mxlmodels 1.0.0__py3-none-any.whl

mxlmodels/matuszynska2016_npq.py

@@ -0,0 +1,683 @@
+"""Matuszynska 2016 NPQ model: non-photochemical quenching via PsbS and xanthophyll cycle.
+
+Reference: Matuszyńska, Anna, et al.
+"A mathematical model of non-photochemical quenching to study short-term light memory in plants."
+Biochimica et Biophysica Acta (BBA)-Bioenergetics 1857.12 (2016): 1860-1869
+"""
+
+import numpy as np
+from mxlpy import Derived, Model
+from mxlpy.surrogates import qss
+
+
+def _ph(
+    h: float,
+) -> float:
+    """Convert lumenal proton concentration to pH (conversion factor 2.5e-4)."""
+    return -np.log10(h * 2.5e-4)
+
+
+def _ph_inv(
+    ph: float,
+) -> float:
+    """Convert pH to lumenal proton concentration (inverse of _ph)."""
+    return 3.2e4 * 10**-ph
+
+
+def _keq_qapq(
+    f: float,
+    e0_qa: float,
+    e0_pq: float,
+    p_h_st: float,
+    r: float,
+    t: float,
+) -> float:
+    """Equilibrium constant for QA -> PQ electron transfer, including stroma pH correction."""
+    RT = r * t
+    DG1 = -f * e0_qa
+    DG2 = -2 * f * e0_pq + 2 * p_h_st * np.log(10) * RT
+    DG0 = -2 * DG1 + DG2
+    return np.exp(-DG0 / RT)
+
+
+def _keq_cytb6f(
+    p_h_lu: float,
+    f: float,
+    e0_pq: float,
+    r: float,
+    t: float,
+    e0_pc: float,
+    p_h_st: float,
+) -> float:
+    """Equilibriu constant of Cytochrome b6f."""
+    RT = r * t
+    DG1 = -2 * f * e0_pq + 2 * RT * np.log(10) * p_h_lu
+    DG2 = -f * e0_pc
+    DG3 = RT * np.log(10) * (p_h_st - p_h_lu)
+    DG = -DG1 + 2 * DG2 + 2 * DG3
+    return np.exp(-DG / RT)
+
+
+def _keq_atp_synth(
+    p_h_lu: float,
+    dg_atp: float,
+    p_h_st: float,
+    r: float,
+    t: float,
+    pi: float,
+) -> float:
+    """Return equilibrium constant of ATP synthase.
+
+    See Matuszynska et al 2016 or Ebenhöh et al. 2011,2014.
+    """
+    RT = r * t
+    DG = dg_atp - np.log(10) * (p_h_st - p_h_lu) * (14 / 3) * RT
+    return pi * np.exp(-DG / RT)
+
+
+def _moiety_1s(
+    x: float,
+    x_total: float,
+) -> float:
+    """Calculate conservation relationship for one substrate.
+
+    Used for creating derived variables that represent moiety conservation,
+    such as calculating the free form of a species when you know the total.
+
+    Parameters
+    ----------
+    x
+        Concentration of one form of the species
+    x_total
+        Total concentration of all forms
+
+    Returns
+    -------
+    Float
+        Concentration of the other form (x_total - x)
+
+    Examples
+    --------
+    >>> moiety_1s(0.3, 1.0)  # If total is 1.0 and one form is 0.3, other is 0.7
+    0.7
+    >>> # Example: If ATP + ADP = total_adenosine
+    >>> moiety_1s(0.8, 1.5)  # [ADP] = total_adenosine - [ATP]
+    0.7
+
+    """
+    return x_total - x
+
+
+def _quencher(
+    psb_s: float,
+    zx: float,
+    psb_sp: float,
+    k_z_sat: float,
+    gamma_0: float,
+    gamma_1: float,
+    gamma_2: float,
+    gamma_3: float,
+) -> float:
+    """Quencher mechanism.
+
+    accepts:
+    psbS: fraction of non-protonated PsbS protein
+    Vx: fraction of Violaxanthin
+    """
+    Zs = zx / (zx + k_z_sat)
+
+    return (
+        gamma_0 * (1 - Zs) * psb_s
+        + gamma_1 * (1 - Zs) * psb_sp
+        + gamma_2 * Zs * psb_sp
+        + gamma_3 * Zs * psb_s
+    )
+
+
+def _b2(
+    pq_ox: float,
+    pq_red: float,
+    quencher: float,
+    pfd: float,
+    k_pqh2: float,
+    keq_qapq: float,
+    kh: float,
+    kf: float,
+    kp: float,
+    psii_tot: float,
+) -> float:
+    """Analytical PSII B2 state (dark-closed, Matuszynska 2016): fraction with PQ reduced."""
+    return (
+        psii_tot
+        * (
+            k_pqh2 * kf**2 * pq_red
+            + 2 * k_pqh2 * kf * kh * pq_red * quencher
+            + k_pqh2 * kf * kp * pq_red
+            + k_pqh2 * kh**2 * pq_red * quencher**2
+            + k_pqh2 * kh * kp * pq_red * quencher
+            + keq_qapq * kf * kp * pfd
+            + keq_qapq * kh * kp * pfd * quencher
+        )
+        / (
+            k_pqh2 * keq_qapq * kf**2 * pq_ox
+            + 2 * k_pqh2 * keq_qapq * kf * kh * pq_ox * quencher
+            + k_pqh2 * keq_qapq * kf * kp * pq_ox
+            + k_pqh2 * keq_qapq * kf * pfd * pq_ox
+            + k_pqh2 * keq_qapq * kh**2 * pq_ox * quencher**2
+            + k_pqh2 * keq_qapq * kh * kp * pq_ox * quencher
+            + k_pqh2 * keq_qapq * kh * pfd * pq_ox * quencher
+            + k_pqh2 * kf**2 * pq_red
+            + 2 * k_pqh2 * kf * kh * pq_red * quencher
+            + k_pqh2 * kf * kp * pq_red
+            + k_pqh2 * kf * pfd * pq_red
+            + k_pqh2 * kh**2 * pq_red * quencher**2
+            + k_pqh2 * kh * kp * pq_red * quencher
+            + k_pqh2 * kh * pfd * pq_red * quencher
+            + k_pqh2 * kp * pfd * pq_red
+            + keq_qapq * kf * kp * pfd
+            + keq_qapq * kh * kp * pfd * quencher
+            + keq_qapq * kp * pfd**2
+        )
+    )
+
+
+def _b0(
+    pq_ox: float,
+    pq_red: float,
+    quencher: float,
+    pfd: float,
+    k_pqh2: float,
+    keq_qapq: float,
+    kh: float,
+    kf: float,
+    kp: float,
+    psii_tot: float,
+) -> float:
+    """Analytical PSII B0 state (dark-closed, Matuszynska 2016): fraction with PQ oxidised."""
+    return (
+        k_pqh2
+        * keq_qapq
+        * pq_ox
+        * psii_tot
+        * (
+            kf**2
+            + 2 * kf * kh * quencher
+            + kf * kp
+            + kh**2 * quencher**2
+            + kh * kp * quencher
+        )
+        / (
+            k_pqh2 * keq_qapq * kf**2 * pq_ox
+            + 2 * k_pqh2 * keq_qapq * kf * kh * pq_ox * quencher
+            + k_pqh2 * keq_qapq * kf * kp * pq_ox
+            + k_pqh2 * keq_qapq * kf * pfd * pq_ox
+            + k_pqh2 * keq_qapq * kh**2 * pq_ox * quencher**2
+            + k_pqh2 * keq_qapq * kh * kp * pq_ox * quencher
+            + k_pqh2 * keq_qapq * kh * pfd * pq_ox * quencher
+            + k_pqh2 * kf**2 * pq_red
+            + 2 * k_pqh2 * kf * kh * pq_red * quencher
+            + k_pqh2 * kf * kp * pq_red
+            + k_pqh2 * kf * pfd * pq_red
+            + k_pqh2 * kh**2 * pq_red * quencher**2
+            + k_pqh2 * kh * kp * pq_red * quencher
+            + k_pqh2 * kh * pfd * pq_red * quencher
+            + k_pqh2 * kp * pfd * pq_red
+            + keq_qapq * kf * kp * pfd
+            + keq_qapq * kh * kp * pfd * quencher
+            + keq_qapq * kp * pfd**2
+        )
+    )
+
+
+def _fluorescence(
+    q: float,
+    _b0: float,
+    _b2: float,
+    k_h: float,
+    k_f: float,
+    k_p: float,
+) -> float:
+    """Fluorescence function."""
+    return k_f / (k_h * q + k_f + k_p) * _b0 + k_f / (k_h * q + k_f) * _b2
+
+
+def _b1(
+    pq_ox: float,
+    pq_red: float,
+    quencher: float,
+    pfd: float,
+    k_pqh2: float,
+    keq_qapq: float,
+    kh: float,
+    kf: float,
+    kp: float,
+    psii_tot: float,
+) -> float:
+    """Analytical PSII B1 state (light-open, Matuszynska 2016): fraction absorbing light with PQ oxidised."""
+    return (
+        k_pqh2
+        * keq_qapq
+        * pfd
+        * pq_ox
+        * psii_tot
+        * (kf + kh * quencher)
+        / (
+            k_pqh2 * keq_qapq * kf**2 * pq_ox
+            + 2 * k_pqh2 * keq_qapq * kf * kh * pq_ox * quencher
+            + k_pqh2 * keq_qapq * kf * kp * pq_ox
+            + k_pqh2 * keq_qapq * kf * pfd * pq_ox
+            + k_pqh2 * keq_qapq * kh**2 * pq_ox * quencher**2
+            + k_pqh2 * keq_qapq * kh * kp * pq_ox * quencher
+            + k_pqh2 * keq_qapq * kh * pfd * pq_ox * quencher
+            + k_pqh2 * kf**2 * pq_red
+            + 2 * k_pqh2 * kf * kh * pq_red * quencher
+            + k_pqh2 * kf * kp * pq_red
+            + k_pqh2 * kf * pfd * pq_red
+            + k_pqh2 * kh**2 * pq_red * quencher**2
+            + k_pqh2 * kh * kp * pq_red * quencher
+            + k_pqh2 * kh * pfd * pq_red * quencher
+            + k_pqh2 * kp * pfd * pq_red
+            + keq_qapq * kf * kp * pfd
+            + keq_qapq * kh * kp * pfd * quencher
+            + keq_qapq * kp * pfd**2
+        )
+    )
+
+
+def _psii(
+    _b1: float,
+    k_p: float,
+) -> float:
+    """Reduction of PQ due to ps2."""
+    return k_p * 0.5 * _b1
+
+
+def _two_divided_value(
+    x: float,
+) -> float:
+    """Return 2/x; used for scaling 2-proton stoichiometry by buffering capacity."""
+    return 2 / x
+
+
+def _ptox(
+    pqh_2: float,
+    pfd: float,
+    k_cytb6f: float,
+    k_ptox: float,
+    o2_ex: float,
+    pq_tot: float,
+    keq_cytb6f: float,
+) -> float:
+    """Oxidation of the PQ pool through cytochrome and PTOX."""
+    kPFD = k_cytb6f * pfd
+    k_ptox = k_ptox * o2_ex
+    a1 = kPFD * keq_cytb6f / (keq_cytb6f + 1)
+    a2 = kPFD / (keq_cytb6f + 1)
+    return (a1 + k_ptox) * pqh_2 - a2 * (pq_tot - pqh_2)
+
+
+def _four_divided_value(
+    x: float,
+) -> float:
+    """Return 4/x; used for scaling 4-proton stoichiometry by buffering capacity."""
+    return 4 / x
+
+
+def _atp_synthase(
+    atp_st: float,
+    at_pase_ac: float,
+    kf_at_psynth: float,
+    keq_at_psynth: float,
+    ap_tot: float,
+) -> float:
+    """Production of ATP by ATPsynthase."""
+    return at_pase_ac * kf_at_psynth * (ap_tot - atp_st - atp_st / keq_at_psynth)
+
+
+def _neg_fourteenthirds_divided_value(
+    x: float,
+) -> float:
+    """Return -(14/3)/x; used for HPR proton stoichiometry of ATP synthase scaled by buffering capacity."""
+    return -(14 / 3) / x
+
+
+def _atp_synthase_activase(
+    at_pase_ac: float,
+    pfd: float,
+    k_act_at_pase: float,
+    k_deact_at_pase: float,
+) -> float:
+    """Activation of ATPsynthase by light."""
+    switch = pfd > 0.0
+    if switch:
+        return k_act_at_pase * (1 - at_pase_ac)
+    return -k_deact_at_pase * at_pase_ac
+
+
+def _proton_leak(
+    h_lu: float,
+    k_leak: float,
+    h_st: float,
+) -> float:
+    """Transmembrane proton leak."""
+    return k_leak * (h_lu - h_st)
+
+
+def _neg_divided_value(
+    x: float,
+) -> float:
+    """Return -1/x; used for negative proton leak stoichiometry scaled by buffering capacity."""
+    return -1 / x
+
+
+def _atp_consumption(
+    atp_st: float,
+    k_at_pconsum: float,
+) -> float:
+    """ATP consuming reaction."""
+    return k_at_pconsum * atp_st
+
+
+def _xantophyll_cycle(
+    vx: float,
+    h_lu: float,
+    nhx: float,
+    k_p_h_sat_inv: float,
+    k_dv: float,
+    k_ez: float,
+    x_tot: float,
+) -> float:
+    """Xanthophyll cycle."""
+    a = h_lu**nhx / (h_lu**nhx + k_p_h_sat_inv**nhx)
+    return k_dv * a * vx - k_ez * (x_tot - vx)
+
+
+def _psbs_protonation(
+    psb_s: float,
+    h_lu: float,
+    nhl: float,
+    k_p_h_sat_lhc_inv: float,
+    k_prot: float,
+    k_deprot: float,
+    psb_s_tot: float,
+) -> float:
+    """Protonation of PsbS protein."""
+    a = h_lu**nhl / (h_lu**nhl + k_p_h_sat_lhc_inv**nhl)
+    return k_prot * a * psb_s - k_deprot * (psb_s_tot - psb_s)
+
+
+def _ps2states_2016a_analytical(
+    pq_ox: float,
+    pq_red: float,
+    quencher: float,
+    pfd: float,
+    k_pqh2: float,
+    keq_qapq: float,
+    kh: float,
+    kf: float,
+    kp: float,
+    psii_tot: float,
+) -> tuple[float, float, float, float]:
+    """PSII state populations (Matuszynska 2016 NPQ, analytical closed-form variant)."""
+    x0 = kf**2
+    x1 = kf * kp
+    x2 = kh * quencher
+    x3 = kp * x2
+    x4 = 2 * x2
+    x5 = kf * x4
+    x6 = kh**2 * quencher**2
+    x7 = keq_qapq * kp
+    x8 = k_pqh2 * pq_ox
+    x9 = keq_qapq * x8
+    x10 = k_pqh2 * pq_red
+    x11 = kf * x10
+    x12 = kp * x10
+    x13 = pfd * x9
+    x14 = x10 * x2
+    x15 = pfd * x7
+    x16 = (
+        keq_qapq * pfd * x1
+        + x0 * x10
+        + x1 * x10
+        + x10 * x3
+        + x10 * x6
+        + x11 * x4
+        + x15 * x2
+    )
+    x17 = psii_tot / (
+        kf * x13
+        + pfd**2 * x7
+        + pfd * x11
+        + pfd * x12
+        + pfd * x14
+        + x0 * x9
+        + x1 * x9
+        + x13 * x2
+        + x16
+        + x2 * x7 * x8
+        + x5 * x9
+        + x6 * x9
+    )
+    x18 = pfd * x17
+    _B0 = x17 * x9 * (x0 + x1 + x3 + x5 + x6)
+    _B1 = x18 * x9 * (kf + x2)
+    _B2 = x16 * x17
+    _B3 = x18 * (x11 + x12 + x14 + x15)
+    return _B0, _B1, _B2, _B3
+
+
+def create_model() -> Model:
+    """Matuszynska 2016 NPQ model: non-photochemical quenching via PsbS and xanthophyll cycle.
+
+    Reference: Matuszyńska, Anna, et al.
+    "A mathematical model of non-photochemical quenching to study short-term light memory in plants."
+    Biochimica et Biophysica Acta (BBA)-Bioenergetics 1857.12 (2016): 1860-1869
+    """
+    m: Model = Model()
+    m = m.add_variable("pq_red", initial_value=0)
+    m = m.add_variable("protons", initial_value=6.32975752e-05)
+    m = m.add_variable("vmax_atp_synthase", initial_value=0)
+    m = m.add_variable("atp", initial_value=25.0)
+    m = m.add_variable("psbs_de", initial_value=1)
+    m = m.add_variable("vx", initial_value=1)
+    m = m.add_parameter("PSII_tot", value=2.5)
+    m = m.add_parameter("PQ_tot", value=20)
+    m = m.add_parameter("AP_tot", value=50)
+    m = m.add_parameter("PsbS_tot", value=1)
+    m = m.add_parameter("X_tot", value=1)
+    m = m.add_parameter("O2_ex", value=8)
+    m = m.add_parameter("Pi", value=0.01)
+    m = m.add_parameter("k_Cytb6f", value=0.104)
+    m = m.add_parameter("k_ActATPase", value=0.01)
+    m = m.add_parameter("k_DeactATPase", value=0.002)
+    m = m.add_parameter("k_ATPsynth", value=20.0)
+    m = m.add_parameter("k_ATPconsum", value=10.0)
+    m = m.add_parameter("k_PQH2", value=250.0)
+    m = m.add_parameter("k_H", value=5000000000.0)
+    m = m.add_parameter("k_F", value=625000000.0)
+    m = m.add_parameter("k_P", value=5000000000.0)
+    m = m.add_parameter("k_PTOX", value=0.01)
+    m = m.add_parameter("pH_st", value=7.8)
+    m = m.add_parameter("k_leak", value=1000)
+    m = m.add_parameter("b_H", value=100)
+    m = m.add_parameter("hpr", value=4.666666666666667)
+    m = m.add_parameter("k_DV", value=0.0024)
+    m = m.add_parameter("k_EZ", value=0.00024)
+    m = m.add_parameter("K_pHSat", value=5.8)
+    m = m.add_parameter("nhx", value=5.0)
+    m = m.add_parameter("K_ZSat", value=0.12)
+    m = m.add_parameter("nhl", value=3)
+    m = m.add_parameter("k_deprot", value=0.0096)
+    m = m.add_parameter("k_prot", value=0.0096)
+    m = m.add_parameter("K_pHSatLHC", value=5.8)
+    m = m.add_parameter("gamma_0", value=0.1)
+    m = m.add_parameter("gamma_1", value=0.25)
+    m = m.add_parameter("gamma_2", value=0.6)
+    m = m.add_parameter("gamma_3", value=0.15)
+    m = m.add_parameter("F", value=96.485)
+    m = m.add_parameter("R", value=0.0083)
+    m = m.add_parameter("T", value=298)
+    m = m.add_parameter("E0_QA", value=-0.14)
+    m = m.add_parameter("E0_PQ", value=0.354)
+    m = m.add_parameter("E0_PC", value=0.38)
+    m = m.add_parameter("DG_ATP", value=30.6)
+    m = m.add_parameter("PPFD", value=100)
+    m = m.add_derived(
+        "pH_lu",
+        fn=_ph,
+        args=["protons"],
+    )
+    m = m.add_derived(
+        "H_st",
+        fn=_ph_inv,
+        args=["pH_st"],
+    )
+    m = m.add_derived(
+        "K_pHSat_inv",
+        fn=_ph_inv,
+        args=["K_pHSat"],
+    )
+    m = m.add_derived(
+        "K_pHSatLHC_inv",
+        fn=_ph_inv,
+        args=["K_pHSatLHC"],
+    )
+    m = m.add_derived(
+        "K_QAPQ",
+        fn=_keq_qapq,
+        args=["F", "E0_QA", "E0_PQ", "pH_st", "R", "T"],
+    )
+    m = m.add_derived(
+        "K_cytb6f",
+        fn=_keq_cytb6f,
+        args=["pH_lu", "F", "E0_PQ", "R", "T", "E0_PC", "pH_st"],
+    )
+    m = m.add_derived(
+        "K_ATPsynth",
+        fn=_keq_atp_synth,
+        args=["pH_lu", "DG_ATP", "pH_st", "R", "T", "Pi"],
+    )
+    m = m.add_derived(
+        "pq_ox",
+        fn=_moiety_1s,
+        args=["pq_red", "PQ_tot"],
+    )
+    m = m.add_derived(
+        "adp",
+        fn=_moiety_1s,
+        args=["atp", "AP_tot"],
+    )
+    m = m.add_derived(
+        "psbs_pr",
+        fn=_moiety_1s,
+        args=["psbs_de", "PsbS_tot"],
+    )
+    m = m.add_derived(
+        "zx",
+        fn=_moiety_1s,
+        args=["vx", "X_tot"],
+    )
+    m = m.add_derived(
+        "Q",
+        fn=_quencher,
+        args=[
+            "psbs_de",
+            "zx",
+            "psbs_pr",
+            "K_ZSat",
+            "gamma_0",
+            "gamma_1",
+            "gamma_2",
+            "gamma_3",
+        ],
+    )
+    m = m.add_derived(
+        "Fluo",
+        fn=_fluorescence,
+        args=["Q", "B0", "B2", "k_H", "k_F", "k_P"],
+    )
+    m = m.add_reaction(
+        "v_PSII",
+        fn=_psii,
+        args=["B1", "k_P"],
+        stoichiometry={
+            "pq_red": 1,
+            "protons": Derived(fn=_two_divided_value, args=["b_H"]),
+        },
+    )
+    m = m.add_reaction(
+        "v_PQ",
+        fn=_ptox,
+        args=["pq_red", "PPFD", "k_Cytb6f", "k_PTOX", "O2_ex", "PQ_tot", "K_cytb6f"],
+        stoichiometry={
+            "pq_red": -1,
+            "protons": Derived(fn=_four_divided_value, args=["b_H"]),
+        },
+    )
+    m = m.add_reaction(
+        "atp_synthase",
+        fn=_atp_synthase,
+        args=["atp", "vmax_atp_synthase", "k_ATPsynth", "K_ATPsynth", "AP_tot"],
+        stoichiometry={
+            "atp": 1,
+            "protons": Derived(fn=_neg_fourteenthirds_divided_value, args=["b_H"]),
+        },
+    )
+    m = m.add_reaction(
+        "atp_activase",
+        fn=_atp_synthase_activase,
+        args=["vmax_atp_synthase", "PPFD", "k_ActATPase", "k_DeactATPase"],
+        stoichiometry={"vmax_atp_synthase": 1},
+    )
+    m = m.add_reaction(
+        "proton_leak",
+        fn=_proton_leak,
+        args=["protons", "k_leak", "H_st"],
+        stoichiometry={"protons": Derived(fn=_neg_divided_value, args=["b_H"])},
+    )
+    m = m.add_reaction(
+        "v_ATPcons",
+        fn=_atp_consumption,
+        args=["atp", "k_ATPconsum"],
+        stoichiometry={"atp": -1},
+    )
+    m = m.add_reaction(
+        "v_Xcyc",
+        fn=_xantophyll_cycle,
+        args=["vx", "protons", "nhx", "K_pHSat_inv", "k_DV", "k_EZ", "X_tot"],
+        stoichiometry={"vx": -1},
+    )
+    m = m.add_reaction(
+        "v_PsbSP",
+        fn=_psbs_protonation,
+        args=[
+            "psbs_de",
+            "protons",
+            "nhl",
+            "K_pHSatLHC_inv",
+            "k_prot",
+            "k_deprot",
+            "PsbS_tot",
+        ],
+        stoichiometry={"psbs_de": -1},
+    )
+    m = m.add_surrogate(
+        "ps2states",
+        qss.Surrogate(
+            model=_ps2states_2016a_analytical,
+            args=[
+                "pq_ox",
+                "pq_red",
+                "Q",
+                "PPFD",
+                "k_PQH2",
+                "K_QAPQ",
+                "k_H",
+                "k_F",
+                "k_P",
+                "PSII_tot",
+            ],
+            outputs=["B0", "B1", "B2", "B3"],
+        ),
+    )
+    return m  # noqa: RET504