Yokota 1985 photorespiration model
The Yokota 1985 model is a kinetic description of the photorespiratory C2 cycle in plant chloroplasts and peroxisomes. Glycolate generated by Rubisco oxygenase flows through glyoxylate, glycine, serine and hydroxypyruvate, while the hydrogen peroxide produced by glycolate oxidase is scavenged by catalase.
Every enzymatic step follows Michaelis–Menten kinetics, so the model traces how carbon and reducing equivalents move through the photorespiratory pathway under varying conditions.
Simulation parameters
Analyses
Simulation
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Model Details
Review and edit model structure, biological variables, and kinetic parameters.
| Name | Tex name | Initial value | Actions |
|---|---|---|---|
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Generated LaTeX Code
\begin{align*}
\frac{d glycolate}{dt} &= kf\_phosphoglycolate\_phosphatase \\
& - \frac{glycolate \cdot vmax\_glycolate\_oxidase}{glycolate + km\_glycolate\_oxidase\_s} \\
\frac{d glyoxylate}{dt} &= \frac{glycolate \cdot vmax\_glycolate\_oxidase}{glycolate + km\_glycolate\_oxidase\_s} \\
& - \frac{glyoxylate \cdot vmax\_glycine\_transaminase}{glyoxylate + km\_glycine\_transaminase\_s} \\
& - \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
\frac{d glycine}{dt} &= \frac{glyoxylate \cdot vmax\_glycine\_transaminase}{glyoxylate + km\_glycine\_transaminase\_s} \\
& - 2 \cdot \frac{glycine \cdot vmax\_glycine\_decarboxylase}{glycine + km\_glycine\_decarboxylase\_s} \\
& + \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
\frac{d serine}{dt} &= \frac{glycine \cdot vmax\_glycine\_decarboxylase}{glycine + km\_glycine\_decarboxylase\_s} \\
& - \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
\frac{d hydroxypyruvate}{dt} &= \frac{glyoxylate \cdot serine \cdot vmax\_serine\_glyoxylate\_transaminase}{glyoxylate \cdot serine + \frac{glyoxylate}{km\_serine\_glyoxylate\_transaminase\_glyoxylate} + \frac{serine}{km\_serine\_glyoxylate\_transaminase\_serine} + \frac{1}{km\_serine\_glyoxylate\_transaminase\_glyoxylate \cdot km\_serine\_glyoxylate\_transaminase\_serine}} \\
& - \frac{hydroxypyruvate \cdot vmax\_glycerate\_dehydrogenase}{hydroxypyruvate + km\_glycerate\_dehydrogenase\_s} \\
\frac{d H2O2}{dt} &= \frac{glycolate \cdot vmax\_glycolate\_oxidase}{glycolate + km\_glycolate\_oxidase\_s} \\
& - \frac{H2O2 \cdot vmax\_catalase}{H2O2 + km\_catalase\_s}
\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.
| 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 |
|---|---|---|---|---|
| kf_phosphoglycolate_phosphatase | — | |||
| E0_glycolate_oxidase | — | |||
| kcat_glycolate_oxidase | — | |||
| km_glycolate_oxidase_s | — | |||
| E0_glycine_transaminase | — | |||
| kcat_glycine_transaminase | — | |||
| km_glycine_transaminase_s | — | |||
| E0_glycine_decarboxylase | — | |||
| kcat_glycine_decarboxylase | — | |||
| km_glycine_decarboxylase_s | — | |||
| E0_serine_glyoxylate_transaminase | — | |||
| kcat_serine_glyoxylate_transaminase | — | |||
| km_serine_glyoxylate_transaminase_glyoxylate | — | |||
| km_serine_glyoxylate_transaminase_serine | — | |||
| E0_glycerate_dehydrogenase | — | |||
| kcat_glycerate_dehydrogenase | — | |||
| km_glycerate_dehydrogenase_s | — | |||
| E0_catalase | — | |||
| kcat_catalase | — | |||
| km_catalase_s | — |