// Created by libAntimony v2.8.0
function function_2(Vm, S, K, R1, KR1, R2, KR2)
  (Vm*S)/(S + K*(1 + R1/KR1 + R2/KR2));
end

function function_7(Vm, S, KA, A, K, R1, KR1, R2, KR2, R3, KR3)
  (Vm*S)/(S*(1 + KA/A) + K*(1 + (1 + KA/A)*(R1/KR1 + R2/KR2 + R3/KR3)));
end

function function_4(Vm, S1, S2, K1, R1, KR1, R2, KR2, R3, KR3, R4, KR41, K2, KR42)
  (Vm*S1*S2)/((S1 + K1*(1 + R1/KR1 + R2/KR2 + R3/KR3))*(S2*(1 + R4/KR41) + K2*(1 + R4/KR42)));
end

function function_6(Vm, s1, s2, K1, K2)
  (Vm*s1*s2)/((s1 + K1)*(s2 + K2));
end

function function_1(Vm, S, K, R1, KR1, R2, KR2, R3, KR3, R4, KR4, R5, KR5)
  (Vm*S)/(S + K*(1 + R1/KR1 + R2/KR2 + R3/KR3 + R4/KR4 + R5/KR5));
end

function function_3(Vm, S, K, R1, KR1)
  (Vm*S)/(S + K*(1 + R1/KR1));
end

function function_5(Vm, S1, S2, K1, K2, R1, KR1, R2, KA1, A1, KA2, A2, KA3, A3)
  (Vm*S1*S2)/((S1 + K1)*(1 + R1/KR1)*(S2 + K2*(1 + (K2*R2)/(KA1*A1 + KA2*A2 + KA3*A3))));
end


model *Arnold2011_Poolman2000_CalvinCycle_Starch()

  // Compartments and Species:
  compartment chloroplast, cytosol;
  species RuBP in chloroplast, PGA in chloroplast, DPGA in chloroplast, GAP in chloroplast;
  species DHAP in chloroplast, FBP in chloroplast, F6P in chloroplast, E4P in chloroplast;
  species SBP in chloroplast, S7P in chloroplast, X5P in chloroplast, R5P in chloroplast;
  species Ru5P in chloroplast, G6P in chloroplast, G1P in chloroplast, ATP in chloroplast;
  species $ADP in chloroplast, $NADPH in chloroplast, $NADP in chloroplast;
  species $H in chloroplast, $Pi_ in chloroplast, $Pext in cytosol;

  // Assignment Rules:
  ADP := 1.5 - ATP;
  Pi_ := 15 - 2*(RuBP + DPGA + FBP + SBP) - (PGA + GAP + DHAP + F6P + E4P + S7P + X5P + R5P + Ru5P + G6P + G1P + ATP);

  // Reactions:
  RuBisCO: RuBP => 2PGA; chloroplast*function_1(RuBisCO_Vm, RuBP, RuBisCO_K, PGA, RuBisCO_KR1, FBP, RuBisCO_KR2, SBP, RuBisCO_KR3, Pi_, RuBisCO_KR4, NADPH, RuBisCO_KR5);
  PGA_K: PGA + ATP -> DPGA + $ADP; chloroplast*(PGA_K_k1*PGA*ATP - PGA_K_k2*DPGA*ADP);
  GAP_DH: DPGA + $NADPH + $H -> GAP + $NADP + $Pi_; chloroplast*(GAP_DH_k1*DPGA*NADPH*H - GAP_DH_k2*GAP*NADP*Pi_);
  TP_I: GAP -> DHAP; chloroplast*(TP_I_k1*GAP - TP_I_k2*DHAP);
  FBP_A: DHAP + GAP -> FBP; chloroplast*(FBP_A_k1*DHAP*GAP - FBP_A_k2*FBP);
  FBPase: FBP => F6P + $Pi_; chloroplast*function_2(FBPase_Vm, FBP, FBPase_K, F6P, FBPase_KR1, Pi_, FBPase_KR2);
  F6P_TK: GAP + F6P -> X5P + E4P; chloroplast*(F6P_TK_k1*GAP*F6P - F6P_TK_k2*X5P*E4P);
  SBP_A: DHAP + E4P -> SBP; chloroplast*(SBP_A_k1*DHAP*E4P - SBP_A_k2*SBP);
  SBPase: SBP => S7P + $Pi_; chloroplast*function_3(SBPase_Vm, SBP, SBPase_K, Pi_, SBPase_KR1);
  S7P_TK: GAP + S7P -> X5P + R5P; chloroplast*(S7P_TK_k1*GAP*S7P - S7P_TK_k2*X5P*R5P);
  R5P_I: R5P -> Ru5P; chloroplast*(R5P_I_k1*R5P - R5P_I_k2*Ru5P);
  Ru5P_E: X5P -> Ru5P; chloroplast*(Ru5P_E_k1*X5P - Ru5P_E_k2*Ru5P);
  Ru5P_K: Ru5P + ATP => RuBP + $ADP; chloroplast*function_4(Ru5P_K_Vm, Ru5P, ATP, Ru5P_K_K1, PGA, Ru5P_K_KR1, RuBP, Ru5P_K_KR2, Pi_, Ru5P_K_KR3, ADP, Ru5P_K_KR41, Ru5P_K_K2, Ru5P_K_KR42);
  PG_I: F6P -> G6P; chloroplast*(PG_I_k1*F6P - PG_I_k2*G6P);
  PG_M: G6P -> G1P; chloroplast*(PG_M_k1*G6P - PG_M_k2*G1P);
  Starch_S: G1P + ATP => ; chloroplast*function_5(Starch_S_Vm, G1P, ATP, Starch_S_K1, Starch_S_K2, ADP, Starch_S_KR1, Pi_, Starch_S_KA1, PGA, Starch_S_KA2, F6P, Starch_S_KA3, FBP);
  Starch_P: $Pi_ => G1P; chloroplast*function_3(Starch_P_Vm, Pi_, Starch_P_K, G1P, Starch_P_KR1);
  ATP_S: $ADP + $Pi_ => ATP; chloroplast*function_6(ATP_S_Vm, ADP, Pi_, ATP_S_K1, ATP_S_K2);
  TPT_PGA: PGA => ; chloroplast*function_7(TPT_PGA_Vm, PGA, TPT_PGA_KA, Pext, TPT_PGA_K, Pi_, TPT_PGA_KR1, GAP, TPT_PGA_KR2, DHAP, TPT_PGA_KR3);
  TPT_GAP: GAP => ; chloroplast*function_7(TPT_GAP_Vm, GAP, TPT_GAP_KA, Pext, TPT_GAP_K, Pi_, TPT_GAP_KR1, PGA, TPT_GAP_KR2, DHAP, TPT_GAP_KR3);
  TPT_DHAP: DHAP => ; chloroplast*function_7(TPT_DHAP_Vm, DHAP, TPT_DHAP_KA, Pext, TPT_DHAP_K, Pi_, TPT_DHAP_KR1, PGA, TPT_DHAP_KR2, GAP, TPT_DHAP_KR3);

  // Species initializations:
  RuBP = 2;
  PGA = 2.4;
  DPGA = 0.0011;
  GAP = 0.02;
  DHAP = 0.48;
  FBP = 0.669999999999999;
  F6P = 0.640764257004719;
  E4P = 0.05;
  SBP = 0.3;
  S7P = 2;
  X5P = 0.0747384155455904;
  R5P = 0.125186846038864;
  Ru5P = 0.0500747384155456;
  G6P = 1.47375779111085;
  G1P = 0.0854779518844294;
  ATP = 0.68;
  NADPH = 0.21;
  NADP = 0.29;
  H = 1.25892541179417e-005;
  Pext = 0.5;

  // Compartment initializations:
  chloroplast = 1;
  cytosol = 1;

  // Variable initializations:
  RuBisCO_Vm = 340;
  RuBisCO_K = 0.02;
  RuBisCO_KR1 = 0.84;
  RuBisCO_KR2 = 0.04;
  RuBisCO_KR3 = 0.0075;
  RuBisCO_KR4 = 0.9;
  RuBisCO_KR5 = 0.07;
  PGA_K_k1 = 500000000;
  PGA_K_k2 = 1612900000000;
  GAP_DH_k1 = 500000000;
  GAP_DH_k2 = 31.25;
  TP_I_k1 = 500000000;
  TP_I_k2 = 22727000;
  FBP_A_k1 = 500000000;
  FBP_A_k2 = 70423000;
  FBPase_Vm = 200;
  FBPase_K = 0.03;
  FBPase_KR1 = 0.7;
  FBPase_KR2 = 12;
  F6P_TK_k1 = 500000000;
  F6P_TK_k2 = 5952400000;
  SBP_A_k1 = 500000000;
  SBP_A_k2 = 38461500;
  SBPase_Vm = 40;
  SBPase_K = 0.02;
  SBPase_KR1 = 12;
  S7P_TK_k1 = 500000000;
  S7P_TK_k2 = 588240000;
  R5P_I_k1 = 500000000;
  R5P_I_k2 = 1250000000;
  Ru5P_E_k1 = 500000000;
  Ru5P_E_k2 = 746269000;
  Ru5P_K_Vm = 1000;
  Ru5P_K_K1 = 0.05;
  Ru5P_K_KR1 = 2;
  Ru5P_K_KR2 = 0.7;
  Ru5P_K_KR3 = 4;
  Ru5P_K_KR41 = 2.5;
  Ru5P_K_K2 = 0.05;
  Ru5P_K_KR42 = 0.4;
  PG_I_k1 = 500000000;
  PG_I_k2 = 217400000;
  PG_M_k1 = 500000000;
  PG_M_k2 = 8621000000;
  Starch_S_Vm = 40;
  Starch_S_K1 = 0.08;
  Starch_S_K2 = 0.08;
  Starch_S_KR1 = 10;
  Starch_S_KA1 = 0.1;
  Starch_S_KA2 = 0.02;
  Starch_S_KA3 = 0.02;
  Starch_P_Vm = 40;
  Starch_P_K = 0.1;
  Starch_P_KR1 = 0.05;
  ATP_S_Vm = 350;
  ATP_S_K1 = 0.014;
  ATP_S_K2 = 0.3;
  TPT_PGA_Vm = 250;
  TPT_PGA_KA = 0.74;
  TPT_PGA_K = 0.25;
  TPT_PGA_KR1 = 0.63;
  TPT_PGA_KR2 = 0.075;
  TPT_PGA_KR3 = 0.077;
  TPT_GAP_Vm = 250;
  TPT_GAP_KA = 0.74;
  TPT_GAP_K = 0.075;
  TPT_GAP_KR1 = 0.63;
  TPT_GAP_KR2 = 0.25;
  TPT_GAP_KR3 = 0.077;
  TPT_DHAP_Vm = 250;
  TPT_DHAP_KA = 0.74;
  TPT_DHAP_K = 0.077;
  TPT_DHAP_KR1 = 0.63;
  TPT_DHAP_KR2 = 0.25;
  TPT_DHAP_KR3 = 0.075;

  // Other declarations:
  const chloroplast, cytosol;

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

  // Display Names:
  RuBisCO is "RuBisCo";
  PGA_K is "PGA kinase";
  GAP_DH is "GAP dehydrogenase";
  TP_I is "TP isomerase";
  FBP_A is "FBP aldolase";
  FBPase is "FBP ase";
  F6P_TK is "F6P transketolase";
  SBP_A is "SBP aldolase";
  SBPase is "SBP ase";
  S7P_TK is "S7P transketolase";
  R5P_I is "R5P isomerase";
  Ru5P_E is "Ru5P epimerase";
  Ru5P_K is "Ru5P kinase";
  PG_I is "PG isomerase";
  PG_M is "PG mutase";
  Starch_S is "starch synthase";
  Starch_P is "starch phosphorylase";
  ATP_S is "ATP synthetase";
  TPT_PGA is "TPT - PGA";
  TPT_GAP is "TPT - GAP";
  TPT_DHAP is "TPT - DHAP";
end