// Created by libAntimony v2.8.0
function oxygenation(phi, Vc, Vj, Vp)
  (phi*((((Vc + Vj) - abs(Vc - Vj))/2 + Vp) - abs(((Vc + Vj) - abs(Vc - Vj))/2 - Vp)))/2;
end

function PGA_consumption(S1, Rp, R, Nt, Vc)
  S1/Rp*(R/Nt)*Vc;
end

function NADPH_production(j, S1, Nt)
  j/2*(S1/Nt);
end

function carboxylation(Vc, Vj, Vp)
  ((((Vc + Vj) - abs(Vc - Vj))/2 + Vp) - abs(((Vc + Vj) - abs(Vc - Vj))/2 - Vp))/2;
end


model *Arnold2011_Sharkey2007_RuBisCO_CalvinCycle()

  // Compartments and Species:
  compartment chloroplast;
  species $RuBP in chloroplast, PGA in chloroplast, NADPH in chloroplast;
  species $CO2 in chloroplast, $O2 in chloroplast, $NADP in chloroplast;

  // Assignment Rules:
  NADP := Nt - NADPH;
  phi := (0.21*((gm*O2)/Ko))/((gm*CO2 - v_c + Rd)/Kc);
  v_c := (abs((abs(Vc + Vj) - abs(Vc - Vj))/2 + Vp) - abs((abs(Vc + Vj) - abs(Vc - Vj))/2 - Vp))/2;
  Vc := (Vcmax*(CO2 - 1/2*((CO2 + Kc*(1 + O2/Ko) + (Vcmax - Rd)/gm) - sqrt((CO2 + Kc*(1 + O2/Ko) + (Vcmax - Rd)/gm)^2 + 4/gm*(Rd*(CO2 + Kc*(1 + O2/Ko)) + Vcmax*(Gamma - CO2))))))/(CO2 - 1/2*((CO2 + Kc*(1 + O2/Ko) + (Vcmax - Rd)/gm) - sqrt((CO2 + Kc*(1 + O2/Ko) + (Vcmax - Rd)/gm)^2 + 4/gm*(Rd*(CO2 + Kc*(1 + O2/Ko)) + Vcmax*(Gamma - CO2)))) + Kc*(1 + O2/Ko));
  Vj := (J/4*(CO2 - 1/2*((CO2 + 2*Gamma + (J - 4*Rd)/(4*gm)) - sqrt((CO2 + 2*Gamma + (J - 4*Rd)/(4*gm))^2 + 4/gm*(Rd*(CO2 + 2*Gamma) + J/4*(Gamma - CO2))))))/(CO2 - 1/2*((CO2 + 2*Gamma + (J - 4*Rd)/(4*gm)) - sqrt((CO2 + 2*Gamma + (J - 4*Rd)/(4*gm))^2 + 4/gm*(Rd*(CO2 + 2*Gamma) + J/4*(Gamma - CO2)))) + 2*Gamma);
  Vp := 3*TPU*((CO2 - (3*TPU - Rd)/gm)/(CO2 - (3*TPU - Rd)/gm - Gamma));

  // Reactions:
  PGA_prod_Vc: $RuBP + $CO2 + 2NADPH => 2PGA; chloroplast*carboxylation(Vc, Vj, Vp);
  PGA_prod_Vo: $RuBP + $O2 + 2NADPH => 1.5PGA; chloroplast*oxygenation(phi, Vc, Vj, Vp);
  PGA_cons: PGA => $RuBP; chloroplast*PGA_consumption(PGA, Rp, NADPH, Nt, Vcmax);
  NADPH_prod: $NADP => NADPH; chloroplast*NADPH_production(J, NADP, Nt);

  // Species initializations:
  RuBP = 2;
  PGA = 2.4;
  NADPH = 0.21;
  CO2 = 24.5;
  O2 = 21;

  // Compartment initializations:
  chloroplast = 1;

  // Variable initializations:
  Nt = 0.5;
  Rp = 3.2;
  Rd = 0.0307674936008629;
  J = 0.0307678189755062;
  gm = 0.0307740792044142;
  Gamma = 3.74116898182615;
  Vcmax = 0.0307602623029146;
  Kc = 27.2372124161502;
  Ko = 16.5788431231261;
  TPU = 0.0307585098788555;

  // Other declarations:
  var phi, v_c, Vc, Vj, Vp;
  const chloroplast, Nt, Rp, Rd, J, gm, Gamma, Vcmax, Kc, Ko, TPU;

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

  // Display Names:
  PGA_prod_Vc is "PGA production - v_c";
  PGA_prod_Vo is "PGA production - v_o";
  PGA_cons is "PGA consumption";
  NADPH_prod is "NADPH production";
end