-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathFig_S6_Freq_analysis_AF.m
258 lines (232 loc) · 11.6 KB
/
Fig_S6_Freq_analysis_AF.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
% AF flag
AF_flag = 1; % 0: nSR; 1: cAF
colorarray = [1 0 0];
if AF_flag == 0
% nSR
load yfin_nSR_0p2Hz
ICs_matrix(1,:) = yfinal;
load yfin_nSR_0p5Hz
ICs_matrix(2,:) = yfinal;
load yfin_nSR_1Hz
ICs_matrix(3,:) = yfinal;
load yfin_nSR_2Hz
ICs_matrix(4,:) = yfinal;
load yfin_nSR_3Hz
ICs_matrix(5,:) = yfinal;
load yfin_nSR_4Hz
ICs_matrix(6,:) = yfinal;
load yfin_nSR_5Hz
ICs_matrix(7,:) = yfinal;
load yfin_nSR_6Hz
ICs_matrix(8,:) = yfinal;
else
% cAF
load yfin_cAF_0p2Hz
ICs_matrix(1,:) = yfinal;
load yfin_cAF_0p5Hz
ICs_matrix(2,:) = yfinal;
load yfin_cAF_1Hz
ICs_matrix(3,:) = yfinal;
load yfin_cAF_2Hz
ICs_matrix(4,:) = yfinal;
load yfin_cAF_3Hz
ICs_matrix(5,:) = yfinal;
load yfin_cAF_4Hz
ICs_matrix(6,:) = yfinal;
load yfin_cAF_5Hz
ICs_matrix(7,:) = yfinal;
load yfin_cAF_6Hz
ICs_matrix(8,:) = yfinal;
end
y0_matrix = ICs_matrix;
cell_par = [AF_flag ISO_flag CCh ACh K2P_cond SK_cond SK_shift Ca_clamp_index Na_clamp_index]; % 5-13
% Parameter array for passing nondefault conditions
p = [prot_par cell_par SA_par];
HR = FREQ; % Hz
outputs = zeros(length(HR),20);
tic
for ii = 1:length(HR)%-2
prot_rate = HR(ii) %#ok<NOPTS> % (Hz)
prot_par = [prot_index prot_rate prot_interval prot_vm]; % 1 2 3 4
p = [prot_par cell_par SA_par];
tspan = [0; simDuration(ii)];
y0 = y0_matrix(ii,:);
[t,y] = ode15s(@human_atrial_model,tspan,y0,options,p);
currents = human_atrial_calcCurrents(t,y,p);
figure(11),subplot(2,4,ii),plot(t,y(:,39),'Color',colorarray)
figure(12),subplot(2,4,ii),plot(t,y(:,38)*1e6,'Color',colorarray)
if prot_rate == 0.5
figure(10),hold on,subplot(2,4,1),plot(t,y(:,39),'Color',colorarray)
figure(10),hold on,subplot(2,4,5),plot(t,y(:,38)*1e6,'Color',colorarray)
elseif prot_rate == 1
figure(10),hold on,subplot(2,4,2),plot(t,y(:,39),'Color',colorarray)
figure(10),hold on,subplot(2,4,6),plot(t,y(:,38)*1e6,'Color',colorarray)
elseif prot_rate == 2
figure(10),hold on,subplot(2,4,3),plot(t,y(:,39),'Color',colorarray)
figure(10),hold on,subplot(2,4,7),plot(t,y(:,38)*1e6,'Color',colorarray)
elseif prot_rate == 3
figure(10),hold on,subplot(2,4,4),plot(t,y(:,39),'Color',colorarray)
figure(10),hold on,subplot(2,4,8),plot(t,y(:,38)*1e6,'Color',colorarray)
end
time = t; % (ms)
Vm = y(:,39); % (mV)
Ca = y(:,38); % (mM)
CaSR = y(:,31); % mM
Na = y(:,34); % (mM)
dVm = currents(:,1); % (mV/ms)
%dVm_delta = (Vm(2:end)-Vm(1:end-1))./(time(2:end)-time(1:end-1));
%dVm = [dVm_delta; dVm_delta(end)];
Jserca = currents(:,2);
Jncx = currents(:,3);
Jpmca = currents(:,4);
period = 1000/prot_rate; % ms
AP_index = 2; % w/ 1 first AP, otherwise last AP
% 1) dVm_max 2) Vm_max 3) -Vm_min 4) AP_amp 5) APD90 6) APD70 7) APD50 8) APD30
% 9) Ca_max 10) Ca_min 11) CaT_amp 12) CaT_rise 13) CaT_decay_50 14) CaT_decay_63
% 15) Na_min 16) CaSR_max 17) CaSR_min 18) B3_serca 19) B3_ncx 20) B3_pmca
%outputs(ii,:) = function_beat_analysis_B3_2018(time,Vm,Ca,CaSR,Na,dVm,Jserca,Jncx,Jpmca,period,AP_index,Ca_clamp_index);
outputs(ii,:) = function_beat_analysis_B3_alt_2019(time,Vm,Ca,CaSR,Na,dVm,Jserca,Jncx,Jpmca,period,AP_index,Ca_clamp_index);
end
toc
figure(11),set(gcf,'color','w')
subplot(2,4,1),set(gca,'box','off','tickdir','out','fontsize',12)
title('0.2 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,2),set(gca,'box','off','tickdir','out','fontsize',12)
title('0.5 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,3),set(gca,'box','off','tickdir','out','fontsize',12)
title('1 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,4),set(gca,'box','off','tickdir','out','fontsize',12)
title('2 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,5),set(gca,'box','off','tickdir','out','fontsize',12)
title('3 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,6),set(gca,'box','off','tickdir','out','fontsize',12)
title('4 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,7),set(gca,'box','off','tickdir','out','fontsize',12)
title('5 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
subplot(2,4,8),set(gca,'box','off','tickdir','out','fontsize',12)
title('6 Hz'),ylabel('Em (mV)'),xlabel('Time (ms)')
figure(12),set(gcf,'color','w')
subplot(2,4,1),set(gca,'box','off','tickdir','out','fontsize',12)
title('0.2 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,2),set(gca,'box','off','tickdir','out','fontsize',12)
title('0.5 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,3),set(gca,'box','off','tickdir','out','fontsize',12)
title('1 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,4),set(gca,'box','off','tickdir','out','fontsize',12)
title('2 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,5),set(gca,'box','off','tickdir','out','fontsize',12)
title('3 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,6),set(gca,'box','off','tickdir','out','fontsize',12)
title('4 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,7),set(gca,'box','off','tickdir','out','fontsize',12)
title('5 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
subplot(2,4,8),set(gca,'box','off','tickdir','out','fontsize',12)
title('6 Hz'),ylabel('[Ca]i (nM)'),xlabel('Time (ms)')
%% Figure 3
figure(3),set(gcf,'color','w')
subplot(4,5,1),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,1),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('UV (mV/ms)')%, xlabel('HR (Hz)')
subplot(4,5,2),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,2),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('AP peak (mV)')%, xlabel('HR (Hz)')
subplot(4,5,3),hold on,plot(HR(HR_low:HR_up),-outputs(HR_low:HR_up,3),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('Em rest (mV)')%, xlabel('HR (Hz)')
subplot(4,5,4),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,4),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('AP amp (mV)')%, xlabel('HR (Hz)')
subplot(4,5,5),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,5),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD90 (ms)')%, xlabel('HR (Hz)')
subplot(4,5,6),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,6),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD70 (ms)')%, xlabel('HR (Hz)')
subplot(4,5,7),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,7),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD50 (ms)')%, xlabel('HR (Hz)')
subplot(4,5,8),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,8),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD30 (ms)')%, xlabel('HR (Hz)')
subplot(4,5,9),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,9)*1e6,'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('syst [Ca] (nM)')%, xlabel('HR (Hz)')
subplot(4,5,10),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,10)*1e6,'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('diast [Ca] (nM)')%, xlabel('HR (Hz)')
subplot(4,5,11),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,11)*1e6,'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT amp (nM)')%, xlabel('HR (Hz)')
subplot(4,5,12),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,12),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT ttp (ms)')%, xlabel('HR (Hz)')
subplot(4,5,13),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,13),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT t50 (ms)')%, xlabel('HR (Hz)')
subplot(4,5,14),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,14),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT tau (ms)')%, xlabel('HR (Hz)')
subplot(4,5,15),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,15),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('diast [Na] (mM)')%, xlabel('HR (Hz)')
subplot(4,5,16),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,16),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaSR max (mM)'), xlabel('HR (Hz)')
subplot(4,5,17),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,17),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaSR min (mM)'), xlabel('HR (Hz)')
subplot(4,5,18),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,18),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('B3 serca (%)'), xlabel('HR (Hz)')
subplot(4,5,19),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,19),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('B3 ncx (%)'), xlabel('HR (Hz)')
subplot(4,5,20),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,20),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('B3 pmca (%)'), xlabel('HR (Hz)')
%% Figure 4
figure(4),set(gcf,'color','w')
subplot(2,3,2),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,5),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD90 (ms)')%, xlabel('HR (Hz)')
subplot(2,3,1),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,7),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD50 (ms)')%, xlabel('HR (Hz)')
subplot(2,3,4),hold on,plot(HR(HR_low:HR_up),-outputs(HR_low:HR_up,3),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('Em rest (mV)'), xlabel('HR (Hz)')
subplot(2,3,5),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,11)*1e6,'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT amp (nM)'), xlabel('HR (Hz)')
subplot(2,3,6),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,15),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('diast [Na] (mM)'), xlabel('HR (Hz)')
%% B3
figure(5),set(gcf,'color','w')
subplot(2,1,2),hold on
bar([46 45 9;outputs(2,18) outputs(2,19) outputs(2,20)]),ylim([0 100])
errorbar([0.78 1 1.22],[46 45 9],[5 6 1],'k.')
set(gca,'box','off','tickdir','out','fontsize',12)
title('cAF @ 0.5 Hz')
ylabel('% contribution')
set(gca, 'XTick', 1:2, 'XTickLabel', {'Experiments','Simulations'})
%%
figure(6),set(gcf,'color','w')
subplot(2,3,1),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,5),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD90 (ms)')%, xlabel('HR (Hz)')
subplot(2,3,2),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,7),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('APD50 (ms)')%, xlabel('HR (Hz)')
subplot(2,3,3),hold on,plot(HR(HR_low:HR_up),-outputs(HR_low:HR_up,3),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('Em rest (mV)')%, xlabel('HR (Hz)')
subplot(2,3,4),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,11)*1e6,'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT amp (nM)'), xlabel('HR (Hz)')
subplot(2,3,5),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,10)*1e6,'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('CaT min (nM)'), xlabel('HR (Hz)')
subplot(2,3,6),hold on,plot(HR(HR_low:HR_up),outputs(HR_low:HR_up,15),'Color',colorarray)
set(gca,'box','off','tickdir','out','fontsize',12)
ylabel('diast [Na] (mM)'), xlabel('HR (Hz)')