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.
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\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*}Edit analysis
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Group 1 - repeat times
PFD Duration (s) Label
Group 2 - repeat times
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Group 3 - repeat times
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