//Created by libAntimony v2.4 model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__environment(time_, pH_cy, pH_calc, CO2_in, HCO3_in, pH_in, MOPSt, clamp) // Assignment Rules: pH_cy := pH_calc; CO2_in := 0.05 * 0.0425 * (760 - 23.8) * 1E-3; HCO3_in := 30E-3; pH_in := 6.157 + log(HCO3_in / CO2_in); MOPSt := 0; // Variable initializations: time_ = ; pH_calc = ; clamp = 1; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__parameters(Vfgly, fracA, KgpA_glyf, KgpA_pi, KgpA_igly, KgpA_ipi, KgpA_glyb, KgpA_g1p, KgpA_ig1p, KgpB_pi, KgpB_ipi, KgpB_iglyf, KgpB_g1p, KgpB_ig1p, KgpB_iglyb, Kgp_amp, nH, Vffpglm, Kpglm_g1p, Kpglm_g6p, Vbbpgi, Kpgi_g6p, Kpgi_f6p, Vffpfk, Kpfk_f6p, Kpfk_f6pT, Kpfk_atp, Kpfk_atpT, Kpfk_fbp, Kpfk_fbpT, Kpfk_adp, Kpfk_adpT, Kpfki, Kmpfk, d, e_, Lo, Vffald, Kald_fbp, Kald_dhap, Kald_gap, Vfftpi, Ktpi_gap, Ktpi_dhap, Vbbg3pdh, Kg3pdh_g3p, Kg3pdh_nad, Kg3pdh_dhap, Kg3pdh_nadh, Vffgad, Kgapdh_gap, Kgapdh_nad, Kgapdh_pi, Kgapdh_bpg, Kgapdh_nadh, Vbbpgk, Kpgk_bpg, Kpgk_adp, Kpgk_3pg, Kpgk_atp, Vffpgm, Kpgm_3pg, Kpgm_2pg, Vffen, Ken_2pg, Ken_pep, Vffpk, Kpk_pep, Kpk_adp, Kpk_pyr, Kpk_atp, Vffldh, Kldh_pyr, Kldh_nadh, Kldh_lac, Kldh_nad, VforCK, Kck_pcr, Kck_iatp, Kck_iadp, Kck_ipcr, Kck_cr, Kck_Iadp, Kck_Ipcr, Kck_Icr, Kck_Iatp, Kck_Ii, Vfadk, Kadk_amp, Kadk_atp, Kadk_adp, kut, VmaxOxPhos, Kmadp, nnHH, Vmax_MCT, Klac1, pKmct1, PSVCO2, X_CA, kf_hydrCO2, Keq_CA, kb_hydrCO2, Flow, V_cell, V_ec, bufcapfixed) // Assignment Rules: Vfgly := 0.0037; fracA := 1E-2; KgpA_glyf := 1.7E-3; KgpA_pi := 4E-3; KgpA_igly := 2E-3; KgpA_ipi := 4.7E-3; KgpA_glyb := 1.5E-4; KgpA_g1p := 2.7E-3; KgpA_ig1p := 1.01E-2; KgpB_pi := 2E-4; KgpB_ipi := 4.6E-3; KgpB_iglyf := 1.5E-2; KgpB_g1p := 1.5E-3; KgpB_ig1p := 7.4E-3; KgpB_iglyb := 4.4E-3; Kgp_amp := 6.46203E-6; nH := 1.6159; Vffpglm := 0.0052; Kpglm_g1p := 6.3E-5; Kpglm_g6p := 3E-5; Vbbpgi := 0.3833; Kpgi_g6p := 4.8E-4; Kpgi_f6p := 1.19E-4; Vffpfk := 0.0037; Kpfk_f6p := 1.8E-4; Kpfk_f6pT := 2E-2; Kpfk_atp := 8E-5; Kpfk_atpT := 2.5E-4; Kpfk_fbp := 4.02E-3; Kpfk_fbpT := 4.02E-3; Kpfk_adp := 2.7E-3; Kpfk_adpT := 2.7E-3; Kpfki := 8.7E-4 * 10; Kmpfk := 6E-5; d := 1E-2; e_ := 1E-2; Lo := 13; Vffald := 0.012; Kald_fbp := 5E-5; Kald_dhap := 2E-3; Kald_gap := 1E-3; Vfftpi := 0.1406; Ktpi_gap := 3.2E-4; Ktpi_dhap := 6.1E-4; Vbbg3pdh := 0.0557; Kg3pdh_g3p := 1.8E-4; Kg3pdh_nad := 1.2E-5; Kg3pdh_dhap := 2.2E-4; Kg3pdh_nadh := 8E-6; Vffgad := 0.0765; Kgapdh_gap := 2.5E-6; Kgapdh_nad := 9E-5; Kgapdh_pi := 2.9E-4; Kgapdh_bpg := 8E-7; Kgapdh_nadh := 3.3E-6; Vbbpgk := 0.0087; Kpgk_bpg := 2E-3; Kpgk_adp := 8E-6; Kpgk_3pg := 1.2E-3; Kpgk_atp := 3.5E-4; Vffpgm := 0.0839; Kpgm_3pg := 2E-4; Kpgm_2pg := 1.4E-5; Vffen := 0.7966; Ken_2pg := 1E-4; Ken_pep := 3.7E-4; Vffpk := 0.0408; Kpk_pep := 8E-5; Kpk_adp := 3E-4; Kpk_pyr := 7.05E-3; Kpk_atp := 1.13E-3; Vffldh := 0.0956; Kldh_pyr := 3.35E-4; Kldh_nadh := 2E-6; Kldh_lac := 1.7E-2; Kldh_nad := 8.49E-4; VforCK := 8.8215; Kck_pcr := 1.11E-3; Kck_iatp := 3.5E-3; Kck_iadp := 1.35E-4; Kck_ipcr := 3.9E-3; Kck_cr := 3.8E-3; Kck_Iadp := 0.015E-3; Kck_Ipcr := 3.9E-3; Kck_Icr := 58E-3; Kck_Iatp := 4.346E-3; Kck_Ii := 1E-3; Vfadk := 2.0299; Kadk_amp := 3.2E-4; Kadk_atp := 2.7E-4; Kadk_adp := 3.5E-4; kut := 0.124547251111437; VmaxOxPhos := 0.0037844; Kmadp := 0.0000419392; nnHH := 2.217962; Vmax_MCT := 0.0007114938; Klac1 := 4E-3; pKmct1 := 8.89; PSVCO2 := 2.3084; X_CA := 740; kf_hydrCO2 := 0.0469 * 60; Keq_CA := power(10, -(6.157)); kb_hydrCO2 := kf_hydrCO2 / Keq_CA; Flow := 4E-3; V_cell := 55E-3 * 0.67 * 1E-3; V_ec := 0.149E-3 - (55E-3 / 1.06) * 1E-3; bufcapfixed := 0.0041388; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__equilibrium_constants(T, I, k, c0, R, B, I1, alphadebye, IcorrpKa, RTalpha, IcorrdeltaGpof, pKa1_Pi, pKamg_Pi, pKak_Pi, P_Pi, HPi2, H2Pi1, kPi, mgPi, Navg_Pi, dNavgPidH, NH_HPi2, deltaGof_HPi2, deltaGpof_HPi2, pKa1_ATP, pKamg_ATP, pKak_ATP, P_ATP, ATP4, HATP3, mgATP2, kATP, Navg_ATP, dNavgATPdH, NH_ATP4, deltaGof_ATP4, deltaGpof_ATP4, pKak_ADP, pKa1_ADP, pKamg_ADP, P_ADP, ADP3, HADP2, mgADP, kADP, Navg_ADP, dNavgADPdH, NH_ADP3, deltaGof_ADP3, deltaGpof_ADP3, pKa1_AMP, pKamg_AMP, P_AMP, AMP2, HAMP1, mgAMP, Navg_AMP, dNavgAMPdH, NH_AMP2, deltaGof_AMP2, deltaGpof_AMP2, pKak_PCR, pKa1_PCR, pKamg_PCR, P_PCR, HPCR, H2PCR, kPCR, mgPCR, Navg_PCR, dNavgPCRdH, NH_HPCR, pKa1_CR, P_CR, HCR, H2CR, Navg_CR, dNavgCRdH, NH_HCR, pKa1_G1P, pKamg_G1P, P_G1P, UG1P, HG1P, mgG1P, Navg_G1P, dNavgG1PdH, NH_UG1P, deltaGof_UG1P, deltaGpof_UG1P, pKa1_G6P, P_G6P, UG6P, HG6P, Navg_G6P, dNavgG6PdH, dNavgG6Pdmg, NH_UG6P, deltaGof_UG6P, deltaGpof_UG6P, pKa1_F6P, P_F6P, UF6P, HF6P, Navg_F6P, dNavgF6PdH, NH_UF6P, deltaGof_UF6P, deltaGpof_UF6P, pKa1_FDP, pKamg_FDP, P_FDP, UFDP, HFDP, mgFDP, Navg_FDP, dNavgFDPdH, NH_UFDP, deltaGof_UFDP, deltaGpof_UFDP, pKa1_GAP, P_GAP, UGAP, HGAP, Navg_GAP, dNavgGAPdH, dNavgGAPdmg, NH_UGAP, deltaGof_UGAP, deltaGpof_UGAP, pKamg_G3P, pKa1_G3P, P_G3P, UG3P, HG3P, mgG3P, Navg_G3P, dNavgG3PdH, NH_UG3P, deltaGof_UG3P, deltaGpof_UG3P, pKa1_DHAP, pKamg_DHAP, P_DHAP, UDHAP, HDHAP, mgDHAP, Navg_DHAP, dNavgDHAPdH, NH_UDHAP, deltaGof_UDHAP, deltaGpof_UDHAP, pKa1_13DPG, P_13DPG, U13DPG, H13DPG, Navg_13DPG, dNavg13DPGdH, NH_U13DPG, deltaGof_U13DPG, deltaGpof_U13DPG, pKa1_3PG, P_3PG, U3PG, H3PG, Navg_3PG, dNavg3PGdH, NH_U3PG, deltaGof_U3PG, deltaGpof_U3PG, pKa1_2PG, pKamg_2PG, pKak_2PG, P_2PG, U2PG, H2PG, mg2PG, k2PG, Navg_2PG, dNavg2PGdH, NH_U2PG, deltaGof_U2PG, deltaGpof_U2PG, pKa1_PEP, pKamg_PEP, pKak_PEP, P_PEP, UPEP, HPEP, kPEP, mgPEP, Navg_PEP, dNavgPEPdH, NH_UPEP, deltaGof_UPEP, deltaGpof_UPEP, pKa1_PYR, P_PYR, UPYR, HPYR, Navg_PYR, dNavgPYRdH, dNavgPYRdmg, NH_UPYR, deltaGof_UPYR, deltaGpof_UPYR, pKamg_LAC, pKa1_LAC, P_LAC, ULAC, HLAC, mgLAC, Navg_LAC, dNavgLACdH, dmgLACdmg, dmgLACdpH, NH_ULAC, deltaGof_ULAC, deltaGpof_ULAC, dNH_GLY, deltaGpo_GLY, NH_NAD, deltaGof_NAD, deltaGpof_NAD, NH_NADH, deltaGof_NADH, deltaGpof_NADH, NH_H2O, deltaGof_H2O, deltaGpof_H2O, NH_H, deltaGof_H, deltaGpof_H, deltaH_CK, slopeint_1, slopeint_2, Kref_CKT, I25, alphadebye1, IcorrneglnKrefCK, neglnKrefCK_Iexp, Kref_CK, deltaGpo_CK, Kapp_CK, deltaH_ADK, deltaGpo_ADK, Kapp_ADK, deltaH_GP, deltaGpo_GP, Kapp_GP, deltaH_PGLM, deltaGpo_PGLM, Kapp_PGLM, deltaH_PGI, deltaGpo_PGI, Kapp_PGI, deltaH_PFK, deltaGpo_PFK, Kapp_PFK, deltaH_ALD, deltaGpo_ALD, Kapp_ALD, deltaH_TPI, deltaGpo_TPI, Kapp_TPI, deltaH_GAPDH, deltaGpo_GAPDH, Kapp_GAPDH, deltaH_G3PDH, deltaGpo_G3PDH, Kapp_G3PDH, deltaH_PGK, deltaGpo_PGK, Kapp_PGK, deltaH_PGM, deltaGpo_PGM, Kapp_PGM, deltaH_ENOL, deltaGpo_ENOL, Kapp_ENOL, deltaH_PK, deltaGpo_PK, Kapp_PK, deltaH_LDH, deltaGpo_LDH, Kapp_LDH, deltaH_ATPase, deltaGpo_ATPase, Kapp_ATPase, mg, pH_cy) // Assignment Rules: T := 298.15; I := 0.17; k := 0.14; c0 := 1; R := 8.314E-3; B := 1.6; I1 := 0.1; alphadebye := 1.17582; IcorrpKa := (alphadebye * (root(I1) / (1 + B * root(I1)) - root(I) / (1 + B * root(I)))) / ln(10); RTalpha := 2.91482; IcorrdeltaGpof := (RTalpha * root(I)) / (1 + B * root(I)); pKa1_Pi := 6.75 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); pKamg_Pi := 1.65 + IcorrpKa * ((power(2, 2) + power(2, 2)) - power(0, 2)); pKak_Pi := 0.5; 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 := H2Pi1; dNavgPidH := (power(10, pKa1_Pi) * P_Pi * (1 - H2Pi1)) / (c0 * 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); pKa1_ATP := 6.48 + IcorrpKa * ((power(4, 2) + power(1, 2)) - power(3, 2)); pKamg_ATP := 4.19 + IcorrpKa * ((power(4, 2) + power(2, 2)) - power(2, 2)); pKak_ATP := 1.17 + IcorrpKa * ((power(4, 2) + power(1, 2)) - power(3, 2)); 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 := HATP3; dNavgATPdH := (power(10, pKa1_ATP) * P_ATP * (1 - HATP3)) / (c0 * 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; pKa1_ADP := 6.38 + IcorrpKa * ((power(3, 2) + power(1, 2)) - power(2, 2)); pKamg_ADP := 3.25 + IcorrpKa * ((power(3, 2) + power(2, 2)) - power(1, 2)); 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 := HADP2; dNavgADPdH := (power(10, pKa1_ADP) * P_ADP * (1 - HADP2)) / (c0 * 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); pKa1_AMP := 6.29 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); pKamg_AMP := 1.92 + IcorrpKa * ((power(2, 2) + power(2, 2)) - power(0, 2)); 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 := HAMP1; dNavgAMPdH := (power(10, pKa1_AMP) * (P_AMP - power(10, - pH_cy + pKa1_AMP))) / (c0 * 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; pKa1_PCR := 4.5 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); pKamg_PCR := 1.6 + IcorrpKa * ((power(2, 2) + power(2, 2)) - power(0, 2)); 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)); 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)); NH_HCR := 9; pKa1_G1P := 6.09 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); pKamg_G1P := 2.48 + IcorrpKa * ((power(2, 2) + power(2, 2)) - power(0, 2)); 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)); 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 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); 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 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); 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)); 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; pKamg_FDP := 2.7; P_FDP := 1 + power(10, - pH_cy + pKa1_FDP) + (mg / c0) * power(10, pKamg_FDP); UFDP := 1 / P_FDP; HFDP := UFDP * power(10, - pH_cy + pKa1_FDP); mgFDP := ((UFDP * mg) / c0) * power(10, pKamg_FDP); Navg_FDP := HFDP; dNavgFDPdH := (power(10, pKa1_FDP) * P_FDP * (1 - HFDP)) / (c0 * 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; pKa1_G3P := 6.22 + IcorrpKa * ((power(2, 2) + power(1, 2)) - power(1, 2)); 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)); 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)); 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)); 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)); 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)); 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)); 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; pKa1_LAC := 3.67 + IcorrpKa * ((power(1, 2) + power(1, 2)) - power(0, 2)); 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)); 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); slopeint_1 := 1000 * 2.04742110212706; slopeint_2 := 1000 * 0.013838383371953; Kref_CKT := exp(slopeint_1 / T + slopeint_2); I25 := 0.25; alphadebye1 := (1.10708 - 1.54508E-3 * T) + 5.95584E-6 * power(T, 2); IcorrneglnKrefCK := alphadebye1 * (root(I25) / (1 + 1.6 * root(I25)) - root(I) / (1 + 1.6 * root(I))); neglnKrefCK_Iexp := -ln(Kref_CKT) + IcorrneglnKrefCK * ((((power(4, 2) + power(0, 2)) - power(2, 2)) - power(3, 2)) - power(1, 2)); Kref_CK := exp(- neglnKrefCK_Iexp); deltaGpo_CK := - R * T * ln(Kref_CK); 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 := (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)); 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: mg = ; pH_cy = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__glycogen_phosphorylase_A(Dglya, pa, VbglyA, glyAF, glyAR, flux_GPa, KgpA_glyf, KgpA_glyb, KgpA_igly, KgpA_pi, KgpA_ipi, KgpA_g1p, KgpA_ig1p, Vfgly, fracA, Gly, Pi_, G1P, pH_cy, Kapp_GP) // Assignment Rules: 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: KgpA_glyf = ; KgpA_glyb = ; KgpA_igly = ; KgpA_pi = ; KgpA_ipi = ; KgpA_g1p = ; KgpA_ig1p = ; Vfgly = ; fracA = ; Gly = ; Pi_ = ; G1P = ; pH_cy = ; Kapp_GP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__glycogen_phosphorylase_B(fracB, M, Dglyb, pb, VbglyB, glyBF, glyBR, flux_GPb, fracA, pH_cy, AMP, Gly, Pi_, G1P, Kapp_GP, nH, Vfgly, Kgp_amp, KgpB_iglyf, KgpB_iglyb, KgpB_pi, KgpB_ipi, KgpB_g1p, KgpB_ig1p) // Assignment Rules: fracB := 1 - fracA; M := power(AMP / Kgp_amp, nH) / (1 + power(AMP / Kgp_amp, nH)); 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 = ; pH_cy = ; AMP = ; Gly = ; Pi_ = ; G1P = ; Kapp_GP = ; nH = ; Vfgly = ; Kgp_amp = ; KgpB_iglyf = ; KgpB_iglyb = ; KgpB_pi = ; KgpB_ipi = ; KgpB_g1p = ; KgpB_ig1p = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGLM(Vfpglm, Vbpglm, v_PGLM, pH_cy, Vffpglm, Kpglm_g1p, Kpglm_g6p, Kapp_PGLM, G1P, G6P) // Assignment Rules: 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 = ; Vffpglm = ; Kpglm_g1p = ; Kpglm_g6p = ; Kapp_PGLM = ; G1P = ; G6P = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGI(Vbpgi, Vfpgi, v_PGI, pH_cy, Vbbpgi, Kpgi_g6p, Kpgi_f6p, Kapp_PGI, G6P, F6P) // Assignment Rules: 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 = ; Vbbpgi = ; Kpgi_g6p = ; Kpgi_f6p = ; Kapp_PGI = ; G6P = ; F6P = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PFK(Vfpfk, Vbpfk, L, alpha, Delta, Deltap, v_PFK, pH_cy, Lo, d, Vffpfk, Kpfk_fbp, Kpfk_adp, Kpfk_f6p, Kpfk_atp, Kpfk_fbpT, Kpfk_adpT, Kpfk_f6pT, Kpfk_atpT, Kapp_PFK, Kmpfk, Kpfki, ATP, ADP, AMP, F6P, FBP) // Assignment Rules: 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 + (exponentiale * 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 = ; Lo = ; d = ; Vffpfk = ; Kpfk_fbp = ; Kpfk_adp = ; Kpfk_f6p = ; Kpfk_atp = ; Kpfk_fbpT = ; Kpfk_adpT = ; Kpfk_f6pT = ; Kpfk_atpT = ; Kapp_PFK = ; Kmpfk = ; Kpfki = ; ATP = ; ADP = ; AMP = ; F6P = ; FBP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__ALD(Vfald, Vbald, v_ALD, pH_cy, Vffald, Kald_gap, Kald_fbp, Kald_dhap, Kapp_ALD, FBP, GAP, DHAP) // Assignment Rules: 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 * 1); 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 = ; Vffald = ; Kald_gap = ; Kald_fbp = ; Kald_dhap = ; Kapp_ALD = ; FBP = ; GAP = ; DHAP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__TPI(Vftpi, Vbtpi, v_TPI, Vfftpi, Ktpi_dhap, Ktpi_gap, Kapp_TPI, GAP, DHAP) // Assignment Rules: 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: Vfftpi = ; Ktpi_dhap = ; Ktpi_gap = ; Kapp_TPI = ; GAP = ; DHAP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__G3PDH(Dg3pdh, Vbg3pdh, Vfg3pdh, v_G3PDH, Vbbg3pdh, Kg3pdh_dhap, Kg3pdh_g3p, Kg3pdh_nadh, Kg3pdh_nad, Kapp_G3PDH, G3P, NADH, DHAP, NAD) // Assignment Rules: 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: Vbbg3pdh = ; Kg3pdh_dhap = ; Kg3pdh_g3p = ; Kg3pdh_nadh = ; Kg3pdh_nad = ; Kapp_G3PDH = ; G3P = ; NADH = ; DHAP = ; NAD = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__GAPDH(Dgap, Vfgad, Vbgad, v_GAPDH, pH_cy, Vffgad, Kgapdh_bpg, Kgapdh_gap, Kgapdh_pi, Kgapdh_nadh, Kgapdh_nad, Kapp_GAPDH, GAP, BPG, NADH, Pi_, NAD) // Assignment Rules: 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 * 1) / (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 = ; Vffgad = ; Kgapdh_bpg = ; Kgapdh_gap = ; Kgapdh_pi = ; Kgapdh_nadh = ; Kgapdh_nad = ; Kapp_GAPDH = ; GAP = ; BPG = ; NADH = ; Pi_ = ; NAD = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGK(Vbpgk, Vfpgk, D_PGK, v_PGK, Vbbpgk, Kpgk_bpg, Kpgk_3pg, Kpgk_atp, Kpgk_adp, Kapp_PGK, P3G, BPG, ATP, ADP, NAD) // Assignment Rules: 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: Vbbpgk = ; Kpgk_bpg = ; Kpgk_3pg = ; Kpgk_atp = ; Kpgk_adp = ; Kapp_PGK = ; P3G = ; BPG = ; ATP = ; ADP = ; NAD = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGM(Vfpgm, Vbpgm, v_PGM, pH_cy, Vffpgm, Kpgm_2pg, Kpgm_3pg, Kapp_PGM, P2G, P3G) // Assignment Rules: 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 = ; Vffpgm = ; Kpgm_2pg = ; Kpgm_3pg = ; Kapp_PGM = ; P2G = ; P3G = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__ENOL(Vfen, Vben, v_ENOL, pH_cy, Vffen, Ken_2pg, Ken_pep, Kapp_ENOL, P2G, PEP) // Assignment Rules: 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: pH_cy = ; Vffen = ; Ken_2pg = ; Ken_pep = ; Kapp_ENOL = ; P2G = ; PEP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PK(Vfpk, Vbpk, v_PK, pH_cy, Vffpk, Kpk_atp, Kpk_adp, Kpk_pep, Kpk_pyr, Kapp_PK, ATP, ADP, PEP, PYR) // Assignment Rules: 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 = ; Vffpk = ; Kpk_atp = ; Kpk_adp = ; Kpk_pep = ; Kpk_pyr = ; Kapp_PK = ; ATP = ; ADP = ; PEP = ; PYR = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__LDH(Vfldh, Vbldh, v_LDH, pH_cy, Vffldh, Kldh_lac, Kldh_pyr, Kldh_nad, Kldh_nadh, Kapp_LDH, PYR, LAC, NAD, NADH) // Assignment Rules: 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 = ; Vffldh = ; Kldh_lac = ; Kldh_pyr = ; Kldh_nad = ; Kldh_nadh = ; Kapp_LDH = ; PYR = ; LAC = ; NAD = ; NADH = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__creatine_kinase(VrevCK, CK, VforCK, Kck_iatp, Kck_iadp, Kck_pcr, Kck_ipcr, Kck_cr, Kapp_CK, ATP, ADP, Cr, PCr) // Assignment Rules: 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: VforCK = ; Kck_iatp = ; Kck_iadp = ; Kck_pcr = ; Kck_ipcr = ; Kck_cr = ; Kapp_CK = ; ATP = ; ADP = ; Cr = ; PCr = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__adenylate_kinase(Vbadk, ADK, Vfadk, Kadk_atp, Kadk_adp, Kadk_amp, Kapp_ADK, ATP, ADP, AMP) // Assignment Rules: 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: Vfadk = ; Kadk_atp = ; Kadk_adp = ; Kadk_amp = ; Kapp_ADK = ; ATP = ; ADP = ; AMP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__ATPase(ATPase, kut, ATP) // Assignment Rules: ATPase := kut * ATP; // Variable initializations: kut = ; ATP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__OXPHOS(oxphos, VmaxOxPhos, nnHH, Kmadp, ADP) // Assignment Rules: oxphos := (VmaxOxPhos * power(ADP / Kmadp, nnHH)) / (1 + power(ADP / Kmadp, nnHH)); // Variable initializations: VmaxOxPhos = ; nnHH = ; Kmadp = ; ADP = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__lactate_transport(Kh, v_MCT, pH_cy, pKmct1, Vmax_MCT, nnHH, Klac1, LAC, pH_ec, LAC_ec) // Assignment Rules: Kh := power(10, - pKmct1); v_MCT := (Vmax_MCT * ((LAC * power(10, - pH_cy)) / (Kh * Klac1) - (LAC_ec * power(10, - pH_ec)) / (Kh * Klac1))) / ((LAC * power(10, - pH_cy)) / (Kh * Klac1) + 2 + power(10, - pH_cy) / Kh + LAC / Klac1 + LAC_ec / Klac1 + power(10, - pH_ec) / Kh + (LAC_ec * power(10, - pH_ec)) / (Klac1 * Kh)); // Variable initializations: pH_cy = ; pKmct1 = ; Vmax_MCT = ; nnHH = ; Klac1 = ; LAC = ; pH_ec = ; LAC_ec = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__CO2_generation_transport(RQ, PO2ratio, fluxO2, fluxCO2, oxphos) // Assignment Rules: RQ := 1; PO2ratio := 4.2; fluxO2 := oxphos / PO2ratio; fluxCO2 := RQ * fluxO2; // Variable initializations: oxphos = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__Passive_permeation_flux(v_psCO2, v_hydrCO2cy, v_hydrCO2ec, pH_cy, X_CA, PSVCO2, kf_hydrCO2, kb_hydrCO2, pH_ec, CO2_ec, HCO3_ec, CO2_cy, HCO3_cy) // Assignment Rules: v_psCO2 := PSVCO2 * (CO2_cy - CO2_ec); v_hydrCO2cy := X_CA * (kf_hydrCO2 * CO2_cy - kb_hydrCO2 * power(10, - pH_cy) * HCO3_cy); v_hydrCO2ec := 1 * (kf_hydrCO2 * CO2_ec - kb_hydrCO2 * power(10, - pH_ec) * HCO3_ec); // Variable initializations: pH_cy = ; X_CA = ; PSVCO2 = ; kf_hydrCO2 = ; kb_hydrCO2 = ; pH_ec = ; CO2_ec = ; HCO3_ec = ; CO2_cy = ; HCO3_cy = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__buffer_capacity(bufcapmetab, c0, 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) // Assignment Rules: 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); // Variable initializations: c0 = ; 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 = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__proton_flux(CKprtflux, glycprtflux, protons_consumed, pHODEterm1, 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, deltaH_ATPase, 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, v_MCT, v_hydrCO2cy, CK, ADK, ATPase, oxphos, bufcapfixed, bufcapmetab) // Assignment Rules: 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; protons_consumed := ((CKprtflux + glycprtflux + deltaH_ATPase * ATPase + - deltaH_ATPase * oxphos + deltaH_ADK * ADK) - v_hydrCO2cy) + v_MCT; pHODEterm1 := protons_consumed / (bufcapfixed + bufcapmetab); // Variable initializations: 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 = ; deltaH_ATPase = ; 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 = ; v_MCT = ; v_hydrCO2cy = ; CK = ; ADK = ; ATPase = ; oxphos = ; bufcapfixed = ; bufcapmetab = ; end model vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__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, LAC_ec, HCO3_cy, CO2_cy, HCO3_ec, CO2_ec, MOPS, MOPSH, pH_ec, dPCrdt, dCrdt, dNADdt, dNADHdt, dATPdt, dADPdt, dAMPdt, dPidt, dglydt, dG1Pdt, dG6Pdt, dF6Pdt, dFBPdt, dDHAPdt, dG3Pdt, dGAPdt, dBPGdt, dP3Gdt, dP2Gdt, dPEPdt, dPYRdt, dLACdt, dmgdt, dpH_calcdt, dLACecdt, dHCO3cydt, dCO2cydt, dHCO3ecdt, dCO2ecdt, MOPS_in, MOPSH_in, v_MOPSbuff, dMOPSdt, dMOPSHdt, dpHecdt, time_, 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, v_MCT, CK, ADK, ATPase, oxphos, pHODEterm1, v_psCO2, v_hydrCO2cy, v_hydrCO2ec, fluxCO2, Flow, V_cell, V_ec, pH_in, MOPSt, CO2_in, HCO3_in, clamp) // Assignment Rules: dPCrdt := clamp * CK; dCrdt := clamp * - CK; dNADdt := clamp * ((- v_GAPDH - v_G3PDH) + v_LDH); dNADHdt := clamp * ((v_GAPDH + v_G3PDH) - v_LDH); dATPdt := clamp * (((((- CK - ADK) - v_PFK) + v_PGK + v_PK) - ATPase) + oxphos); dADPdt := clamp * (((((CK + 2 * ADK + v_PFK) - v_PGK) - v_PK) + ATPase) - oxphos); dAMPdt := clamp * - ADK; dPidt := clamp * (((-(flux_GPa + flux_GPb) - v_GAPDH) + ATPase) - oxphos); dglydt := clamp * -(flux_GPa + flux_GPb); dG1Pdt := clamp * ((flux_GPa + flux_GPb) - v_PGLM); dG6Pdt := clamp * (v_PGLM - v_PGI); dF6Pdt := clamp * (v_PGI - v_PFK); dFBPdt := clamp * (v_PFK - v_ALD); dDHAPdt := clamp * (v_ALD + v_TPI + v_G3PDH); dG3Pdt := clamp * - v_G3PDH; dGAPdt := clamp * ((v_ALD - v_TPI) - v_GAPDH); dBPGdt := clamp * (v_GAPDH - v_PGK); dP3Gdt := clamp * (v_PGK - v_PGM); dP2Gdt := clamp * (v_PGM - v_ENOL); dPEPdt := clamp * (v_ENOL - v_PK); dPYRdt := clamp * (v_PK - v_LDH); dLACdt := clamp * (v_LDH - v_MCT); dmgdt := clamp * 0; dpH_calcdt := clamp * pHODEterm1; dLACecdt := clamp * ((V_cell * v_MCT) / V_ec - (Flow * LAC_ec) / V_ec); dHCO3cydt := clamp * v_hydrCO2cy; dCO2cydt := clamp * ((fluxCO2 - v_hydrCO2cy) - v_psCO2); dHCO3ecdt := clamp * ((Flow * (HCO3_in - HCO3_ec)) / V_ec + v_hydrCO2ec); dCO2ecdt := clamp * (((Flow * (CO2_in - CO2_ec)) / V_ec + (v_psCO2 * V_cell) / V_ec) - v_hydrCO2ec); MOPS_in := MOPSt / 2; MOPSH_in := MOPSt / 2; v_MOPSbuff := 1E7 * (power(10, -(7.184)) * MOPS - MOPSH * power(10, - pH_ec)); dMOPSdt := clamp * ((Flow * (MOPS_in - MOPS)) / V_ec - v_MOPSbuff); dMOPSHdt := clamp * ((Flow * (MOPSH_in - MOPSH)) / V_ec + v_MOPSbuff); dpHecdt := (clamp * ((Flow * (power(10, - pH_in) - power(10, - pH_ec))) / V_ec + v_hydrCO2ec / 1 + v_MOPSbuff / 1 + (V_cell * v_MCT) / (V_ec * 1))) / (-ln(10) * power(10, - pH_ec)); // 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' = dBPGdt; P3G' = dP3Gdt; P2G' = dP2Gdt; PEP' = dPEPdt; PYR' = dPYRdt; LAC' = dLACdt; mg' = dmgdt; pH_calc' = dpH_calcdt; LAC_ec' = dLACecdt; HCO3_cy' = dHCO3cydt; CO2_cy' = dCO2cydt; HCO3_ec' = dHCO3ecdt; CO2_ec' = dCO2ecdt; MOPS' = dMOPSdt; MOPSH' = dMOPSHdt; pH_ec' = dpHecdt; // Variable initializations: PCr = 14.5e-3; Cr = 0.0075; NAD = 0.000406654344; NADH = 0.0000000406654344; ATP = 0.0055; ADP = 1e-5; AMP = 1e-8; Pi_ = 0.0054; Gly = 0.02; 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 = 1e-3; pH_calc = 7.14; LAC_ec = 0; HCO3_cy = 15e-3; CO2_cy = 0.001564425; HCO3_ec = 30e-3; CO2_ec = 0.001564425; MOPS = 0; MOPSH = 0; pH_ec = 7.439766507222684; time_ = ; 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 = ; v_MCT = ; CK = ; ADK = ; ATPase = ; oxphos = ; pHODEterm1 = ; v_psCO2 = ; v_hydrCO2cy = ; v_hydrCO2ec = ; fluxCO2 = ; Flow = ; V_cell = ; V_ec = ; pH_in = ; MOPSt = ; CO2_in = ; HCO3_in = ; clamp = ; end model *vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus____main() // Sub-modules, and any changes to those submodules: environment: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__environment(time_, pH_cy, pH_calc, CO2_in, HCO3_in, pH_in, MOPSt, clamp); parameters: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__parameters(Vfgly, fracA, KgpA_glyf, KgpA_pi, KgpA_igly, KgpA_ipi, KgpA_glyb, KgpA_g1p, KgpA_ig1p, KgpB_pi, KgpB_ipi, KgpB_iglyf, KgpB_g1p, KgpB_ig1p, KgpB_iglyb, Kgp_amp, nH, Vffpglm, Kpglm_g1p, Kpglm_g6p, Vbbpgi, Kpgi_g6p, Kpgi_f6p, Vffpfk, Kpfk_f6p, Kpfk_f6pT, Kpfk_atp, Kpfk_atpT, Kpfk_fbp, Kpfk_fbpT, Kpfk_adp, Kpfk_adpT, Kpfki, Kmpfk, d, e_, Lo, Vffald, Kald_fbp, Kald_dhap, Kald_gap, Vfftpi, Ktpi_gap, Ktpi_dhap, Vbbg3pdh, Kg3pdh_g3p, Kg3pdh_nad, Kg3pdh_dhap, Kg3pdh_nadh, Vffgad, Kgapdh_gap, Kgapdh_nad, Kgapdh_pi, Kgapdh_bpg, Kgapdh_nadh, Vbbpgk, Kpgk_bpg, Kpgk_adp, Kpgk_3pg, Kpgk_atp, Vffpgm, Kpgm_3pg, Kpgm_2pg, Vffen, Ken_2pg, Ken_pep, Vffpk, Kpk_pep, Kpk_adp, Kpk_pyr, Kpk_atp, Vffldh, Kldh_pyr, Kldh_nadh, Kldh_lac, Kldh_nad, VforCK, Kck_pcr, Kck_iatp, Kck_iadp, Kck_ipcr, Kck_cr, Kck_Iadp, Kck_Ipcr, Kck_Icr, Kck_Iatp, Kck_Ii, Vfadk, Kadk_amp, Kadk_atp, Kadk_adp, kut, VmaxOxPhos, Kmadp, nnHH, Vmax_MCT, Klac1, pKmct1, PSVCO2, X_CA, kf_hydrCO2, Keq_CA, kb_hydrCO2, Flow, V_cell, V_ec, bufcapfixed); equilibrium_constants: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__equilibrium_constants(T, I, k, c0, R, B, I1, alphadebye, IcorrpKa, RTalpha, IcorrdeltaGpof, pKa1_Pi, pKamg_Pi, pKak_Pi, P_Pi, HPi2, H2Pi1, kPi, mgPi, Navg_Pi, dNavgPidH, NH_HPi2, deltaGof_HPi2, deltaGpof_HPi2, pKa1_ATP, pKamg_ATP, pKak_ATP, P_ATP, ATP4, HATP3, mgATP2, kATP, Navg_ATP, dNavgATPdH, NH_ATP4, deltaGof_ATP4, deltaGpof_ATP4, pKak_ADP, pKa1_ADP, pKamg_ADP, P_ADP, ADP3, HADP2, mgADP, kADP, Navg_ADP, dNavgADPdH, NH_ADP3, deltaGof_ADP3, deltaGpof_ADP3, pKa1_AMP, pKamg_AMP, P_AMP, AMP2, HAMP1, mgAMP, Navg_AMP, dNavgAMPdH, NH_AMP2, deltaGof_AMP2, deltaGpof_AMP2, pKak_PCR, pKa1_PCR, pKamg_PCR, P_PCR, HPCR, H2PCR, kPCR, mgPCR, Navg_PCR, dNavgPCRdH, NH_HPCR, pKa1_CR, P_CR, HCR, H2CR, Navg_CR, dNavgCRdH, NH_HCR, pKa1_G1P, pKamg_G1P, P_G1P, UG1P, HG1P, mgG1P, Navg_G1P, dNavgG1PdH, NH_UG1P, deltaGof_UG1P, deltaGpof_UG1P, pKa1_G6P, P_G6P, UG6P, HG6P, Navg_G6P, dNavgG6PdH, dNavgG6Pdmg, NH_UG6P, deltaGof_UG6P, deltaGpof_UG6P, pKa1_F6P, P_F6P, UF6P, HF6P, Navg_F6P, dNavgF6PdH, NH_UF6P, deltaGof_UF6P, deltaGpof_UF6P, pKa1_FDP, pKamg_FDP, P_FDP, UFDP, HFDP, mgFDP, Navg_FDP, dNavgFDPdH, NH_UFDP, deltaGof_UFDP, deltaGpof_UFDP, pKa1_GAP, P_GAP, UGAP, HGAP, Navg_GAP, dNavgGAPdH, dNavgGAPdmg, NH_UGAP, deltaGof_UGAP, deltaGpof_UGAP, pKamg_G3P, pKa1_G3P, P_G3P, UG3P, HG3P, mgG3P, Navg_G3P, dNavgG3PdH, NH_UG3P, deltaGof_UG3P, deltaGpof_UG3P, pKa1_DHAP, pKamg_DHAP, P_DHAP, UDHAP, HDHAP, mgDHAP, Navg_DHAP, dNavgDHAPdH, NH_UDHAP, deltaGof_UDHAP, deltaGpof_UDHAP, pKa1_13DPG, P_13DPG, U13DPG, H13DPG, Navg_13DPG, dNavg13DPGdH, NH_U13DPG, deltaGof_U13DPG, deltaGpof_U13DPG, pKa1_3PG, P_3PG, U3PG, H3PG, Navg_3PG, dNavg3PGdH, NH_U3PG, deltaGof_U3PG, deltaGpof_U3PG, pKa1_2PG, pKamg_2PG, pKak_2PG, P_2PG, U2PG, H2PG, mg2PG, k2PG, Navg_2PG, dNavg2PGdH, NH_U2PG, deltaGof_U2PG, deltaGpof_U2PG, pKa1_PEP, pKamg_PEP, pKak_PEP, P_PEP, UPEP, HPEP, kPEP, mgPEP, Navg_PEP, dNavgPEPdH, NH_UPEP, deltaGof_UPEP, deltaGpof_UPEP, pKa1_PYR, P_PYR, UPYR, HPYR, Navg_PYR, dNavgPYRdH, dNavgPYRdmg, NH_UPYR, deltaGof_UPYR, deltaGpof_UPYR, pKamg_LAC, pKa1_LAC, P_LAC, ULAC, HLAC, mgLAC, Navg_LAC, dNavgLACdH, dmgLACdmg, dmgLACdpH, NH_ULAC, deltaGof_ULAC, deltaGpof_ULAC, dNH_GLY, deltaGpo_GLY, NH_NAD, deltaGof_NAD, deltaGpof_NAD, NH_NADH, deltaGof_NADH, deltaGpof_NADH, NH_H2O, deltaGof_H2O, deltaGpof_H2O, NH_H, deltaGof_H, deltaGpof_H, deltaH_CK, slopeint_1, slopeint_2, Kref_CKT, I25, alphadebye1, IcorrneglnKrefCK, neglnKrefCK_Iexp, Kref_CK, deltaGpo_CK, Kapp_CK, deltaH_ADK, deltaGpo_ADK, Kapp_ADK, deltaH_GP, deltaGpo_GP, Kapp_GP, deltaH_PGLM, deltaGpo_PGLM, Kapp_PGLM, deltaH_PGI, deltaGpo_PGI, Kapp_PGI, deltaH_PFK, deltaGpo_PFK, Kapp_PFK, deltaH_ALD, deltaGpo_ALD, Kapp_ALD, deltaH_TPI, deltaGpo_TPI, Kapp_TPI, deltaH_GAPDH, deltaGpo_GAPDH, Kapp_GAPDH, deltaH_G3PDH, deltaGpo_G3PDH, Kapp_G3PDH, deltaH_PGK, deltaGpo_PGK, Kapp_PGK, deltaH_PGM, deltaGpo_PGM, Kapp_PGM, deltaH_ENOL, deltaGpo_ENOL, Kapp_ENOL, deltaH_PK, deltaGpo_PK, Kapp_PK, deltaH_LDH, deltaGpo_LDH, Kapp_LDH, deltaH_ATPase, deltaGpo_ATPase, Kapp_ATPase, mg, pH_cy); glycogen_phosphorylase_A: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__glycogen_phosphorylase_A(Dglya, pa, VbglyA, glyAF, glyAR, flux_GPa, KgpA_glyf, KgpA_glyb, KgpA_igly, KgpA_pi, KgpA_ipi, KgpA_g1p, KgpA_ig1p, Vfgly, fracA, Gly, Pi_, G1P, pH_cy, Kapp_GP); glycogen_phosphorylase_B: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__glycogen_phosphorylase_B(fracB, M, Dglyb, pb, VbglyB, glyBF, glyBR, flux_GPb, fracA, pH_cy, AMP, Gly, Pi_, G1P, Kapp_GP, nH, Vfgly, Kgp_amp, KgpB_iglyf, KgpB_iglyb, KgpB_pi, KgpB_ipi, KgpB_g1p, KgpB_ig1p); PGLM: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGLM(Vfpglm, Vbpglm, v_PGLM, pH_cy, Vffpglm, Kpglm_g1p, Kpglm_g6p, Kapp_PGLM, G1P, G6P); PGI: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGI(Vbpgi, Vfpgi, v_PGI, pH_cy, Vbbpgi, Kpgi_g6p, Kpgi_f6p, Kapp_PGI, G6P, F6P); PFK: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PFK(Vfpfk, Vbpfk, L, alpha, Delta, Deltap, v_PFK, pH_cy, Lo, d, Vffpfk, Kpfk_fbp, Kpfk_adp, Kpfk_f6p, Kpfk_atp, Kpfk_fbpT, Kpfk_adpT, Kpfk_f6pT, Kpfk_atpT, Kapp_PFK, Kmpfk, Kpfki, ATP, ADP, AMP, F6P, FBP); ALD: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__ALD(Vfald, Vbald, v_ALD, pH_cy, Vffald, Kald_gap, Kald_fbp, Kald_dhap, Kapp_ALD, FBP, GAP, DHAP); TPI: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__TPI(Vftpi, Vbtpi, v_TPI, Vfftpi, Ktpi_dhap, Ktpi_gap, Kapp_TPI, GAP, DHAP); G3PDH: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__G3PDH(Dg3pdh, Vbg3pdh, Vfg3pdh, v_G3PDH, Vbbg3pdh, Kg3pdh_dhap, Kg3pdh_g3p, Kg3pdh_nadh, Kg3pdh_nad, Kapp_G3PDH, G3P, NADH, DHAP, NAD); GAPDH: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__GAPDH(Dgap, Vfgad, Vbgad, v_GAPDH, pH_cy, Vffgad, Kgapdh_bpg, Kgapdh_gap, Kgapdh_pi, Kgapdh_nadh, Kgapdh_nad, Kapp_GAPDH, GAP, BPG, NADH, Pi_, NAD); PGK: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGK(Vbpgk, Vfpgk, D_PGK, v_PGK, Vbbpgk, Kpgk_bpg, Kpgk_3pg, Kpgk_atp, Kpgk_adp, Kapp_PGK, P3G, BPG, ATP, ADP, NAD); PGM: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PGM(Vfpgm, Vbpgm, v_PGM, pH_cy, Vffpgm, Kpgm_2pg, Kpgm_3pg, Kapp_PGM, P2G, P3G); ENOL: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__ENOL(Vfen, Vben, v_ENOL, pH_cy, Vffen, Ken_2pg, Ken_pep, Kapp_ENOL, P2G, PEP); PK: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__PK(Vfpk, Vbpk, v_PK, pH_cy, Vffpk, Kpk_atp, Kpk_adp, Kpk_pep, Kpk_pyr, Kapp_PK, ATP, ADP, PEP, PYR); LDH: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__LDH(Vfldh, Vbldh, v_LDH, pH_cy, Vffldh, Kldh_lac, Kldh_pyr, Kldh_nad, Kldh_nadh, Kapp_LDH, PYR, LAC, NAD, NADH); creatine_kinase: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__creatine_kinase(VrevCK, CK, VforCK, Kck_iatp, Kck_iadp, Kck_pcr, Kck_ipcr, Kck_cr, Kapp_CK, ATP, ADP, Cr, PCr); adenylate_kinase: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__adenylate_kinase(Vbadk, ADK, Vfadk, Kadk_atp, Kadk_adp, Kadk_amp, Kapp_ADK, ATP, ADP, AMP); ATPase: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__ATPase(ATPase0, kut, ATP); OXPHOS: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__OXPHOS(oxphos, VmaxOxPhos, nnHH, Kmadp, ADP); lactate_transport: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__lactate_transport(Kh, v_MCT, pH_cy, pKmct1, Vmax_MCT, nnHH, Klac1, LAC, pH_ec, LAC_ec); CO2_generation_transport: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__CO2_generation_transport(RQ, PO2ratio, fluxO2, fluxCO2, oxphos); Passive_permeation_flux: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__Passive_permeation_flux(v_psCO2, v_hydrCO2cy, v_hydrCO2ec, pH_cy, X_CA, PSVCO2, kf_hydrCO2, kb_hydrCO2, pH_ec, CO2_ec, HCO3_ec, CO2_cy, HCO3_cy); buffer_capacity: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__buffer_capacity(bufcapmetab, c0, 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); proton_flux: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__proton_flux(CKprtflux, glycprtflux, protons_consumed, pHODEterm1, 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, deltaH_ATPase, 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, v_MCT, v_hydrCO2cy, CK, ADK, ATPase0, oxphos, bufcapfixed, bufcapmetab); differential_equations: vinnakota_rusk_palmer_shankland_kushmeric_2010_soleus__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, LAC_ec, HCO3_cy, CO2_cy, HCO3_ec, CO2_ec, MOPS, MOPSH, pH_ec, dPCrdt, dCrdt, dNADdt, dNADHdt, dATPdt, dADPdt, dAMPdt, dPidt, dglydt, dG1Pdt, dG6Pdt, dF6Pdt, dFBPdt, dDHAPdt, dG3Pdt, dGAPdt, dBPGdt, dP3Gdt, dP2Gdt, dPEPdt, dPYRdt, dLACdt, dmgdt, dpH_calcdt, dLACecdt, dHCO3cydt, dCO2cydt, dHCO3ecdt, dCO2ecdt, MOPS_in, MOPSH_in, v_MOPSbuff, dMOPSdt, dMOPSHdt, dpHecdt, time_, 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, v_MCT, CK, ADK, ATPase0, oxphos, pHODEterm1, v_psCO2, v_hydrCO2cy, v_hydrCO2ec, fluxCO2, Flow, V_cell, V_ec, pH_in, MOPSt, CO2_in, HCO3_in, clamp); end