \\
& + ATP \cdot Ru5P \cdot k9 + ATP \cdot HP \cdot k10 \\
& + ATP \cdot GA \cdot k21 + ATP \cdot GmA \cdot NH3 \cdot k22 \\
\frac{d Pi}{dt} &= - ADP \cdot Pi \cdot k2 + ATP \cdot PGA \cdot k3 \\
& + k4 \cdot {TP}^{2} + E4P \cdot TP \cdot k6 \\
& + 2 \cdot ATP \cdot HP \cdot k10 - GG \cdot Pi \cdot k11 \\
& + Pio \cdot TP \cdot k12 + PGl \cdot k17 \\
& + ATP \cdot GmA \cdot NH3 \cdot k22 \\
\frac{d TP}{dt} &= ATP \cdot PGA \cdot k3 - 2 \cdot k4 \cdot {TP}^{2} \\
& - E4P \cdot TP \cdot k6 - TP \cdot TPGA \cdot k8 \\
& - Pio \cdot TP \cdot k12 \\
\frac{d HP}{dt} &= k4 \cdot {TP}^{2} - HP \cdot k5 - ATP \cdot HP \cdot k10 \\
& + GG \cdot Pi \cdot k11 \\
\frac{d GG}{dt} &= ATP \cdot HP \cdot k10 - GG \cdot Pi \cdot k11 \\
\frac{d Pio}{dt} &= - Pio \cdot TP \cdot k12 + k13 \cdot {TPo}^{2} \\
& - Pio \cdot UDP \cdot k14 + 3 \cdot HPo \cdot UTP \cdot k15 \\
\frac{d TPo}{dt} &= Pio \cdot TP \cdot k12 - 2 \cdot k13 \cdot {TPo}^{2} \\
\frac{d HPo}{dt} &= k13 \cdot {TPo}^{2} - 2 \cdot HPo \cdot UTP \cdot k15 \\
\frac{d UDP}{dt} &= - Pio \cdot UDP \cdot k14 + HPo \cdot UTP \cdot k15 \\
\frac{d GF}{dt} &= HPo \cdot UTP \cdot k15 - GF \cdot rd - phis \cdot (GF - E) \\
& - D \cdot (GF - GFV) \\
\frac{d GFV}{dt} &= D \cdot (GF - GFV) \\
\frac{d TPGA}{dt} &= HP \cdot k5 + S7P \cdot k7 - TP \cdot TPGA \cdot k8 \\
\frac{d E4P}{dt} &= HP \cdot k5 - E4P \cdot TP \cdot k6 \\
\frac{d S7P}{dt} &= E4P \cdot TP \cdot k6 - S7P \cdot k7 \\
\frac{d Ru5P}{dt} &= S7P \cdot k7 + TP \cdot TPGA \cdot k8 \\
& - ATP \cdot Ru5P \cdot k9 \\
\frac{d PGl}{dt} &= O2 \cdot RuBP \cdot k16 - PGl \cdot k17 \\
\frac{d Gl}{dt} &= PGl \cdot k17 - 2 \cdot O2 \cdot k18 \cdot {Gl}^{2} \\
\frac{d Gx}{dt} &= 2 \cdot O2 \cdot k18 \cdot {Gl}^{2} - Gx \cdot Sn \cdot k19 \\
& - GmA \cdot Gx \cdot k24 \\
\frac{d Sn}{dt} &= - Gx \cdot Sn \cdot k19 + k20 \cdot {Gn}^{2} \\
\frac{d Gn}{dt} &= Gx \cdot Sn \cdot k19 - 2 \cdot k20 \cdot {Gn}^{2} \\
& + GmA \cdot Gx \cdot k24 \\
\frac{d GA}{dt} &= Gx \cdot Sn \cdot k19 - ATP \cdot GA \cdot k21 \\
\frac{d GmA}{dt} &= - ATP \cdot GmA \cdot NH3 \cdot k22 \\
& + 2 \cdot Glm \cdot OxA \cdot k23 - GmA \cdot Gx \cdot k24 \\
\frac{d Glm}{dt} &= ATP \cdot GmA \cdot NH3 \cdot k22 - Glm \cdot OxA \cdot k23 \\
\frac{d OxA}{dt} &= - Glm \cdot OxA \cdot k23 + GmA \cdot Gx \cdot k24 \\
\frac{d NH3}{dt} &= k20 \cdot {Gn}^{2} - ATP \cdot GmA \cdot NH3 \cdot k22 \\
\frac{d CO2}{dt} &= - CO2 \cdot RuBP \cdot k1 + k20 \cdot {Gn}^{2} \\
& + 12 \cdot GF \cdot rd + Ci \cdot kc1 - CO2 \cdot kc2 \\
\frac{d O2}{dt} &= - 0.5 \cdot CO2 \cdot RuBP \cdot k1 \\
& + 0.5 \cdot ATP \cdot PGA \cdot k3 \\
& + 0.5 \cdot HPo \cdot UTP \cdot k15 \\
& - O2 \cdot RuBP \cdot k16 - 0.5 \cdot k20 \cdot {Gn}^{2} \\
& + 0.5 \cdot ATP \cdot GmA \cdot NH3 \cdot k22 \\
& - 12 \cdot GF \cdot rd + Oi \cdot ko1 - O2 \cdot ko2 \\
\frac{d Ci}{dt} &= - Ci \cdot kc1 + CO2 \cdot kc2 + phic \cdot (Ca - Ci) \\
\frac{d Oi}{dt} &= - Oi \cdot ko1 + O2 \cdot ko2 + phio \cdot (Oa - Oi) \\
\frac{d AP\_tot}{dt} &= 0 \\
\frac{d UP\_tot}{dt} &= 0
\end{align*}