// Created by libAntimony v2.13.0
function Constant_flux__irreversible(v)
  v;
end

Constant_flux__irreversible is "Constant flux (irreversible)"

function Henri_Michaelis_Menten__irreversible(substrate, Km, V)
  V*substrate/(Km + substrate);
end

Henri_Michaelis_Menten__irreversible is "Henri-Michaelis-Menten (irreversible)"

function Function_for_Sucrose_Formation_TrioseP(k4, EtrioseP, trioseP)
  k4*EtrioseP*trioseP;
end

Function_for_Sucrose_Formation_TrioseP is "Function_for_Sucrose_Formation_TrioseP"

function Function_for_Sucrose_Consumption_Ephe(k9, sucr, Ephe, f_I_phe)
  k9*sucr*Ephe*f_I_phe;
end

Function_for_Sucrose_Consumption_Ephe is "Function_for_Sucrose_Consumption_Ephe"

function Function_for_Sucrose_Consumption_PCF(k5, sucr, f_act_pcf)
  k5*sucr*f_act_pcf;
end

Function_for_Sucrose_Consumption_PCF is "Function_for_Sucrose_Consumption_PCF"

function Function_for_Sucrose_Consumption_PCF_Lignin(k14, k15, sucr)
  (k14 + k15)*sucr;
end

Function_for_Sucrose_Consumption_PCF_Lignin is "Function_for_Sucrose_Consumption_PCF_Lignin"

function Function_for_Sucrose_Formation_Starch(k37, starch, Estarch)
  k37*starch*Estarch;
end

Function_for_Sucrose_Formation_Starch is "Function_for_Sucrose_Formation_Starch"

function Function_for_EtrioseP_Consumption_Sucrose(k2, sucr, EtrioseP, k3)
  k2*sucr*EtrioseP/(k3 + EtrioseP);
end

Function_for_EtrioseP_Consumption_Sucrose is "Function_for_EtrioseP_Consumption_Sucrose"

function Function_for_Next_Consumption(g, k11, Next, Enitrate)
  g*k11*Next*Enitrate;
end

Function_for_Next_Consumption is "Function_for_Next_Consumption"

function Function_for_TrioseP_Formation(k29, f_act_trioseP, ECO2)
  k29*f_act_trioseP*ECO2;
end

Function_for_TrioseP_Formation is "Function_for_TrioseP_Formation"

function Function_for_ECO2_Consumption(k31, trioseP, ECO2, k32)
  k31*trioseP*ECO2/(k32 + ECO2);
end

Function_for_ECO2_Consumption is "Function_for_ECO2_Consumption"

function Function_for_Ephe_Formation_Sucrose(k6, sucr, f_I_E_phe_outfl)
  k6*sucr*f_I_E_phe_outfl;
end

Function_for_Ephe_Formation_Sucrose is "Function_for_Ephe_Formation_Sucrose"

function Function_for_Enitrate_Consumption(k27, N, Enitrate, k28)
  k27*N*Enitrate/(k28 + Enitrate);
end

Function_for_Enitrate_Consumption is "Function_for_Enitrate_Consumption"

function Function_for_Estarch_Consumption(k35, sucr, Estarch, k36)
  k35*sucr*Estarch/(k36 + Estarch);
end

Function_for_Estarch_Consumption is "Function_for_Estarch_Consumption"

function Function_for_N_Formation(k11, Next, Enitrate)
  k11*Next*Enitrate;
end

Function_for_N_Formation is "Function_for_N_Formation"


model *Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles()

  // Compartments and Species:
  compartment compartment_;
  species sucr in compartment_, EtrioseP in compartment_, Ephe in compartment_;
  species N in compartment_, starch in compartment_, $Next in compartment_;
  species Enitrate in compartment_, trioseP in compartment_, $ECO2 in compartment_;
  species Estarch in compartment_;

  // Assignment Rules:
  k29 := piecewise(10.1, Light_Dark_Tracker < 0, 0);
  Light_Dark_Tracker := (time%24) - 12;
  f_I_phe := k38/(k38 + N);
  f_act_pcf := N/(k13 + N);
  f_I_E_phe_outfl := k39/(k39 + N);
  f_act_trioseP := N/(k33 + N);

  // Reactions:
  Sucrose_Formation_TrioseP: trioseP => sucr; compartment_*Function_for_Sucrose_Formation_TrioseP(k4, EtrioseP, trioseP);
  Sucrose_Consumption_Ephe: sucr => ; compartment_*Function_for_Sucrose_Consumption_Ephe(k9, sucr, Ephe, f_I_phe);
  Sucrose_Consumption_PCF: sucr => ; compartment_*Function_for_Sucrose_Consumption_PCF(k5, sucr, f_act_pcf);
  Sucrose_Consumption_PCF_Lignin: sucr => ; compartment_*Function_for_Sucrose_Consumption_PCF_Lignin(k14, k15, sucr);
  Sucrose_Formation_Starch: starch => sucr; compartment_*Function_for_Sucrose_Formation_Starch(k37, starch, Estarch);
  EtrioseP_Formation_Constant:  => EtrioseP; compartment_*Constant_flux__irreversible(k1);
  EtrioseP_Consumption_Sucrose: EtrioseP => ; compartment_*Function_for_EtrioseP_Consumption_Sucrose(k2, sucr, EtrioseP, k3);
  Ephe_Formation_Sucrose:  => Ephe; compartment_*Function_for_Ephe_Formation_Sucrose(k6, sucr, f_I_E_phe_outfl);
  Ephe_Consumption: Ephe => ; compartment_*Henri_Michaelis_Menten__irreversible(Ephe, k8, k7);
  N_Formation:  => N; compartment_*Function_for_N_Formation(k11, Next, Enitrate);
  N_Consumption: N => ; compartment_*k12*N;
  Next_Consumption: $Next => ; compartment_*Function_for_Next_Consumption(g, k11, Next, Enitrate);
  Starch_Formation: trioseP => starch; compartment_*k10*trioseP;
  Enitrate_Formation:  => Enitrate; compartment_*Constant_flux__irreversible(k26);
  Enitrate_Consumption: Enitrate => ; compartment_*Function_for_Enitrate_Consumption(k27, N, Enitrate, k28);
  TrioseP_Formation:  => trioseP; compartment_*Function_for_TrioseP_Formation(k29, f_act_trioseP, ECO2);
  ECO2_Formation:  => $ECO2; compartment_*Constant_flux__irreversible(k30);
  ECO2_Consumption: $ECO2 => ; compartment_*Function_for_ECO2_Consumption(k31, trioseP, ECO2, k32);
  Estarch_Formation:  => Estarch; compartment_*Constant_flux__irreversible(k34);
  Estarch_Consumption: Estarch => ; compartment_*Function_for_Estarch_Consumption(k35, sucr, Estarch, k36);

  // Species initializations:
  sucr = 0.748;
  EtrioseP = 2.825;
  Ephe = 9.751e-07;
  N = 4.998;
  starch = 6.041;
  Next = 20;
  Enitrate = 18.742;
  trioseP = 0;
  ECO2 = 1;
  Estarch = 5.95;

  // Compartment initializations:
  compartment_ = 1;

  // Variable initializations:
  k1 = 1;
  k2 = 1;
  k3 = 1e-05;
  k4 = 5;
  k5 = 5.5;
  k6 = 10;
  k7 = 9.8;
  k8 = 1e-06;
  k9 = 1;
  k10 = 10;
  k11 = 0.2;
  k12 = 15;
  k13 = 1;
  k14 = 0.2;
  k15 = 0.2;
  k26 = 0.5;
  k27 = 0.1;
  k28 = 1e-06;
  k30 = 0;
  k31 = 0;
  k32 = 1e-05;
  k33 = 1e-11;
  k34 = 9.8;
  k35 = 10;
  k36 = 0.0001;
  k37 = 0.1;
  k38 = 0.02;
  k39 = 1000;
  g = 1;

  // Other declarations:
  var k29, Light_Dark_Tracker, f_I_phe, f_act_pcf, f_I_E_phe_outfl, f_act_trioseP;
  const compartment_, k1, k2, k3, k4, k5, k6, k7, k8, k9, k10, k11, k12, k13;
  const k14, k15, k26, k27, k28, k30, k31, k32, k33, k34, k35, k36, k37, k38;
  const k39, g;

  // Unit definitions:
  unit volume = 1e-3 litre;
  unit substance = 1e-3 mole;

  // Display Names:
  compartment_ is "compartment";

  // CV terms:
  compartment_ hypernym "http://identifiers.org/po/PO:0009002"
  sucr identity "http://identifiers.org/chebi/CHEBI:17992"
  EtrioseP property "http://identifiers.org/ncit/C49887"
  EtrioseP property "http://identifiers.org/chebi/CHEBI:27137"
  Ephe property "http://identifiers.org/chebi/CHEBI:15882"
  Ephe property "http://identifiers.org/ncit/C49887"
  N identity "http://identifiers.org/chebi/CHEBI:17632"
  starch identity "http://identifiers.org/chebi/CHEBI:28017"
  Next identity "http://identifiers.org/chebi/CHEBI:17632"
  Next container "http://identifiers.org/go/GO:0005576"
  Enitrate property "http://identifiers.org/chebi/CHEBI:17632"
  Enitrate property "http://identifiers.org/ncit/C49887"
  trioseP hypernym "http://identifiers.org/chebi/CHEBI:27137"
  trioseP property "http://identifiers.org/pato/PATO:0002220"
  ECO2 property "http://identifiers.org/ncit/C49887"
  ECO2 property "http://identifiers.org/chebi/CHEBI:16526"
  Estarch property "http://identifiers.org/chebi/CHEBI:28017"
  Estarch property "http://identifiers.org/ncit/C49887"
  Sucrose_Formation_TrioseP hypernym "http://identifiers.org/sbo/SBO:0000393"
  Sucrose_Consumption_Ephe hypernym "http://identifiers.org/sbo/SBO:0000394"
  Sucrose_Consumption_PCF hypernym "http://identifiers.org/sbo/SBO:0000394"
  Sucrose_Consumption_PCF_Lignin hypernym "http://identifiers.org/sbo/SBO:0000394"
  Sucrose_Formation_Starch hypernym "http://identifiers.org/sbo/SBO:0000393"
  EtrioseP_Formation_Constant hypernym "http://identifiers.org/sbo/SBO:0000393"
  EtrioseP_Consumption_Sucrose hypernym "http://identifiers.org/sbo/SBO:0000394"
  Ephe_Formation_Sucrose hypernym "http://identifiers.org/sbo/SBO:0000393"
  Ephe_Consumption hypernym "http://identifiers.org/sbo/SBO:0000394"
  N_Formation hypernym "http://identifiers.org/sbo/SBO:0000393"
  N_Consumption hypernym "http://identifiers.org/sbo/SBO:0000394"
  Next_Consumption hypernym "http://identifiers.org/sbo/SBO:0000394"
  Starch_Formation hypernym "http://identifiers.org/sbo/SBO:0000393"
  Enitrate_Formation hypernym "http://identifiers.org/sbo/SBO:0000393"
  Enitrate_Consumption hypernym "http://identifiers.org/sbo/SBO:0000394"
  TrioseP_Formation hypernym "http://identifiers.org/sbo/SBO:0000393"
  TrioseP_Formation description "http://identifiers.org/pubmed/27164436"
  ECO2_Formation hypernym "http://identifiers.org/sbo/SBO:0000393"
  ECO2_Consumption hypernym "http://identifiers.org/sbo/SBO:0000394"
  Estarch_Formation hypernym "http://identifiers.org/sbo/SBO:0000393"
  Estarch_Consumption hypernym "http://identifiers.org/sbo/SBO:0000394"
end

Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles is "Larbat2016.2 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles)"

Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles description "http://identifiers.org/pubmed/27164436"
Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles model_entity_is "http://identifiers.org/biomodels.db/MODEL1911130005",
                                                                                                                                                                              "http://identifiers.org/biomodels.db/BIOMD0000000858"
Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles property "http://identifiers.org/go/GO:0018958"
Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles property "http://identifiers.org/mamo/MAMO_0000046"
Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles property "http://identifiers.org/go/GO:0005985"
Larbat2016_2___Modeling_the_diversion_of_primary_carbon_flux_into_secondary_metabolism_under_variable_nitrate_and_light_or_dark_conditions__Light_Dark_Cycles property "http://identifiers.org/go/GO:0005982"
