-
Notifications
You must be signed in to change notification settings - Fork 0
/
FI_Ini.m
171 lines (145 loc) · 11 KB
/
FI_Ini.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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_Init.m This is the routine that initialize the parameters, initial conditions for simulation of fluorescence induction curve.
% The following information is initialized sequentially 1) Rate constants; 2) Initial concentration ( or conditions); 3) THe maximum
% concentration of components of photosystems.
function FI_Con = FI_Ini(begin)
global FIRatio;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initilization of the rate constant %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The rate constant used in the model
% The rate constant used in the model
% The rate constant used in the model
% Reference
kA_d = 2*10^8*FIRatio(1); % The rate constant of heat dissipation from peripheral antenna Lazar (1999), 0.25~1 *10^(9)
kA_f = 6.3 *10^6 *0.2 *FIRatio(2); % The rate constant of fluorescence emission from peripheral antenna; based on the fact that the natural lifetime of chlorophyll a is 15.9 ns; This value is correct and should not be changed by any.
kA_U = 10^10*FIRatio(3) ; % The rate constant of exciton transfer from periphral antenna to core antenna Reference needed, a guess
kU_A = 10^10*FIRatio(4) ; % The rate constant of exciton transfer from core antenna to peripheral antenna Reference needed, a guess
kU_d = 2*10^8*FIRatio(5) ; % The rate constant of the heat dissipation from core antenna; Laverage and Trissl, 1995
kU_f = 6.3 *10^6 *0.2*FIRatio(6) ; % The rate constant of the fluorescence emission from the core antenna; Laverage and Trissl 1995
k1 = 2.5 * 10^11*FIRatio(7) ; % The rate constant of primary charge separation for open reaction center
k_r1 = 3*10^8*FIRatio(8) ; % The rate constant of charge recombination for open reactoin center; Lazar, 1999;
kz = 5*10^6*FIRatio(9) ; % The rate constant of the Tyrosine oxidation Lazar (1999); 3.8~50 * 10^6
k12 = 30000*FIRatio(10) ; % The rate constant of the S1 to S2 transition Lazar (1999); 0.667~33.3 * 10^3
k23 = 10000*FIRatio(11) ; % The rate constant of the S2 to S3 transition Lazar (1999); 0.667~33.3 * 10^3
k30 = 3000*FIRatio(12) ; % The rate constant of the S3 to S0 transition Lazar (1999); 0.667~33.3 * 10^3
k01 = 500*FIRatio(13) ; % The rate constant of the S0 to S1 transition Lazar (1999); 0.667~33.3 * 10^3
k2 = 2*10^9*FIRatio(14) ; % The rate constant of the QA reduction by Pheo- Lazar (1999); 2~2.3 * 10^9
kAB1 = 2500*FIRatio(15) ; % The rate constant of QAQB-->QAQB- Lazar (1999); 2.5~5 * 10^3
kBA1 = 200*FIRatio(16) ; % The rate constant of the QAQB- -->QAQB Lazar (1999)
kAB2 = 3300*FIRatio(17) ; % The rate constant of the QAQB- --> QAQB2- Lazar (1999); 1.25~3.33 * 10^3
kBA2 = 250*FIRatio(18) ; % The rate constant of the QAQB2- --> QAQB- Lazar (1999), or same as kAB2 depend on the equilibium constant
k3 = 800 *FIRatio(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 = 80 *FIRatio(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= 500 *FIRatio(21); % The rate constant of the PQH2 oxidation Lazar (1999),50~500
% The rate constant used in the model
global FI_RC;
FI_RC= zeros(5,1);
% The rate constant used in the model
% The rate constant used in the model
FI_RC ( 1 ) = kA_d ; % The rate constant of heat dissipation from peripheral antenna Lazar (1999), 0.25~1 *10^(9)
FI_RC ( 2 ) = kA_f ; % The rate constant of fluorescence emission from peripheral antenna Lazar 1999, with a lifetime of 5 ns at closed reaction center
FI_RC ( 3 ) = kA_U ; % The rate constant of exciton transfer from periphral antenna to core antenna Reference needed, a guess
FI_RC ( 4 ) = kU_A ; % The rate constant of exciton transfer from core antenna to peripheral antenna Reference needed, a guess
FI_RC ( 5 ) = kU_d ; % The rate constant of heat emission from core antenna
FI_RC ( 6 ) = kU_f ; % The rate constant of fluorescence emission from core antenna
FI_RC ( 7 ) = k1 ; % The rate constant of primary charge separation for open reaction center
FI_RC ( 8 ) = k_r1 ; % The rate constant of charge recombination for open reactoin center
FI_RC ( 9 ) = kz ; % The rate constant of the Tyrosine oxidation Lazar (1999); 3.8~50 * 10^6
FI_RC ( 10 ) = k12 ; % The rate constant of the S1 to S2 transition Lazar (1999); 0.667~33.3 * 10^3
FI_RC ( 11 ) = k23 ; % The rate constant of the S2 to S3 transition Lazar (1999); 0.667~33.3 * 10^3
FI_RC ( 12 ) = k30 ; % The rate constant of the S3 to S0 transition Lazar (1999); 0.667~33.3 * 10^3
FI_RC ( 13 ) = k01 ; % The rate constant of the S0 to S1 transition Lazar (1999); 0.667~33.3 * 10^3
FI_RC ( 14 ) = k2 ; % The rate constant of the QA reduction by Pheo- Lazar (1999); 2~2.3 * 10^9
FI_RC ( 15 ) = kAB1 ; % The rate constant of QAQB-->QAQB- Lazar (1999); 2.5~5 * 10^3
FI_RC ( 16 ) = kBA1 ; % The rate constant of the QAQB- -->QAQB Lazar (1999)
FI_RC ( 17 ) = kAB2 ; % The rate constant of the QAQB- --> QAQB2- Lazar (1999); 1.25~3.33 * 10^3
FI_RC ( 18 ) = kBA2 ; % The rate constant of the QAQB2- --> QAQB- Lazar (1999), or same as kAB2 depend on the equilibium constant
FI_RC ( 19 ) = k3 ; % 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
FI_RC ( 20 ) = k_r3 ; % The rate constant of the exchange of QB and PQH2 Lazar (1999), since the equilibrium constant is 1 (205 in Lazar, 1999)
FI_RC ( 21 ) = k_pq_oxy ; % The rate constant of the PQH2 oxidation Lazar (1999),50~500
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialization of the initial concentration of the different component %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialize the leaves for a dark adapted leaves;
% Unit micro mol per m2
% Initialize the leaves for a dark adapted leaves;
% mircomol per m2
% Initialize the leaves for a dark adapted leaves;
% Micro mol m2
A = 0 ; % The concentration of excitons in the peripheral antenna
U = 0 ; % The concentration fo excitons in the core antenna
P680Pheo = 1 ; % The concentration of the P680Pheo
P680pPheon = 0 ; % The concentration for the P680+ Pheo-
P680pPheo = 0 ; % The concentration of P680+ Pheo
P680Pheon = 0 ; % The concentration of P680Pheo-
Yz = 1; % The concentration of reduced tyrosine
S1T = 0.8 ; % The concentration of S1 in combination with reduced tyrosine
S2T = 0 ; % The concentration of S2 in combination with reduced tyrosine
S3T = 0 ; % The concentration of S3 in combination with reduced tyrosine
S0T = 0.2 ; % The concentration of S0 in combination with reduced tyrosine
S1Tp = 0 ; % The concentration of S1 in combination with oxidized tyrosine
S2Tp = 0 ; % The concentration of S2 in combination with oxidized tyrosine
S3Tp = 0 ; % The concentration of S3 in combination with oxidized tyrosine
S0Tp = 0 ; % The concentration of S0 in combination with oxidized tyrosine
QAQB = 1 ; % The concentration of [QAQB]
QAnQB = 0 ; % The concentration of [QA-QB];
QAQBn = 0 ; % The concentration of [QAQB-]
QAnQBn = 0 ; % The concentration of [QA-QB-];
QAQB2n = 0 ; % The concentration of [QAQB2-]
QAnQB2n = 0 ; % The concentration of [QA-QB2-];
PQn = 5 ; % The concentration of reduced PQ, i.e. PQH2;
% Assign the value to a array
% FI_ini.m
% This is the program that initialize the major variables used in the fluorescence induction system.In this file, the n represent negative charges, _red represent that the components are associated with the closed reaction center; while _ox represent a system with open reaction center.
global FI_Con;
FI_Con ( 1 ) = A ; % The concentration of excitons in the peripheral antenna
FI_Con ( 2 ) = U ; % The concentration fo excitons in the core antenna
FI_Con ( 3 ) = P680Pheo ; % The concentration of the P680Pheo
FI_Con ( 4 ) = P680pPheon ; % The concentration for the P680+ Pheo-
FI_Con ( 5 ) = P680pPheo ; % The concentration of P680+ Pheo
FI_Con ( 6 ) = P680Pheon ; % The concentration of P680Pheo-
FI_Con ( 7 ) = Yz ; % The concentration of reduced tyrosine
FI_Con ( 8 ) = S1T ; % The concentration of S1 in combination with reduced tyrosine
FI_Con ( 9 ) = S2T ; % The concentration of S2 in combination with reduced tyrosine
FI_Con ( 10 ) = S3T ; % The concentration of S3 in combination with reduced tyrosine
FI_Con ( 11 ) = S0T ; % The concentration of S0 in combination with reduced tyrosine
FI_Con ( 12 ) = S1Tp ; % The concentration of S1 in combination with oxidized tyrosine
FI_Con ( 13 ) = S2Tp ; % The concentration of S2 in combination with oxidized tyrosine
FI_Con ( 14 ) = S3Tp ; % The concentration of S3 in combination with oxidized tyrosine
FI_Con ( 15 ) = S0Tp ; % The concentration of S0 in combination with oxidized tyrosine
FI_Con ( 16 ) = QAQB ; % The concentration of [QAQB]
FI_Con ( 17 ) = QAnQB ; % The concentration of [QA-QB];
FI_Con ( 18 ) = QAQBn ; % The concentration of [QAQB-]
FI_Con ( 19 ) = QAnQBn ; % The concentration of [QA-QB-];
FI_Con ( 20 ) = QAQB2n ; % The concentration of [QAQB2-]
FI_Con ( 21 ) = QAnQB2n ; % The concentration of [QA-QB2-];
FI_Con ( 22 ) = PQn ; % The concentration of reduced PQ, i.e. PQH2;
global FI_Pool;
QBt = 1*FIRatio(22); % The total concentration of Qb site;
PQT = 8*FIRatio(23); % The total concentration of PQ;
FI_Pool(1) = QBt;
FI_Pool(2) = PQT;
global FIBF_AUX;
FIBF_AUX = zeros(5,1);
global FI_RC_Reg_o;
FI_RC_Reg_o(1) = FI_RC(11);
FI_RC_Reg_o(2) = FI_RC(12);
FI_RC_Reg_o(3) = FI_RC(13);
FI_RC_Reg_o(4) = FI_RC(7);