//Created by libAntimony v2.4 model vinnakota_kemp_kushmeric_2006_exp45__environment(time_, pH_cy, Par_97, Par_98, pH_calc) // Assignment Rules: pH_cy := piecewise( pH_calc , (( time_ <= 1) || ((time_ > 1) && ((addbuffer == 0)) )), pHstat ); addbuffer := Par_97; pHstat := Par_98; // Variable initializations: time_ = ; Par_97 = ; Par_98 = ; pH_calc = ; end model vinnakota_kemp_kushmeric_2006_exp45__global_parameters(R, T1, T, I, Par_90, Par_94) // Assignment Rules: T := Par_94; I := Par_90; // Variable initializations: R = 8.314e-3; T1 = 298.15; Par_90 = ; Par_94 = ; end model vinnakota_kemp_kushmeric_2006_exp45__parameters(Par_1, Par_2, Par_3, Par_4, Par_5, Par_6, Par_7, Par_8, Par_9, Par_10, Par_11, Par_12, Par_13, Par_14, Par_15, Par_16, Par_17, Par_18, Par_19, Par_20, Par_21, Par_22, Par_23, Par_24, Par_25, Par_26, Par_27, Par_28, Par_29, Par_30, Par_31, Par_32, Par_33, Par_34, Par_35, Par_36, Par_37, Par_38, Par_39, Par_40, Par_41, Par_42, Par_43, Par_44, Par_45, Par_46, Par_47, Par_48, Par_49, Par_50, Par_51, Par_52, Par_53, Par_54, Par_55, Par_56, Par_57, Par_58, Par_59, Par_60, Par_61, Par_62, Par_63, Par_64, Par_65, Par_66, Par_67, Par_68, Par_69, Par_70, Par_71, Par_72, Par_73, Par_74, Par_75, Par_76, Par_77, Par_78, Par_79, Par_80, Par_81, Par_82, Par_83, Par_84, Par_85, Par_86, Par_87, Par_88, Par_89, Par_90, Par_91, Par_92, Par_93, Par_94, Par_95, Par_96, Par_97, Par_98, Par_99, Par_100) // Assignment Rules: Par_1 := 1.9 * 5E-2; Par_2 := 0.002; Par_3 := 1.7E-3; Par_4 := 4E-3; Par_5 := 2E-3; Par_6 := 4.7E-3; Par_7 := 1.5E-4; Par_8 := 2.7E-3; Par_9 := 1.01E-2; Par_10 := 2E-4; Par_11 := 4.6E-3; Par_12 := 1.5E-2; Par_13 := 1.5E-3; Par_14 := 7.4E-3; Par_15 := 4.4E-3; Par_16 := 0.00266054976219; Par_17 := 2E-2; Par_18 := 1.7505240494613; Par_19 := 1.9 * 4.8E-1; Par_20 := 6.3E-5; Par_21 := 3E-5; Par_22 := 1.9 * 8.8E-1; Par_23 := 4.8E-4; Par_24 := 1.19E-4; Par_25 := 1.9 * 5.6E-2; Par_26 := 1.8E-4; Par_27 := 2E-2; Par_28 := 8E-5; Par_29 := 2.5E-4; Par_30 := 4.02E-3; Par_31 := 4.02E-3; Par_32 := 2.7E-3; Par_33 := 2.7E-3; Par_34 := 8.7E-4; Par_35 := 6E-5; Par_36 := 1E-2; Par_37 := 1E-2; Par_38 := 13; Par_39 := 1.9 * 0.01065914307349; Par_40 := 5E-5; Par_41 := 2E-3; Par_42 := 1E-3; Par_43 := 1.9 * 12; Par_44 := 3.2E-4; Par_45 := 6.1E-4; Par_46 := 1.9 * 8.25E-2; Par_47 := 1.8E-4; Par_48 := 1.2E-5; Par_49 := 2.2E-4; Par_50 := 8E-6; Par_51 := 1.9 * 1.265E0; Par_52 := 2.5E-6; Par_53 := 9E-5; Par_54 := 2.9E-4; Par_55 := 8E-7; Par_56 := 3.3E-6; Par_57 := 1.9 * 1.12E0; Par_58 := 2E-3; Par_59 := 8E-6; Par_60 := 1.2E-3; Par_61 := 3.5E-4; Par_62 := 1.9 * 1.12E0; Par_63 := 2E-4; Par_64 := 1.4E-5; Par_65 := 1.9 * 1.92E-1; Par_66 := 1E-4; Par_67 := 3.7E-4; Par_68 := 1.9 * 1.44E0; Par_69 := 8E-5; Par_70 := 3E-4; Par_71 := 7.05E-3; Par_72 := 1.13E-3; Par_73 := 1.9 * 1.92E0; Par_74 := 3.35E-4; Par_75 := 2E-6; Par_76 := 1.7E-2; Par_77 := 8.49E-4; Par_78 := 1.9 * 5E-1; Par_79 := 1.11E-3; Par_80 := 3.5E-3; Par_81 := 1.35E-4; Par_82 := 3.9E-3; Par_83 := 3.8E-3; Par_84 := 1.9 * 8.8E-1; Par_85 := 3.2E-4; Par_86 := 2.7E-4; Par_87 := 3.5E-4; Par_88 := 5E-3; Par_89 := 1E-4; Par_90 := 1E-1; Par_91 := 1.5E-2; Par_92 := 2.5E-2; Par_93 := 1E-2; Par_94 := 310.15; Par_95 := 0.005; Par_96 := 0.08; Par_97 := 1; Par_98 := 7.3; Par_99 := 0; Par_100 := 45; end model vinnakota_kemp_kushmeric_2006_exp45__equilibrium_constants(mgT, k, c0, Par_95, Par_96) // Assignment Rules: mgT := Par_95; k := Par_96; c0 := 1; // Variable initializations: Par_95 = ; Par_96 = ; end model vinnakota_kemp_kushmeric_2006_exp45__correction_factors(mgPi, dNavgPidH, dNavgPidmg, dmgPidmg, dmgPidpH, mgATP2, dNavgATPdH, dNavgATPdmg, dmgATP2dmg, dmgATP2dpH, mgADP, dNavgADPdH, dNavgADPdmg, dmgADPdmg, dmgADPdpH, mgAMP, dNavgAMPdH, dNavgAMPdmg, dmgAMPdmg, dmgAMPdpH, mgPCR, dNavgPCRdH, dNavgPCRdmg, dmgPCRdmg, dmgPCRdpH, dNavgCRdH, dNavgCRdmg, mgG1P, dNavgG1PdH, dNavgG1Pdmg, dmgG1Pdmg, dmgG1PdpH, dNavgG6PdH, dNavgG6Pdmg, dNavgF6PdH, dNavgF6Pdmg, mgFDP, dNavgFDPdH, dNavgFDPdmg, dmgFDPdmg, dmgFDPdpH, dNavgGAPdH, dNavgGAPdmg, mgG3P, dNavgG3PdH, dNavgG3Pdmg, dmgG3Pdmg, dmgG3PdpH, mgDHAP, dNavgDHAPdH, dNavgDHAPdmg, dmgDHAPdmg, dmgDHAPdpH, dNavg13DPGdH, dNavg13DPGdmg, dNavg3PGdH, dNavg3PGdmg, mg2PG, dNavg2PGdH, dNavg2PGdmg, dmg2PGdmg, dmg2PGdpH, mgPEP, dNavgPEPdH, dNavgPEPdmg, dmgPEPdmg, dmgPEPdpH, dNavgPYRdH, dNavgPYRdmg, mgLAC, dNavgLACdH, dNavgLACdmg, dmgLACdmg, dmgLACdpH, deltaH_CK, Kapp_CK, deltaH_ADK, Kapp_ADK, deltaH_GP, Kapp_GP, deltaH_PGLM, Kapp_PGLM, deltaH_PGI, Kapp_PGI, deltaH_PFK, Kapp_PFK, deltaH_ALD, Kapp_ALD, deltaH_TPI, Kapp_TPI, deltaH_GAPDH, Kapp_GAPDH, deltaH_G3PDH, Kapp_G3PDH, deltaH_PGK, Kapp_PGK, deltaH_PGM, Kapp_PGM, deltaH_ENOL, Kapp_ENOL, deltaH_PK, Kapp_PK, deltaH_LDH, Kapp_LDH, deltaH_ATPase, Kapp_ATPase, R, T1, T, I, mgT, k, c0, mg, pH_cy) // Assignment Rules: RT2dadT := 1.4775; B := 1.6; Icorr := (RT2dadT * root(I)) / (1 + B * root(I)); I1 := 0.1; alphadebye := 1.17582; IcorrpKa := (1 * alphadebye * (root(I1) / (1 + B * root(I1)) - root(I) / (1 + B * root(I)))) / ln(10); TcorrpKa := (1 / T - 1 / T1) / (ln(10) * R); RTalpha := 2.91482; IcorrdeltaGpof := (RTalpha * root(I)) / (1 + B * root(I)); pKak_Pi := 0.5; deltaH1o_Pi := 3; deltaHmgo_Pi := -(2.9); deltaH1_Pi := deltaH1o_Pi + Icorr * ((power(2, 2) + power(1, 2)) - power(1, 2)); deltaHmg_Pi := deltaHmgo_Pi + Icorr * ((power(2, 2) + power(2, 2)) - power(0, 2)); pKa1_Pi := 6.75 + (IcorrpKa / 1) * ((power(2, 2) + power(1, 2)) - power(1, 2)) + TcorrpKa * deltaH1_Pi; pKamg_Pi := 1.65 + (IcorrpKa / 1) * ((power(2, 2) + power(1, 2)) - power(1, 2)) + TcorrpKa * deltaHmg_Pi; P_Pi := 1 + power(10, - pH_cy + pKa1_Pi) + (mg / c0) * power(10, pKamg_Pi) + (k / c0) * power(10, pKak_Pi); HPi2 := 1 / P_Pi; H2Pi1 := power(10, - pH_cy + pKa1_Pi) * HPi2; kPi := (k / c0) * power(10, pKak_Pi) * HPi2; mgPi := (mg / c0) * power(10, pKamg_Pi) * HPi2; Navg_Pi := 1 * H2Pi1; dNavgPidH := (power(10, pKa1_Pi) * (P_Pi - power(10, - pH_cy + pKa1_Pi))) / (c0 * power(P_Pi, 2)); dNavgPidmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_Pi + pKamg_Pi)) / power(P_Pi, 2); dmgPidmg := ((P_Pi * power(10, pKamg_Pi)) / c0 - ((mg / c0) * power(10, 2 * pKamg_Pi)) / c0) / power(P_Pi, 2); dmgPidpH := ((mg / c0) * power(10, - pH_cy + pKa1_Pi + pKamg_Pi) * ln(10)) / power(P_Pi, 2); NH_HPi2 := 1; deltaGof_HPi2 := -(1096.1); deltaGpof_HPi2 := (deltaGof_HPi2 + NH_HPi2 * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_HPi2); deltaH1o_ATP := -(5); deltaHmgo_ATP := -(18); deltaHko_ATP := -(1); deltaH1_ATP := deltaH1o_ATP + Icorr * ((power(4, 2) + power(1, 2)) - power(3, 2)); deltaHmg_ATP := deltaHmgo_ATP + Icorr * ((power(4, 2) + power(2, 2)) - power(2, 2)); deltaHk_ATP := deltaHko_ATP + Icorr * ((power(4, 2) + power(1, 2)) - power(3, 2)); pKa1_ATP := 6.48 + (IcorrpKa / 1) * ((power(4, 2) + power(1, 2)) - power(3, 2)) + TcorrpKa * deltaH1_ATP; pKamg_ATP := 4.19 + (IcorrpKa / 1) * ((power(4, 2) + power(2, 2)) - power(2, 2)) + TcorrpKa * deltaHmg_ATP; pKak_ATP := 1.17 + (IcorrpKa / 1) * ((power(4, 2) + power(1, 2)) - power(3, 2)) + TcorrpKa * deltaHk_ATP; P_ATP := 1 + power(10, - pH_cy + pKa1_ATP) + (mg / c0) * power(10, pKamg_ATP) + (k / c0) * power(10, pKak_ATP); ATP4 := 1 / P_ATP; HATP3 := power(10, - pH_cy + pKa1_ATP) * ATP4; mgATP2 := (mg / c0) * power(10, pKamg_ATP) * ATP4; kATP := (k / c0) * power(10, pKak_ATP) * ATP4; Navg_ATP := 0 * ATP4 + 1 * HATP3 + 0 * mgATP2 + 0 * kATP; dNavgATPdH := (power(10, pKa1_ATP) * (P_ATP - power(10, - pH_cy + pKa1_ATP))) / (c0 * power(P_ATP, 2)); dNavgATPdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_ATP + pKamg_ATP)) / power(P_ATP, 2); dmgATP2dmg := ((P_ATP * power(10, pKamg_ATP)) / c0 - ((mg / c0) * power(10, 2 * pKamg_ATP)) / c0) / power(P_ATP, 2); dmgATP2dpH := ((mg / c0) * power(10, - pH_cy + pKa1_ATP + pKamg_ATP) * ln(10)) / power(P_ATP, 2); NH_ATP4 := 12; deltaGof_ATP4 := -(2768.1); deltaGpof_ATP4 := (deltaGof_ATP4 + NH_ATP4 * R * T * ln(10) * pH_cy) - IcorrdeltaGpof * (16 - NH_ATP4); pKak_ADP := 1; deltaH1o_ADP := -(3); deltaHmgo_ADP := -(15); deltaH1_ADP := deltaH1o_ADP + Icorr * ((power(3, 2) + power(1, 2)) - power(2, 2)); deltaHmg_ADP := deltaHmgo_ADP + Icorr * ((power(3, 2) + power(2, 2)) - power(1, 2)); pKa1_ADP := 6.38 + (IcorrpKa / 1) * ((power(3, 2) + power(1, 2)) - power(2, 2)) + TcorrpKa * deltaH1_ADP; pKamg_ADP := 3.25 + (IcorrpKa / 1) * ((power(3, 2) + power(2, 2)) - power(1, 2)) + TcorrpKa * deltaHmg_ADP; P_ADP := 1 + power(10, - pH_cy + pKa1_ADP) + (mg / c0) * power(10, pKamg_ADP) + (k / c0) * power(10, pKak_ADP); ADP3 := 1 / P_ADP; HADP2 := power(10, - pH_cy + pKa1_ADP) * ADP3; mgADP := ((ADP3 * mg) / c0) * power(10, pKamg_ADP); kADP := ((ADP3 * k) / c0) * power(10, pKak_ADP); Navg_ADP := 0 * ADP3 + 1 * HADP2 + 0 * mgADP + 0 * kADP; dNavgADPdH := (power(10, pKa1_ADP) * (P_ADP - power(10, - pH_cy + pKa1_ADP))) / (c0 * power(P_ADP, 2)); dNavgADPdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_ADP + pKamg_ADP)) / power(P_ADP, 2); dmgADPdmg := ((P_ADP * power(10, pKamg_ADP)) / c0 - ((mg / c0) * power(10, 2 * pKamg_ADP)) / c0) / power(P_ADP, 2); dmgADPdpH := ((mg / c0) * power(10, - pH_cy + pKa1_ADP + pKamg_ADP) * ln(10)) / power(P_ADP, 2); NH_ADP3 := 12; deltaGof_ADP3 := -(1906.13); deltaGpof_ADP3 := (deltaGof_ADP3 + NH_ADP3 * R * T * ln(10) * pH_cy) - IcorrdeltaGpof * (9 - NH_ADP3); deltaH1o_AMP := -(3); deltaHmgo_AMP := -(7.5); deltaH1_AMP := deltaH1o_AMP + Icorr * ((power(2, 2) + power(1, 2)) - power(1, 2)); deltaHmg_AMP := deltaHmgo_AMP + Icorr * ((power(2, 2) + power(2, 2)) - power(0, 2)); pKa1_AMP := 6.29 + (IcorrpKa / 1) * ((power(2, 2) + power(1, 2)) - power(1, 2)) + TcorrpKa * deltaH1_AMP; pKamg_AMP := 1.92 + (IcorrpKa / 1) * ((power(2, 2) + power(2, 2)) - power(0, 2)) + TcorrpKa * deltaHmg_AMP; P_AMP := 1 + power(10, pKa1_AMP - pH_cy) + (mg / c0) * power(10, pKamg_AMP); AMP2 := 1 / P_AMP; HAMP1 := AMP2 * power(10, pKa1_AMP - pH_cy); mgAMP := (mg / c0) * power(10, pKamg_AMP) * AMP2; Navg_AMP := 0 * AMP2 + HAMP1 + 0 * mgAMP; dNavgAMPdH := (power(10, pKa1_AMP) * (P_AMP - power(10, - pH_cy + pKa1_AMP))) / (c0 * power(P_AMP, 2)); dNavgAMPdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_AMP + pKamg_AMP)) / power(P_AMP, 2); dmgAMPdmg := ((P_AMP * power(10, pKamg_AMP)) / c0 - ((mg / c0) * power(10, 2 * pKamg_AMP)) / c0) / power(P_AMP, 2); dmgAMPdpH := ((mg / c0) * power(10, - pH_cy + pKa1_AMP + pKamg_AMP) * ln(10)) / power(P_AMP, 2); NH_AMP2 := 12; deltaGof_AMP2 := -(1040.45); deltaGpof_AMP2 := (deltaGof_AMP2 + NH_AMP2 * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_AMP2); pKak_PCR := 0.31; deltaH1o_PCR := 2.66; deltaHmgo_PCR := 8.19; deltaH1_PCR := deltaH1o_PCR + Icorr * ((power(2, 2) + power(1, 2)) - power(1, 2)); deltaHmg_PCR := deltaHmgo_PCR + Icorr * ((power(2, 2) + power(2, 2)) - power(0, 2)); pKa1_PCR := 4.5 + (IcorrpKa / 1) * ((power(2, 2) + power(1, 2)) - power(1, 2)) + TcorrpKa * deltaH1_PCR; pKamg_PCR := 1.6 + (IcorrpKa / 1) * ((power(2, 2) + power(2, 2)) - power(0, 2)) + TcorrpKa * deltaHmg_PCR; P_PCR := 1 + power(10, - pH_cy + pKa1_PCR) + (mg / c0) * power(10, pKamg_PCR) + (k / c0) * power(10, pKak_PCR); HPCR := 1 / P_PCR; H2PCR := power(10, - pH_cy + pKa1_PCR) * HPCR; kPCR := (k / c0) * power(10, pKak_PCR) * HPCR; mgPCR := (mg / c0) * power(10, pKamg_PCR) * HPCR; Navg_PCR := H2PCR; dNavgPCRdH := (power(10, pKa1_PCR) * (P_PCR - power(10, - pH_cy + pKa1_PCR))) / (c0 * power(P_PCR, 2)); dNavgPCRdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_PCR + pKamg_PCR)) / power(P_PCR, 2); dmgPCRdmg := ((P_PCR * power(10, pKamg_PCR)) / c0 - ((mg / c0) * power(10, 2 * pKamg_PCR)) / c0) / power(P_PCR, 2); dmgPCRdpH := ((mg / c0) * power(10, - pH_cy + pKa1_PCR + pKamg_PCR) * ln(10)) / power(P_PCR, 2); NH_HPCR := 8; pKa1_CR := 2.3; P_CR := 1 + power(10, - pH_cy + pKa1_CR); HCR := 1 / P_CR; H2CR := HCR * power(10, - pH_cy + pKa1_CR); Navg_CR := 0 * HCR + 1 * H2CR; dNavgCRdH := (power(10, pKa1_CR) * (P_CR - power(10, - pH_cy + pKa1_CR))) / (c0 * power(P_CR, 2)); dNavgCRdmg := 0; NH_HCR := 9; deltaH1o_G1P := -(1.7); deltaHmgo_G1P := -(12); deltaH1_G1P := deltaH1o_G1P + Icorr * ((power(2, 2) + power(1, 2)) - power(1, 2)); deltaHmg_G1P := deltaHmgo_G1P + Icorr * ((power(2, 2) + power(2, 2)) - power(0, 2)); pKa1_G1P := 6.09 + (IcorrpKa / 1) * ((power(2, 2) + power(1, 2)) - power(1, 2)) + TcorrpKa * deltaH1_G1P; pKamg_G1P := 2.48 + (IcorrpKa / 1) * ((power(2, 2) + power(2, 2)) - power(0, 2)) + TcorrpKa * deltaHmg_G1P; P_G1P := 1 + power(10, - pH_cy) * power(10, pKa1_G1P) + (mg / c0) * power(10, pKamg_G1P); UG1P := 1 / P_G1P; HG1P := UG1P * power(10, - pH_cy + pKa1_G1P); mgG1P := ((UG1P * mg) / c0) * power(10, pKamg_G1P); Navg_G1P := HG1P; dNavgG1PdH := (power(10, pKa1_G1P) * (P_G1P - power(10, - pH_cy + pKa1_G1P))) / (c0 * power(P_G1P, 2)); dNavgG1Pdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_G1P + pKamg_G1P)) / power(P_G1P, 2); dmgG1Pdmg := ((P_G1P * power(10, pKamg_G1P)) / c0 - ((mg / c0) * power(10, 2 * pKamg_G1P)) / c0) / power(P_G1P, 2); dmgG1PdpH := ((mg / c0) * power(10, - pH_cy + pKa1_G1P + pKamg_G1P) * ln(10)) / power(P_G1P, 2); NH_UG1P := 11; deltaGof_UG1P := -(1756.87); deltaGpof_UG1P := (deltaGof_UG1P + NH_UG1P * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_UG1P); pKa1_G6P := 6.11; P_G6P := 1 + power(10, - pH_cy + pKa1_G6P); UG6P := 1 / P_G6P; HG6P := UG6P * power(10, - pH_cy + pKa1_G6P); Navg_G6P := HG6P; dNavgG6PdH := (power(10, pKa1_G6P) * (P_G6P - power(10, - pH_cy + pKa1_G6P))) / (c0 * power(P_G6P, 2)); dNavgG6Pdmg := 0; NH_UG6P := 11; deltaGof_UG6P := -(1763.94); deltaGpof_UG6P := (deltaGof_UG6P + NH_UG6P * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_UG6P); pKa1_F6P := 5.89; P_F6P := 1 + power(10, - pH_cy + pKa1_F6P); UF6P := 1 / P_F6P; HF6P := UF6P * power(10, - pH_cy + pKa1_F6P); Navg_F6P := HF6P; dNavgF6PdH := (power(10, pKa1_F6P) * (P_F6P - power(10, - pH_cy + pKa1_F6P))) / (c0 * power(P_F6P, 2)); dNavgF6Pdmg := 0; NH_UF6P := 11; deltaGof_UF6P := -(1760.8); deltaGpof_UF6P := (deltaGof_UF6P + NH_UF6P * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_UF6P); pKa1_FDP := 6.4; pKa2_FDP := 5.92; pKamg_FDP := 2.7; P_FDP := 1 + power(10, - pH_cy + pKa1_FDP) + power(10, -(2) * pH_cy + pKa1_FDP + pKa2_FDP) + (mg / c0) * power(10, pKamg_FDP); UFDP := 1 / P_FDP; HFDP := UFDP * power(10, - pH_cy + pKa1_FDP); H2FDP := UFDP * power(10, -(2) * pH_cy + pKa1_FDP + pKa2_FDP); mgFDP := ((UFDP * mg) / c0) * power(10, pKamg_FDP); Navg_FDP := HFDP + 2 * H2FDP; dNavgFDPdH := (P_FDP * (power(10, pKa1_FDP) + 2 * power(10, - pH_cy + pKa1_FDP + pKa2_FDP)) - (power(10, - pH_cy + pKa1_FDP) + 2 * power(10, -(2) * pH_cy + pKa1_FDP + pKa2_FDP)) * (power(10, pKa1_FDP) + 2 * power(10, - pH_cy + pKa1_FDP + pKa2_FDP))) / (c0 * power(P_FDP, 2)); dNavgFDPdmg := (-(power(10, - pH_cy + pKa1_FDP) + 2 * power(10, -(2) * pH_cy + pKa1_FDP + pKa2_FDP)) * power(10, pKamg_FDP)) / (c0 * power(P_FDP, 2)); dmgFDPdmg := ((P_FDP * power(10, pKamg_FDP)) / c0 - ((mg / c0) * power(10, 2 * pKamg_FDP)) / c0) / power(P_FDP, 2); dmgFDPdpH := ((mg / c0) * power(10, pKamg_FDP) * (P_FDP * power(10, - pH_cy + pKa1_FDP) * ln(10) - power(10, -(2) * pH_cy + pKa1_FDP + pKa2_FDP) * 2 * ln(10))) / power(P_FDP, 2); NH_UFDP := 10; deltaGof_UFDP := -(2601.4); deltaGpof_UFDP := (deltaGof_UFDP + NH_UFDP * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (16 - NH_UFDP); pKa1_GAP := 6.45; P_GAP := 1 + power(10, - pH_cy + pKa1_GAP); UGAP := 1 / P_GAP; HGAP := UGAP * power(10, - pH_cy + pKa1_GAP); Navg_GAP := HGAP; dNavgGAPdH := (power(10, pKa1_GAP) * (P_GAP - power(10, - pH_cy + pKa1_GAP))) / (c0 * power(P_GAP, 2)); dNavgGAPdmg := 0; NH_UGAP := 5; deltaGof_UGAP := -(1288.6); deltaGpof_UGAP := (deltaGof_UGAP + NH_UGAP * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_UGAP); pKamg_G3P := 1.63; deltaH1o_G3P := -(3.1); deltaH1_G3P := deltaH1o_G3P + Icorr * ((power(2, 2) + power(1, 2)) - power(1, 2)); pKa1_G3P := 6.22 + (IcorrpKa / 1) * ((power(2, 2) + power(1, 2)) - power(1, 2)) + TcorrpKa * deltaH1_G3P; P_G3P := 1 + power(10, - pH_cy + pKa1_G3P) + (mg / c0) * power(10, pKamg_G3P); UG3P := 1 / P_G3P; HG3P := UG3P * power(10, - pH_cy + pKa1_G3P); mgG3P := ((UG3P * mg) / c0) * power(10, pKamg_G3P); Navg_G3P := HG3P; dNavgG3PdH := (power(10, pKa1_G3P) * (P_G3P - power(10, - pH_cy + pKa1_G3P))) / (c0 * power(P_G3P, 2)); dNavgG3Pdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_G3P + pKamg_G3P)) / power(P_G3P, 2); dmgG3Pdmg := ((P_G3P * power(10, pKamg_G3P)) / c0 - ((mg / c0) * power(10, 2 * pKamg_G3P)) / c0) / power(P_G3P, 2); dmgG3PdpH := ((mg / c0) * power(10, - pH_cy + pKa1_G3P + pKamg_G3P) * ln(10)) / power(P_G3P, 2); NH_UG3P := 7; deltaGof_UG3P := -(1339.25); deltaGpof_UG3P := (deltaGof_UG3P + NH_UG3P * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_UG3P); pKa1_DHAP := 5.9; pKamg_DHAP := 1.57; P_DHAP := 1 + power(10, - pH_cy + pKa1_DHAP) + (mg / c0) * power(10, pKamg_DHAP); UDHAP := 1 / P_DHAP; HDHAP := UDHAP * power(10, - pH_cy + pKa1_DHAP); mgDHAP := ((UDHAP * mg) / c0) * power(10, pKamg_DHAP); Navg_DHAP := HDHAP; dNavgDHAPdH := (power(10, pKa1_DHAP) * (P_DHAP - power(10, - pH_cy + pKa1_DHAP))) / (c0 * power(P_DHAP, 2)); dNavgDHAPdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_DHAP + pKamg_DHAP)) / power(P_DHAP, 2); dmgDHAPdmg := ((P_DHAP * power(10, pKamg_DHAP)) / c0 - ((mg / c0) * power(10, 2 * pKamg_DHAP)) / c0) / power(P_DHAP, 2); dmgDHAPdpH := ((mg / c0) * power(10, - pH_cy + pKa1_DHAP + pKamg_DHAP) * ln(10)) / power(P_DHAP, 2); NH_UDHAP := 5; deltaGof_UDHAP := -(1296.26); deltaGpof_UDHAP := (deltaGof_UDHAP + NH_UDHAP * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_UDHAP); pKa1_13DPG := 7.5; P_13DPG := 1 + power(10, - pH_cy + pKa1_13DPG); U13DPG := 1 / P_13DPG; H13DPG := U13DPG * power(10, - pH_cy + pKa1_13DPG); Navg_13DPG := H13DPG; dNavg13DPGdH := (power(10, pKa1_13DPG) * (P_13DPG - power(10, - pH_cy + pKa1_13DPG))) / (c0 * power(P_13DPG, 2)); dNavg13DPGdmg := 0; NH_U13DPG := 4; deltaGof_U13DPG := -(2356.14); deltaGpof_U13DPG := (deltaGof_U13DPG + NH_U13DPG * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (16 - NH_U13DPG); pKa1_3PG := 6.21; P_3PG := 1 + power(10, - pH_cy + 6.21); U3PG := 1 / P_3PG; H3PG := U3PG * power(10, - pH_cy + 6.21); Navg_3PG := H3PG; dNavg3PGdH := (power(10, pKa1_3PG) * (P_3PG - power(10, - pH_cy + pKa1_3PG))) / (c0 * power(P_3PG, 2)); dNavg3PGdmg := 0; NH_U3PG := 4; deltaGof_U3PG := -(1502.54); deltaGpof_U3PG := (deltaGof_U3PG + NH_U3PG * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (9 - NH_U3PG); pKa1_2PG := 7; pKamg_2PG := 2.45; pKak_2PG := 1.18; P_2PG := 1 + power(10, - pH_cy + pKa1_2PG) + (mg / c0) * power(10, pKamg_2PG) + (k / c0) * power(10, pKak_2PG); U2PG := 1 / P_2PG; H2PG := U2PG * power(10, - pH_cy + pKa1_2PG); mg2PG := ((U2PG * mg) / c0) * power(10, pKamg_2PG); k2PG := ((U2PG * k) / c0) * power(10, pKak_2PG); Navg_2PG := H2PG; dNavg2PGdH := (power(10, pKa1_2PG) * (P_2PG - power(10, - pH_cy + pKa1_2PG))) / (c0 * power(P_2PG, 2)); dNavg2PGdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_2PG + pKamg_2PG)) / power(P_2PG, 2); dmg2PGdmg := ((P_2PG * power(10, pKamg_2PG)) / c0 - ((mg / c0) * power(10, 2 * pKamg_2PG)) / c0) / power(P_2PG, 2); dmg2PGdpH := ((mg / c0) * power(10, - pH_cy + pKa1_2PG + pKamg_2PG) * ln(10)) / power(P_2PG, 2); NH_U2PG := 4; deltaGof_U2PG := -(1496.38); deltaGpof_U2PG := (deltaGof_U2PG + NH_U2PG * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (9 - NH_U2PG); pKa1_PEP := 6.35; pKamg_PEP := 2.26; pKak_PEP := 1.08; P_PEP := 1 + power(10, pKa1_PEP - pH_cy) + (mg / c0) * power(10, pKamg_PEP) + (k / c0) * power(10, pKak_PEP); UPEP := 1 / P_PEP; HPEP := UPEP * power(10, pKa1_PEP - pH_cy); kPEP := ((UPEP * k) / c0) * power(10, pKak_PEP); mgPEP := ((UPEP * mg) / c0) * power(10, pKamg_PEP); Navg_PEP := HPEP; dNavgPEPdH := (power(10, pKa1_PEP) * (P_PEP - power(10, - pH_cy + pKa1_PEP))) / (c0 * power(P_PEP, 2)); dNavgPEPdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_PEP + pKamg_PEP)) / power(P_PEP, 2); dmgPEPdmg := ((P_PEP * power(10, pKamg_PEP)) / c0 - ((mg / c0) * power(10, 2 * pKamg_PEP)) / c0) / power(P_PEP, 2); dmgPEPdpH := ((mg / c0) * power(10, - pH_cy + pKa1_PEP + pKamg_PEP) * ln(10)) / power(P_PEP, 2); NH_UPEP := 2; deltaGof_UPEP := -(1263.65); deltaGpof_UPEP := (deltaGof_UPEP + NH_UPEP * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (9 - NH_UPEP); pKa1_PYR := 2.49; P_PYR := 1 + power(10, - pH_cy + pKa1_PYR); UPYR := 1 / P_PYR; HPYR := UPYR * power(10, - pH_cy + pKa1_PYR); Navg_PYR := HPYR; dNavgPYRdH := (power(10, pKa1_PYR) * (P_PYR - power(10, - pH_cy + pKa1_PYR))) / (c0 * power(P_PYR, 2)); dNavgPYRdmg := 0; NH_UPYR := 3; deltaGof_UPYR := -(472.27); deltaGpof_UPYR := (deltaGof_UPYR + NH_UPYR * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (1 - NH_UPYR); pKamg_LAC := 0.98; deltaH1o_LAC := -(0.33); deltaH1_LAC := deltaH1o_LAC + Icorr * ((power(1, 2) + power(1, 2)) - power(0, 2)); pKa1_LAC := 3.67 + (IcorrpKa / 1) * ((power(1, 2) + power(1, 2)) - power(0, 2)) + TcorrpKa * deltaH1_LAC; P_LAC := 1 + power(10, - pH_cy + pKa1_LAC) + (mg / c0) * power(10, pKamg_LAC); ULAC := 1 / P_LAC; HLAC := ULAC * power(10, - pH_cy + pKa1_LAC); mgLAC := (mg / c0) * power(10, pKamg_LAC) * ULAC; Navg_LAC := HLAC; dNavgLACdH := (power(10, pKa1_LAC) * (P_LAC - power(10, - pH_cy + pKa1_LAC))) / (c0 * power(P_LAC, 2)); dNavgLACdmg := ((-power(10, - pH_cy) / c0) * power(10, pKa1_LAC + pKamg_LAC)) / power(P_LAC, 2); dmgLACdmg := ((P_LAC * power(10, pKamg_LAC)) / c0 - ((mg / c0) * power(10, 2 * pKamg_LAC)) / c0) / power(P_LAC, 2); dmgLACdpH := ((mg / c0) * power(10, - pH_cy + pKa1_LAC + pKamg_LAC) * ln(10)) / power(P_LAC, 2); NH_ULAC := 5; deltaGof_ULAC := -(516.72); deltaGpof_ULAC := (deltaGof_ULAC + NH_ULAC * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (1 - NH_ULAC); dNH_GLY := -(10); deltaGpo_GLY := 655.7 + dNH_GLY * ln(10) * R * T * pH_cy; NH_NAD := 26; deltaGof_NAD := 0; deltaGpof_NAD := (deltaGof_NAD + NH_NAD * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (1 - NH_NAD); NH_NADH := 27; deltaGof_NADH := 22.65; deltaGpof_NADH := (deltaGof_NADH + NH_NADH * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (4 - NH_NADH); NH_H2O := 2; deltaGof_H2O := -(237.19); deltaGpof_H2O := (deltaGof_H2O + NH_H2O * ln(10) * R * T * pH_cy) - IcorrdeltaGpof * (0 - NH_H2O); NH_H := 1; deltaGof_H := 0; deltaGpof_H := deltaGof_H + NH_H * ln(10) * R * T * pH_cy; deltaH_CK := (((Navg_ATP + Navg_CR) - Navg_PCR) - Navg_ADP) + (((NH_ATP4 + NH_HCR) - NH_HPCR) - NH_ADP3); Kref_CK := 2.58E8; deltaHo_CKo := -(17.55); deltaH1_CK := deltaHo_CKo + Icorr * (((power(2, 2) + power(3, 2) + power(1, 2)) - power(4, 2)) - power(0, 2)); Kref_CKI := exp(ln(Kref_CK) + (alphadebye * root(I) * (((power(2, 2) + power(3, 2) + power(1, 2)) - power(4, 2)) - power(0, 2))) / (1 + B * root(I))); Kref_CKT := power(10, log(Kref_CKI) - TcorrpKa * deltaH1_CK); deltaGpo_CK := - R * T * ln(Kref_CKT); Kapp_CK := (exp(- deltaGpo_CK / (R * T)) * power(10, - pH_cy) * P_ATP * P_CR) / (P_PCR * P_ADP); deltaH_ADK := ((2 * Navg_ADP - Navg_ATP) - Navg_AMP) + ((2 * NH_ADP3 - NH_ATP4) - NH_AMP2); deltaGpo_ADK := (2 * deltaGpof_ADP3 - deltaGpof_ATP4) - deltaGpof_AMP2; Kapp_ADK := (exp(- deltaGpo_ADK / (R * T)) * power(P_ADP, 2)) / (P_ATP * P_AMP); deltaH_GP := (Navg_G1P - Navg_Pi) + (1 - NH_HPi2); deltaGpo_GP := (deltaGpo_GLY + deltaGpof_UG1P) - deltaGpof_HPi2; Kapp_GP := (exp(- deltaGpo_GP / (R * T)) * P_G1P) / P_Pi; deltaH_PGLM := (Navg_G6P - Navg_G1P) + (NH_UG6P - NH_UG1P); deltaGpo_PGLM := deltaGpof_UG6P - deltaGpof_UG1P; Kapp_PGLM := (exp(- deltaGpo_PGLM / (R * T)) * P_G6P) / P_G1P; deltaH_PGI := (Navg_F6P - Navg_G6P) + (NH_UF6P - NH_UG6P); deltaGpo_PGI := deltaGpof_UF6P - deltaGpof_UG6P; Kapp_PGI := (exp(- deltaGpo_PGI / (R * T)) * P_F6P) / P_G6P; deltaH_PFK := (((((Navg_ADP + Navg_FDP) - Navg_F6P) - Navg_ATP) + NH_ADP3 + NH_UFDP) - NH_UF6P) - NH_ATP4; deltaGpo_PFK := ((deltaGpof_UFDP + deltaGpof_ADP3 + deltaGpof_H) - deltaGpof_UF6P) - deltaGpof_ATP4; Kapp_PFK := (exp(- deltaGpo_PFK / (R * T)) * P_FDP * P_ADP) / (P_F6P * P_ATP * power(10, - pH_cy)); deltaH_ALD := ((Navg_DHAP + Navg_GAP) - Navg_FDP) + ((NH_UDHAP + NH_UGAP) - NH_UFDP); deltaGpo_ALD := (deltaGpof_UDHAP + deltaGpof_UGAP) - deltaGpof_UFDP; Kapp_ALD := (1 * exp(- deltaGpo_ALD / (R * T)) * P_GAP * P_FDP) / P_DHAP; deltaH_TPI := (Navg_DHAP - Navg_GAP) + (NH_UDHAP - NH_UGAP); deltaGpo_TPI := deltaGpof_UDHAP - deltaGpof_UGAP; Kapp_TPI := (exp(- deltaGpo_TPI / (R * T)) * P_DHAP) / P_GAP; deltaH_GAPDH := ((Navg_13DPG - Navg_GAP) - Navg_Pi) + ((((NH_U13DPG + NH_NADH) - NH_UGAP) - NH_HPi2) - NH_NAD); deltaGpo_GAPDH := (((deltaGpof_U13DPG + deltaGpof_NADH + deltaGpof_H) - deltaGpof_HPi2) - deltaGpof_UGAP) - deltaGpof_NAD; Kapp_GAPDH := (exp(- deltaGpo_GAPDH / (R * T)) * P_13DPG) / (P_Pi * P_GAP * power(10, - pH_cy) * 1); deltaH_G3PDH := (Navg_DHAP - Navg_G3P) + (((NH_UDHAP + NH_NADH) - NH_NAD) - NH_UG3P); deltaGpo_G3PDH := ((deltaGpof_H + deltaGpof_NADH + deltaGpof_UDHAP) - deltaGpof_NAD) - deltaGpof_UG3P; Kapp_G3PDH := (exp(- deltaGpo_G3PDH / (R * T)) * P_DHAP) / (P_G3P * power(10, - pH_cy)); deltaH_PGK := (((Navg_3PG + Navg_ATP) - Navg_13DPG) - Navg_ADP) + (((NH_U3PG + NH_ATP4) - NH_U13DPG) - NH_ADP3); deltaGpo_PGK := ((deltaGpof_ATP4 + deltaGpof_U3PG) - deltaGpof_U13DPG) - deltaGpof_ADP3; Kapp_PGK := (exp(- deltaGpo_PGK / (R * T)) * P_ATP * P_3PG) / (P_13DPG * P_ADP); deltaH_PGM := (Navg_2PG - Navg_3PG) + (NH_U2PG - NH_U3PG); deltaGpo_PGM := deltaGpof_U2PG - deltaGpof_U3PG; Kapp_PGM := (exp(- deltaGpo_PGM / (R * T)) * P_2PG) / P_3PG; deltaH_ENOL := (Navg_PEP - Navg_2PG) + ((NH_H2O + NH_UPEP) - NH_U2PG); deltaGpo_ENOL := (deltaGpof_H2O + deltaGpof_UPEP) - deltaGpof_U2PG; Kapp_ENOL := (exp(- deltaGpo_ENOL / (R * T)) * P_PEP) / P_2PG; deltaH_PK := (((Navg_PYR + Navg_ATP) - Navg_PEP) - Navg_ADP) + (((NH_UPYR + NH_ATP4) - NH_UPEP) - NH_ADP3); deltaGpo_PK := (((deltaGpof_UPYR + deltaGpof_ATP4) - deltaGpof_H) - deltaGpof_UPEP) - deltaGpof_ADP3; Kapp_PK := (exp(- deltaGpo_PK / (R * T)) * P_PYR * P_ATP * power(10, - pH_cy)) / (P_PEP * P_ADP); deltaH_LDH := (Navg_LAC - Navg_PYR) + (((NH_ULAC + NH_NAD) - NH_UPYR) - NH_NADH); deltaGpo_LDH := (((deltaGpof_ULAC + deltaGpof_NAD) - deltaGpof_UPYR) - deltaGpof_NADH) - deltaGpof_H; Kapp_LDH := (exp(- deltaGpo_LDH / (R * T)) * P_LAC * power(10, - pH_cy)) / P_PYR; deltaH_ATPase := ((Navg_ADP + Navg_Pi) - Navg_ATP) + (((NH_ADP3 + NH_HPi2) - NH_ATP4) - NH_H2O); deltaGpo_ATPase := ((deltaGpof_ADP3 + deltaGpof_HPi2 + deltaGpof_H) - deltaGpof_H2O) - deltaGpof_ATP4; Kapp_ATPase := (exp(- deltaGpo_ATPase / (R * T)) * P_ADP * P_Pi) / (P_ATP * power(10, - pH_cy)); // Variable initializations: R = ; T1 = ; T = ; I = ; mgT = ; k = ; c0 = ; mg = ; pH_cy = ; end model vinnakota_kemp_kushmeric_2006_exp45__glycogen_phosphorylase(Vfgly, expno, fracA, flux_GPa, time_, G1P, Pi_, Gly, pH_cy, Kapp_GP, Par_1, Par_2, Par_3, Par_4, Par_5, Par_6, Par_7, Par_8, Par_9, Par_100) // Assignment Rules: Vfgly := Par_1; expno := Par_100; fracA := piecewise( Par_2 , expno != 45 , 0.001 , time_ < 40 , 0.004 , ( geq(time_, 40)) && (time_ < 80 ), 0.01 , ( geq(time_, 80)) && (time_ < 100 ), 0.04 , geq(time_, 100) ); KgpA_glyf := Par_3; KgpA_pi := Par_4; KgpA_igly := Par_5; KgpA_ipi := Par_6; KgpA_glyb := Par_7; KgpA_g1p := Par_8; KgpA_ig1p := Par_9; Dglya := 1 + Gly / KgpA_glyf + Pi_ / KgpA_pi + (Gly * Pi_) / (KgpA_glyf * KgpA_ipi) + Gly / KgpA_glyb + G1P / KgpA_g1p + (Gly * G1P) / (KgpA_ig1p * KgpA_glyb); pa := 1.404 / (1 + power(10, 5.94 - pH_cy) + power(10, pH_cy - 7.29)); VbglyA := (pa * Vfgly * KgpA_glyb * KgpA_ig1p) / (KgpA_igly * KgpA_pi * Kapp_GP); glyAF := ((pa * Vfgly * Pi_) / (KgpA_igly * KgpA_pi)) / Dglya; glyAR := ((VbglyA * Gly) / (KgpA_glyb * KgpA_ig1p)) / Dglya; flux_GPa := fracA * (Gly * glyAF - G1P * glyAR); // Variable initializations: time_ = ; G1P = ; Pi_ = ; Gly = ; pH_cy = ; Kapp_GP = ; Par_1 = ; Par_2 = ; Par_3 = ; Par_4 = ; Par_5 = ; Par_6 = ; Par_7 = ; Par_8 = ; Par_9 = ; Par_100 = ; end model vinnakota_kemp_kushmeric_2006_exp45__glycogen_phosphorylase_B(flux_GPb, fracA, Vfgly, AMP, G1P, Gly, Pi_, Kapp_GP, pH_cy, Par_10, Par_11, Par_12, Par_13, Par_14, Par_15, Par_16, Par_17, Par_18) // Assignment Rules: fracB := 1 - fracA; KgpB_pi := Par_10; KgpB_ipi := Par_11; KgpB_iglyf := Par_12; KgpB_g1p := Par_13; KgpB_ig1p := Par_14; KgpB_iglyb := Par_15; Kgp_amp := Par_16; interactioncoeff := Par_17; nH := Par_18; M := (power(AMP / Kgp_amp, nH) / interactioncoeff) / (1 + power(AMP / Kgp_amp, nH) / interactioncoeff); Dglyb := 1 + Gly / KgpB_iglyf + Pi_ / KgpB_ipi + Gly / KgpB_iglyb + G1P / KgpB_ig1p + (Gly * Pi_) / (KgpB_iglyf * KgpB_pi) + (Gly * G1P) / (KgpB_g1p * KgpB_iglyb); pb := 1.75 / (1 + power(10, 6.12 - pH_cy) + power(10, pH_cy - 7.03)); VbglyB := (pb * Vfgly * KgpB_g1p * KgpB_iglyb) / (KgpB_iglyf * KgpB_pi * Kapp_GP); glyBF := ((pb * M * Vfgly * Pi_) / (KgpB_iglyf * KgpB_pi)) / Dglyb; glyBR := ((M * VbglyB * Gly) / (KgpB_g1p * KgpB_iglyb)) / Dglyb; flux_GPb := fracB * (Gly * glyBF - G1P * glyBR); // Variable initializations: fracA = ; Vfgly = ; AMP = ; G1P = ; Gly = ; Pi_ = ; Kapp_GP = ; pH_cy = ; Par_10 = ; Par_11 = ; Par_12 = ; Par_13 = ; Par_14 = ; Par_15 = ; Par_16 = ; Par_17 = ; Par_18 = ; end model vinnakota_kemp_kushmeric_2006_exp45__PGLM(v_PGLM, pH_cy, Kapp_PGLM, G1P, G6P, Par_19, Par_20, Par_21) // Assignment Rules: Vffpglm := Par_19; Kpglm_g1p := Par_20; Kpglm_g6p := Par_21; Vfpglm := (Vffpglm * 1.329) / (1 + power(10, - pH_cy + 6.64) + power(10, pH_cy - 8.36)); Vbpglm := (Vfpglm * Kpglm_g6p) / (Kpglm_g1p * Kapp_PGLM); v_PGLM := ((Vfpglm * G1P) / Kpglm_g1p - (Vbpglm * G6P) / Kpglm_g6p) / (1 + G1P / Kpglm_g1p + G6P / Kpglm_g6p); // Variable initializations: pH_cy = ; Kapp_PGLM = ; G1P = ; G6P = ; Par_19 = ; Par_20 = ; Par_21 = ; end model vinnakota_kemp_kushmeric_2006_exp45__PGI(v_PGI, pH_cy, Kapp_PGI, F6P, G6P, Par_22, Par_23, Par_24) // Assignment Rules: Vbbpgi := Par_22; Kpgi_g6p := Par_23; Kpgi_f6p := Par_24; Vbpgi := Vbbpgi / (1 + power(10, - pH_cy + 6.94) + power(10, pH_cy - 9.35)); Vfpgi := ((Vbpgi * Kpgi_g6p) / Kpgi_f6p) * Kapp_PGI; v_PGI := ((Vfpgi * G6P) / Kpgi_g6p - (Vbpgi * F6P) / Kpgi_f6p) / (1 + F6P / Kpgi_f6p + G6P / Kpgi_g6p); // Variable initializations: pH_cy = ; Kapp_PGI = ; F6P = ; G6P = ; Par_22 = ; Par_23 = ; Par_24 = ; end model vinnakota_kemp_kushmeric_2006_exp45__PFK(v_PFK, pH_cy, Kapp_PFK, F6P, FBP, AMP, ADP, ATP, Par_25, Par_26, Par_27, Par_28, Par_29, Par_30, Par_31, Par_32, Par_33, Par_34, Par_35, Par_36, Par_37, Par_38) // Assignment Rules: Vffpfk := Par_25; Kpfk_f6p := Par_26; Kpfk_f6pT := Par_27; Kpfk_atp := Par_28; Kpfk_atpT := Par_29; Kpfk_fbp := Par_30; Kpfk_fbpT := Par_31; Kpfk_adp := Par_32; Kpfk_adpT := Par_33; Kpfki := Par_34; Kmpfk := Par_35; d := Par_36; e_ := Par_37; Lo := Par_38; Vfpfk := Vffpfk / (1 + power(pH_cy / 6.8, -(30))); Vbpfk := (Vfpfk * Kpfk_fbp * Kpfk_adp) / (Kpfk_f6p * Kpfk_atp * Kapp_PFK); L := Lo * power((((1 + ATP / Kpfki) / (1 + (d * ATP) / Kpfki)) * (1 + (e_ * AMP) / Kmpfk)) / (1 + AMP / Kmpfk), 4); alpha := (Kpfk_f6p * Kpfk_atp) / (Kpfk_f6pT * Kpfk_atpT); Delta := (1 + F6P / Kpfk_f6p) * (1 + ATP / Kpfk_atp) + FBP / Kpfk_fbp + (ADP / Kpfk_adp) * (1 + FBP / Kpfk_fbp); Deltap := (1 + F6P / Kpfk_f6pT) * (1 + ATP / Kpfk_atpT) + FBP / Kpfk_fbpT + (ADP / Kpfk_adpT) * (1 + FBP / Kpfk_fbpT); v_PFK := ((((Vfpfk * F6P * ATP) / (Kpfk_f6p * Kpfk_atp)) / Delta - ((Vbpfk * ADP * FBP) / (Kpfk_adp * Kpfk_fbp)) / Delta) * (1 + alpha * L * power(Deltap / Delta, 3))) / (1 + L * power(Deltap / Delta, 4)); // Variable initializations: pH_cy = ; Kapp_PFK = ; F6P = ; FBP = ; AMP = ; ADP = ; ATP = ; Par_25 = ; Par_26 = ; Par_27 = ; Par_28 = ; Par_29 = ; Par_30 = ; Par_31 = ; Par_32 = ; Par_33 = ; Par_34 = ; Par_35 = ; Par_36 = ; Par_37 = ; Par_38 = ; end model vinnakota_kemp_kushmeric_2006_exp45__ALD(v_ALD, pH_cy, Kapp_ALD, DHAP, FBP, GAP, Par_39, Par_40, Par_41, Par_42) // Assignment Rules: Vffald := Par_39; Kald_fbp := Par_40; Kald_dhap := Par_41; Kald_gap := Par_42; Vfald := (Vffald * 1.013) / (1 + power(10, - pH_cy + 5.32) + power(10, pH_cy - 9.15)); Vbald := (Vfald * Kald_gap * Kald_dhap) / (Kald_fbp * Kapp_ALD); v_ALD := ((Vfald * FBP) / Kald_fbp - (Vbald * GAP * DHAP) / (Kald_gap * Kald_dhap)) / (1 + FBP / Kald_fbp + GAP / Kald_gap + DHAP / Kald_dhap); // Variable initializations: pH_cy = ; Kapp_ALD = ; DHAP = ; FBP = ; GAP = ; Par_39 = ; Par_40 = ; Par_41 = ; Par_42 = ; end model vinnakota_kemp_kushmeric_2006_exp45__TPI(v_TPI, Kapp_TPI, DHAP, GAP, Par_43, Par_44, Par_45) // Assignment Rules: Vfftpi := Par_43; Ktpi_gap := Par_44; Ktpi_dhap := Par_45; Vftpi := Vfftpi; Vbtpi := (Vftpi * Ktpi_dhap) / (Ktpi_gap * Kapp_TPI); v_TPI := ((Vftpi * GAP) / Ktpi_gap - (Vbtpi * DHAP) / Ktpi_dhap) / (1 + GAP / Ktpi_gap + DHAP / Ktpi_dhap); // Variable initializations: Kapp_TPI = ; DHAP = ; GAP = ; Par_43 = ; Par_44 = ; Par_45 = ; end model vinnakota_kemp_kushmeric_2006_exp45__G3PDH(v_G3PDH, Kapp_G3PDH, DHAP, G3P, NAD, NADH, Par_46, Par_47, Par_48, Par_49, Par_50) // Assignment Rules: Vbbg3pdh := Par_46; Kg3pdh_g3p := Par_47; Kg3pdh_nad := Par_48; Kg3pdh_dhap := Par_49; Kg3pdh_nadh := Par_50; Dg3pdh := (1 + G3P / Kg3pdh_g3p + NADH / Kg3pdh_nadh) * (1 + DHAP / Kg3pdh_dhap + NAD / Kg3pdh_nadh); Vbg3pdh := Vbbg3pdh; Vfg3pdh := (Vbg3pdh * Kg3pdh_g3p * Kg3pdh_nad * Kapp_G3PDH) / (Kg3pdh_dhap * Kg3pdh_nadh); v_G3PDH := ((Vfg3pdh * G3P * NAD) / (Kg3pdh_g3p * Kg3pdh_nad) - (Vbg3pdh * DHAP * NADH) / (Kg3pdh_dhap * Kg3pdh_nadh)) / Dg3pdh; // Variable initializations: Kapp_G3PDH = ; DHAP = ; G3P = ; NAD = ; NADH = ; Par_46 = ; Par_47 = ; Par_48 = ; Par_49 = ; Par_50 = ; end model vinnakota_kemp_kushmeric_2006_exp45__GAPDH(v_GAPDH, pH_cy, Kapp_GAPDH, BPG, GAP, NAD, NADH, Pi_, Par_51, Par_52, Par_53, Par_54, Par_55, Par_56) // Assignment Rules: Vffgad := Par_51; Kgapdh_gap := Par_52; Kgapdh_nad := Par_53; Kgapdh_pi := Par_54; Kgapdh_bpg := Par_55; Kgapdh_nadh := Par_56; Dgap := 1 + Pi_ / Kgapdh_pi + GAP / Kgapdh_gap + NAD / Kgapdh_nad + (GAP * NAD) / (Kgapdh_gap * Kgapdh_nad) + (GAP * NAD * Pi_) / (Kgapdh_gap * Kgapdh_nad * Kgapdh_pi) + BPG / Kgapdh_bpg + NADH / Kgapdh_nadh + (BPG * NADH) / (Kgapdh_nadh * Kgapdh_bpg); Vfgad := Vffgad * 0.0007 * exp(pH_cy * 0.8979); Vbgad := (Vfgad * Kgapdh_bpg * Kgapdh_nadh) / (Kgapdh_gap * Kgapdh_pi * Kgapdh_nad * Kapp_GAPDH); v_GAPDH := ((Vfgad * GAP * NAD * Pi_) / (Kgapdh_nad * Kgapdh_gap * Kgapdh_pi) - (Vbgad * BPG * NADH) / (Kgapdh_bpg * Kgapdh_nadh)) / Dgap; // Variable initializations: pH_cy = ; Kapp_GAPDH = ; BPG = ; GAP = ; NAD = ; NADH = ; Pi_ = ; Par_51 = ; Par_52 = ; Par_53 = ; Par_54 = ; Par_55 = ; Par_56 = ; end model vinnakota_kemp_kushmeric_2006_exp45__PGK(v_PGK, Kapp_PGK, BPG, P3G, ADP, ATP, Par_57, Par_58, Par_59, Par_60, Par_61) // Assignment Rules: Vbbpgk := Par_57; Kpgk_bpg := Par_58; Kpgk_adp := Par_59; Kpgk_3pg := Par_60; Kpgk_atp := Par_61; Vbpgk := Vbbpgk; Vfpgk := ((Vbpgk * Kpgk_bpg * Kpgk_adp) / (Kpgk_3pg * Kpgk_atp)) * Kapp_PGK; D_PGK := 1 + ADP / Kpgk_adp + BPG / Kpgk_bpg + (BPG * ADP) / (Kpgk_bpg * Kpgk_adp) + P3G / Kpgk_3pg + ATP / Kpgk_atp + (P3G * ATP) / (Kpgk_3pg * Kpgk_atp); v_PGK := ((Vfpgk * BPG * ADP) / (Kpgk_adp * Kpgk_bpg) - (Vbpgk * ATP * P3G) / (Kpgk_atp * Kpgk_3pg)) / D_PGK; // Variable initializations: Kapp_PGK = ; BPG = ; P3G = ; ADP = ; ATP = ; Par_57 = ; Par_58 = ; Par_59 = ; Par_60 = ; Par_61 = ; end model vinnakota_kemp_kushmeric_2006_exp45__PGM(v_PGM, pH_cy, Kapp_PGM, P2G, P3G, Par_62, Par_63, Par_64) // Assignment Rules: Vffpgm := Par_62; Kpgm_3pg := Par_63; Kpgm_2pg := Par_64; Vfpgm := (Vffpgm * 0.989) / (1 + power(10, - pH_cy + 5.62) + power(10, pH_cy - 8.74)); Vbpgm := (Vfpgm * Kpgm_2pg) / (Kpgm_3pg * Kapp_PGM); v_PGM := ((Vfpgm * P3G) / Kpgm_3pg - (Vbpgm * P2G) / Kpgm_2pg) / (1 + P3G / Kpgm_3pg + P2G / Kpgm_2pg); // Variable initializations: pH_cy = ; Kapp_PGM = ; P2G = ; P3G = ; Par_62 = ; Par_63 = ; Par_64 = ; end model vinnakota_kemp_kushmeric_2006_exp45__ENOL(v_ENOL, Kapp_ENOL, P2G, PEP, Par_65, Par_66, Par_67) // Assignment Rules: Vffen := Par_65; Ken_2pg := Par_66; Ken_pep := Par_67; Vfen := Vffen; Vben := (Vfen * Ken_pep) / (Ken_2pg * Kapp_ENOL); v_ENOL := ((Vfen * P2G) / Ken_2pg - (Vben * PEP) / Ken_pep) / (1 + PEP / Ken_pep + P2G / Ken_2pg); // Variable initializations: Kapp_ENOL = ; P2G = ; PEP = ; Par_65 = ; Par_66 = ; Par_67 = ; end model vinnakota_kemp_kushmeric_2006_exp45__PK(v_PK, pH_cy, Kapp_PK, PEP, PYR, ADP, ATP, Par_68, Par_69, Par_70, Par_71, Par_72) // Assignment Rules: Vffpk := Par_68; Kpk_pep := Par_69; Kpk_adp := Par_70; Kpk_pyr := Par_71; Kpk_atp := Par_72; Vfpk := (Vffpk * 1.05) / (1 + power(10, - pH_cy + 5.58) + power(10, pH_cy - 8.79)); Vbpk := (Vfpk * Kpk_pyr * Kpk_atp) / (Kpk_pep * Kpk_adp * Kapp_PK); v_PK := ((Vfpk * PEP * ADP) / (Kpk_pep * Kpk_adp) - (Vbpk * PYR * ATP) / (Kpk_pyr * Kpk_atp)) / (1 + PEP / Kpk_pep + ADP / Kpk_adp + (PEP * ADP) / (Kpk_pep * Kpk_adp) + ATP / Kpk_atp + PYR / Kpk_pyr + (PYR * ATP) / (Kpk_pyr * Kpk_atp)); // Variable initializations: pH_cy = ; Kapp_PK = ; PEP = ; PYR = ; ADP = ; ATP = ; Par_68 = ; Par_69 = ; Par_70 = ; Par_71 = ; Par_72 = ; end model vinnakota_kemp_kushmeric_2006_exp45__LDH(v_LDH, pH_cy, Kapp_LDH, LAC, NAD, NADH, PYR, Par_73, Par_74, Par_75, Par_76, Par_77) // Assignment Rules: Vffldh := Par_73; Kldh_pyr := Par_74; Kldh_nadh := Par_75; Kldh_lac := Par_76; Kldh_nad := Par_77; Vfldh := Vffldh * (-(0.1134) * pH_cy + 1.6069); Vbldh := (Vfldh * Kldh_lac * Kldh_nad) / (Kldh_pyr * Kldh_nadh * Kapp_LDH); v_LDH := ((Vfldh * PYR * NADH) / (Kldh_pyr * Kldh_nadh) - (Vbldh * LAC * NAD) / (Kldh_lac * Kldh_nad)) / (1 + PYR / Kldh_pyr + NADH / Kldh_nadh + (PYR * NADH) / (Kldh_pyr * Kldh_nadh) + LAC / Kldh_lac + NAD / Kldh_nad + (LAC * NAD) / (Kldh_lac * Kldh_nad)); // Variable initializations: pH_cy = ; Kapp_LDH = ; LAC = ; NAD = ; NADH = ; PYR = ; Par_73 = ; Par_74 = ; Par_75 = ; Par_76 = ; Par_77 = ; end model vinnakota_kemp_kushmeric_2006_exp45__ATPase(ATPase, time_, ATP, expno, Par_88, Par_89) // Assignment Rules: VmaxATPase := piecewise( Par_88 , ( (expno != 5)) && ((expno != 45) ), Par_88 , (( (expno != 5)) && ((expno == 45)) && (geq(time_, 110) )), Par_88 , ( (expno == 5)) && (time_ > 30 ), 0 ); Katp_ATPase := Par_89; ATPase := (VmaxATPase * ATP) / (Katp_ATPase + ATP); // Variable initializations: time_ = ; ATP = ; expno = ; Par_88 = ; Par_89 = ; end model vinnakota_kemp_kushmeric_2006_exp45__creatine_kinase(CK, Kapp_CK, ADP, ATP, Cr, PCr, Par_78, Par_79, Par_80, Par_81, Par_82, Par_83) // Assignment Rules: VforCK := Par_78; Kck_pcr := Par_79; Kck_iatp := Par_80; Kck_iadp := Par_81; Kck_ipcr := Par_82; Kck_cr := Par_83; VrevCK := ((VforCK / Kapp_CK) * Kck_iatp * Kck_cr) / (Kck_iadp * Kck_pcr); CK := ((VrevCK * ATP * Cr) / (Kck_iatp * Kck_cr) - (VforCK * ADP * PCr) / (Kck_iadp * Kck_pcr)) / (1 + ADP / Kck_iadp + PCr / Kck_ipcr + (PCr * ADP) / (Kck_iadp * Kck_pcr) + ATP / Kck_iatp + (Cr * ATP) / (Kck_cr * Kck_iatp)); // Variable initializations: Kapp_CK = ; ADP = ; ATP = ; Cr = ; PCr = ; Par_78 = ; Par_79 = ; Par_80 = ; Par_81 = ; Par_82 = ; Par_83 = ; end model vinnakota_kemp_kushmeric_2006_exp45__adenylate_kinase(ADK, Kapp_ADK, AMP, ADP, ATP, Par_84, Par_85, Par_86, Par_87) // Assignment Rules: Vfadk := Par_84; Kadk_amp := Par_85; Kadk_atp := Par_86; Kadk_adp := Par_87; Vbadk := (Vfadk * power(Kadk_adp, 2)) / (Kadk_amp * Kadk_atp * Kapp_ADK); ADK := ((Vfadk * ATP * AMP) / (Kadk_atp * Kadk_amp) - Vbadk * power(ADP / Kadk_adp, 2)) / (1 + ATP / Kadk_atp + AMP / Kadk_amp + (ATP * AMP) / (Kadk_atp * Kadk_amp) + (2 * ADP) / Kadk_adp + power(ADP, 2) / power(Kadk_adp, 2)); // Variable initializations: Kapp_ADK = ; AMP = ; ADP = ; ATP = ; Par_84 = ; Par_85 = ; Par_86 = ; Par_87 = ; end model vinnakota_kemp_kushmeric_2006_exp45__buffer_capacity(protons_consumed, pHODEterm1, pHODEterm2, denom_mgODE, RHSterm1_mgODE, denomMgpHODE, pH_cy, PCr, Cr, NAD, NADH, ATP, ADP, AMP, Pi_, Gly, G1P, G6P, F6P, FBP, DHAP, G3P, GAP, BPG, P3G, P2G, PEP, PYR, LAC, ADK, CK, dNavg13DPGdH, dNavg3PGdH, dNavg2PGdH, dNavgADPdH, dNavgAMPdH, dNavgATPdH, dNavgCRdH, dNavgDHAPdH, dNavgF6PdH, dNavgFDPdH, dNavgG1PdH, dNavgG3PdH, dNavgG6PdH, dNavgGAPdH, dNavgLACdH, dNavgPCRdH, dNavgPEPdH, dNavgPYRdH, dNavgPidH, deltaH_ADK, deltaH_ALD, deltaH_CK, deltaH_ENOL, deltaH_G3PDH, deltaH_GAPDH, deltaH_GP, deltaH_LDH, deltaH_PFK, deltaH_PGI, deltaH_PGK, deltaH_PGLM, deltaH_PGM, deltaH_PK, deltaH_TPI, dNavg13DPGdmg, dNavg2PGdmg, dNavg3PGdmg, dNavgADPdmg, dNavgAMPdmg, dNavgATPdmg, dNavgCRdmg, dNavgDHAPdmg, dNavgF6Pdmg, dNavgFDPdmg, dNavgG1Pdmg, dNavgG3Pdmg, dNavgG6Pdmg, dNavgGAPdmg, dNavgLACdmg, dNavgPCRdmg, dNavgPEPdmg, dNavgPYRdmg, dNavgPidmg, dmg2PGdmg, dmgATP2dmg, dmgADPdmg, dmgAMPdmg, dmgDHAPdmg, dmgFDPdmg, dmgG1Pdmg, dmgG3Pdmg, dmgLACdmg, dmgPCRdmg, dmgPEPdmg, dmgPidmg, dmg2PGdpH, dmgADPdpH, dmgAMPdpH, dmgATP2dpH, dmgDHAPdpH, dmgFDPdpH, dmgG1PdpH, dmgG3PdpH, dmgLACdpH, dmgPCRdpH, dmgPEPdpH, dmgPidpH, flux_GPa, flux_GPb, v_ALD, v_ENOL, v_G3PDH, v_GAPDH, v_LDH, v_PFK, v_PGI, v_PGK, v_PGLM, v_PGM, v_PK, v_TPI, c0, Par_91, Par_92, Par_93) // Assignment Rules: carnosine := Par_92; tris := Par_91; acetate := Par_93; bufcapfixed := (ln(10) * carnosine * power(10, - pH_cy - 6.87)) / power(power(10, - pH_cy) + power(10, -(6.87)), 2) + (ln(10) * tris * power(10, - pH_cy - 8.3)) / power(power(10, - pH_cy) + power(10, -(8.3)), 2) + (ln(10) * acetate * power(10, - pH_cy - 4.8)) / power(power(10, - pH_cy) + power(10, -(4.8)), 2); bufcapmetab := ln(10) * power(10, - pH_cy) * c0 * (1 + dNavgPidH * Pi_ + dNavgATPdH * ATP + dNavgADPdH * ADP + dNavgAMPdH * AMP + dNavgPCRdH * PCr + dNavgCRdH * Cr + dNavgG1PdH * G1P + dNavgG6PdH * G6P + dNavgF6PdH * F6P + dNavgFDPdH * FBP + dNavgGAPdH * GAP + dNavgDHAPdH * DHAP + dNavgG3PdH * G3P + dNavg13DPGdH * BPG + dNavg3PGdH * P3G + dNavg2PGdH * P2G + dNavgPEPdH * PEP + dNavgPYRdH * PYR + dNavgLACdH * LAC); protons_consumed := deltaH_CK * - CK + deltaH_ADK * ADK + deltaH_PGLM * v_PGLM + deltaH_GP * (flux_GPa + flux_GPb) + deltaH_PGI * v_PGI + deltaH_PFK * v_PFK + deltaH_ALD * v_ALD + deltaH_TPI * v_TPI + deltaH_GAPDH * v_GAPDH + deltaH_PGK * v_PGK + deltaH_PGM * v_PGM + deltaH_ENOL * v_ENOL + deltaH_PK * v_PK + deltaH_LDH * v_LDH + deltaH_G3PDH * v_G3PDH; CKprtflux := deltaH_CK * - CK; glycprtflux := deltaH_PGLM * v_PGLM + deltaH_GP * (flux_GPa + flux_GPb) + deltaH_PGI * v_PGI + deltaH_PFK * v_PFK + deltaH_ALD * v_ALD + deltaH_TPI * v_TPI + deltaH_GAPDH * v_GAPDH + deltaH_PGK * v_PGK + deltaH_PGM * v_PGM + deltaH_ENOL * v_ENOL + deltaH_PK * v_PK + deltaH_LDH * v_LDH + deltaH_G3PDH * v_G3PDH; pHODEterm1 := protons_consumed / (bufcapfixed + bufcapmetab); pHODEterm2 := (dNavgPidmg * Pi_ + dNavgATPdmg * ATP + dNavgADPdmg * ADP + dNavgAMPdmg * AMP + dNavgPCRdmg * PCr + dNavgCRdmg * Cr + dNavgG1Pdmg * G1P + dNavgG6Pdmg * G6P + dNavgF6Pdmg * F6P + dNavgFDPdmg * FBP + dNavgGAPdmg * GAP + dNavgDHAPdmg * DHAP + dNavgG3Pdmg * G3P + dNavg13DPGdmg * BPG + dNavg3PGdmg * P3G + dNavg2PGdmg * P2G + dNavgPEPdmg * PEP + dNavgPYRdmg * PYR + dNavgLACdmg * LAC) / (bufcapfixed + bufcapmetab); denom_mgODE := -(1) - (dmgATP2dmg * ATP + dmgADPdmg * ADP + dmgAMPdmg * AMP + dmgPidmg * Pi_ + dmgPCRdmg * PCr + dmgG1Pdmg * G1P + dmgFDPdmg * FBP + dmgG3Pdmg * G3P + dmgDHAPdmg * DHAP + dmgPEPdmg * PEP + dmg2PGdmg * P2G + dmgLACdmg * LAC); RHSterm1_mgODE := (dmgATP2dpH * ATP + dmgADPdpH * ADP + dmgAMPdpH * AMP + dmgPidpH * Pi_ + dmgPCRdpH * PCr + dmgG1PdpH * G1P + dmgFDPdpH * FBP + dmgG3PdpH * G3P + dmgDHAPdpH * DHAP + dmgPEPdpH * PEP + dmg2PGdpH * P2G + dmgLACdpH * LAC) / denom_mgODE; denomMgpHODE := 1 - RHSterm1_mgODE * pHODEterm2; // Variable initializations: pH_cy = ; PCr = ; Cr = ; NAD = ; NADH = ; ATP = ; ADP = ; AMP = ; Pi_ = ; Gly = ; G1P = ; G6P = ; F6P = ; FBP = ; DHAP = ; G3P = ; GAP = ; BPG = ; P3G = ; P2G = ; PEP = ; PYR = ; LAC = ; ADK = ; CK = ; dNavg13DPGdH = ; dNavg3PGdH = ; dNavg2PGdH = ; dNavgADPdH = ; dNavgAMPdH = ; dNavgATPdH = ; dNavgCRdH = ; dNavgDHAPdH = ; dNavgF6PdH = ; dNavgFDPdH = ; dNavgG1PdH = ; dNavgG3PdH = ; dNavgG6PdH = ; dNavgGAPdH = ; dNavgLACdH = ; dNavgPCRdH = ; dNavgPEPdH = ; dNavgPYRdH = ; dNavgPidH = ; deltaH_ADK = ; deltaH_ALD = ; deltaH_CK = ; deltaH_ENOL = ; deltaH_G3PDH = ; deltaH_GAPDH = ; deltaH_GP = ; deltaH_LDH = ; deltaH_PFK = ; deltaH_PGI = ; deltaH_PGK = ; deltaH_PGLM = ; deltaH_PGM = ; deltaH_PK = ; deltaH_TPI = ; dNavg13DPGdmg = ; dNavg2PGdmg = ; dNavg3PGdmg = ; dNavgADPdmg = ; dNavgAMPdmg = ; dNavgATPdmg = ; dNavgCRdmg = ; dNavgDHAPdmg = ; dNavgF6Pdmg = ; dNavgFDPdmg = ; dNavgG1Pdmg = ; dNavgG3Pdmg = ; dNavgG6Pdmg = ; dNavgGAPdmg = ; dNavgLACdmg = ; dNavgPCRdmg = ; dNavgPEPdmg = ; dNavgPYRdmg = ; dNavgPidmg = ; dmg2PGdmg = ; dmgATP2dmg = ; dmgADPdmg = ; dmgAMPdmg = ; dmgDHAPdmg = ; dmgFDPdmg = ; dmgG1Pdmg = ; dmgG3Pdmg = ; dmgLACdmg = ; dmgPCRdmg = ; dmgPEPdmg = ; dmgPidmg = ; dmg2PGdpH = ; dmgADPdpH = ; dmgAMPdpH = ; dmgATP2dpH = ; dmgDHAPdpH = ; dmgFDPdpH = ; dmgG1PdpH = ; dmgG3PdpH = ; dmgLACdpH = ; dmgPCRdpH = ; dmgPEPdpH = ; dmgPidpH = ; flux_GPa = ; flux_GPb = ; v_ALD = ; v_ENOL = ; v_G3PDH = ; v_GAPDH = ; v_LDH = ; v_PFK = ; v_PGI = ; v_PGK = ; v_PGLM = ; v_PGM = ; v_PK = ; v_TPI = ; c0 = ; Par_91 = ; Par_92 = ; Par_93 = ; end model vinnakota_kemp_kushmeric_2006_exp45__differential_equations(PCr, Cr, NAD, NADH, ATP, ADP, AMP, Pi_, Gly, G1P, G6P, F6P, FBP, DHAP, G3P, GAP, BPG, P3G, P2G, PEP, PYR, LAC, Mg, pH_calc, protonload, time_, ADK, CK, flux_GPa, flux_GPb, v_ALD, v_ENOL, v_G3PDH, v_GAPDH, v_LDH, v_PFK, v_PGI, v_PGK, v_PGLM, v_PGM, v_PK, v_TPI, ATPase, protons_consumed, pHODEterm1, pHODEterm2, denom_mgODE, RHSterm1_mgODE, mg2PG, mgATP2, mgADP, mgAMP, mgDHAP, mgFDP, mgG1P, mgG3P, mgLAC, mgPCR, mgPEP, mgPi, Par_99) // Assignment Rules: RHSterm2_mgODE := (mgATP2 * dATPdt + mgADP * dADPdt + mgAMP * dAMPdt + mgPi * dPidt + mgPCR * dPCrdt + mgG1P * dG1Pdt + mgFDP * dFBPdt + mgG3P * dG3Pdt + mgDHAP * dDHAPdt + mgPEP * dPEPdt + mg2PG * dP2Gdt + mgLAC * dLACdt) / denom_mgODE; fixmg := 1; fixpH := Par_99; dATPdt := (((- CK - ADK) - v_PFK) + v_PGK + v_PK) - ATPase; dADPdt := (((CK + 2 * ADK + v_PFK) - v_PGK) - v_PK) + ATPase; dAMPdt := - ADK; dDHAPdt := v_ALD + v_TPI + v_G3PDH; dFBPdt := v_PFK - v_ALD; dG1Pdt := (flux_GPa + flux_GPb) - v_PGLM; dG3Pdt := - v_G3PDH; dLACdt := v_LDH; dP2Gdt := v_PGM - v_ENOL; dPCrdt := CK; dPEPdt := v_ENOL - v_PK; dPidt := (-(flux_GPa + flux_GPb) - v_GAPDH) + ATPase; dCrdt := - CK; dNADdt := (- v_GAPDH - v_G3PDH) + v_LDH; dNADHdt := (v_GAPDH + v_G3PDH) - v_LDH; dGlydt := -(flux_GPa + flux_GPb); dG6Pdt := v_PGLM - v_PGI; dF6Pdt := v_PGI - v_PFK; dGAPdt := (v_ALD - v_TPI) - v_GAPDH; dBGPdt := v_GAPDH - v_PGK; dP3Gdt := v_PGK - v_PGM; dPYRdt := v_PK - v_LDH; // Rate Rules: PCr' = dPCrdt; Cr' = dCrdt; NAD' = dNADdt; NADH' = dNADHdt; ATP' = dATPdt; ADP' = dADPdt; AMP' = dAMPdt; Pi_' = dPidt; Gly' = dGlydt; G1P' = dG1Pdt; G6P' = dG6Pdt; F6P' = dF6Pdt; FBP' = dFBPdt; DHAP' = dDHAPdt; G3P' = dG3Pdt; GAP' = dGAPdt; BPG' = dBGPdt; P3G' = dP3Gdt; P2G' = dP2Gdt; PEP' = dPEPdt; PYR' = dPYRdt; LAC' = dLACdt; Mg' = piecewise( (fixmg * (RHSterm2_mgODE + RHSterm1_mgODE * pHODEterm1)) / (1 - RHSterm1_mgODE * pHODEterm2) , time_ <= 1 , fixmg * RHSterm2_mgODE ); pH_calc' = (fixpH * (pHODEterm1 + RHSterm2_mgODE * pHODEterm2)) / (1 - RHSterm1_mgODE * pHODEterm2); protonload' = - protons_consumed; // Variable initializations: PCr = 1e-9; Cr = 0.029999999; NAD = 0.0005; NADH = 1e-9; ATP = 0.005; ADP = 1e-9; AMP = 1e-9; Pi_ = 0.035; Gly = 0.04; G1P = 1e-9; G6P = 1e-9; F6P = 1e-9; FBP = 1e-9; DHAP = 1e-9; G3P = 1e-9; GAP = 1e-9; BPG = 1e-9; P3G = 1e-9; P2G = 1e-9; PEP = 1e-9; PYR = 1e-9; LAC = 1e-9; Mg = 4.913450725e-4; pH_calc = 7.3; protonload = 0; time_ = ; ADK = ; CK = ; flux_GPa = ; flux_GPb = ; v_ALD = ; v_ENOL = ; v_G3PDH = ; v_GAPDH = ; v_LDH = ; v_PFK = ; v_PGI = ; v_PGK = ; v_PGLM = ; v_PGM = ; v_PK = ; v_TPI = ; ATPase = ; protons_consumed = ; pHODEterm1 = ; pHODEterm2 = ; denom_mgODE = ; RHSterm1_mgODE = ; mg2PG = ; mgATP2 = ; mgADP = ; mgAMP = ; mgDHAP = ; mgFDP = ; mgG1P = ; mgG3P = ; mgLAC = ; mgPCR = ; mgPEP = ; mgPi = ; Par_99 = ; end model *vinnakota_kemp_kushmeric_2006_exp45____main() // Sub-modules, and any changes to those submodules: environment: vinnakota_kemp_kushmeric_2006_exp45__environment(time_, pH_cy, Par_97, Par_98, pH_calc); global_parameters: vinnakota_kemp_kushmeric_2006_exp45__global_parameters(R, T1, T, I, Par_90, Par_94); parameters: vinnakota_kemp_kushmeric_2006_exp45__parameters(Par_1, Par_2, Par_3, Par_4, Par_5, Par_6, Par_7, Par_8, Par_9, Par_10, Par_11, Par_12, Par_13, Par_14, Par_15, Par_16, Par_17, Par_18, Par_19, Par_20, Par_21, Par_22, Par_23, Par_24, Par_25, Par_26, Par_27, Par_28, Par_29, Par_30, Par_31, Par_32, Par_33, Par_34, Par_35, Par_36, Par_37, Par_38, Par_39, Par_40, Par_41, Par_42, Par_43, Par_44, Par_45, Par_46, Par_47, Par_48, Par_49, Par_50, Par_51, Par_52, Par_53, Par_54, Par_55, Par_56, Par_57, Par_58, Par_59, Par_60, Par_61, Par_62, Par_63, Par_64, Par_65, Par_66, Par_67, Par_68, Par_69, Par_70, Par_71, Par_72, Par_73, Par_74, Par_75, Par_76, Par_77, Par_78, Par_79, Par_80, Par_81, Par_82, Par_83, Par_84, Par_85, Par_86, Par_87, Par_88, Par_89, Par_90, Par_91, Par_92, Par_93, Par_94, Par_95, Par_96, Par_97, Par_98, Par_99, Par_100); equilibrium_constants: vinnakota_kemp_kushmeric_2006_exp45__equilibrium_constants(mgT, k, c0, Par_95, Par_96); correction_factors: vinnakota_kemp_kushmeric_2006_exp45__correction_factors(mgPi, dNavgPidH, dNavgPidmg, dmgPidmg, dmgPidpH, mgATP2, dNavgATPdH, dNavgATPdmg, dmgATP2dmg, dmgATP2dpH, mgADP, dNavgADPdH, dNavgADPdmg, dmgADPdmg, dmgADPdpH, mgAMP, dNavgAMPdH, dNavgAMPdmg, dmgAMPdmg, dmgAMPdpH, mgPCR, dNavgPCRdH, dNavgPCRdmg, dmgPCRdmg, dmgPCRdpH, dNavgCRdH, dNavgCRdmg, mgG1P, dNavgG1PdH, dNavgG1Pdmg, dmgG1Pdmg, dmgG1PdpH, dNavgG6PdH, dNavgG6Pdmg, dNavgF6PdH, dNavgF6Pdmg, mgFDP, dNavgFDPdH, dNavgFDPdmg, dmgFDPdmg, dmgFDPdpH, dNavgGAPdH, dNavgGAPdmg, mgG3P, dNavgG3PdH, dNavgG3Pdmg, dmgG3Pdmg, dmgG3PdpH, mgDHAP, dNavgDHAPdH, dNavgDHAPdmg, dmgDHAPdmg, dmgDHAPdpH, dNavg13DPGdH, dNavg13DPGdmg, dNavg3PGdH, dNavg3PGdmg, mg2PG, dNavg2PGdH, dNavg2PGdmg, dmg2PGdmg, dmg2PGdpH, mgPEP, dNavgPEPdH, dNavgPEPdmg, dmgPEPdmg, dmgPEPdpH, dNavgPYRdH, dNavgPYRdmg, mgLAC, dNavgLACdH, dNavgLACdmg, dmgLACdmg, dmgLACdpH, deltaH_CK, Kapp_CK, deltaH_ADK, Kapp_ADK, deltaH_GP, Kapp_GP, deltaH_PGLM, Kapp_PGLM, deltaH_PGI, Kapp_PGI, deltaH_PFK, Kapp_PFK, deltaH_ALD, Kapp_ALD, deltaH_TPI, Kapp_TPI, deltaH_GAPDH, Kapp_GAPDH, deltaH_G3PDH, Kapp_G3PDH, deltaH_PGK, Kapp_PGK, deltaH_PGM, Kapp_PGM, deltaH_ENOL, Kapp_ENOL, deltaH_PK, Kapp_PK, deltaH_LDH, Kapp_LDH, deltaH_ATPase, Kapp_ATPase, R, T1, T, I, mgT, k, c0, mg, pH_cy); glycogen_phosphorylase: vinnakota_kemp_kushmeric_2006_exp45__glycogen_phosphorylase(Vfgly, expno, fracA, flux_GPa, time_, G1P, Pi_, Gly, pH_cy, Kapp_GP, Par_1, Par_2, Par_3, Par_4, Par_5, Par_6, Par_7, Par_8, Par_9, Par_100); glycogen_phosphorylase_B: vinnakota_kemp_kushmeric_2006_exp45__glycogen_phosphorylase_B(flux_GPb, fracA, Vfgly, AMP, G1P, Gly, Pi_, Kapp_GP, pH_cy, Par_10, Par_11, Par_12, Par_13, Par_14, Par_15, Par_16, Par_17, Par_18); PGLM: vinnakota_kemp_kushmeric_2006_exp45__PGLM(v_PGLM, pH_cy, Kapp_PGLM, G1P, G6P, Par_19, Par_20, Par_21); PGI: vinnakota_kemp_kushmeric_2006_exp45__PGI(v_PGI, pH_cy, Kapp_PGI, F6P, G6P, Par_22, Par_23, Par_24); PFK: vinnakota_kemp_kushmeric_2006_exp45__PFK(v_PFK, pH_cy, Kapp_PFK, F6P, FBP, AMP, ADP, ATP, Par_25, Par_26, Par_27, Par_28, Par_29, Par_30, Par_31, Par_32, Par_33, Par_34, Par_35, Par_36, Par_37, Par_38); ALD: vinnakota_kemp_kushmeric_2006_exp45__ALD(v_ALD, pH_cy, Kapp_ALD, DHAP, FBP, GAP, Par_39, Par_40, Par_41, Par_42); TPI: vinnakota_kemp_kushmeric_2006_exp45__TPI(v_TPI, Kapp_TPI, DHAP, GAP, Par_43, Par_44, Par_45); G3PDH: vinnakota_kemp_kushmeric_2006_exp45__G3PDH(v_G3PDH, Kapp_G3PDH, DHAP, G3P, NAD, NADH, Par_46, Par_47, Par_48, Par_49, Par_50); GAPDH: vinnakota_kemp_kushmeric_2006_exp45__GAPDH(v_GAPDH, pH_cy, Kapp_GAPDH, BPG, GAP, NAD, NADH, Pi_, Par_51, Par_52, Par_53, Par_54, Par_55, Par_56); PGK: vinnakota_kemp_kushmeric_2006_exp45__PGK(v_PGK, Kapp_PGK, BPG, P3G, ADP, ATP, Par_57, Par_58, Par_59, Par_60, Par_61); PGM: vinnakota_kemp_kushmeric_2006_exp45__PGM(v_PGM, pH_cy, Kapp_PGM, P2G, P3G, Par_62, Par_63, Par_64); ENOL: vinnakota_kemp_kushmeric_2006_exp45__ENOL(v_ENOL, Kapp_ENOL, P2G, PEP, Par_65, Par_66, Par_67); PK: vinnakota_kemp_kushmeric_2006_exp45__PK(v_PK, pH_cy, Kapp_PK, PEP, PYR, ADP, ATP, Par_68, Par_69, Par_70, Par_71, Par_72); LDH: vinnakota_kemp_kushmeric_2006_exp45__LDH(v_LDH, pH_cy, Kapp_LDH, LAC, NAD, NADH, PYR, Par_73, Par_74, Par_75, Par_76, Par_77); ATPase: vinnakota_kemp_kushmeric_2006_exp45__ATPase(ATPase0, time_, ATP, expno, Par_88, Par_89); creatine_kinase: vinnakota_kemp_kushmeric_2006_exp45__creatine_kinase(CK, Kapp_CK, ADP, ATP, Cr, PCr, Par_78, Par_79, Par_80, Par_81, Par_82, Par_83); adenylate_kinase: vinnakota_kemp_kushmeric_2006_exp45__adenylate_kinase(ADK, Kapp_ADK, AMP, ADP, ATP, Par_84, Par_85, Par_86, Par_87); buffer_capacity: vinnakota_kemp_kushmeric_2006_exp45__buffer_capacity(protons_consumed, pHODEterm1, pHODEterm2, denom_mgODE, RHSterm1_mgODE, denomMgpHODE, pH_cy, PCr, Cr, NAD, NADH, ATP, ADP, AMP, Pi_, Gly, G1P, G6P, F6P, FBP, DHAP, G3P, GAP, BPG, P3G, P2G, PEP, PYR, LAC, ADK, CK, dNavg13DPGdH, dNavg3PGdH, dNavg2PGdH, dNavgADPdH, dNavgAMPdH, dNavgATPdH, dNavgCRdH, dNavgDHAPdH, dNavgF6PdH, dNavgFDPdH, dNavgG1PdH, dNavgG3PdH, dNavgG6PdH, dNavgGAPdH, dNavgLACdH, dNavgPCRdH, dNavgPEPdH, dNavgPYRdH, dNavgPidH, deltaH_ADK, deltaH_ALD, deltaH_CK, deltaH_ENOL, deltaH_G3PDH, deltaH_GAPDH, deltaH_GP, deltaH_LDH, deltaH_PFK, deltaH_PGI, deltaH_PGK, deltaH_PGLM, deltaH_PGM, deltaH_PK, deltaH_TPI, dNavg13DPGdmg, dNavg2PGdmg, dNavg3PGdmg, dNavgADPdmg, dNavgAMPdmg, dNavgATPdmg, dNavgCRdmg, dNavgDHAPdmg, dNavgF6Pdmg, dNavgFDPdmg, dNavgG1Pdmg, dNavgG3Pdmg, dNavgG6Pdmg, dNavgGAPdmg, dNavgLACdmg, dNavgPCRdmg, dNavgPEPdmg, dNavgPYRdmg, dNavgPidmg, dmg2PGdmg, dmgATP2dmg, dmgADPdmg, dmgAMPdmg, dmgDHAPdmg, dmgFDPdmg, dmgG1Pdmg, dmgG3Pdmg, dmgLACdmg, dmgPCRdmg, dmgPEPdmg, dmgPidmg, dmg2PGdpH, dmgADPdpH, dmgAMPdpH, dmgATP2dpH, dmgDHAPdpH, dmgFDPdpH, dmgG1PdpH, dmgG3PdpH, dmgLACdpH, dmgPCRdpH, dmgPEPdpH, dmgPidpH, flux_GPa, flux_GPb, v_ALD, v_ENOL, v_G3PDH, v_GAPDH, v_LDH, v_PFK, v_PGI, v_PGK, v_PGLM, v_PGM, v_PK, v_TPI, c0, Par_91, Par_92, Par_93); differential_equations: vinnakota_kemp_kushmeric_2006_exp45__differential_equations(PCr, Cr, NAD, NADH, ATP, ADP, AMP, Pi_, Gly, G1P, G6P, F6P, FBP, DHAP, G3P, GAP, BPG, P3G, P2G, PEP, PYR, LAC, mg, pH_calc, protonload, time_, ADK, CK, flux_GPa, flux_GPb, v_ALD, v_ENOL, v_G3PDH, v_GAPDH, v_LDH, v_PFK, v_PGI, v_PGK, v_PGLM, v_PGM, v_PK, v_TPI, ATPase0, protons_consumed, pHODEterm1, pHODEterm2, denom_mgODE, RHSterm1_mgODE, mg2PG, mgATP2, mgADP, mgAMP, mgDHAP, mgFDP, mgG1P, mgG3P, mgLAC, mgPCR, mgPEP, mgPi, Par_99); end