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PSRate.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 PSr = PSRate(t,PSs,Param)
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;
% For output of the flux
global PS_VEL;
global PS_TIME_N;
global PS_OLD_TIME;
PsCA = PS_C_CA;
PsCP = PS_C_CP;
PsCN = PS_C_CN;
PsPEXT = PS_PEXT;
% First the physical and chemical constant for all the 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 KM11 ;
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 KM231 ;
global KM232 ;
global KM233 ;
global KM234 ;
global KA231 ;
global KI231 ;
global KVmo ;
global KE23 ;
global KM241;
global KM242;
global KE24;
global KE25;
global KE6;
global KE7;
global KE8;
global KE9;
global KE10;
global KE13;
global KE16;
global KM103;
global KM163;
% Set the value to the local variables: for example: PrKM11
PsKM11 = KM11 ; % CO2 1 RuBP+CO2->2PGA
PsKM12 = KM12 ; % O2 1 RuBP+CO2->2PGA
PsKM13 = KM13 ; % RuBP 1 RuBP+CO2->2PGA
PsKI11 = KI11 ; % PGA
PsKI12 = KI12 ; % FBP
PsKI13 = KI13 ; % SBP
PsKI14 = KI14 ; % Pi
PsKI15 = KI15 ; % NADPH
PsKM21 = KM21 ; % PGA 2 PGA+ATP <-> ADP + DPGA
PsKM22 = KM22 ; % ATP 2 PGA+ATP <-> ADP + DPGA
PsKM23 = KM23 ; % ADP
PsKM31a = KM31a ; % BPGA 3 DPGA+NADPH <->GAP + OP+NADP
PsKM32b = KM32b ; % NADPH 3 DPGA+NADPH <->GAP + OP+NADP
PsKM41 = KM41 ; % DHAP 4 DHAP <->GAP
PsKM42 = KM42 ; % GAP 4 DHAP <->GAP
PsKE4 = KE4 ;
PsKM51 = KM51 ; % GAP 5 GAP+DHAP <->FBP
PsKM52 = KM52 ; % DHAP 5 GAP+DHAP <->FBP
PsKM53 = KM53 ; % FBP 5 GAP+DHAP <->FBP
PsKE5 = KE5 ;
PsKM61 = KM61 ; % FBP 6 FBP<->F6P+OP
PsKI61 = KI61 ;
PsKI62 = KI62 ;
PsKM71 = KM71 ; % Xu5P 7 F6P+GAP<->E4P+Xu5P
PsKM72 = KM72 ; % E4P 7 F6P+GAP<->E4P+Xu5P
PsKM73 = KM73 ; % Estimate for F6P
PsKM74 = KM74 ; % Estimate for GAP
PsKM8 = KM8 ; % SBP 8 E4P+DHAP<->SBP
PsKM81 = KM81 ; % DHAP
PsKM82 = KM82 ; % E4P
PsKM9 = KM9 ; % SBP 9 SBP<->S7P+OP
PsKI9 = KI9 ;
PsKM10 = KM10 ; % R5P 10 S7P+GAP<->Ri5P+Xu5P
PsKM101 = KM101 ; % Xu5P
PsKM102 = KM102 ; % GAP estimate
PsKM103 = KM103 ; % S7P estimate
PsKE11 = KE11 ; % Equilibrium Constant 11 Ri5P<-->Ru5P
PsKE12 = KE12 ; % Equilibrium Constant 12 Xu5P<-->Ru5P
PsKM131 = KM131 ; % Ru5P 13 Ru5P+ATP<->RuBP+ADP
PsKM132 = KM132 ; % ATP 13 Ru5P+ATP<->RuBP+ADP
PsKI131 = KI131 ; % PGA
PsKI132 = KI132 ; % RuBP
PsKI133 = KI133 ; % Pi
PsKI134 = KI134 ; % ADP
PsKI135 = KI135 ; % ADP
PsKM161 = KM161 ; % ADP 16 ADP+Pi<->ATP
PsKM162 = KM162 ; % Pi 16 ADP+Pi<-> ATP
PsKE21 = KE21 ; % Equilibrium constant 21 F6P<->G6P
PsKE22 = KE22 ; % Equilibrium constant 22 G6P<->G1P
PsKM311 = KM311 ; % DHAP 31 DHAPi<->DHAPo
PsKM312 = KM312 ; % Pi 31 DHAPi<->DHAPo
PsKM313 = KM313 ; % Pext 31 DHAPi<->DHAPo
PsKM32 = KM32 ; % PGA 32 PGAi<->PGAo
PsKM33 = KM33 ; % GAP 33 GAPi<->GAPo
PsKM231 = KM231 ;
PsKM232 = KM232;
PsKM233 = KM233 ;
PsKM234 = KM234 ;
PsKA231 = KA231 ;
PsKI231 = KI231 ;
PsKVmo = KVmo ;
PsKE23 = KE23 ;
PsKM241 = KM241;
PsKM242 = KM242;
PsKE24 = KE24;
PsKE25 = KE25;
PsKE6 = KE6;
PsKE7 = KE7;
PsKE8 = KE8;
PsKE9 = KE9;
PsKE10 = KE10;
PsKE13 = KE13;
PsKE16 = KE16;
PsKM103 = KM103;
PsKM163 = KM163;
% Initialize the PrVmax of the different reactions based on the global variables Vmax
global V1; % (Harris & Koniger, 1997) 1 Rubisco RuBP+CO2<->2PGA
global V2; % (Harris & Koniger, 1997) 2 PGA Kinase PGA+ATP <-> ADP + DPGA
global V3; % (Harris & Koniger, 1997) 3 GAP dehydragenase DPGA+NADPH <->GAP + OP+NADP
global V4; % (Harris & Koniger, 1997) 4 Triose phosphate isomerase DHAP <->GAP
global V5; % (Harris & Koniger, 1997) 5 Aldolase GAP+DHAP <->FBP
global V6; % (Harris & Koniger, 1997) 6 FBPase FBP<->F6P+OP
global V7; % (Harris & Koniger, 1997) 7 Transketolase F6P+GAP<->E4P+Xu5P
global V8; % (Harris & Koniger, 1997) 8 Aldolase E4P+DHAP<->SBP
global V9; % (Harris & Koniger, 1997) 9 SBPase SBP<->S7P+OP
global V10; % (Harris & Koniger, 1997) 10 Transketolase S7P+GAP<->Ri5P+Xu5P
global V11; % (Harris & Koniger, 1997) 11 Pentosephosphate isomerase Ri5P<-->Ru5P
global V12; % (Harris & Koniger, 1997) 12 Pentosephosphate epimerase Xu5P<-->Ru5P
global V13; % (Harris & Koniger, 1997) 13 Ribulosebiphosphate kinase Ru5P+ATP<->RuBP+ADP
global V16; % (Aflalo & Shavit, 1983, Davenport & McLeod, 1986) 16 ATP synthase ADP+Pi<->ATP
global V21; % 21 Hexose phosphate isomerase F6P<->G6P
global V22; % 22 Phosphoglucomutase G6P<->G1P
global V23; % (Latzko, Steup & Schachtele, 1981) 23 ATP + G-1P --> ADPG + PPi
global V31; % (Lilley, Chon, Mosbach & Heldt, 1977b) 31 Phosphate translocator DHAPi<->DHAPo
global V32; % (Lilley et al., 1977b) 32 Phosphate translocator PGAi<->PGAo
global V33; % (Lilley et al., 1977b) 33 Phosphate translocator GAPi<->GAPo
global V24; % % ADPG --> ADP + Gn
% Get the values of the global variables of Vmax for different reactions
global FIBF_PSPR_com;
global DPH;
global ATPActive;
RegFactor = 1;
PsV1 = V1 ; % 1 Rubisco RuBP+CO2<->2PGA
PsV2 = V2 ; % 2 PGA Kinase PGA+ATP <-> ADP + DPGA
PsV3 = V3 ; % 3 GAP dehydragenase DPGA+NADPH <->GAP + OP+NADP
PsV4 = V4 ; % 4 Triose phosphate isomerase DHAP <->GAP
PsV5 = V5 ; % 5 Aldolase GAP+DHAP <->FBP
PsV6 = V6 ; % 6 FBPase FBP<->F6P+OP
PsV7 = V7 ; % 7 Transketolase F6P+GAP<->E4P+Xu5P
PsV8 = V8 ; % 8 Aldolase E4P+DHAP<->SBP
PsV9 = V9 ; % 9 SBPase SBP<->S7P+OP
PsV10 = V10 ; % 10 Transketolase S7P+GAP<->Ri5P+Xu5P
PsV11 = V11 ; % 11 Pentosephosphate isomerase Ri5P<-->Ru5P
PsV12 = V12 ; % 12 Pentosephosphate epimerase Xu5P<-->Ru5P
PsV13 = V13; % 13 Ribulosebiphosphate kinase Ru5P+ATP<->RuBP+ADP
PsV16 = V16 ; % 16 ATP synthase ADP+Pi<->ATP
PsV21 = V21 ; % 21 Hexose phosphate isomerase F6P<->G6P
PsV22 = V22 ; % 22 Phosphoglucomutase G6P<->G1P
PsV23 = V23 ;% 23 ATP + G-1P -> ADPG + PPi
PsV31 = V31 * RegFactor; % 31 Phosphate translocator DHAPi<->DHAPo
PsV32 = V32 * RegFactor; % 32 Phosphate translocator PGAi<->PGAo
PsV33 = V33 * RegFactor; % 33 Phosphate translocator GAPi<->GAPo
PsV24 = V24; % 24 ADPG --> ADP + Gn
global SUCS2PS_Pic;
global PSPR_SUCS_com;
if PSPR_SUCS_com ==1
PsPEXT = SUCS2PS_Pic;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% First here is one way of the redox regulation, assuming the regulation is instataneous.
global RedoxReg_RA_com; % This part is essentially not used now. This part is left here only
% in case that there are more work using the equilibrium of Thio with enzyme
% as a way to regulate enzyme activities.
global Redox2PS_V6;
global Redox2PS_V9;
global Redox2PS_V13;
global Redox2PS_V16;
if RedoxReg_RA_com == 2
PsV6 = Redox2PS_V6;
PsV9 = Redox2PS_V9;
PsV13 = Redox2PS_V13;
PsV16 = Redox2PS_V16;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The second method of the redox regulation.
% First set the global poool from the RROEA.
global RROEA_Pool;
global RROEA_EPS_com;
global RROEA2PS_GAPDH;
global RROEA2PS_FBPase;
global RROEA2PS_SBPase;
global RROEA2PS_PRK;
global RROEA2PS_ATPase;
global RROEA2PS_ATPGPP;
if RROEA_EPS_com ==0
% ATPreg = ATP/3;
% ATPreg = PGA/3; % If there is no regulation of enzyme activity, some forcing needed to be added.
else
ATPreg = 1;
GAPDHT = RROEA_Pool ( 1 );
FBPaseT = RROEA_Pool ( 2 );
SBPaseT = RROEA_Pool ( 3 );
PRKT = RROEA_Pool ( 4 );
ATPaseT = RROEA_Pool ( 5 );
ATPGPPT = RROEA_Pool ( 6 );
PsV3 = V3 * RROEA2PS_GAPDH/GAPDHT;
PsV9 = V9 * RROEA2PS_SBPase/SBPaseT;
PsV13 = V13 * RROEA2PS_PRK/PRKT;
PsV16 = V16 * RROEA2PS_ATPase/ATPaseT;
PsV23 = V23 * RROEA2PS_ATPGPP/ATPGPPT;
end
% Setting the concentration
RuBP = PSs(1) ;
PGA = PSs(2) ;
DPGA = PSs(3) ;
T3P = PSs(4) ;
ADPG = PSs(5) ;
FBP = PSs(6) ;
E4P = PSs(7) ;
S7P = PSs(8) ;
SBP = PSs(9) ;
ATP = PSs(10) ;
NADPH = PSs(11) ;
CO2 = PSs(12) ;
O2 = PSs(13) ;
HexP = PSs(14);
PenP = PSs(15);
% Assuming that the regulation exists no matter there is enzyme regulation or not. ATPReg is
% used to regulate the TP export and starch synthesis.
% Now Calculate the concentration of the auxiliary variables.
global RuACT_EPS_com;
global PS2EPS_NADPH;
PS2EPS_NADPH = NADPH;
global PR_PS_com; % This is a variable indicating whether the PR model is actually need to be combined with PS or not. If 1 then means combined; 0 means not.
global StomCond_TrDynaPS_com; % Notice here only if there is no stomata conductance we need to use the
% external CO2 directly.
if StomCond_TrDynaPS_com ==0
global O2_cond;
global CO2_cond;
CO2 = CO2_cond;
O2 = O2_cond;
end
DHAP= T3P/(1+KE4);
GAP = KE4*T3P/(1+KE4);
%%%%%%%%%%%%%%%%%%%%%%%%%
% DHAP= T3P*KE4/(1+KE4); %%WY201803
% GAP = T3P/(1+KE4);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
ATPreg = DHAP/3; % If there is no regulation of enzyme activity, some forcing needed to be added.
if ATPreg >1
ATPreg =1;
end
NADP = PS_C_CN - NADPH;
ADP = PS_C_CA - ATP ;
F6P = (HexP /PsKE21)/(1+1/PsKE21+PsKE22);
G6P = HexP /(1+1/PsKE21+PsKE22);
G1P = (HexP *PsKE22)/(1+1/PsKE21+PsKE22);
Ru5P = PenP /(1+1/PsKE11+1/PsKE12);
Ri5P = (PenP/PsKE11) /(1+1/PsKE11+1/PsKE12);
Xu5P = (PenP/PsKE12) /(1+1/PsKE11+1/PsKE12);
PR2PS_Pgca = Param(2);
Pit = PS_C_CP - PGA - 2*DPGA-GAP-DHAP-2*FBP-F6P-E4P-2*SBP-S7P-Xu5P-Ri5P-Ru5P-2*RuBP-G6P-G1P- ATP -PR2PS_Pgca;
Pi = 0.5 * (-PsKE25 + (PsKE25 * PsKE25 + 4 * Pit * PsKE25)^0.5);
OPOP = Pit - Pi;
global V1Reg;
global RUBISCOMETHOD;
global RUBISCOTOTAL;
global ATPActive;
global RedoxReg_RA_com;
if RedoxReg_RA_com ==0
ATPreg = PGA/3;
else
ATPreg = 1;
end
V1Reg = 1+PGA/PsKI11+FBP/PsKI12+SBP/PsKI13 + Pi/PsKI14+NADPH/PsKI15;
if RUBISCOMETHOD ==2
tmp = PsV1 * RuBP/(RuBP+PsKM13*V1Reg);
v1 = tmp*CO2/(CO2+PsKM11*(1+O2/PsKM12));
if RuBP<PsV1/2.5
v1 = v1 * RuBP/(PsV1/2.5);
end
elseif RUBISCOMETHOD==1
v1 = PsV1*CO2/(CO2+PsKM11*(1+O2/PsKM12));
if RuBP<PsV1/2.5
v1 = v1 * RuBP/(PsV1/2.5);
end
end
v2 = PsV2 * PGA * ATP /((PGA + PsKM21)*(ATP+PsKM22*(1+ADP/PsKM23)));
v3 = PsV3 * DPGA * NADPH/((DPGA+PsKM31a)*(NADPH+PsKM32b));
v5 = PsV5 * (GAP * DHAP-FBP/PsKE5)/((PsKM51*PsKM52)*(1+GAP/PsKM51+DHAP/PsKM52+FBP/PsKM53+GAP*DHAP/(PsKM51*PsKM52)));
v8 = PsV8 * (DHAP *E4P-SBP/PsKE8)/((E4P+PsKM82)*(DHAP + PsKM81));
KE57 = 1.005 * 0.1*PSRatio(94);
Km8p5p = 0.118*PSRatio(95);
Km5p5p = 0.616*PSRatio(96);
KE810 = 0.8446*PSRatio(97);
Km5gap = 0.2727*PSRatio(98);
Km8f6p = 0.5443*PSRatio(99);
Km8s7p = 0.01576*PSRatio(100);
Km8gap = 0.09*PSRatio(101);
Den = 1 + (1+GAP/Km5gap)*(F6P/Km8f6p+S7P/Km8s7p)+GAP/Km8gap + 1/Km8p5p*(Xu5P*(1+E4P*Ri5P/Km5p5p)+E4P+Ri5P);
v7 = PsV7 * (F6P * GAP *KE57 - E4P * Xu5P)/(Km8p5p*Km5p5p*Den);
v10 = PsV7 * (S7P * GAP * KE810 - Xu5P * Ri5P)/(Km8p5p*Km5p5p*Den);
v6 = PsV6 * (FBP-F6P * Pi/PsKE6)/(FBP + PsKM61*(1+F6P/PsKI61+Pi/PsKI62));
v9 = PsV9 * (SBP-Pi * S7P/PsKE9) /(SBP + PsKM9*(1+Pi/PsKI9));
v13 = PsV13 * (ATP * Ru5P-ADP * RuBP/PsKE13)/((ATP*(1+ADP/PsKI134) + PsKM132*(1+ADP/PsKI135))*(Ru5P+PsKM131*(1+PGA/PsKI131+RuBP/PsKI132+Pi/PsKI133)));
v16 = PsV16 * (ADP * Pi-ATP/PsKE16)/(PsKM161*PsKM162 * (1+ADP/PsKM161 + Pi/PsKM162 + ATP/PsKM163 + ADP * Pi /(PsKM161 * PsKM162)));
Va = PsKVmo + PsV23 * (PGA/(PsKA231*(1+PGA/PsKA231)));
v23num = Va * (ATP * G1P - ADPG * OPOP/PsKE23); % The reason we set this here is to assume that we can obtain a reverse reaction here. However, a more realistic
% way to achieve the homeostasis might be to allow starch breakdown and allow regulation of SBPase and FBPase.
% WY 201803
%v23den = PsKM231 * PsKM232 * (1 + ATP/PsKM232 + G1P/PsKM231 + ATP * G1P/(PsKM231 * PsKM232) + ADPG/PsKM233 + OPOP/PsKM234 + ADPG * OPOP/(PsKM233 * PsKM234) + Pi/PsKI231);
v23den2 = (1+ Pi/PsKI231)*PsKM231 * PsKM232 * (1 + ATP/PsKM232 + G1P/PsKM231 + ATP * G1P/(PsKM231 * PsKM232) + ADPG/PsKM233 + OPOP/PsKM234 + ADPG * OPOP/(PsKM233 * PsKM234) );
v23 = v23num/v23den2;
%v23 = v23num/v23den;
v24num = PsV24 * (ADPG); % Similar to the argument for reaction 23. The control of homeostasis might be better enforced at the point of reaction 23.
v24dem = PsKM241 * (1+ ADPG/PsKM241);
v24 = v24num/v24dem;
MaxCoeff = 5*PSRatio(102);
V25max = 0.5*PSRatio(103)/100/5; %WY201803
v25 = V25max * (1- RuBP/MaxCoeff) * ATP/(ATP + 1);
%WY201803
% N = 1 + (1+ PsKM313/PsPEXT)*(Pi/PsKM312+PGA/PsKM32+GAP/PsKM33+DHAP/PsKM311);
% v31 = PsV31 * DHAP/(N*PsKM311) ;
% v32 = PsV32 * PGA/(N*PsKM32);
% v33 = PsV33 * GAP/(N * PsKM33);
%
v31= PsV31 * DHAP/(DHAP+PsKM311)*PsPEXT/(PsPEXT+ PsKM313);
v32 = PsV32 * PGA/(PGA+PsKM32)*PsPEXT/(PsPEXT+ PsKM313);
v33 = PsV33 * GAP/(GAP+PsKM33)*PsPEXT/(PsPEXT+ PsKM313);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
v31 = v31 * ATPreg ;
v32 = v32 * ATPreg ;
v33 = v33 * ATPreg ;
global EPS_ADP; % This variable is used in the BF_Rate when EPS is used.
EPS_ADP = ADP;
global EPS_Pi; % This variable is used in the BF_Rate when EPS is used.
EPS_Pi = Pi;
global PS2EPS_V16;
PS2EPS_V16 = v16;
global EPS_ADP; % This variable is used in the BF_Rate when EPS is used.
EPS_ADP = ADP;
global EPS_Pi; % This variable is used in the BF_Rate when EPS is used.
EPS_Pi = Pi;
global PS2EPS_v3;
PS2EPS_v3 = v3;
global PSPR_RA_O2; % RA is the combined EPS and Rubisco activase.
global PSPR_RA_CO2;
PSPR_RA_O2 = O2;
PSPR_RA_CO2 = CO2;
global PS2RA_ATP;
PS2RA_ATP = ATP;
% information is sent back to PR by PS2PR_Pi global variable.
global PS2PR_Pi;
PS2PR_Pi = Pi;
global PS2PR_ATP;
PS2PR_ATP = ATP;
global PS2PR_ADP;
PS2PR_ADP = ADP;
global PS2BF_ATP;
PS2BF_ATP = ATP;
global PS2BF_ADP;
PS2BF_ADP = ADP;
global PS2BF_Pi;
PS2BF_Pi = Pi;
global PS2SUCS_PGA;
PS2SUCS_PGA = PGA;
% Notice the series PS2CM is used both in the CM model and the FPSReg model and thereafter.
global PS2CM_vdhap;
PS2CM_vdhap = v31;
global PS2CM_vpga;
PS2CM_vpga = v32;
global PS2CM_vgap;
PS2CM_vgap = v33;
global PS2PRC;
global PS2PRO;
PS2PRC = CO2;
PS2PRO = O2;
global PS2RubACC;
global PS2RubACO;
PS2RubACC = CO2;
PS2RubACO = O2;
global PS2Stom_CO2_consum;
PS2Stom_CO2_consum = v1;
PSr = zeros(16,1);
PSr(1) = v1 ;
PSr(2) = v2 ;
PSr(3) = v3 ;
PSr(4) = 0 ;
PSr(5) = v5 ;
PSr(6) = v6 ;
PSr(7) = v7 ;
PSr(8) = v8 ;
PSr(9) = v9 ;
PSr(10) = v10 ;
PSr(11) = v13 ;
PSr(12) = v16 ;
PSr(13) = v23 ;
PSr(14) = v31 ;
PSr(15) = v32;
PSr(16) = v33;
PSr(17) = v24;
PSr(18) = v25;
PSr;
% Getting the information for output as figures.
if (PS_TIME_N ==0)
PS_TIME_N = 1;
end
if (t > PS_OLD_TIME)
PS_TIME_N = PS_TIME_N + 1;
PS_OLD_TIME = t;
end
PS_VEL(1,PS_TIME_N) = t;
PS_VEL(2,PS_TIME_N) = v1;
PS_VEL(3,PS_TIME_N) = v2;
PS_VEL(4,PS_TIME_N) = v3;
PS_VEL(5,PS_TIME_N) = 0;
PS_VEL(6,PS_TIME_N) = v5;
PS_VEL(7,PS_TIME_N) = v6;
PS_VEL(8,PS_TIME_N) = v7;
PS_VEL(9,PS_TIME_N) = v8;
PS_VEL(10,PS_TIME_N) = v9;
PS_VEL(11,PS_TIME_N) = v10;
PS_VEL(12,PS_TIME_N) = v13;
PS_VEL(13,PS_TIME_N) = v16;
PS_VEL(14,PS_TIME_N) = v23;
PS_VEL(15,PS_TIME_N) = v31;
PS_VEL(16,PS_TIME_N) = v32;
PS_VEL(17,PS_TIME_N) = v33;
PS_VEL(18,PS_TIME_N) = Pi;
PS_VEL(19,PS_TIME_N) = v24;
PS_VEL(20,PS_TIME_N) = v25;
% Transfer the variables for output
global PS2OUT;
PS2OUT = zeros(5,1);
PS2OUT(1) = RuBP;
PS2OUT(2) = PGA;
PS2OUT(3) = DPGA;
PS2OUT(4) = T3P;
PS2OUT(5) = ADPG;
PS2OUT(6) = FBP;
PS2OUT(7) = E4P;
PS2OUT(8) = S7P;
PS2OUT(9) = SBP;
PS2OUT(10) = ATP;
PS2OUT(11) = NADPH;
PS2OUT(12) = CO2;
PS2OUT(13) = O2;
PS2OUT(14) = HexP;
PS2OUT(15) = PenP;
PS2OUT(16) = Pi;
PS2OUT(17) = ADP;
PS2OUT(18) = v1;