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BF_MB.m
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BF_MB.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 BF_mb = BF_Mb(t,BF_Con,BF_Param)
global GLight;
fini = Condition (t);
light = GLight;
BF_Param(1) = light;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate the rates BFrst %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BF_Vel = BF_Rate(t,BF_Con, BF_Param);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Get the rate of different reactions%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Assign velocities of different reactions in the model
Vbf1 = BF_Vel ( 1 ) ;
Vbf2 = BF_Vel ( 2 ) ;
Vbf3 = BF_Vel ( 3 ) ;
Vbf4 = BF_Vel ( 4 ) ;
Vbf5 = BF_Vel ( 5 ) ;
Vbf6 = BF_Vel ( 6 ) ;
Vbf7 = BF_Vel ( 7 ) ;
Vbf8 = BF_Vel ( 8 ) ;
Vbf9 = BF_Vel ( 9 ) ;
Vbf10 = BF_Vel ( 10 ) ;
Vbf11 = BF_Vel ( 11 ) ;
Vqi = BF_Vel ( 12 ) ;
Vipc = BF_Vel ( 13 ) ;
Vicp = BF_Vel ( 14 ) ;
Vinc = BF_Vel ( 15 ) ;
Vinp = BF_Vel ( 16 ) ;
Vdp = BF_Vel ( 17 ) ;
Vdc = BF_Vel ( 18 ) ;
Vfp = BF_Vel ( 19 ) ;
Vfc = BF_Vel ( 20 ) ;
Vsfd = BF_Vel ( 21 ) ;
VsATP = BF_Vel ( 22 ) ;
VgPQH2 = BF_Vel ( 23 ) ;
Vbf12 = BF_Vel ( 24 ) ;
Vbf13 = BF_Vel ( 25 ) ;
Vbf14 = BF_Vel ( 26 ) ;
Vbf15 = BF_Vel ( 27 ) ;
Vbf16 = BF_Vel ( 28 ) ;
vbfn2 = BF_Vel ( 29 ) ;
VsNADPH = BF_Vel ( 30 ) ;
vcet = BF_Vel ( 31 ) ;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Get the mass balance equation %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BF_mb = zeros(5,1);
global AVR;
CoeffVol = AVR; % This is the conversion factor between volume and area.
BF_mb ( 1 ) = Vbf2 - Vbf8 ; % ISPHr The reduced ion sulfer protein (ISPH)
BF_mb ( 2 ) = Vbf9 - Vbf8 ; % cytc1 The oxidized state of cytc1
BF_mb ( 3 ) = Vbf8 - Vbf1 ; % ISPo The oxidized ion sulfer protein (ISP)
BF_mb ( 4 ) = Vbf1 - Vbf2 ; % ISPoQH2 The complex of oxidized ion sulfer protein and reduced quinone
BF_mb ( 5 ) = Vbf2 - Vbf3 ; % QHsemi Semiquinone
BF_mb ( 6 ) = Vbf4 - Vbf3 ; % cytbL The oxidized cytbL
BF_mb ( 7 ) = Vbf7-Vbf5 - vcet; % Qi The quinone bound in the Qi site of cytbf complex ????
% DEBUG
BF_mb ( 8 ) = Vbf3 - Vbf7 - VgPQH2 ; % Q Quinone in thylakoid membrane in free form
BF_mb ( 9 ) = Vbf6 - Vbf4 +Vbf5 ; % cytbH The oxidized form of cytbH
BF_mb ( 10 ) = Vbf5 - Vbf6 + vcet; % Qn Q-
BF_mb ( 11 ) = Vbf6 - Vqi/2 ; % Qr Q2-
BF_mb ( 12 ) = Vqi/2 - Vbf1 + VgPQH2; % QH2 The PQH2 concentration; the coefficient 2 represent the fact that 2 protons were taken up by one Q2-.
BF_mb ( 13 ) = Vbf10 - Vbf9; % cytc2 oxidized cytc2
BF_mb ( 14 ) = Vbf10 - Vbf15; % P700 The reduced state of P700, including both P700 and excited P700
BF_mb ( 16 ) = 0 ; % Pi Phosphate in stroma
BF_mb ( 15 ) = VsATP - Vbf11 ; % ADP ADP in stroma
BF_mb ( 17 ) = Vbf11 - VsATP ; % ATP ATP in stroma
BF_mb ( 18 ) = Vbf12 ; % Ks K ions in stroma
BF_mb ( 19 ) = Vbf13 ; % Mgs Mg ions in stroma
BF_mb ( 20 ) = Vbf14 ; % Cls Cl ions in stroma
BF_mb ( 21 ) = Vicp + Vinp - Vipc - Vdp - Vfp ; % Aip The number of photons in peripheral antenna
BF_mb ( 22 ) = Vipc + Vinc - Vicp - Vdc - Vfc ; % Ui The number of photons in core antenna
BF_mb ( 23 ) = Vbf15 - Vbf16 ; % An: the reduced electron acceptor in PSI
%BF_mb ( 24 ) = Vbf16 - vbfn2 * CoeffVol - vcet; % Fdn The reduced ferrodoxin; unit: mircomol m-2; Therefore,the the rate of NADPH formation need to micromole per meter square.
BF_mb ( 24 ) = Vbf16/2 - vbfn2/2 * CoeffVol - vcet/2;
vqb = VgPQH2 * 2; % The rate of quinone protonation
roe = VgPQH2 * 2 ; % The rate of proton generation from oxygen evolution complex
Hroe = roe/CoeffVol ; % Convert the unit of rate of oxygen evolution (roe) from micormole per meter square per second to mM s-1
Hrqb = vqb/CoeffVol ; % Convert the unit of vqb from micormole per meter square per second to mM s-1; vqb is the rate of QB2- reduction in thylakoid membrane.
Hvqo1 = Vbf8/CoeffVol ; % The rate of release of protons into lumen through Qo site
Hvqo2 = Vbf3/CoeffVol ; % The rate of proton release into lumen through Qo site
sink = 0 ; % The sinks of electron in stroma
Hvqi = Vqi/CoeffVol ; % The rate of proton uptake from stroma at Qi site of cytbc1 complex
global HPR;
BF_mb ( 25 ) = (HPR * Vbf11 - Hrqb - Hvqi - vbfn2); % BFHs The proton and protonated buffer species in stroma. The proton concentration is not used in the MB procedure. The reason is that the proton concentration is buffered and therefore did not changed linerly with the generation of the protons.
BF_mb ( 26 ) = (Hvqo1 + Hvqo2 + Hroe - HPR * Vbf11); % BFHl The proton and protonated buffer species in lumen, similarly, we can only use the buff concentration, but, the proton concentration can not be used here.
BF_mb ( 27 ) = -(HPR * Vbf11 - Hrqb - Hvqi - vbfn2)/1000/0.015; % PHs, The changes of PH in stoma, 0.03 mol /PH from Laisk et al.
BF_mb ( 28 ) = -(Hvqo1 + Hvqo2 + Hroe - HPR * Vbf11)/1000/0.015; % PHl The changes in PH of lumen, 0.03 is from Curz et al., 2001, Biochemistry.
BF_mb ( 29 ) = vbfn2 - VsNADPH ;