//Created by libAntimony v2.4 model vanbeek_model_2007__environment(time_) // Variable initializations: time_ = ; end model vanbeek_model_2007__ATP_cyt(ATP_cyt, J_hyd, J_CKMM, J_diff_ATP, V_cyt, time_) // Rate Rules: ATP_cyt' = (J_diff_ATP - (J_hyd + J_CKMM)) / V_cyt; // Variable initializations: ATP_cyt = 5912.77; J_hyd = ; J_CKMM = ; J_diff_ATP = ; V_cyt = ; time_ = ; end model vanbeek_model_2007__ADP_cyt(ADP_cyt, J_hyd, J_CKMM, J_diff_ADP, V_cyt, time_) // Rate Rules: ADP_cyt' = (J_diff_ADP + J_hyd + J_CKMM) / V_cyt; // Variable initializations: ADP_cyt = 64; J_hyd = ; J_CKMM = ; J_diff_ADP = ; V_cyt = ; time_ = ; end model vanbeek_model_2007__PCr_cyt(PCr_cyt, J_CKMM, J_diff_PCr, V_cyt, time_) // Rate Rules: PCr_cyt' = (J_diff_PCr + J_CKMM) / V_cyt; // Variable initializations: PCr_cyt = 5000; J_CKMM = ; J_diff_PCr = ; V_cyt = ; time_ = ; end model vanbeek_model_2007__Cr_cyt(Cr_cyt, J_CKMM, J_diff_Cr, V_cyt, time_) // Rate Rules: Cr_cyt' = (J_diff_Cr - J_CKMM) / V_cyt; // Variable initializations: Cr_cyt = 10500; J_CKMM = ; J_diff_Cr = ; V_cyt = ; time_ = ; end model vanbeek_model_2007__Pi_cyt(Pi_cyt, J_hyd, J_diff_Pi, V_cyt, time_) // Rate Rules: Pi_cyt' = (J_diff_Pi + J_hyd) / V_cyt; // Variable initializations: Pi_cyt = 913; J_hyd = ; J_diff_Pi = ; V_cyt = ; time_ = ; end model vanbeek_model_2007__ATP_ims(ATP_ims, J_CKMi, J_syn, J_diff_ATP, V_ims, time_) // Rate Rules: ATP_ims' = (J_syn - (J_diff_ATP + J_CKMi)) / V_ims; // Variable initializations: ATP_ims = 5912.77; J_CKMi = ; J_syn = ; J_diff_ATP = ; V_ims = ; time_ = ; end model vanbeek_model_2007__ADP_ims(ADP_ims, J_CKMi, J_syn, J_diff_ADP, V_ims, time_) // Rate Rules: ADP_ims' = (J_CKMi - (J_syn + J_diff_ADP)) / V_ims; // Variable initializations: ADP_ims = 39; J_CKMi = ; J_syn = ; J_diff_ADP = ; V_ims = ; time_ = ; end model vanbeek_model_2007__PCr_ims(PCr_ims, J_CKMi, J_diff_PCr, V_ims, time_) // Rate Rules: PCr_ims' = (J_CKMi - J_diff_PCr) / V_ims; // Variable initializations: PCr_ims = 5000; J_CKMi = ; J_diff_PCr = ; V_ims = ; time_ = ; end model vanbeek_model_2007__Cr_ims(Cr_ims, J_CKMi, J_diff_Cr, V_ims, time_) // Rate Rules: Cr_ims' = -(J_CKMi + J_diff_Cr) / V_ims; // Variable initializations: Cr_ims = 10500; J_CKMi = ; J_diff_Cr = ; V_ims = ; time_ = ; end model vanbeek_model_2007__Pi_ims(Pi_ims, J_syn, J_diff_Pi, V_ims, time_) // Rate Rules: Pi_ims' = -(J_syn + J_diff_Pi) / V_ims; // Variable initializations: Pi_ims = 910; J_syn = ; J_diff_Pi = ; V_ims = ; time_ = ; end model vanbeek_model_2007__J_CKMM(J_CKMM, ATP_cyt, ADP_cyt, PCr_cyt, Cr_cyt) // Assignment Rules: J_CKMM := (Vmax_MM_f * ((ATP_cyt * Cr_cyt) / (Kia * Kb)) - Vmax_MM_b * ((ADP_cyt * PCr_cyt) / (Kic * Kd))) / Den_MMCK; Den_MMCK := 1.0 + Cr_cyt / Kib + PCr_cyt / Kid + ATP_cyt * (1.0 / Kia + Cr_cyt / (Kia * Kb)) + ADP_cyt * (1.0 / Kic + PCr_cyt / (Kid * Kc) + Cr_cyt / (Kic * KIb)); KIb := Kib; Kc := (Kic * Kd) / Kid; // Variable initializations: ATP_cyt = ; ADP_cyt = ; PCr_cyt = ; Cr_cyt = ; Kia = 9.0E2; Kb = 1.55E4; Kib = 3.49E4; Kic = 2.224E2; Kd = 1.67E3; Kid = 4.73E3; Vmax_MM_f = 1.144E4; Vmax_MM_b = 4.804E4; end model vanbeek_model_2007__J_CKMi(J_CKMi, ATP_ims, ADP_ims, PCr_ims, Cr_ims) // Assignment Rules: J_CKMi := (Vmax_Mi_f * ((ATP_ims * Cr_ims) / (Kia * Kb)) - Vmax_Mi_b * ((ADP_ims * PCr_ims) / (Kic * Kd))) / Den_MiCK; Den_MiCK := 1.0 + Cr_ims / Kib + PCr_ims / Kid + ATP_ims * (1.0 / Kia + Cr_ims / (Kia * Kb)) + ADP_ims * (1.0 / Kic + PCr_ims / (Kid * Kc) + Cr_ims / (Kic * KIb)); KIb := Kib; Kc := (Kic * Kd) / Kid; // Variable initializations: ATP_ims = ; ADP_ims = ; PCr_ims = ; Cr_ims = ; Kia = 7.5E2; Kb = 5.2E3; Kib = 2.88E4; Kic = 2.048E2; Kd = 5.0E2; Kid = 1.6E3; Vmax_Mi_f = 8.82E2; Vmax_Mi_b = 3.704E3; end model vanbeek_model_2007__J_hyd(J_hyd, time_) // Assignment Rules: J_hyd := piecewise( ((H_ATPmax * ltime) / t_cycle) * 6 , ( geq(ltime, 0)) && (ltime < (1 / 6) * t_cycle ), H_ATPmax * (1 - 6 * (ltime / t_cycle - 1 / 6)) , ( geq(ltime, (1 / 6) * t_cycle)) && (ltime < (1 / 3) * t_cycle ), 0 , ( geq(ltime, (1 / 3) * t_cycle)) && (ltime < t_cycle ) ); H_ATPmax := piecewise( 6 * J_hyd_basis_1 , time_ <= duration_1 , 6 * J_hyd_basis_2 ); t_cycle_1 := 60 / freq_1; t_cycle_2 := 60 / freq_2; t_cycle := piecewise( t_cycle_1 , time_ <= duration_1 , t_cycle_2 ); duration_1 := nb_of_cycles_1 * t_cycle_1; ltime := piecewise( time_ - t_cycle_1 * floor(time_ / t_cycle_1) , time_ <= duration_1 , (time_ - duration_1) - t_cycle_2 * floor((time_ - duration_1) / t_cycle_2) ); // Variable initializations: J_hyd_basis_1 = 4.865e2; J_hyd_basis_2 = 6.276e2; freq_1 = 135; freq_2 = 220; nb_of_cycles_1 = 5; time_ = ; end model vanbeek_model_2007__J_syn(J_syn, Pi_ims, ADP_ims) // Assignment Rules: J_syn := V_max_syn * ((ADP_ims * Pi_ims) / (KPi * KADP * Den_syn)); Den_syn := 1.0 + ADP_ims / KADP + Pi_ims / KPi + (ADP_ims * Pi_ims) / (KADP * KPi); // Variable initializations: Pi_ims = ; ADP_ims = ; KPi = 8E2; KADP = 25; V_max_syn = 1.504E4; end model vanbeek_model_2007__J_diff_ATP(J_diff_ATP, ATP_ims, ATP_cyt) // Assignment Rules: J_diff_ATP := PS_tot_ATP * (ATP_ims - ATP_cyt); // Variable initializations: ATP_ims = ; ATP_cyt = ; PS_tot_ATP = 13.3; end model vanbeek_model_2007__J_diff_ADP(J_diff_ADP, ADP_ims, ADP_cyt) // Assignment Rules: J_diff_ADP := PS_tot_ADP * (ADP_ims - ADP_cyt); // Variable initializations: ADP_ims = ; ADP_cyt = ; PS_tot_ADP = 13.3; end model vanbeek_model_2007__J_diff_PCr(J_diff_PCr, PCr_ims, PCr_cyt) // Assignment Rules: J_diff_PCr := PS_tot_PCr * (PCr_ims - PCr_cyt); // Variable initializations: PCr_ims = ; PCr_cyt = ; PS_tot_PCr = 155.0; end model vanbeek_model_2007__J_diff_Cr(J_diff_Cr, Cr_ims, Cr_cyt) // Assignment Rules: J_diff_Cr := PS_tot_Cr * (Cr_ims - Cr_cyt); // Variable initializations: Cr_ims = ; Cr_cyt = ; PS_tot_Cr = 155.0; end model vanbeek_model_2007__J_diff_Pi(J_diff_Pi, Pi_ims, Pi_cyt) // Assignment Rules: J_diff_Pi := PS_tot_Pi * (Pi_ims - Pi_cyt); // Variable initializations: Pi_ims = ; Pi_cyt = ; PS_tot_Pi = 194.0; end model vanbeek_model_2007__fractional_volumes(V_cyt, V_ims) // Variable initializations: V_cyt = 0.75; V_ims = 0.0625; end model *vanbeek_model_2007____main() // Sub-modules, and any changes to those submodules: environment: vanbeek_model_2007__environment(time_); ATP_cyt: vanbeek_model_2007__ATP_cyt(ATP_cyt0, J_hyd0, J_CKMM0, J_diff_ATP0, V_cyt, time_); ADP_cyt: vanbeek_model_2007__ADP_cyt(ADP_cyt0, J_hyd0, J_CKMM0, J_diff_ADP0, V_cyt, time_); PCr_cyt: vanbeek_model_2007__PCr_cyt(PCr_cyt0, J_CKMM0, J_diff_PCr0, V_cyt, time_); Cr_cyt: vanbeek_model_2007__Cr_cyt(Cr_cyt0, J_CKMM0, J_diff_Cr0, V_cyt, time_); Pi_cyt: vanbeek_model_2007__Pi_cyt(Pi_cyt0, J_hyd0, J_diff_Pi0, V_cyt, time_); ATP_ims: vanbeek_model_2007__ATP_ims(ATP_ims0, J_CKMi0, J_syn0, J_diff_ATP0, V_ims, time_); ADP_ims: vanbeek_model_2007__ADP_ims(ADP_ims0, J_CKMi0, J_syn0, J_diff_ADP0, V_ims, time_); PCr_ims: vanbeek_model_2007__PCr_ims(PCr_ims0, J_CKMi0, J_diff_PCr0, V_ims, time_); Cr_ims: vanbeek_model_2007__Cr_ims(Cr_ims0, J_CKMi0, J_diff_Cr0, V_ims, time_); Pi_ims: vanbeek_model_2007__Pi_ims(Pi_ims0, J_syn0, J_diff_Pi0, V_ims, time_); J_CKMM: vanbeek_model_2007__J_CKMM(J_CKMM0, ATP_cyt0, ADP_cyt0, PCr_cyt0, Cr_cyt0); J_CKMi: vanbeek_model_2007__J_CKMi(J_CKMi0, ATP_ims0, ADP_ims0, PCr_ims0, Cr_ims0); J_hyd: vanbeek_model_2007__J_hyd(J_hyd0, time_); J_syn: vanbeek_model_2007__J_syn(J_syn0, Pi_ims0, ADP_ims0); J_diff_ATP: vanbeek_model_2007__J_diff_ATP(J_diff_ATP0, ATP_ims0, ATP_cyt0); J_diff_ADP: vanbeek_model_2007__J_diff_ADP(J_diff_ADP0, ADP_ims0, ADP_cyt0); J_diff_PCr: vanbeek_model_2007__J_diff_PCr(J_diff_PCr0, PCr_ims0, PCr_cyt0); J_diff_Cr: vanbeek_model_2007__J_diff_Cr(J_diff_Cr0, Cr_ims0, Cr_cyt0); J_diff_Pi: vanbeek_model_2007__J_diff_Pi(J_diff_Pi0, Pi_ims0, Pi_cyt0); fractional_volumes: vanbeek_model_2007__fractional_volumes(V_cyt, V_ims); end