//Created by libAntimony v2.4

// Warnings from automatic translation:
//    Unable to use the formula "Qv * Na_v - Qa * Na_a" to set the assignment rule for Jv_Na:  Loop detected:  Jv_Na's definition (Qv * Na_v - Qa * Na_a) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5').
//    Unable to use the formula "Qv * K_v - Qa * K_a" to set the assignment rule for Jv_K:  Loop detected:  Jv_K's definition (Qv * K_v - Qa * K_a) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5').
//    Unable to use the formula "Qv * Cl_v - Qa * Cl_a" to set the assignment rule for Jv_Cl:  Loop detected:  Jv_Cl's definition (Qv * Cl_v - Qa * Cl_a) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5').
//    Unable to use the formula "Qv - Qa" to set the assignment rule for Jv_H2O:  Loop detected:  Jv_H2O's definition (Qv - Qa) either includes itself directly (i.e. 's5 := 6 + s5') or by proxy (i.e. 's5 := 8*d3' and 'd3 := 9*s5').
//    In module 'yi_2003____main', the variables capillary_space.Qa and Qa were unable to be set as equivalent:  Loop detected:  'capillary_space.Qa' may not be set to be equal to 'Qa' because Qa's definition already includes capillary_space.Qa either directly or by proxy.
//    In module 'yi_2003____main', the variables arterial_space.Pr_v and Pr_v were unable to be set as equivalent:  Loop detected:  'arterial_space.Pr_v' may not be set to be equal to 'Pr_v' because Pr_v's definition already includes arterial_space.Pr_v either directly or by proxy.

model yi_2003__environment(time_)

  // Variable initializations:
  time_ = ;
end

model yi_2003__intracellular_space(delta, delta_eq, V_i, R, T, F, C_m, Lie_p, pi_i, pi_e, P_h, delta_eh, X_e, time_, Na_e, Na_i, K_e, K_i, Cl_e, Cl_i, V_e, delta_e)

  // Assignment Rules:
  pi_i := R * T * (Na_i + K_i + Cl_i + X_i / V_i);
  pi_e := R * T * (Na_e + K_e + Cl_e + X_e / V_e);
  delta_init := delta_i - delta_e;
  X_i := (V_i * ((Na_i + K_i) - Cl_i)) / z_i;

  // Rate Rules:
  delta' = (V_i * F * R * T * ((Na_i + K_i) - (Cl_i + (z_i * X_i) / V_i))) / (C_m * A_s);
  V_i' = Lie_p * (pi_i - pi_e);

  // Variable initializations:
  delta = -80.0;
  delta_eq = -70.0;
  V_i = 3.80E-8;
  R = 8.314;
  T = 310.0;
  F = 96.5;
  C_m = 1.0;
  Lie_p = 1.21E12;
  P_h = 6.0E-10;
  delta_eh = ;
  delta_i = ;
  z_i = 1.44;
  A_s = 7.67E-5;
  X_e = ;
  time_ = ;
  Na_e = ;
  Na_i = ;
  K_e = ;
  K_i = ;
  Cl_e = ;
  Cl_i = ;
  V_e = ;
  delta_e = ;
end

model yi_2003__intracellular_sodium_m_gate(m_infinity, delta, delta_eq)

  // Assignment Rules:
  m_infinity := A_m / (A_m + B_m);
  A_m := (0.1 * ((25.0 - delta) + delta_eq)) / (exp(0.1 * ((25.0 - delta) + delta_eq)) - 1.0);
  B_m := 4.0 * exp((- delta + delta_eq) / 18.0);

  // Variable initializations:
  delta = ;
  delta_eq = ;
end

model yi_2003__intracellular_sodium_h_gate(h_infinity, delta, delta_eq)

  // Assignment Rules:
  h_infinity := A_h / (A_h + B_h);
  A_h := 0.07 * exp(0.05 * (- delta + delta_eq));
  B_h := 1.0 / (exp(0.1 * ((30.0 - delta) + delta_eq)) + 1.0);

  // Variable initializations:
  delta = ;
  delta_eq = ;
end

model yi_2003__intracellular_sodium(Na_i, g_Na, delta_Na, time_, Na_e, P, R, F, T, delta, delta_eq, m_infinity, h_infinity)

  // Sub-modules, and any changes to those submodules:
  intracellular_sodium_m_gate: yi_2003__intracellular_sodium_m_gate(m_infinity, delta, delta_eq);
  intracellular_sodium_h_gate: yi_2003__intracellular_sodium_h_gate(h_infinity, delta, delta_eq);

  // Assignment Rules:
  g_Na := g_b_Na + g_Na_max * power(m_infinity, 3.0) * h_infinity;
  delta_Na := ((R * T) / F) * ln(Na_e / Na_i);

  // Rate Rules:
  Na_i' = -((g_Na / F) * (delta - delta_Na) + 3.0 * P);

  // Variable initializations:
  Na_i = 11.2;
  g_b_Na = 3.31E-5;
  g_Na_max = 3.69E-2;
  time_ = ;
  Na_e = ;
  P = ;
  R = ;
  F = ;
  T = ;
end

model yi_2003__intracellular_potassium_n_gate(n_infinity, delta, delta_eq)

  // Assignment Rules:
  n_infinity := A_n / (A_n + B_n);
  A_n := (0.01 * ((10.0 - delta) + delta_eq)) / (exp(0.1 * ((10.0 - delta) + delta_eq)) - 1.0);
  B_n := 0.125 * exp((- delta + delta_eq) / 80.0);

  // Variable initializations:
  delta = ;
  delta_eq = ;
end

model yi_2003__intracellular_potassium(K_i, g_K, delta_K, time_, K_e, P, R, F, T, delta, delta_eq, n_infinity)

  // Sub-modules, and any changes to those submodules:
  intracellular_potassium_n_gate: yi_2003__intracellular_potassium_n_gate(n_infinity, delta, delta_eq);

  // Assignment Rules:
  g_K := g_b_K + g_K_max * power(n_infinity, 4.0);
  delta_K := ((R * T) / F) * ln(K_e / K_i);

  // Rate Rules:
  K_i' = -((g_K / F) * (delta - delta_K) - 2.0 * P);

  // Variable initializations:
  K_i = 139.0;
  g_b_K = 8.33E-4;
  g_K_max = 1.28E-2;
  time_ = ;
  K_e = ;
  P = ;
  R = ;
  F = ;
  T = ;
end

model yi_2003__intracellular_chloride(Cl_i, g_Cl, delta_Cl, time_, Cl_e, R, F, T, delta)

  // Assignment Rules:
  delta_Cl := ((R * T) / (-1.0 * F)) * ln(Cl_e / Cl_i);

  // Rate Rules:
  Cl_i' = (g_Cl / F) * (delta + delta_Cl);

  // Variable initializations:
  Cl_i = 4.95;
  g_Cl = 2.81E-4;
  time_ = ;
  Cl_e = ;
  R = ;
  F = ;
  T = ;
  delta = ;
end

model yi_2003__extracellular_sodium(Na_e, delta_Na, time_, g_Na, P, R, F, T, delta, Jv_Na, Jh_Na)

  // Rate Rules:
  Na_e' = ((g_Na / F) * (delta - delta_Na) + 3.0 * P) - (Jv_Na + Jh_Na);

  // Variable initializations:
  Na_e = 140.0;
  delta_Na = ;
  time_ = ;
  g_Na = ;
  P = ;
  R = ;
  F = ;
  T = ;
  delta = ;
  Jv_Na = ;
  Jh_Na = ;
end

model yi_2003__extracellular_potassium(K_e, g_K, delta_K, time_, P, R, F, T, delta, Jv_K, Jh_K)

  // Rate Rules:
  K_e' = ((g_K / F) * (delta - delta_K) - 2.0 * P) - (Jv_K + Jh_K);

  // Variable initializations:
  K_e = 5.4;
  g_K = ;
  delta_K = ;
  time_ = ;
  P = ;
  R = ;
  F = ;
  T = ;
  delta = ;
  Jv_K = ;
  Jh_K = ;
end

model yi_2003__extracellular_chloride(Cl_e, g_Cl, delta_Cl, time_, R, F, T, delta, Jv_Cl, Jh_Cl)

  // Rate Rules:
  Cl_e' = -((g_Cl / F) * (delta + delta_Cl)) - (Jv_Cl + Jh_Cl);

  // Variable initializations:
  Cl_e = 110.0;
  g_Cl = ;
  delta_Cl = ;
  time_ = ;
  R = ;
  F = ;
  T = ;
  delta = ;
  Jv_Cl = ;
  Jh_Cl = ;
end

model yi_2003__extracellular_space(V_e, delta_e, X_e, Lie_p, pi_i, pi_e, time_, Jv_H2O, Jh_H2O, Cl_e, Na_e, K_e)

  // Assignment Rules:
  X_e := (V_e * ((Na_e + K_e) - Cl_e)) / z_e;

  // Rate Rules:
  V_e' = Lie_p * (pi_e - pi_i) - (Jv_H2O + Jh_H2O);

  // Variable initializations:
  V_e = 9.50E-9;
  delta_e = ;
  z_e = 85.4;
  Lie_p = ;
  pi_i = ;
  pi_e = ;
  time_ = ;
  Jv_H2O = ;
  Jh_H2O = ;
  Cl_e = ;
  Na_e = ;
  K_e = ;
end

model yi_2003__water_flux(Jh_H2O, V_i, V_e, time_)

  // Assignment Rules:
  Jh_H2O := -((1.0 / tau_1) * (V_infinity_e - V_e) + (1.0 / tau_2) * (V_infinity_T - (V_i + V_e)));

  // Variable initializations:
  V_infinity_e = ;
  V_infinity_T = ;
  tau_1 = 3.3;
  tau_2 = 33.0;
  V_i = ;
  V_e = ;
  time_ = ;
end

model yi_2003__sodium_flux(Jh_Na, Na_e, delta_eh, time_, R, T, F, P_h, Jh_H2O)

  // Assignment Rules:
  Jh_Na := P_h * alpha_Na * ((Na_infinity_e - Na_e * exp(alpha_Na)) / (1.0 - exp(alpha_Na)));
  alpha_Na := Jh_H2O / P_h - (1.0 * F) / (R * T * delta_eh);

  // Variable initializations:
  Na_infinity_e = ;
  Na_e = ;
  delta_eh = ;
  time_ = ;
  R = ;
  T = ;
  F = ;
  P_h = ;
  Jh_H2O = ;
end

model yi_2003__potassium_flux(Jh_K, K_e, delta_eh, time_, R, T, F, P_h, Jh_H2O)

  // Assignment Rules:
  Jh_K := P_h * alpha_K * ((K_infinity_e - K_e * exp(alpha_K)) / (1.0 - exp(alpha_K)));
  alpha_K := Jh_H2O / P_h - (1.0 * F) / (R * T * delta_eh);

  // Variable initializations:
  K_infinity_e = ;
  K_e = ;
  delta_eh = ;
  time_ = ;
  R = ;
  T = ;
  F = ;
  P_h = ;
  Jh_H2O = ;
end

model yi_2003__chloride_flux(Jh_Cl, Cl_e, delta_eh, time_, R, T, F, P_h, Jh_H2O)

  // Assignment Rules:
  Jh_Cl := P_h * alpha_Cl * ((Cl_infinity_e - Cl_e * exp(alpha_Cl)) / (1.0 - exp(alpha_Cl)));
  alpha_Cl := Jh_H2O / P_h - (-1.0 * F) / (R * T * delta_eh);

  // Variable initializations:
  Cl_infinity_e = ;
  Cl_e = ;
  delta_eh = ;
  time_ = ;
  R = ;
  T = ;
  F = ;
  P_h = ;
  Jh_H2O = ;
end

model yi_2003__capillary_compartment_sodium(Na_v, delta_ev_Na, Jv_Na, time_, Na_a, Na_e, Qv, Qa, R, T, F)

  // Assignment Rules:
  Na_v := (Qa * Na_a + Jv_Na) / Qv;
  delta_ev_Na := ((R * T) / F) * ln(Na_v / Na_e);

  // Variable initializations:
  Jv_Na = 0.0;
  time_ = ;
  Na_a = ;
  Na_e = ;
  Qv = ;
  Qa = ;
  R = ;
  T = ;
  F = ;
end

model yi_2003__capillary_compartment_potassium(K_v, delta_ev_K, Jv_K, time_, K_a, K_e, Qv, Qa, R, T, F)

  // Assignment Rules:
  K_v := (Qa * K_a + Jv_K) / Qv;
  delta_ev_K := ((R * T) / F) * ln(K_v / K_e);

  // Variable initializations:
  Jv_K = 0.0;
  time_ = ;
  K_a = ;
  K_e = ;
  Qv = ;
  Qa = ;
  R = ;
  T = ;
  F = ;
end

model yi_2003__capillary_compartment_chloride(Cl_v, delta_ev_Cl, Jv_Cl, time_, Cl_a, Cl_e, Qv, Qa, R, T, F)

  // Assignment Rules:
  Cl_v := (Qa * Cl_a + Jv_Cl) / Qv;
  delta_ev_Cl := ((R * T) / F) * ln(Cl_v / Cl_e);

  // Variable initializations:
  Jv_Cl = 0.0;
  time_ = ;
  Cl_a = ;
  Cl_e = ;
  Qv = ;
  Qa = ;
  R = ;
  T = ;
  F = ;
end

model yi_2003__capillary_space(pi_v, Qv, Pr_v, Jv_H2O, Qa, Na_v, K_v, Cl_v, pi_e, time_)

  // Assignment Rules:
  pi_v := Na_v + K_v + Cl_v + Pr_v;
  Qv := Qa + Jv_H2O;
  Pr_v := (Na_v + K_v + - Cl_v) / z_v;

  // Variable initializations:
  Jv_H2O = ;
  z_v = 24.4;
  Qa = ;
  Na_v = ;
  K_v = ;
  Cl_v = ;
  pi_e = ;
  time_ = ;
end

model yi_2003__arterial_space(Qa, Na_a, K_a, Cl_a, time_, Pr_v, Qv)

  // Assignment Rules:
  Qa := (Qv * Pr_v) / Pr_a;

  // Variable initializations:
  Na_a = 140.0;
  K_a = 5.4;
  Cl_a = 110.0;
  Pr_a = 1.45;
  time_ = ;
  Pr_v = ;
  Qv = ;
end

model yi_2003__pump_rate(P, time_, K_e, Na_i, Na_e, R, F, T, delta)

  // Assignment Rules:
  P := a_t * P_max * f_NaK * (1.0 / (1.0 + power(Km_Na_i / Na_i, 1.5))) * (K_e / (Km_K_e + K_e));
  f_NaK := 1.0 / (1.0 + 0.1245 * exp((-0.1 * delta * F) / (R * T)) + (0.0365 * 7.0 * exp((-0.1 * delta * F) / (R * T)) * exp(Na_e / 67.3) - 1.0));
  a_t := power(0.35, time_ / 15.0);

  // Variable initializations:
  P_max = 4.6E-8;
  Km_Na_i = 10.0;
  Km_K_e = 1.5;
  time_ = ;
  K_e = ;
  Na_i = ;
  Na_e = ;
  R = ;
  F = ;
  T = ;
  delta = ;
end

model *yi_2003____main()

  // Sub-modules, and any changes to those submodules:
  environment: yi_2003__environment(time_);
  intracellular_space: yi_2003__intracellular_space(delta, delta_eq, V_i, R, T, F, C_m, Lie_p, pi_i, pi_e, P_h, delta_eh, X_e, time_, Na_e, Na_i, K_e, K_i, Cl_e, Cl_i, V_e, delta_e);
  intracellular_sodium: yi_2003__intracellular_sodium(Na_i, g_Na, delta_Na, time_, Na_e, P, R, F, T, delta, delta_eq, m_infinity, h_infinity);
  intracellular_potassium: yi_2003__intracellular_potassium(K_i, g_K, delta_K, time_, K_e, P, R, F, T, delta, delta_eq, n_infinity);
  intracellular_chloride: yi_2003__intracellular_chloride(Cl_i, g_Cl, delta_Cl, time_, Cl_e, R, F, T, delta);
  extracellular_sodium: yi_2003__extracellular_sodium(Na_e, delta_Na, time_, g_Na, P, R, F, T, delta, Jv_Na, Jh_Na);
  extracellular_potassium: yi_2003__extracellular_potassium(K_e, g_K, delta_K, time_, P, R, F, T, delta, Jv_K, Jh_K);
  extracellular_chloride: yi_2003__extracellular_chloride(Cl_e, g_Cl, delta_Cl, time_, R, F, T, delta, Jv_Cl, Jh_Cl);
  extracellular_space: yi_2003__extracellular_space(V_e, delta_e, X_e, Lie_p, pi_i, pi_e, time_, Jv_H2O, Jh_H2O, Cl_e, Na_e, K_e);
  water_flux: yi_2003__water_flux(Jh_H2O, V_i, V_e, time_);
  sodium_flux: yi_2003__sodium_flux(Jh_Na, Na_e, delta_eh, time_, R, T, F, P_h, Jh_H2O);
  potassium_flux: yi_2003__potassium_flux(Jh_K, K_e, delta_eh, time_, R, T, F, P_h, Jh_H2O);
  chloride_flux: yi_2003__chloride_flux(Jh_Cl, Cl_e, delta_eh, time_, R, T, F, P_h, Jh_H2O);
  capillary_compartment_sodium: yi_2003__capillary_compartment_sodium(Na_v, delta_ev_Na, Jv_Na, time_, Na_a, Na_e, Qv, Qa, R, T, F);
  capillary_compartment_potassium: yi_2003__capillary_compartment_potassium(K_v, delta_ev_K, Jv_K, time_, K_a, K_e, Qv, Qa, R, T, F);
  capillary_compartment_chloride: yi_2003__capillary_compartment_chloride(Cl_v, delta_ev_Cl, Jv_Cl, time_, Cl_a, Cl_e, Qv, Qa, R, T, F);
  capillary_space: yi_2003__capillary_space(pi_v, Qv, Pr_v, Jv_H2O, Qa0, Na_v, K_v, Cl_v, pi_e, time_);
  arterial_space: yi_2003__arterial_space(Qa, Na_a, K_a, Cl_a, time_, Pr_v0, Qv);
  pump_rate: yi_2003__pump_rate(P, time_, K_e, Na_i, Na_e, R, F, T, delta);
end