-
Notifications
You must be signed in to change notification settings - Fork 3
/
BF_Ini.m
287 lines (233 loc) · 16.5 KB
/
BF_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
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 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_con = BF_Ini(begin)
global BFVmax;
global cATPsyn;
global CPSi;
global cNADPHsyn;
% cATPsyn=1.0447;%1.01866 WY201803
% CPSi=1.0131;% 1.0237 WY201803
% cNADPHsyn=1.094468408;%1.0388 WY201803
K1 = 10^6 ; % The rate constant for formation of ISP.QH2 complex; Vmax is used here.
K2 = 500 ; % The rate constant for ISP.QH2-->QH(semi) + ISPH(red)
K3 = 5 * 10^7 ; % The rate constant for QH. + cytbL --> Q + cytbL- + H+;
K4 = 5 * 10^7 ; % The rate constant for cytbL- + cytbH --> cytbL + cytbH-
K5 = 5 * 10^7 ; % The rate constant for CytbH- + Q --> cytbH + Q-
K6 = 5 * 10^7 ; % The rate constant for CytbH- + Q- --> cytbH + Q2-
K7 = 10^4 ; % The rate constant for Q binding to Qi site
K8 = 1000 ; % The rate constant for ISPH + CytC1 --> ISPH(ox) + CytC1+
K9 = 8.3 * 10^6 ; % The rate constant for the electron transport from cytc1 to cytc2
K10 = 8 * 10 ^ 8 ; % The rate constant for the electron transport from cytc2 to P700
Vmax11 = 6 *cATPsyn; % WY201803 The maximum rate of ATP synthesis; unit: mmol l-1 s-1; default 1.47;
Kqi = 10^ 3 ; % The rate constant for the uptake of 2 protons from stroma; Unit: s-1; the calculation is done based on a simplified assumption of first order kinetics for these reaction. The half time for the uptake of two protons is assumed, following Crofts "http://pop.life.uiuc.edu/~a-crofts/ahab/qcycle1.html"--The modified Q cycle, as <150 microsecond. 150 microsecond is used as an estimate of the halftime for this electron transfer.
PMODTEM = 1;
PK = 3.6 * 10^(-8) * PMODTEM; % The permeability constant for K, cm s-1
PMg = 3.6 * 10^(-8) * PMODTEM; % The permeability constant for Mg, cm s-1
PCl = 1.8 * 10^(-8) * PMODTEM; % The permeability constant for Cl, cm s-1
Kau = 10^10 ; % The rate constant for exciton transfer from perpheral antenna to core antenna, see FI, unit: s-1
Kua = 10^10 ; % The rate constant for exciton transfer from core antenna to peripheral antenna, SEE FI, unit: s-1
Kf = 6.3 * 10 ^6 ; % The rate constant for fluorescence emission, see the note in FI, unit: s-1
Kd = 2 * 10^8 ; % The rate constant for heat dissipation; see the note for FI, unit: s-1
K15 = 10^10*CPSi ; % WY 201803 The rate constant for the primary charge sepration in PSI, assuming the half time 30ps, unit: s-1
K16 = 10^5 ; % The rate constant for the electron transfer from electron acceptor A- to Fd, unit: s-1; following reference of Setif PQ and Bottin H, 1995, Biochemistry.
Em_ISP = 0.31 ; % The midpoint potential fo ISP; unit: V
Em_CytC1 = 0.27 ; % The midpoint potential for cytc1; unit: V
Em_CytbL = -0.09 ; % The midpoint potential for cytbL; unit: V
Em_CytbH = 0.05 ; % The midpoint potential for cytbH; UNIT: V
Em_CytC2 = 0.35 ; % The midpoint potential for cytc2, unit: V
% ISPHr + cytc1 --> ISPHox + cytc1-
DeltaEm = Em_CytC1 - Em_ISP ;
DeltaG = DeltaEm *(-9.649) * 10^4 ;
RT = 8.314 * 298;
KE8 = exp(-DeltaG/RT) ;
% cytc1- + cytc2 --> cytc1 + cytc2-
DeltaEm = Em_CytC2 - Em_CytC1 ;
DeltaG = DeltaEm *(-9.649) * 10^4 ;
RT = 8.314 * 298;
KE9 = exp(-DeltaG/RT) ;
MemCap = 0.6 * 10^(-6) ; % The membrane capacity, microFarady/cm2.
RVA = 8*10^(-10) ; % THe ratio of the lumen volume to thylakoid membrane; unit: L/cm2. The data from Cruz 2001.
KBs = 1.1*10^(-8) ; % The buffer equilibrium constant
KBl = 5.1 * 10^(-6) ; % The buffer equilibrium constant
KM1ATP = 0.12;
KM1ADP = 0.014; % Originally
KM1PI = 0.3; % Originally
KM2NADP = 0.05; % From Fridlyand and Scheibe 1999
KM2NADPH= 0.035; % From Fridlyand and Scheibe 1999
V2M = 27.8*cNADPHsyn;%WY 201803 % Calcualted based on 6.4 mmol (mg chl)-1h-1; Unit: mmol/l/s;
KE2 = 495; % From Fridlyand paper , 1999, BBA, 1413, 1, 31-42
K1=BFVmax(1);
K2=BFVmax(2);
K3=BFVmax(3);
K4=BFVmax(4);
K5=BFVmax(5);
K6=BFVmax(6);
K7=BFVmax(7);
K8=BFVmax(8);
K9=BFVmax(9);
K10=BFVmax(10);
Vmax11=BFVmax(11)*cATPsyn;;
Kau=BFVmax(12);
Kua=BFVmax(13);
Kf=BFVmax(14);
Kd=BFVmax(15);
K15=BFVmax(16)*CPSi;
K16=BFVmax(17);
V2M=BFVmax(18)*cNADPHsyn;
% The rate constant used in the model
global BF_RC;
BF_RC= zeros(5,1);
% Assign values to the array for rate constant
BF_RC ( 1 ) = K1 ; % The rate constant for formation of ISP.QH2 complex; unit: per second
BF_RC ( 2 ) = K2 ; % The rate constant for ISP.QH2-->QH(semi) + ISPH(red) ; unit: per second
BF_RC ( 3 ) = K3 ; % The rate constant for QH. + cytbL --> Q + cytbL- + H+ Unit: s-1
BF_RC ( 4 ) = K4 ; % The rate constant for cytbL- + cytbH --> cytbL + cytbH- Unit: s-1
BF_RC ( 5 ) = K5 ; % The rate constant for CytbH- + Q --> cytbH + Q- Unit: s-1
BF_RC ( 6 ) = K6 ; % The rate constant for CytbH- + Q- --> cytbH + Q2- Unit: s-1
BF_RC ( 7 ) = K7 ; % The rate constant for Q binding to Qi site; which assumed half time as 200 us, following Croft's website Unit: s-1
BF_RC ( 8 ) = K8 ; % The rate constant for ISPH + CytC1 --> ISPH(ox) + CytC1+ Unit: s-1
BF_RC ( 9 ) = K9 ; % The rate constant for the electron transport from cytc1 to cytc2 Unit: s-1
BF_RC ( 10 ) = K10 ; % The rate constant for the electron transport from cytc2 to P700 Unit: s-1
BF_RC ( 11 ) = Vmax11 ; % The maximum rate of ATP synthesis Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 12 ) = Kqi ; % The rate constant for uptake of two protons from the stroma to Q2- s-1
BF_RC ( 13 ) = PK ; % The permeability constant for K Unit: cm s-1
BF_RC ( 14 ) = PMg ; % The permeability constant for Mg Unit: cm s-1
BF_RC ( 15 ) = PCl ; % The permeability constant for Cl Unit: cm s-1
BF_RC ( 16 ) = Kau ; % The rate constant for exciton transfer from perpheral antenna to core antenna, see FI Unit: s-1
BF_RC ( 17 ) = Kua ; % The rate constant for exciton transfer from core antenna to peripheral antenna, SEE FI Unit: s-1
BF_RC ( 18 ) = Kf ; % The rate constant for fluorescence emission, see the note in FI Unit: s-1
BF_RC ( 19 ) = Kd ; % The rate constant for heat dissipation; see the note for FI Unit: s-1
BF_RC ( 20 ) = KE8 ; % ISPHr + cytc1 --> ISPHox + cytc1- Unit: s-1
BF_RC ( 21 ) = KE9 ; % cytc1- + cytc2 --> cytc1 + cytc2- Unit: s-1
BF_RC ( 22 ) = K15 ; % The rate constant for primary charge separation in PSI Unit: s-1
BF_RC ( 23 ) = K16 ; % The rate constant for electron tranfer from electron acceptor of PSI to Fd Unit: s-1
BF_RC ( 24 ) = MemCap ; % The membrane capacity
BF_RC ( 25 ) = RVA ; % The ratio of lumen volume to thylakoid membrane area
BF_RC ( 26 ) = KBs ; % The buffer equilibrium constant in stroma
BF_RC ( 27 ) = KBl ; % The buffer equilibrium constant in lumen
BF_RC ( 28 ) = KM1ATP ; % The michaelis menton constant for ATP for ATP synthesis
BF_RC ( 29 ) = KM1ADP ; % The michaelis menton constant for ATP for ADP synthesis
BF_RC ( 30 ) = KM1PI ; % The michaelis menton constant for ATP for PI synthesis
BF_RC ( 31 ) = KM2NADP ; % The michaelis menten constant for NADP Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 32 ) = KM2NADPH ; % The michaelis menten constant for NADPH Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 33 ) = V2M ; % The maximum rate of NADPH formation Unit: mmol l-1 s-1; The unit for the reactions occurrs in stroma is mmol l-1 s-1
BF_RC ( 34 ) = KE2 ; % Equilibrium constatn
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialization of the initial concentration of the different component %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialize the leaves for a dark adapted leaves;
% Unit micro mol per m2 or mmol l-2 stroma volume
% The initialization of the model with concentration of each substrate in dark-adapted leaves
% The total concentration of PSII is assumed to be 1 micromole per meter square
ISPHr = 0 ; % The reduced ion sulfer protein (ISPH); unit: micromole per m2
cytc1 = 1 ; % The oxidized state of cytc1; unit: micromole per meter square
ISPo = 1 ; % The oxidized ion sulfer protein (ISP); unit: micromole per meter square
ISPoQH2 = 0 ; % The complex of oxidized ion sulfer protein and reduced quinone; unit: micromole per meter square
QHsemi = 0 ; % Semiquinone; micromole per meter square
cytbL = 1 ; % The oxidized cytbL; micromole per meter square
Qi = 0 ; % The binding quinone on the quinone site; micromole per meter square
Q = 1 ; % Quinone; micromole per meter square
cytbH =1 ; % The oxidized form of cytbH; micromole per meter square
Qn = 0 ; % Q- ; unit: micromole per meter square
Qr = 0 ; % The reduced quinone Q2- ; micromole per meter square
QH2 = 5 ; % The reduced quinone PQH2; micromole per meter square
cytc2 = 1 ; % oxidized cytc2; micromole per meter square
P700 = 0.5 ; % The reduced state of P700, including both P700 and excited P700; micromole per meter square
ADP = 0.82 ; % ADP in stroma, from the earlier photorespiration model; mmol l-1
Pi = 0.9 ; % Phosphate in stroma, from the photorespiration model; mmol l-1
ATP = 0.68 ; % ATP in stroma, from the photorespiration model; mmol l-1
Ks = 10 ; % K ions in stroma, mM, from the literature; mmol l-1; 90 might be an default;
Mgs = 5;%2.5 ; % Mg ions in stroma, mM, from the literature of the ion estimate
Cls = 1 ; % Cl ions in stroma, mM, from the literature of the ion estimate
Aip = 0 ; % The number of photons in peripheral antenna; micromole per meter square
U = 0 ; % The number of photons in core antenna; micromole per meter square
An = 0 ; % The reduced electron acceptor in PSI; micromole per meter square
Fdn = 0.3 ; % The reduced ferrodoxin; micromole per meter square leaf area
BFHs = 19.0001; %50.0001 ; % The protonated buffer species and free proton together in stroma; mmol l-1; The value follows Laisk and Walker, 1989. But they did not give reference about the source of this number.; default 25
BFHl = 19.0001; % The protonated buffer species and free proton together in lumen; mmol l-1; The value follows Laisk and Walker, 1989. But they did not give reference about the source of this number. ; default 5
PHs = 7 ; % PH of stroma
PHl = 7 ; % PH of lumen
NADPH = 0.21; % The NADPH concentration in stroma at dark
% Assign the value to a array
% BF_ini.m
% This is the initialization step for the module of the Q cycle, and ATP synthesis steps
global BF_con;
BF_con ( 1 ) = ISPHr ; % The reduced ion sulfer protein (ISPH)
BF_con ( 2 ) = cytc1 ; % The oxidized state of cytc1
BF_con ( 3 ) = ISPo ; % The oxidized ion sulfer protein (ISP)
BF_con ( 4 ) = ISPoQH2 ; % The complex of oxidized ion sulfer protein and reduced quinone
BF_con ( 5 ) = QHsemi ; % Semiquinone
BF_con ( 6 ) = cytbL ; % The oxidized cytbL
BF_con ( 7 ) = Qi ; % The binding Quinone
BF_con ( 8 ) = Q ; % Quinone
BF_con ( 9 ) = cytbH ; % The oxidized form of cytbH
BF_con ( 10 ) = Qn ; % Q-
BF_con ( 11 ) = Qr ; % Q2-
BF_con ( 12 ) = QH2 ; % QH2
BF_con ( 13 ) = cytc2 ; % oxidized cytc2
BF_con ( 14 ) = P700 ; % The reduced state of P700, including both P700 and excited P700
BF_con ( 15 ) = ADP ; % ADP in stroma
BF_con ( 16 ) = Pi ; % Phosphate in stroma
BF_con ( 17 ) = ATP ; % ATP in stroma
BF_con ( 18 ) = Ks ; % K ions in stroma
BF_con ( 19 ) = Mgs ; % Mg ions in stroma
BF_con ( 20 ) = Cls ; % Cl ions in stroma
BF_con ( 21 ) = Aip ; % The number of photons in peripheral antenna
BF_con ( 22 ) = U ; % The number of photons in core antenna
BF_con ( 23 ) = An ; % The reduced electron acceptor in PSI
BF_con ( 24 ) = Fdn ; % The reduced ferrodoxin
BF_con ( 25 ) = BFHs ; % The total concentration of proton and protonated buffer species in stroma, put in unit: mmol l-1
BF_con ( 26 ) = BFHl ; % The total concentration of proton and protonated buffer species in lumen, unit: mmol l-1
BF_con ( 27 ) = PHs ; % The PH value of the stroma
BF_con ( 28 ) = PHl ; % The PH value of the lumen
BF_con ( 29 ) = NADPH ; % The NADPH concentration in stroma, Unit: mmol l-1;
% Assigning the pool variables
% The sizes of different pools in the model
Tcyt = 1 ; % Unit: micromole m-2 The total concentration of cytochrome. It is assumed that the concentration of cytbL, cytbH, and cytc1 is equal as Tcyt.
Tcytc2 = 1 ; % Unit: micromole m-2 The total concentration of cytc2, as Tcyt , the unit is micromole per meter square leaf area
TK = 20 ; % Unit: mmol l-1 The total concentration of potassium, 180 mM, in the bigining assuming the concentration of ions in stroma and lumen are same
TMg = 10 ; % Unit: mmol l-1 The total concentraiton of Mg2+, 18 mM, in the beginning assuming the concentration of the ions in the stroma and lumen are same
TCl = 2;%1 ; % Unit: mmol l-1 The total concentraiton of Cl-, 1 mM, assuming equal concentrations of ion concentrations in stroma and lumen in the beginning.
TFd = 1 ; % Unit: micromole m-2 The total concentration of Ferrodoxin, this assumed that only 1 Fd is associated with one PSI unit.
TA = 1 ; % Unit: micromole m-2 The total concentration of electron acceptor of PSI
TQ = 8 ; % Unit: micromole m-2 The total concentration of quinone at all different states
BFTs = 38 ; % Unit: mmol l-1 The total concentration of buffer in stroma;
BFTl = 38 ; % Unit: mmol l-1 The total concentration of buffer in lumen
P700T = 1 ; % % The total number of P700 unit: micromole m-2 leaf area
NADPHT = 1; % The total concentration of NADPH in stroma; 1 is an guessed value;
% Assign the pools to the global pool variables
global BF_Pool;
BF_Pool = zeros(5,1);
BF_Pool ( 1 ) = Tcyt; % The total amount of cytbH or cytbL; Unit: micromole m-2 leaf area
BF_Pool ( 2 ) = Tcytc2; % The total amount of cytc; Unit: micromole m-2 leaf area
BF_Pool ( 3 ) = TK ; % The total concentration of K in both stroma and lumen. Unit: mmol l-1. In this model, it was assumed that the total concentration of K, and Mg and Cl as well, is constant.
BF_Pool ( 4 ) = TMg ; % The total concentration of Mg in both stroma and lumen. Unit: mmol l-1. In this model, it was assumed that the total concentration of Mg, and K and Cl as well, is constant.
BF_Pool ( 5 ) = TCl ; % The total concentration of Cl in both stroma and lumen. Unit: mmol l-1. In this model, it was assumed that the total concentration of Cl in both stroma and lumen is constant.
BF_Pool ( 6 ) = TFd ; % The total concentration of Ferrodoxin
BF_Pool ( 7 ) = TA ; % The total concentration of the primary electron acceptor of PSI; Unit: micromole m-2 leaf area
BF_Pool ( 8 ) = TQ ; % The total concentration of plastoquinone in thylakoid membrane. ; Unit: micromole m-2 leaf area
BF_Pool ( 9 ) = BFTs ; % The total concentration of buffer in stroma; unit: mmol per liter
BF_Pool ( 10 ) = BFTl ; % The total concentration of buffer in lumen; unit: mmol per liter
BF_Pool ( 11 ) = P700T ; % The total number of P700; unit: micromole m-2 leaf area
BF_Pool ( 12 ) = NADPHT ; % The total concentration of NADPH in stroma; 1 is an guessed value;
global HPR ;
HPR = 4.66;
global BF2RROEA_Fdn;
global BF2RROEA_FdT;
BF2RROEA_Fdn = Fdn;
BF2RROEA_FdT = TFd;