//Created by libAntimony v2.4
model cloutier_2009b__environment(time_)

  // Variable initializations:
  time_ = ;
end

model cloutier_2009b__F6P(F6P, V_hk, V_pfk, V_pfk2, time_)

  // Rate Rules:
  F6P' = V_hk - (V_pfk - V_pfk2);

  // Variable initializations:
  F6P = 0.2;
  V_hk = ;
  V_pfk = ;
  V_pfk2 = ;
  time_ = ;
end

model cloutier_2009b__F26P(F26P, V_pfk2, time_)

  // Rate Rules:
  F26P' = V_pfk2;

  // Variable initializations:
  F26P = 0.001;
  V_pfk2 = ;
  time_ = ;
end

model cloutier_2009b__GAP(GAP, V_pk, V_pfk, time_)

  // Rate Rules:
  GAP' = 2.0 * V_pfk - V_pk;

  // Variable initializations:
  GAP = 0.0405;
  V_pk = ;
  V_pfk = ;
  time_ = ;
end

model cloutier_2009b__PYR(PYR, V_pk, V_ldh, V_op, time_)

  // Rate Rules:
  PYR' = V_pk - (V_op + V_ldh);

  // Variable initializations:
  PYR = 0.1;
  V_pk = ;
  V_ldh = ;
  V_op = ;
  time_ = ;
end

model cloutier_2009b__LAC(LAC, V_lac, V_ldh, time_)

  // Rate Rules:
  LAC' = 2.25 * V_ldh + V_lac;

  // Variable initializations:
  LAC = 0.5;
  V_lac = ;
  V_ldh = ;
  time_ = ;
end

model cloutier_2009b__ATP(ATP, V_hk, V_pfk, V_pfk2, V_pk, V_ATPase, V_op, V_ck, dAMP_dATP, time_)

  // Rate Rules:
  ATP' = ((2.0 * V_pk + 15.0 * V_op + V_ck) - (V_hk + V_pfk + V_pfk2 + V_ATPase)) * power(1 - dAMP_dATP, -1);

  // Variable initializations:
  ATP = 2.402;
  V_hk = ;
  V_pfk = ;
  V_pfk2 = ;
  V_pk = ;
  V_ATPase = ;
  V_op = ;
  V_ck = ;
  dAMP_dATP = ;
  time_ = ;
end

model cloutier_2009b__PCr(PCr, V_ck, time_)

  // Rate Rules:
  PCr' = - V_ck;

  // Variable initializations:
  PCr = 18.14;
  V_ck = ;
  time_ = ;
end

model cloutier_2009b__V_hk(V_hk, F6P, ATP)

  // Assignment Rules:
  V_hk := Vmax_hk * (ATP / (ATP + Km_ATP_hk)) * power(1 + power(F6P / KI_F6P, 4), -1);

  // Variable initializations:
  Vmax_hk = 2.5;
  Km_ATP_hk = 0.5;
  KI_F6P = 0.068;
  F6P = ;
  ATP = ;
end

model cloutier_2009b__V_pfk(V_pfk, ATP, F6P, F26P, AMP_act, ATP_inh)

  // Assignment Rules:
  V_pfk := Vmax_pfk * (F6P / (F6P + Km_F6P_pfk)) * (ATP / (ATP + Km_ATP_pfk)) * (F26P / (F26P + Km_F26P_pfk)) * ATP_inh * AMP_act;

  // Variable initializations:
  Vmax_pfk = 3.85;
  Km_ATP_pfk = 0.05;
  Km_F6P_pfk = 0.18;
  Km_F26P_pfk = 0.01;
  ATP = ;
  F6P = ;
  F26P = ;
  AMP_act = ;
  ATP_inh = ;
end

model cloutier_2009b__V_pfk2(V_pfk2, ATP, F6P, F26P, AMP_pfk2)

  // Assignment Rules:
  V_pfk2 := Vmaxf_pfk2 * (ATP / (ATP + Km_ATP_pfk2)) * (F6P / (F6P + Km_F6P_pfk2)) * AMP_pfk2 - Vmaxr_pfk2 * (F26P / (F26P + Km_F26P_pfk2));

  // Variable initializations:
  Vmaxf_pfk2 = 0;
  Vmaxr_pfk2 = 0;
  Km_ATP_pfk2 = 0.05;
  Km_F6P_pfk2 = 0.01;
  Km_F26P_pfk2 = 0.0001;
  ATP = ;
  F6P = ;
  F26P = ;
  AMP_pfk2 = ;
end

model cloutier_2009b__V_pk(V_pk, ADP, GAP, ATP_inh)

  // Assignment Rules:
  V_pk := Vmax_pk * (GAP / (GAP + Km_GAP_pk)) * (ADP / (ADP + Km_ADP_pk)) * ATP_inh;

  // Variable initializations:
  Vmax_pk = 5.0;
  Km_ADP_pk = 0.005;
  Km_GAP_pk = 0.4;
  ADP = ;
  GAP = ;
  ATP_inh = ;
end

model cloutier_2009b__V_op(V_op, ATP, ADP, PYR)

  // Assignment Rules:
  V_op := Vmax_op * (PYR / (PYR + Km_PYR_op)) * (ADP / (ADP + Km_ADP_op)) * (1 / (1 + 0.1 * 24));

  // Variable initializations:
  Vmax_op = 1.0;
  Km_ADP_op = 0.005;
  Km_PYR_op = 0.5;
  ATP = ;
  ADP = ;
  PYR = ;
end

model cloutier_2009b__V_ldh(V_ldh, LAC, PYR)

  // Assignment Rules:
  V_ldh := kf_ldh * PYR - kr_ldh * LAC;

  // Variable initializations:
  kf_ldh = 0;
  kr_ldh = 0;
  LAC = ;
  PYR = ;
end

model cloutier_2009b__V_ck(V_ck, Cr, PCr, ADP, ATP)

  // Assignment Rules:
  V_ck := kf_ck * PCr * ADP - kr_ck * Cr * ATP;

  // Variable initializations:
  kf_ck = 0;
  kr_ck = 0;
  Cr = ;
  PCr = ;
  ADP = ;
  ATP = ;
end

model cloutier_2009b__Cr(Cr, PCr)

  // Assignment Rules:
  Cr := PCrtot - PCr;

  // Variable initializations:
  PCrtot = 20.0;
  PCr = ;
end

model cloutier_2009b__V_ATPase(V_ATPase, ATP, v_stim)

  // Assignment Rules:
  V_ATPase := Vmax_ATPase * (ATP / (ATP + Km_ATP)) * (1 + v_stim);

  // Variable initializations:
  Vmax_ATPase = 0.9355;
  Km_ATP = 0.5;
  ATP = ;
  v_stim = ;
end

model cloutier_2009b__V_lac(V_lac, LAC, v_stim)

  // Assignment Rules:
  V_lac := Vlac_0 * (1 + v_stim * K_LAC) - K_LAC_eff * LAC;

  // Variable initializations:
  Vlac_0 = 0.355;
  K_LAC_eff = 0.71;
  K_LAC = 0.641;
  LAC = ;
  v_stim = ;
end

model cloutier_2009b__ADP(ADP, u, ATP, ANP, Q_adk)

  // Assignment Rules:
  ADP := (ATP / 2) * (- Q_adk + root(u));
  u := power(Q_adk, 2) + 4 * Q_adk * (ANP / ATP - 1);

  // Variable initializations:
  ATP = ;
  ANP = ;
  Q_adk = ;
end

model cloutier_2009b__dAMP_dATP(dAMP_dATP, ATP, ANP, u, Q_adk)

  // Assignment Rules:
  dAMP_dATP := -(1) + Q_adk / 2 + -(0.5 * root(u)) + Q_adk * (ANP / (ATP * root(u)));

  // Variable initializations:
  ATP = ;
  ANP = ;
  u = ;
  Q_adk = ;
end

model cloutier_2009b__AMP(AMP, ANP, ATP, ADP)

  // Assignment Rules:
  AMP := ANP - (ATP + ADP);

  // Variable initializations:
  ANP = ;
  ATP = ;
  ADP = ;
end

model cloutier_2009b__ATP_inh(ATP_inh, ATP)

  // Assignment Rules:
  ATP_inh := power((1 + nATP * (ATP / KI_ATP)) / (1 + ATP / KI_ATP), 4);

  // Variable initializations:
  nATP = 0.4;
  KI_ATP = 1.0;
  ATP = ;
end

model cloutier_2009b__AMP_act(AMP_act, AMP)

  // Assignment Rules:
  AMP_act := power((1 + AMP / Ka_AMP) / (1 + nAMP * (AMP / Ka_AMP)), 4);

  // Variable initializations:
  nAMP = 0.5;
  Ka_AMP = 0.05;
  AMP = ;
end

model cloutier_2009b__v_stim(v_stim, time_)

  // Assignment Rules:
  v_stim := stim * (v1_n + v2_n * ((time_ - to) / t_n_stim) * exp(-((time_ - to) * (unitpulseSB / t_n_stim)))) * unitpulseSB;
  unitpulseSB := piecewise( 1 , ( geq(time_, to)) && (time_ <= to + tend ), 0 );

  // Variable initializations:
  stim = 1;
  to = 50;
  tend = 200;
  v1_n = 0.5;
  v2_n = 0.0;
  t_n_stim = 2;
  time_ = ;
end

model cloutier_2009b__model_parameters(ANP, Q_adk)

  // Variable initializations:
  ANP = 2.51;
  Q_adk = 0.92;
end

model cloutier_2009b__AMP_pfk2(AMP_pfk2, AMP)

  // Assignment Rules:
  AMP_pfk2 := power(AMP / Kamp_pfk2, nh_amp) / (1 + power(AMP / Kamp_pfk2, nh_amp));

  // Variable initializations:
  Kamp_pfk2 = 0.005;
  nh_amp = 2;
  AMP = ;
end

model *cloutier_2009b____main()

  // Sub-modules, and any changes to those submodules:
  environment: cloutier_2009b__environment(time_);
  F6P: cloutier_2009b__F6P(F6P0, V_hk0, V_pfk0, V_pfk20, time_);
  F26P: cloutier_2009b__F26P(F26P0, V_pfk20, time_);
  GAP: cloutier_2009b__GAP(GAP0, V_pk0, V_pfk0, time_);
  PYR: cloutier_2009b__PYR(PYR0, V_pk0, V_ldh0, V_op0, time_);
  LAC: cloutier_2009b__LAC(LAC0, V_lac0, V_ldh0, time_);
  ATP: cloutier_2009b__ATP(ATP0, V_hk0, V_pfk0, V_pfk20, V_pk0, V_ATPase0, V_op0, V_ck0, dAMP_dATP0, time_);
  PCr: cloutier_2009b__PCr(PCr0, V_ck0, time_);
  V_hk: cloutier_2009b__V_hk(V_hk0, F6P0, ATP0);
  V_pfk: cloutier_2009b__V_pfk(V_pfk0, ATP0, F6P0, F26P0, AMP_act0, ATP_inh0);
  V_pfk2: cloutier_2009b__V_pfk2(V_pfk20, ATP0, F6P0, F26P0, AMP_pfk20);
  V_pk: cloutier_2009b__V_pk(V_pk0, ADP0, GAP0, ATP_inh0);
  V_op: cloutier_2009b__V_op(V_op0, ATP0, ADP0, PYR0);
  V_ldh: cloutier_2009b__V_ldh(V_ldh0, LAC0, PYR0);
  V_ck: cloutier_2009b__V_ck(V_ck0, Cr0, PCr0, ADP0, ATP0);
  Cr: cloutier_2009b__Cr(Cr0, PCr0);
  V_ATPase: cloutier_2009b__V_ATPase(V_ATPase0, ATP0, v_stim0);
  V_lac: cloutier_2009b__V_lac(V_lac0, LAC0, v_stim0);
  ADP: cloutier_2009b__ADP(ADP0, u, ATP0, ANP, Q_adk);
  dAMP_dATP: cloutier_2009b__dAMP_dATP(dAMP_dATP0, ATP0, ANP, u, Q_adk);
  AMP: cloutier_2009b__AMP(AMP0, ANP, ATP0, ADP0);
  ATP_inh: cloutier_2009b__ATP_inh(ATP_inh0, ATP0);
  AMP_act: cloutier_2009b__AMP_act(AMP_act0, AMP0);
  v_stim: cloutier_2009b__v_stim(v_stim0, time_);
  model_parameters: cloutier_2009b__model_parameters(ANP, Q_adk);
  AMP_pfk2: cloutier_2009b__AMP_pfk2(AMP_pfk20, AMP0);
end