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FI_Rate.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 FI_Vel = FI_Rate(t,FI_Con, FI_Param)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Step 1 Get the rate constant and the initial concentrations %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global FI_RC;
% The rate constant used in the model
kA_d = FI_RC ( 1 ) ; % The rate constant of heat dissipation from peripheral antenna Lazar (1999), 0.25~1 *10^(9)
kA_f = FI_RC ( 2 ) ; % The rate constant of fluorescence emission from peripheral antenna Lazar 1999, with a lifetime of 5 ns at closed reaction center
kA_U = FI_RC ( 3 ) ; % The rate constant of exciton transfer from periphral antenna to core antenna Reference needed, a guess
kU_A = FI_RC ( 4 ) ; % The rate constant of exciton transfer from core antenna to peripheral antenna Reference needed, a guess
kU_d = FI_RC ( 5 ) ; % The rate constant of heat emission from core antenna
kU_f = FI_RC ( 6 ) ; % The rate constant of fluorescence emission from core antenna
k1 = FI_RC ( 7 ) ; % The rate constant of primary charge separation for open reaction center
k_r1 = FI_RC ( 8 ) ; % The rate constant of charge recombination for open reactoin center
kz = FI_RC ( 9 ) ; % The rate constant of the Tyrosine oxidation Lazar (1999); 3.8~50 * 10^6
k12 = FI_RC ( 10 ) ; % The rate constant of the S1 to S2 transition Lazar (1999); 0.667~33.3 * 10^3
k23 = FI_RC ( 11 ) ; % The rate constant of the S2 to S3 transition Lazar (1999); 0.667~33.3 * 10^3
k30 = FI_RC ( 12 ) ; % The rate constant of the S3 to S0 transition Lazar (1999); 0.667~33.3 * 10^3
k01 = FI_RC ( 13 ) ; % The rate constant of the S0 to S1 transition Lazar (1999); 0.667~33.3 * 10^3
k2 = FI_RC ( 14 ) ; % The rate constant of the QA reduction by Pheo- Lazar (1999); 2~2.3 * 10^9
kAB1 = FI_RC ( 15 ) ; % The rate constant of QAQB-->QAQB- Lazar (1999); 2.5~5 * 10^3
kBA1 = FI_RC ( 16 ) ; % The rate constant of the QAQB- -->QAQB Lazar (1999)
kAB2 = FI_RC ( 17 ) ; % The rate constant of the QAQB- --> QAQB2- Lazar (1999); 1.25~3.33 * 10^3
kBA2 = FI_RC ( 18 ) ; % The rate constant of the QAQB2- --> QAQB- Lazar (1999), or same as kAB2 depend on the equilibium constant
k3 = FI_RC ( 19 ) ; % The rate constant of the exchange of PQ and QBH2 Lazar (1999),0.12~1 for the fast PQ pool, or 3~8 for the slow recycling PQ pool
k_r3 = FI_RC ( 20 ) ; % The rate constant of the exchange of QB and PQH2 Lazar (1999), since the equilibrium constant is 1 (205 in Lazar, 1999)
k_pq_oxy = FI_RC ( 21 ) ; % The rate constant of the PQH2 oxidation Lazar (1999),50~500
A = FI_Con ( 1 ) ; % The concentration of excitons in the peripheral antenna
U = FI_Con ( 2 ) ; % The concentration fo excitons in the core antenna
P680ePheo = FI_Con ( 3 ); %QF add
P680pPheon = FI_Con ( 4 ) ; % The concentration for the P680+ Pheo-
P680pPheo = FI_Con ( 5 ) ; % The concentration of P680+ Pheo
P680Pheon = FI_Con ( 6 ) ; % The concentration of P680Pheo-
Yz = FI_Con ( 7 ) ; % The concentration of reduced tyrosine
S1T = FI_Con ( 8 ) ; % The concentration of S1 in combination with reduced tyrosine
S2T = FI_Con ( 9 ) ; % The concentration of S2 in combination with reduced tyrosine
S3T = FI_Con ( 10 ) ; % The concentration of S3 in combination with reduced tyrosine
S0T = FI_Con ( 11 ) ; % The concentration of S0 in combination with reduced tyrosine
S1Tp = FI_Con ( 12 ) ; % The concentration of S1 in combination with oxidized tyrosine
S2Tp = FI_Con ( 13 ) ; % The concentration of S2 in combination with oxidized tyrosine
S3Tp = FI_Con ( 14 ) ; % The concentration of S3 in combination with oxidized tyrosine
S0Tp = FI_Con ( 15 ) ; % The concentration of S0 in combination with oxidized tyrosine
QAQB = FI_Con ( 16 ) ; % The concentration of [QAQB]
QAnQB = FI_Con ( 17 ) ; % The concentration of [QA-QB];
QAQBn = FI_Con ( 18 ) ; % The concentration of [QAQB-]
QAnQBn = FI_Con ( 19 ) ; % The concentration of [QA-QB-];
QAQB2n = FI_Con ( 20 ) ; % The concentration of [QAQB2-]
QAnQB2n = FI_Con ( 21 ) ; % The concentration of [QA-QB2-];
PQn = FI_Con ( 22 ) ; % The concentration of reduced PQ, i.e. PQH2;
global FI_Pool;
PQT = FI_Pool (2); % The total concentraion of PQH2 and PQ;
global FIBF_AUX;
PQa = FIBF_AUX(2);
PQ = PQT - PQn - PQa;
global BF_FI_com;
if BF_FI_com ==1
global FIBF2FI_PQ;
PQ = FIBF2FI_PQ;
end
P680PheoT = 1 ;
global ChlT2;
global ChlT;
global ChlPSI;
% ChlT = 70 ; % The amount of chl molecules in U in one meter square leaf area; unit: micor mole per meter square
% ChlT2 = 290; % The total amoutn of chlorophyll in one PSII unit, inclusing both U and A.
P680Pheo = P680PheoT - P680pPheo - P680Pheon - P680pPheon - P680ePheo; %QF add '- P680ePheo'
%P680ePheo = U /(ChlT) * P680Pheo ; % The amount of excitons on P680 molecules; the difference in the energy of P680 and antenna chlorophyll is not incorporated
n = FI_Param(2) ; % n The ratio of the number of PSI to PSII
It = FI_Param(1) ; % It The total incident light intensity
% rate: U -> U*
Ic = It * ChlT/(ChlT2 + ChlPSI) ; % Ic The incident light on the core antenna; ChlT is defined in upper lines as the total amount of Chl in one U.
% rate: A -> A*
Ia = It * (ChlT2 - ChlT)/(ChlT2 + ChlPSI) ; % Ia The incident light on the peripheral antenna
% Ic = It * ChlT/(ChlT2 + 200*n) ; % Ic The incident light on the core antenna; ChlT is defined in upper lines as the total amount of Chl in one U.
% Ia = It * (ChlT2 - ChlT)/(ChlT2 + 200*n) ; % Ia The incident light on the peripheral antenna
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate the rate of different reactions %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
q = (QAQB+QAQBn+QAQB2n)/(QAQB + QAQBn+ QAQB2n + QAnQB + QAnQBn+QAnQB2n);
vA_d = A * kA_d ; % vA_d The rate of heat dissipation from peripheral antenna
vA_f = A * kA_f ; % vA_f The rate of fluorescence emission from peripheral antenna
vA_U = A * kA_U ; % vA_U The rate of exciton transfer from peripheral antenna to core antenna in open reaction center
vU_A = U * kU_A ; % vU_A The rate of exciton transfer from core antenna to perpheral antenna in open center
vU_f = U * kU_f ; % vU_f The rate of fluorescence emission from core antenna
vU_d = U * kU_d *(1-q) ; % vU_d The rate of heat dissipation from core antenna
P = 1;
% energy flow:
vU_P680 = Ic + vA_U - vU_A -vU_f - vU_d; %QF add , total energy coming to P680 and == the rate of P680 -> P680*, except f and d, energy is transport to P680 reaction center
vP680_d = P680ePheo * kU_d *(1-q);
v1 = P680ePheo * k1 * q + P680ePheo * P * (1-q) * k1/6.2 + P680ePheo * (1-P)* (1-q) * k1; % v1 The rate of primary charge separation
v_r1 = P680pPheon * k_r1*q + P680pPheon *(1-q)* k_r1*3 ; % v_r1 The rate of charge recombination
vP680_f = vU_P680 - (v1 - v_r1) - vP680_d;
vS1_S2 = S1Tp * k12 ; % vS1_S2 The rate of transition from S1 to S2
vS2_S3 = S2Tp * k23 ; % vS2_S3 The rate of transition from S2 to S3
vS3_S0 = S3Tp * k30 ; % vS3_S0 The rate of transition from S3 to S0
vS0_S1 = S0Tp * k01 ; % vS0_S1 The rate of transition from S0 to S1
Coeff = P680pPheon/P680PheoT ;
v1z_1 = S1T * kz * Coeff ; % v1z_1 The rate of oxidation of S1T by P680pPheon
v2z_1 = S2T* kz* Coeff ; % v2z_1 The rate of oxidation of S2T by P680pPheon
v3z_1 = S3T* kz* Coeff ; % v3z_1 The rate of oxidation of S3T by P680pPheon
v0z_1 = S0T * kz* Coeff ; % v0z_1 The rate of oxidation of S0T by P680pPheon
vz_1 = v1z_1 + v2z_1 + v3z_1 + v0z_1 ; % vz_1 The rate of P680pPheon reduction
Coeff = P680pPheo/P680PheoT ;
v1z_2 = S1T * kz * Coeff ; % v1z_2 The rate of oxidation of S1T by P680pPheo
v2z_2 = S2T* kz* Coeff ; % v2z_2 The rate of oxidation of S2T by P680pPheo
v3z_2 = S3T* kz* Coeff ; % v3z_2 The rate of oxidation of S3T by P680pPheo
v0z_2 = S0T * kz* Coeff ; % v0z_2 The rate of oxidation of S0T by P680pPheo
vz_2 = v1z_2 + v2z_2 + v3z_2 + v0z_2 ; % vz_2 The rate of P680pPheo reduction
v1z = v1z_1 + v1z_2 ;
v2z = v2z_1 + v2z_2 ;
v3z = v3z_1 + v3z_2 ;
v0z = v0z_1 + v0z_2 ;
vAB1 = QAnQB * kAB1 ; % vAB1 The rate of electron transfer from QA- to QB
vBA1 = QAQBn * kBA1 ; % vBA1 The rate of electron transfer from QB- to QA
vAB2 = QAnQBn * kAB2 ; % vAB2 The rate of electron transfer from QA- to QB-
vBA2 = QAQB2n * kBA2 ; % vBA2 The rate of electron transfer from QB2- TO QA
v3 = QAQB2n * PQ * k3/PQT ; % v3 The rate of exchange of QAQBH2 with PQ
v_r3 = QAQB * PQn * k_r3/PQT ; % v_r3 The rate of exchange of QAQB with PQH2
v3_n = QAnQB2n * PQ * k3/PQT ; % v3_n The rate of exchange of QAnQBH2 with PQ
v_r3_n = QAnQB * PQn * k_r3/PQT ; % v_r3_n The rate of exchange of QAnQB with PQH2
v_pq_ox = PQn * k_pq_oxy ; % v_pq_ox The rate of PQH2 oxidation
v2_1 = P680pPheon * k2 *q ; % v2_1 The rate of P680pPheon oxidation
v2_2 = P680Pheon * k2 *q ; % v2_1 The rate of P680pPheon oxidation
a = QAQB/(QAQB+QAQBn + QAQB2n) ; % a
b = QAQBn/(QAQB+QAQBn + QAQB2n) ; % b
c = QAQB2n/(QAQB+QAQBn + QAQB2n) ; % c
v2_00_1 = v2_1 * a ; % v2_00_1 The rate of reduction of QAQB by P680pPheon
v2_01_1 = v2_1 * b ; % v2_01_1 The rate of reduction of QAQBn by P680pPheon
v2_02_1 = v2_1 * c ; % v2_02_1 The rate of reduction of QAQB2n by P680pPheon
v2_00_2 = v2_2 * a ; % v2_00_2 The rate of reduction of QAQB by P680Pheon
v2_01_2 = v2_2 * b ; % v2_01_2 The rate of reduction of QAQBn by P680Pheon
v2_02_2 = v2_2 * c ; % v2_02_2 The rate of reduction of QAQB2n by P680Pheon
KE = 1000000 ;
Coeff1 = P680pPheo/P680PheoT ; % Coeff1
vr2_00_1 = QAnQB * k2/KE *Coeff1 ; % vr2_00_1 The reverse reaction of The rate of reduction of QAQB by P680pPheon
vr2_01_1 = QAnQBn * k2/KE *Coeff1 ; % vr2_01_1 The reverse reaction of The rate of reduction of QAQBn by P680pPheon
vr2_02_1 = QAnQB2n * k2/KE *Coeff1 ; % vr2_02_1 The reverse reaction of The rate of reduction of QAQB2n by P680pPheon
vr2_1 = vr2_00_1 + vr2_01_1 + vr2_02_1 ; % vr2_1
Coeff2 = P680Pheo/P680PheoT ; % Coeff2
vr2_00_2 = QAnQB * k2/KE *Coeff2 ; % vr2_00_2 The reverse reaction of The rate of reduction of QAQB by P680Pheon
vr2_01_2 = QAnQBn * k2/KE *Coeff2 ; % vr2_01_2 The reverse reaction of The rate of reduction of QAQBn by P680Pheon
vr2_02_2 = QAnQB2n * k2/KE *Coeff2 ; % vr2_02_2 The reverse reaction of The rate of reduction of QAQB2n by P680Pheon
vr2_2 = vr2_00_2 + vr2_01_2 + vr2_02_2 ; % vr2_2
vP680qU = 10^9 * U * (P680pPheo + P680pPheon) + U * 0.15 * (kU_f + kU_d) * PQ/PQT;
vP680qA = 10^9 * A * (P680pPheo + P680pPheon) + A * 0.15 * (kA_f + kA_d) * PQ/PQT;
%%%%%%%%%%%%%%%%%%%%
%%% FOR TESITNG %%
f = vA_f + vU_f;
%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Part V Output of Velocity for plot %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global FI_OLD_TIME;
global FI_TIME_N;
global FI_VEL;
global FI_CON;
if (FI_TIME_N ==0)
FI_TIME_N = 1;
end
if (t > FI_OLD_TIME)
FI_TIME_N = FI_TIME_N + 1;
FI_OLD_TIME = t;
end
FI_VEL ( FI_TIME_N , 1 ) = t;
FI_VEL ( FI_TIME_N , 2 ) = vA_d;
FI_VEL ( FI_TIME_N , 3 ) = vA_f;
FI_VEL ( FI_TIME_N , 4 ) = vA_U;
FI_VEL ( FI_TIME_N , 5 ) = vU_A;
FI_VEL ( FI_TIME_N , 6 ) = vU_f;
FI_VEL ( FI_TIME_N , 7 ) = vU_d;
FI_VEL ( FI_TIME_N , 8 ) = v1;
FI_VEL ( FI_TIME_N , 9 ) = v_r1;
FI_VEL ( FI_TIME_N , 10 ) = vS1_S2;
FI_VEL ( FI_TIME_N , 11 ) = vS2_S3;
FI_VEL ( FI_TIME_N , 12 ) = vS3_S0;
FI_VEL ( FI_TIME_N , 13 ) = vS0_S1;
FI_VEL ( FI_TIME_N , 14 ) = vz_1;
FI_VEL ( FI_TIME_N , 15 ) = v1z_1;
FI_VEL ( FI_TIME_N , 16 ) = v2z_1;
FI_VEL ( FI_TIME_N , 17 ) = v3z_1;
FI_VEL ( FI_TIME_N , 18 ) = v0z_1;
FI_VEL ( FI_TIME_N , 19 ) = vz_2;
FI_VEL ( FI_TIME_N , 20 ) = v1z_2;
FI_VEL ( FI_TIME_N , 21 ) = v2z_2;
FI_VEL ( FI_TIME_N , 22 ) = v3z_2;
FI_VEL ( FI_TIME_N , 23 ) = v0z_2;
FI_VEL ( FI_TIME_N , 24 ) = v1z;
FI_VEL ( FI_TIME_N , 25 ) = v2z;
FI_VEL ( FI_TIME_N , 26 ) = v3z;
FI_VEL ( FI_TIME_N , 27 ) = v0z;
FI_VEL ( FI_TIME_N , 28 ) = vAB1;
FI_VEL ( FI_TIME_N , 29 ) = vBA1;
FI_VEL ( FI_TIME_N , 30 ) = vAB2;
FI_VEL ( FI_TIME_N , 31 ) = vBA2;
FI_VEL ( FI_TIME_N , 32 ) = v3;
FI_VEL ( FI_TIME_N , 33 ) = v_r3;
FI_VEL ( FI_TIME_N , 34 ) = v3_n;
FI_VEL ( FI_TIME_N , 35 ) = v_r3_n;
FI_VEL ( FI_TIME_N , 36 ) = v_pq_ox;
FI_VEL ( FI_TIME_N , 37 ) = Ic ;
FI_VEL ( FI_TIME_N , 38 ) = Ia;
FI_VEL ( FI_TIME_N , 39 ) = v2_1;
FI_VEL ( FI_TIME_N , 40 ) = v2_2;
FI_VEL ( FI_TIME_N , 41 ) = v2_00_1;
FI_VEL ( FI_TIME_N , 42 ) = v2_01_1;
FI_VEL ( FI_TIME_N , 43 ) = v2_02_1;
FI_VEL ( FI_TIME_N , 44 ) = v2_00_2;
FI_VEL ( FI_TIME_N , 45 ) = v2_01_2;
FI_VEL ( FI_TIME_N , 46 ) = v2_02_2;
FI_VEL ( FI_TIME_N , 47 ) = vr2_00_1;
FI_VEL ( FI_TIME_N , 48 ) = vr2_01_1;
FI_VEL ( FI_TIME_N , 49 ) = vr2_02_1;
FI_VEL ( FI_TIME_N , 50 ) = vr2_1;
FI_VEL ( FI_TIME_N , 51 ) = vr2_00_2;
FI_VEL ( FI_TIME_N , 52 ) = vr2_01_2;
FI_VEL ( FI_TIME_N , 53 ) = vr2_02_2;
FI_VEL ( FI_TIME_N , 54 ) = vr2_2;
FI_VEL ( FI_TIME_N , 55 ) = vP680qU ; % vr2_2
FI_VEL ( FI_TIME_N , 56 ) = vP680qA ; % vr2_2
FI_VEL ( FI_TIME_N , 57 ) = vU_P680;
FI_VEL ( FI_TIME_N , 58 ) = vP680_d;
FI_VEL ( FI_TIME_N , 59 ) = vP680_f;
FI_CON(FI_TIME_N,1) = t;
FI_CON(FI_TIME_N,2) = f;
FI_CON(FI_TIME_N,3) = 1-q;
FI_CON(FI_TIME_N,4) = vA_d + vU_d;
FI_CON(FI_TIME_N,5) = vS3_S0;
if It ==0
fPSII = 0;
else
It2 = It * 27/47;
fPSII = (It2 - f - vA_d - vU_d)/It2;
end
FI_CON(FI_TIME_N,6) = fPSII;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Assign table
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
global FI_Vel;
FI_Vel ( 1 ) = vA_d ; % vA_d The rate of heat dissipation from peripheral antenna
FI_Vel ( 2 ) = vA_f ; % vA_f The rate of fluorescence emission from peripheral antenna
FI_Vel ( 3 ) = vA_U ; % vA_U The rate of exciton transfer from peripheral antenna to core antenna in open reaction center
FI_Vel ( 4 ) = vU_A ; % vU_A The rate of exciton transfer from core antenna to perpheral antenna in open center
FI_Vel ( 5 ) = vU_f ; % vU_f The rate of fluorescence emission from core antenna
FI_Vel ( 6 ) = vU_d ; % vU_d The rate of heat dissipation from core antenna
FI_Vel ( 7 ) = v1 ; % v1 The rate of primary charge separation
FI_Vel ( 8 ) = v_r1 ; % v_r1 The rate of charge recombination
FI_Vel ( 9 ) = vS1_S2 ; % vS1_S2 The rate of transition from S1 to S2
FI_Vel ( 10 ) = vS2_S3 ; % vS2_S3 The rate of transition from S2 to S3
FI_Vel ( 11 ) = vS3_S0 ; % vS3_S0 The rate of transition from S3 to S0
FI_Vel ( 12 ) = vS0_S1 ; % vS0_S1 The rate of transition from S0 to S1
FI_Vel ( 13 ) = vz_1 ; % vz_1 The rate of P680p reduction
FI_Vel ( 14 ) = v1z_1 ; % v1z_1 The rate of oxidation of S1T by P680pPheon
FI_Vel ( 15 ) = v2z_1 ; % v2z_1 The rate of oxidation of S2T by P680pPheon
FI_Vel ( 16 ) = v3z_1 ; % v3z_1 The rate of oxidation of S3T by P680pPheon
FI_Vel ( 17 ) = v0z_1 ; % v0z_1 The rate of oxidation of S0T by P680pPheon
FI_Vel ( 18 ) = vz_2 ; % vz_2 The rate of P680pPheon reduction
FI_Vel ( 19 ) = v1z_2 ; % v1z_2 The rate of oxidation of S1T by P680pPheo
FI_Vel ( 20 ) = v2z_2 ; % v2z_2 The rate of oxidation of S2T by P680pPheo
FI_Vel ( 21 ) = v3z_2 ; % v3z_2 The rate of oxidation of S3T by P680pPheo
FI_Vel ( 22 ) = v0z_2 ; % v0z_2 The rate of oxidation of S0T by P680pPheo
FI_Vel ( 23 ) = v1z ; % v1z
FI_Vel ( 24 ) = v2z ; % v2z
FI_Vel ( 25 ) = v3z ; % v3z
FI_Vel ( 26 ) = v0z ; % v0z
FI_Vel ( 27 ) = vAB1 ; % vAB1 The rate of electron transfer from QA- to QB
FI_Vel ( 28 ) = vBA1 ; % vBA1 The rate of electron transfer from QB- to QA
FI_Vel ( 29 ) = vAB2 ; % vAB2 The rate of electron transfer from QA- to QB-
FI_Vel ( 30 ) = vBA2 ; % vBA2 The rate of electron transfer from QB2- TO QA
FI_Vel ( 31 ) = v3 ; % v3 The rate of exchange of QAQBH2 with PQ
FI_Vel ( 32 ) = v_r3 ; % v_r3 The rate of exchange of QAQB with PQH2
FI_Vel ( 33 ) = v3_n ; % v3_n The rate of exchange of QAnQBH2 with PQ
FI_Vel ( 34 ) = v_r3_n ; % v_r3_n The rate of exchange of QAnQB with PQH2
FI_Vel ( 35 ) = v_pq_ox ; % v_pq_ox The rate of PQH2 oxidation
FI_Vel ( 36 ) = Ic ; % Ic The incident light on the core antenna
FI_Vel ( 37 ) = Ia ; % Ia The incident light on the peripheral antenna
FI_Vel ( 38 ) = v2_1 ; % v2_1 The rate of P680pPheon oxidation
FI_Vel ( 39 ) = v2_2 ; % v2_1 The rate of P680pPheon oxidation
FI_Vel ( 40 ) = v2_00_1 ; % v2_00_1 The rate of reduction of QAQB by P680pPheon
FI_Vel ( 41 ) = v2_01_1 ; % v2_01_1 The rate of reduction of QAQBn by P680pPheon
FI_Vel ( 42 ) = v2_02_1 ; % v2_02_1 The rate of reduction of QAQB2n by P680pPheon
FI_Vel ( 43 ) = v2_00_2 ; % v2_00_2 The rate of reduction of QAQB by P680Pheon
FI_Vel ( 44 ) = v2_01_2 ; % v2_01_2 The rate of reduction of QAQBn by P680Pheon
FI_Vel ( 45 ) = v2_02_2 ; % v2_02_2 The rate of reduction of QAQB2n by P680Pheon
FI_Vel ( 46 ) = vr2_00_1 ; % vr2_00_1 The reverse reaction of The rate of reduction of QAQB by P680pPheon
FI_Vel ( 47 ) = vr2_01_1 ; % vr2_01_1 The reverse reaction of The rate of reduction of QAQBn by P680pPheon
FI_Vel ( 48 ) = vr2_02_1 ; % vr2_02_1 The reverse reaction of The rate of reduction of QAQB2n by P680pPheon
FI_Vel ( 49 ) = vr2_1 ; % vr2_1
FI_Vel ( 50 ) = vr2_00_2 ; % vr2_00_2 The reverse reaction of The rate of reduction of QAQB by P680Pheon
FI_Vel ( 51 ) = vr2_01_2 ; % vr2_01_2 The reverse reaction of The rate of reduction of QAQBn by P680Pheon
FI_Vel ( 52 ) = vr2_02_2 ; % vr2_02_2 The reverse reaction of The rate of reduction of QAQB2n by P680Pheon
FI_Vel ( 53 ) = vr2_2 ; % vr2_2
FI_Vel ( 54 ) = vP680qU ; % vr2_2
FI_Vel ( 55 ) = vP680qA ; % vr2_2
FI_Vel ( 56 ) = vU_P680;
FI_Vel ( 57 ) = vP680_d;
FI_Vel ( 58 ) = vP680_f;