mxlmodels 1.0.0__py3-none-any.whl

mxlmodels/poolman2000.py

@@ -0,0 +1,685 @@
+"""Poolman 2000 Calvin-Benson-Bassham cycle model.
+
+Reference: Poolman, Mark G., David A. Fell, and Simon Thomas.
+"Modelling photosynthesis and its control."
+Journal of experimental botany 51.suppl_1 (2000): 319-328
+"""
+
+from mxlpy import Model
+
+
+def _moiety_1(
+    concentration: float,
+    total: float,
+) -> float:
+    """Conservation moiety: total - concentration."""
+    return total - concentration
+
+
+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 _mass_action_1s(
+    s1: float,
+    k_fwd: float,
+) -> float:
+    """Mass-action rate for one substrate."""
+    return k_fwd * s1
+
+
+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 _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_atp_synthase_2000(
+    adp: float,
+    pi: float,
+    v16: float,
+    km161: float,
+    km162: float,
+) -> float:
+    """ATP synthase rate (Poolman 2000): bi-substrate Michaelis-Menten on ADP and Pi."""
+    return v16 * adp * pi / ((adp + km161) * (pi + km162))
+
+
+def create_model() -> Model:
+    """Poolman 2000 Calvin-Benson-Bassham cycle model.
+
+    Reference: Poolman, Mark G., David A. Fell, and Simon Thomas.
+    "Modelling photosynthesis and its control."
+    Journal of experimental botany 51.suppl_1 (2000): 319-328
+    """
+    m: Model = Model()
+    m = m.add_variable("3PGA", initial_value=0.6387788347932627)
+    m = m.add_variable("BPGA", initial_value=0.0013570885908749779)
+    m = m.add_variable("GAP", initial_value=0.011259431827358068)
+    m = m.add_variable("DHAP", initial_value=0.24770748227012374)
+    m = m.add_variable("FBP", initial_value=0.01980222074817044)
+    m = m.add_variable("F6P", initial_value=1.093666906864421)
+    m = m.add_variable("G6P", initial_value=2.5154338857582377)
+    m = m.add_variable("G1P", initial_value=0.14589516537322303)
+    m = m.add_variable("SBP", initial_value=0.09132688566151095)
+    m = m.add_variable("S7P", initial_value=0.23281380022778891)
+    m = m.add_variable("E4P", initial_value=0.02836065066520614)
+    m = m.add_variable("X5P", initial_value=0.03647242425941113)
+    m = m.add_variable("R5P", initial_value=0.06109130988031577)
+    m = m.add_variable("RUBP", initial_value=0.2672164362349537)
+    m = m.add_variable("RU5P", initial_value=0.0244365238237522)
+    m = m.add_variable("ATP", initial_value=0.43633201706180874)
+    m = m.add_parameter("CO2 (dissolved)", value=0.2)
+    m = m.add_parameter("NADPH", value=0.21)
+    m = m.add_parameter("protons", value=1.2589254117941661e-05)
+    m = m.add_parameter("A*P", value=0.5)
+    m = m.add_parameter("NADP*", value=0.5)
+    m = m.add_parameter("Pi_tot", value=15.0)
+    m = m.add_parameter("E0_rubisco_carboxylase", 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("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("E0_ex_g1p", value=1.0)
+    m = m.add_parameter("kcat_ex_g1p", value=0.32)
+    m = m.add_parameter("km_atp_synthase_ADP", value=0.014)
+    m = m.add_parameter("km_atp_synthase_Orthophosphate", value=0.3)
+    m = m.add_parameter("kcat_atp_synthase", value=2.8)
+    m = m.add_parameter("E0_atp_synthase", value=1.0)
+    m = m.add_derived(
+        "ADP",
+        fn=_moiety_1,
+        args=["ATP", "A*P"],
+    )
+    m = m.add_derived(
+        "NADP",
+        fn=_moiety_1,
+        args=["NADPH", "NADP*"],
+    )
+    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(
+        "vmax_rubisco_carboxylase",
+        fn=_mass_action_1s,
+        args=["kcat_rubisco_carboxylase", "E0_rubisco_carboxylase"],
+    )
+    m = m.add_derived(
+        "vmax_fbpase",
+        fn=_mass_action_1s,
+        args=["kcat_fbpase", "E0_fbpase"],
+    )
+    m = m.add_derived(
+        "vmax_SBPase",
+        fn=_mass_action_1s,
+        args=["kcat_SBPase", "E0_SBPase"],
+    )
+    m = m.add_derived(
+        "vmax_phosphoribulokinase",
+        fn=_mass_action_1s,
+        args=["kcat_phosphoribulokinase", "E0_phosphoribulokinase"],
+    )
+    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(
+        "vmax_ex_g1p",
+        fn=_mass_action_1s,
+        args=["kcat_ex_g1p", "E0_ex_g1p"],
+    )
+    m = m.add_derived(
+        "vmax_atp_synthase",
+        fn=_mass_action_1s,
+        args=["kcat_atp_synthase", "E0_atp_synthase"],
+    )
+    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={"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(
+        "atp_synthase",
+        fn=_rate_atp_synthase_2000,
+        args=[
+            "ADP",
+            "Orthophosphate",
+            "vmax_atp_synthase",
+            "km_atp_synthase_ADP",
+            "km_atp_synthase_Orthophosphate",
+        ],
+        stoichiometry={"ATP": 1.0},
+    )
+    return m  # noqa: RET504