Matuszyńska 2016 NPQ model
The Matuszyńska 2016 NPQ model is an ODE model of photoprotection in plant photosystem II. It tracks the PSII open and closed states, the plastoquinone (PQ/PQH₂) redox pool, lumenal proton buffering, ATP synthesis, PsbS protonation and xanthophyll de-epoxidation (zeaxanthin formation) — the molecular machinery underlying non-photochemical quenching.
The model can be run under PAM fluorescence protocols, reproducing the Fm/Fm′ quenching observed experimentally and linking the fast photoprotective response to the redox state of the electron transport chain.
Simulation parameters
Analyses
Simulation
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PAM Fluorescence
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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 pq\_red}{dt} &= 0.5 \cdot ps2states \cdot k\_P \\
& - pq\_red \cdot (O2\_ex \cdot k\_PTOX + \frac{K\_cytb6f \cdot PPFD \cdot k\_Cytb6f}{1 + K\_cytb6f}) - \frac{PPFD \cdot k\_Cytb6f \cdot (PQ\_tot - pq\_red)}{1 + K\_cytb6f} \\
\frac{d protons}{dt} &= \frac{2}{b\_H} \cdot 0.5 \cdot ps2states \cdot k\_P \\
& + \frac{4}{b\_H} \cdot pq\_red \cdot (O2\_ex \cdot k\_PTOX + \frac{K\_cytb6f \cdot PPFD \cdot k\_Cytb6f}{1 + K\_cytb6f}) - \frac{PPFD \cdot k\_Cytb6f \cdot (PQ\_tot - pq\_red)}{1 + K\_cytb6f} \\
& - \frac{4.666666666666667}{b\_H} \cdot k\_ATPsynth \cdot vmax\_atp\_synthase \cdot (AP\_tot - atp - \frac{atp}{K\_ATPsynth}) \\
& - \frac{1}{b\_H} \cdot k\_leak \cdot (protons - H\_st) \\
\frac{d vmax\_atp\_synthase}{dt} &= \begin{cases}k\_ActATPase \cdot (1 - vmax\_atp\_synthase) & PPFD > 0 \\ - k\_DeactATPase \cdot vmax\_atp\_synthase & \text{else}\end{cases} \\
\frac{d atp}{dt} &= k\_ATPsynth \cdot vmax\_atp\_synthase \cdot (AP\_tot - atp - \frac{atp}{K\_ATPsynth}) \\
& - atp \cdot k\_ATPconsum \\
\frac{d psbs\_de}{dt} &= - - k\_deprot \cdot (PsbS\_tot - psbs\_de) + \frac{k\_prot \cdot psbs\_de \cdot {protons}^{nhl}}{{K\_pHSatLHC\_inv}^{nhl} + {protons}^{nhl}} \\
\frac{d vx}{dt} &= - - k\_EZ \cdot (X\_tot - vx) + \frac{k\_DV \cdot vx \cdot {protons}^{nhx}}{{K\_pHSat\_inv}^{nhx} + {protons}^{nhx}}
\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 |
|---|---|---|---|---|
| PSII_tot | — | |||
| PQ_tot | — | |||
| AP_tot | — | |||
| PsbS_tot | — | |||
| X_tot | — | |||
| O2_ex | — | |||
| Pi | — | |||
| k_Cytb6f | — | |||
| k_ActATPase | — | |||
| k_DeactATPase | — | |||
| k_ATPsynth | — | |||
| k_ATPconsum | — | |||
| k_PQH2 | — | |||
| k_H | — | |||
| k_F | — | |||
| k_P | — | |||
| k_PTOX | — | |||
| pH_st | — | |||
| k_leak | — | |||
| b_H | — | |||
| hpr | — | |||
| k_DV | — | |||
| k_EZ | — | |||
| K_pHSat | — | |||
| nhx | — | |||
| K_ZSat | — | |||
| nhl | — | |||
| k_deprot | — | |||
| k_prot | — | |||
| K_pHSatLHC | — | |||
| gamma_0 | — | |||
| gamma_1 | — | |||
| gamma_2 | — | |||
| gamma_3 | — | |||
| F | — | |||
| R | — | |||
| T | — | |||
| E0_QA | — | |||
| E0_PQ | — | |||
| E0_PC | — | |||
| DG_ATP | — | |||
| PPFD | — |