// Created by libAntimony v2.8.0 model *Singh2006_TCA_mtu_model2() // Compartments and Species: compartment cell; species $aca in cell, $oaa in cell, $coa in cell, cit in cell, icit in cell; species akg in cell, ssa in cell, suc in cell, sca in cell, fa in cell; species mal in cell, gly in cell, $biosyn in cell; // Reactions: CS: $aca + $oaa -> $coa + cit; cell*((CS_Vf_cs*(aca/CS_Kaca_cs)*(oaa/CS_Koaa_cs) - CS_Vr_cs*(coa/CS_Kcoa_cs)*(cit/CS_Kcit_cs))/((1 + aca/CS_Kaca_cs + coa/CS_Kcoa_cs)*(1 + oaa/CS_Koaa_cs + cit/CS_Kcit_cs))); ACN: cit -> icit; cell*((ACN_Vf_acn*(cit/ACN_Kcit_acn) - ACN_Vr_acn*(icit/ACN_Kicit_acn))/(1 + cit/ACN_Kcit_acn + icit/ACN_Kicit_acn)); ICD1: icit -> akg; cell*((ICD1_Vf_icd1*(icit/ICD1_Kicit_icd1) - ICD1_Vr_icd1*(akg/ICD1_Kakg_icd1))/(1 + icit/ICD1_Kicit_icd1 + akg/ICD1_Kakg_icd1)); ICD2: icit -> akg; cell*((ICD2_Vf_icd2*(icit/ICD2_Kicit_icd2) - ICD2_Vr_icd2*(akg/ICD2_Kakg_icd2))/(1 + icit/ICD2_Kicit_icd2 + akg/ICD2_Kakg_icd2)); KGD: akg -> ssa; cell*((KGD_Vf_kgd*(akg/KGD_Kakg_kgd) - KGD_Vr_kgd*(ssa/KGD_Kssa_kgd))/(1 + akg/KGD_Kakg_kgd + ssa/KGD_Kssa_kgd)); SSADH: ssa -> suc; cell*((SSADH_Vf_ssadh*(ssa/SSADH_Kssa_ssadh) - SSADH_Vr_ssadh*(suc/SSADH_Ksuc_ssadh))/(1 + ssa/SSADH_Kssa_ssadh + suc/SSADH_Ksuc_ssadh)); ScAS: sca -> suc; cell*((ScAS_Vf_scas*(sca/ScAS_Ksca_scas) - ScAS_Vr_scas*(suc/ScAS_Ksuc_scas))/(1 + sca/ScAS_Ksca_scas + suc/ScAS_Ksuc_scas)); SDH: suc -> fa; cell*((SDH_Vf_sdh*(suc/SDH_Ksuc_sdh) - SDH_Vr_sdh*(fa/SDH_Kfa_sdh))/(1 + suc/SDH_Ksuc_sdh + fa/SDH_Kfa_sdh)); FUM: fa -> mal; cell*((FUM_Vf_fum*(fa/FUM_Kfa_fum) - FUM_Vr_fum*(mal/FUM_Kmal_fum))/(1 + fa/FUM_Kfa_fum + mal/FUM_Kmal_fum)); MDH: mal -> $oaa; cell*((MDH_Vf_mdh*(mal/MDH_Kmal_mdh) - MDH_Vr_mdh*(oaa/MDH_Koaa_mdh))/(1 + mal/MDH_Kmal_mdh + oaa/MDH_Koaa_mdh)); ICL1: icit -> suc + gly; cell*((ICL1_Vf_icl1*(icit/ICL1_Kicit_icl1) - ICL1_Vr_icl1*(suc/ICL1_Ksuc_icl1)*(gly/ICL1_Kgly_icl1))/(1 + icit/ICL1_Kicit_icl1 + suc/ICL1_Ksuc_icl1 + gly/ICL1_Kgly_icl1 + icit/ICL1_Kicit_icl1*(suc/ICL1_Ksuc_icl1) + suc/ICL1_Ksuc_icl1*(gly/ICL1_Kgly_icl1))); ICL2: icit -> suc + gly; cell*((ICL2_Vf_icl2*(icit/ICL2_Kicit_icl2) - ICL2_Vr_icl2*(suc/ICL2_Ksuc_icl2)*(gly/ICL2_Kgly_icl2))/(1 + icit/ICL2_Kicit_icl2 + suc/ICL2_Ksuc_icl2 + gly/ICL2_Kgly_icl2 + icit/ICL2_Kicit_icl2*(suc/ICL2_Ksuc_icl2) + suc/ICL2_Ksuc_icl2*(gly/ICL2_Kgly_icl2))); MS: gly + $aca -> mal + $coa; cell*((MS_Vf_ms*(gly/MS_Kgly_ms)*(aca/MS_Kaca_ms) - MS_Vr_ms*(mal/MS_Kmal_ms)*(coa/MS_Kcoa_ms))/((1 + gly/MS_Kgly_ms + mal/MS_Kmal_ms)*(1 + aca/MS_Kaca_ms + coa/MS_Kcoa_ms))); SYN: akg -> $biosyn; cell*0.0341*((SYN_Vf_icd1*(icit/SYN_Kicit_icd1) - SYN_Vr_icd1*(akg/SYN_Kakg_icd1))/(1 + icit/SYN_Kicit_icd1 + akg/SYN_Kakg_icd1) + (SYN_Vf_icd2*(icit/SYN_Kicit_icd2) - SYN_Vr_icd2*(akg/SYN_Kakg_icd2))/(1 + icit/SYN_Kicit_icd2 + akg/SYN_Kakg_icd2)); // Species initializations: aca = 0.5; oaa = 0.0003; coa = 0.0001; cit = 3.4; icit = 0.06; akg = 0.96; ssa = 0.03; suc = 2.464; sca = 0.04; fa = 0.08528; mal = 0.408; gly = 0.114; biosyn = 0.1; // Compartment initializations: cell = 1; // Variable initializations: CS_Vf_cs = 64.8; CS_Vf_cs has mmlmin; CS_Kaca_cs = 0.05; CS_Kaca_cs has mml; CS_Koaa_cs = 0.012; CS_Koaa_cs has mml; CS_Vr_cs = 0.648; CS_Vr_cs has mmlmin; CS_Kcoa_cs = 0.5; CS_Kcoa_cs has mml; CS_Kcit_cs = 0.12; CS_Kcit_cs has mml; ACN_Vf_acn = 31.2; ACN_Vf_acn has mmlmin; ACN_Kcit_acn = 1.7; ACN_Kcit_acn has mml; ACN_Vr_acn = 0.312; ACN_Vr_acn has mmlmin; ACN_Kicit_acn = 0.7; ACN_Kicit_acn has mml; ICD1_Vf_icd1 = 10.2; ICD1_Vf_icd1 has mmlmin; ICD1_Kicit_icd1 = 0.03; ICD1_Kicit_icd1 has mml; ICD1_Vr_icd1 = 0.102; ICD1_Vr_icd1 has mmlmin; ICD1_Kakg_icd1 = 0.3; ICD1_Kakg_icd1 has mml; ICD2_Vf_icd2 = 9.965; ICD2_Vf_icd2 has mmlmin; ICD2_Kicit_icd2 = 0.06; ICD2_Kicit_icd2 has mml; ICD2_Vr_icd2 = 0.09965; ICD2_Vr_icd2 has mmlmin; ICD2_Kakg_icd2 = 0.6; ICD2_Kakg_icd2 has mml; KGD_Vf_kgd = 48.3; KGD_Vf_kgd has mmlmin; KGD_Kakg_kgd = 0.48; KGD_Kakg_kgd has mml; KGD_Vr_kgd = 0.483; KGD_Vr_kgd has mmlmin; KGD_Kssa_kgd = 4.8; KGD_Kssa_kgd has mml; SSADH_Vf_ssadh = 6.51; SSADH_Vf_ssadh has mmlmin; SSADH_Kssa_ssadh = 0.015; SSADH_Kssa_ssadh has mml; SSADH_Vr_ssadh = 0.0651; SSADH_Vr_ssadh has mmlmin; SSADH_Ksuc_ssadh = 0.15; SSADH_Ksuc_ssadh has mml; ScAS_Vf_scas = 1.2; ScAS_Vf_scas has mmlmin; ScAS_Ksca_scas = 0.02; ScAS_Ksca_scas has mml; ScAS_Vr_scas = 0.012; ScAS_Vr_scas has mmlmin; ScAS_Ksuc_scas = 5; ScAS_Ksuc_scas has mml; SDH_Vf_sdh = 1.02; SDH_Vf_sdh has mmlmin; SDH_Ksuc_sdh = 0.12; SDH_Ksuc_sdh has mml; SDH_Vr_sdh = 1.02; SDH_Vr_sdh has mmlmin; SDH_Kfa_sdh = 0.15; SDH_Kfa_sdh has mml; FUM_Vf_fum = 87.7; FUM_Vf_fum has mmlmin; FUM_Kfa_fum = 0.25; FUM_Kfa_fum has mml; FUM_Vr_fum = 87.7; FUM_Vr_fum has mmlmin; FUM_Kmal_fum = 2.38; FUM_Kmal_fum has mml; MDH_Vf_mdh = 184; MDH_Vf_mdh has mmlmin; MDH_Kmal_mdh = 0.833; MDH_Kmal_mdh has mml; MDH_Vr_mdh = 184; MDH_Vr_mdh has mmlmin; MDH_Koaa_mdh = 0.0443; MDH_Koaa_mdh has mml; ICL1_Vf_icl1 = 1.172; ICL1_Vf_icl1 has mmlmin; ICL1_Kicit_icl1 = 0.145; ICL1_Kicit_icl1 has mml; ICL1_Vr_icl1 = 0.01172; ICL1_Vr_icl1 has mmlmin; ICL1_Ksuc_icl1 = 0.59; ICL1_Ksuc_icl1 has mml; ICL1_Kgly_icl1 = 0.13; ICL1_Kgly_icl1 has mml; ICL2_Vf_icl2 = 0.391; ICL2_Vf_icl2 has mmlmin; ICL2_Kicit_icl2 = 1.3; ICL2_Kicit_icl2 has mml; ICL2_Vr_icl2 = 0.00391; ICL2_Vr_icl2 has mmlmin; ICL2_Ksuc_icl2 = 5.9; ICL2_Ksuc_icl2 has mml; ICL2_Kgly_icl2 = 1.3; ICL2_Kgly_icl2 has mml; MS_Vf_ms = 20; MS_Vf_ms has mmlmin; MS_Kgly_ms = 0.057; MS_Kgly_ms has mml; MS_Kaca_ms = 0.03; MS_Kaca_ms has mml; MS_Vr_ms = 0.2; MS_Vr_ms has mmlmin; MS_Kmal_ms = 1; MS_Kmal_ms has mml; MS_Kcoa_ms = 0.1; MS_Kcoa_ms has mml; SYN_Vf_icd1 = 10.2; SYN_Vf_icd1 has mmlmin; SYN_Kicit_icd1 = 0.03; SYN_Kicit_icd1 has mml; SYN_Vr_icd1 = 0.102; SYN_Vr_icd1 has mmlmin; SYN_Kakg_icd1 = 0.3; SYN_Kakg_icd1 has mml; SYN_Vf_icd2 = 9.965; SYN_Vf_icd2 has mmlmin; SYN_Kicit_icd2 = 0.06; SYN_Kicit_icd2 has mml; SYN_Vr_icd2 = 0.09965; SYN_Vr_icd2 has mmlmin; SYN_Kakg_icd2 = 0.6; SYN_Kakg_icd2 has mml; // Other declarations: const cell; // Unit definitions: unit time_unit = 60 second; unit substance = 1e-3 mole; unit mmlmin = 1e-3 mole / (litre * 60 second); unit mml = 1e-3 mole / litre; // Display Names: time_unit is "min"; substance is "mmole"; mmlmin is "mM_per_min"; mml is "mM"; end