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PSI.m
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PSI.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 = PSI(Begin);
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;
PS_C_CA =1.5;
PS_C_CN =1;
PS_PEXT =0.5;
global PSPR_RA_CA;
PSPR_RA_CA = PS_C_CA;
RuBP = 2.000;
PGA =2.400;
DPGA =0.0011;
T3P =0.5;
NONE =0;
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 = 0.264;
PSs(1) =RuBP;
PSs(2) =PGA;
PSs(3) =DPGA;
PSs(4) =T3P;
PSs(5) =NONE;
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;
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 KM231 ;
global KM232 ;
global KA231 ;
global KA232 ;
global KA233 ;
global KI23 ;
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; % CO2 1 RuBP+CO2->2PGA
KM12 = 0.222; % O2 1 RuBP+CO2->2PGA 0.28 DEFAUL.
KM13 = 0.02; % RuBP 1 RuBP+CO2->2PGA
KI11 = 0.84 ; % PGA
KI12 =0.04 ; % FBP
KI13 = 0.075 ; % SBP
KI14 = 0.9 ; % Pi
KI15 = 0.07 ; % NADPH
KM21 = 0.240; % PGA 2 PGA+ATP <-> ADP + DPGA
KM22 = 0.390; % ATP 2 PGA+ATP <-> ADP + DPGA
KM23 = 0.23 ; % ADP
KM31a = 0.004; % BPGA 3 DPGA+NADPH <->GAP + OP+NADP
KM32b = 0.1 ; % NADPH 3 DPGA+NADPH <->GAP + OP+NADP
KM41 = 2.5 ; % DHAP 4 DHAP <->GAP
KM42 = 0.68; % GAP 4 DHAP <->GAP
KE4 = 0.05; % Using the value from Patterson
KM51 = 0.3 ; % GAP 5 GAP+DHAP <->FBP
KM52 = 0.4 ; % DHAP 5 GAP+DHAP <->FBP
KM53 = 0.02; % FBP 5 GAP+DHAP <->FBP % Original Value: 0.02
KE5 = 7.100; % Defult: 7.1
KM61 = 0.033; % FBP 6 FBP<->F6P+OP
KI61 = 0.7 ; % F6P
KI62 = 12 ; % Pi
KE6 = 6.66 * 10^5; % The equilibrium constant for this reaction % New mM Laisk or Bassham and Krause 1969 BBA
KM71 = 0.100; % Xu5P 7 F6P+GAP<->E4P+Xu5P % jn
KM72 = 0.100; % E4P 7 F6P+GAP<->E4P+Xu5P
KM73 = 0.1; % F6P This value was based on estimate
KM74 = 0.1000; % Estimate for GAP ORIGINAL 0.1
KE7 = 10 ; % The equilibrium constant for this reaction % New Laisk Bassham and Krause 1969 BBA
KM8 = 0.02; % SBP 8 E4P+DHAP<->SBP
KM81 = 0.4 ; % DHAP
KM82 = 0.2 ; % E4P estimate
KE8 = 1.017 ; % The equilibrium constant for this reaction % New mM-1 Laisk Bassham and Krause 1969 BBA. Default: 1.107
KM9 = 0.05; % SBP 9 SBP<->S7P+OP
KI9 = 12 ; % The inibintion constant for Pi;
KE9 = 6.66 * 10^5 ; % The equilibrium constant of this reaction % New mM Laisk Bassham and Krause 1969 BBA
KM10 = 1.5 ; % R5P 10 S7P+GAP<->Ri5P+Xu5P
KM101 = 0.1 ; % Xu5P
KM102 = 0.072 ; % Estimate for GAP
KM103 = 0.46 ; % Estimate for S7P % New
KE10 = 1/0.85 ; % The equilibrium constant for this reaction % New From Laisk or Bassham and Krause 1969 BBA
KE11 = 0.4 ; % Equilibrium Constant 11 Ri5P<-->Ru5P
KE12 = 0.67; % Equilibrium Constant 12 Xu5P<-->Ru5P
KM131 = 0.05; % Ru5P 13 Ru5P+ATP<->RuBP+ADP
KM132 = 0.059; % ATP 13 Ru5P+ATP<->RuBP+ADP
KI131 = 2 ; % PGA 13 Ru5P+ATP<->RuBP+ADP
KI132 = 0.7 ; % RuBP 13 Ru5P+ATP<->RuBP+ADP
KI133 = 4 ; % Pi 13 Ru5P+ATP<->RuBP+ADP
KI134 = 2.5 ; % ADP 13 Ru5P+ATP<->RuBP+ADP
KI135 = 0.4 ; % ADP 13 Ru5P+ATP<->RuBP+ADP
KE13 = 6.846 * 10^3; % The equilibrium constant for this reaction % New From Laisk or Bassham and Krause 1969 BBA
KM161 = 0.014; % ADP 16 ADP+Pi<->ATP
KM162 = 0.3; % Pi 16 ADP+Pi<-> ATP
KM163 = 0.3; % ATP 16 ADP+Pi<-> ATP % New Based on Laisk
KE16 = 5.734; % The equilibrium constant for this reaction % NEW, From Laisk or Bassham and Krause 1969 BBA
KE21 = 2.3; % Equilibrium constant 21 F6P<->G6P
KE22 = 0.058; % 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; % DHAP 31 DHAPi<->DHAPo
KM312 = 0.63; % Pi 31 DHAPi<->DHAPo
KM313 = 0.74; % Pext 31 DHAPi<->DHAPo
KM32 = 0.25; % PGA 32 PGAi<->PGAo
KM33 = 0.075; % GAP 33 GAPi<->GAPo
% Initialize the Vmax for different reactions
global V1 ;
global V2 ;
global V3 ;
% global V4 ;
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 ;
% FC is a fussl factor here.
FC = 1; % Defulat is 2.5.
fc16 = 1; % default 1.5.
SC = 1; % Scalling coefficient for the stroma volume per mg chl. defualt 2
V31 = 3.73/3 ; % 1.05 *SC *1.0 ; % (Lilley, Chon, Mosbach & Heldt, 1977b) 31 Phosphate translocator DHAPi<->DHAPo 1.05 defulat
V32 = 3.73/3 ; %1.05 *SC *1.0; % (Lilley et al., 1977b) 32 Phosphate translocator PGAi<->PGAo 1.05 default
V33 = 3.73/3 ; %1.05 *SC * 1.0; % (Lilley et al., 1977b) 33 Phosphate translocator GAPi<->GAPo 1.05 default
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%H%%%%%%%%
% 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 V31_ps2ca;
global V32_ps2ca;
global V33_ps2ca;
V31_ps2ca = V31;
V32_ps2ca = V32;
V33_ps2ca = V33;