mxlmodels 1.0.0__py3-none-any.whl

mxlmodels/saadat2021.py

@@ -0,0 +1,1871 @@
+"""Saadat 2021 chloroplast model with ROS scavenging, Calvin cycle, and thioredoxin regulation.
+
+Reference: Saadat, Nima P., et al.
+"Computational analysis of alternative photosynthetic electron flows linked with oxidative stress."
+Frontiers in plant science 12 (2021): 750580
+"""
+
+import math
+
+import numpy as np
+from mxlpy import Derived, Model
+from mxlpy.surrogates import qss
+
+
+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 _moiety_1(
+    concentration: float,
+    total: float,
+) -> float:
+    """Conservation moiety: total - concentration."""
+    return total - concentration
+
+
+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 _pi_cbb(
+    phosphate_total: float,
+    pga: float,
+    bpga: float,
+    gap: float,
+    dhap: float,
+    fbp: float,
+    f6p: float,
+    g6p: float,
+    g1p: float,
+    sbp: float,
+    s7p: float,
+    e4p: float,
+    x5p: float,
+    r5p: float,
+    rubp: float,
+    ru5p: float,
+    atp: float,
+) -> float:
+    """Free orthophosphate from total minus all phosphorylated CBB intermediates (bisphosphates count twice)."""
+    return phosphate_total - (
+        pga
+        + 2 * bpga
+        + gap
+        + dhap
+        + 2 * fbp
+        + f6p
+        + g6p
+        + g1p
+        + 2 * sbp
+        + s7p
+        + e4p
+        + x5p
+        + r5p
+        + 2 * rubp
+        + ru5p
+        + atp
+    )
+
+
+def _moiety_2(
+    x1: float,
+    x2: float,
+    total: float,
+) -> float:
+    """Conservation moiety: total - x1 - x2."""
+    return total - x1 - x2
+
+
+def _glutathion_moiety(
+    gssg: float,
+    gs_total: float,
+) -> float:
+    """Conservation moiety: GSH = total - 2*GSSG (one GSSG releases two GSH)."""
+    return gs_total - 2 * gssg
+
+
+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 _mul(
+    x: float,
+    y: float,
+) -> float:
+    """Calculate the product of two values.
+
+    Parameters
+    ----------
+    x
+        First factor
+    y
+        Second factor
+
+    Returns
+    -------
+    Float
+        Product of x and y (x * y)
+
+    Examples
+    --------
+    >>> mul(2.0, 3.0)
+    6.0
+    >>> mul(0.5, 4.0)
+    2.0
+
+    """
+    return x * y
+
+
+def _rate_translocator(
+    pi: float,
+    pga: float,
+    gap: float,
+    dhap: float,
+    k_pxt: float,
+    p_ext: float,
+    k_pi: float,
+    k_pga: float,
+    k_gap: float,
+    k_dhap: float,
+) -> float:
+    """Denominator term N for the phosphate translocator shared by all triose-P export reactions."""
+    return 1 + (1 + k_pxt / p_ext) * (
+        pi / k_pi + pga / k_pga + gap / k_gap + dhap / k_dhap
+    )
+
+
+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_atp_synthase_2019(
+    atp: float,
+    adp: float,
+    keq_at_psynthase: float,
+    k_at_psynth: float,
+    convf: float,
+) -> float:
+    """ATP synthase rate (2019 formulation): same as 2016 but ADP/ATP scaled by convf."""
+    return k_at_psynth * (adp / convf - atp / convf / keq_at_psynthase)
+
+
+def _neg_div(
+    x: float,
+    y: float,
+) -> float:
+    """Return -x / y."""
+    return -x / y
+
+
+def _value(
+    x: float,
+) -> float:
+    """Return x unchanged."""
+    return x
+
+
+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_fnr_2019(
+    fd_ox: float,
+    fd_red: float,
+    nadph: float,
+    nadp: float,
+    km_fnr_f: float,
+    km_fnr_n: float,
+    vmax: float,
+    keq_fnr: float,
+    convf: float,
+) -> float:
+    """FNR rate (2019 formulation): same as 2016 but NADP/H concentrations scaled by convf."""
+    fdred = fd_red / km_fnr_f
+    fdox = fd_ox / km_fnr_f
+    nadph = nadph / convf / km_fnr_n
+    nadp = nadp / convf / km_fnr_n
+    return (
+        vmax
+        * (fdred**2 * nadp - fdox**2 * nadph / keq_fnr)
+        / ((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_ferredoxin_reductase(
+    fd: float,
+    fdred: float,
+    a1: float,
+    a2: float,
+    k_fdred: float,
+    keq_fa_fd: float,
+) -> float:
+    """Rate of the redcution of Fd by the activity of PSI.
+
+    used to be equall to the rate of PSI but now
+    alternative electron pathway from Fd allows for the production of ROS
+    hence this rate has to be separate.
+    """
+    return k_fdred * fd * a1 - k_fdred / keq_fa_fd * fdred * a2
+
+
+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 _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 _rate_poolman_5i(
+    rubp: float,
+    pga: float,
+    co2: float,
+    vmax: float,
+    kms_rubp: float,
+    kms_co2: float,
+    # inhibitors
+    ki_pga: float,
+    fbp: float,
+    ki_fbp: float,
+    sbp: float,
+    ki_sbp: float,
+    pi: float,
+    ki_p: float,
+    nadph: float,
+    ki_nadph: float,
+) -> float:
+    """Rubisco carboxylation rate (Poolman 2000): bi-substrate with 5 competitive inhibitors."""
+    top = vmax * rubp * co2
+    btm = (
+        rubp
+        + kms_rubp
+        * (
+            1
+            + pga / ki_pga
+            + fbp / ki_fbp
+            + sbp / ki_sbp
+            + pi / ki_p
+            + nadph / ki_nadph
+        )
+    ) * (co2 + kms_co2)
+    return top / btm
+
+
+def _rapid_equilibrium_2s_2p(
+    s1: float,
+    s2: float,
+    p1: float,
+    p2: float,
+    k_re: float,
+    q: float,
+) -> float:
+    """Rapid-equilibrium rate for two substrates, two products."""
+    return k_re * (s1 * s2 - p1 * p2 / q)
+
+
+def _rapid_equilibrium_3s_3p(
+    s1: float,
+    s2: float,
+    s3: float,
+    p1: float,
+    p2: float,
+    p3: float,
+    k_re: float,
+    q: float,
+) -> float:
+    """Rapid-equilibrium rate for three substrates, three products."""
+    return k_re * (s1 * s2 * s3 - p1 * p2 * p3 / q)
+
+
+def _rapid_equilibrium_1s_1p(
+    s1: float,
+    p1: float,
+    k_re: float,
+    q: float,
+) -> float:
+    """Rapid-equilibrium rate for one substrate, one product."""
+    return k_re * (s1 - p1 / q)
+
+
+def _rapid_equilibrium_2s_1p(
+    s1: float,
+    s2: float,
+    p1: float,
+    k_re: float,
+    q: float,
+) -> float:
+    """Rapid-equilibrium rate for two substrates, one product."""
+    return k_re * (s1 * s2 - p1 / q)
+
+
+def _michaelis_menten_1s_2i(
+    s: float,
+    i1: float,
+    i2: float,
+    vmax: float,
+    km: float,
+    ki1: float,
+    ki2: float,
+) -> float:
+    """Irreversible Michaelis-Menten rate for one substrate with two inhibitors."""
+    return vmax * s / (s + km * (1 + i1 / ki1 + i2 / ki2))
+
+
+def _michaelis_menten_1s_1i(
+    s: float,
+    i: float,
+    vmax: float,
+    km: float,
+    ki: float,
+) -> float:
+    """Irreversible Michaelis-Menten rate for one substrate with one inhibitor."""
+    return vmax * s / (s + km * (1 + i / ki))
+
+
+def _rate_prk(
+    ru5p: float,
+    atp: float,
+    pi: float,
+    pga: float,
+    rubp: float,
+    adp: float,
+    v13: float,
+    km131: float,
+    km132: float,
+    ki131: float,
+    ki132: float,
+    ki133: float,
+    ki134: float,
+    ki135: float,
+) -> float:
+    """Phosphoribulokinase rate: ordered bi-substrate kinetics with PGA, RuBP, Pi and ADP inhibition."""
+    return (
+        v13
+        * ru5p
+        * atp
+        / (
+            (ru5p + km131 * (1 + pga / ki131 + rubp / ki132 + pi / ki133))
+            * (atp * (1 + adp / ki134) + km132 * (1 + adp / ki135))
+        )
+    )
+
+
+def _rate_out(
+    s1: float,
+    n_total: float,
+    vmax_efflux: float,
+    k_efflux: float,
+) -> float:
+    """Individual substrate export rate normalised by the translocator occupancy N."""
+    return vmax_efflux * s1 / (n_total * k_efflux)
+
+
+def _rate_starch(
+    g1p: float,
+    atp: float,
+    adp: float,
+    pi: float,
+    pga: float,
+    f6p: float,
+    fbp: float,
+    v_st: float,
+    kmst1: float,
+    kmst2: float,
+    ki_st: float,
+    kast1: float,
+    kast2: float,
+    kast3: float,
+) -> float:
+    """Starch synthesis rate via G1P+ATP with ADP inhibition and allosteric activation by PGA/F6P/FBP."""
+    return (
+        v_st
+        * g1p
+        * atp
+        / (
+            (g1p + kmst1)
+            * (
+                (1 + adp / ki_st) * (atp + kmst2)
+                + kmst2 * pi / (kast1 * pga + kast2 * f6p + kast3 * fbp)
+            )
+        )
+    )
+
+
+def _rate_mda_reductase1(
+    mda: float,
+    k3: float,
+) -> float:
+    """MDA reductase rate: second-order disproportionation of monodehydroascorbate."""
+    return k3 * mda**2
+
+
+def _rate_mda_reductase2(
+    nadph: float,
+    mda: float,
+    vmax: float,
+    km_nadph: float,
+    km_mda: float,
+) -> float:
+    """Compare Valero et al. 2016."""
+    nom = vmax * nadph * mda
+    denom = km_nadph * mda + km_mda * nadph + nadph * mda + km_nadph * km_mda
+    return nom / denom
+
+
+def _rate_ascorbate_peroxidase(
+    a: float,
+    h: float,
+    kf1: float,
+    kr1: float,
+    kf2: float,
+    kr2: float,
+    kf3: float,
+    kf4: float,
+    kr4: float,
+    kf5: float,
+    xt: float,
+) -> float:
+    """Lumped reaction of ascorbate peroxidase.
+
+    the cycle stretched to a linear chain with
+    two steps producing the MDA
+    two steps releasing ASC
+    and one step producing hydrogen peroxide.
+    """
+    nom = a * h * xt
+    denom = (
+        a * h * (1 / kf3 + 1 / kf5)
+        + a / kf1
+        + h / kf4
+        + h * kr4 / (kf4 * kf5)
+        + h / kf2
+        + h * kr2 / (kf2 * kf3)
+        + kr1 / (kf1 * kf2)
+        + kr1 * kr2 / (kf1 * kf2 * kf3)
+    )
+    return nom / denom
+
+
+def _rate_glutathion_reductase(
+    nadph: float,
+    gssg: float,
+    vmax: float,
+    km_nadph: float,
+    km_gssg: float,
+) -> float:
+    """Glutathione reductase rate: bi-substrate Michaelis-Menten for NADPH + GSSG."""
+    nom = vmax * nadph * gssg
+    denom = km_nadph * gssg + km_gssg * nadph + nadph * gssg + km_nadph * km_gssg
+    return nom / denom
+
+
+def _rate_dhar(
+    dha: float,
+    gsh: float,
+    vmax: float,
+    km_dha: float,
+    km_gsh: float,
+    k: float,
+) -> float:
+    """Dehydroascorbate reductase rate: bi-substrate random-order Michaelis-Menten."""
+    nom = vmax * dha * gsh
+    denom = k + km_dha * gsh + km_gsh * dha + dha * gsh
+    return nom / denom
+
+
+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 _ps1states_2021_surrogate(
+    pc_ox: float,
+    pc_red: float,
+    fd_ox: float,
+    fd_red: float,
+    ps2cs: float,
+    ps1_tot: float,
+    k_fd_red: float,
+    keq_f: float,
+    keq_c: float,
+    k_pc_ox: float,
+    pfd: float,
+    k0: float,
+    o2: float,
+) -> tuple[float, float, float]:
+    """QSSA calculates open state of PSI.
+
+    depends on reduction states of plastocyanin and ferredoxin
+    C = [PC], F = [Fd] (ox. forms).
+    """
+    kLI = (1 - ps2cs) * pfd
+
+    y0 = (
+        keq_c
+        * keq_f
+        * pc_red
+        * ps1_tot
+        * k_pc_ox
+        * (fd_ox * k_fd_red + o2 * k0)
+        / (
+            fd_ox * keq_c * keq_f * pc_red * k_fd_red * k_pc_ox
+            + fd_ox * keq_f * k_fd_red * (keq_c * kLI + pc_ox * k_pc_ox)
+            + fd_red * k_fd_red * (keq_c * kLI + pc_ox * k_pc_ox)
+            + keq_c * keq_f * o2 * pc_red * k0 * k_pc_ox
+            + keq_c * keq_f * pc_red * kLI * k_pc_ox
+            + keq_f * o2 * k0 * (keq_c * kLI + pc_ox * k_pc_ox)
+        )
+    )
+
+    y1 = (
+        ps1_tot
+        * (
+            fd_red * k_fd_red * (keq_c * kLI + pc_ox * k_pc_ox)
+            + keq_c * keq_f * pc_red * kLI * k_pc_ox
+        )
+        / (
+            fd_ox * keq_c * keq_f * pc_red * k_fd_red * k_pc_ox
+            + fd_ox * keq_f * k_fd_red * (keq_c * kLI + pc_ox * k_pc_ox)
+            + fd_red * k_fd_red * (keq_c * kLI + pc_ox * k_pc_ox)
+            + keq_c * keq_f * o2 * pc_red * k0 * k_pc_ox
+            + keq_c * keq_f * pc_red * kLI * k_pc_ox
+            + keq_f * o2 * k0 * (keq_c * kLI + pc_ox * k_pc_ox)
+        )
+    )
+    y2 = ps1_tot - y0 - y1
+
+    return y0, y1, y2
+
+
+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:
+    """Saadat 2021 chloroplast model with ROS scavenging, Calvin cycle, and thioredoxin regulation.
+
+    Reference: Saadat, Nima P., et al.
+    "Computational analysis of alternative photosynthetic electron flows linked with oxidative stress."
+    Frontiers in plant science 12 (2021): 750580
+    """
+    m: Model = Model()
+    m = m.add_variable("3PGA", initial_value=0.9167729479368978)
+    m = m.add_variable("BPGA", initial_value=0.0003814495319659031)
+    m = m.add_variable("GAP", initial_value=0.00580821050261484)
+    m = m.add_variable("DHAP", initial_value=0.1277806166216142)
+    m = m.add_variable("FBP", initial_value=0.005269452472931973)
+    m = m.add_variable("F6P", initial_value=0.2874944558066638)
+    m = m.add_variable("G6P", initial_value=0.6612372482712676)
+    m = m.add_variable("G1P", initial_value=0.03835176039761378)
+    m = m.add_variable("SBP", initial_value=0.011101373736607443)
+    m = m.add_variable("S7P", initial_value=0.1494578301900007)
+    m = m.add_variable("E4P", initial_value=0.00668295494870102)
+    m = m.add_variable("X5P", initial_value=0.020988553174809618)
+    m = m.add_variable("R5P", initial_value=0.035155825913785584)
+    m = m.add_variable("RUBP", initial_value=0.11293260727162346)
+    m = m.add_variable("RU5P", initial_value=0.014062330254191594)
+    m = m.add_variable("ATP", initial_value=1.4612747767895344)
+    m = m.add_variable("Ferredoxine (oxidised)", initial_value=3.715702384326767)
+    m = m.add_variable("protons_lumen", initial_value=0.002086128887296243)
+    m = m.add_variable("Light-harvesting complex", initial_value=0.7805901436176024)
+    m = m.add_variable("NADPH", initial_value=0.5578718406315588)
+    m = m.add_variable("Plastocyanine (oxidised)", initial_value=1.8083642974980014)
+    m = m.add_variable("Plastoquinone (oxidised)", initial_value=10.251099271612473)
+    m = m.add_variable("PsbS (de-protonated)", initial_value=0.9667381262477079)
+    m = m.add_variable("Violaxanthin", initial_value=0.9629870646993118)
+    m = m.add_variable("MDA", initial_value=2.0353396709300447e-07)
+    m = m.add_variable("H2O2", initial_value=1.2034405327140102e-07)
+    m = m.add_variable("DHA", initial_value=1.0296456279861962e-11)
+    m = m.add_variable("GSSG", initial_value=4.99986167652437e-12)
+    m = m.add_variable("Thioredoxin (oxidised)", initial_value=0.9334426859846461)
+    m = m.add_variable("E_inactive", initial_value=3.6023635680406634)
+    m = m.add_parameter("PPFD", value=100.0)
+    m = m.add_parameter("CO2 (dissolved)", value=0.2)
+    m = m.add_parameter("O2 (dissolved)_lumen", value=8.0)
+    m = m.add_parameter("pH", value=7.9)
+    m = m.add_parameter("protons", value=1.2589254117941661e-05)
+    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("convf", value=0.032)
+    m = m.add_parameter("R", value=0.0083)
+    m = m.add_parameter("T", value=298.0)
+    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("Thioredoxin_tot", value=1.0)
+    m = m.add_parameter("E_total", value=6.0)
+    m = m.add_parameter("NADP*", value=0.8)
+    m = m.add_parameter("A*P", value=2.55)
+    m = m.add_parameter("Pi_tot", value=17.05)
+    m = m.add_parameter("kf_ferredoxin_thioredoxin_reductase", value=1.0)
+    m = m.add_parameter("kf_tr_activation", value=1.0)
+    m = m.add_parameter("kf_tr_inactivation", value=0.1)
+    m = m.add_parameter("ASC_tot*", value=10)
+    m = m.add_parameter("Glutathion_tot", value=10.0)
+    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("km_fnr_Ferredoxine (reduced)", value=1.56)
+    m = m.add_parameter("km_fnr_NADP", value=0.22)
+    m = m.add_parameter("E0_fnr", value=3.0)
+    m = m.add_parameter("kcat_fnr", value=500.0)
+    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("kMehler", value=1.0)
+    m = m.add_parameter("E0_ferredoxin_reductase", value=1.0)
+    m = m.add_parameter("kcat_ferredoxin_reductase", value=250000.0)
+    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("E0_rubisco", value=1.0)
+    m = m.add_parameter("kcat_rubisco_carboxylase", value=2.72)
+    m = m.add_parameter("km_rubisco_carboxylase_RUBP", value=0.02)
+    m = m.add_parameter("km_rubisco_carboxylase_CO2 (dissolved)", value=0.0107)
+    m = m.add_parameter("ki_rubisco_carboxylase_3PGA", value=0.04)
+    m = m.add_parameter("ki_rubisco_carboxylase_FBP", value=0.04)
+    m = m.add_parameter("ki_rubisco_carboxylase_SBP", value=0.075)
+    m = m.add_parameter("ki_rubisco_carboxylase_Orthophosphate", value=0.9)
+    m = m.add_parameter("ki_rubisco_carboxylase_NADPH", value=0.07)
+    m = m.add_parameter("kre_phosphoglycerate_kinase", value=800000000.0)
+    m = m.add_parameter("keq_phosphoglycerate_kinase", value=0.00031)
+    m = m.add_parameter("kre_gadph", value=800000000.0)
+    m = m.add_parameter("keq_gadph", value=16000000.0)
+    m = m.add_parameter("kre_triose_phosphate_isomerase", value=800000000.0)
+    m = m.add_parameter("keq_triose_phosphate_isomerase", value=22.0)
+    m = m.add_parameter("kre_aldolase_dhap_gap", value=800000000.0)
+    m = m.add_parameter("keq_aldolase_dhap_gap", value=7.1)
+    m = m.add_parameter("kre_aldolase_dhap_e4p", value=800000000.0)
+    m = m.add_parameter("keq_aldolase_dhap_e4p", value=13.0)
+    m = m.add_parameter("E0_fbpase", value=1.0)
+    m = m.add_parameter("kcat_fbpase", value=1.6)
+    m = m.add_parameter("km_fbpase_s", value=0.03)
+    m = m.add_parameter("ki_fbpase_F6P", value=0.7)
+    m = m.add_parameter("ki_fbpase_Orthophosphate", value=12.0)
+    m = m.add_parameter("kre_transketolase_gap_f6p", value=800000000.0)
+    m = m.add_parameter("keq_transketolase_gap_f6p", value=0.084)
+    m = m.add_parameter("kre_transketolase_gap_s7p", value=800000000.0)
+    m = m.add_parameter("keq_transketolase_gap_s7p", value=0.85)
+    m = m.add_parameter("E0_SBPase", value=1.0)
+    m = m.add_parameter("kcat_SBPase", value=0.32)
+    m = m.add_parameter("km_SBPase_s", value=0.013)
+    m = m.add_parameter("ki_SBPase_Orthophosphate", value=12.0)
+    m = m.add_parameter("kre_ribose_phosphate_isomerase", value=800000000.0)
+    m = m.add_parameter("keq_ribose_phosphate_isomerase", value=0.4)
+    m = m.add_parameter("kre_ribulose_phosphate_epimerase", value=800000000.0)
+    m = m.add_parameter("keq_ribulose_phosphate_epimerase", value=0.67)
+    m = m.add_parameter("E0_phosphoribulokinase", value=1.0)
+    m = m.add_parameter("kcat_phosphoribulokinase", value=7.9992)
+    m = m.add_parameter("km_phosphoribulokinase_RU5P", value=0.05)
+    m = m.add_parameter("km_phosphoribulokinase_ATP", value=0.05)
+    m = m.add_parameter("ki_phosphoribulokinase_3PGA", value=2.0)
+    m = m.add_parameter("ki_phosphoribulokinase_RUBP", value=0.7)
+    m = m.add_parameter("ki_phosphoribulokinase_Orthophosphate", value=4.0)
+    m = m.add_parameter("ki_phosphoribulokinase_4", value=2.5)
+    m = m.add_parameter("ki_phosphoribulokinase_5", value=0.4)
+    m = m.add_parameter("kre_g6pi", value=800000000.0)
+    m = m.add_parameter("keq_g6pi", value=2.3)
+    m = m.add_parameter("kre_phosphoglucomutase", value=800000000.0)
+    m = m.add_parameter("keq_phosphoglucomutase", value=0.058)
+    m = m.add_parameter("Orthophosphate (external)", value=0.5)
+    m = m.add_parameter("km_ex_pga", value=0.25)
+    m = m.add_parameter("km_ex_gap", value=0.075)
+    m = m.add_parameter("km_ex_dhap", value=0.077)
+    m = m.add_parameter("km_N_translocator_Orthophosphate (external)", value=0.74)
+    m = m.add_parameter("km_N_translocator_Orthophosphate", value=0.63)
+    m = m.add_parameter("kcat_N_translocator", value=2.0)
+    m = m.add_parameter("E0_N_translocator", value=1.0)
+    m = m.add_parameter("E0_ex_g1p", value=1.0)
+    m = m.add_parameter("km_ex_g1p_G1P", value=0.08)
+    m = m.add_parameter("km_ex_g1p_ATP", value=0.08)
+    m = m.add_parameter("ki_ex_g1p", value=10.0)
+    m = m.add_parameter("ki_ex_g1p_3PGA", value=0.1)
+    m = m.add_parameter("ki_ex_g1p_F6P", value=0.02)
+    m = m.add_parameter("ki_ex_g1p_FBP", value=0.02)
+    m = m.add_parameter("kcat_ex_g1p", value=0.32)
+    m = m.add_parameter("kf_mda_reductase_1", value=500.0)
+    m = m.add_parameter("E0_mda_reductase_2", value=0.002)
+    m = m.add_parameter("kcat_mda_reductase_2", value=300.0)
+    m = m.add_parameter("km_mda_reductase_2_NADPH", value=0.023)
+    m = m.add_parameter("km_mda_reductase_2_MDA", value=0.0014)
+    m = m.add_parameter("kf1", value=10000.0)
+    m = m.add_parameter("kr1", value=220.0)
+    m = m.add_parameter("kf2", value=10000.0)
+    m = m.add_parameter("kr2", value=4000.0)
+    m = m.add_parameter("kf3", value=2510.0)
+    m = m.add_parameter("kf4", value=10000.0)
+    m = m.add_parameter("kr4", value=4000.0)
+    m = m.add_parameter("kf5", value=2510.0)
+    m = m.add_parameter("XT", value=0.07)
+    m = m.add_parameter("E0_glutathion_reductase", value=0.0014)
+    m = m.add_parameter("kcat_glutathion_reductase", value=595)
+    m = m.add_parameter("km_glutathion_reductase_NADPH", value=0.003)
+    m = m.add_parameter("km_glutathion_reductase_GSSG", value=0.2)
+    m = m.add_parameter("km_dehydroascorbate_reductase_DHA", value=0.07)
+    m = m.add_parameter("km_dehydroascorbate_reductase_GSH", value=2.5)
+    m = m.add_parameter("K", value=0.5)
+    m = m.add_parameter("E0_dehydroascorbate_reductase", value=0.0017)
+    m = m.add_parameter("kcat_dehydroascorbate_reductase", value=142)
+    m = m.add_parameter("kf_ex_atp", value=0.2)
+    m = m.add_parameter("kf_ex_nadph", value=0.2)
+    m = m.add_derived(
+        "RT",
+        fn=_mass_action_1s,
+        args=["R", "T"],
+    )
+    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(
+        "Thioredoxin (reduced)",
+        fn=_moiety_1,
+        args=["Thioredoxin (oxidised)", "Thioredoxin_tot"],
+    )
+    m = m.add_derived(
+        "E_active",
+        fn=_moiety_1,
+        args=["E_inactive", "E_total"],
+    )
+    m = m.add_derived(
+        "NADP",
+        fn=_moiety_1,
+        args=["NADPH", "NADP*"],
+    )
+    m = m.add_derived(
+        "ADP",
+        fn=_moiety_1,
+        args=["ATP", "A*P"],
+    )
+    m = m.add_derived(
+        "Orthophosphate",
+        fn=_pi_cbb,
+        args=[
+            "Pi_tot",
+            "3PGA",
+            "BPGA",
+            "GAP",
+            "DHAP",
+            "FBP",
+            "F6P",
+            "G6P",
+            "G1P",
+            "SBP",
+            "S7P",
+            "E4P",
+            "X5P",
+            "R5P",
+            "RUBP",
+            "RU5P",
+            "ATP",
+        ],
+    )
+    m = m.add_derived(
+        "ascorbate",
+        fn=_moiety_2,
+        args=["MDA", "DHA", "ASC_tot*"],
+    )
+    m = m.add_derived(
+        "GSH",
+        fn=_glutathion_moiety,
+        args=["GSSG", "Glutathion_tot"],
+    )
+    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(
+        "vmax_ferredoxin_reductase",
+        fn=_mass_action_1s,
+        args=["kcat_ferredoxin_reductase", "E0_ferredoxin_reductase"],
+    )
+    m = m.add_derived(
+        "E0_rubisco_active",
+        fn=_mul,
+        args=["E0_rubisco", "E_active"],
+    )
+    m = m.add_derived(
+        "vmax_rubisco_carboxylase",
+        fn=_mass_action_1s,
+        args=["kcat_rubisco_carboxylase", "E0_rubisco_active"],
+    )
+    m = m.add_derived(
+        "E0_fbpase_active",
+        fn=_mul,
+        args=["E0_fbpase", "E_active"],
+    )
+    m = m.add_derived(
+        "vmax_fbpase",
+        fn=_mass_action_1s,
+        args=["kcat_fbpase", "E0_fbpase_active"],
+    )
+    m = m.add_derived(
+        "E0_SBPase_active",
+        fn=_mul,
+        args=["E0_SBPase", "E_active"],
+    )
+    m = m.add_derived(
+        "vmax_SBPase",
+        fn=_mass_action_1s,
+        args=["kcat_SBPase", "E0_SBPase_active"],
+    )
+    m = m.add_derived(
+        "E0_phosphoribulokinase_active",
+        fn=_mul,
+        args=["E0_phosphoribulokinase", "E_active"],
+    )
+    m = m.add_derived(
+        "vmax_phosphoribulokinase",
+        fn=_mass_action_1s,
+        args=["kcat_phosphoribulokinase", "E0_phosphoribulokinase_active"],
+    )
+    m = m.add_derived(
+        "vmax_ex_pga",
+        fn=_mass_action_1s,
+        args=["kcat_N_translocator", "E0_N_translocator"],
+    )
+    m = m.add_derived(
+        "N_translocator",
+        fn=_rate_translocator,
+        args=[
+            "Orthophosphate",
+            "3PGA",
+            "GAP",
+            "DHAP",
+            "km_N_translocator_Orthophosphate (external)",
+            "Orthophosphate (external)",
+            "km_N_translocator_Orthophosphate",
+            "km_ex_pga",
+            "km_ex_gap",
+            "km_ex_dhap",
+        ],
+    )
+    m = m.add_derived(
+        "E0_ex_g1p_active",
+        fn=_mul,
+        args=["E0_ex_g1p", "E_active"],
+    )
+    m = m.add_derived(
+        "vmax_ex_g1p",
+        fn=_mass_action_1s,
+        args=["kcat_ex_g1p", "E0_ex_g1p_active"],
+    )
+    m = m.add_derived(
+        "vmax_mda_reductase_2",
+        fn=_mass_action_1s,
+        args=["kcat_mda_reductase_2", "E0_mda_reductase_2"],
+    )
+    m = m.add_derived(
+        "vmax_glutathion_reductase",
+        fn=_mass_action_1s,
+        args=["kcat_glutathion_reductase", "E0_glutathion_reductase"],
+    )
+    m = m.add_derived(
+        "vmax_dehydroascorbate_reductase",
+        fn=_mass_action_1s,
+        args=["kcat_dehydroascorbate_reductase", "E0_dehydroascorbate_reductase"],
+    )
+    m = m.add_reaction(
+        "ferredoxin_thioredoxin_reductase",
+        fn=_mass_action_2s,
+        args=[
+            "Thioredoxin (oxidised)",
+            "Ferredoxine (reduced)",
+            "kf_ferredoxin_thioredoxin_reductase",
+        ],
+        stoichiometry={"Thioredoxin (oxidised)": -1, "Ferredoxine (oxidised)": 1},
+    )
+    m = m.add_reaction(
+        "tr_activation",
+        fn=_mass_action_2s,
+        args=["E_inactive", "Thioredoxin (reduced)", "kf_tr_activation"],
+        stoichiometry={"E_inactive": -5, "Thioredoxin (oxidised)": 5},
+    )
+    m = m.add_reaction(
+        "tr_inactivation",
+        fn=_mass_action_1s,
+        args=["E_active", "kf_tr_inactivation"],
+        stoichiometry={"E_inactive": 5},
+    )
+    m = m.add_reaction(
+        "atp_synthase",
+        fn=_rate_atp_synthase_2019,
+        args=["ATP", "ADP", "keq_atp_synthase", "kf_atp_synthase", "convf"],
+        stoichiometry={
+            "protons_lumen": Derived(fn=_neg_div, args=["HPR", "bH"]),
+            "ATP": Derived(fn=_value, args=["convf"]),
+        },
+    )
+    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_fnr_2019,
+        args=[
+            "Ferredoxine (oxidised)",
+            "Ferredoxine (reduced)",
+            "NADPH",
+            "NADP",
+            "km_fnr_Ferredoxine (reduced)",
+            "km_fnr_NADP",
+            "vmax_fnr",
+            "keq_fnr",
+            "convf",
+        ],
+        stoichiometry={
+            "Ferredoxine (oxidised)": 2,
+            "NADPH": Derived(fn=_value, args=["convf"]),
+        },
+    )
+    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=["A0", "PSII_cross_section", "PPFD"],
+        stoichiometry={"Plastocyanine (oxidised)": 1},
+    )
+    m = m.add_reaction(
+        "mehler",
+        fn=_mass_action_2s,
+        args=["A1", "O2 (dissolved)_lumen", "kMehler"],
+        stoichiometry={"H2O2": Derived(fn=_value, args=["convf"])},
+    )
+    m = m.add_reaction(
+        "ferredoxin_reductase",
+        fn=_rate_ferredoxin_reductase,
+        args=[
+            "Ferredoxine (oxidised)",
+            "Ferredoxine (reduced)",
+            "A1",
+            "A2",
+            "vmax_ferredoxin_reductase",
+            "keq_ferredoxin_reductase",
+        ],
+        stoichiometry={"Ferredoxine (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(
+        "rubisco_carboxylase",
+        fn=_rate_poolman_5i,
+        args=[
+            "RUBP",
+            "3PGA",
+            "CO2 (dissolved)",
+            "vmax_rubisco_carboxylase",
+            "km_rubisco_carboxylase_RUBP",
+            "km_rubisco_carboxylase_CO2 (dissolved)",
+            "ki_rubisco_carboxylase_3PGA",
+            "FBP",
+            "ki_rubisco_carboxylase_FBP",
+            "SBP",
+            "ki_rubisco_carboxylase_SBP",
+            "Orthophosphate",
+            "ki_rubisco_carboxylase_Orthophosphate",
+            "NADPH",
+            "ki_rubisco_carboxylase_NADPH",
+        ],
+        stoichiometry={"RUBP": -1.0, "3PGA": 2.0},
+    )
+    m = m.add_reaction(
+        "phosphoglycerate_kinase",
+        fn=_rapid_equilibrium_2s_2p,
+        args=[
+            "3PGA",
+            "ATP",
+            "BPGA",
+            "ADP",
+            "kre_phosphoglycerate_kinase",
+            "keq_phosphoglycerate_kinase",
+        ],
+        stoichiometry={"3PGA": -1.0, "ATP": -1.0, "BPGA": 1.0},
+    )
+    m = m.add_reaction(
+        "gadph",
+        fn=_rapid_equilibrium_3s_3p,
+        args=[
+            "BPGA",
+            "NADPH",
+            "protons",
+            "GAP",
+            "NADP",
+            "Orthophosphate",
+            "kre_gadph",
+            "keq_gadph",
+        ],
+        stoichiometry={"NADPH": -1.0, "BPGA": -1.0, "GAP": 1.0},
+    )
+    m = m.add_reaction(
+        "triose_phosphate_isomerase",
+        fn=_rapid_equilibrium_1s_1p,
+        args=[
+            "GAP",
+            "DHAP",
+            "kre_triose_phosphate_isomerase",
+            "keq_triose_phosphate_isomerase",
+        ],
+        stoichiometry={"GAP": -1, "DHAP": 1},
+    )
+    m = m.add_reaction(
+        "aldolase_dhap_gap",
+        fn=_rapid_equilibrium_2s_1p,
+        args=["GAP", "DHAP", "FBP", "kre_aldolase_dhap_gap", "keq_aldolase_dhap_gap"],
+        stoichiometry={"GAP": -1, "DHAP": -1, "FBP": 1},
+    )
+    m = m.add_reaction(
+        "aldolase_dhap_e4p",
+        fn=_rapid_equilibrium_2s_1p,
+        args=["DHAP", "E4P", "SBP", "kre_aldolase_dhap_e4p", "keq_aldolase_dhap_e4p"],
+        stoichiometry={"DHAP": -1, "E4P": -1, "SBP": 1},
+    )
+    m = m.add_reaction(
+        "fbpase",
+        fn=_michaelis_menten_1s_2i,
+        args=[
+            "FBP",
+            "F6P",
+            "Orthophosphate",
+            "vmax_fbpase",
+            "km_fbpase_s",
+            "ki_fbpase_F6P",
+            "ki_fbpase_Orthophosphate",
+        ],
+        stoichiometry={"FBP": -1, "F6P": 1},
+    )
+    m = m.add_reaction(
+        "transketolase_gap_f6p",
+        fn=_rapid_equilibrium_2s_2p,
+        args=[
+            "GAP",
+            "F6P",
+            "E4P",
+            "X5P",
+            "kre_transketolase_gap_f6p",
+            "keq_transketolase_gap_f6p",
+        ],
+        stoichiometry={"GAP": -1, "F6P": -1, "E4P": 1, "X5P": 1},
+    )
+    m = m.add_reaction(
+        "transketolase_gap_s7p",
+        fn=_rapid_equilibrium_2s_2p,
+        args=[
+            "GAP",
+            "S7P",
+            "R5P",
+            "X5P",
+            "kre_transketolase_gap_s7p",
+            "keq_transketolase_gap_s7p",
+        ],
+        stoichiometry={"GAP": -1, "S7P": -1, "R5P": 1, "X5P": 1},
+    )
+    m = m.add_reaction(
+        "SBPase",
+        fn=_michaelis_menten_1s_1i,
+        args=[
+            "SBP",
+            "Orthophosphate",
+            "vmax_SBPase",
+            "km_SBPase_s",
+            "ki_SBPase_Orthophosphate",
+        ],
+        stoichiometry={"SBP": -1, "S7P": 1},
+    )
+    m = m.add_reaction(
+        "ribose_phosphate_isomerase",
+        fn=_rapid_equilibrium_1s_1p,
+        args=[
+            "R5P",
+            "RU5P",
+            "kre_ribose_phosphate_isomerase",
+            "keq_ribose_phosphate_isomerase",
+        ],
+        stoichiometry={"R5P": -1, "RU5P": 1},
+    )
+    m = m.add_reaction(
+        "ribulose_phosphate_epimerase",
+        fn=_rapid_equilibrium_1s_1p,
+        args=[
+            "X5P",
+            "RU5P",
+            "kre_ribulose_phosphate_epimerase",
+            "keq_ribulose_phosphate_epimerase",
+        ],
+        stoichiometry={"X5P": -1, "RU5P": 1},
+    )
+    m = m.add_reaction(
+        "phosphoribulokinase",
+        fn=_rate_prk,
+        args=[
+            "RU5P",
+            "ATP",
+            "Orthophosphate",
+            "3PGA",
+            "RUBP",
+            "ADP",
+            "vmax_phosphoribulokinase",
+            "km_phosphoribulokinase_RU5P",
+            "km_phosphoribulokinase_ATP",
+            "ki_phosphoribulokinase_3PGA",
+            "ki_phosphoribulokinase_RUBP",
+            "ki_phosphoribulokinase_Orthophosphate",
+            "ki_phosphoribulokinase_4",
+            "ki_phosphoribulokinase_5",
+        ],
+        stoichiometry={"RU5P": -1.0, "ATP": -1.0, "RUBP": 1.0},
+    )
+    m = m.add_reaction(
+        "g6pi",
+        fn=_rapid_equilibrium_1s_1p,
+        args=["F6P", "G6P", "kre_g6pi", "keq_g6pi"],
+        stoichiometry={"F6P": -1, "G6P": 1},
+    )
+    m = m.add_reaction(
+        "phosphoglucomutase",
+        fn=_rapid_equilibrium_1s_1p,
+        args=["G6P", "G1P", "kre_phosphoglucomutase", "keq_phosphoglucomutase"],
+        stoichiometry={"G6P": -1, "G1P": 1},
+    )
+    m = m.add_reaction(
+        "ex_pga",
+        fn=_rate_out,
+        args=["3PGA", "N_translocator", "vmax_ex_pga", "km_ex_pga"],
+        stoichiometry={"3PGA": -1},
+    )
+    m = m.add_reaction(
+        "ex_gap",
+        fn=_rate_out,
+        args=["GAP", "N_translocator", "vmax_ex_pga", "km_ex_gap"],
+        stoichiometry={"GAP": -1},
+    )
+    m = m.add_reaction(
+        "ex_dhap",
+        fn=_rate_out,
+        args=["DHAP", "N_translocator", "vmax_ex_pga", "km_ex_dhap"],
+        stoichiometry={"DHAP": -1},
+    )
+    m = m.add_reaction(
+        "ex_g1p",
+        fn=_rate_starch,
+        args=[
+            "G1P",
+            "ATP",
+            "ADP",
+            "Orthophosphate",
+            "3PGA",
+            "F6P",
+            "FBP",
+            "vmax_ex_g1p",
+            "km_ex_g1p_G1P",
+            "km_ex_g1p_ATP",
+            "ki_ex_g1p",
+            "ki_ex_g1p_3PGA",
+            "ki_ex_g1p_F6P",
+            "ki_ex_g1p_FBP",
+        ],
+        stoichiometry={"G1P": -1.0, "ATP": -1.0},
+    )
+    m = m.add_reaction(
+        "mda_reductase_1",
+        fn=_rate_mda_reductase1,
+        args=["MDA", "kf_mda_reductase_1"],
+        stoichiometry={"MDA": -2, "DHA": 1},
+    )
+    m = m.add_reaction(
+        "mda_reductase_2",
+        fn=_rate_mda_reductase2,
+        args=[
+            "NADPH",
+            "MDA",
+            "vmax_mda_reductase_2",
+            "km_mda_reductase_2_NADPH",
+            "km_mda_reductase_2_MDA",
+        ],
+        stoichiometry={"NADPH": -1, "MDA": -2},
+    )
+    m = m.add_reaction(
+        "ascorbate_peroxidase",
+        fn=_rate_ascorbate_peroxidase,
+        args=[
+            "ascorbate",
+            "H2O2",
+            "kf1",
+            "kr1",
+            "kf2",
+            "kr2",
+            "kf3",
+            "kf4",
+            "kr4",
+            "kf5",
+            "XT",
+        ],
+        stoichiometry={"H2O2": -1, "MDA": 2},
+    )
+    m = m.add_reaction(
+        "glutathion_reductase",
+        fn=_rate_glutathion_reductase,
+        args=[
+            "NADPH",
+            "GSSG",
+            "vmax_glutathion_reductase",
+            "km_glutathion_reductase_NADPH",
+            "km_glutathion_reductase_GSSG",
+        ],
+        stoichiometry={"NADPH": -1, "GSSG": -1},
+    )
+    m = m.add_reaction(
+        "dehydroascorbate_reductase",
+        fn=_rate_dhar,
+        args=[
+            "DHA",
+            "GSH",
+            "vmax_dehydroascorbate_reductase",
+            "km_dehydroascorbate_reductase_DHA",
+            "km_dehydroascorbate_reductase_GSH",
+            "K",
+        ],
+        stoichiometry={"DHA": -1, "GSSG": 1},
+    )
+    m = m.add_reaction(
+        "ex_atp",
+        fn=_mass_action_1s,
+        args=["ATP", "kf_ex_atp"],
+        stoichiometry={"ATP": -1},
+    )
+    m = m.add_reaction(
+        "ex_nadph",
+        fn=_mass_action_1s,
+        args=["NADPH", "kf_ex_nadph"],
+        stoichiometry={"NADPH": -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_surrogate(
+        "ps1states",
+        qss.Surrogate(
+            model=_ps1states_2021_surrogate,
+            args=[
+                "Plastocyanine (oxidised)",
+                "Plastocyanine (reduced)",
+                "Ferredoxine (oxidised)",
+                "Ferredoxine (reduced)",
+                "PSII_cross_section",
+                "PSI_total",
+                "kFdred",
+                "keq_ferredoxin_reductase",
+                "keq_PCP700",
+                "kPCox",
+                "PPFD",
+                "kMehler",
+                "O2 (dissolved)_lumen",
+            ],
+            outputs=["A0", "A1", "A2"],
+        ),
+    )
+    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(
+        "NADPH/tot",
+        fn=_div,
+        args=["NADPH", "NADP*"],
+    )
+    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