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FI_MB.m
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FI_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/>.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% FI_mb.m This is the routine for calculation of the mass balance equations for the fluorescence induction model
% This routine is composed of two components;
% 1) The initialization of the rates that was transfered from the FI_Rate routine
% 2) The computation of the mass balance equations
function FI_mb = FI_Mb(t,FI_Con,FI_Param)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate the rates first %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%global GLight;
global LI;
%fini = Condition (t);
light = LI*30;
FI_Param(1) = light;
FI_Vel = FI_Rate(t,FI_Con, FI_Param);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Get the rate of different reactions%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
vA_d = FI_Vel ( 1 ) ; % vA_d The rate of heat dissipation from peripheral antenna
vA_f = FI_Vel ( 2 ) ; % vA_f The rate of fluorescence emission from peripheral antenna
vA_U = FI_Vel ( 3 ) ; % vA_U The rate of exciton transfer from peripheral antenna to core antenna in open reaction center
vU_A = FI_Vel ( 4 ) ; % vU_A The rate of exciton transfer from core antenna to perpheral antenna in open center
vU_f = FI_Vel ( 5 ) ; % vU_f The rate of fluorescence emission from core antenna
vU_d = FI_Vel ( 6 ) ; % vU_d The rate of heat dissipation from core antenna
v1 = FI_Vel ( 7 ) ; % v1 The rate of primary charge separation
v_r1 = FI_Vel ( 8 ) ; % v_r1 The rate of charge recombination
vS1_S2 = FI_Vel ( 9 ) ; % vS1_S2 The rate of transition from S1 to S2
vS2_S3 = FI_Vel ( 10 ) ; % vS2_S3 The rate of transition from S2 to S3
vS3_S0 = FI_Vel ( 11 ) ; % vS3_S0 The rate of transition from S3 to S0
vS0_S1 = FI_Vel ( 12 ) ; % vS0_S1 The rate of transition from S0 to S1
vz_1 = FI_Vel ( 13 ) ; % vz_1 The rate of P680p reduction
v1z_1 = FI_Vel ( 14 ) ; % v1z_1 The rate of oxidation of S1T by P680pPheon
v2z_1 = FI_Vel ( 15 ) ; % v2z_1 The rate of oxidation of S2T by P680pPheon
v3z_1 = FI_Vel ( 16 ) ; % v3z_1 The rate of oxidation of S3T by P680pPheon
v0z_1 = FI_Vel ( 17 ) ; % v0z_1 The rate of oxidation of S0T by P680pPheon
vz_2 = FI_Vel ( 18 ) ; % vz_2 The rate of P680pPheon reduction
v1z_2 = FI_Vel ( 19 ) ; % v1z_2 The rate of oxidation of S1T by P680pPheo
v2z_2 = FI_Vel ( 20 ) ; % v2z_2 The rate of oxidation of S2T by P680pPheo
v3z_2 = FI_Vel ( 21 ) ; % v3z_2 The rate of oxidation of S3T by P680pPheo
v0z_2 = FI_Vel ( 22 ) ; % v0z_2 The rate of oxidation of S0T by P680pPheo
v1z = FI_Vel ( 23 ) ; % v1z
v2z = FI_Vel ( 24 ) ; % v2z
v3z = FI_Vel ( 25 ) ; % v3z
v0z = FI_Vel ( 26 ) ; % v0z
vAB1 = FI_Vel ( 27 ) ; % vAB1 The rate of electron transfer from QA- to QB
vBA1 = FI_Vel ( 28 ) ; % vBA1 The rate of electron transfer from QB- to QA
vAB2 = FI_Vel ( 29 ) ; % vAB2 The rate of electron transfer from QA- to QB-
vBA2 = FI_Vel ( 30 ) ; % vBA2 The rate of electron transfer from QB2- TO QA
v3 = FI_Vel ( 31 ) ; % v3 The rate of exchange of QAQBH2 with PQ
v_r3 = FI_Vel ( 32 ) ; % v_r3 The rate of exchange of QAQB with PQH2
v3_n = FI_Vel ( 33 ) ; % v3_n The rate of exchange of QAnQBH2 with PQ
v_r3_n = FI_Vel ( 34 ) ; % v_r3_n The rate of exchange of QAnQB with PQH2
v_pq_ox = FI_Vel ( 35 ) ; % v_pq_ox The rate of PQH2 oxidation
Ic = FI_Vel ( 36 ) ; % Ic The incident light on the core antenna
Ia = FI_Vel ( 37 ) ; % Ia The incident light on the peripheral antenna
v2_1 = FI_Vel ( 38 ) ; % v2_1 The rate of P680pPheon oxidation
v2_2 = FI_Vel ( 39 ) ; % v2_1 The rate of P680pPheon oxidation
v2_00_1 = FI_Vel ( 40 ) ; % v2_00_1 The rate of reduction of QAQB by P680pPheon
v2_01_1 = FI_Vel ( 41 ) ; % v2_01_1 The rate of reduction of QAQBn by P680pPheon
v2_02_1 = FI_Vel ( 42 ) ; % v2_02_1 The rate of reduction of QAQB2n by P680pPheon
v2_00_2 = FI_Vel ( 43 ) ; % v2_00_2 The rate of reduction of QAQB by P680Pheon
v2_01_2 = FI_Vel ( 44 ) ; % v2_01_2 The rate of reduction of QAQBn by P680Pheon
v2_02_2 = FI_Vel ( 45 ) ; % v2_02_2 The rate of reduction of QAQB2n by P680Pheon
vr2_00_1 = FI_Vel ( 46 ) ; % vr2_00_1 The reverse reaction of The rate of reduction of QAQB by P680pPheon
vr2_01_1 = FI_Vel ( 47 ) ; % vr2_01_1 The reverse reaction of The rate of reduction of QAQBn by P680pPheon
vr2_02_1 = FI_Vel ( 48 ) ; % vr2_02_1 The reverse reaction of The rate of reduction of QAQB2n by P680pPheon
vr2_1 = FI_Vel ( 49 ) ; % vr2_1
vr2_00_2 = FI_Vel ( 50 ) ; % vr2_00_2 The reverse reaction of The rate of reduction of QAQB by P680Pheon
vr2_01_2 = FI_Vel ( 51 ) ; % vr2_01_2 The reverse reaction of The rate of reduction of QAQBn by P680Pheon
vr2_02_2 = FI_Vel ( 52 ) ; % vr2_02_2 The reverse reaction of The rate of reduction of QAQB2n by P680Pheon
vr2_2 = FI_Vel ( 53 ) ; % vr2_2
vP680qU = FI_Vel ( 54 ) ; % vP680qU
vP680qA = FI_Vel ( 55 ) ; % vP680qA
vU_P680 = FI_Vel (56);
vP680_d = FI_Vel (57);
vP680_f = FI_Vel (58);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Get the mass balance equation %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This page defines the mass balance equation for the system under study
% One problem need to be taken care of is the variables needed to transfer from FI_CalV to FI_mb
% The Major Variables
FI_mb = zeros(5,1) ;
%FI_mb ( 1 ) = Ia - vA_f - vA_d - vA_U + vU_A - vP680qA ; % A
FI_mb ( 1 ) = Ia - vA_f - vA_d - vA_U + vU_A; % A 6
FI_mb ( 2 ) = Ic + vA_U - vU_A -vU_f - vU_d - v1 + v_r1 - vP680qU ; % U
FI_mb ( 3 ) = vU_P680 + v_r1 - v1 - vP680_d; % P680ePheo QF add
FI_mb ( 4 ) = v1 - v_r1 - vz_1 - v2_1 + vr2_1 ; % P680pPheon
FI_mb ( 5 ) = v2_1 - vr2_1 - vz_2 ; % P680pPheo
FI_mb ( 6 ) = vz_1- v2_2 + vr2_2 ; % P680Pheon
FI_mb ( 7 ) = vS1_S2 + vS2_S3 + vS3_S0 + vS0_S1 - vz_1 - vz_2 ; % Yz
FI_mb ( 8 ) = vS0_S1 - v1z ; % S1T
FI_mb ( 9 ) = vS1_S2 - v2z ; % S2T
FI_mb ( 10 ) = vS2_S3 - v3z ; % S3T
FI_mb ( 11 ) = vS3_S0 - v0z ; % S0T
FI_mb ( 12 ) = v1z - vS1_S2 ; % S1Tp
FI_mb ( 13 ) = v2z - vS2_S3 ; % S2Tp
FI_mb ( 14 ) = v3z - vS3_S0 ; % S3Tp
FI_mb ( 15 ) = v0z - vS0_S1 ; % S0Tp
FI_mb ( 16 ) = v3 - v_r3 -v2_00_1 - v2_00_2 + vr2_00_1 + vr2_00_2 ; % QAQB
FI_mb ( 17 ) = v2_00_1 + v2_00_2 - vr2_00_1 - vr2_00_2- vAB1 + vBA1 + v3_n - v_r3_n ; % QAnQB
FI_mb ( 18 ) = vAB1 -vBA1 - v2_01_1-v2_01_2 +vr2_01_1+vr2_01_2 ; % QAQBn
FI_mb ( 19 ) = vBA2 - vAB2 + v2_01_1+v2_01_2 -vr2_01_1-vr2_01_2 ; % QAnQBn
FI_mb ( 20 ) = vAB2 - vBA2 - v3 + v_r3 - v2_02_1-v2_02_2 +vr2_02_1+vr2_02_2 ; % QAQB2n
FI_mb ( 21 ) = 0-v3_n + v_r3_n + v2_02_1+v2_02_2 -vr2_02_1-vr2_02_2 ; % QAnQB2n
FI_mb ( 22 ) = v3 + v3_n - v_r3 - v_r3_n - v_pq_ox ; % PQn