-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathC4Drive.m
159 lines (144 loc) · 4.39 KB
/
C4Drive.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
% Copyright Wang Y and Zhu X-G, 2014.
% CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai,200031
% A mixed pathway model of C4 photosynthesis
% The CO2 uptake and metabolite concentraion changes with time.
clear all;
Input=importdata('C4model_input.txt');
InputData=Input.data;
Ca_Input=InputData(:,ismember(Input.colheaders,'CO2')==1);
Light_Input=InputData(:,ismember(Input.colheaders,'Light')==1);
Pathway_Input=InputData(:,ismember(Input.colheaders,'Pathway_type')==1);
global phi;
global Lpd;
global I;
global U;
global V;
global Ratio;
global CI
global O2;
global Bchl_CP;
global MC_CP;
global Mchl_CP;
I = Light_Input/1000;%mmol m-2 s-1 light intensity input
CI=Ca_Input*0.45/(3 * 10^4);%0.006;%intercellular CO2 concentration
phi=0.03; %¦Õ=0.03 plasmodesmata proportion
Lpd=400; % plasmodesmata length lPD=0.4¦Ìm
U=0;% light partition coefficient
V=0;% Jmax partition coefficient
Ratio=4; % % Enezyme activity variation factor for PCK pathway
O2= 0.2646;% O2 concentration
Bchl_CP= 25.0;%Total phosphate concentration in bundle sheath chloroplast
MC_CP=15.0;%Total phosphate concentration in mesophyll cell cytosol
Mchl_CP=15.0;%Total phosphate concentration in mesophyll cell chloroplast
global pathway_option;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
pathway_option=Pathway_Input;
%%% 0 normal NADP-ME type
%%% 1 Asp+Mal transport and ME type
%%% 2 Asp+Mal and PCK type
%%% 3 Asp+Mal and PCK+ME type
%%% 4 Asp and PCK only type
%%% 6 DiT2 mutant
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Ini=C4Ini;
time=3000;%simulation time
[Tt, d]=ode15s(@C4MB, [0, time], Ini);
global Result;
Result =[Tt,d];
gm=0.7;%molm-2 bar-10.2
Sc=3*10^4;%3.36*10^4;%ubarL/mmol
vinf=gm*Sc*10^(-3)*(CI-d(:,56));%vinf=gm*Sc*10^(-3)*(CI-MC_CO2);
figure;
plot(Tt,vinf*1000) %CO2 influx of the model
xlabel('TIme (s)');
ylabel('CO_2 uptake rate (\mumolm^-^2 s^-^1)');
ylim([0,60]);
figure
subplot(5,10,1); plot(Tt,d(:,1));
title('MC.HCO3');
subplot(5,10,2); plot(Tt,d(:,2));
title('MC.OAA');
subplot(5,10,3); plot(Tt,d(:,3));
title('MC.PEP');
subplot(5,10,4); plot(Tt,d(:,4));
title('MC.Malate');
subplot(5,10,5); plot(Tt,d(:,5));
title('MC.Pyruvate');
subplot(5,10,6); plot(Tt,d(:,6));
title('MC.PGA');
subplot(5,10,7); plot(Tt,d(:,7));
title('MC.FBP');
subplot(5,10,8); plot(Tt,d(:,8));
title('MC.UDPG');
subplot(5,10,9); plot(Tt,d(:,9));
title('MC.SUCP');
subplot(5,10,10); plot(Tt,d(:,10));
title('MC.SUC');
subplot(5,10,11); plot(Tt,d(:,11));
title('MC.F26BP');
subplot(5,10,12); plot(Tt,d(:,12));
title('MC.ATP');
subplot(5,10,13); plot(Tt,d(:,13));
title('MC.T3P');
subplot(5,10,14); plot(Tt,d(:,14));
title('MC.HexP');
subplot(5,10,15); plot(Tt,d(:,15));
title('MC.Sucrose');
subplot(5,10,16); plot(Tt,d(:,16));
title('Mchl.OAA');
subplot(5,10,17); plot(Tt,d(:,17));
title('Mchl.Malate');
subplot(5,10,18); plot(Tt,d(:,18));
title('Mchl.PEP');
subplot(5,10,19); plot(Tt,d(:,19));
title('Mchl.Pyruvate');
subplot(5,10,20); plot(Tt,d(:,20));
title('Mchl.NADPH');
subplot(5,10,21); plot(Tt,d(:,21));
title('Mchl.ATP');
subplot(5,10,22); plot(Tt,d(:,22));
title('Mchl.PGA');
subplot(5,10,23); plot(Tt,d(:,24));
title('Mchl.T3P');
subplot(5,10,24); plot(Tt,d(:,25));
title('BSC.T3P');
subplot(5,10,25); plot(Tt,d(:,26));
title('BSC.PGA');
subplot(5,10,26); plot(Tt,d(:,27));
title('BSC.Malate');
subplot(5,10,27); plot(Tt,d(:,28));
title('BSC.Pyruvate');
subplot(5,10,28); plot(Tt,d(:,29));
title('BSC.CO2');
subplot(5,10,29); plot(Tt,d(:,30));
title('Bchl.CO2');
subplot(5,10,30); plot(Tt,d(:,31));
title('Bchl.RuBP');
subplot(5,10,31); plot(Tt,d(:,32));
title('Bchl.PGA');
subplot(5,10,32); plot(Tt,d(:,34));
title('Bchl.ATP');
subplot(5,10,33); plot(Tt,d(:,35));
title('Bchl.NADPH');
subplot(5,10,34); plot(Tt,d(:,36));
title('Bchl.SBP');
subplot(5,10,35); plot(Tt,d(:,37));
title('Bchl.S7P');
subplot(5,10,36); plot(Tt,d(:,38));
title('Bchl.FBP');
subplot(5,10,37); plot(Tt,d(:,39));
title('Bchl.E4P');
subplot(5,10,38); plot(Tt,d(:,40));
title('Bchl.Starch');
subplot(5,10,39); plot(Tt,d(:,41));
title('Bchl.Rubisco');
subplot(5,10,40); plot(Tt,d(:,42));
title('Bchl.T3P');
subplot(5,10,41); plot(Tt,d(:,43));
title('Bchl.HexP');
subplot(5,10,42); plot(Tt,d(:,44));
title('Bchl.Pent');
subplot(5,10,43); plot(Tt,d(:,45));
title('Bchl.Malate');
subplot(5,10,44); plot(Tt,d(:,46));
title('Bchl.Pyruvate');