//Created by libAntimony v2.4
model wu_jeneson_beard_2006__Environment(time_, O2_x, X_AtC)

  // Variable initializations:
  time_ = ;
  O2_x = 3.48e-5;
  X_AtC = 0e-4;
end

model wu_jeneson_beard_2006__fixed_parameters(RT, F, dG_C1op, dG_C3op, dG_C4op, dG_F1o, dG_H, k_dHPI, k_dHatp, k_dHadp, K_DT, K_DD, K_AK, K_CK, W_m, W_c, W_x, W_i, V_cyto, V_mito, Rm_cyto, Rm_cell, Rc_cell, n_A, C_tot, CR_tot, Q_tot, NAD_tot, H_c, K_c, H_i, K_i, H_x, deltaPsi)

  // Assignment Rules:
  dG_C1op := dG_C1o - 1 * RT * ln(H_x / 1E-7);
  dG_C3op := dG_C3o + 2 * RT * ln(H_x / 1E-7);
  dG_C4op := dG_C4o - 2 * RT * ln(H_x / 1E-7);
  dG_H := F * deltaPsi + RT * ln(H_i / H_x);
  k_dHPI := 1 * power(10, -(6.75));
  k_dHatp := 1 * power(10, -(6.48));
  k_dHadp := 1 * power(10, -(6.29));
  W_m := 0.664 * 1.09;
  W_c := 0.807 * 1.044;
  W_x := 0.9 * W_m;
  W_i := 0.1 * W_m;
  Rm_cyto := V_mito / V_cyto;
  Rm_cell := V_mito;
  Rc_cell := V_cyto;
  H_c := 1 * power(10, - pH_C);
  H_i := H_c;
  K_i := K_c;

  // Variable initializations:
  RT = 2.5775;
  F = 0.096484;
  dG_C1o = -69.37;
  dG_C3o = -32.53;
  dG_C4o = -122.94;
  dG_F1o = 36.03;
  K_DT = 24e-6;
  K_DD = 347e-6;
  K_AK = 0.4331;
  K_CK = 1.66e9;
  V_cyto = 0.894;
  V_mito = 0.056;
  n_A = 3;
  C_tot = 2.7e-3;
  CR_tot = 42.7e-3;
  Q_tot = 1.35e-3;
  NAD_tot = 2.97e-3;
  pH_C = 7;
  K_c = 0.15;
  H_x = ;
  deltaPsi = ;
end

model wu_jeneson_beard_2006__adjustable_parameters(k_PI1, k_PI2, k_PI3, k_PI4, k_PIH, r, X_DH, X_C1, X_C3, X_C4, X_F1, X_ANT, X_PI1, X_KH, X_Hle, X_K, k_mADP, X_AK, X_CK, X_MgA, k_O2, x_buff, C_IM, X_A, X_PI2, gamma)

  // Variable initializations:
  k_PI1 = 0.1553e-3;
  k_PI2 = 0.8222e-3;
  k_PI3 = 0.3601e-3;
  k_PI4 = 5.651e-3;
  k_PIH = 2.542e-4;
  r = 4.559;
  X_DH = 0.0866;
  X_C1 = 4.405e3;
  X_C3 = 4.887;
  X_C4 = 6.766e-5;
  X_F1 = 1e3;
  X_ANT = 8.123e-3;
  X_PI1 = 3.85e5;
  X_KH = 5.651e7;
  X_Hle = 200;
  X_K = 0;
  k_mADP = 3.5e-6;
  X_AK = 1e7;
  X_CK = 1e7;
  X_MgA = 1e7;
  k_O2 = 1.2e-4;
  x_buff = 100;
  C_IM = 6.75e-6;
  X_A = 85;
  X_PI2 = 327;
  gamma = 5.99;
end

model wu_jeneson_beard_2006__dNAD_x_dt(NAD_x, NAD_tot, NADH_x)

  // Assignment Rules:
  NAD_x := NAD_tot - NADH_x;

  // Variable initializations:
  NAD_tot = ;
  NADH_x = ;
end

model wu_jeneson_beard_2006__dQH2_x_dt(QH2_x, Q_tot, Q_x)

  // Assignment Rules:
  QH2_x := Q_tot - Q_x;

  // Variable initializations:
  Q_tot = ;
  Q_x = ;
end

model wu_jeneson_beard_2006__dCred_x_dt(Cred_x, C_tot, Cox_x)

  // Assignment Rules:
  Cred_x := C_tot - Cox_x;

  // Variable initializations:
  C_tot = ;
  Cox_x = ;
end

model wu_jeneson_beard_2006__dATP_fx_dt(ATP_fx, ATP_x, ATP_mx)

  // Assignment Rules:
  ATP_fx := ATP_x - ATP_mx;

  // Variable initializations:
  ATP_x = ;
  ATP_mx = ;
end

model wu_jeneson_beard_2006__dADP_fx_dt(ADP_fx, ADP_x, ADP_mx)

  // Assignment Rules:
  ADP_fx := ADP_x - ADP_mx;

  // Variable initializations:
  ADP_x = ;
  ADP_mx = ;
end

model wu_jeneson_beard_2006__dH_x_dt(pH_x, H_x, time_, n_A, x_buff, J_DH, J_C1, J_C3, J_C4, J_F1, J_PI1, J_KH, J_Hle, W_x)

  // Assignment Rules:
  H_x := 1 * power(10, - pH_x);

  // Rate Rules:
  pH_x' = ((-(1) / 2.303) * x_buff * ((((((J_DH - 5 * J_C1) - 2 * J_C3) - 4 * J_C4) + (n_A - 1) * J_F1 + 2 * J_PI1) - J_KH) + J_Hle)) / W_x;

  // Variable initializations:
  pH_x = 7;
  time_ = ;
  n_A = ;
  x_buff = ;
  J_DH = ;
  J_C1 = ;
  J_C3 = ;
  J_C4 = ;
  J_F1 = ;
  J_PI1 = ;
  J_KH = ;
  J_Hle = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dK_x_dt(K_x, time_, J_K, J_KH, W_x)

  // Rate Rules:
  K_x' = (J_KH + J_K) / W_x;

  // Variable initializations:
  K_x = 0.14661;
  time_ = ;
  J_K = ;
  J_KH = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dMg_x_dt(Mg_x, time_, J_MgATP_x, J_MgADP_x, W_x)

  // Rate Rules:
  Mg_x' = (- J_MgADP_x - J_MgATP_x) / W_x;

  // Variable initializations:
  Mg_x = 1.0229e-3;
  time_ = ;
  J_MgATP_x = ;
  J_MgADP_x = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dNADH_x_dt(NADH_x, time_, J_DH, J_C1, W_x)

  // Rate Rules:
  NADH_x' = (J_DH - J_C1) / W_x;

  // Variable initializations:
  NADH_x = 0.0015723;
  time_ = ;
  J_DH = ;
  J_C1 = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dQ_x_dt(Q_x, time_, J_C1, J_C3, W_x)

  // Rate Rules:
  Q_x' = -(J_C1 - J_C3) / W_x;

  // Variable initializations:
  Q_x = 6.75e-4;
  time_ = ;
  J_C1 = ;
  J_C3 = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dCox_x_dt(Cox_x, time_, J_C3, J_C4, W_x)

  // Rate Rules:
  Cox_x' = -(2 * J_C3 - 2 * J_C4) / W_x;

  // Variable initializations:
  Cox_x = 1.35e-3;
  time_ = ;
  J_C3 = ;
  J_C4 = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dATP_x_dt(ATP_x, time_, J_F1, J_ANT, W_x)

  // Rate Rules:
  ATP_x' = (J_F1 - J_ANT) / W_x;

  // Variable initializations:
  ATP_x = 0.0026657;
  time_ = ;
  J_F1 = ;
  J_ANT = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dADP_x_dt(ADP_x, time_, J_F1, J_ANT, W_x)

  // Rate Rules:
  ADP_x' = (- J_F1 + J_ANT) / W_x;

  // Variable initializations:
  ADP_x = 0.0073343;
  time_ = ;
  J_F1 = ;
  J_ANT = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dATP_mx_dt(ATP_mx, time_, J_MgATP_x, W_x)

  // Rate Rules:
  ATP_mx' = J_MgATP_x / W_x;

  // Variable initializations:
  ATP_mx = 0.0026046;
  time_ = ;
  J_MgATP_x = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dADP_mx_dt(ADP_mx, time_, J_MgADP_x, W_x)

  // Rate Rules:
  ADP_mx' = J_MgADP_x / W_x;

  // Variable initializations:
  ADP_mx = 0.0054765;
  time_ = ;
  J_MgADP_x = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dPI_x_dt(PI_x, time_, J_F1, J_PI1, W_x)

  // Rate Rules:
  PI_x' = (- J_F1 + J_PI1) / W_x;

  // Variable initializations:
  PI_x = 1.72e-4;
  time_ = ;
  J_F1 = ;
  J_PI1 = ;
  W_x = ;
end

model wu_jeneson_beard_2006__dATP_fi_dt(ATP_fi, ATP_i, ATP_mi)

  // Assignment Rules:
  ATP_fi := ATP_i - ATP_mi;

  // Variable initializations:
  ATP_i = ;
  ATP_mi = ;
end

model wu_jeneson_beard_2006__dADP_fi_dt(ADP_fi, ADP_i, ADP_mi)

  // Assignment Rules:
  ADP_fi := ADP_i - ADP_mi;

  // Variable initializations:
  ADP_i = ;
  ADP_mi = ;
end

model wu_jeneson_beard_2006__dATP_i_dt(ATP_i, time_, J_ATP, J_ANT, J_AKi, W_i)

  // Rate Rules:
  ATP_i' = (J_ATP + J_ANT + J_AKi) / W_i;

  // Variable initializations:
  ATP_i = 0.0065339;
  time_ = ;
  J_ATP = ;
  J_ANT = ;
  J_AKi = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dADP_i_dt(ADP_i, time_, J_ADP, J_ANT, J_AKi, W_i)

  // Rate Rules:
  ADP_i' = ((J_ADP - J_ANT) - 2 * J_AKi) / W_i;

  // Variable initializations:
  ADP_i = 6.5773e-5;
  time_ = ;
  J_ADP = ;
  J_ANT = ;
  J_AKi = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dAMP_i_dt(AMP_i, time_, J_AMP, J_ANT, J_AKi, W_i)

  // Rate Rules:
  AMP_i' = (J_AMP + J_AKi) / W_i;

  // Variable initializations:
  AMP_i = 2.8837e-7;
  time_ = ;
  J_AMP = ;
  J_ANT = ;
  J_AKi = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dATP_mi_dt(ATP_mi, time_, J_MgATP_i, W_i)

  // Rate Rules:
  ATP_mi' = J_MgATP_i / W_i;

  // Variable initializations:
  ATP_mi = 0.0063812;
  time_ = ;
  J_MgATP_i = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dADP_mi_dt(ADP_mi, time_, J_MgADP_i, W_i)

  // Rate Rules:
  ADP_mi' = J_MgADP_i / W_i;

  // Variable initializations:
  ADP_mi = 4.8866e-5;
  time_ = ;
  J_MgADP_i = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dPI_i_dt(PI_i, time_, J_PI1, J_PI2, W_i)

  // Rate Rules:
  PI_i' = (- J_PI1 + J_PI2) / W_i;

  // Variable initializations:
  PI_i = 1.72e-4;
  time_ = ;
  J_PI1 = ;
  J_PI2 = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dMg_i_dt(Mg_i, time_, J_MgATP_i, J_MgADP_i, W_i)

  // Rate Rules:
  Mg_i' = (- J_MgADP_i - J_MgATP_i) / W_i;

  // Variable initializations:
  Mg_i = 0.0010029;
  time_ = ;
  J_MgATP_i = ;
  J_MgADP_i = ;
  W_i = ;
end

model wu_jeneson_beard_2006__dATP_c_dt(ATP_c, time_, J_ATP, J_AKc, J_AtC, J_CKc, W_c, Rm_cyto, Rc_cell)

  // Rate Rules:
  ATP_c' = (((- Rm_cyto * J_ATP + J_AKc) - J_AtC / Rc_cell) + J_CKc) / W_c;

  // Variable initializations:
  ATP_c = 0.0081312;
  time_ = ;
  J_ATP = ;
  J_AKc = ;
  J_AtC = ;
  J_CKc = ;
  W_c = ;
  Rm_cyto = ;
  Rc_cell = ;
end

model wu_jeneson_beard_2006__dADP_c_dt(ADP_c, time_, J_ADP, J_AKc, J_AtC, J_CKc, W_c, Rm_cyto, Rc_cell)

  // Rate Rules:
  ADP_c' = (((- Rm_cyto * J_ADP - 2 * J_AKc) + J_AtC / Rc_cell) - J_CKc) / W_c;

  // Variable initializations:
  ADP_c = 6.85e-5;
  time_ = ;
  J_ADP = ;
  J_AKc = ;
  J_AtC = ;
  J_CKc = ;
  W_c = ;
  Rm_cyto = ;
  Rc_cell = ;
end

model wu_jeneson_beard_2006__dAMP_c_dt(AMP_c, time_, J_AMP, J_AKc, W_c, Rm_cyto)

  // Rate Rules:
  AMP_c' = (- Rm_cyto * J_AMP + J_AKc) / W_c;

  // Variable initializations:
  AMP_c = 3.0911e-7;
  time_ = ;
  J_AMP = ;
  J_AKc = ;
  W_c = ;
  Rm_cyto = ;
end

model wu_jeneson_beard_2006__dATP_mc_dt(ATP_mc, time_, J_MgATP_c, W_c)

  // Rate Rules:
  ATP_mc' = J_MgATP_c / W_c;

  // Variable initializations:
  ATP_mc = 0.0079786;
  time_ = ;
  J_MgATP_c = ;
  W_c = ;
end

model wu_jeneson_beard_2006__dADP_mc_dt(ADP_mc, time_, J_MgADP_c, W_c)

  // Rate Rules:
  ADP_mc' = J_MgADP_c / W_c;

  // Variable initializations:
  ADP_mc = 5.1958e-5;
  time_ = ;
  J_MgADP_c = ;
  W_c = ;
end

model wu_jeneson_beard_2006__dPI_c_dt(PI_c, time_, J_PI2, J_AtC, W_c, Rm_cyto, Rc_cell)

  // Rate Rules:
  PI_c' = (- J_PI2 * Rm_cyto + J_AtC / Rc_cell) / W_c;

  // Variable initializations:
  PI_c = 8.7702e-3;
  time_ = ;
  J_PI2 = ;
  J_AtC = ;
  W_c = ;
  Rm_cyto = ;
  Rc_cell = ;
end

model wu_jeneson_beard_2006__dMg_c_dt(Mg_c, time_, J_MgATP_c, J_MgADP_c, W_c)

  // Rate Rules:
  Mg_c' = (- J_MgATP_c - J_MgADP_c) / W_c;

  // Variable initializations:
  Mg_c = 0.001003;
  time_ = ;
  J_MgATP_c = ;
  J_MgADP_c = ;
  W_c = ;
end

model wu_jeneson_beard_2006__dPCr_c_dt(PCr_c, time_, J_CKc, W_c)

  // Rate Rules:
  PCr_c' = - J_CKc / W_c;

  // Variable initializations:
  PCr_c = 23.589e-3;
  time_ = ;
  J_CKc = ;
  W_c = ;
end

model wu_jeneson_beard_2006__dATP_fc_dt(ATP_fc, ATP_c, ATP_mc)

  // Assignment Rules:
  ATP_fc := ATP_c - ATP_mc;

  // Variable initializations:
  ATP_c = ;
  ATP_mc = ;
end

model wu_jeneson_beard_2006__dADP_fc_dt(ADP_fc, ADP_c, ADP_mc)

  // Assignment Rules:
  ADP_fc := ADP_c - ADP_mc;

  // Variable initializations:
  ADP_c = ;
  ADP_mc = ;
end

model wu_jeneson_beard_2006__dCr_c_dt(Cr_c, CR_tot, PCr_c)

  // Assignment Rules:
  Cr_c := CR_tot - PCr_c;

  // Variable initializations:
  CR_tot = ;
  PCr_c = ;
end

model wu_jeneson_beard_2006__ddeltaPsi_dt(deltaPsi, time_, J_C1, J_C3, J_C4, J_F1, J_ANT, J_Hle, J_K, n_A, C_IM)

  // Rate Rules:
  deltaPsi' = (((((4 * J_C1 + 2 * J_C3 + 4 * J_C4) - n_A * J_F1) - J_ANT) - J_Hle) - J_K) / C_IM;

  // Variable initializations:
  deltaPsi = 166.67;
  time_ = ;
  J_C1 = ;
  J_C3 = ;
  J_C4 = ;
  J_F1 = ;
  J_ANT = ;
  J_Hle = ;
  J_K = ;
  n_A = ;
  C_IM = ;
end

model wu_jeneson_beard_2006__J_DH(J_DH, X_DH, r, NAD_x, NADH_x, PI_x, k_PI1, k_PI2)

  // Assignment Rules:
  J_DH := (X_DH * (r * NAD_x - NADH_x) * (1 + PI_x / k_PI1)) / (1 + PI_x / k_PI2);

  // Variable initializations:
  X_DH = ;
  r = ;
  NAD_x = ;
  NADH_x = ;
  PI_x = ;
  k_PI1 = ;
  k_PI2 = ;
end

model wu_jeneson_beard_2006__J_C1(J_C1, X_C1, NAD_x, NADH_x, Q_x, QH2_x, RT, k_PI1, k_PI2, dG_C1op, dG_H)

  // Assignment Rules:
  J_C1 := X_C1 * (exp(-(dG_C1op + 4 * dG_H) / RT) * NADH_x * Q_x - NAD_x * QH2_x);

  // Variable initializations:
  X_C1 = ;
  NAD_x = ;
  NADH_x = ;
  Q_x = ;
  QH2_x = ;
  RT = ;
  k_PI1 = ;
  k_PI2 = ;
  dG_C1op = ;
  dG_H = ;
end

model wu_jeneson_beard_2006__J_C3(J_C3, X_C3, Cox_x, Cred_x, Q_x, QH2_x, PI_x, F, RT, deltaPsi, k_PI3, k_PI4, dG_C3op, dG_H)

  // Assignment Rules:
  J_C3 := ((X_C3 * (1 + PI_x / k_PI3)) / (1 + PI_x / k_PI4)) * (exp(-((dG_C3op + 4 * dG_H) - 2 * F * deltaPsi) / (2 * RT)) * Cox_x * root(QH2_x) - Cred_x * root(Q_x));

  // Variable initializations:
  X_C3 = ;
  Cox_x = ;
  Cred_x = ;
  Q_x = ;
  QH2_x = ;
  PI_x = ;
  F = ;
  RT = ;
  deltaPsi = ;
  k_PI3 = ;
  k_PI4 = ;
  dG_C3op = ;
  dG_H = ;
end

model wu_jeneson_beard_2006__J_C4(J_C4, X_C4, C_tot, Cred_x, Cox_x, O2_x, RT, F, deltaPsi, k_O2, dG_C4op, dG_H)

  // Assignment Rules:
  J_C4 := piecewise( 0 , O2_x < 1E-12 , ((X_C4 * O2_x) / (O2_x + k_O2)) * (Cred_x / C_tot) * (exp(-(dG_C4op + 2 * dG_H) / (2 * RT)) * Cred_x * power(O2_x / 1, 0.25) - Cox_x * exp((F * deltaPsi) / RT)) );

  // Variable initializations:
  X_C4 = ;
  C_tot = ;
  Cred_x = ;
  Cox_x = ;
  O2_x = ;
  RT = ;
  F = ;
  deltaPsi = ;
  k_O2 = ;
  dG_C4op = ;
  dG_H = ;
end

model wu_jeneson_beard_2006__J_F1(J_F1, X_F1, ATP_mx, ADP_mx, PI_x, n_A, deltaPsi, F, RT, K_DD, K_DT, dG_F1o, dG_H)

  // Assignment Rules:
  J_F1 := X_F1 * (((exp(-(dG_F1o - n_A * dG_H) / RT) * K_DD) / K_DT) * ADP_mx * PI_x - ATP_mx * 1);

  // Variable initializations:
  X_F1 = ;
  ATP_mx = ;
  ADP_mx = ;
  PI_x = ;
  n_A = ;
  deltaPsi = ;
  F = ;
  RT = ;
  K_DD = ;
  K_DT = ;
  dG_F1o = ;
  dG_H = ;
end

model wu_jeneson_beard_2006__J_ANT(J_ANT, X_ANT, ATP_fx, ADP_fx, ATP_fi, ADP_fi, k_mADP, deltaPsi, F, RT)

  // Assignment Rules:
  J_ANT := piecewise( X_ANT * (ADP_fi / (ADP_fi + ATP_fi * exp((- F * Psi_i) / RT)) - ADP_fx / (ADP_fx + ATP_fx * exp((- F * Psi_x) / RT))) * (ADP_fi / (ADP_fi + k_mADP)) , ( ADP_fi > mincon) || (ATP_fi > mincon ), 0 );
  Psi_x := -(0.65) * deltaPsi;
  Psi_i := 0.35 * deltaPsi;

  // Variable initializations:
  mincon = 1e-9;
  X_ANT = ;
  ATP_fx = ;
  ADP_fx = ;
  ATP_fi = ;
  ADP_fi = ;
  k_mADP = ;
  deltaPsi = ;
  F = ;
  RT = ;
end

model wu_jeneson_beard_2006__J_PI1(J_PI1, PI_i, PI_x, H_i, H_x, k_dHPI, k_PIH, H2PIi, H2PIx, X_PI1)

  // Assignment Rules:
  J_PI1 := (X_PI1 * (H_i * H2PIi - H_x * H2PIx)) / (H2PIi + k_PIH);
  H2PIi := (PI_i * H_i) / (H_i + k_dHPI);
  H2PIx := (PI_x * H_x) / (H_x + k_dHPI);

  // Variable initializations:
  PI_i = ;
  PI_x = ;
  H_i = ;
  H_x = ;
  k_dHPI = ;
  k_PIH = ;
  X_PI1 = ;
end

model wu_jeneson_beard_2006__J_Hle(J_Hle, X_Hle, PI_i, PI_x, H_i, H_x, deltaPsi, F, RT)

  // Assignment Rules:
  J_Hle := piecewise( (X_Hle * deltaPsi * (H_i * exp((F * deltaPsi) / RT) - H_x)) / (exp((F * deltaPsi) / RT) - 1) , abs(deltaPsi) > mincond , (X_Hle * RT * (H_i - H_x)) / F );

  // Variable initializations:
  X_Hle = ;
  PI_i = ;
  PI_x = ;
  H_i = ;
  H_x = ;
  deltaPsi = ;
  F = ;
  RT = ;
  mincond = 1e-6;
end

model wu_jeneson_beard_2006__J_KH(J_KH, K_x, K_i, H_x, H_i, X_KH)

  // Assignment Rules:
  J_KH := X_KH * (K_i * H_x - K_x * H_i);

  // Variable initializations:
  K_x = ;
  K_i = ;
  H_x = ;
  H_i = ;
  X_KH = ;
end

model wu_jeneson_beard_2006__J_K(J_K, K_x, K_i, X_K, deltaPsi, F, RT)

  // Assignment Rules:
  J_K := piecewise( (X_K * deltaPsi * (K_i * exp((F * deltaPsi) / RT) - K_x)) / (exp((F * deltaPsi) / RT) - 1) , abs(deltaPsi) > mincond , (X_K * RT * (K_i - K_x)) / F );

  // Variable initializations:
  K_x = ;
  K_i = ;
  X_K = ;
  deltaPsi = ;
  F = ;
  RT = ;
  mincond = 1e-6;
end

model wu_jeneson_beard_2006__J_AMP(J_AMP, AMP_c, AMP_i, gamma, X_A)

  // Assignment Rules:
  J_AMP := gamma * X_A * (AMP_c - AMP_i);

  // Variable initializations:
  AMP_c = ;
  AMP_i = ;
  gamma = ;
  X_A = ;
end

model wu_jeneson_beard_2006__J_ADP(J_ADP, ADP_c, ADP_i, gamma, X_A)

  // Assignment Rules:
  J_ADP := gamma * X_A * (ADP_c - ADP_i);

  // Variable initializations:
  ADP_c = ;
  ADP_i = ;
  gamma = ;
  X_A = ;
end

model wu_jeneson_beard_2006__J_ATP(J_ATP, ATP_c, ATP_i, gamma, X_A)

  // Assignment Rules:
  J_ATP := gamma * X_A * (ATP_c - ATP_i);

  // Variable initializations:
  ATP_c = ;
  ATP_i = ;
  gamma = ;
  X_A = ;
end

model wu_jeneson_beard_2006__J_PI2(J_PI2, PI_c, PI_i, gamma, X_PI2)

  // Assignment Rules:
  J_PI2 := gamma * X_PI2 * (PI_c - PI_i);

  // Variable initializations:
  PI_c = ;
  PI_i = ;
  gamma = ;
  X_PI2 = ;
end

model wu_jeneson_beard_2006__J_MgATP_x(J_MgATP_x, X_MgA, ATP_fx, Mg_x, ATP_mx, K_DT)

  // Assignment Rules:
  J_MgATP_x := X_MgA * (ATP_fx * Mg_x - K_DT * ATP_mx);

  // Variable initializations:
  X_MgA = ;
  ATP_fx = ;
  Mg_x = ;
  ATP_mx = ;
  K_DT = ;
end

model wu_jeneson_beard_2006__J_MgADP_x(J_MgADP_x, X_MgA, ADP_fx, Mg_x, ADP_mx, K_DD)

  // Assignment Rules:
  J_MgADP_x := X_MgA * (ADP_fx * Mg_x - K_DD * ADP_mx);

  // Variable initializations:
  X_MgA = ;
  ADP_fx = ;
  Mg_x = ;
  ADP_mx = ;
  K_DD = ;
end

model wu_jeneson_beard_2006__J_MgATP_i(J_MgATP_i, X_MgA, ATP_fi, Mg_i, ATP_mi, K_DT)

  // Assignment Rules:
  J_MgATP_i := X_MgA * (ATP_fi * Mg_i - K_DT * ATP_mi);

  // Variable initializations:
  X_MgA = ;
  ATP_fi = ;
  Mg_i = ;
  ATP_mi = ;
  K_DT = ;
end

model wu_jeneson_beard_2006__J_MgADP_i(J_MgADP_i, X_MgA, ADP_fi, Mg_i, ADP_mi, K_DD)

  // Assignment Rules:
  J_MgADP_i := X_MgA * (ADP_fi * Mg_i - K_DD * ADP_mi);

  // Variable initializations:
  X_MgA = ;
  ADP_fi = ;
  Mg_i = ;
  ADP_mi = ;
  K_DD = ;
end

model wu_jeneson_beard_2006__J_MgATP_c(J_MgATP_c, X_MgA, ATP_fc, Mg_c, ATP_mc, K_DT)

  // Assignment Rules:
  J_MgATP_c := X_MgA * 1 * (ATP_fc * Mg_c - K_DT * ATP_mc);

  // Variable initializations:
  X_MgA = ;
  ATP_fc = ;
  Mg_c = ;
  ATP_mc = ;
  K_DT = ;
end

model wu_jeneson_beard_2006__J_MgADP_c(J_MgADP_c, X_MgA, ADP_fc, Mg_c, ADP_mc, K_DD)

  // Assignment Rules:
  J_MgADP_c := X_MgA * 1 * (ADP_fc * Mg_c - K_DD * ADP_mc);

  // Variable initializations:
  X_MgA = ;
  ADP_fc = ;
  Mg_c = ;
  ADP_mc = ;
  K_DD = ;
end

model wu_jeneson_beard_2006__J_AKi(J_AKi, X_AK, ATP_i, ADP_i, AMP_i, K_AK)

  // Assignment Rules:
  J_AKi := X_AK * (K_AK * ADP_i * ADP_i - AMP_i * ATP_i);

  // Variable initializations:
  X_AK = ;
  ATP_i = ;
  ADP_i = ;
  AMP_i = ;
  K_AK = ;
end

model wu_jeneson_beard_2006__J_AKc(J_AKc, X_AK, ATP_c, ADP_c, AMP_c, K_AK)

  // Assignment Rules:
  J_AKc := X_AK * 1 * (K_AK * ADP_c * ADP_c - AMP_c * ATP_c);

  // Variable initializations:
  X_AK = ;
  ATP_c = ;
  ADP_c = ;
  AMP_c = ;
  K_AK = ;
end

model wu_jeneson_beard_2006__J_AtC(J_AtC, X_AtC)

  // Assignment Rules:
  J_AtC := X_AtC;

  // Variable initializations:
  X_AtC = ;
end

model wu_jeneson_beard_2006__J_CKc(J_CKc, X_CK, K_CK, ATP_c, ADP_c, H_c, PCr_c, Cr_c)

  // Assignment Rules:
  J_CKc := X_CK * 1 * (K_CK * ADP_c * PCr_c * H_c - ATP_c * Cr_c);

  // Variable initializations:
  X_CK = ;
  K_CK = ;
  ATP_c = ;
  ADP_c = ;
  H_c = ;
  PCr_c = ;
  Cr_c = ;
end

model *wu_jeneson_beard_2006____main()

  // Sub-modules, and any changes to those submodules:
  Environment: wu_jeneson_beard_2006__Environment(time_, O2_x, X_AtC);
  fixed_parameters: wu_jeneson_beard_2006__fixed_parameters(RT, F, dG_C1op, dG_C3op, dG_C4op, dG_F1o, dG_H, k_dHPI, k_dHatp, k_dHadp, K_DT, K_DD, K_AK, K_CK, W_m, W_c, W_x, W_i, V_cyto, V_mito, Rm_cyto, Rm_cell, Rc_cell, n_A, C_tot, CR_tot, Q_tot, NAD_tot, H_c, K_c, H_i, K_i, H_x, deltaPsi);
  adjustable_parameters: wu_jeneson_beard_2006__adjustable_parameters(k_PI1, k_PI2, k_PI3, k_PI4, k_PIH, r, X_DH, X_C1, X_C3, X_C4, X_F1, X_ANT, X_PI1, X_KH, X_Hle, X_K, k_mADP, X_AK, X_CK, X_MgA, k_O2, x_buff, C_IM, X_A, X_PI2, gamma);
  dNAD_x_dt: wu_jeneson_beard_2006__dNAD_x_dt(NAD_x, NAD_tot, NADH_x);
  dQH2_x_dt: wu_jeneson_beard_2006__dQH2_x_dt(QH2_x, Q_tot, Q_x);
  dCred_x_dt: wu_jeneson_beard_2006__dCred_x_dt(Cred_x, C_tot, Cox_x);
  dATP_fx_dt: wu_jeneson_beard_2006__dATP_fx_dt(ATP_fx, ATP_x, ATP_mx);
  dADP_fx_dt: wu_jeneson_beard_2006__dADP_fx_dt(ADP_fx, ADP_x, ADP_mx);
  dH_x_dt: wu_jeneson_beard_2006__dH_x_dt(pH_x, H_x, time_, n_A, x_buff, J_DH0, J_C10, J_C30, J_C40, J_F10, J_PI10, J_KH0, J_Hle0, W_x);
  dK_x_dt: wu_jeneson_beard_2006__dK_x_dt(K_x, time_, J_K0, J_KH0, W_x);
  dMg_x_dt: wu_jeneson_beard_2006__dMg_x_dt(Mg_x, time_, J_MgATP_x0, J_MgADP_x0, W_x);
  dNADH_x_dt: wu_jeneson_beard_2006__dNADH_x_dt(NADH_x, time_, J_DH0, J_C10, W_x);
  dQ_x_dt: wu_jeneson_beard_2006__dQ_x_dt(Q_x, time_, J_C10, J_C30, W_x);
  dCox_x_dt: wu_jeneson_beard_2006__dCox_x_dt(Cox_x, time_, J_C30, J_C40, W_x);
  dATP_x_dt: wu_jeneson_beard_2006__dATP_x_dt(ATP_x, time_, J_F10, J_ANT0, W_x);
  dADP_x_dt: wu_jeneson_beard_2006__dADP_x_dt(ADP_x, time_, J_F10, J_ANT0, W_x);
  dATP_mx_dt: wu_jeneson_beard_2006__dATP_mx_dt(ATP_mx, time_, J_MgATP_x0, W_x);
  dADP_mx_dt: wu_jeneson_beard_2006__dADP_mx_dt(ADP_mx, time_, J_MgADP_x0, W_x);
  dPI_x_dt: wu_jeneson_beard_2006__dPI_x_dt(PI_x, time_, J_F10, J_PI10, W_x);
  dATP_fi_dt: wu_jeneson_beard_2006__dATP_fi_dt(ATP_fi, ATP_i, ATP_mi);
  dADP_fi_dt: wu_jeneson_beard_2006__dADP_fi_dt(ADP_fi, ADP_i, ADP_mi);
  dATP_i_dt: wu_jeneson_beard_2006__dATP_i_dt(ATP_i, time_, J_ATP0, J_ANT0, J_AKi0, W_i);
  dADP_i_dt: wu_jeneson_beard_2006__dADP_i_dt(ADP_i, time_, J_ADP0, J_ANT0, J_AKi0, W_i);
  dAMP_i_dt: wu_jeneson_beard_2006__dAMP_i_dt(AMP_i, time_, J_AMP0, J_ANT0, J_AKi0, W_i);
  dATP_mi_dt: wu_jeneson_beard_2006__dATP_mi_dt(ATP_mi, time_, J_MgATP_i0, W_i);
  dADP_mi_dt: wu_jeneson_beard_2006__dADP_mi_dt(ADP_mi, time_, J_MgADP_i0, W_i);
  dPI_i_dt: wu_jeneson_beard_2006__dPI_i_dt(PI_i, time_, J_PI10, J_PI20, W_i);
  dMg_i_dt: wu_jeneson_beard_2006__dMg_i_dt(Mg_i, time_, J_MgATP_i0, J_MgADP_i0, W_i);
  dATP_c_dt: wu_jeneson_beard_2006__dATP_c_dt(ATP_c, time_, J_ATP0, J_AKc0, J_AtC0, J_CKc0, W_c, Rm_cyto, Rc_cell);
  dADP_c_dt: wu_jeneson_beard_2006__dADP_c_dt(ADP_c, time_, J_ADP0, J_AKc0, J_AtC0, J_CKc0, W_c, Rm_cyto, Rc_cell);
  dAMP_c_dt: wu_jeneson_beard_2006__dAMP_c_dt(AMP_c, time_, J_AMP0, J_AKc0, W_c, Rm_cyto);
  dATP_mc_dt: wu_jeneson_beard_2006__dATP_mc_dt(ATP_mc, time_, J_MgATP_c0, W_c);
  dADP_mc_dt: wu_jeneson_beard_2006__dADP_mc_dt(ADP_mc, time_, J_MgADP_c0, W_c);
  dPI_c_dt: wu_jeneson_beard_2006__dPI_c_dt(PI_c, time_, J_PI20, J_AtC0, W_c, Rm_cyto, Rc_cell);
  dMg_c_dt: wu_jeneson_beard_2006__dMg_c_dt(Mg_c, time_, J_MgATP_c0, J_MgADP_c0, W_c);
  dPCr_c_dt: wu_jeneson_beard_2006__dPCr_c_dt(PCr_c, time_, J_CKc0, W_c);
  dATP_fc_dt: wu_jeneson_beard_2006__dATP_fc_dt(ATP_fc, ATP_c, ATP_mc);
  dADP_fc_dt: wu_jeneson_beard_2006__dADP_fc_dt(ADP_fc, ADP_c, ADP_mc);
  dCr_c_dt: wu_jeneson_beard_2006__dCr_c_dt(Cr_c, CR_tot, PCr_c);
  ddeltaPsi_dt: wu_jeneson_beard_2006__ddeltaPsi_dt(deltaPsi, time_, J_C10, J_C30, J_C40, J_F10, J_ANT0, J_Hle0, J_K0, n_A, C_IM);
  J_DH: wu_jeneson_beard_2006__J_DH(J_DH0, X_DH, r, NAD_x, NADH_x, PI_x, k_PI1, k_PI2);
  J_C1: wu_jeneson_beard_2006__J_C1(J_C10, X_C1, NAD_x, NADH_x, Q_x, QH2_x, RT, k_PI1, k_PI2, dG_C1op, dG_H);
  J_C3: wu_jeneson_beard_2006__J_C3(J_C30, X_C3, Cox_x, Cred_x, Q_x, QH2_x, PI_x, F, RT, deltaPsi, k_PI3, k_PI4, dG_C3op, dG_H);
  J_C4: wu_jeneson_beard_2006__J_C4(J_C40, X_C4, C_tot, Cred_x, Cox_x, O2_x, RT, F, deltaPsi, k_O2, dG_C4op, dG_H);
  J_F1: wu_jeneson_beard_2006__J_F1(J_F10, X_F1, ATP_mx, ADP_mx, PI_x, n_A, deltaPsi, F, RT, K_DD, K_DT, dG_F1o, dG_H);
  J_ANT: wu_jeneson_beard_2006__J_ANT(J_ANT0, X_ANT, ATP_fx, ADP_fx, ATP_fi, ADP_fi, k_mADP, deltaPsi, F, RT);
  J_PI1: wu_jeneson_beard_2006__J_PI1(J_PI10, PI_i, PI_x, H_i, H_x, k_dHPI, k_PIH, H2PIi, H2PIx, X_PI1);
  J_Hle: wu_jeneson_beard_2006__J_Hle(J_Hle0, X_Hle, PI_i, PI_x, H_i, H_x, deltaPsi, F, RT);
  J_KH: wu_jeneson_beard_2006__J_KH(J_KH0, K_x, K_i, H_x, H_i, X_KH);
  J_K: wu_jeneson_beard_2006__J_K(J_K0, K_x, K_i, X_K, deltaPsi, F, RT);
  J_AMP: wu_jeneson_beard_2006__J_AMP(J_AMP0, AMP_c, AMP_i, gamma, X_A);
  J_ADP: wu_jeneson_beard_2006__J_ADP(J_ADP0, ADP_c, ADP_i, gamma, X_A);
  J_ATP: wu_jeneson_beard_2006__J_ATP(J_ATP0, ATP_c, ATP_i, gamma, X_A);
  J_PI2: wu_jeneson_beard_2006__J_PI2(J_PI20, PI_c, PI_i, gamma, X_PI2);
  J_MgATP_x: wu_jeneson_beard_2006__J_MgATP_x(J_MgATP_x0, X_MgA, ATP_fx, Mg_x, ATP_mx, K_DT);
  J_MgADP_x: wu_jeneson_beard_2006__J_MgADP_x(J_MgADP_x0, X_MgA, ADP_fx, Mg_x, ADP_mx, K_DD);
  J_MgATP_i: wu_jeneson_beard_2006__J_MgATP_i(J_MgATP_i0, X_MgA, ATP_fi, Mg_i, ATP_mi, K_DT);
  J_MgADP_i: wu_jeneson_beard_2006__J_MgADP_i(J_MgADP_i0, X_MgA, ADP_fi, Mg_i, ADP_mi, K_DD);
  J_MgATP_c: wu_jeneson_beard_2006__J_MgATP_c(J_MgATP_c0, X_MgA, ATP_fc, Mg_c, ATP_mc, K_DT);
  J_MgADP_c: wu_jeneson_beard_2006__J_MgADP_c(J_MgADP_c0, X_MgA, ADP_fc, Mg_c, ADP_mc, K_DD);
  J_AKi: wu_jeneson_beard_2006__J_AKi(J_AKi0, X_AK, ATP_i, ADP_i, AMP_i, K_AK);
  J_AKc: wu_jeneson_beard_2006__J_AKc(J_AKc0, X_AK, ATP_c, ADP_c, AMP_c, K_AK);
  J_AtC: wu_jeneson_beard_2006__J_AtC(J_AtC0, X_AtC);
  J_CKc: wu_jeneson_beard_2006__J_CKc(J_CKc0, X_CK, K_CK, ATP_c, ADP_c, H_c, PCr_c, Cr_c);
end