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GC_biophys.m
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GC_biophys.m
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function strct = GC_biophys(options)
% options:
% -p include passive parameters (default)
% -a include active parameters (default)
% -o old AH99....also calcium channels with uncorrected Ca buffer shell model
% -s orig na8st vshifts and rates as in SH10
% -n latest changes as published in Beining et al 2017
%% Paramters
%Kir parameter
Kirusemodel = 'Own'; % 'Own', 'Hanuschkin'
%Kv4.2 parameter
Kv4model = {'Amarillo','Barghaan'};
Kv4composition = 4; % {'wt','wt + KChIP2','wt + DPPX','wt + KChIP2 + DPPX'};
Kv4usethismodel = 2;
Ca_tau = 240; %calcium decay! orig 9 ms
if ~isempty(strfind(options,'-n'))
on = struct('HCN',1,'Kir',1.07,'Kv11',0.5/4,'Kv14',0.5/4,'Kv21',0.6*1.3/1.1 ,'Kv33',0,'Kv34',5 /4/2*2.5,'Kv42',0.145 *3 *2/2/2 *2,'Kv72u3',6.7,'Na',1.728,'Nav19',0,'NCa',0.5,'LCa',6,'TCa',0.33,'BK',1*1.5*2*2/1.5,'SK',0.2/2);%*3
elseif ~isempty(strfind(options,'-k'))
on = struct('HCN',1,'Kir',1.07*0.95,'Kv11',0.5/4,'Kv14',0.5/4,'Kv21',0.6*1.3 ,'Kv33',0,'Kv34',5 /4/2,'Kv42',0.145 *3 *2/2/2,'Kv72u3',6.7,'Na',1.728,'Nav19',0,'NCa',0.5,'LCa',6,'TCa',0.33,'BK',1*1.5*2*2,'SK',0.2/2);%*3
else
on = struct('HCN',1,'Kir',1.07,'Kv11',0,'Kv14',0.5/4,'Kv21',0.6*1.3/1.1 ,'Kv33',0,'Kv34',5 /4/2,'Kv42',0.145 *3 *2/2/2,'Kv72u3',6.7,'Na',1.728,'Nav19',0,'NCa',0.5,'LCa',6,'TCa',0.33,'BK',1*1.5*2*2,'SK',0.2/2);
end
if nargin < 1 || isempty(options)
options = '-a-p';
end
strct = struct;
if ~isempty(strfind(options,'-p'))
if isempty(strfind(options,'-o')) % new model
if ~isempty(strfind(options,'-y'))
e_pas = -70;%-96.5 ; % chloride has ecl of -40mV !
e_pas_axon = -70;
else
e_pas = -80;%-96.5 ; % chloride has ecl of -40mV ! TRP channels...
e_pas_axon = -80;
end
% -80.4 for SH07 pure passive model reproduction
Rm = 36.4;
if ~isempty(strfind(options,'-n'))
chg = 0.48;
gax = chg*0.5;
chg = chg * 1.05;
else
chg = 0.48;
gax = chg;
end
if ~isempty(strfind(options,'-ra'))
on.Kir = on.Kir * 2.5;2.7;%2.5
end
if ~isempty(strfind(options,'-cm'))
cm = 0.7;
Ra = 200; % 200 as SH2010 did...
else
cm = 0.9;
Ra = 200; %200 as SH2010 did...
end
Raax = 100;
if isempty(strfind(options,'-a')) % do not change the passive parameters from their original values if not active model
chg = 1;
gax = 1;
end
strct.GCL.pas = struct('cm',cm ,'Ra', Ra,'g',(chg)/(Rm*1000),'e',e_pas); %SH07 cell4,6,7
strct.adendIML.pas = struct('cm',cm ,'Ra', Ra,'g',(chg)/(Rm*1000),'e',e_pas); %SH07 cell4,6,7
strct.adendMML.pas = struct('cm',cm ,'Ra', Ra,'g',(chg)/(Rm*1000),'e',e_pas); %SH07 cell4,6,7
strct.adendOML.pas = struct('cm',cm ,'Ra', Ra,'g',(chg)/(Rm*1000),'e',e_pas); %SH07 cell4,6,7
strct.soma.pas = struct('cm',cm ,'Ra', Ra,'g',chg/(Rm*1000),'e',e_pas); %SH07 cell4,6,7
strct.axon.pas = struct('cm',cm, 'Ra', Raax, 'g',gax/(Rm*1000),'e',e_pas_axon); % Ra of 120 because of SH10 saying in distal axon there is less Ra
strct.axonh.pas = struct('cm',cm, 'Ra', Ra, 'g',gax/(Rm*1000),'e',e_pas_axon);
else % AH99 model
e_pas = -70;
strct.all.pas = struct('e',e_pas,'g',2.5e-5,'Ra',210,'cm',1);
strct.adendIML.pas = struct('e',e_pas,'g',4e-5,'Ra',210,'cm',1.6);
strct.adendMML.pas = struct('e',e_pas,'g',4e-5,'Ra',210,'cm',1.6);
strct.adendOML.pas = struct('e',e_pas,'g',4e-5,'Ra',210,'cm',1.6);
end
end
if ~isempty(strfind(options,'-a'))
if isempty(strfind(options,'-o'))
%%
if on.Kir > 0
Kirdistr = [1, 0.286, 0.143, 0.143, 0.143];
% Kir in axons probably only for G-Protein activated Kirs (Kir3.x)...
switch Kirusemodel
case 'Own'
gkbar_Kir = 7e-4; %0.0007
% Kir current
spm_i = 3.5;%µM %7.5; %sollte über 3.5 sein für tau bei tiefen vclamps %-10 possible!
chg_Kir = on.Kir * gkbar_Kir;%5.3; %2.5;
gsub = 0.15; % substate conductance (between 0.2 (spermidine) and 0.07 (spermine) Liu 2012)
fac = 0.001;
vshiftbs = 10;
vshiftbb = 0;
shiftmg = 1;
mg_i = 4;
b = 0.105;
fac = 0.005 ;
mg_i = 4;
if ~isempty(strfind(options,'-n'))
Kirdistr = [1.05, 1.05, 1.05, 1.05, 1.05, 0.5]*0.9;
else
Kirdistr = [1, 1, 1, 1, 1, 1]*0.9;
end
chg_Kir = chg_Kir *0.2;
gsub = 0.25 ;
spm_i = 1;
shiftmg = 0.5 ; % means only 0.5 of ek shift
vshiftbs = 0;
cas = 1/7; % tau made larger due to kir 2.3
As = 0.2;
strct.soma.Kir21 = struct('gkbar',Kirdistr(1)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
strct.GCL.Kir21 = struct('gkbar',Kirdistr(2)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
strct.adendIML.Kir21 = struct('gkbar',Kirdistr(3)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
strct.adendMML.Kir21 = struct('gkbar',Kirdistr(4)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
strct.adendOML.Kir21 = struct('gkbar',Kirdistr(5)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
strct.axon.Kir21 = struct('gkbar',Kirdistr(end)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
strct.axonh.Kir21 = struct('gkbar',Kirdistr(end)*chg_Kir,'mg_i',mg_i,'spm_i',spm_i,'gsub',gsub,'fac',fac,'vshiftbs',vshiftbs,'vshiftbb',vshiftbb,'b',b,'shiftmg',shiftmg,'cas',cas,'As',As);
case 'Hanuschkin'
Kirdistr(:) = 1;
vhalfl_kir_fit = -107.609612;
kl_kir_fit = 10; % // NOTE: sign changed in comparison with publication
vhalft_kir_fit = 67.0828 ;
at_kir_fit = 0.00610779;
bt_kir_fit = 0.0817741 ; % // NOTE: error in publication (here the correct value)
gkbar_kir_fit = 9.1016e-5; % this is what hanuschkin used in his paper
chg_Kir = on.Kir * gkbar_kir_fit;
strct.soma.HKir = struct('gkbar',Kirdistr(1)*chg_Kir,'vhalfl',vhalfl_kir_fit,'kl',kl_kir_fit,'vhalft',vhalft_kir_fit,'at',at_kir_fit,'bt',bt_kir_fit);
strct.GCL.HKir = struct('gkbar',Kirdistr(2)*chg_Kir,'vhalfl',vhalfl_kir_fit,'kl',kl_kir_fit,'vhalft',vhalft_kir_fit,'at',at_kir_fit,'bt',bt_kir_fit);
strct.adendIML.HKir = struct('gkbar',1.5*Kirdistr(3)*chg_Kir,'vhalfl',vhalfl_kir_fit,'kl',kl_kir_fit,'vhalft',vhalft_kir_fit,'at',at_kir_fit,'bt',bt_kir_fit);
strct.adendMML.HKir = struct('gkbar',2*Kirdistr(4)*chg_Kir,'vhalfl',vhalfl_kir_fit,'kl',kl_kir_fit,'vhalft',vhalft_kir_fit,'at',at_kir_fit,'bt',bt_kir_fit);
strct.adendOML.HKir = struct('gkbar',2.5*Kirdistr(5)*chg_Kir,'vhalfl',vhalfl_kir_fit,'kl',kl_kir_fit,'vhalft',vhalft_kir_fit,'at',at_kir_fit,'bt',bt_kir_fit);
end
end
if on.HCN > 0
e_hcn = -41.9;
vhalfl_hcn = -100; % shifted hcn since is much more left in other models. Furthermore, I have much Mg2+ and I have implemented the cAMP dependency
kl_hcn = 8; %// NOTE: sign changed in comparison with publication
vhalft_hcn = 30.4; %// (see manuscript)
at_hcn = 0.00052;
bt_hcn = 0.2151;
cAMP = 0; % mM cAMP concentration
ghcnbar = 4e-6; %1.7561e-5;
% according to Notomi und Shigemoto 2004 only in dendrites
strct.adendIML.HCN = struct('cAMP',cAMP,'e',e_hcn,'gbar',on.HCN*ghcnbar,'vhalfl',vhalfl_hcn,'kl',kl_hcn,'vhalft',vhalft_hcn,'at',at_hcn,'bt',bt_hcn);
strct.adendMML.HCN = struct('cAMP',cAMP,'e',e_hcn,'gbar',on.HCN*ghcnbar,'vhalfl',vhalfl_hcn,'kl',kl_hcn,'vhalft',vhalft_hcn,'at',at_hcn,'bt',bt_hcn);
strct.adendOML.HCN = struct('cAMP',cAMP,'e',e_hcn,'gbar',on.HCN*ghcnbar,'vhalfl',vhalfl_hcn,'kl',kl_hcn,'vhalft',vhalft_hcn,'at',at_hcn,'bt',bt_hcn);
end
% Na channel
if on.Na>0
%**********
if ~isempty(strfind(options,'-s'))
addShift = 0; %no additional shift in SH10
else
addShift = 10; % additional shift in my model
end
if ~isempty(strfind(options,'-y'))
vShift = 12+addShift ; %12 is default
vShift_inact = 22-vShift;
else
vShift = 12+addShift ; %12 is default
vShift_inact = 22-vShift;
end
%**********
f = fopen('lib_mech/soma_st8.txt','r');
rates_soma = textscan(f, '%.20f','Delimiter','\n');
fclose(f);
f = fopen('lib_mech/axon_st8.txt','r');
rates_axon = textscan(f, '%.20f','Delimiter','\n');
fclose(f);
gnabar_soma = on.Na*0.03 * 1.7; %conversion to siemens;
gnabar_axonh= on.Na*0.2*1.5;
gnabar_axon = on.Na*0.03 * 1.7; %siemens;
gnabar_dend = 0*on.Na*0.0005; % only for test purpose
if isempty(strfind(options,'-s'))
rates_axon{1}(13:end) = [2.9807,0.4679,--0.0596,0.3962,2982.1,0.0635];% ah = [0.3962,2982.1,0.0635]; bh = [2.9807,0.4679,--0.0596];
rates_soma{1}(13:end) = [2.9713,0.6443,--0.0594,1.5860,2306.7,0.0493]; % new fitted inactivation kinetics since SH10 seems not to consider recov from inact values
end
strct.axon.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_axon);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.axonh.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_axonh);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.soma.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_soma);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
if gnabar_dend > 0
ax=1; % give dendritic na8st the axon rates
if ax
strct.GCL.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.adendIML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.adendMML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.adendOML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
else
strct.GCL.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.adendIML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.adendMML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
strct.adendOML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
end
end
% else
% % this is the old SH10 na8st channel distribution which is
% % distance dependent and thus need the tree morphology for
% % calculation of distribution. Is not used in the model
% if isempty(tree)
% warning('Tree not given to GC_biophys. 8st sodium channel model cannot be inserted!')
% else
%
% toaxon = false(numel(tree.X),1);
% toaxon(tree.R == find(strcmp(tree.rnames,'axon')) | tree.R == find(strcmp(tree.rnames,'axonh'))) = true;
% [tree2,order] = redirect_tree(tree,find(Pvec_tree(tree,toaxon)==1,1,'first')); % redirect tree so that first axon point is root node (axon initial segment)
% plen = Pvec_tree(tree2); % get distances from axon initial segment
% plen(order) = plen; % get original order (from soma root node)
%
% gnabar = NaN(numel(tree.X),1);
%
% gnabar_axon= 38.6152 *nafac / 1000; %conversion to siemens;
% gnabar_soma = 18.8 *nafac / 1000; %conversion to siemens;
% gnabar_dend = 3.8 *nafac / 1000;%3.8 *nafac / 1000;
% a0 = 18.015027;
% gnabar(toaxon) = gnabar_soma + (gnabar_axon - gnabar_soma) .* (1-exp(-plen(toaxon)/5)) .* (1+ a0 * exp(-plen(toaxon)/10));
% gnabar(~toaxon) = gnabar_dend + (gnabar_soma - gnabar_dend) ./ (1+ exp((abs(plen(~toaxon))-80)/40));
% gnabar(~toaxon & gnabar == gnabar_dend) = NaN;
%
% gnabar(toaxon & gnabar == gnabar_axon) = NaN;
% gnabar(~toaxon & gnabar == gnabar_soma) = NaN;%
%
% rates = NaN(numel(rates_axon{1}),numel(tree.X));
% for r = 1:numel(rates_axon{1})
% rates(r,toaxon) = rates_axon{1}(r) - (rates_axon{1}(r) - rates_soma{1}(r))./(1+exp((plen(toaxon)-2)/2));
% rates(r,~toaxon) = rates_axon{1}(r) - (rates_axon{1}(r) - rates_soma{1}(r))./(1+exp((-plen(~toaxon)-2)/2));
% % ranged rates outside soma can be
% % ignored anyways because lambda of
% % change is only 2 µm --> rate soma is
% % reached already in the soma
% if any(strcmp(tree.rnames,'axonh'))
% rates(r,~(tree.R == find(strcmp(tree.rnames,'axonh'))) & ~(tree.R == find(strcmp(tree.rnames,'axon'))) & ~(tree.R == find(strcmp(tree.rnames,'soma')))) = NaN; % really...no Na in dendrites
% else
% rates(r,~(tree.R == find(strcmp(tree.rnames,'axon'))) & ~(tree.R == find(strcmp(tree.rnames,'soma')))) = NaN; % really...no Na in dendrites
% end
% end
% strct.range.na8st = struct('a1_0',rates(1,:),'a1_1',rates(2,:),'b1_0',rates(3,:),'b1_1',rates(4,:),'a2_0',rates(5,:),'a2_1',rates(6,:),'b2_0',rates(7,:),'b2_1',rates(8,:),'a3_0',rates(9,:),'a3_1',rates(10,:),'b3_0',rates(11,:),'b3_1',rates(12,:),'bh_0',rates(13,:),'bh_1',rates(14,:),'bh_2',rates(15,:),'ah_0',rates(16,:),'ah_1',rates(17,:),'ah_2',rates(18,:),'gbar',gnabar);
% strct.axon.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_axon);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.axonh.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_axon{1}(1),'a1_1',rates_axon{1}(2),'b1_0',rates_axon{1}(3),'b1_1',rates_axon{1}(4),'a2_0',rates_axon{1}(5),'a2_1',rates_axon{1}(6),'b2_0',rates_axon{1}(7),'b2_1',rates_axon{1}(8),'a3_0',rates_axon{1}(9),'a3_1',rates_axon{1}(10),'b3_0',rates_axon{1}(11),'b3_1',rates_axon{1}(12),'bh_0',rates_axon{1}(13),'bh_1',rates_axon{1}(14),'bh_2',rates_axon{1}(15),'ah_0',rates_axon{1}(16),'ah_1',rates_axon{1}(17),'ah_2',rates_axon{1}(18),'gbar',gnabar_axon);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.soma.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_soma);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.GCL.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.adendIML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.adendMML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.adendOML.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% strct.adendOMLout.na8st = struct('vShift',vShift,'vShift_inact',vShift_inact,'a1_0',rates_soma{1}(1),'a1_1',rates_soma{1}(2),'b1_0',rates_soma{1}(3),'b1_1',rates_soma{1}(4),'a2_0',rates_soma{1}(5),'a2_1',rates_soma{1}(6),'b2_0',rates_soma{1}(7),'b2_1',rates_soma{1}(8),'a3_0',rates_soma{1}(9),'a3_1',rates_soma{1}(10),'b3_0',rates_soma{1}(11),'b3_1',rates_soma{1}(12),'bh_0',rates_soma{1}(13),'bh_1',rates_soma{1}(14),'bh_2',rates_soma{1}(15),'ah_0',rates_soma{1}(16),'ah_1',rates_soma{1}(17),'ah_2',rates_soma{1}(18),'gbar',gnabar_dend);%,'maxrate',8000,'vshift_inact',vshift_inact,'vShift',vdonnan,);
% end
end
if on.Nav19 > 0 % persistent sodium channel (as Krueppel 2011 proposed)
vshift = -18;
strct.GCL.Nav19 = struct('gbar', on.Nav19 * 0.0002,'vshift',vshift);
strct.adendIML.Nav19 = struct('gbar', on.Nav19 * 0.0002,'vshift',vshift);
strct.adendMML.Nav19 = struct('gbar', on.Nav19 * 0.0002,'vshift',vshift);
strct.adendOML.Nav19 = struct('gbar', on.Nav19 * 0.0002,'vshift',vshift);
strct.adendOMLout.Nav19 = struct('gbar', on.Nav19 * 0.0002,'vshift',vshift);
end
%% A-type Potassium
% Kv1.1
if on.Kv11 > 0
kfac = on.Kv11;
vshift = 0;
gbdef = 0.002;
strct.axon.Kv11 = struct('gkbar',gbdef*kfac,'vshift',vshift);%,'mk',-8.1,'md',-32);
strct.axonh.Kv11 = struct('gkbar',gbdef*kfac,'vshift',vshift);%,'mk',-8.1,'md',-32);
end
% Kv1.4
if on.Kv14 > 0 % Protein nearly only in axon!
vshift = 0;
strct.axon.Kv14 = struct('gkbar',0.008*on.Kv14,'vshift',vshift); % scale_i von 3 möglich um inactivatin schneller zu machen wegen kvbeta1.1
strct.axonh.Kv14 = struct('gkbar',0.008*on.Kv14,'vshift',vshift);
end
%Kv2.1
if on.Kv21 > 0
strct.soma.Kv21 = struct('gkbar',on.Kv21 * 0.01);
end
% Kv3.3 und Kv3.4 Protein nearly only in axon!
if on.Kv33 > 0
strct.axon.Kv33 = struct('gkbar',on.Kv33 * 0.002 );
strct.axonh.Kv33 = struct('gkbar',on.Kv33 * 0.02 );
end
if on.Kv34 > 0
if ~isempty(strfind(options,'-k'))
scale_a = 2.5;
ksl= 0.75;
else
scale_a = 4;%2.5;
ksl= 0.5;%0.75;
end
strct.axon.Kv34 = struct('gkbar',on.Kv34 * 0.0049 ,'scale_a',scale_a,'ksl',ksl); % 0.00325
strct.axonh.Kv34 = struct('gkbar',on.Kv34 * 0.0197 ,'scale_a',scale_a,'ksl',ksl); % 0.0325
end
%Kv4.2
if on.Kv42 > 0
kafac = on.Kv42 * 1;
gdist = [0.0005,0.001,0.001,0.001]; % GCL IML MML OML
% gdist = [0.0002,0.001,0.003,0.003]; % GCL IML MML OML
switch Kv4model{Kv4usethismodel}
case 'Amarillo'
switch Kv4composition
case 1
% Kv4.2 alone
strct.GCL.Kv42b = struct('gkbar',kafac * gdist(1),'a0', 1.589,'za',0.64,'b0', 0.0184,'zb', -1.31,'c0',6.668,'zc', 0.15,'d0', 2.381,'zd', -1.21,'e0',0.503,'ze',0.07,'f0',0.174,'zf',-0.25,'kci', 0.047,'kic', 0.00003,'kappa1', 0.229,'lambda1', 0.151,'kappa2',0.0487,'lambda2',0.0065);
strct.adendIML.Kv42b = struct('gkbar',kafac * gdist(2),'a0', 1.589,'za',0.64,'b0', 0.0184,'zb', -1.31,'c0',6.668,'zc', 0.15,'d0', 2.381,'zd', -1.21,'e0',0.503,'ze',0.07,'f0',0.174,'zf',-0.25,'kci', 0.047,'kic', 0.00003,'kappa1', 0.229,'lambda1', 0.151,'kappa2',0.0487,'lambda2',0.0065);
strct.adendMML.Kv42b = struct('gkbar',kafac * gdist(3),'a0', 1.589,'za',0.64,'b0', 0.0184,'zb', -1.31,'c0',6.668,'zc', 0.15,'d0', 2.381,'zd', -1.21,'e0',0.503,'ze',0.07,'f0',0.174,'zf',-0.25,'kci', 0.047,'kic', 0.00003,'kappa1', 0.229,'lambda1', 0.151,'kappa2',0.0487,'lambda2',0.0065);
strct.adendOML.Kv42b = struct('gkbar',kafac * gdist(4),'a0', 1.589,'za',0.64,'b0', 0.0184,'zb', -1.31,'c0',6.668,'zc', 0.15,'d0', 2.381,'zd', -1.21,'e0',0.503,'ze',0.07,'f0',0.174,'zf',-0.25,'kci', 0.047,'kic', 0.00003,'kappa1', 0.229,'lambda1', 0.151,'kappa2',0.0487,'lambda2',0.0065);
case 3
% + DPPX
strct.GCL.Kv42b = struct('gkbar',kafac * gdist(1),'a0',3.282,'za',0.64,'b0', 0.01,'zb', -1.31,'c0',7.22,'zc', 0.15,'d0', 0.588,'zd', -1.21,'e0',1.101,'ze',0.07,'f0',0.673,'zf',-0.25,'kci', 0.072,'kic', 0.00046,'kappa1', 0.108,'lambda1', 0.034,'kappa2',0.0206,'lambda2',0.0086);
strct.adendIML.Kv42b = struct('gkbar',kafac * gdist(2),'a0',3.282,'za',0.64,'b0', 0.01,'zb', -1.31,'c0',7.22,'zc', 0.15,'d0', 0.588,'zd', -1.21,'e0',1.101,'ze',0.07,'f0',0.673,'zf',-0.25,'kci', 0.072,'kic', 0.00046,'kappa1', 0.108,'lambda1', 0.034,'kappa2',0.0206,'lambda2',0.0086);
strct.adendMML.Kv42b = struct('gkbar',kafac * gdist(3),'a0',3.282,'za',0.64,'b0', 0.01,'zb', -1.31,'c0',7.22,'zc', 0.15,'d0', 0.588,'zd', -1.21,'e0',1.101,'ze',0.07,'f0',0.673,'zf',-0.25,'kci', 0.072,'kic', 0.00046,'kappa1', 0.108,'lambda1', 0.034,'kappa2',0.0206,'lambda2',0.0086);
strct.adendOML.Kv42b = struct('gkbar',kafac * gdist(4),'a0',3.282,'za',0.64,'b0', 0.01,'zb', -1.31,'c0',7.22,'zc', 0.15,'d0', 0.588,'zd', -1.21,'e0',1.101,'ze',0.07,'f0',0.673,'zf',-0.25,'kci', 0.072,'kic', 0.00046,'kappa1', 0.108,'lambda1', 0.034,'kappa2',0.0206,'lambda2',0.0086);
case 2
% + KChIP1
strct.GCL.Kv42b = struct('gkbar',kafac * gdist(1),'a0',1.443,'za',0.64,'b0', 0.0019,'zb', -1.31,'c0',5.556,'zc', 0.15,'d0', 0.155,'zd', -1.21,'e0',0.559,'ze',0.07,'f0',0.621,'zf',-0.25,'kci', 0.029,'kic', 0.00014,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
strct.adendIML.Kv42b = struct('gkbar',kafac * gdist(2),'a0',1.443,'za',0.64,'b0', 0.0019,'zb', -1.31,'c0',5.556,'zc', 0.15,'d0', 0.155,'zd', -1.21,'e0',0.559,'ze',0.07,'f0',0.621,'zf',-0.25,'kci', 0.029,'kic', 0.00014,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
strct.adendMML.Kv42b = struct('gkbar',kafac * gdist(3),'a0',1.443,'za',0.64,'b0', 0.0019,'zb', -1.31,'c0',5.556,'zc', 0.15,'d0', 0.155,'zd', -1.21,'e0',0.559,'ze',0.07,'f0',0.621,'zf',-0.25,'kci', 0.029,'kic', 0.00014,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
strct.adendOML.Kv42b = struct('gkbar',kafac * gdist(4),'a0',1.443,'za',0.64,'b0', 0.0019,'zb', -1.31,'c0',5.556,'zc', 0.15,'d0', 0.155,'zd', -1.21,'e0',0.559,'ze',0.07,'f0',0.621,'zf',-0.25,'kci', 0.029,'kic', 0.00014,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
case 4
% + KChIP1 and DPPX (ternary)
strct.GCL.Kv42b = struct('gkbar',kafac * gdist(1),'a0',2.577,'za',0.64,'b0', 0.0028,'zb', -1.31,'c0',4.318,'zc', 0.15,'d0', 0.38,'zd', -1.21,'e0',0.466,'ze',0.07,'f0',0.277,'zf',-0.25,'kci', 0.054,'kic', 0.00044,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
strct.adendIML.Kv42b = struct('gkbar',kafac * gdist(2),'a0',2.577,'za',0.64,'b0', 0.0028,'zb', -1.31,'c0',4.318,'zc', 0.15,'d0', 0.38,'zd', -1.21,'e0',0.466,'ze',0.07,'f0',0.277,'zf',-0.25,'kci', 0.054,'kic', 0.00044,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
strct.adendMML.Kv42b = struct('gkbar',kafac * gdist(3),'a0',2.577,'za',0.64,'b0', 0.0028,'zb', -1.31,'c0',4.318,'zc', 0.15,'d0', 0.38,'zd', -1.21,'e0',0.466,'ze',0.07,'f0',0.277,'zf',-0.25,'kci', 0.054,'kic', 0.00044,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
strct.adendOML.Kv42b = struct('gkbar',kafac * gdist(4),'a0',2.577,'za',0.64,'b0', 0.0028,'zb', -1.31,'c0',4.318,'zc', 0.15,'d0', 0.38,'zd', -1.21,'e0',0.466,'ze',0.07,'f0',0.277,'zf',-0.25,'kci', 0.054,'kic', 0.00044,'kappa1', 0,'lambda1', 100,'kappa2',0,'lambda2',100);
end
case 'Barghaan'
vshift = -15-5; % don't ask why but activation is ~ 15 mV right shifted in the model compared to the measurements (Suppl Fig1 Barghaan 2008), additional -5mV shift due to uncorrected LJP of 4.9
kafac = kafac * 10; %optional raise this..
switch Kv4composition
case 1
strct.GCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.175,'za', 2.7,'b0', 0.003598,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.267,'zoc', -0.047,'kci', 0.02392,'kic', 0.000037,'koi', 0.194,'kio', 0.03686,'vshift',vshift);
strct.SGCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.175,'za', 2.7,'b0', 0.003598,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.267,'zoc', -0.047,'kci', 0.02392,'kic', 0.000037,'koi', 0.194,'kio', 0.03686,'vshift',vshift);
strct.adendIML.Kv42 = struct('gkbar',kafac * gdist(2),'a0', 0.175,'za', 2.7,'b0', 0.003598,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.267,'zoc', -0.047,'kci', 0.02392,'kic', 0.000037,'koi', 0.194,'kio', 0.03686,'vshift',vshift);
strct.adendMML.Kv42 = struct('gkbar',kafac * gdist(3),'a0', 0.175,'za', 2.7,'b0', 0.003598,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.267,'zoc', -0.047,'kci', 0.02392,'kic', 0.000037,'koi', 0.194,'kio', 0.03686,'vshift',vshift);
strct.adendOML.Kv42 = struct('gkbar',kafac * gdist(4),'a0', 0.175,'za', 2.7,'b0', 0.003598,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.267,'zoc', -0.047,'kci', 0.02392,'kic', 0.000037,'koi', 0.194,'kio', 0.03686,'vshift',vshift);
case 2
strct.GCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.175,'za', 2.7,'b0', 0.01947,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.670,'zoc', -0.047,'kci', 0.03061,'kic', 0.00018,'koi', 0.04308,'kio', 0.1099,'vshift',vshift);
strct.SGCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.175,'za', 2.7,'b0', 0.01947,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.670,'zoc', -0.047,'kci', 0.03061,'kic', 0.00018,'koi', 0.04308,'kio', 0.1099,'vshift',vshift);
strct.adendIML.Kv42 = struct('gkbar',kafac * gdist(2),'a0', 0.175,'za', 2.7,'b0', 0.01947,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.670,'zoc', -0.047,'kci', 0.03061,'kic', 0.00018,'koi', 0.04308,'kio', 0.1099,'vshift',vshift);
strct.adendMML.Kv42 = struct('gkbar',kafac * gdist(3),'a0', 0.175,'za', 2.7,'b0', 0.01947,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.670,'zoc', -0.047,'kci', 0.03061,'kic', 0.00018,'koi', 0.04308,'kio', 0.1099,'vshift',vshift);
strct.adendOML.Kv42 = struct('gkbar',kafac * gdist(4),'a0', 0.175,'za', 2.7,'b0', 0.01947,'zb', -1.742,'kco0', 0.347,'zco', 0.185,'koc0', 1.670,'zoc', -0.047,'kci', 0.03061,'kic', 0.00018,'koi', 0.04308,'kio', 0.1099,'vshift',vshift);
case 3
strct.GCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.416,'za', 1.1,'b0', 0.009,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.267,'zoc', 0,'kci', 0.03807,'kic', 0.00011,'koi', 0.3,'kio', 0.01424,'vshift',vshift);
strct.SGCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.416,'za', 1.1,'b0', 0.009,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.267,'zoc', 0,'kci', 0.03807,'kic', 0.00011,'koi', 0.3,'kio', 0.01424,'vshift',vshift);
strct.adendIML.Kv42 = struct('gkbar',kafac * gdist(2),'a0', 0.416,'za', 1.1,'b0', 0.009,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.267,'zoc', 0,'kci', 0.03807,'kic', 0.00011,'koi', 0.3,'kio', 0.01424,'vshift',vshift);
strct.adendMML.Kv42 = struct('gkbar',kafac * gdist(3),'a0', 0.416,'za', 1.1,'b0', 0.009,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.267,'zoc', 0,'kci', 0.03807,'kic', 0.00011,'koi', 0.3,'kio', 0.01424,'vshift',vshift);
strct.adendOML.Kv42 = struct('gkbar',kafac * gdist(4),'a0', 0.416,'za', 1.1,'b0', 0.009,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.267,'zoc', 0,'kci', 0.03807,'kic', 0.00011,'koi', 0.3,'kio', 0.01424,'vshift',vshift);
case 4
strct.GCL.Kv42 = struct('gkbar',kafac * gdist(1),'a0', 0.416,'za', 1.1,'b0', 0.0486,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.670,'zoc', 0,'kci', 0.04873,'kic', 0.000537,'koi', 0.0669,'kio', 0.04246,'vshift',vshift);
strct.adendIML.Kv42 = struct('gkbar',kafac * gdist(2),'a0', 0.416,'za', 1.1,'b0', 0.0486,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.670,'zoc', 0,'kci', 0.04873,'kic', 0.000537,'koi', 0.0669,'kio', 0.04246,'vshift',vshift);
strct.adendMML.Kv42 = struct('gkbar',kafac * gdist(3),'a0', 0.416,'za', 1.1,'b0', 0.0486,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.670,'zoc', 0,'kci', 0.04873,'kic', 0.000537,'koi', 0.0669,'kio', 0.04246,'vshift',vshift);
strct.adendOML.Kv42 = struct('gkbar',kafac * gdist(4),'a0', 0.416,'za', 1.1,'b0', 0.0486,'zb', -1.556,'kco0', 0.347,'zco', 0,'koc0', 1.670,'zoc', 0,'kci', 0.04873,'kic', 0.000537,'koi', 0.0669,'kio', 0.04246,'vshift',vshift);
end
end
end
%Kv7.2/3 (M current)
if on.Kv72u3 > 0
Dtaumult = 6;
tau0mult = 0.2;
% on.Kv72u3 = on.Kv72u3 * 2
strct.axonh.Kv723 = struct('gkbar',on.Kv72u3 * 0.0005 *2,'Dtaumult1',Dtaumult,'Dtaumult2',Dtaumult,'tau0mult',tau0mult);
strct.axon.Kv723 = struct('gkbar',on.Kv72u3 * 0.0001 *2,'Dtaumult1',Dtaumult,'Dtaumult2',Dtaumult,'tau0mult',tau0mult);
end
%AH Calcium channels
if on.TCa > 0 || on.NCa > 0 || on.LCa > 0
strct.all.Cabuffer = struct('brat',50,'tau',Ca_tau );
strct.axon.Cabuffer = struct('brat',10,'tau',43 );
strct.soma.Cabuffer = struct('brat',200,'tau',Ca_tau );
strct.all.Cabuffer.depth = 0.05; %µm
tfac = on.TCa ;
fac = 10 * 1.5 ;
fac3 = fac * 5 / 6;
on.LCa = on.LCa /30;
on.NCa = on.NCa *3;
kf = 0.0005; % = 0.5µM = 500 nM
vdi12 = 1; % voltage dependent inactivation of the channel (0-1)
vdi13 = 0.85; % voltage dependent inactivation of the channel (0-1)
strct.axon.Cav22 = struct('gbar', on.NCa * 0.0001 * 5 / fac,'hTau',80);
strct.axonh.Cav22 = struct('gbar', on.NCa * 0.0001 * 5/ fac,'hTau',80);
strct.soma.Cav22 = struct('gbar', on.NCa * 0.0015 *2 / fac,'hTau',80);
strct.SGCL.Cav22 = struct('gbar', on.NCa * 0.0001 *5 / fac,'hTau',80);
strct.GCL.Cav22 = struct('gbar', on.NCa * 0.0001 *5 / fac);
strct.adendIML.Cav22 = struct('gbar', on.NCa * 0.0001 *5 / fac,'hTau',80);
strct.adendMML.Cav22 = struct('gbar', on.NCa * 0.0001 *5 / fac,'hTau',80);
strct.adendOML.Cav22 = struct('gbar', on.NCa * 0.0001 *5 / fac,'hTau',80);
strct.axonh.Cav12 = struct('gbar', on.LCa * 0.0005 * 3/2 / fac,'kf',kf,'VDI',vdi12);
strct.soma.Cav12 = struct('gbar', on.LCa * 0.0015 / fac,'kf',kf,'VDI',vdi12);
strct.SGCL.Cav12 = struct('gbar', on.LCa * 0.0005 * 3/2 / fac,'kf',kf,'VDI',vdi12);
strct.GCL.Cav12 = struct('gbar', on.LCa * 0.0005 * 3/2 / fac,'kf',kf,'VDI',vdi12);
strct.adendIML.Cav12 = struct('gbar', on.LCa * 0.0005 * 3/2 * 4 / fac,'kf',kf,'VDI',vdi12);
strct.adendMML.Cav12 = struct('gbar', on.LCa * 0.0005 * 3/2 * 4 / fac,'kf',kf,'VDI',vdi12);
strct.adendOML.Cav12 = struct('gbar', on.LCa * 0.0005 * 3/2 * 4 / fac,'kf',kf,'VDI',vdi12);
strct.axon.Cav13 = struct('gbar', on.LCa * 0.0005 / 2 / fac3,'kf',kf,'VDI',vdi13);
strct.axonh.Cav13 = struct('gbar', on.LCa * 0.0005 / fac3,'kf',kf,'VDI',vdi13);
strct.soma.Cav13 = struct('gbar', on.LCa * 0.0005 * 2 / fac3,'kf',kf,'VDI',vdi13);
strct.SGCL.Cav13 = struct('gbar', on.LCa * 0.0005 /2 / fac3,'kf',kf,'VDI',vdi13);
strct.GCL.Cav13 = struct('gbar', on.LCa * 0.0005 /2 / fac3,'kf',kf,'VDI',vdi13);
strct.adendIML.Cav13 = struct('gbar', on.LCa * 0.0005 * 4/2 / 2 / fac3,'kf',kf,'VDI',vdi13);
strct.adendMML.Cav13 = struct('gbar', on.LCa * 0.0005 * 4/2 / 2 / fac3,'kf',kf,'VDI',vdi13);
strct.adendOML.Cav13 = struct('gbar', on.LCa * 0.0005 * 4/2 / 2 / fac3,'kf',kf,'VDI',vdi13);
%
strct.axon.Cav32 = struct('gbar', 0.0005/1.375 *tfac / fac);% no T-type in axon bouton (Li,Bischofberger 2007) but Martinello finds some immunogold...
strct.axonh.Cav32 = struct('gbar', 0.0005/1.375 *tfac / fac);
strct.soma.Cav32 = struct('gbar', 0.001 *tfac / fac);
strct.SGCL.Cav32 = struct('gbar', 0.0002 * 2.5 *2 *tfac / fac);
strct.GCL.Cav32 = struct('gbar', 0.0002 * 2.5 *2 *tfac / fac);
strct.adendIML.Cav32 = struct('gbar', 0.0002 * 2.5 *2 *tfac / fac);
strct.adendMML.Cav32 = struct('gbar', 0.0002 * 2.5 *2 *tfac / fac);
strct.adendOML.Cav32 = struct('gbar', 0.0002 * 2.5 *2 *tfac / fac);
end
if on.BK > 0
gabk = 13 * 0.0003 * on.BK ;
if ~isempty(strfind(options,'-n'))
base = 4;
diffsoma = 1.5;%0.3;
gak = gabk * 4;
gabk_soma = gabk / 4;
gak_soma = gabk * 4 / 4;
else
base = 2;
diffsoma = 1;%0.3;
gabk_soma = gabk / 2;
gak = 0;%gak / 2 ;
gak_soma = 0;
end
% BK: 0.05 - 0.3 S/cm²! (from model)
strct.axon.BK = struct('gabkbar', gabk,'gakbar', gak,'diff',100000,'base',base); % no Calcium channel - BK clusters in axon, this is why high diff value
strct.axonh.BK = struct('gabkbar', gabk,'gakbar', gak,'diff',100000,'base',base); % axonh i dont know, but made it same as axon...
% ab is slow bk type I, a is fast bk type II
strct.soma.BK = struct('gabkbar', gabk_soma,'gakbar', gak_soma,'diff',diffsoma,'base',base); % also more gak because there might be heteromeric BKs with less than 4 ß4 subunits
end
if on.SK > 0
Q10 = 5;
skfac = on.SK / 24;
dif = 3;
strct.soma.SK2 = struct('gkbar',0.004 / 20 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320); % this is not really SK2 but SK1
strct.axonh.SK2 = struct('gkbar',0.02* skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320); % this is not really SK2 but SK1
strct.axon.SK2 = struct('gkbar',0.003 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320); % this is not really SK2 but SK1/3
strct.SGCL.SK2 = struct('gkbar',0.0002 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320);
strct.GCL.SK2 = struct('gkbar',0.0004 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320);
strct.adendIML.SK2 = struct('gkbar',0.00105 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.08*4,'invc2',0.08*4,'dirc4',80*4); % ~ 35 mal weniger SK3 in soma als in IML/OML (Ballesteros-Merino 2014)
strct.adendMML.SK2 = struct('gkbar',0.00105 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320);
strct.adendOML.SK2 = struct('gkbar',0.00105 * skfac,'diff',dif,'Q10',Q10,'fac',2.5,'diro2',0.1,'invc3',0.09,'invc1',0.16*2,'invc2',0.16*2,'dirc4',320);
end
strct.all.k_ion = struct('ek',-103); % calculated from concentrations in Mongiat paper (SH07 very similar)
strct.all.na_ion = struct('ena',87); % calculated from concentrations in Mongiat paper (SH07 very similar)
strct.all.ca_ion = struct('cao0',2,'cai0',0.00007); % calculated from concentrations in Mongiat paper (SH07 very similar)
else
%already with corrected Ca buffer model...
strct.axon.ichan3 = struct('gnabar',0.21,'gkfbar',0.028,'gksbar',0,'gkabar',0.004);
strct.axonh.ichan3 = struct('gnabar',0.21,'gkfbar',0.028,'gksbar',0,'gkabar',0.004);
strct.soma.ichan3 = struct('gnabar',0.12,'gkfbar',0.016,'gksbar',0.003,'gkabar',0.012);
strct.soma.Caold = struct('gtcabar',0.00015,'gncabar',0.002,'glcabar',0.01);
strct.soma.CadepK = struct('gbkbar',0.0003,'gskbar',0.0005);
strct.GCL.ichan3 = struct('gnabar',0.018,'gkfbar',0.004,'gksbar',0.003,'gkabar',0);
strct.SGCL.ichan3 = struct('gnabar',0.018,'gkfbar',0.004,'gksbar',0.003,'gkabar',0);
strct.GCL.Caold = struct('gtcabar',0.0003,'gncabar',0.003,'glcabar',0.015);
strct.GCL.CadepK = struct('gbkbar',0.0003,'gskbar',0.0002);
strct.SGCL.Caold = struct('gtcabar',0.0003,'gncabar',0.003,'glcabar',0.015);
strct.SGCL.CadepK = struct('gbkbar',0.0003,'gskbar',0.0002);
strct.adendIML.ichan3 = struct('gnabar',0.013,'gkfbar',0.004,'gksbar',0.003,'gkabar',0);
strct.adendIML.Caold = struct('gtcabar',0.001,'gncabar',0.001,'glcabar',0.015);
strct.adendIML.CadepK = struct('gbkbar',0.0005,'gskbar',0.0001);
strct.adendMML.ichan3 = struct('gnabar',0.008,'gkfbar',0.001,'gksbar',0.003,'gkabar',0);
strct.adendMML.Caold = struct('gtcabar',0.002,'gncabar',0.001,'glcabar',0.001);
strct.adendMML.CadepK = struct('gbkbar',0.0012,'gskbar',0);
strct.adendOML.ichan3 = struct('gnabar',0,'gkfbar',0.001,'gksbar',0.004,'gkabar',0);
strct.adendOML.Caold = struct('gtcabar',0.002,'gncabar',0.001,'glcabar',0);
strct.adendOML.CadepK = struct('gbkbar',0.0012,'gskbar',0);
strct.all.k_ion = struct('ek',-85); % calculated from concentrations in Mongiat paper (SH07 very similar)
strct.all.na_ion = struct('ena',45); % % calculated from concentrations in Mongiat paper (SH07 very similar)
strct.all.ca_ion = struct('cao0',2,'cai0',0.00007); % calculated from concentrations in Mongiat paper (SH07 very similar)
end
end