mxlmodels 1.0.0__py3-none-any.whl

mxlmodels/matuszynska2016_phd.py

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+"""Matuszynska 2016 PhD photosynthesis model.
+
+Full chloroplast electron transport chain with non-photochemical quenching (NPQ)
+and LHC state transitions. Covers PSII/PSI, cytochrome b6f, FNR, ATP synthase,
+the xanthophyll cycle (violaxanthin ↔ zeaxanthin), PsbS protonation, and
+cyclic electron flow around PSI.
+
+Reference: Matuszyńska, Anna Barbara.
+Mathematical models of light acclimation mechanisms in higher plants and green algae.
+Dissertation, Düsseldorf, Heinrich-Heine-Universität, 2016.
+"""
+
+import math
+
+import numpy as np
+from mxlpy import Derived, Model
+from mxlpy.surrogates import qss
+
+
+def _moiety_1(
+    concentration: float,
+    total: float,
+) -> float:
+    """Conservation moiety: total - concentration."""
+    return total - concentration
+
+
+def _mass_action_1s(
+    s1: float,
+    k_fwd: float,
+) -> float:
+    """Mass-action rate for one substrate."""
+    return k_fwd * s1
+
+
+def _dg_ph(
+    r: float,
+    t: float,
+) -> float:
+    """Thermodynamic coefficient dG/dpH = RT*ln(10) in kJ/mol."""
+    return np.log(10) * r * t
+
+
+def _ph_lumen(
+    protons: float,
+) -> float:
+    """Lumenal pH from proton concentration in mmol/mmol_Chl (conversion factor 0.00025)."""
+    return -np.log10(protons * 0.00025)
+
+
+def _quencher(
+    psbs: float,
+    vx: float,
+    psbsp: float,
+    zx: float,
+    y0: float,
+    y1: float,
+    y2: float,
+    y3: float,
+    k_z_sat: float,
+) -> float:
+    """co-operative 4-state quenching mechanism.
+
+    gamma0: slow quenching of (Vx - protonation)
+    gamma1: fast quenching (Vx + protonation)
+    gamma2: fastest possible quenching (Zx + protonation)
+    gamma3: slow quenching of Zx present (Zx - protonation).
+    """
+    ZAnt = zx / (zx + k_z_sat)
+    return y0 * vx * psbs + y1 * vx * psbsp + y2 * ZAnt * psbsp + y3 * ZAnt * psbs
+
+
+def _keq_pq_red(
+    e0_qa: float,
+    f: float,
+    e0_pq: float,
+    p_hstroma: float,
+    d_g_p_h: float,
+    rt: float,
+) -> float:
+    """Equilibrium constant for PQ reduction by QA, pH-corrected via stroma proton contribution."""
+    dg1 = -e0_qa * f
+    dg2 = -2 * e0_pq * f
+    dg = -2 * dg1 + dg2 + 2 * p_hstroma * d_g_p_h
+    return np.exp(-dg / rt)
+
+
+def _ps2_crosssection(
+    lhc: float,
+    static_ant_ii: float,
+    static_ant_i: float,
+) -> float:
+    """Equilibrium constant for PQ reduction by QA, pH-corrected via stroma proton contribution."""
+    return static_ant_ii + (1 - static_ant_ii - static_ant_i) * lhc
+
+
+def _keq_atp(
+    p_h: float,
+    delta_g0_atp: float,
+    d_g_p_h: float,
+    hpr: float,
+    p_hstroma: float,
+    pi_mol: float,
+    rt: float,
+) -> float:
+    """Equilibrium constant for ATP synthase, driven by the transmembrane proton gradient."""
+    delta_g = delta_g0_atp - d_g_p_h * hpr * (p_hstroma - p_h)
+    return pi_mol * math.exp(-delta_g / rt)
+
+
+def _keq_cytb6f(
+    p_h: float,
+    f: float,
+    e0_pq: float,
+    e0_pc: float,
+    p_hstroma: float,
+    rt: float,
+    d_g_p_h: float,
+) -> float:
+    """Equilibrium constant of cytochrome b6f from redox potentials and transmembrane pH gradient."""
+    DG1 = -2 * f * e0_pq
+    DG2 = -f * e0_pc
+    DG = -(DG1 + 2 * d_g_p_h * p_h) + 2 * DG2 + 2 * d_g_p_h * (p_hstroma - p_h)
+    return math.exp(-DG / rt)
+
+
+def _keq_fnr(
+    e0_fd: float,
+    f: float,
+    e0_nadp: float,
+    p_hstroma: float,
+    d_g_p_h: float,
+    rt: float,
+) -> float:
+    """Equilibrium constant for FNR: Fd-mediated NADP+ reduction, pH-corrected."""
+    dg1 = -e0_fd * f
+    dg2 = -2 * e0_nadp * f
+    dg = -2 * dg1 + dg2 + d_g_p_h * p_hstroma
+    return math.exp(-dg / rt)
+
+
+def _keq_pcp700(
+    e0_pc: float,
+    f: float,
+    eo_p700: float,
+    rt: float,
+) -> float:
+    """Equilibrium constant for PC -> P700 electron transfer from standard redox potentials."""
+    dg1 = -e0_pc * f
+    dg2 = -eo_p700 * f
+    dg = -dg1 + dg2
+    return math.exp(-dg / rt)
+
+
+def _keq_faf_d(
+    e0_fa: float,
+    f: float,
+    e0_fd: float,
+    rt: float,
+) -> float:
+    """Equilibrium constant for FA -> Fd electron transfer from standard redox potentials."""
+    dg1 = -e0_fa * f
+    dg2 = -e0_fd * f
+    dg = -dg1 + dg2
+    return math.exp(-dg / rt)
+
+
+def _ps1states_2019(
+    pc_px: float,
+    pc_red: float,
+    fd_ox: float,
+    fd_red: float,
+    ps2cs: float,
+    psi_tot: float,
+    k_fd_red: float,
+    keq_fafd: float,
+    keq_pcp700: float,
+    k_pc_ox: float,
+    pfd: float,
+) -> float:
+    """QSSA calculates open state of PSI.
+
+    depends on reduction states of plastocyanin and ferredoxin
+    C = [PC], F = [Fd] (ox. forms).
+    """
+    L = (1 - ps2cs) * pfd
+    return psi_tot / (
+        1
+        + L / (k_fd_red * fd_ox)
+        + (1 + fd_red / (keq_fafd * fd_ox))
+        * (pc_px / (keq_pcp700 * pc_red) + L / (k_pc_ox * pc_red))
+    )
+
+
+def _rate_atp_synthase_2016(
+    atp: float,
+    adp: float,
+    keq_at_psynthase: float,
+    k_at_psynth: float,
+) -> float:
+    """ATP synthase rate (2016 formulation): linear reversible kinetics driven by Keq."""
+    return k_at_psynth * (adp - atp / keq_at_psynthase)
+
+
+def _neg_div(
+    x: float,
+    y: float,
+) -> float:
+    """Return -x / y."""
+    return -x / y
+
+
+def _b6f(
+    pc_ox: float,
+    pq_ox: float,
+    pq_red: float,
+    pc_red: float,
+    keq_b6f: float,
+    k_cytb6f: float,
+) -> float:
+    """Cytochrome b6f rate: reversible mass action clamped to -kCytb6f to avoid runaway reverse flux."""
+    return max(
+        k_cytb6f * (pq_red * pc_ox**2 - pq_ox * pc_red**2 / keq_b6f),
+        -k_cytb6f,
+    )
+
+
+def _four_div_by(
+    x: float,
+) -> float:
+    """Return 4/x; used for the 4-proton stoichiometry of b6f scaled by buffering capacity."""
+    return 4.0 / x
+
+
+def _protons_stroma_2016(
+    ph: float,
+) -> float:
+    """Convert stromal pH to proton concentration (µmol/L).
+
+    Introduced by the Matuszynska 2016 PhD model.
+    """
+    return 4000.0 * 10 ** (-ph)
+
+
+def _protonation_hill(
+    vx: float,
+    h: float,
+    nh: float,
+    k_fwd: float,
+    k_ph_sat: float,
+) -> float:
+    """Hill-type protonation rate scaled by lumenal proton concentration."""
+    return k_fwd * (h**nh / (h**nh + _protons_stroma_2016(k_ph_sat) ** nh)) * vx  # type: ignore
+
+
+def _rate_cyclic_electron_flow(
+    pox: float,
+    fdred: float,
+    kcyc: float,
+) -> float:
+    """Cyclic electron flow rate: mass action on Fd_red^2 and PQ_ox."""
+    return kcyc * fdred**2 * pox
+
+
+def _rate_protonation_hill(
+    vx: float,
+    h: float,
+    k_fwd: float,
+    n_h: float,
+    kph_sat: float,
+) -> float:
+    """Hill-type deepoxidase rate activated by lumenal proton concentration."""
+    return k_fwd * (h**n_h / (h**n_h + _protons_stroma_2016(kph_sat) ** n_h)) * vx  # type: ignore
+
+
+def _rate_fnr2016(
+    fd_ox: float,
+    fd_red: float,
+    nadph: float,
+    nadp: float,
+    vmax: float,
+    km_fd_red: float,
+    km_nadph: float,
+    keq: float,
+) -> float:
+    """FNR rate (2016 formulation): reversible ping-pong with Fd^2 stoichiometry, mmol/mmol_Chl units."""
+    fdred = fd_red / km_fd_red
+    fdox = fd_ox / km_fd_red
+    nadph = nadph / km_nadph
+    nadp = nadp / km_nadph
+    return (
+        vmax
+        * (fdred**2 * nadp - fdox**2 * nadph / keq)
+        / ((1 + fdred + fdred**2) * (1 + nadp) + (1 + fdox + fdox**2) * (1 + nadph) - 1)
+    )
+
+
+def _rate_ps2(
+    b1: float,
+    k2: float,
+) -> float:
+    """PSII electron transfer rate from the open-excited state B1 and photochemistry rate constant k2."""
+    return 0.5 * k2 * b1
+
+
+def _two_div_by(
+    x: float,
+) -> float:
+    """Return 2/x; used for the 2-proton stoichiometry of PSII scaled by buffering capacity."""
+    return 2.0 / x
+
+
+def _rate_ps1(
+    a: float,
+    ps2cs: float,
+    pfd: float,
+) -> float:
+    """PSI electron transfer rate: open PSI centers (a) * light absorbed by PSI antenna."""
+    return (1 - ps2cs) * pfd * a
+
+
+def _rate_leak(
+    protons_lumen: float,
+    ph_stroma: float,
+    k_leak: float,
+) -> float:
+    """Passive proton leak across the thylakoid membrane, proportional to the proton gradient."""
+    return k_leak * (protons_lumen - _protons_stroma_2016(ph_stroma))
+
+
+def _neg_one_div_by(
+    x: float,
+) -> float:
+    """Return -1/x; used for negated unit stoichiometry scaled by buffering capacity."""
+    return -1.0 / x
+
+
+def _mass_action_2s(
+    s1: float,
+    s2: float,
+    k_fwd: float,
+) -> float:
+    """Mass-action rate for two substrates."""
+    return k_fwd * s1 * s2
+
+
+def _rate_state_transition_ps1_ps2(
+    ant: float,
+    pox: float,
+    p_tot: float,
+    k_stt7: float,
+    km_st: float,
+    n_st: float,
+) -> float:
+    """STT7-kinase phosphorylation of LHC; inhibited by oxidised PQ (state 1 → 2 transition)."""
+    return k_stt7 * (1 / (1 + (pox / p_tot / km_st) ** n_st)) * ant
+
+
+def _ps2states_2016_phd_surrogate(
+    pq_ox: float,
+    pq_red: float,
+    ps2cs: float,
+    quencher: float,
+    psii_tot: float,
+    k2: float,
+    k_f: float,
+    _kh: float,
+    keq_pq_red: float,
+    k_pq_red: float,
+    pfd: float,
+    k_h0: float,
+) -> tuple[float, float, float, float]:
+    """PSII state populations (PHD quenching model, 2016) via analytical closed-form surrogate."""
+    x0 = k_f**2
+    x1 = k_h0**2
+    x2 = k2 * k_f
+    x3 = k2 * k_h0
+    x4 = 2 * k_f
+    x5 = k_h0 * x4
+    x6 = _kh * quencher
+    x7 = k2 * x6
+    x8 = x4 * x6
+    x9 = 2 * x6
+    x10 = k_h0 * x9
+    x11 = _kh**2 * quencher**2
+    x12 = k2 * keq_pq_red
+    x13 = k_pq_red * keq_pq_red * pq_ox
+    x14 = k_pq_red * pq_red
+    x15 = k2 * x14
+    x16 = pfd * ps2cs
+    x17 = k_f * x14
+    x18 = k_h0 * x14
+    x19 = x14 * x6
+    x20 = x13 * x16
+    x21 = keq_pq_red * x16
+    x22 = (
+        x0 * x14
+        + x1 * x14
+        + x11 * x14
+        + x14 * x2
+        + x14 * x3
+        + x14 * x5
+        + x14 * x7
+        + x14 * x8
+        + x18 * x9
+        + x2 * x21
+        + x21 * x3
+        + x21 * x7
+    )
+    x23 = psii_tot / (
+        k_f * x20
+        + k_h0 * x20
+        + pfd**2 * ps2cs**2 * x12
+        + x0 * x13
+        + x1 * x13
+        + x10 * x13
+        + x11 * x13
+        + x13 * x2
+        + x13 * x3
+        + x13 * x5
+        + x13 * x7
+        + x13 * x8
+        + x15 * x16
+        + x16 * x17
+        + x16 * x18
+        + x16 * x19
+        + x20 * x6
+        + x22
+    )
+    x24 = x16 * x23
+    _B0 = x13 * x23 * (x0 + x1 + x10 + x11 + x2 + x3 + x5 + x7 + x8)
+    _B1 = x13 * x24 * (k_f + k_h0 + x6)
+    _B2 = x22 * x23
+    _B3 = x24 * (x12 * x16 + x15 + x17 + x18 + x19)
+    return _B0, _B1, _B2, _B3
+
+
+def _div(
+    x: float,
+    y: float,
+) -> float:
+    """Return x / y."""
+    return x / y
+
+
+def _rate_fluorescence(
+    q: float,
+    b0: float,
+    b2: float,
+    ps2cs: float,
+    k2: float,
+    k_f: float,
+    k_h: float,
+) -> float:
+    """Chlorophyll fluorescence yield from open (B0) and closed (B2) PSII centres."""
+    return ps2cs * k_f * b0 / (k_f + k2 + k_h * q) + ps2cs * k_f * b2 / (k_f + k_h * q)
+
+
+def create_model() -> Model:
+    """Matuszynska 2016 PhD photosynthesis model.
+
+    Full chloroplast electron transport chain with non-photochemical quenching (NPQ)
+    and LHC state transitions. Covers PSII/PSI, cytochrome b6f, FNR, ATP synthase,
+    the xanthophyll cycle (violaxanthin ↔ zeaxanthin), PsbS protonation, and
+    cyclic electron flow around PSI.
+
+    Reference: Matuszyńska, Anna Barbara.
+    Mathematical models of light acclimation mechanisms in higher plants and green algae.
+    Dissertation, Düsseldorf, Heinrich-Heine-Universität, 2016.
+    """
+    m: Model = Model()
+    m = m.add_variable("ATP", initial_value=1.6999999999999997)
+    m = m.add_variable("Plastoquinone (oxidised)", initial_value=4.706348349506148)
+    m = m.add_variable("Plastocyanine (oxidised)", initial_value=3.9414515288091567)
+    m = m.add_variable("Ferredoxine (oxidised)", initial_value=3.7761613271207324)
+    m = m.add_variable("protons_lumen", initial_value=7.737821100836988)
+    m = m.add_variable("Light-harvesting complex", initial_value=0.5105293511676007)
+    m = m.add_variable("PsbS (de-protonated)", initial_value=0.5000000001374878)
+    m = m.add_variable("Violaxanthin", initial_value=0.09090909090907397)
+    m = m.add_parameter("pH", value=7.9)
+    m = m.add_parameter("PPFD", value=100.0)
+    m = m.add_parameter("NADPH", value=0.6)
+    m = m.add_parameter("O2 (dissolved)_lumen", value=8.0)
+    m = m.add_parameter("bH", value=100.0)
+    m = m.add_parameter("F", value=96.485)
+    m = m.add_parameter("E^0_PC", value=0.38)
+    m = m.add_parameter("E^0_P700", value=0.48)
+    m = m.add_parameter("E^0_FA", value=-0.55)
+    m = m.add_parameter("E^0_Fd", value=-0.43)
+    m = m.add_parameter("E^0_NADP", value=-0.113)
+    m = m.add_parameter("NADP*", value=0.8)
+    m = m.add_parameter("R", value=0.0083)
+    m = m.add_parameter("T", value=298.0)
+    m = m.add_parameter("A*P", value=2.55)
+    m = m.add_parameter("Carotenoids_tot", value=1.0)
+    m = m.add_parameter("Fd*", value=5.0)
+    m = m.add_parameter("PC_tot", value=4.0)
+    m = m.add_parameter("PSBS_tot", value=1.0)
+    m = m.add_parameter("LHC_tot", value=1.0)
+    m = m.add_parameter("gamma0", value=0.1)
+    m = m.add_parameter("gamma1", value=0.25)
+    m = m.add_parameter("gamma2", value=0.6)
+    m = m.add_parameter("gamma3", value=0.15)
+    m = m.add_parameter("kZSat", value=0.12)
+    m = m.add_parameter("E^0_QA", value=-0.14)
+    m = m.add_parameter("E^0_PQ", value=0.354)
+    m = m.add_parameter("PQ_tot", value=17.5)
+    m = m.add_parameter("staticAntII", value=0.1)
+    m = m.add_parameter("staticAntI", value=0.37)
+    m = m.add_parameter("kf_atp_synthase", value=20.0)
+    m = m.add_parameter("HPR", value=4.666666666666667)
+    m = m.add_parameter("Pi_mol", value=0.01)
+    m = m.add_parameter("DeltaG0_ATP", value=30.6)
+    m = m.add_parameter("kcat_b6f", value=2.5)
+    m = m.add_parameter("kh_lhc_protonation", value=3.0)
+    m = m.add_parameter("kf_lhc_protonation", value=0.0096)
+    m = m.add_parameter("ksat_lhc_protonation", value=5.8)
+    m = m.add_parameter("kf_lhc_deprotonation", value=0.0096)
+    m = m.add_parameter("kf_cyclic_electron_flow", value=1.0)
+    m = m.add_parameter("kf_violaxanthin_deepoxidase", value=0.0024)
+    m = m.add_parameter("kh_violaxanthin_deepoxidase", value=5.0)
+    m = m.add_parameter("ksat_violaxanthin_deepoxidase", value=5.8)
+    m = m.add_parameter("kf_zeaxanthin_epoxidase", value=0.00024)
+    m = m.add_parameter("E0_fnr", value=3.0)
+    m = m.add_parameter("kcat_fnr", value=500.0)
+    m = m.add_parameter("km_fnr_Ferredoxine (reduced)", value=1.56)
+    m = m.add_parameter("km_fnr_NADP", value=0.22)
+    m = m.add_parameter("kf_ndh", value=0.002)
+    m = m.add_parameter("PSII_total", value=2.5)
+    m = m.add_parameter("PSI_total", value=2.5)
+    m = m.add_parameter("kH0", value=500000000.0)
+    m = m.add_parameter("kPQred", value=250.0)
+    m = m.add_parameter("kPCox", value=2500.0)
+    m = m.add_parameter("kFdred", value=250000.0)
+    m = m.add_parameter("k2", value=5000000000.0)
+    m = m.add_parameter("kH", value=5000000000.0)
+    m = m.add_parameter("kF", value=625000000.0)
+    m = m.add_parameter("convf", value=0.032)
+    m = m.add_parameter("kf_proton_leak", value=10.0)
+    m = m.add_parameter("kPTOX", value=0.01)
+    m = m.add_parameter("kStt7", value=0.0035)
+    m = m.add_parameter("km_lhc_state_transition_12", value=0.2)
+    m = m.add_parameter("n_ST", value=2.0)
+    m = m.add_parameter("kPph1", value=0.0013)
+    m = m.add_parameter("kf_ex_atp", value=10.0)
+    m = m.add_derived(
+        "NADP",
+        fn=_moiety_1,
+        args=["NADPH", "NADP*"],
+    )
+    m = m.add_derived(
+        "RT",
+        fn=_mass_action_1s,
+        args=["R", "T"],
+    )
+    m = m.add_derived(
+        "ADP",
+        fn=_moiety_1,
+        args=["ATP", "A*P"],
+    )
+    m = m.add_derived(
+        "dG_pH",
+        fn=_dg_ph,
+        args=["R", "T"],
+    )
+    m = m.add_derived(
+        "pH_lumen",
+        fn=_ph_lumen,
+        args=["protons_lumen"],
+    )
+    m = m.add_derived(
+        "Zeaxanthin",
+        fn=_moiety_1,
+        args=["Violaxanthin", "Carotenoids_tot"],
+    )
+    m = m.add_derived(
+        "Ferredoxine (reduced)",
+        fn=_moiety_1,
+        args=["Ferredoxine (oxidised)", "Fd*"],
+    )
+    m = m.add_derived(
+        "Plastocyanine (reduced)",
+        fn=_moiety_1,
+        args=["Plastocyanine (oxidised)", "PC_tot"],
+    )
+    m = m.add_derived(
+        "PsbS (protonated)",
+        fn=_moiety_1,
+        args=["PsbS (de-protonated)", "PSBS_tot"],
+    )
+    m = m.add_derived(
+        "Light-harvesting complex (protonated)",
+        fn=_moiety_1,
+        args=["Light-harvesting complex", "LHC_tot"],
+    )
+    m = m.add_derived(
+        "Q",
+        fn=_quencher,
+        args=[
+            "PsbS (de-protonated)",
+            "Violaxanthin",
+            "PsbS (protonated)",
+            "Zeaxanthin",
+            "gamma0",
+            "gamma1",
+            "gamma2",
+            "gamma3",
+            "kZSat",
+        ],
+    )
+    m = m.add_derived(
+        "keq_Plastoquinone (reduced)",
+        fn=_keq_pq_red,
+        args=["E^0_QA", "F", "E^0_PQ", "pH", "dG_pH", "RT"],
+    )
+    m = m.add_derived(
+        "Plastoquinone (reduced)",
+        fn=_moiety_1,
+        args=["Plastoquinone (oxidised)", "PQ_tot"],
+    )
+    m = m.add_derived(
+        "PSII_cross_section",
+        fn=_ps2_crosssection,
+        args=["Light-harvesting complex", "staticAntII", "staticAntI"],
+    )
+    m = m.add_derived(
+        "keq_atp_synthase",
+        fn=_keq_atp,
+        args=["pH_lumen", "DeltaG0_ATP", "dG_pH", "HPR", "pH", "Pi_mol", "RT"],
+    )
+    m = m.add_derived(
+        "keq_b6f",
+        fn=_keq_cytb6f,
+        args=["pH_lumen", "F", "E^0_PQ", "E^0_PC", "pH", "RT", "dG_pH"],
+    )
+    m = m.add_derived(
+        "keq_fnr",
+        fn=_keq_fnr,
+        args=["E^0_Fd", "F", "E^0_NADP", "pH", "dG_pH", "RT"],
+    )
+    m = m.add_derived(
+        "vmax_fnr",
+        fn=_mass_action_1s,
+        args=["kcat_fnr", "E0_fnr"],
+    )
+    m = m.add_derived(
+        "keq_PCP700",
+        fn=_keq_pcp700,
+        args=["E^0_PC", "F", "E^0_P700", "RT"],
+    )
+    m = m.add_derived(
+        "keq_ferredoxin_reductase",
+        fn=_keq_faf_d,
+        args=["E^0_FA", "F", "E^0_Fd", "RT"],
+    )
+    m = m.add_derived(
+        "A1",
+        fn=_ps1states_2019,
+        args=[
+            "Plastocyanine (oxidised)",
+            "Plastocyanine (reduced)",
+            "Ferredoxine (oxidised)",
+            "Ferredoxine (reduced)",
+            "PSII_cross_section",
+            "PSI_total",
+            "kFdred",
+            "keq_ferredoxin_reductase",
+            "keq_PCP700",
+            "kPCox",
+            "PPFD",
+        ],
+    )
+    m = m.add_reaction(
+        "atp_synthase",
+        fn=_rate_atp_synthase_2016,
+        args=["ATP", "ADP", "keq_atp_synthase", "kf_atp_synthase"],
+        stoichiometry={
+            "ATP": 1.0,
+            "protons_lumen": Derived(fn=_neg_div, args=["HPR", "bH"]),
+        },
+    )
+    m = m.add_reaction(
+        "b6f",
+        fn=_b6f,
+        args=[
+            "Plastocyanine (oxidised)",
+            "Plastoquinone (oxidised)",
+            "Plastoquinone (reduced)",
+            "Plastocyanine (reduced)",
+            "keq_b6f",
+            "kcat_b6f",
+        ],
+        stoichiometry={
+            "Plastocyanine (oxidised)": -2,
+            "Plastoquinone (oxidised)": 1,
+            "protons_lumen": Derived(fn=_four_div_by, args=["bH"]),
+        },
+    )
+    m = m.add_reaction(
+        "lhc_protonation",
+        fn=_protonation_hill,
+        args=[
+            "PsbS (de-protonated)",
+            "protons_lumen",
+            "kh_lhc_protonation",
+            "kf_lhc_protonation",
+            "ksat_lhc_protonation",
+        ],
+        stoichiometry={"PsbS (de-protonated)": -1},
+    )
+    m = m.add_reaction(
+        "lhc_deprotonation",
+        fn=_mass_action_1s,
+        args=["PsbS (protonated)", "kf_lhc_deprotonation"],
+        stoichiometry={"PsbS (de-protonated)": 1},
+    )
+    m = m.add_reaction(
+        "cyclic_electron_flow",
+        fn=_rate_cyclic_electron_flow,
+        args=[
+            "Plastoquinone (oxidised)",
+            "Ferredoxine (reduced)",
+            "kf_cyclic_electron_flow",
+        ],
+        stoichiometry={"Plastoquinone (oxidised)": -1, "Ferredoxine (oxidised)": 2},
+    )
+    m = m.add_reaction(
+        "violaxanthin_deepoxidase",
+        fn=_rate_protonation_hill,
+        args=[
+            "Violaxanthin",
+            "protons_lumen",
+            "kf_violaxanthin_deepoxidase",
+            "kh_violaxanthin_deepoxidase",
+            "ksat_violaxanthin_deepoxidase",
+        ],
+        stoichiometry={"Violaxanthin": -1},
+    )
+    m = m.add_reaction(
+        "zeaxanthin_epoxidase",
+        fn=_mass_action_1s,
+        args=["Zeaxanthin", "kf_zeaxanthin_epoxidase"],
+        stoichiometry={"Violaxanthin": 1},
+    )
+    m = m.add_reaction(
+        "fnr",
+        fn=_rate_fnr2016,
+        args=[
+            "Ferredoxine (oxidised)",
+            "Ferredoxine (reduced)",
+            "NADPH",
+            "NADP",
+            "vmax_fnr",
+            "km_fnr_Ferredoxine (reduced)",
+            "km_fnr_NADP",
+            "keq_fnr",
+        ],
+        stoichiometry={"Ferredoxine (oxidised)": 2},
+    )
+    m = m.add_reaction(
+        "ndh",
+        fn=_mass_action_1s,
+        args=["Plastoquinone (oxidised)", "kf_ndh"],
+        stoichiometry={"Plastoquinone (oxidised)": -1},
+    )
+    m = m.add_reaction(
+        "PSII",
+        fn=_rate_ps2,
+        args=["B1", "k2"],
+        stoichiometry={
+            "Plastoquinone (oxidised)": -1,
+            "protons_lumen": Derived(fn=_two_div_by, args=["bH"]),
+        },
+    )
+    m = m.add_reaction(
+        "PSI",
+        fn=_rate_ps1,
+        args=["A1", "PSII_cross_section", "PPFD"],
+        stoichiometry={"Ferredoxine (oxidised)": -1, "Plastocyanine (oxidised)": 1},
+    )
+    m = m.add_reaction(
+        "proton_leak",
+        fn=_rate_leak,
+        args=["protons_lumen", "pH", "kf_proton_leak"],
+        stoichiometry={"protons_lumen": Derived(fn=_neg_one_div_by, args=["bH"])},
+    )
+    m = m.add_reaction(
+        "PTOX",
+        fn=_mass_action_2s,
+        args=["Plastoquinone (reduced)", "O2 (dissolved)_lumen", "kPTOX"],
+        stoichiometry={"Plastoquinone (oxidised)": 1},
+    )
+    m = m.add_reaction(
+        "lhc_state_transition_12",
+        fn=_rate_state_transition_ps1_ps2,
+        args=[
+            "Light-harvesting complex",
+            "Plastoquinone (oxidised)",
+            "PQ_tot",
+            "kStt7",
+            "km_lhc_state_transition_12",
+            "n_ST",
+        ],
+        stoichiometry={"Light-harvesting complex": -1},
+    )
+    m = m.add_reaction(
+        "lhc_state_transition_21",
+        fn=_mass_action_1s,
+        args=["Light-harvesting complex (protonated)", "kPph1"],
+        stoichiometry={"Light-harvesting complex": 1},
+    )
+    m = m.add_reaction(
+        "ex_atp",
+        fn=_mass_action_1s,
+        args=["ATP", "kf_ex_atp"],
+        stoichiometry={"ATP": -1},
+    )
+    m = m.add_surrogate(
+        "ps2states",
+        qss.Surrogate(
+            model=_ps2states_2016_phd_surrogate,
+            args=[
+                "Plastoquinone (oxidised)",
+                "Plastoquinone (reduced)",
+                "PSII_cross_section",
+                "Q",
+                "PSII_total",
+                "k2",
+                "kF",
+                "kH",
+                "keq_Plastoquinone (reduced)",
+                "kPQred",
+                "PPFD",
+                "kH0",
+            ],
+            outputs=["B0", "B1", "B2", "B3"],
+        ),
+    )
+    m = m.add_readout(
+        "PQ_ox/tot",
+        fn=_div,
+        args=["Plastoquinone (reduced)", "PQ_tot"],
+    )
+    m = m.add_readout(
+        "Fd_ox/tot",
+        fn=_div,
+        args=["Ferredoxine (reduced)", "Fd*"],
+    )
+    m = m.add_readout(
+        "PC_ox/tot",
+        fn=_div,
+        args=["Plastocyanine (reduced)", "PC_tot"],
+    )
+    m = m.add_readout(
+        "ATP/tot",
+        fn=_div,
+        args=["ATP", "A*P"],
+    )
+    m = m.add_readout(
+        "Fluo",
+        fn=_rate_fluorescence,
+        args=["Q", "B0", "B2", "PSII_cross_section", "k2", "kF", "kH"],
+    )
+    return m  # noqa: RET504