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C4Ini.m
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% Copyright Wang Y and Zhu X-G, 2014.
% CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
% A mixed pathway model of C4 photosynthesis
%the code for initial concentrations of metabolites, and parameters .
function con = C4Ini()%
global Bchl_CA;
global Bchl_CN;
Bchl_CA= 1.5;
Bchl_CN= 0.5;
global MC_CU;
global MC_CA;
MC_CU=1.5;
MC_CA=1.0;
global Mchl_CA;
global Mchl_CN;
Mchl_CA= 1.5;
Mchl_CN= 0.5;
global MC_UTP;
MC_UTP=1.26;%0.75
global Bper_GLU;
global Bper_KG;
global Bper_NADH;
global Bper_NAD;
Bper_GLU=24;
Bper_KG=0.4;
Bper_NADH=0.47;
Bper_NAD=0.4;
global CI;
global O2;
%MC mesophyll cell cytosol
MC_HCO3= 0.005;
MC_OAA=0.01;
MC_PEP=0.1;
MC_Malate=1.0;
MC_Pyruvate=2;%
MC_PGA=0.3;
MC_FBP=0.04;
MC_UDPG=0.035;
MC_SUCP=0.0;
MC_SUC=0.0;
MC_F26BP=7.8E-5;
MC_ATP=0.35;%
MC_T3P=0.55;
MC_HexP=2.4;
MC_Sucrose=0.0;
%Mchl mesophyll chloroplast
Mchl_OAA= 0.005;
Mchl_Malate =1.8;
Mchl_PEP =0.1;
Mchl_Pyruvate= 0.01;
Mchl_NADPH= 0.21;
Mchl_ATP= 1.4;
Mchl_PGA= 0.04;
Mchl_DPGA= 0.0;
Mchl_T3P= 0.6;
%BSC bundle sheath cell cytosol
BSC_T3P= 0.45;
BSC_PGA= 0.2;
BSC_Malate=0.8;
BSC_Pyruvate= 2;%
BSC_CO2= 0.001;
%Bchl bundle sheath chloroplast
Bchl_CO2= 0.01;
Bchl_RuBP= 2.0;
Bchl_PGA= 0.3;
Bchl_DPGA= 0;
Bchl_ATP= 1.4;
Bchl_NADPH= 0.1;
Bchl_SBP= 0.015;
Bchl_S7P= 0.045;
Bchl_FBP= 0.06;
Bchl_E4P= 0.05;
Bchl_Starch= 0.0;
Bchl_Rubisco= 1.456965457;
Bchl_T3P= 0.5;
Bchl_HexP= 2.2;
Bchl_Pent =0.05;
Bchl_Malate= 0.3;
Bchl_Pyruvate= 0.23;
Bchl_PGCA=0.0029;
Bchl_GCA=0.36;
Bchl_GCEA=0.1812;
Bper_GCA=0.36;
Bper_GOA=0.028;
Bper_GLY=1.8;
Bper_SER=7.5;
Bper_HPR=0.0035;
Bper_GCEA=0.1812;
Bchl_PPi=0;
Bchl_ADPG=0;
MC_CO2=0.5*CI;
MC_Glu=15;
MC_OxoG=3;
MC_Asp=0;
MC_Ala=0;
BSC_OxoG=3;
BSC_Glu=15;
BSC_Asp=0;
BSC_Ala=0;
BSC_OAA=0;
BSC_PEP=0.1;
BSC_ATP=0.5;
Bchl_OAA=0;
MC_O2=O2;
Mchl_O2=O2;
BSC_O2=O2;
Bchl_O2=O2;
con=zeros(1,74);
con(1)=MC_HCO3;
con(2)=MC_OAA;
con(3)=MC_PEP;
con(4)=MC_Malate;
con(5)=MC_Pyruvate;
con(6)=MC_PGA;
con(7)=MC_FBP;
con(8)=MC_UDPG;
con(9)=MC_SUCP;
con(10)=MC_SUC;
con(11)=MC_F26BP;
con(12)=MC_ATP;
con(13)=MC_T3P;
con(14)=MC_HexP;
con(15)=MC_Sucrose;
con(16)=Mchl_OAA;
con(17)=Mchl_Malate;
con(18)=Mchl_PEP;
con(19)=Mchl_Pyruvate;
con(20)=Mchl_NADPH;
con(21)=Mchl_ATP;
con(22)=Mchl_PGA;
con(23)=Mchl_DPGA;
con(24)=Mchl_T3P;
con(25)=BSC_T3P;
con(26)=BSC_PGA;
con(27)=BSC_Malate;
con(28)=BSC_Pyruvate;
con(29)=BSC_CO2;
con(30)=Bchl_CO2;
con(31)=Bchl_RuBP;
con(32)=Bchl_PGA;
con(33)=Bchl_DPGA;
con(34)=Bchl_ATP;
con(35)=Bchl_NADPH;
con(36)=Bchl_SBP;
con(37)=Bchl_S7P;
con(38)=Bchl_FBP;
con(39)=Bchl_E4P;
con(40)=Bchl_Starch;
con(41)=Bchl_Rubisco;
con(42)=Bchl_T3P;
con(43)=Bchl_HexP;
con(44)=Bchl_Pent;
con(45)=Bchl_Malate;
con(46)=Bchl_Pyruvate;
con(47)=Bchl_PGCA;
con(48)=Bchl_GCA;
con(49)=Bchl_GCEA;
con(50)=Bper_GCA;
con(51)=Bper_GOA;
con(52)=Bper_GLY;
con(53)=Bper_SER;
con(54)=Bper_HPR;
con(55)=Bper_GCEA;
con(56)=MC_CO2;
con(57)=Bchl_PPi;
con(58)=Bchl_ADPG;
con(59)=MC_Glu;
con(60)=MC_OxoG;
con(61)=MC_Asp;
con(62)=MC_Ala;
con(63)=BSC_OxoG;
con(64)=BSC_Glu;
con(65)=BSC_Asp;
con(66)=BSC_Ala;
con(67)=BSC_OAA;
con(68)=BSC_PEP;
con(69)=BSC_ATP;
con(70)=Bchl_OAA;
con(71)=MC_O2;
con(72)=Mchl_O2;
con(73)=BSC_O2;
con(74)=Bchl_O2;
%Km Ki(mM)
%4.2.1.1 1
KmCO2_1 = 2.8;%2.8;
Ke_1 =11.2;%20;%;% No unit
%4.1.1.31 2
KmHCO3_2 =0.02; KmPEP_2 =1; Kimal_2 =1;
%1.1.1.82 3
KmNADPH_3 =0.024; KmOAA_3 =0.056; KmNADP_3 =0.073; Kmmal_3 =32.0;
Ke_3 =4450.0; % No unit
%1.1.1.40 4
KmCO2_4 =1.1; KmNADP_4 =0.0080; KmNADPH_4 =0.045; KmPyr_4 =3; Kmmal_4 =0.23; Ke_4 =0.051;%0.0344 KmNADP_4 =0.008
%2.7.9.1 5
KiPEP_5 =0.15; KmATP_5 =0.082; KmPyr_5 =0.082;%
%4.1.1.39 6
KmCO2_6 =0.0162; KmO2_6 =0.183; KmRuBP_6 =0.02; KiPGA_6 =2.52; KiFBP_6 =0.04; KiSBP_6 =0.075; KiPi_6 =0.9*3; KiNADPH_6 =0.07*3;%KiNADPH_6 =0.07;KiPi_6 =0.9
%2.7.2.3 7
KmADP_7 =0.5; KmATP_7 =0.3; KmPGA_7 =2.4;
%1.2.1.13 8
KmDPGA_8 =0.4; KmNADPH_8=0.1;
%5.3.1.1 9
Ke_9=0.05;
%4.1.2.13FBP 10
KmDHAP_10 =0.45; KmFBP_10 =0.0923; KmGAP_10 =0.04;
Ke_10 =7.1; % 1/millimolarity
%3.1.3.11
KiF6P_11 =0.7; KiPi_11 =12.0; KmFBP_11 =0.066; Ke_11 =666000.0;
%4.1.2.13SBP 12
KmDHAP_12 =0.4; KmE4P_12 =0.2;
Ke_12 =1.017; % 1/millimolarity
%3.1.3.37 13
KiPi_13 =12.0; KmSBP_13 =0.05; Ke_13 =666000.0;
%2.2.1.1X 14
KmE4P_14 =0.1; KmF6P_14 =0.1; KmGAP_14 =0.1; KmXu5P =0.1;
Ke_14 =0.084; % No unit
%2.2.1.1R 15
KmGAP_15 =0.072; KmRi5P_15 =1.5; KmS7P_15 =0.015; KmXu5P_15 =0.1;
Ke_15 =0.9;%
%5.3.1.6:Chl 16
Ke_16=0.4;
%5.1.3.1:Chl 17
Ke_17=0.67;
%2.7.1.19 18
KiADP_18 =2.5; Ki_ADP_18 =0.4; KiPGA_18 =2.0; KiPi_18 =4.0; KiRuBP_18 =0.7; KmATP_18 =0.625; KmRu5P_18 =0.05; % KiPi_18 =4.0;
Ke_18 =6846.0; % No unit
%2.7.2.3:MChl 7Mchl
KmADP_7Mchl =0.5; KmATP_7Mchl =0.3; KmPGA_7Mchl =2.4;
%1.2.1.13:MChl 8Mchl
KmDPGA_8Mchl =0.4; KmNADPH_8Mchl =0.1;
%StarchSynthesis:Chl Starchsyn
KiADP_Starch =10.0; KmATP_Starch =0.08; KmG1P_Starch =0.48; KaF6P_Starch =0.12; KaFBP_Starch =0.12; KaPGA_Starch =0.3;% Ka (No unit)KmG1P_Starch =0.08; KaF6P_Starch =0.02; KaFBP_Starch =0.02; KaPGA_Starch =0.1
Ke_Starch1=2.3; Ke_Starch2=0.058;
%PGASink
KmPGA_PGASink=1;%
%4.1.2.13FBP:Cel Suc1
KmDHAP_Suc1 =0.45; KmGAP_Suc1 =0.04/2; KmFBP_Suc1 =0.0023; %KmDHAP_Suc1 =0.4; KmGAP_Suc1 =0.1; KmFBP_Suc1 =0.2;
Ke_Suc1 =12;%12.0; 10000 % 1/millimolarity
%3.1.3.11:Cel
KiF26BP_Suc2 =0.00007; KiF6P_Suc2 =0.7; KiPi_Suc2 =12.0; KmFBP_Suc2 =0.00108; Ke_Suc2 =174.0;
%5.3.1.9:Cel Suc5
Ke_Suc5=2.3;
%5.4.2.2:Cel Suc6
Ke_Suc6=0.0584;
%2.7.7.9:Cel Suc7
KmG1P_Suc7 =0.14; KmPPi_Suc7 =0.11; KmUDPG_Suc7 =0.12; KmUTP_Suc7 =0.1;
Ke_Suc7 =0.31;%0.31; % No unit
%2.4.1.14:Cel Suc8
KiFBP_Suc8 =0.8; KiPi_Suc8 =5.0; KiSuc_Suc8 =50.0; KiSucP_Suc8 =0.4; KiUDP_Suc8 =0.7; KmF6P_Suc8 =0.8; KmUDPG_Suc8 =1.3;
Ke_Suc8 =10.0; % No unit
%3.1.3.24:Cel Suc9
KmSuc_Suc9 =80.0; KmSucP_Suc9 =0.35; Ke_Suc9 =780.0;
%SUCSink:Cel Suc10
KmSuc_Suc10 =1.5;
%2.7.1.105:Cel Suc3
KiADP_Suc3 =0.16; KIDHAP_Suc3 =0.7; KmATP_Suc3 =1.32; KmF26BP_Suc3 =0.021; KmF6P_Suc3 =1.4;
Ke_Suc3 =590.0;% No unit
%3.1.3.46:Cel Suc4
KiF6P_Suc4 =0.1; KiPi_Suc4 =0.5*10; KmF26BP_Suc4= 0.032;
%3.6.1.1:Cel
KePi=128.4;
%3.6.3.14:MChl ATPM
KmADP_ATPM =0.014; KmATP_ATPM =0.11; KmPi_ATPM =0.3;
Ke_ATPM =5.734; %1/millimolarity
X =0.667; Y =0.6; F =0.7225; Q =0.7; D =1;% No unit
%1.18.1.2:MChl NADPHM
KmNADP_NADPHM =0.05; KmNADPH_NADPHM =0.058; %
Ke_NADPHM =502; E =0.5; % No unit
%V3.6.3.14:Chl ATPB
KmADP_ATPB =0.014; KmPi_ATPB =0.11; KmATP_ATPB =0.3;
Ke_ATPB =5.734; % 1/millimolarity
G =0.667; % No unit
%1.18.1.2:BChl NADPHB
KmNADP_NADPHB =0.05; KmNADPH_NADPHB =0.058;
Ke_NADPHB =502; % No unit
%4.1.1.39 O2 1
KmCO2_PR1=0.0162; KmO2_PR1=0.183; KmRuBP_PR1=0.02; KiPGA_PR1=2.52; KiFBP_PR1=0.04; KiSBP_PR1=0.75; KiPi_PR1=0.9*3; KiNADPH_PR1=0.21;
%3.1.3.18 2
KmPGCA_PR2=0.026; KiPI_PR2=2.55; KiGCA_PR2=94.0;
%1.1.3.15 3
KmGCA_PR3= 0.1;
%2.6.1.4 4
Ke_PS4= 607.0; KmGOA_PS4=0.15; KmGLU_PS4= 1.7; KiGLY_PS4=2.0;
%GLY_SER:Mit 5
KmGLY_PS5= 6.0; KiSER_PS5=4.0;
%2.6.1.45 6
Ke_PR6= 0.24; KmGOA_PR6=0.15; KmSER_PR6=2.7; KmGLY_PR6=33.0;
%1.1.1.29 7
Ke_PR7= 250000.0; KiHPR_PR7= 12.0; KmHPR_PR7=0.09;
%2.7.1.31 8
Ke_PR8= 300.0; KmATP_PR8= 0.21; KmGCEA_PR8=0.25; KiPGA_PR8=0.72;
%Tgca 9
KmGCA_PR9= 0.2; KiGCEA_PR9= 0.22;
%Tgcea 10
KmGCEA_PR10= 0.39; KiGCA_PR10= 0.28;
% Transport coeffcient (1/second)
Voaa =1.5;
Vmal =1.5;
Vpyr =1.5;
Vpep =1.5;
Vt =1.5;
Vleak=1;
Vpga=2;
KmPGA_62 = 0.08;
KmPEP_62 = 0.3;
Ke_62=0.4302;%
global KValue;
KValue=zeros(48,10);
KValue(1,1)=KmCO2_1; KValue(1,2)=Ke_1;
KValue(2,1)=KmHCO3_2; KValue(2,2)= KmPEP_2; KValue(2,3)=Kimal_2;
KValue(3,1)=KmNADPH_3; KValue(3,2)=KmOAA_3; KValue(3,3)=KmNADP_3; KValue(3,4)=Kmmal_3; KValue(3,5)=Ke_3;
KValue(4,1)=KmCO2_4; KValue(4,2)=KmNADP_4; KValue(4,3)=KmNADPH_4; KValue(4,4)=KmPyr_4; KValue(4,5)=Kmmal_4; KValue(4,6)=Ke_4;
KValue(5,1)=KiPEP_5; KValue(5,2)=KmATP_5; KValue(5,3)=KmPyr_5;
KValue(6,1)=KmCO2_6; KValue(6,2)=KmO2_6; KValue(6,3)=KmRuBP_6; KValue(6,4)=KiPGA_6; KValue(6,5)=KiFBP_6; KValue(6,6)=KiSBP_6; KValue(6,7)=KiPi_6; KValue(6,8)=KiNADPH_6;
KValue(7,1)=KmADP_7; KValue(7,2)=KmATP_7; KValue(7,3)=KmPGA_7;
KValue(8,1)=KmDPGA_8; KValue(8,2)=KmNADPH_8;
KValue(9,1)=Ke_9;
KValue(10,1)=KmDHAP_10; KValue(10,2)=KmFBP_10; KValue(10,3)=KmGAP_10; KValue(10,4)=Ke_10;
KValue(11,1)=KiF6P_11; KValue(11,2)=KiPi_11; KValue(11,3)=KmFBP_11; KValue(11,4)=Ke_11;
KValue(12,1)=KmDHAP_12; KValue(12,2)=KmE4P_12; KValue(12,3)=Ke_12;
KValue(13,1)=KiPi_13; KValue(13,2)=KmSBP_13; KValue(13,3)=Ke_13;
KValue(14,1)=KmE4P_14; KValue(14,2)=KmF6P_14; KValue(14,3)=KmGAP_14; KValue(14,4)=KmXu5P; KValue(14,5)=Ke_14;
KValue(15,1)=KmGAP_15; KValue(15,2)=KmRi5P_15; KValue(15,3)=KmS7P_15; KValue(15,4)=KmXu5P_15; KValue(15,5)=Ke_15;
KValue(16,1)=Ke_16;
KValue(17,1)=Ke_17;
KValue(18,1)=KiADP_18; KValue(18,2)=Ki_ADP_18; KValue(18,3)=KiPGA_18; KValue(18,4)=KiPi_18; KValue(18,5)=KiRuBP_18; KValue(18,6)=KmATP_18; KValue(18,7)=KmRu5P_18; KValue(18,8)=Ke_18;
KValue(19,1)=KmADP_7Mchl; KValue(19,2)=KmATP_7Mchl; KValue(19,3)=KmPGA_7Mchl;
KValue(20,1)=KmDPGA_8Mchl; KValue(20,1)=KmNADPH_8Mchl;
KValue(21,1)=KiADP_Starch; KValue(21,2)=KmATP_Starch; KValue(21,3)=KmG1P_Starch; KValue(21,4)=KaF6P_Starch; KValue(21,5)=KaFBP_Starch; KValue(21,6)=KaPGA_Starch; KValue(21,7)=Ke_Starch1; KValue(21,8)=Ke_Starch2;
KValue(22,1)=KmPGA_PGASink;
KValue(23,1)=KmDHAP_Suc1; KValue(23,2)=KmGAP_Suc1; KValue(23,3)=KmFBP_Suc1; KValue(23,4)=Ke_Suc1;
KValue(24,1)=KiF26BP_Suc2; KValue(24,2)=KiF6P_Suc2; KValue(24,3)=KiPi_Suc2; KValue(24,4)=KmFBP_Suc2; KValue(24,5)=Ke_Suc2;
KValue(25,1)=Ke_Suc5; KValue(25,2)=Ke_Suc6;
KValue(26,1)=KmG1P_Suc7; KValue(26,2)=KmPPi_Suc7; KValue(26,3)=KmUDPG_Suc7; KValue(26,4)=KmUTP_Suc7; KValue(26,5)=Ke_Suc7;
KValue(27,1)=KiFBP_Suc8; KValue(27,2)=KiPi_Suc8; KValue(27,3)=KiSuc_Suc8; KValue(27,4)=KiSucP_Suc8; KValue(27,5)=KiUDP_Suc8; KValue(27,6)=KmF6P_Suc8; KValue(27,7)=KmUDPG_Suc8; KValue(27,8)=Ke_Suc8;
KValue(28,1)=KmSuc_Suc9; KValue(28,2)=KmSucP_Suc9; KValue(28,3)=Ke_Suc9;
KValue(29,1)=KmSuc_Suc10;
KValue(30,1)=KiADP_Suc3; KValue(30,2)=KIDHAP_Suc3; KValue(30,3)=KmATP_Suc3; KValue(30,4)=KmF26BP_Suc3; KValue(30,5)=KmF6P_Suc3; KValue(30,6)=Ke_Suc3;
KValue(31,1)=KiF6P_Suc4; KValue(31,2)=KiPi_Suc4; KValue(31,3)=KmF26BP_Suc4;
KValue(36,1)=KePi;
KValue(32,1)=KmADP_ATPM; KValue(32,2)=KmATP_ATPM; KValue(32,3)=KmPi_ATPM; KValue(32,4)=X; KValue(32,5)=Y; KValue(32,6)=F; KValue(32,7)=Q; KValue(32,8)=D; KValue(32,9)=Ke_ATPM;
KValue(33,1)=KmNADP_NADPHM; KValue(33,2)=KmNADPH_NADPHM; KValue(33,3)=Ke_NADPHM; KValue(33,4)=E;
KValue(34,1)=KmADP_ATPB; KValue(34,2)=KmPi_ATPB; KValue(34,3)=KmATP_ATPB; KValue(34,4)=Ke_ATPB; KValue(34,5)=G;
KValue(37,1)=KmNADP_NADPHB; KValue(37,2)=KmNADPH_NADPHB; KValue(37,3)=Ke_NADPHB;
KValue(35,1)=Voaa; KValue(35,2)=Vmal; KValue(35,3)=Vpyr; KValue(35,4)=Vpep; KValue(35,5)=Vt; KValue(35,6)=Vleak; KValue(35,7)=Vpga;
KValue(38,1)= KmCO2_PR1; KValue(38,2)= KmO2_PR1; KValue(38,3)=KmRuBP_PR1; KValue(38,4)=KiPGA_PR1; KValue(38,5)=KiFBP_PR1; KValue(38,6)=KiSBP_PR1; KValue(38,7)=KiPi_PR1; KValue(38,8)=KiNADPH_PR1;
KValue(39,1)=KmPGCA_PR2; KValue(39,2)=KiPI_PR2; KValue(39,3)=KiGCA_PR2;
KValue(40,1)=KmGCA_PR3;
KValue(41,1)=Ke_PS4; KValue(41,2)=KmGOA_PS4; KValue(41,3)=KmGLU_PS4; KValue(41,4)=KiGLY_PS4;
KValue(42,1)=KmGLY_PS5; KValue(42,2)=KiSER_PS5;
KValue(43,1)=Ke_PR6; KValue(43,2)=KmGOA_PR6; KValue(43,3)=KmSER_PR6; KValue(43,4)=KmGLY_PR6;
KValue(44,1)=Ke_PR7; KValue(44,2)=KiHPR_PR7; KValue(44,3)=KmHPR_PR7;
KValue(45,1)=Ke_PR8; KValue(45,2)=KmATP_PR8; KValue(45,3)=KmGCEA_PR8; KValue(45,4)=KiPGA_PR8;
KValue(46,1)=KmGCA_PR9; KValue(46,2)=KiGCEA_PR9;
KValue(47,1)=KmGCEA_PR10; KValue(47,2)=KiGCA_PR10;
KValue(48,1)=KmPGA_62; KValue(48,2)=KmPEP_62; KValue(48,3)=Ke_62;
%mM/(L*s)
Vm_1 = 200;
Vm_2 = 0.18;
Vm_3 = 0.09;
Vm_4 = 0.09;
Vm_5 = 0.09;
Vm_6 = 0.065;
Vm_78= 0.2;
Vm_8 = 0;
Vm_10 = 0.0731;
Vm_11 =0.0654;
Vm_12 =0.1097;
Vm_13 =0.0292;
Vm_14 =0.2810;
Vm_15 = 0.2810;
Vm_18 = 0.9751;
Vm_78Mchl=0.3;
Vm_8Mchl =0;
Vm_Starch =0;
Vm_Sta1=0.03;
Vm_Sta2=1;
Vm_Sta3=0.025;
Vm_PGASink = 0.002;
Vm_Suc1 = 0.0081;
Vm_Suc2 = 0.0064;
Vm_Suc7 = 0.0058;
Vm_Suc8 = 0.0278;
Vm_Suc9 = 0.0278;
Vm_Suc10 =0.0035;
Vm_Suc3 =0.001;
Vm_Suc4 =8.4096e-004;
global I;
Jmax =0.5;
Vm_ATPM = 0.3;
Vm_NADPHM = 0.2;
Vm_ATPB = 0.3;
Vm_NADPHB= 0.2;
Vm_PR1= Vm_6*0.11;%(Cousins 2010 0.11)
Vm_PR2= 2.6210;
Vm_PR3= 0.0728;
Vm_PR4= 0.1373;
Vm_PR5= 0.1247;
Vm_PR6= 0.1653;
Vm_PR7= 0.5005;
Vm_PR8= 0.2858;
VTgca_PR9=0.3;
VTgcea_PR10=0.25;
Vm_62 =0.001;
Vm_OAA_M=0.08;
Vm_PYR_B=0.2;
Vm_PYR_M=0.2;
Vm_PEP_M=0.15;
global Vtpt_Bchl;
global Vtpt_Mchl;
Vtpt_Bchl=0.75;
Vtpt_Mchl=0.75;
Vtp_Bchl=Vtpt_Bchl;
Vtp_Mchl=Vtpt_Mchl;
Vm_MAL_B=0.15;
Vm_MAL_M=0.15;
% transport between two cell types
global phi;
global Lpd;
Pmal=0.0421*(phi/0.03)/(Lpd/400);
Ppyr=0.0436*(phi/0.03)/(Lpd/400);
Pco2=0.1139*(phi/0.03)/(Lpd/400);
global PC3P;
PC3P=0.0327;
Pc3p=PC3P*(phi/0.03)/(Lpd/400);
Pco2_B=0.2;
global vrpd;
vrpd=0.0005;
global Velocity_s;
Velocity_s=zeros(60,1);
Velocity_s(1)=Vm_1;
Velocity_s(2)=Vm_2;
Velocity_s(3)=Vm_3;
Velocity_s(4)=Vm_4;
Velocity_s(5)=Vm_5;
Velocity_s(6)=Vm_6;
Velocity_s(7)=Vm_78;
Velocity_s(8)=Vm_8;
Velocity_s(9)=Vm_10;
Velocity_s(10)=Vm_11;
Velocity_s(11)=Vm_12;
Velocity_s(12)=Vm_13;
Velocity_s(13)=Vm_14;
Velocity_s(14)=Vm_15;
Velocity_s(15)=Vm_18;
Velocity_s(16)=Vm_78Mchl;
Velocity_s(17)=Vm_8Mchl;
Velocity_s(18)=Vm_Starch;
Velocity_s(19)=Vm_PGASink;
Velocity_s(20)=Vm_Suc1;
Velocity_s(21)=Vm_Suc2;
Velocity_s(22)=Vm_Suc7;
Velocity_s(23)=Vm_Suc8;
Velocity_s(24)=Vm_Suc9;
Velocity_s(25)=Vm_Suc10;
Velocity_s(26)=Vm_Suc3;
Velocity_s(27)=Vm_Suc4;
Velocity_s(28)=I;
Velocity_s(29)=Jmax;
Velocity_s(30)=Vm_ATPM;
Velocity_s(31)=Vm_NADPHM;
Velocity_s(32)=Vm_ATPB;
Velocity_s(33)=Vm_NADPHB;
Velocity_s(34)=Vm_PR1;
Velocity_s(35)=Vm_PR2;
Velocity_s(36)=Vm_PR3;
Velocity_s(37)=Vm_PR4;
Velocity_s(38)=Vm_PR5;
Velocity_s(39)=Vm_PR6;
Velocity_s(40)=Vm_PR7;
Velocity_s(41)=Vm_PR8;
Velocity_s(42)=VTgca_PR9;
Velocity_s(43)=VTgcea_PR10;
Velocity_s(44)=Vm_62;
Velocity_s(45)=Vtp_Bchl;
Velocity_s(46)=Vtp_Mchl;
Velocity_s(47)=Vm_Sta1;
Velocity_s(48)=Vm_Sta2;
Velocity_s(49)=Vm_Sta3;
Velocity_s(50)=Vm_OAA_M;
Velocity_s(51)=Vm_PYR_B;
Velocity_s(52)=Vm_PYR_M;
Velocity_s(53)=Vm_PEP_M;
Velocity_s(54)=Pmal;
Velocity_s(55)=Ppyr;
Velocity_s(56)=Pco2;
Velocity_s(57)=Pc3p;
Velocity_s(58)=Pco2_B;
Velocity_s(59)=Vm_MAL_B;
Velocity_s(60)=Vm_MAL_M;
%Velocity_s=Velocity_s/20; % unit conversion