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PSInitial.m
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PSInitial.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright Xin-Guang Zhu, Yu Wang, Donald R. ORT and Stephen P. LONG
%CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
%China Institute of Genomic Biology and Department of Plant Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
%University of Illinois at Urbana Champaign
%Global Change and Photosynthesis Research Unit, USDA/ARS, 1406 Institute of Genomic Biology, Urbana, IL 61801, USA.
% This file is part of e-photosynthesis.
% e-photosynthesis is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation;
% e-photosynthesis is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
% You should have received a copy of the GNU General Public License (GPL)
% along with this program. If not, see <http://www.gnu.org/licenses/>.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function PSs = PSInitial(Begin)
global PSRatio;
global PS_C_CA; % Global constant for the total adenylates
global PS_C_CP; % Global constant for the total phosphate
global PS_C_CN; % Global constant for the total NADP+NADPH
global PS_PEXT; % Global constant for the cytosolic Phosphate concentration;
PS_C_CP = 15*PSRatio(1);
PS_C_CA =1.5*PSRatio(2);
PS_C_CN =1*PSRatio(3);
PS_PEXT =0.5*PSRatio(4);
global PSPR_RA_CA;
PSPR_RA_CA = PS_C_CA;
RuBP = 2.000;
PGA = 2.400;
DPGA =0.0011;
T3P = 0.5;
ADPG = 0.005;
FBP =0.670;
E4P =0.050;
S7P = 2.000;
SBP = 0.300;
ATP = 0.68;
NADPH = 0.21;
HexP = 2.2;
PenP = 0.25;
CO2 = 0.012;
O2 = 0.21*1.26 ;
PSs(1) =RuBP;
PSs(2) =PGA;
PSs(3) =DPGA;
PSs(4) =T3P;
PSs(5) =ADPG;
PSs(6) =FBP;
PSs(7) =E4P;
PSs(8) =S7P;
PSs(9) =SBP;
PSs(10) =ATP;
PSs(11) =NADPH;
PSs(12) = CO2;
PSs(13) = O2;
PSs(14) = HexP;
PSs(15) = PenP;
% Initialize the constants for the different reactions
global KM11 ;
global KM12 ;
global KM13 ;
global KI11 ;
global KI12 ;
global KI13 ;
global KI14 ;
global KI15 ;
global KM21 ;
global KM22 ;
global KM23 ;
global KM31a ;
global KM32b ;
global KM41 ;
global KM42 ;
global KE4 ;
global KM51 ;
global KM52 ;
global KM53 ;
global KE5 ;
global KM61 ;
global KI61 ;
global KI62 ;
global KM71 ;
global KM72 ;
global KM73 ;
global KM74 ;
global KM8 ;
global KM81 ;
global KM82 ;
global KM9 ;
global KI9 ;
global KM10 ;
global KM101 ;
global KM102 ;
global KM103 ;
global KE11 ;
global KE12 ;
global KM131 ;
global KM132 ;
global KI131 ;
global KI132 ;
global KI133 ;
global KI134 ;
global KI135 ;
global KM161 ;
global KM162 ;
global KE21 ;
global KE22 ;
global KM311 ;
global KM312 ;
global KM313 ;
global KM32 ;
global KM33 ;
global KE6;
global KE7;
global KE8;
global KE9;
global KE10;
global KE13;
global KE16;
global KM103;
global KM163;
KM11 = 0.0115*PSRatio(20); % CO2 1 RuBP+CO2->2PGA
KM12 = 0.222*PSRatio(21); % O2 1 RuBP+CO2->2PGA
KM13 = 0.02*PSRatio(22); % RuBP 1 RuBP+CO2->2PGA
KI11 = 0.84*PSRatio(23) ; % PGA
KI12 = 0.04*PSRatio(24) ; % FBP
KI13 = 0.075*PSRatio(25); % SBP
KI14 = 0.9*PSRatio(26) ; % Pi
KI15 = 0.07*PSRatio(27) ; % NADPH
KM21 = 0.240*PSRatio(28); % PGA 2 PGA+ATP <-> ADP + DPGA
KM22 = 0.390*PSRatio(29); % ATP 2 PGA+ATP <-> ADP + DPGA
KM23 = 0.23*PSRatio(30) ; % ADP
KM31a = 0.004*PSRatio(31); % BPGA 3 DPGA+NADPH <->GAP + OP+NADP
KM32b = 0.1*PSRatio(32) ; % NADPH 3 DPGA+NADPH <->GAP + OP+NADP
KM41 = 2.5*PSRatio(33) ; % DHAP 4 DHAP <->GAP
KM42 = 0.68*PSRatio(34); % GAP 4 DHAP <->GAP
KE4 = 1/0.05*PSRatio(35); % Using the value from Patterson
KM51 = 0.3*PSRatio(36); % GAP 5 GAP+DHAP <->FBP
KM52 = 0.4*PSRatio(37) ; % DHAP 5 GAP+DHAP <->FBP
KM53 = 0.02*PSRatio(38); % FBP 5 GAP+DHAP <->FBP % Original Value: 0.02
KE5 = 7.100*PSRatio(39); % Defult: 7.1
KM61 = 0.033*PSRatio(40); % FBP 6 FBP<->F6P+OP
KI61 = 0.7*PSRatio(41) ; % F6P
KI62 = 12*PSRatio(42) ; % Pi
KE6 = 6.66 * 10^5*PSRatio(43); % The equilibrium constant for this reaction % New mM Laisk or Bassham and Krause 1969 BBA
KM71 = 0.100*PSRatio(44); % Xu5P 7 F6P+GAP<->E4P+Xu5P % jn
KM72 = 0.100*PSRatio(45); % E4P 7 F6P+GAP<->E4P+Xu5P
KM73 = 0.1*PSRatio(46); % F6P This value was based on estimate
KM74 = 0.1000*PSRatio(47); % Estimate for GAP ORIGINAL 0.1
KE7 = 0.1*PSRatio(48) ; % The equilibrium constant for this reaction % New Laisk Bassham and Krause 1969 BBA
KM8 = 0.02*PSRatio(49); % SBP 8 E4P+DHAP<->SBP
KM81 = 0.4*PSRatio(50) ; % DHAP
KM82 = 0.2*PSRatio(51) ; % E4P estimate
KE8 = 1.017*PSRatio(52) ; % The equilibrium constant for this reaction % New mM-1 Laisk Bassham and Krause 1969 BBA. Default: 1.107
KM9 = 0.05*PSRatio(53); % SBP 9 SBP<->S7P+OP
KI9 = 12*PSRatio(54) ; % The inibintion constant for Pi;
KE9 = 6.66 * 10^5*PSRatio(55) ; % The equilibrium constant of this reaction % New mM Laisk Bassham and Krause 1969 BBA
KM10 = 0.5*PSRatio(56) ; % R5P 10 S7P+GAP<->Ri5P+Xu5P
KM101 = 0.1*PSRatio(57) ; % Xu5P
KM102 = 0.09*PSRatio(58) ; % Estimate for GAP
KM103 = 0.015*PSRatio(59) ; % Estimate for S7P % New
KE10 = 1/0.85*PSRatio(60) ; % The equilibrium constant for this reaction % New From Laisk or Bassham and Krause 1969 BBA
KE11 = 0.4*PSRatio(61) ; % Equilibrium Constant 11 Ri5P<-->Ru5P
KE12 = 0.67*PSRatio(62); % Equilibrium Constant 12 Xu5P<-->Ru5P
KM131 = 0.05*PSRatio(63); % Ru5P 13 Ru5P+ATP<->RuBP+ADP
KM132 = 0.059*PSRatio(64); % ATP 13 Ru5P+ATP<->RuBP+ADP
KI131 = 2*PSRatio(65) ; % PGA 13 Ru5P+ATP<->RuBP+ADP
KI132 = 0.7*PSRatio(66) ; % RuBP 13 Ru5P+ATP<->RuBP+ADP
KI133 = 4*PSRatio(67) ; % Pi 13 Ru5P+ATP<->RuBP+ADP
KI134 = 2.5*PSRatio(68) ; % ADP 13 Ru5P+ATP<->RuBP+ADP
KI135 = 0.4*PSRatio(69) ; % ADP 13 Ru5P+ATP<->RuBP+ADP
KE13 = 6.846 * 10^3*PSRatio(70); % The equilibrium constant for this reaction % New From Laisk or Bassham and Krause 1969 BBA
KM161 = 0.014*PSRatio(71); % ADP 16 ADP+Pi<->ATP
KM162 = 0.3*PSRatio(72); % Pi 16 ADP+Pi<-> ATP
KM163 = 0.3*PSRatio(73); % ATP 16 ADP+Pi<-> ATP % New Based on Laisk
KE16 = 5.734*PSRatio(74); % The equilibrium constant for this reaction % NEW, From Laisk or Bassham and Krause 1969 BBA
KE21 = 2.3*PSRatio(75); % Equilibrium constant 21 F6P<->G6P
KE22 = 0.058*PSRatio(76); % Equilibrium constant 22 G6P<->G1P
% KM231 = 0.08; % G1P 23 G1P+ATP+Gn<->PPi+ADP+Gn+1
% KM232 = 0.08; % ATP 23 G1P+ATP+Gn<->PPi+ADP+Gn+1
% KA231 = 0.1; % PGA 23 G1P+ATP+Gn<->PPi+ADP+Gn+1
% KA232 = 0.02; % F6P 23 G1P+ATP+Gn<->PPi+ADP+Gn+1
% KA233 = 0.02; % FBP 23 G1P+ATP+Gn<->PPi+ADP+Gn+1
% KI23 = 10; % ADP 23 G1P+ATP+Gn<->PPi+ADP+Gn+1
KM311 = 0.077*PSRatio(77); % DHAP 31 DHAPi<->DHAPo
KM312 = 0.63*PSRatio(78); % Pi 31 DHAPi<->DHAPo
KM313 = 0.74*PSRatio(79); % Pext 31 DHAPi<->DHAPo
KM32 = 0.25*PSRatio(80); % PGA 32 PGAi<->PGAo
KM33 = 0.075*PSRatio(81); % GAP 33 GAPi<->GAPo
% Now put in the constant for the new ADPG Pyrophosphorylase and starch
% synthase
% ATP + Glucose-1-Phosphate --> ADPG + PPi
global KM231 ;
global KM232 ;
global KM233 ;
global KM234 ;
global KA231 ;
global KI231 ;
global KVmo ;
global KE23 ;
KM231 = 0.031*PSRatio(82); % G1P 23 G1P+ATP<->ADPG + PPi Laisk et al 1989
KM232 = 0.045*PSRatio(83); % ATP 23 G1P+ATP<->ADPG + PPi Laisk et al 1989
KM233 = 0.14*PSRatio(84); % ADPG 23 G1P+ATP<->ADPG + PPi Laisk et al 1989
KM234 = 0.8*PSRatio(85); % PPi 23 G1P+ATP<->ADPG + PPi Laisk et al 1989
KE23 = 7.6 * 10^(-3)*PSRatio(86); % PPi 23 G1P+ATP<->ADPG + PPi Laisk et al 1989
KA231 = 0.23*PSRatio(87); % PGA 23 G1P+ATP<->ADPG + PPi Laisk et al 1989
KI231 = 0.9*PSRatio(88);%0.9 ; % Pi 23 G1P+ATP<->ADPG + PPi Laisk et al 1989 WY201803
KVmo = 0.007*PSRatio(89); % The minimum maximum velocity Laisk et al 1989
% ADPG --> ADP + Gn % The starch synthesis reaction 24. Laisk et al
% 1989
global KM241;
global KM242;
global KE24;
KM241 = 0.2*PSRatio(90) ; % ADPG ADPG --> ADP + Gn Laisk et al 1989
KM242 = 0.6*PSRatio(91) ; % ADP ADPG --> ADP + Gn Laisk et al 1989
KE24 = 7.4 * 10^5*PSRatio(92) ; % ADP ADPG --> ADP + Gn Laisk et al 1989
global KE25;
KE25 = 1.2 * 107*PSRatio(93);
% Initialize the Vmax for different reactions
global V1 ;
global V2 ;
global V3 ;
global V5 ;
global V6 ;
global V7 ;
global V8 ;
global V9 ;
global V10 ;
global V11 ;
global V12 ;
global V13 ;
global V16 ;
global V21 ;
global V22 ;
global V23 ;
global V31 ;
global V32 ;
global V33 ;
global V24 ;
global GP;
if GP ==0
% FC is a fussl factor here.
FC = 1; % Defulat is 2.5.
fc16 = 1; % default 1.5.
% Initialize the values of the global variables
SC = 1; % Scalling coefficient for the stroma volume per mg chl. defualt 2
SC1 = 1;
SC222 = 2;
STOM1 = 1;
STOM2 = 1;
V1 = 2.93 * SC1 /STOM1*PSRatio(5) ; % (Harris & Koniger, 1997)
V2 = 30.15 * SC * STOM2 *PSRatio(6); % (Harris & Koniger, 1997)
V3 = 4.04 * SC * STOM2*PSRatio(7);% 1.57*SC ; % (Harris & Koniger, 1997)
V5 = 1.22*SC*PSRatio(8) ; % (Harris & Koniger, 1997)
V6 = 0.734*SC/STOM1*PSRatio(9) ; % (Harris & Koniger, 1997)
V7 = 3.12*SC * 4*PSRatio(10); % (Harris & Koniger, 1997)
V8 = 1.22*SC *PSRatio(11) ; % (Harris & Koniger, 1997)
V9 = 0.32 *3 *PSRatio(12) ; % 0.17*SC *FC ; % (Harris & Koniger, 1997) *3.
V10 = V7; % (Harris & Koniger, 1997)
V13 = 10.81*SC1*PSRatio(13) ; % (Harris & Koniger, 1997)
V16 = 5.47*PSRatio(14); % (Aflalo & Shavit, 1983, Davenport & McLeod, 1986)
V23 = 2 *PSRatio(15) ;
end
V24 = 2*PSRatio(16);
V31 = 1.0*PSRatio(17)*20 ;
V32 = 1.0*PSRatio(18);
V33 = 1.0*PSRatio(19)*20; %WY 2018103
global Cond_V16; % This parameter is used to modifying the V16 if needed.
Cond_V16 = V16;
global PS2SUCSV32;
PS2SUCSV32 = V32;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Here is the location for transfering variables%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global PS2RA_RuBP_ini;
PS2RA_RuBP_ini = RuBP;
global BF_FI_com;
global PS2BF_ATP;
global PS2BF_ADP;
global PS2BF_Pi;
PS2BF_ATP = ATP;
PS2BF_ADP = PS_C_CA - ATP;
global PS2PR_V1;
PS2PR_V1 = V1;
global CO2_PS2StomCond;
CO2_PS2StomCond = CO2;
global PS2SUCS_PGA;
PS2SUCS_PGA = PGA;