clc
clear all
%close all
%
Surface_area_node = 2.59415600000000*pi*1e-8 ; %cm2
Surface_area_MYSA = 8*3*pi*1e-8 ; %cm2
Surface_area_FLUT = 8*8.05888*pi*1e-8 ; %cm2
Surface_area_STIN = 8*19.641280*pi*1e-8 ; %cm2
%
Left_Trans_Leak = csvread('MYSARpn1x2_TransmembraneCurrent_Leak_Leftside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
Left_Trans_Cap = csvread('MYSARpn1x2_TransmembraneCurrent_Capacitive_Leftside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
Right_Trans_Leak = csvread('MYSARpn1x2_TransmembraneCurrent_Leak_Rightside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
Right_Trans_Cap = csvread('MYSARpn1x2_TransmembraneCurrent_Capacitive_Rightside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
[soton satr] = size(Left_Trans_Leak) ;
time = Left_Trans_Leak(:,1) ;
% changing the unit from mA/cm2 to nA
for i=2:22
Left_Trans_Leak(:,i) = Left_Trans_Leak(:,i)*Surface_area_STIN ; % mA
Left_Trans_Leak(:,i) = Left_Trans_Leak(:,i)*1e6 ; % nA
end
for i=23:27
Left_Trans_Leak(:,i) = Left_Trans_Leak(:,i)*Surface_area_FLUT ; % mA
Left_Trans_Leak(:,i) = Left_Trans_Leak(:,i)*1e6 ; % nA
end
for i=28
Left_Trans_Leak(:,i) = Left_Trans_Leak(:,i)*Surface_area_MYSA ; % mA
Left_Trans_Leak(:,i) = Left_Trans_Leak(:,i)*1e6 ; % nA
end
%%%%%%%%%%%%%%%
for i=2:22
Left_Trans_Cap(:,i) = Left_Trans_Cap(:,i)*Surface_area_STIN ; % mA
Left_Trans_Cap(:,i) = Left_Trans_Cap(:,i)*1e6 ; % nA
end
for i=23:27
Left_Trans_Cap(:,i) = Left_Trans_Cap(:,i)*Surface_area_FLUT ; % mA
Left_Trans_Cap(:,i) = Left_Trans_Cap(:,i)*1e6 ; % nA
end
for i=28
Left_Trans_Cap(:,i) = Left_Trans_Cap(:,i)*Surface_area_MYSA ; % mA
Left_Trans_Cap(:,i) = Left_Trans_Cap(:,i)*1e6 ; % nA
end
for i=2:22
Right_Trans_Leak(:,i) = Right_Trans_Leak(:,i)*Surface_area_STIN ; % mA
Right_Trans_Leak(:,i) = Right_Trans_Leak(:,i)*1e6 ; % nA
end
for i=23:27
Right_Trans_Leak(:,i) = Right_Trans_Leak(:,i)*Surface_area_FLUT ; % mA
Right_Trans_Leak(:,i) = Right_Trans_Leak(:,i)*1e6 ; % nA
end
for i=28
Right_Trans_Leak(:,i) = Right_Trans_Leak(:,i)*Surface_area_MYSA ; % mA
Right_Trans_Leak(:,i) = Right_Trans_Leak(:,i)*1e6 ; % nA
end
%%%%%%%%%%%%%%%
for i=2:22
Right_Trans_Cap(:,i) = Right_Trans_Cap(:,i)*Surface_area_STIN ; % mA
Right_Trans_Cap(:,i) = Right_Trans_Cap(:,i)*1e6 ; % nA
end
for i=23:27
Right_Trans_Cap(:,i) = Right_Trans_Cap(:,i)*Surface_area_FLUT ; % mA
Right_Trans_Cap(:,i) = Right_Trans_Cap(:,i)*1e6 ; % nA
end
for i=28
Right_Trans_Cap(:,i) = Right_Trans_Cap(:,i)*Surface_area_MYSA ; % mA
Right_Trans_Cap(:,i) = Right_Trans_Cap(:,i)*1e6 ; % nA
end
%
startColor = [1, 1, 1];
xx = startColor ;
figure
for i=2:satr
if i<25
m=0.008 ;
xx = xx - m ;
else
m=0.2 ;
xx = xx - m ;
end
plot(time , Left_Trans_Leak(:,i) ,'--' ,'color', xx , 'LineWidth' , 2 ) ;
hold on
end
xlabel('time(ms)')
ylabel('transmembrane-il (nA)')
title('Left side')
xlim([0.95 4])
% for i=2:satr
%
% plot(time , Right_Trans_Leak(:,i) , 'LineWidth' , 2)
% hold on
%
%
% end
% xlabel('time(ms)')
% ylabel('transmembrane_il (nA)')
% title('Right side')
%%
xx = startColor ;
figure
for i=2:satr
if i<25
m=0.008 ;
xx = xx - m ;
else
m=0.2 ;
xx = xx - m ;
end
plot(time , Left_Trans_Cap(:,i) ,'--', 'color', xx , 'LineWidth' , 2)
hold on
end
xlabel('time(ms)')
ylabel('icap (nA)')
title('Left side')
xlim([0.95 4])
% for i=2:satr
%
% plot(time , Right_Trans_Cap(:,i) , 'LineWidth' , 2)
% hold on
%
%
% end
% xlabel('time(ms)')
% ylabel('icap (nA)')
% title('Right side')
%% vext0
Rpn0 = 429128.527578172*1e6*1e-4 ; %ohm/micron node and MYSA
Rpn2 = 108066.18906880693*1e6*1e-4 ; %ohm/micron FLUT
Rpx = 108066.18906880693*1e6*1e-4 ; %ohm/micron STIN
Left_vext0 = csvread('MYSARpn1x2_vext0_Leftside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
%
j=1 ;
for i=2:42
I_vext0_left(:,j) = (Left_vext0(:,i) - Left_vext0(:,i+1))/Rpx ; %mA.micron
I_vext0_left(:,j) = I_vext0_left(:,j)/9.8205 ; %mA
I_vext0_left(:,j) = I_vext0_left(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=43:52
I_vext0_left(:,j) = (Left_vext0(:,i) - Left_vext0(:,i+1))/Rpn2 ; %mA.micron
I_vext0_left(:,j) = I_vext0_left(:,j)/4.0294 ; %mA
I_vext0_left(:,j) = I_vext0_left(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=53:54
I_vext0_left(:,j) = (Left_vext0(:,i) - Left_vext0(:,i+1))/Rpn0 ; %mA.micron
I_vext0_left(:,j) = I_vext0_left(:,j)/1.5 ; %mA
I_vext0_left(:,j) = I_vext0_left(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=55
I_vext0_left(:,j) = (Left_vext0(:,i) - Left_vext0(:,i+1))/Rpn0 ; %mA.micron
I_vext0_left(:,j) = I_vext0_left(:,j)/0.5 ; %mA
I_vext0_left(:,j) = I_vext0_left(:,j)*1e6 ; % nA
j=j+1 ;
end
startColor = [1, 1, 1];
xx = startColor ;
figure
for i=2:54
if i<48
m=0.005 ;
xx = xx - m ;
else
m=0.1 ;
xx = xx - m ;
end
plot(time , I_vext0_left(:,i) ,'--' , 'Color' , xx ,'LineWidth' , 2)
hold on
end
xlabel('time(ms)')
ylabel('periaxonal current (nA)')
title('Left side')
xlim([0.95 4])
%%
Right_vext0 = csvread('MYSARpn1x2_vext0_Rightside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
j=1 ;
for i=2:42
I_vext0_right(:,j) = (Right_vext0(:,i) - Right_vext0(:,i+1))/Rpx ; %mA.micron
I_vext0_right(:,j) = I_vext0_right(:,j)/9.8205 ; %mA
I_vext0_right(:,j) = I_vext0_right(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=43:52
I_vext0_right(:,j) = (Right_vext0(:,i) - Right_vext0(:,i+1))/Rpn2 ; %mA.micron
I_vext0_right(:,j) = I_vext0_right(:,j)/4.0294 ; %mA
I_vext0_right(:,j) = I_vext0_right(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=53:54
I_vext0_right(:,j) = (Right_vext0(:,i) - Right_vext0(:,i+1))/Rpn0 ; %mA.micron
I_vext0_right(:,j) = I_vext0_right(:,j)/1.5 ; %mA
I_vext0_right(:,j) = I_vext0_right(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=55
I_vext0_right(:,j) = (Right_vext0(:,i) - Right_vext0(:,i+1))/Rpn0 ; %mA.micron
I_vext0_right(:,j) = I_vext0_right(:,j)/0.5 ; %mA
I_vext0_right(:,j) = I_vext0_right(:,j)*1e6 ; % nA
j=j+1 ;
end
% figure
% for i=2:54
%
% plot(time , I_vext0_right(:,i) , '--' , 'LineWidth' , 2)
% hold on
%
%
% end
% xlabel('time(ms)')
% ylabel('periaxonal current (nA)')
% title('Right side')
%% vext1
xr = 95769.75706051444*1e6*1e-4 ; %ohm/micron
Left_vext1 = csvread('MYSARpn1x2_vext1_Leftside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
%
j=1 ;
for i=2:42
I_vext1_left(:,j) = (Left_vext1(:,i) - Left_vext1(:,i+1))/xr ; %mA.micron
I_vext1_left(:,j) = I_vext1_left(:,j)/9.8205 ; %mA
I_vext1_left(:,j) = I_vext1_left(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=43:52
I_vext1_left(:,j) = (Left_vext1(:,i) - Left_vext1(:,i+1))/xr ; %mA.micron
I_vext1_left(:,j) = I_vext1_left(:,j)/4.0294 ; %mA
I_vext1_left(:,j) = I_vext1_left(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=53:54
I_vext1_left(:,j) = (Left_vext1(:,i) - Left_vext1(:,i+1))/xr ; %mA.micron
I_vext1_left(:,j) = I_vext1_left(:,j)/1.5 ; %mA
I_vext1_left(:,j) = I_vext1_left(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=55
I_vext1_left(:,j) = (Left_vext1(:,i) - Left_vext1(:,i+1))/xr ; %mA.micron
I_vext1_left(:,j) = I_vext1_left(:,j)/0.5 ; %mA
I_vext1_left(:,j) = I_vext1_left(:,j)*1e6 ; % nA
j=j+1 ;
end
% figure
% startColor = [1, 1, 1];
% xx = startColor ;
%
%
% for i=2:54
%
%
%
% if i<30
% m=0.005 ;
% xx = xx - m ;
% else
% m=0.1 ;
% xx = xx - m ;
% end
%
% plot(time , I_vext1_left(:,i) ,'--' , 'LineWidth' , 2)
% hold on
%
%
% end
xlabel('time(ms)')
ylabel('Longitudinal current (nA)')
title('Left side')
xlim([0.95 4])
%%
Right_vext1 = csvread('MYSARpn1x2_vext1_Rightside_Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv');
j=1 ;
for i=2:42
I_vext1_right(:,j) = (Right_vext1(:,i) - Right_vext1(:,i+1))/xr ; %mA.micron
I_vext1_right(:,j) = I_vext1_right(:,j)/9.8205 ; %mA
I_vext1_right(:,j) = I_vext1_right(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=43:52
I_vext1_right(:,j) = (Right_vext1(:,i) - Right_vext1(:,i+1))/xr ; %mA.micron
I_vext1_right(:,j) = I_vext1_right(:,j)/4.0294 ; %mA
I_vext1_right(:,j) = I_vext1_right(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=53:54
I_vext1_right(:,j) = (Right_vext1(:,i) - Right_vext1(:,i+1))/xr ; %mA.micron
I_vext1_right(:,j) = I_vext1_right(:,j)/1.5 ; %mA
I_vext1_right(:,j) = I_vext1_right(:,j)*1e6 ; % nA
j=j+1 ;
end
for i=55
I_vext1_right(:,j) = (Right_vext1(:,i) - Right_vext1(:,i+1))/xr ; %mA.micron
I_vext1_right(:,j) = I_vext1_right(:,j)/0.5 ; %mA
I_vext1_right(:,j) = I_vext1_right(:,j)*1e6 ; % nA
j=j+1 ;
end
startColor = [1, 1, 1];
xx = startColor ;
% figure
%
% for i=1:54
%
%
% if i<48
% m=0.005 ;
% xx = xx - m ;
% else
% m=0.1 ;
% xx = xx - m ;
% end
%
% plot(time , I_vext1_right(:,i) , 'LineWidth' , 2)
% hold on
%
%
% end
xlabel('time(ms)')
ylabel('Longitudinal current (nA)')
title('Right side')
xlim([0.95 4])
%%
Surface_area_node = 2.59415600000000*pi ; %micron2
Surface_area_MYSA = 8*3*pi ;
Surface_area_FLUT = 8*8.05888*pi ;
Surface_area_STIN = 8*19.641280*pi ;
%%%%%%%% I4
XG = 7.08e+04 *1e-8 ; %S/micron2
IT = (Left_vext0(:,56)-Right_vext1(:,56))*XG ;
IT = IT * Surface_area_node*1e6 ;
figure
plot(time , IT , '--' , 'LineWidth' , 2)
xlabel('time(ms)')
ylabel('IT (nA)')
xlim([0.95 4])
%% to the neaby fiber
N = csvread('MYSARpn1x2_vext1_Abeta1_stimulateonlyAbeta0_edgedist0.1_.csv');
I_nearby = (Right_vext1(:,56)-N(:,2))*XG ;
I_nearby = I_nearby * Surface_area_node*1e6 ;
figure
plot(time , I_nearby , '--', 'LineWidth' , 2)
xlabel('time(ms)')
ylabel('I-nearby (nA)')
xlim([0.95 4])
%% to boundary
B = csvread('MYSARpn1x2_Boundary_stimulateonlyAbeta0_edgedist0.1_.csv');
I_boundary = (Right_vext1(:,56)-B(:,2))*16.1*1e-8 ;
I_boundary = I_boundary * Surface_area_node*1e6 ;
figure
plot(time , I_boundary , '--' , 'LineWidth' , 2)
xlabel('time(ms)')
ylabel('I-boundary (nA)')
xlim([0.95 4])
%% node icap and Na
Surface_area_node = 2.59415600000000*pi*1e-8 ; %cm2
node_icapp = csvread('MYSARpn1x2_icap_Node15Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv'); %mA/cm2
node_icap = node_icapp(:,2)*Surface_area_node*1e6 ;
figure
plot(time , node_icap , 'LineWidth' , 2)
xlabel('time(ms)')
ylabel('node,icap (nA)')
node_inaa = csvread('MYSARpn1x2_ina_Node15Abeta0_stimulateonlyAbeta0_edgedist0.1_.csv'); %mA/cm2
node_ina = node_inaa(:,2)*Surface_area_node*1e6 ;
figure
plot(time , node_ina , 'LineWidth' , 2)
xlabel('time(ms)')
ylabel('node,ina (nA)')
xlim([0.95 4])
%%
mycm=0.1 ;
mygm=0.001 ;
nl = 104 ;
xg0_MYSA = (mygm/(nl*2))*1e-8 ; %S/micron2
C_MYSA = (mycm/(nl*2))*1e-6*1e-8 ; %Farad/micron2
k=1 ;
for i=2:2:42
Left_myelin_leak(:,k) = (Left_vext0(:,i)-Left_vext1(:,i))* xg0_MYSA ;
Left_myelin_leak(:,k) = Left_myelin_leak(:,k)*Surface_area_STIN*1e6 ;
clear C
C = (Left_vext0(:,i)-Left_vext1(:,i)) ;
dvdt = gradient(C(:)) ./ gradient(time(:));
Left_myelin_cap(:,k) = dvdt*C_MYSA ;
Left_myelin_cap(:,k) = Left_myelin_cap(:,k) *Surface_area_STIN*1e6 ;
k=k+1 ;
end
for i=44:2:52
Left_myelin_leak(:,k) = (Left_vext0(:,i)-Left_vext1(:,i))* xg0_MYSA ;
Left_myelin_leak(:,k) = Left_myelin_leak(:,k)*Surface_area_FLUT*1e6 ;
clear C
C = (Left_vext0(:,i)-Left_vext1(:,i)) ;
dvdt = gradient(C(:)) ./ gradient(time(:));
Left_myelin_cap(:,k) = dvdt*C_MYSA ;
Left_myelin_cap(:,k) = Left_myelin_cap(:,k) *Surface_area_FLUT*1e6 ;
k=k+1 ;
end
for i=54
Left_myelin_leak(:,k) = (Left_vext0(:,i)-Left_vext1(:,i))* xg0_MYSA ;
Left_myelin_leak(:,k) = Left_myelin_leak(:,k)*Surface_area_MYSA*1e6 ;
clear C
C = (Left_vext0(:,i)-Left_vext1(:,i)) ;
dvdt = gradient(C(:)) ./ gradient(time(:));
Left_myelin_cap(:,k) = dvdt*C_MYSA ;
Left_myelin_cap(:,k) = Left_myelin_cap(:,k) *Surface_area_MYSA*1e6 ;
k=k+1 ;
end
startColor = [1, 1, 1];
xx = startColor ;
figure
for i=1:27
if i<20
m=0.005 ;
xx = xx - m ;
else
m=0.1 ;
xx = xx - m ;
end
plot(time , Left_myelin_leak(:,i) , '--' , 'LineWidth' , 2)
hold on
end
xlabel('time(ms)')
ylabel('myelin-leak (nA)')
title('left')
startColor = [1, 1, 1];
xx = startColor ;
figure
for i=1:27
if i<20
m=0.005 ;
xx = xx - m ;
else
m=0.1 ;
xx = xx - m ;
end
plot(time , Left_myelin_cap(:,i) , '--' , 'LineWidth' , 2)
hold on
end
xlabel('time(ms)')
ylabel('myelin-cap (nA)')
title('left')
xlim([0.95 4])
%%
mycm=0.1 ;
mygm=0.001 ;
nl = 104 ;
xg0_MYSA = (mygm/(nl*2))*1e-8 ; %S/micron2
C_MYSA = (mycm/(nl*2))*1e-6*1e-8 ; %Farad/micron2
k=1 ;
for i=2:2:42
Right_myelin_leak(:,k) = (Right_vext0(:,i)-Right_vext1(:,i))* xg0_MYSA ;
Right_myelin_leak(:,k) = Right_myelin_leak(:,k)*Surface_area_STIN*1e6 ;
clear C
C = (Right_vext0(:,i)-Right_vext1(:,i)) ;
dvdt = gradient(C(:)) ./ gradient(time(:));
right_myelin_cap(:,k) = dvdt*C_MYSA ;
right_myelin_cap(:,k) = right_myelin_cap(:,k) *Surface_area_STIN*1e6 ;
k=k+1 ;
end
for i=44:2:52
Right_myelin_leak(:,k) = (Right_vext0(:,i)-Right_vext1(:,i))* xg0_MYSA ;
Right_myelin_leak(:,k) = Right_myelin_leak(:,k)*Surface_area_FLUT*1e6 ;
clear C
C = (Right_vext0(:,i)-Right_vext1(:,i)) ;
dvdt = gradient(C(:)) ./ gradient(time(:));
right_myelin_cap(:,k) = dvdt*C_MYSA ;
right_myelin_cap(:,k) = right_myelin_cap(:,k) *Surface_area_FLUT*1e6 ;
k=k+1 ;
end
for i=54
Right_myelin_leak(:,k) = (Right_vext0(:,i)-Right_vext1(:,i))* xg0_MYSA ;
Right_myelin_leak(:,k) = Right_myelin_leak(:,k)*Surface_area_MYSA*1e6 ;
clear C
C = (Right_vext0(:,i)-Right_vext1(:,i)) ;
dvdt = gradient(C(:)) ./ gradient(time(:));
right_myelin_cap(:,k) = dvdt*C_MYSA ;
right_myelin_cap(:,k) = right_myelin_cap(:,k) *Surface_area_MYSA*1e6 ;
k=k+1 ;
end
startColor = [1, 1, 1];
xx = startColor ;
figure
for i=1:27
if i<20
m=0.005 ;
xx = xx - m ;
else
m=0.1 ;
xx = xx - m ;
end
plot(time , Right_myelin_leak(:,i) , '--' , 'LineWidth' , 2)
hold on
end
xlabel('time(ms)')
ylabel('myelin-leak (nA)')
title('right')
xlim([0.95 4])
%%
startColor = [1, 1, 1];
xx = startColor ;
figure
for i=20:27
if i<20
m=0.005 ;
xx = xx - m ;
else
m=0.1 ;
xx = xx - m ;
end
plot(time , right_myelin_cap(:,i) , '--' , 'Color' ,xx, 'LineWidth' , 2)
hold on
end
xlabel('time(ms)')
ylabel('myelin-cap (nA)')
title('right')
xlim([0.95 4])