//Created by libAntimony v2.4
model tran_2009__environment(time_)

  // Variable initializations:
  time_ = ;
end

model tran_2009__sarcomere_geometry(SOVFThick, SOVFThin, len_thin, len_thick, len_hbare, SL)

  // Assignment Rules:
  SOVFThick := (len_sovr * 2) / (len_thick - len_hbare);
  SOVFThin := len_sovr / len_thin;
  sovr_ze := piecewise( len_thick / 2 , len_thick / 2 < SL / 2 , SL / 2 );
  sovr_cle := piecewise( SL / 2 - (SL - len_thin) , SL / 2 - (SL - len_thin) > len_hbare / 2 , len_hbare / 2 );
  len_sovr := sovr_ze - sovr_cle;

  // Variable initializations:
  len_thin = ;
  len_thick = ;
  len_hbare = ;
  SL = ;
end

model tran_2009__Ca_binding_to_troponin_to_thin_filament_regulation(TRPNCaL, TRPNCaH, dTRPNCaL, dTRPNCaH, kn_pT, kp_nT, H, H_cons, time_, TmpC, Cai, SOVFThin)

  // Assignment Rules:
  dTRPNCaL := konT * Cai * (1 - TRPNCaL) - koffLT * TRPNCaL;
  dTRPNCaH := konT * Cai * (1 - TRPNCaH) - koffHT * TRPNCaH;
  kn_pT := kn_p * permtot * power(Qkn_p, (TmpC - 37) / 10);
  kp_nT := kp_n * inprmt * power(Qkp_n, (TmpC - 37) / 10);
  H := 10E6 * power(10, - pH);
  H_cons := 10E6 * power(10, -7.15);
  konT := ((power(kdHCa, m) + power(H_cons, m)) / (power(kdHCa, m) + power(H, m))) * (kon * power(Qkon, (TmpC - 37) / 10));
  koffLT := koffL * koffmod * power(Qkoff, (TmpC - 37) / 10);
  koffHT := koffH * koffmod * power(Qkoff, (TmpC - 37) / 10);
  Tropreg := (1 - SOVFThin) * TRPNCaL + SOVFThin * TRPNCaH;
  permtot := root(abs(1 / (1 + power(perm50 / Tropreg, nperm))));
  inprmt := piecewise( 1 / permtot , 1 / permtot < 100 , 100 );

  // Rate Rules:
  TRPNCaL' = dTRPNCaL;
  TRPNCaH' = dTRPNCaH;

  // Variable initializations:
  TRPNCaL = 0.0147730085063734;
  TRPNCaH = 0.13066096561522;
  Qkon = 1.5;
  Qkoff = 1.3;
  Qkn_p = 1.6;
  Qkp_n = 1.6;
  kon = 0.05;
  koffL = 0.25;
  koffH = 0.025;
  perm50 = 0.5;
  nperm = 15;
  kn_p = 0.5;
  kp_n = 0.05;
  koffmod = 1;
  pH = 7.15;
  m = 1;
  kdHCa = 2e-2;
  time_ = ;
  TmpC = ;
  Cai = ;
  SOVFThin = ;
end

model tran_2009__thin_filament_regulation_and_crossbridge_cycling_rates(fappT, gappT, hfT, hbT, gxbT, fapp, gapp, hf, hb, gxb, x_0, TmpC, SOVFThick, xXBpostr, xXBprer)

  // Assignment Rules:
  fappT := fapp * xbmodsp * power(Qfapp, (TmpC - 37) / 10);
  gappT := gapp * gapslmd * xbmodsp * power(Qgapp, (TmpC - 37) / 10);
  hfT := hf * hfmd * xbmodsp * power(Qhf, (TmpC - 37) / 10);
  hbT := hb * hbmd * xbmodsp * power(Qhb, (TmpC - 37) / 10);
  gxbT := gxb * gxbmd * xbmodsp * power(Qgxb, (TmpC - 37) / 10);
  hfmd := exp((- xXBprer / abs(xXBprer)) * hfmdc * power(xXBprer / x_0, 2));
  hbmd := exp(((xXBpostr - x_0) / abs(xXBpostr - x_0)) * hbmdc * power((xXBpostr - x_0) / x_0, 2));
  gxbmd := piecewise( exp(sigmap * power((x_0 - xXBpostr) / x_0, 2)) , xXBpostr < x_0 , exp(sigman * power((xXBpostr - x_0) / x_0, 2)) );
  gapslmd := 1 + (1 - SOVFThick) * gslmod;

  // Variable initializations:
  fapp = 0.5;
  gapp = 0.07;
  hf = 2;
  hb = 0.4;
  gxb = 0.07;
  gslmod = 6;
  hfmdc = 5;
  hbmdc = 0;
  sigmap = 8;
  sigman = 1;
  xbmodsp = 0.2;
  Qfapp = 6.25;
  Qgapp = 2.5;
  Qhf = 6.25;
  Qhb = 6.25;
  Qgxb = 6.25;
  x_0 = ;
  TmpC = ;
  SOVFThick = ;
  xXBpostr = ;
  xXBprer = ;
end

model tran_2009__regulation_and_crossbridge_cycling_state_equations(XBpostr, XBprer, dXBpostr, dXBprer, alpha1_plus, alpha2_plus, alpha3_plus, alpha1_minus, alpha2_minus, alpha3_minus, kMgATP, kdADP, xPi_cons, MgATP_cons, time_, fappT, gappT, hfT, hbT, gxbT, kn_pT, kp_nT, H, H_cons)

  // Assignment Rules:
  dXBpostr := (alpha3_minus * P + alpha2_plus * XBprer) - (alpha2_minus + alpha3_plus) * XBpostr;
  dXBprer := (alpha1_plus * P + alpha2_minus * XBpostr) - (alpha1_minus + alpha2_plus) * XBprer;
  alpha1_plus := fappT;
  alpha2_plus := hfT;
  alpha3_plus := MgATP * (gxbT / MgATP_cons) * ((kdADP + MgADP_cons) / (kdADP + MgADP));
  alpha1_minus := xPi * (gappT / xPi_cons);
  alpha2_minus := H * (hbT / H_cons) * ((kdADP + MgADP_cons) / MgADP_cons) * (MgADP / (kdADP + MgADP));
  alpha3_minus := fxbT;
  fxbT := (kdADP * fappT * hfT * (gxbT / MgATP_cons)) / ((gappT / xPi_cons) * (hbT / H_cons) * kMgATP);
  N := 1 - (P + XBprer + XBpostr);

  // Rate Rules:
  XBpostr' = dXBpostr;
  XBprer' = dXBprer;
  N_NoXB' = kp_nT * P_NoXB - kn_pT * N_NoXB;
  P_NoXB' = kn_pT * N_NoXB - kp_nT * P_NoXB;
  P' = kn_pT * N - (kp_nT + alpha1_plus) * P;

  // Variable initializations:
  XBpostr = 1.81017564383744e-6;
  XBprer = 3.0494964880038e-7;
  kMgATP = 15400e6;
  kdADP = 4;
  xPi_cons = 2e3;
  MgATP_cons = 5e3;
  N_NoXB = 0.999999959256274;
  P_NoXB = 4.07437173988636e-8;
  P = 0.999997834540066;
  MgADP_cons = 36;
  xPi = 2e3;
  MgATP = 5e3;
  MgADP = 36.3;
  time_ = ;
  fappT = ;
  gappT = ;
  hfT = ;
  hbT = ;
  gxbT = ;
  kn_pT = ;
  kp_nT = ;
  H = ;
  H_cons = ;
end

model tran_2009__mean_strain_of_strongly_bound_states(xXBpostr, xXBprer, dxXBpostr, dxXBprer, time_, alpha1_plus, alpha2_plus, alpha3_plus, alpha1_minus, alpha2_minus, alpha3_minus, dSL, x_0, fappT, gappT, hfT, hbT, gxbT)

  // Assignment Rules:
  dxXBpostr := dSL / 2 + (xPsi / dutypostr) * (alpha2_plus * ((xXBprer + x_0) - xXBpostr));
  dxXBprer := dSL / 2 + (xPsi / dutyprer) * (-(alpha1_plus * xXBprer) + alpha2_minus * (xXBpostr - (x_0 + xXBprer)));
  dutyprer := (alpha3_minus * alpha2_minus + alpha3_plus * alpha1_plus + alpha2_minus * alpha1_plus) / (alpha1_plus * alpha2_plus + alpha3_minus * alpha1_minus + alpha3_minus * alpha2_plus + alpha3_minus * alpha2_minus + alpha3_plus * alpha1_plus + alpha2_minus * alpha1_plus + alpha2_plus * alpha3_plus + alpha3_minus * alpha1_minus + alpha3_plus * alpha1_minus);
  dutypostr := (alpha1_plus * alpha2_plus + alpha3_minus * alpha1_minus + alpha3_minus * alpha2_plus) / (alpha1_plus * alpha2_plus + alpha3_minus * alpha1_minus + alpha3_minus * alpha2_plus + alpha3_minus * alpha2_minus + alpha3_plus * alpha1_plus + alpha2_minus * alpha1_plus + alpha2_plus * alpha3_plus + alpha3_minus * alpha1_minus + alpha3_plus * alpha1_minus);

  // Rate Rules:
  xXBpostr' = dxXBpostr;
  xXBprer' = dxXBprer;

  // Variable initializations:
  xXBpostr = 0.00700005394873882;
  xXBprer = 3.41212828972468e-8;
  xPsi = 2;
  time_ = ;
  alpha1_plus = ;
  alpha2_plus = ;
  alpha3_plus = ;
  alpha1_minus = ;
  alpha2_minus = ;
  alpha3_minus = ;
  dSL = ;
  x_0 = ;
  fappT = ;
  gappT = ;
  hfT = ;
  hbT = ;
  gxbT = ;
end

model tran_2009__normalised_active_and_passive_force(SSXBpostr, SSXBprer, dSL, SL, MgATP_cons, xPi_cons, H_cons, kMgATP, kdADP, x_0, fapp, gapp, hf, hb, gxb, time_, fappT, gappT, hfT, hbT, gxbT, XBpostr, XBprer, xXBpostr, xXBprer, SOVFThick)

  // Assignment Rules:
  SSXBpostr := (fapp * hf + fxb * gapp + fxb * hb) / (hf * gxb + hb * gapp + gxb * gapp + fxb * hb + gxb * fapp + hb * fapp + fxb * gapp + fapp * hf + fxb * hb);
  SSXBprer := (fxb * hb + gxb * fapp + hbT * fapp) / (hf * gxb + hb * gapp + gxb * gapp + fxb * hb + gxb * fapp + hb * fapp + fxb * gapp + fapp * hf + fxb * hb);
  dSL := 0;
  Fnordv := kxb * x_0 * SSXBpostr;
  force := kxb * SOVFThick * (xXBpostr * XBpostr + xXBprer * XBprer);
  active := (1 * force) / Fnordv;
  ppforce := ppforce_t + ppforce_c;
  ppforce_t := ((SL - SLrest) / abs(SL - SLrest)) * PCon_t * (exp(PExp_t * abs(SL - SLrest)) - 1);
  ppforce_c := piecewise( PCon_c * (exp(PExp_c * abs(SL - SL_c)) - 1) , SL > SL_c , 0 );
  preload := (abs(SLset - SLrest) / (SLset - SLrest)) * PCon_t * (exp(PExp_t * abs(SLset - SLrest)) - 1);
  afterload := piecewise( KSE * (SLset - SL) , SEon == 1 , 0 );
  fxb := (kdADP * fapp * hf * (gxb / MgATP_cons)) / ((gapp / xPi_cons) * (hb / H_cons) * kMgATP);

  // Rate Rules:
  SL' = dSL;
  intf' = (preload + afterload) - (ppforce + active);

  // Variable initializations:
  SL = 2.2;
  kxb = 120;
  intf = -4.5113452510363e-6;
  SL_c = 2.25;
  SLrest = 1.85;
  SLset = 1.9;
  PCon_t = 0.002;
  PExp_t = 10;
  PCon_c = 0.02;
  PExp_c = 70;
  KSE = 1;
  MgATP_cons = ;
  xPi_cons = ;
  H_cons = ;
  kMgATP = ;
  kdADP = ;
  x_0 = ;
  fapp = ;
  gapp = ;
  hf = ;
  hb = ;
  gxb = ;
  time_ = ;
  fappT = ;
  gappT = ;
  hfT = ;
  hbT = ;
  gxbT = ;
  XBpostr = ;
  XBprer = ;
  xXBpostr = ;
  xXBprer = ;
  SOVFThick = ;
  SEon = 1;
end

model tran_2009__calculation_of_micromolar_per_millisecondes_of_Ca_for_apparent_Ca_binding(dSL, SL, dXBpostr, dXBprer, dxXBpostr, dxXBprer, XBpostr, XBprer, xXBpostr, xXBprer, SSXBpostr, SSXBprer, SOVFThick, SOVFThin, len_thin, len_thick, len_hbare, TRPNCaL, TRPNCaH, dTRPNCaL, dTRPNCaH)

  // Assignment Rules:
  FrSBXB := (XBpostr + XBprer) / (SSXBpostr + SSXBprer);
  dFrSBXB := (dXBpostr + dXBprer) / (SSXBpostr + SSXBprer);
  dsovr_ze := piecewise( -(0.5) * dSL , SL < len_thick , 0 );
  dsovr_cle := piecewise( -(0.5) * dSL , 2 * len_thin - SL > len_hbare , 0 );
  dlen_sovr := dsovr_ze - dsovr_cle;
  dSOVFThick := (2 * dlen_sovr) / (len_thick - len_hbare);
  dSOVFThin := dlen_sovr / len_thin;
  dforce := kxb * dSOVFThick * (xXBpostr * XBpostr + xXBprer * XBprer) + kxb * SOVFThick * (dxXBpostr * XBpostr + xXBpostr * dXBpostr + dxXBprer * XBprer + xXBprer * dXBprer);
  TropTot := Trop_conc * ((1 - SOVFThin) * TRPNCaL + SOVFThin * (FrSBXB * TRPNCaH + (1 - FrSBXB) * TRPNCaL));
  dTropTot := Trop_conc * (- dSOVFThin * TRPNCaL + (1 - SOVFThin) * dTRPNCaL + dSOVFThin * (FrSBXB * TRPNCaH + (1 - FrSBXB) * TRPNCaL) + SOVFThin * ((dFrSBXB * TRPNCaH + FrSBXB * dTRPNCaH + (1 - FrSBXB) * dTRPNCaL) - dFrSBXB * TRPNCaL));

  // Variable initializations:
  kxb = 120;
  Trop_conc = 70;
  dSL = ;
  SL = ;
  dXBpostr = ;
  dXBprer = ;
  dxXBpostr = ;
  dxXBprer = ;
  XBpostr = ;
  XBprer = ;
  xXBpostr = ;
  xXBprer = ;
  SSXBpostr = ;
  SSXBprer = ;
  SOVFThick = ;
  SOVFThin = ;
  len_thin = ;
  len_thick = ;
  len_hbare = ;
  TRPNCaL = ;
  TRPNCaH = ;
  dTRPNCaL = ;
  dTRPNCaH = ;
end

model tran_2009__model_parameters(Cai, len_thin, len_thick, len_hbare, TmpC, x_0)

  // Variable initializations:
  Cai = 200.0;
  len_thin = 1.2;
  len_thick = 1.65;
  len_hbare = 0.1;
  TmpC = 22;
  x_0 = 0.007;
end

model *tran_2009____main()

  // Sub-modules, and any changes to those submodules:
  environment: tran_2009__environment(time_);
  sarcomere_geometry: tran_2009__sarcomere_geometry(SOVFThick, SOVFThin, len_thin, len_thick, len_hbare, SL);
  Ca_binding_to_troponin_to_thin_filament_regulation: tran_2009__Ca_binding_to_troponin_to_thin_filament_regulation(TRPNCaL, TRPNCaH, dTRPNCaL, dTRPNCaH, kn_pT, kp_nT, H, H_cons, time_, TmpC, Cai, SOVFThin);
  thin_filament_regulation_and_crossbridge_cycling_rates: tran_2009__thin_filament_regulation_and_crossbridge_cycling_rates(fappT, gappT, hfT, hbT, gxbT, fapp, gapp, hf, hb, gxb, x_0, TmpC, SOVFThick, xXBpostr, xXBprer);
  regulation_and_crossbridge_cycling_state_equations: tran_2009__regulation_and_crossbridge_cycling_state_equations(XBpostr, XBprer, dXBpostr, dXBprer, alpha1_plus, alpha2_plus, alpha3_plus, alpha1_minus, alpha2_minus, alpha3_minus, kMgATP, kdADP, xPi_cons, MgATP_cons, time_, fappT, gappT, hfT, hbT, gxbT, kn_pT, kp_nT, H, H_cons);
  mean_strain_of_strongly_bound_states: tran_2009__mean_strain_of_strongly_bound_states(xXBpostr, xXBprer, dxXBpostr, dxXBprer, time_, alpha1_plus, alpha2_plus, alpha3_plus, alpha1_minus, alpha2_minus, alpha3_minus, dSL, x_0, fappT, gappT, hfT, hbT, gxbT);
  normalised_active_and_passive_force: tran_2009__normalised_active_and_passive_force(SSXBpostr, SSXBprer, dSL, SL, MgATP_cons, xPi_cons, H_cons, kMgATP, kdADP, x_0, fapp, gapp, hf, hb, gxb, time_, fappT, gappT, hfT, hbT, gxbT, XBpostr, XBprer, xXBpostr, xXBprer, SOVFThick);
  calculation_of_micromolar_per_millisecondes_of_Ca_for_apparent_Ca_binding: tran_2009__calculation_of_micromolar_per_millisecondes_of_Ca_for_apparent_Ca_binding(dSL, SL, dXBpostr, dXBprer, dxXBpostr, dxXBprer, XBpostr, XBprer, xXBpostr, xXBprer, SSXBpostr, SSXBprer, SOVFThick, SOVFThin, len_thin, len_thick, len_hbare, TRPNCaL, TRPNCaH, dTRPNCaL, dTRPNCaH);
  model_parameters: tran_2009__model_parameters(Cai, len_thin, len_thick, len_hbare, TmpC, x_0);
end