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define_global.m
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define_global.m
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function [] = define_global()
% This function is used to define global variables used in the simulation.
global iPO2 idPsi iH_x iATP_x iADP_x iAMP_x iGTP_x iGDP_x iPI_x iNADH_x iQH2_x ...
iOAA_x iACCOA_x iCIT_x iICIT_x iAKG_x iSCOA_x iCOASH_x iSUC_x iFUM_x ...
iMAL_x iGLU_x iASP_x iK_x iMg_x iCO2tot_x iCred_i iATP_i iADP_i iAMP_i ...
iPI_i iH_i iMg_i iK_i iATP_c iADP_c iPI_c iH_c iMg_c iK_c iPYR_x iPYR_i ...
iPYR_c iCIT_i iCIT_c iAKG_i iAKG_c iSUC_i iSUC_c iMAL_i iMAL_c iASP_i ...
iASP_c iGLU_i iGLU_c iFUM_i iFUM_c iICIT_i iICIT_c iPCr_c iAMP_c iCr_c;
global i_J_C1 i_J_C3 i_J_C4 i_J_F1 i_J_ANT i_J_PI1 i_J_Hle i_J_KH i_J_pdh i_J_cits ...
i_J_acon i_J_isod i_J_akgd i_J_scoas i_J_sdh i_J_fum i_J_mdh i_J_ndk i_J_got ...
i_J_PI2 i_J_ATPt i_J_ADPt i_J_AMPt i_J_PYR_H i_J_GLU_H i_J_CIT_MAL i_J_SUC_MAL ...
i_J_AKG_MAL i_J_MAL_PI i_J_ASP_GLU i_J_PYRt i_J_CITt i_J_ICITt i_J_MALt ...
i_J_AKGt i_J_SUCt i_J_FUMt i_J_GLUt i_J_ASPt i_J_CKe i_J_AKe i_J_AtC...
iC16Carn_m iC16CoA_m iC16EnoylCoA_m iC16OHCoA_m iC16KetoCoA_m...
iC14Carn_cy iC14Carn_m iC14CoA_m iC14EnoylCoA_m iC14OHCoA_m...
iC14KetoCoA_m iC12Carn_cy iC12Carn_m iC12CoA_m iC12EnoylCoA_m iC12OHCoA_m...
iC12KetoCoA_m iC10Carn_cy iC10Carn_m iC10CoA_m iC10EnoylCoA_m iC10OHCoA_m...
iC10KetoCoA_m iC8Carn_cy iC8Carn_m iC8CoA_m iC8EnoylCoA_m iC8OHCoA_m...
iC8KetoCoA_m iC6Carn_cy iC6Carn_m iC6CoA_m iC6EnoylCoA_m iC6OHCoA_m...
iC6KetoCoA_m iC4Carn_cy iC4Carn_m iC4CoA_m...
iC4EnoylCoA_m iC4OHCoA_m iC4KetoCoA_m iAcetylCoAMAT iFADH_m iNADHm iCoAMAT...
iC16AcylCoACYT iC16Carn_cy;
%% define indices for all state variables
% For biochemical concentration variables the notations
% "_x", "_i", and "_c" denote matrix, im space, and cytoplasm,
% respectively. Thus iATP_x indexes ATP in the matrix.
%
% (i) oxygen species
iPO2 = 1;
% (ii) Matrix species and dPsi
idPsi = 2;
iH_x = 3;
iATP_x = 4;
iADP_x = 5;
iAMP_x = 6;
iGTP_x = 7;
iGDP_x = 8;
iPI_x = 9;
iNADH_x = 10;
iQH2_x = 11;
iOAA_x = 12;
iACCOA_x = 13;
iCIT_x = 14;
iICIT_x = 15;
iAKG_x = 16;
iSCOA_x = 17;
iCOASH_x = 18;
iSUC_x = 19;
iFUM_x = 20;
iMAL_x = 21;
iGLU_x = 22;
iASP_x = 23;
iK_x = 24;
iMg_x = 25;
iCO2tot_x = 26;
% (iii) IM space species
iCred_i = 27;
iATP_i = 28;
iADP_i = 29;
iAMP_i = 30;
iPI_i = 31;
iH_i = 32;
iMg_i = 33;
iK_i = 34;
% (iv) Cytoplasmic species
iATP_c = 35;
iADP_c = 36;
iPI_c = 37;
iH_c = 38;
iMg_c = 39;
iK_c = 40;
% others
iPYR_x = 41;
iPYR_i = 42;
iPYR_c = 43;
iCIT_i = 44;
iCIT_c = 45;
iAKG_i = 46;
iAKG_c = 47;
iSUC_i = 48;
iSUC_c = 49;
iMAL_i = 50;
iMAL_c = 51;
iASP_i = 52;
iASP_c = 53;
iGLU_i = 54;
iGLU_c = 55;
iFUM_i = 56;
iFUM_c = 57;
iICIT_i = 58;
iICIT_c = 59;
iPCr_c = 60;
iAMP_c = 61;
iCr_c = 62;
iC16Carn_cy = 63; % C16 AcylCarnitine cytosol
iC16Carn_m = 64; % C16 AcylCarnitine Matrix
iC16CoA_m = 65; % C16 AcylCoA Matrix
iC16EnoylCoA_m = 66; % C16 EnoylCoA Matrix
iC16OHCoA_m = 67; % C16 HydroxoxyacylCoA Matrix
iC16KetoCoA_m = 68; % C16 KetoacylCoA Matrix
iC14Carn_cy = 69; % C14 AcylCarnitine cytosol
iC14Carn_m = 70; % C14 AcylCarnitine Matrix
iC14CoA_m = 71; % C14 AcylCoA Matrix
iC14EnoylCoA_m = 72; % C14 EnoylCoA Matrix
iC14OHCoA_m = 73; % C14 HydroxoxyacylCoA Matrix
iC14KetoCoA_m = 74;
iC12Carn_cy = 75;
iC12Carn_m = 76;
iC12CoA_m = 77;
iC12EnoylCoA_m = 78;
iC12OHCoA_m = 79;
iC12KetoCoA_m = 80;
iC10Carn_cy = 81;
iC10Carn_m = 82;
iC10CoA_m = 83;
iC10EnoylCoA_m = 84;
iC10OHCoA_m = 85;
iC10KetoCoA_m = 86;
iC8Carn_cy = 87;
iC8Carn_m = 88;
iC8CoA_m = 89;
iC8EnoylCoA_m = 90;
iC8OHCoA_m = 91;
iC8KetoCoA_m = 92;
iC6Carn_cy = 93;
iC6Carn_m = 94;
iC6CoA_m = 95;
iC6EnoylCoA_m = 96;
iC6OHCoA_m = 97;
iC6KetoCoA_m = 98;
iC4Carn_cy = 99;
iC4Carn_m = 100;
iC4CoA_m = 101;
iC4EnoylCoA_m = 102;
iC4OHCoA_m = 103;
iC4KetoCoA_m = 104;
%State variables that are involved in both TCA/Oxphos and b oxidation
iAcetylCoAMAT = 105;
iFADH_m = 106;
iNADHm = 107;
iCoAMAT = 108;
iC16AcylCoACYT = 109;
%% Defining indices for all fluxes
i_J_C1 = 4 ;
i_J_C3 = 5;
i_J_C4 = 6;
i_J_F1 = 7;
i_J_ANT = 8;
i_J_PI1 = 9;
i_J_Hle = 10;
i_J_KH = 11;
i_J_pdh = 12;
i_J_cits = 13;
i_J_acon = 14;
i_J_isod = 15;
i_J_akgd = 16;
i_J_scoas = 17;
i_J_sdh = 18;
i_J_fum = 19;
i_J_mdh = 20;
i_J_ndk = 21;
i_J_got = 22;
i_J_PI2 = 23;
i_J_ATPt = 24;
i_J_ADPt = 25;
i_J_AMPt = 26;
i_J_PYR_H = 27;
i_J_GLU_H = 28;
i_J_CIT_MAL = 29;
i_J_SUC_MAL = 30;
i_J_AKG_MAL = 31;
i_J_MAL_PI = 32;
i_J_ASP_GLU = 33;
i_J_PYRt = 34;
i_J_CITt = 35;
i_J_ICITt = 36;
i_J_MALt = 37;
i_J_AKGt = 38;
i_J_SUCt = 39;
i_J_FUMt = 40;
i_J_GLUt = 41;
i_J_ASPt = 42;
i_J_CKe = 43;
i_J_AKe = 44;
i_J_AtC = 45;