-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathRROEA_Rate.m
185 lines (142 loc) · 6.2 KB
/
RROEA_Rate.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
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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 RROEA_Vel = RROEA_Rate(t,RROEA_Con, RROEA_Param)
global RROEA_RC;
light = RROEA_Param(1);
ke2GAPDH = RROEA_RC ( 1 ) ; % The rate constant of electron transfer to GAPDH. From literature.
ke2MDH = RROEA_RC ( 2 ) ; % The rate constant of electront transfer to MDH, this rate is totally ASSUMED.
ke2FBPase = RROEA_RC ( 3 ) ; % The rate constant of electron transfer from thioredoxin to FBPase.
ke2SBPase = RROEA_RC ( 4 ) ; % The rate constant of electron tranfer from thioredoxin to SBPase
ke2PRK = RROEA_RC ( 5 ) ; % The rate constant of electron transfer from thioredoxin to PRK, Phosphoribulase kinase
ke2RuACT = RROEA_RC ( 6 ) ; % The rate constant of electron transfer from thioredoxin to Rubisco activase
ke2Fd = RROEA_RC ( 7 ) ; % The rate constant of electron transfer to fe
keFd2Thio = RROEA_RC ( 8 ) ; % The rate constant of electron transfer from fd to thio
keFd2Calvin = RROEA_RC ( 9 ) ; % The rate constant of electron transfer from fd to Calvin cycle
ke2ATPGPP = RROEA_RC ( 10 ) ; % The rate constant of electron transfer from fd to ATPGPP
global RROEA_KE;
KEe2FBPase = RROEA_KE ( 1 ) ;
KEe2SBPase = RROEA_KE ( 2 ) ;
KEe2PRK = RROEA_KE ( 3 ) ;
KEe2ATPase = RROEA_KE ( 4 ) ;
KEe2RuACT = RROEA_KE ( 5 ) ;
KEe2GAPDH = RROEA_KE ( 6 ) ;
KEe2MDH = RROEA_KE ( 7 ) ;
KEe2ATPGPP = RROEA_KE ( 8 ) ;
KEeFd2Thio = RROEA_KE ( 9 ) ;
GAPDH =RROEA_Con ( 1 ) ; % The concentration of active GAPDH
FBPase = RROEA_Con ( 2 ) ; % The concentration of active FBPase
SBPase = RROEA_Con ( 3 ) ; % The concentration of active SBPase
PRK = RROEA_Con ( 4 ) ; % The concentration of actove PRK
ATPase = RROEA_Con ( 5 ) ; % The concentration of actove ATPase
ATPGPP = RROEA_Con ( 6 ) ; % The concentration of actove ATPGPP
MDH = RROEA_Con ( 7 ) ; % The concentration of actove MDH
Thio = RROEA_Con (8 ); % The concentration of
Fd = RROEA_Con ( 9 ) ; % The concentration of reduced ferrodoxin
RuACT = RROEA_Con (10) ; % The concentration of Rubisco activase
global RROEA_Pool;
GAPDHT = RROEA_Pool ( 1 ) ;
FBPaseT = RROEA_Pool ( 2 ) ;
SBPaseT = RROEA_Pool ( 3 ) ;
PRKT = RROEA_Pool ( 4 );
ATPaseT = RROEA_Pool ( 5 ) ;
ATPGPPT = RROEA_Pool ( 6 ) ;
MDHT = RROEA_Pool ( 7 ) ;
ThioT = RROEA_Pool (8);
FdT = RROEA_Pool (9);
RuACTT = RROEA_Pool (10);
GAPDHo = GAPDHT - GAPDH;
FBPaseo = FBPaseT - FBPase;
SBPaseo = SBPaseT - SBPase;
PRKo = PRKT - PRK;
ATPaseo = ATPaseT - ATPase;
ATPGPPo = ATPGPPT - ATPGPP;
MDHo = MDHT - MDH;
Thioo = ThioT - Thio;
Fdo = FdT - Fd;
RuACTo = RuACTT - RuACT;
ve2GAPDH = ke2GAPDH * ( Thio * GAPDHo - Thioo * GAPDH/KEe2GAPDH) ;
ve2FBPase = ke2FBPase * ( Thio * FBPaseo - Thioo * FBPase/KEe2FBPase) ;
ve2SBPase = ke2SBPase * ( Thio * SBPaseo - Thioo * SBPase/KEe2SBPase) ;
ve2PRK = ke2PRK * ( Thio * PRKo - Thioo * PRK/KEe2PRK) ;
KEe2ATPase = 1;
ke2ATPase = 1;
ve2ATPase = ke2ATPase * ( Thio * ATPaseo - Thioo * ATPase/KEe2ATPase);
ve2ATPGPP = ke2ATPGPP * ( Thio * ATPGPPo - Thioo * ATPGPP/KEe2ATPGPP) ;
ve2MDH = ke2MDH * ( Thio * MDHo - Thioo * MDH/KEe2MDH) -MDH;
if light > 500
ve2Fd = ke2Fd * Fdo;
else
ve2Fd = ke2Fd * light/500 * Fdo;
end
veFd2Thio = keFd2Thio * (Fd * Thioo - Thio * Fdo/KEeFd2Thio);
veFd2Calvin = Fd * keFd2Calvin * (FBPase/FBPaseT);
ve2RuACT = ke2RuACT * ( Thio * RuACTo - Thioo * RuACT/KEe2RuACT);
global RROEA_OLD_TIME;
global RROEA_TIME_N;
global RROEA_VEL;
global RROEA_CON;
if (RROEA_TIME_N ==0)
RROEA_TIME_N = 1;
end
if (t > RROEA_OLD_TIME)
RROEA_TIME_N = RROEA_TIME_N + 1;
RROEA_OLD_TIME = t;
end
RROEA_VEL ( RROEA_TIME_N , 1 ) = t;
RROEA_VEL ( RROEA_TIME_N , 2 ) = ve2GAPDH ;
RROEA_VEL ( RROEA_TIME_N , 3 ) = ve2FBPase ;
RROEA_VEL ( RROEA_TIME_N , 4 ) = ve2SBPase ;
RROEA_VEL ( RROEA_TIME_N , 5 ) = ve2PRK ;
RROEA_VEL ( RROEA_TIME_N , 6 ) = ve2ATPase ;
RROEA_VEL ( RROEA_TIME_N , 7 ) = ve2ATPGPP ;
RROEA_VEL ( RROEA_TIME_N , 8 ) = ve2MDH ;
RROEA_VEL ( RROEA_TIME_N , 9 ) = ve2Fd ;
RROEA_VEL ( RROEA_TIME_N , 10 ) = veFd2Thio ;
RROEA_VEL ( RROEA_TIME_N , 11 ) = veFd2Calvin ;
RROEA_VEL ( RROEA_TIME_N , 12 ) = ve2RuACT ;
RROEA_CON(RROEA_TIME_N,1) = t;
RROEA_CON(RROEA_TIME_N,2) = Thioo;
RROEA_Vel ( 1 ) = ve2GAPDH ;
RROEA_Vel ( 2 ) = ve2FBPase ;
RROEA_Vel ( 3 ) = ve2SBPase ;
RROEA_Vel ( 4 ) = ve2PRK ;
RROEA_Vel ( 5 ) = ve2ATPase ;
RROEA_Vel ( 6 ) = ve2ATPGPP ;
RROEA_Vel ( 7 ) = ve2MDH ;
RROEA_Vel ( 8 ) = ve2Fd ;
RROEA_Vel ( 9 ) = veFd2Thio ;
RROEA_Vel ( 10 ) = veFd2Calvin ;
RROEA_Vel ( 11 ) = ve2RuACT ;
global RROEA2PS_GAPDH;
global RROEA2PS_FBPase;
global RROEA2PS_SBPase;
global RROEA2PS_PRK;
global RROEA2PS_ATPase;
global RROEA2PS_ATPGPP;
RROEA2PS_GAPDH = GAPDH;
RROEA2PS_FBPase =FBPase;
RROEA2PS_SBPase = SBPase;
RROEA2PS_PRK = PRK;
RROEA2PS_ATPase = ATPase;
RROEA2PS_ATPGPP = ATPGPP;
global RROEA2RuACT_RuAC;
RROEA2RuACT_RuAC = RuACT;
global RROEA2trDynaPS_ve2Fd;
RROEA2trDynaPS_ve2Fd = ve2Fd;
global RROEA2trDynaPS_veFd2Calvin;
RROEA2trDynaPS_veFd2Calvin = veFd2Calvin;