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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 Q\_active}{dt} &= \frac{k3 \cdot (1 - Q\_active)}{1 + {\frac{keq\_NPQ}{H\_lumen}}^{n\_NPQ}} \\
& - Q\_active \cdot k4 \\
\frac{d PQ}{dt} &= - 0.5 \cdot PQ \cdot RCII\_closed \cdot k1p - PQH\_2 \cdot RCII\_open \cdot k1m \\
& + 0.5 \cdot PQH\_2 \cdot PSI\_ox \cdot k2p - PQ \cdot PSI\_red \cdot k2m \\
& + PQH\_2 \cdot k\_X \\
\frac{d PSI\_ox}{dt} &= \frac{L\_PSI \cdot osc\_light \cdot sigma\_PSI\_0 \cdot stoic\_PSI \cdot (stoic\_PSI - PSI\_ox)}{L\_PSI + osc\_light} \\
& - PQH\_2 \cdot PSI\_ox \cdot k2p - PQ \cdot PSI\_red \cdot k2m \\
\frac{d H\_lumen}{dt} &= \frac{bH}{N\_A \cdot V\_lumen} \cdot osc\_light \cdot sigma\_PSII \cdot stoic\_PSII \cdot (1 - RCII\_closed) \\
& + \frac{bH}{N\_A \cdot V\_lumen} \cdot PQH\_2 \cdot PSI\_ox \cdot k2p - PQ \cdot PSI\_red \cdot k2m \\
& - \frac{4.666666666666667 \cdot V\_stroma \cdot bH}{V\_lumen} \cdot k5 \cdot (ADP\_st - \frac{ATP\_st \cdot {\frac{H\_stroma}{H\_lumen}}^{4.666666666666667}}{cEqP}) \\
& - k7 \cdot (H\_lumen - H\_stroma) \\
\frac{d ATP\_st}{dt} &= k5 \cdot (ADP\_st - \frac{ATP\_st \cdot {\frac{H\_stroma}{H\_lumen}}^{4.666666666666667}}{cEqP}) \\
& - ATP\_st \cdot k6
\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
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| Parameter | Fit | Log-space | Initial guess / fixed value | Fitted value |
|---|---|---|---|---|
| stoic_PSII | — | |||
| stoic_PSI | — | |||
| PQ_tot | — | |||
| H_stroma | — | |||
| AP_tot | — | |||
| V_lumen | — | |||
| V_stroma | — | |||
| sigma_PSI_0 | — | |||
| k1p | — | |||
| k1m | — | |||
| k2p | — | |||
| k2m | — | |||
| k3 | — | |||
| k4 | — | |||
| k5 | — | |||
| k6 | — | |||
| k7 | — | |||
| k_X | — | |||
| L_PSI | — | |||
| bH | — | |||
| NPQ_max | — | |||
| cEqP | — | |||
| keq_NPQ | — | |||
| n_NPQ | — | |||
| N_A | — | |||
| PPFD | — | |||
| PPFD_add | — | |||
| f | — | |||
| PSI_total | — | |||
| Fluo_0 | — | |||
| Q_total | — |
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