//Created by libAntimony v2.4
model nazaret_2009__environment(time_)

  // Variable initializations:
  time_ = ;
end

model nazaret_2009__p(p, v1, v2, v7, tau)

  // Rate Rules:
  p' = v1 - (v2 + v7);

  // Variable initializations:
  p = 0.154;
  v1 = ;
  v2 = ;
  v7 = ;
  tau = ;
end

model nazaret_2009__a(a, v2, v3, epsilon1, tau)

  // Rate Rules:
  a' = (v2 - v3) / epsilon1;

  // Variable initializations:
  a = 0.063;
  v2 = ;
  v3 = ;
  epsilon1 = ;
  tau = ;
end

model nazaret_2009__c(c, v3, v4, epsilon2, tau)

  // Rate Rules:
  c' = (v3 - v4) / epsilon2;

  // Variable initializations:
  c = 0.44;
  v3 = ;
  v4 = ;
  epsilon2 = ;
  tau = ;
end

model nazaret_2009__k(k, v4, v5, v6, epsilon3, tau)

  // Rate Rules:
  k' = ((v4 + v6) - v5) / epsilon3;

  // Variable initializations:
  k = 0.225;
  v4 = ;
  v5 = ;
  v6 = ;
  epsilon3 = ;
  tau = ;
end

model nazaret_2009__o(o, v3, v5, v6, v7, v8, epsilon4, tau)

  // Rate Rules:
  o' = ((v5 + v7) - (v3 + v8 + v6)) / epsilon4;

  // Variable initializations:
  o = 0.005;
  v3 = ;
  v5 = ;
  v6 = ;
  v7 = ;
  v8 = ;
  epsilon4 = ;
  tau = ;
end

model nazaret_2009__n(n, v2, v4, v5, vresp, epsilon5, tau)

  // Rate Rules:
  n' = (vresp - (v2 + v4 + 2.0 * v5)) / epsilon5;

  // Variable initializations:
  n = 0.856;
  v2 = ;
  v4 = ;
  v5 = ;
  vresp = ;
  epsilon5 = ;
  tau = ;
end

model nazaret_2009__en(en, vATP, vANT, v5, v7, epsilon6, tau)

  // Rate Rules:
  en' = ((vATP + v5) - (vANT + v7)) / epsilon6;

  // Variable initializations:
  en = 3.536;
  vATP = ;
  vANT = ;
  v5 = ;
  v7 = ;
  epsilon6 = ;
  tau = ;
end

model nazaret_2009__s(s, vresp, vANT, vleak, vATP, epsilon7, tau)

  // Rate Rules:
  s' = (10 * vresp - (3 * vATP + vleak + vANT)) / epsilon7;

  // Variable initializations:
  s = 150.0;
  vresp = ;
  vANT = ;
  vleak = ;
  vATP = ;
  epsilon7 = ;
  tau = ;
end

model nazaret_2009__v1(v1)

  // Assignment Rules:
  v1 := 1;
end

model nazaret_2009__v2(v2, beta2, p, n)

  // Assignment Rules:
  v2 := beta2 * p * n;

  // Variable initializations:
  beta2 = ;
  p = ;
  n = ;
end

model nazaret_2009__v3(v3, beta3, o, a)

  // Assignment Rules:
  v3 := beta3 * o * a;

  // Variable initializations:
  beta3 = ;
  o = ;
  a = ;
end

model nazaret_2009__v4(v4, beta4, c, n)

  // Assignment Rules:
  v4 := beta4 * c * n;

  // Variable initializations:
  beta4 = ;
  c = ;
  n = ;
end

model nazaret_2009__v5(v5, beta5, en, k, n)

  // Assignment Rules:
  v5 := beta5 * k * n * (1 - en);

  // Variable initializations:
  beta5 = ;
  en = ;
  k = ;
  n = ;
end

model nazaret_2009__v6(v6, delta_6, beta6, o, k)

  // Assignment Rules:
  v6 := beta6 * (o - delta_6 * k);

  // Variable initializations:
  delta_6 = ;
  beta6 = ;
  o = ;
  k = ;
end

model nazaret_2009__v7(v7, beta7, p, en)

  // Assignment Rules:
  v7 := beta7 * p * en;

  // Variable initializations:
  beta7 = ;
  p = ;
  en = ;
end

model nazaret_2009__v8(v8, beta8, o)

  // Assignment Rules:
  v8 := beta8 * o;

  // Variable initializations:
  beta8 = ;
  o = ;
end

model nazaret_2009__vANT(vANT, beta_ANT, en)

  // Assignment Rules:
  vANT := beta_ANT * en;

  // Variable initializations:
  beta_ANT = ;
  en = ;
end

model nazaret_2009__vleak(vleak, beta_leak, s)

  // Assignment Rules:
  vleak := beta_leak * s;

  // Variable initializations:
  beta_leak = ;
  s = ;
end

model nazaret_2009__vresp(vresp, beta_resp, delta_r1, delta_r2, s, n)

  // Assignment Rules:
  vresp := beta_resp * ((1 - n) / ((delta_r1 + 1) - n)) * (1 / (1 + exp(delta_r2 * (s - 1))));

  // Variable initializations:
  beta_resp = ;
  delta_r1 = ;
  delta_r2 = ;
  s = ;
  n = ;
end

model nazaret_2009__vATP(vATP, beta_ATP, delta_atp, en, en_crit, s)

  // Assignment Rules:
  vATP := beta_ATP * (2 / (1 + exp(delta_atp * (en - en_crit * s))) - 1);

  // Variable initializations:
  beta_ATP = ;
  delta_atp = ;
  en = ;
  en_crit = ;
  s = ;
end

model nazaret_2009__en_crit(en_crit, Kapp_dash, delta_crit, s)

  // Assignment Rules:
  en_crit := Kapp_dash / (Kapp_dash + exp(-1 * delta_crit * s));

  // Variable initializations:
  Kapp_dash = ;
  delta_crit = ;
  s = ;
end

model nazaret_2009__normalised_constants(beta2, beta3, beta4, beta5, beta6, beta7, beta8, epsilon1, epsilon2, epsilon3, epsilon4, epsilon5, epsilon6, epsilon7, beta_ANT, beta_leak, beta_resp, beta_ATP, delta_6, delta_r1, delta_r2, delta_atp, delta_crit, Kapp_dash, tau, p, a, c, k, o, n, en, s, time_)

  // Assignment Rules:
  beta2 := (k2 / k1) * Nt * Pyr_bar;
  beta3 := (k3 / k1) * OAA_bar * AcCoA_bar;
  beta4 := (k4 / k1) * Nt * Cit_bar;
  beta5 := (k5 / k1) * Nt * At_ * KG_bar;
  beta6 := (k6 / k1) * OAA_bar;
  beta7 := (k7 / k1) * At_ * Pyr_bar;
  beta8 := (k8 / k1) * OAA_bar;
  epsilon1 := AcCoA_bar / Pyr_bar;
  epsilon2 := Cit_bar / Pyr_bar;
  epsilon3 := KG_bar / Pyr_bar;
  epsilon4 := OAA_bar / Pyr_bar;
  epsilon5 := Nt / Pyr_bar;
  epsilon6 := At_ / Pyr_bar;
  epsilon7 := (delta_psi_m / Pyr_bar) * C;
  beta_ANT := (kANT / k1) * At_;
  beta_leak := (kleak / k1) * delta_psi_m;
  beta_resp := kresp / k1;
  beta_ATP := kATP / k1;
  delta_6 := KG_bar / (OAA_bar * Keq);
  delta_r1 := K / Nt;
  delta_r2 := alpha * delta_psi_m;
  delta_atp := b * At_;
  delta_crit := 3 * ((1.2 * F * delta_psi_m) / (R * T));
  Kapp_dash := Kapp * Pi_;
  tau := (k1 / Pyr_bar) * time_;

  // Variable initializations:
  At_ = 4.160;
  Nt = 1.070;
  Pyr_bar = 0.161;
  Cit_bar = 0.460;
  AcCoA_bar = 0.105;
  KG_bar = 0.146;
  OAA_bar = 0.004;
  k1 = 38;
  k2 = 152;
  k3 = 57142;
  k4 = 53;
  k5 = 40;
  k6 = 82361;
  k7 = 3.2e-3;
  k8 = 3.6;
  kresp = 2.5;
  kATP = 131.9;
  kANT = 0.1;
  kleak = 0.426;
  Keq = 0.3975;
  K = 2;
  alpha = 0.100;
  b = 0.004;
  delta_psi_m = 150.0;
  R = 8.314;
  T = 298;
  F = 96485;
  C = 6.75e-06;
  Kapp = 4.4e-6;
  Pi_ = 2.440;
  p = ;
  a = ;
  c = ;
  k = ;
  o = ;
  n = ;
  en = ;
  s = ;
  time_ = ;
end

model *nazaret_2009____main()

  // Sub-modules, and any changes to those submodules:
  environment: nazaret_2009__environment(time_);
  p: nazaret_2009__p(p0, v10, v20, v70, tau);
  a: nazaret_2009__a(a0, v20, v30, epsilon1, tau);
  c: nazaret_2009__c(c0, v30, v40, epsilon2, tau);
  k: nazaret_2009__k(k0, v40, v50, v60, epsilon3, tau);
  o: nazaret_2009__o(o0, v30, v50, v60, v70, v80, epsilon4, tau);
  n: nazaret_2009__n(n0, v20, v40, v50, vresp0, epsilon5, tau);
  en: nazaret_2009__en(en0, vATP0, vANT0, v50, v70, epsilon6, tau);
  s: nazaret_2009__s(s0, vresp0, vANT0, vleak0, vATP0, epsilon7, tau);
  v1: nazaret_2009__v1(v10);
  v2: nazaret_2009__v2(v20, beta2, p0, n0);
  v3: nazaret_2009__v3(v30, beta3, o0, a0);
  v4: nazaret_2009__v4(v40, beta4, c0, n0);
  v5: nazaret_2009__v5(v50, beta5, en0, k0, n0);
  v6: nazaret_2009__v6(v60, delta_6, beta6, o0, k0);
  v7: nazaret_2009__v7(v70, beta7, p0, en0);
  v8: nazaret_2009__v8(v80, beta8, o0);
  vANT: nazaret_2009__vANT(vANT0, beta_ANT, en0);
  vleak: nazaret_2009__vleak(vleak0, beta_leak, s0);
  vresp: nazaret_2009__vresp(vresp0, beta_resp, delta_r1, delta_r2, s0, n0);
  vATP: nazaret_2009__vATP(vATP0, beta_ATP, delta_atp, en0, en_crit0, s0);
  en_crit: nazaret_2009__en_crit(en_crit0, Kapp_dash, delta_crit, s0);
  normalised_constants: nazaret_2009__normalised_constants(beta2, beta3, beta4, beta5, beta6, beta7, beta8, epsilon1, epsilon2, epsilon3, epsilon4, epsilon5, epsilon6, epsilon7, beta_ANT, beta_leak, beta_resp, beta_ATP, delta_6, delta_r1, delta_r2, delta_atp, delta_crit, Kapp_dash, tau, p0, a0, c0, k0, o0, n0, en0, s0, time_);
end