//Created by libAntimony v2.4

// Warnings from automatic translation:
//    Unable to use the formula "pi * preplength * power(radius, 2)" to set the assignment rule for volume:  The variable 'volume' is the type Unit Definition, and may not have an assignment rule associated with it.

model clancy_rudy_2002__environment(time_)

  // Variable initializations:
  time_ = ;
end

model clancy_rudy_2002__membrane(V, R, T, F, time_, i_Na, i_Ca_L, i_Ca_T, i_Kr, i_Ks, i_K_Na, i_K_ATP, i_to, i_NaCa, i_K1, i_Kp, i_p_Ca, i_Na_b, i_Ca_b, i_NaK, i_ns_Ca, dVdt)

  // Assignment Rules:
  I_st := piecewise( stim_amplitude , (( geq(time_, stim_start)) && (time_ <= stim_end) && ((time_ - stim_start) - floor((time_ - stim_start) / stim_period) * stim_period <= stim_duration )), 0 );
  dVdt := (-(1) / Cm) * (i_Na + i_Ca_L + i_Ca_T + i_Kr + i_Ks + i_K_Na + i_K_ATP + i_to + i_K1 + i_Kp + i_NaCa + i_p_Ca + i_Na_b + i_Ca_b + i_NaK + i_ns_Ca + I_st);

  // Rate Rules:
  V' = (-(1) / Cm) * (i_Na + i_Ca_L + i_Ca_T + i_Kr + i_Ks + i_K_Na + i_K_ATP + i_to + i_K1 + i_Kp + i_NaCa + i_p_Ca + i_Na_b + i_Ca_b + i_NaK + i_ns_Ca + I_st);

  // Variable initializations:
  V = -89.179;
  R = 8314;
  T = 310;
  F = 96485;
  Cm = 0.001;
  time_ = ;
  i_Na = ;
  i_Ca_L = ;
  i_Ca_T = ;
  i_Kr = ;
  i_Ks = ;
  i_K_Na = ;
  i_K_ATP = ;
  i_to = ;
  i_NaCa = ;
  i_K1 = ;
  i_Kp = ;
  i_p_Ca = ;
  i_Na_b = ;
  i_Ca_b = ;
  i_NaK = ;
  i_ns_Ca = ;
  stim_start = 3;
  stim_end = 9;
  stim_period = 1;
  stim_duration = 0.002;
  stim_amplitude = -50;
end

model clancy_rudy_2002__Na_channel_states(P_O_Na, time_, V)

  // Assignment Rules:
  P_O_Na := P_LO + P_UO;
  alpha_11 := 3802 / (0.1027 * exp(- V / 17) + 0.2 * exp(- V / 150));
  beta_11 := 191.7 * exp(- V / 20.3);
  alpha_12 := 3802 / (0.1027 * exp(- V / 15) + 0.23 * exp(- V / 150));
  beta_12 := 200 * exp(-(V - 5) / 20.3);
  alpha_13 := 3802 / (0.1027 * exp(- V / 12) + 0.25 * exp(- V / 150));
  beta_13 := 220 * exp(-(V - 10) / 20.3);
  alpha_2 := 9178 * exp(V / 29.68);
  beta_2 := (alpha_13 * alpha_2 * alpha_3) / (beta_13 * beta_3);
  alpha_3 := (3.7933E-4 * exp(- V / 7.7)) / 2.5;
  beta_3 := 8.4 + 0.02 * V;
  alpha_4 := alpha_2 / 100;
  beta_4 := alpha_3;
  alpha_5 := alpha_2 / 3.5E4;
  beta_5 := alpha_3 / 20;

  // Rate Rules:
  P_LO' = -(9.5E-1 + beta_13) * P_LO + 1E-4 * P_UO + alpha_13 * P_LC1;
  P_UO' = -(alpha_2 + beta_13 + 1E-4) * P_UO + beta_2 * P_UIF + alpha_13 * P_UC1 + 9.5E-1 * P_LO;
  P_LC1' = -(beta_12 + alpha_13 + 9.5E-1) * P_LC1 + alpha_12 * P_LC2 + beta_13 * P_LO + 1E-4 * P_UC1;
  P_LC2' = -(beta_11 + 9.5E-1 + alpha_12) * P_LC2 + alpha_11 * P_LC3 + beta_12 * P_LC1 + 1E-4 * P_UC2;
  P_LC3' = -(9.5E-1 + alpha_11) * P_LC3 + 1E-4 * P_UC3 + beta_11 * P_LC2;
  P_UIF' = -(beta_2 + alpha_3 + alpha_4 + beta_12) * P_UIF + beta_3 * P_UC1 + beta_4 * P_UIM1 + alpha_2 * P_UO + alpha_12 * P_UIC2;
  P_UC1' = -(beta_12 + alpha_13 + beta_3 + 1E-4) * P_UC1 + alpha_12 * P_UC2 + beta_13 * P_UO + alpha_3 * P_UIF + 9.5E-1 * P_LC1;
  P_UC2' = -(beta_11 + beta_3 + alpha_12 + 1E-4) * P_UC2 + alpha_11 * P_UC3 + beta_12 * P_UC1 + alpha_3 * P_UIC2 + 9.5E-1 * P_LC2;
  P_UC3' = -(beta_3 + alpha_11 + 1E-4) * P_UC3 + alpha_3 * P_UIC3 + beta_11 * P_UC2 + 9.5E-1 * P_LC3;
  P_UIC3' = -(alpha_3 + alpha_11) * P_UIC3 + beta_3 * P_UC3 + beta_11 * P_UIC2;
  P_UIC2' = -(alpha_3 + alpha_12 + beta_11) * P_UIC2 + beta_3 * P_UC2 + beta_12 * P_UIF + alpha_11 * P_UIC3;
  P_UIM1' = -(alpha_5 + beta_4) * P_UIM1 + beta_5 * P_UIM2 + alpha_4 * P_UIF;
  P_UIM2' = alpha_5 * P_UIM1 - beta_5 * P_UIM2;

  // Variable initializations:
  P_LO = 4.128e-17;
  P_UO = 3.923e-13;
  P_LC1 = 5.498e-14;
  P_LC2 = 1.186e-11;
  P_LC3 = 9.604e-10;
  P_UIF = 2.127e-10;
  P_UC1 = 5.224e-10;
  P_UC2 = 1.127e-7;
  P_UC3 = 9.126e-6;
  P_UIC3 = 3.715e-6;
  P_UIC2 = 4.589e-8;
  P_UIM1 = 5.952e-11;
  P_UIM2 = 9.56e-13;
  time_ = ;
  V = ;
end

model clancy_rudy_2002__fast_sodium_current(i_Na, E_Na, time_, V, R, T, F, Nao, Nai, P_O_Na)

  // Sub-modules, and any changes to those submodules:
  Na_channel_states: clancy_rudy_2002__Na_channel_states(P_O_Na, time_, V);

  // Assignment Rules:
  i_Na := g_Na * P_O_Na * (V - E_Na);
  E_Na := ((R * T) / F) * ln(Nao / Nai);

  // Variable initializations:
  g_Na = 23.5;
  R = ;
  T = ;
  F = ;
  Nao = ;
  Nai = ;
end

model clancy_rudy_2002__L_type_Ca_channel_d_gate(d, V, time_)

  // Assignment Rules:
  alpha_d := d_infinity / tau_d;
  beta_d := (1 - d_infinity) / tau_d;
  d_infinity := 1 / (1 + exp(- E0_d / 6.24));
  tau_d := piecewise( 0.001 / (0.035 * 6.24) , abs(E0_d) < 1E-5 , (0.001 * d_infinity * (1 - exp(- E0_d / 6.24))) / (0.035 * E0_d) );
  E0_d := V + 10;

  // Rate Rules:
  d' = alpha_d * (1 - d) - beta_d * d;

  // Variable initializations:
  d = 3.085e-6;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__L_type_Ca_channel_f_gate(f, V, time_)

  // Assignment Rules:
  alpha_f := f_infinity / tau_f;
  beta_f := (1 - f_infinity) / tau_f;
  f_infinity := 1 / (1 + exp((V + 32) / 8)) + 0.6 / (1 + exp((50 - V) / 20));
  tau_f := 0.001 / (0.0197 * exp(-power(0.0337 * (V + 10), 2)) + 0.02);

  // Rate Rules:
  f' = alpha_f * (1 - f) - beta_f * f;

  // Variable initializations:
  f = 0.9998;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__L_type_Ca_channel_f_Ca_gate(f_Ca, V, time_, Cai)

  // Assignment Rules:
  f_Ca := 1 / (1 + Cai / Km_Ca);

  // Variable initializations:
  Km_Ca = 0.0006;
  V = ;
  time_ = ;
  Cai = ;
end

model clancy_rudy_2002__L_type_Ca_channel(i_Ca_L, i_CaCa, i_CaK, i_CaNa, gamma_Nai, gamma_Nao, gamma_Ki, gamma_Ko, time_, V, Cai, R, T, F, Cao, Nao, Ko, Nai, Ki, d, f, f_Ca)

  // Sub-modules, and any changes to those submodules:
  L_type_Ca_channel_d_gate: clancy_rudy_2002__L_type_Ca_channel_d_gate(d, V, time_);
  L_type_Ca_channel_f_gate: clancy_rudy_2002__L_type_Ca_channel_f_gate(f, V, time_);
  L_type_Ca_channel_f_Ca_gate: clancy_rudy_2002__L_type_Ca_channel_f_Ca_gate(f_Ca, V, time_, Cai);

  // Assignment Rules:
  i_Ca_L := i_CaCa + i_CaK + i_CaNa;
  i_CaCa := d * f * f_Ca * I_CaCa;
  i_CaK := d * f * f_Ca * I_CaK;
  i_CaNa := d * f * f_Ca * I_CaNa;
  I_CaCa := (((P_Ca * power(2, 2) * V * power(F, 2)) / (R * T)) * (gamma_Cai * Cai * exp((2 * V * F) / (R * T)) - gamma_Cao * Cao)) / (exp((2 * V * F) / (R * T)) - 1);
  I_CaK := (((P_K * power(1, 2) * V * power(F, 2)) / (R * T)) * (gamma_Ki * Ki * exp((1 * V * F) / (R * T)) - gamma_Ko * Ko)) / (exp((1 * V * F) / (R * T)) - 1);
  I_CaNa := (((P_Na * power(1, 2) * V * power(F, 2)) / (R * T)) * (gamma_Nai * Nai * exp((1 * V * F) / (R * T)) - gamma_Nao * Nao)) / (exp((1 * V * F) / (R * T)) - 1);

  // Variable initializations:
  gamma_Nai = 0.75;
  gamma_Nao = 0.75;
  gamma_Ki = 0.75;
  gamma_Ko = 0.75;
  P_Ca = 0.00054;
  P_Na = 6.75e-7;
  P_K = 1.93e-7;
  gamma_Cai = 1;
  gamma_Cao = 0.341;
  R = ;
  T = ;
  F = ;
  Cao = ;
  Nao = ;
  Ko = ;
  Nai = ;
  Ki = ;
end

model clancy_rudy_2002__T_type_Ca_channel_b_gate(b, V, time_)

  // Assignment Rules:
  b_inf := 1 / (1 + exp(-(V + 14) / 10.8));
  tau_b := 0.0037 + 0.0061 / (1 + exp((V + 25) / 4.5));

  // Rate Rules:
  b' = (b_inf - b) / tau_b;

  // Variable initializations:
  b = 0.00095;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__T_type_Ca_channel_g_gate(g, V, time_)

  // Assignment Rules:
  g_inf := 1 / (1 + exp((V + 60) / 5.6));
  tau_g := piecewise( -(0.000875) * V + 0.012 , V <= 0 , 0.012 );

  // Rate Rules:
  g' = (g_inf - g) / tau_g;

  // Variable initializations:
  g = 0.9946;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__T_type_Ca_channel(i_Ca_T, E_Ca, time_, V, b, g)

  // Sub-modules, and any changes to those submodules:
  T_type_Ca_channel_b_gate: clancy_rudy_2002__T_type_Ca_channel_b_gate(b, V, time_);
  T_type_Ca_channel_g_gate: clancy_rudy_2002__T_type_Ca_channel_g_gate(g, V, time_);

  // Assignment Rules:
  i_Ca_T := g_CaT * b * b * g * (V - E_Ca);

  // Variable initializations:
  g_CaT = 0.05;
  E_Ca = ;
end

model clancy_rudy_2002__Kr_channel_states(P_O, time_, V, Ko)

  // Assignment Rules:
  alpha := 55.5 * exp(0.05547153 * (V - 12));
  beta := 2.357 * exp(-(0.036588) * V);
  alpha_alpha := 65.5 * exp(0.05547153 * (V - 36));
  beta_beta := 2.9357 * exp(-(0.02158) * V);
  alpha_i := (439 * exp(-(0.02352) * (V + 25)) * 4.5) / Ko;
  beta_i := (656 * exp(0.000942 * V) * power(4.5, 0.3)) / power(Ko, 0.3);
  mu := (alpha_i * beta_beta * alpha_alpha) / (alpha_alpha * beta_i);

  // Rate Rules:
  P_O' = -(beta_beta + beta_i) * P_O + alpha_alpha * P_C1 + alpha_i * P_I;
  P_C1' = -(beta_in + alpha_alpha + alpha_alpha) * P_C1 + alpha_in * P_C2 + beta_beta * P_O + mu * P_I;
  P_C2' = -(beta + alpha_in) * P_C2 + alpha * P_C3 + beta_in * P_C1;
  P_C3' = beta * P_C2 - alpha * P_C3;
  P_I' = -(mu + alpha_i) * P_I + alpha_alpha * P_C1 + beta_i * P_O;

  // Variable initializations:
  P_O = 1.032e-10;
  P_C1 = 3.286e-8;
  P_C2 = 1.63e-8;
  P_C3 = 4.95e-6;
  P_I = 3.135e-11;
  alpha_in = 2172;
  beta_in = 1077;
  time_ = ;
  V = ;
  Ko = ;
end

model clancy_rudy_2002__rapid_delayed_rectifier_potassium_current(i_Kr, time_, V, Ko, Ki, R, T, F, P_O)

  // Sub-modules, and any changes to those submodules:
  Kr_channel_states: clancy_rudy_2002__Kr_channel_states(P_O, time_, V, Ko);

  // Assignment Rules:
  i_Kr := g_Kr * P_O * (V - E_Kr);
  g_Kr := 0.0135 * power(Ko, 0.59);
  E_Kr := ((R * T) / F) * ln(Ko / Ki);

  // Variable initializations:
  Ki = ;
  R = ;
  T = ;
  F = ;
end

model clancy_rudy_2002__slow_delayed_rectifier_potassium_current_xs1_gate(xs1, V, time_)

  // Assignment Rules:
  xs1_infinity := 1 / (1 + exp(-(V - 1.5) / 16.7));
  tau_xs1 := 0.001 / ((7.19E-5 * (V + 30)) / (1 - exp(-(0.148) * (V + 30))) + (0.000131 * (V + 30)) / (exp(0.0687 * (V + 30)) - 1));

  // Rate Rules:
  xs1' = (xs1_infinity - xs1) / tau_xs1;

  // Variable initializations:
  xs1 = 0.00437;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__slow_delayed_rectifier_potassium_current_xs2_gate(xs2, V, time_)

  // Assignment Rules:
  xs2_infinity := 1 / (1 + exp(-(V - 1.5) / 16.7));
  tau_xs2 := (4 * 0.001) / ((7.19E-5 * (V + 30)) / (1 - exp(-(0.148) * (V + 30))) + (0.000131 * (V + 30)) / (exp(0.0687 * (V + 30)) - 1));

  // Rate Rules:
  xs2' = (xs2_infinity - xs2) / tau_xs2;

  // Variable initializations:
  xs2 = 0.00437;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__slow_delayed_rectifier_potassium_current(i_Ks, time_, V, R, T, F, Ko, Ki, Nao, Nai, Cai, xs1, xs2)

  // Sub-modules, and any changes to those submodules:
  slow_delayed_rectifier_potassium_current_xs1_gate: clancy_rudy_2002__slow_delayed_rectifier_potassium_current_xs1_gate(xs1, V, time_);
  slow_delayed_rectifier_potassium_current_xs2_gate: clancy_rudy_2002__slow_delayed_rectifier_potassium_current_xs2_gate(xs2, V, time_);

  // Assignment Rules:
  i_Ks := g_Ks * xs1 * xs2 * (V - E_Ks);
  g_Ks := 0.968 * 0.433 * (1 + 0.6 / (1 + power(3.8E-5 / Cai, 1.4)));
  E_Ks := ((R * T) / F) * ln((Ko + PNaK * Nao) / (Ki + PNaK * Nai));

  // Variable initializations:
  PNaK = 0.01833;
  R = ;
  T = ;
  F = ;
  Ko = ;
  Ki = ;
  Nao = ;
  Nai = ;
  Cai = ;
end

model clancy_rudy_2002__time_independent_potassium_current_K1_gate(K1_infinity, V, time_, E_K)

  // Assignment Rules:
  K1_infinity := alpha_K1 / (alpha_K1 + beta_K1);
  alpha_K1 := 1020 / (1 + exp(0.2385 * ((V - E_K) - 59.215)));
  beta_K1 := (1000 * (0.49124 * exp(0.08032 * ((V - E_K) + 5.476)) + exp(0.06175 * ((V - E_K) - 594.31)))) / (1 + exp(-(0.5143) * ((V - E_K) + 4.753)));

  // Variable initializations:
  V = ;
  time_ = ;
  E_K = ;
end

model clancy_rudy_2002__time_independent_potassium_current(i_K1, E_K, time_, V, Ko, Ki, R, T, F, K1_infinity)

  // Sub-modules, and any changes to those submodules:
  time_independent_potassium_current_K1_gate: clancy_rudy_2002__time_independent_potassium_current_K1_gate(K1_infinity, V, time_, E_K);

  // Assignment Rules:
  i_K1 := g_K1 * K1_infinity * (V - E_K);
  E_K := ((R * T) / F) * ln(Ko / Ki);
  g_K1 := 0.75 * root(Ko / 5.4);

  // Variable initializations:
  Ko = ;
  Ki = ;
  R = ;
  T = ;
  F = ;
end

model clancy_rudy_2002__plateau_potassium_current(i_Kp, time_, V, E_K)

  // Assignment Rules:
  i_Kp := g_Kp * Kp * (V - E_K);
  Kp := 1 / (1 + exp((7.488 - V) / 5.98));

  // Variable initializations:
  g_Kp = 0.00552;
  time_ = ;
  V = ;
  E_K = ;
end

model clancy_rudy_2002__sodium_activated_potassium_current(i_K_Na, time_, V, Nai, E_K)

  // Assignment Rules:
  i_K_Na := g_K_Na * pona * pov * (V - E_K);
  g_K_Na := 0 * 0.12848;
  pona := 0.85 / (1 + power(kdKNa / Nai, nKNa));
  pov := 0.8 - 0.65 / (1 + exp((V + 125) / 15));

  // Variable initializations:
  nKNa = 2.8;
  kdKNa = 66;
  time_ = ;
  V = ;
  Nai = ;
  E_K = ;
end

model clancy_rudy_2002__ATP_sensitive_potassium_current(i_K_ATP, time_, V, Ko, E_K)

  // Assignment Rules:
  i_K_ATP := GKbaraATP * (V - E_K);
  g_K_ATP := (i_K_ATP_on * 0.000193) / nicholsarea;
  pATP := 1 / (1 + power(ATPi / kATP, hATP));
  GKbaraATP := g_K_ATP * pATP * power(Ko / 4, nATP);

  // Variable initializations:
  i_K_ATP_on = 1;
  nATP = 0.24;
  nicholsarea = 5e-5;
  ATPi = 3;
  hATP = 2;
  kATP = 0.00025;
  time_ = ;
  V = ;
  Ko = ;
  E_K = ;
end

model clancy_rudy_2002__transient_outward_current_zdv_gate(zdv, V, time_)

  // Assignment Rules:
  alpha_zdv := (10000 * exp((V - 40) / 25)) / (1 + exp((V - 40) / 25));
  beta_zdv := (10000 * exp(-(V + 90) / 25)) / (1 + exp(-(V + 90) / 25));
  tau_zdv := 1 / (alpha_zdv + beta_zdv);
  zdv_ss := alpha_zdv / (alpha_zdv + beta_zdv);

  // Rate Rules:
  zdv' = (zdv_ss - zdv) / tau_zdv;

  // Variable initializations:
  zdv = 0.0114;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__transient_outward_current_ydv_gate(ydv, V, time_)

  // Assignment Rules:
  alpha_ydv := 15 / (1 + exp((V + 60) / 5));
  beta_ydv := (100 * exp((V + 25) / 5)) / (1 + exp((V + 25) / 5));
  tau_ydv := 1 / (alpha_ydv + beta_ydv);
  ydv_ss := alpha_ydv / (alpha_ydv + beta_ydv);

  // Rate Rules:
  ydv' = (ydv_ss - ydv) / tau_ydv;

  // Variable initializations:
  ydv = 0.99998;
  V = ;
  time_ = ;
end

model clancy_rudy_2002__transient_outward_current(i_to, E_K, V, time_, zdv, ydv)

  // Sub-modules, and any changes to those submodules:
  transient_outward_current_zdv_gate: clancy_rudy_2002__transient_outward_current_zdv_gate(zdv, V, time_);
  transient_outward_current_ydv_gate: clancy_rudy_2002__transient_outward_current_ydv_gate(ydv, V, time_);

  // Assignment Rules:
  i_to := g_to * power(zdv, 3) * ydv * rvdv * (V - E_K);
  g_to := 0.05;
  rvdv := exp(V / 100);

  // Variable initializations:
  E_K = ;
end

model clancy_rudy_2002__sarcolemmal_calcium_pump(i_p_Ca, time_, Cai)

  // Assignment Rules:
  i_p_Ca := (I_pCa * Cai) / (K_mpCa + Cai);

  // Variable initializations:
  K_mpCa = 0.0005;
  I_pCa = 1.15;
  time_ = ;
  Cai = ;
end

model clancy_rudy_2002__sodium_background_current(i_Na_b, time_, V, E_Na)

  // Assignment Rules:
  i_Na_b := g_Nab * (V - E_Na);

  // Variable initializations:
  g_Nab = 0.004;
  time_ = ;
  V = ;
  E_Na = ;
end

model clancy_rudy_2002__calcium_background_current(i_Ca_b, E_Ca, time_, V, R, T, F, Cai, Cao)

  // Assignment Rules:
  i_Ca_b := g_Cab * (V - E_Ca);
  E_Ca := ((R * T) / (2 * F)) * ln(Cao / Cai);

  // Variable initializations:
  g_Cab = 0.003016;
  time_ = ;
  V = ;
  R = ;
  T = ;
  F = ;
  Cai = ;
  Cao = ;
end

model clancy_rudy_2002__sodium_potassium_pump(i_NaK, time_, V, R, T, F, Nai, Nao, Ko)

  // Assignment Rules:
  i_NaK := (((I_NaK * f_NaK * 1) / (1 + power(K_mNai / Nai, 2))) * Ko) / (Ko + K_mKo);
  f_NaK := 1 / (1 + 0.1245 * exp((-(0.1) * V * F) / (R * T)) + 0.0365 * sigma * exp((- V * F) / (R * T)));
  sigma := (1 / 7) * (exp(Nao / 67.3) - 1);

  // Variable initializations:
  I_NaK = 2.25;
  K_mNai = 10;
  K_mKo = 1.5;
  time_ = ;
  V = ;
  R = ;
  T = ;
  F = ;
  Nai = ;
  Nao = ;
  Ko = ;
end

model clancy_rudy_2002__non_specific_calcium_activated_current(i_ns_Ca, i_ns_Na, i_ns_K, gamma_Nai, gamma_Nao, gamma_Ki, gamma_Ko, R, T, F, Cao, Nao, Ko, Nai, Ki, time_, Cai, V)

  // Assignment Rules:
  i_ns_Ca := i_ns_Na + i_ns_K;
  i_ns_Na := (I_ns_Na * 1) / (1 + power(K_m_ns_Ca / Cai, 3));
  i_ns_K := (I_ns_K * 1) / (1 + power(K_m_ns_Ca / Cai, 3));
  P_ns_Ca := 0 * 1.75E-7;
  I_ns_Na := (((P_ns_Ca * power(1, 2) * V * power(F, 2)) / (R * T)) * (gamma_Nai * Nai * exp((1 * V * F) / (R * T)) - gamma_Nao * Nao)) / (exp((1 * V * F) / (R * T)) - 1);
  I_ns_K := (((P_ns_Ca * power(1, 2) * V * power(F, 2)) / (R * T)) * (gamma_Ki * Ki * exp((1 * V * F) / (R * T)) - gamma_Ko * Ko)) / (exp((1 * V * F) / (R * T)) - 1);

  // Variable initializations:
  gamma_Nai = ;
  gamma_Nao = ;
  gamma_Ki = ;
  gamma_Ko = ;
  R = ;
  T = ;
  F = ;
  Cao = ;
  Nao = ;
  Ko = ;
  Nai = ;
  Ki = ;
  K_m_ns_Ca = 0.0012;
  time_ = ;
  Cai = ;
  V = ;
end

model clancy_rudy_2002__Na_Ca_exchanger(i_NaCa, time_, V, R, T, F, Nai, Nao, Cai, Cao)

  // Assignment Rules:
  i_NaCa := (c1 * exp(((gamma - 1) * V * F) / (R * T)) * (exp((V * F) / (R * T)) * power(Nai, 3) * Cao - power(Nao, 3) * Cai)) / (1 + c2 * exp(((gamma - 1) * V * F) / (R * T)) * (exp((V * F) / (R * T)) * power(Nai, 3) * Cao + power(Nao, 3) * Cai));

  // Variable initializations:
  c1 = 0.00025;
  c2 = 0.0001;
  gamma = 0.15;
  time_ = ;
  V = ;
  R = ;
  T = ;
  F = ;
  Nai = ;
  Nao = ;
  Cai = ;
  Cao = ;
end

model clancy_rudy_2002__calcium_dynamics(i_rel, i_up, i_leak, i_tr, time_, F, Cai, Cao, Ca_JSR, Ca_NSR, V_myo, A_cap, i_NaCa, i_CaCa, i_p_Ca, i_Ca_b, i_Ca_T, dVdt)

  // Assignment Rules:
  i_rel := G_rel * (Ca_JSR - Cai);
  i_up := (I_up * Cai) / (Cai + K_mup);
  i_leak := K_leak * Ca_NSR;
  i_tr := (Ca_NSR - Ca_JSR) / tau_tr;
  G_rel := piecewise( ((G_rel_max * (Cainfluxtrack - delta_Ca_ith)) / ((K_mrel + Cainfluxtrack) - delta_Ca_ith)) * (1 - APtrack2) * APtrack2 , Cainfluxtrack > delta_Ca_ith , G_rel_overload * (1 - OVRLDtrack2) * OVRLDtrack2 , ( Cainfluxtrack <= delta_Ca_ith) && (OVRLDtrack2 > 0 ), 0 );
  K_leak := I_up / Ca_NSR_max;
  V_JSR := (0.0048 / 0.68) * V_myo;
  V_NSR := (0.0552 / 0.68) * V_myo;

  // Rate Rules:
  Cai' = (1 / (1 + (CMDN_max * K_mCMDN) / power(K_mCMDN + Cai, 2) + (Tn_max * K_mTn) / power(K_mTn + Cai, 2))) * ((- A_cap * (((i_CaCa + i_Ca_T) - 2 * i_NaCa) + i_p_Ca + i_Ca_b)) / (2 * V_myo * F) + (i_rel * V_JSR) / V_myo + ((i_leak - i_up) * V_NSR) / V_myo);
  Ca_JSR' = (1 / (1 + (CSQN_max * K_mCSQN) / power(K_mCSQN + Ca_JSR, 2))) * (i_tr - i_rel);
  Ca_NSR' = ((- i_tr * V_JSR) / V_NSR - i_leak) + i_up;
  APtrack' = piecewise( 100000 * (1 - APtrack) - 500 * APtrack , dVdt > 150000 , -(500) * APtrack );
  APtrack2' = piecewise( 100000 * (1 - APtrack2) - 500 * APtrack2 , ( APtrack < 0.2) && (APtrack > 0.18 ), -(500) * APtrack2 );
  APtrack3' = piecewise( 100000 * (1 - APtrack3) - 500 * APtrack3 , ( APtrack < 0.2) && (APtrack > 0.18 ), -(10) * APtrack3 );
  Cainfluxtrack' = piecewise( (- A_cap * (((i_CaCa + i_Ca_T) - i_NaCa) + i_p_Ca + i_Ca_b)) / (2 * V_myo * F) , APtrack > 0.2 , 0 , ( APtrack2 > 0.01) && (APtrack <= 0.2 ), -(500) * Cainfluxtrack );
  OVRLDtrack' = piecewise( 50000 * (1 - OVRLDtrack) , (( 1 / (1 + K_mCSQN / Ca_NSR) > CSQNthresh) && (OVRLDtrack3 < 0.37) && (APtrack3 < 0.37 )), -(500) * OVRLDtrack );
  OVRLDtrack2' = piecewise( 50000 * (1 - OVRLDtrack2) , ( OVRLDtrack > Logicthresh) && (OVRLDtrack2 < Logicthresh ), -(500) * OVRLDtrack2 );
  OVRLDtrack3' = piecewise( 50000 * (1 - OVRLDtrack3) , ( OVRLDtrack > Logicthresh) && (OVRLDtrack3 < Logicthresh ), -(10) * OVRLDtrack3 );

  // Variable initializations:
  G_rel_max = 60000;
  G_rel_overload = 4000;
  tau_tr = 0.18;
  K_mrel = 0.0008;
  delta_Ca_ith = 0.00018;
  CSQN_max = 10;
  K_mCSQN = 0.8;
  K_mup = 0.00092;
  I_up = 8.75;
  Ca_NSR_max = 15;
  time_ = ;
  F = ;
  Cai = 0.000123;
  Cao = 1.8;
  Ca_JSR = 1.762;
  Ca_NSR = 1.764;
  V_myo = ;
  A_cap = ;
  i_NaCa = ;
  i_CaCa = ;
  i_p_Ca = ;
  i_Ca_b = ;
  i_Ca_T = ;
  K_mTn = 0.0005;
  K_mCMDN = 0.00238;
  Tn_max = 0.07;
  CMDN_max = 0.05;
  dVdt = ;
  APtrack = 0;
  APtrack2 = 0;
  APtrack3 = 0;
  Cainfluxtrack = 0;
  OVRLDtrack = 0;
  OVRLDtrack2 = 0;
  OVRLDtrack3 = 0;
  CSQNthresh = 0.7;
  Logicthresh = 0.98;
end

model clancy_rudy_2002__ionic_concentrations(Nai, Nao, Ki, Ko, A_cap, V_myo, time_, F, i_Na, i_CaNa, i_Na_b, i_ns_Na, i_NaCa, i_NaK, i_CaK, i_Kr, i_Ks, i_K1, i_Kp, i_K_Na, i_K_ATP, i_ns_K, i_to)

  // Assignment Rules:
  V_myo := 0.68 * volume;

  // Rate Rules:
  Nai' = (-(i_Na + i_CaNa + i_Na_b + i_ns_Na + i_NaCa * 3 + i_NaK * 3) * A_cap) / (V_myo * F);
  Ki' = (-(i_CaK + i_Kr + i_Ks + i_K1 + i_Kp + i_K_Na + i_K_ATP + i_to + i_ns_K + - i_NaK * 2) * A_cap) / (V_myo * F);

  // Variable initializations:
  Nai = 12.3;
  Nao = 132;
  Ki = 140.22;
  Ko = 4.5;
  A_cap = 1.434e-7;
  preplength = 0.001;
  radius = 1.1e-4;
  time_ = ;
  F = ;
  i_Na = ;
  i_CaNa = ;
  i_Na_b = ;
  i_ns_Na = ;
  i_NaCa = ;
  i_NaK = ;
  i_CaK = ;
  i_Kr = ;
  i_Ks = ;
  i_K1 = ;
  i_Kp = ;
  i_K_Na = ;
  i_K_ATP = ;
  i_ns_K = ;
  i_to = ;

  // Unit definitions:
  unit volume = litre;
end

model *clancy_rudy_2002____main()

  // Sub-modules, and any changes to those submodules:
  environment: clancy_rudy_2002__environment(time_);
  membrane: clancy_rudy_2002__membrane(V, R, T, F, time_, i_Na, i_Ca_L, i_Ca_T, i_Kr, i_Ks, i_K_Na, i_K_ATP, i_to, i_NaCa, i_K1, i_Kp, i_p_Ca, i_Na_b, i_Ca_b, i_NaK, i_ns_Ca, dVdt);
  fast_sodium_current: clancy_rudy_2002__fast_sodium_current(i_Na, E_Na, time_, V, R, T, F, Nao, Nai, P_O_Na);
  L_type_Ca_channel: clancy_rudy_2002__L_type_Ca_channel(i_Ca_L, i_CaCa, i_CaK, i_CaNa, gamma_Nai, gamma_Nao, gamma_Ki, gamma_Ko, time_, V, Cai, R, T, F, Cao, Nao, Ko, Nai, Ki, d, f, f_Ca);
  T_type_Ca_channel: clancy_rudy_2002__T_type_Ca_channel(i_Ca_T, E_Ca, time_, V, b, g);
  rapid_delayed_rectifier_potassium_current: clancy_rudy_2002__rapid_delayed_rectifier_potassium_current(i_Kr, time_, V, Ko, Ki, R, T, F, P_O);
  slow_delayed_rectifier_potassium_current: clancy_rudy_2002__slow_delayed_rectifier_potassium_current(i_Ks, time_, V, R, T, F, Ko, Ki, Nao, Nai, Cai, xs1, xs2);
  time_independent_potassium_current: clancy_rudy_2002__time_independent_potassium_current(i_K1, E_K, time_, V, Ko, Ki, R, T, F, K1_infinity);
  plateau_potassium_current: clancy_rudy_2002__plateau_potassium_current(i_Kp, time_, V, E_K);
  sodium_activated_potassium_current: clancy_rudy_2002__sodium_activated_potassium_current(i_K_Na, time_, V, Nai, E_K);
  ATP_sensitive_potassium_current: clancy_rudy_2002__ATP_sensitive_potassium_current(i_K_ATP, time_, V, Ko, E_K);
  transient_outward_current: clancy_rudy_2002__transient_outward_current(i_to, E_K, V, time_, zdv, ydv);
  sarcolemmal_calcium_pump: clancy_rudy_2002__sarcolemmal_calcium_pump(i_p_Ca, time_, Cai);
  sodium_background_current: clancy_rudy_2002__sodium_background_current(i_Na_b, time_, V, E_Na);
  calcium_background_current: clancy_rudy_2002__calcium_background_current(i_Ca_b, E_Ca, time_, V, R, T, F, Cai, Cao);
  sodium_potassium_pump: clancy_rudy_2002__sodium_potassium_pump(i_NaK, time_, V, R, T, F, Nai, Nao, Ko);
  non_specific_calcium_activated_current: clancy_rudy_2002__non_specific_calcium_activated_current(i_ns_Ca, i_ns_Na, i_ns_K, gamma_Nai, gamma_Nao, gamma_Ki, gamma_Ko, R, T, F, Cao, Nao, Ko, Nai, Ki, time_, Cai, V);
  Na_Ca_exchanger: clancy_rudy_2002__Na_Ca_exchanger(i_NaCa, time_, V, R, T, F, Nai, Nao, Cai, Cao);
  calcium_dynamics: clancy_rudy_2002__calcium_dynamics(i_rel, i_up, i_leak, i_tr, time_, F, Cai, Cao, Ca_JSR, Ca_NSR, V_myo, A_cap, i_NaCa, i_CaCa, i_p_Ca, i_Ca_b, i_Ca_T, dVdt);
  ionic_concentrations: clancy_rudy_2002__ionic_concentrations(Nai, Nao, Ki, Ko, A_cap, V_myo, time_, F, i_Na, i_CaNa, i_Na_b, i_ns_Na, i_NaCa, i_NaK, i_CaK, i_Kr, i_Ks, i_K1, i_Kp, i_K_Na, i_K_ATP, i_ns_K, i_to);
end