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get_PFC_cell.m
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function spec = get_PFC_cell(type,N)
% specification=get_PFC_cell(type,N)
% purpose: retrieve DynaSim specification for single-cell PFC models.
% options:
% type (default: 'DS02PY'):
% PFC cell models:
% 'DS02PY' : two-compartment pyramidal cell ('Es','Ed') (from [DS02])
% 'DS02FS' : FS interneuron ('FS') (from [DS02])
% 'DS02KS14FS' : FS interneuron ('FS') (IN from [DS02] w/ FS modifications from [KS14] soma)
% 'DS02KS14RSNP': RSNP interneuron ('RSNP') (IN from [DS02] w/ RS modifications from [KS14] soma)
% 'DS02PYjs' : Custom two-compartment pyramidal cell ('Es','Ed') ([DS02] + [TW03] dend ih)
% 'DS02FSjs' : Custom FS interneuron ('FS') (IN from [DS02] w/ JSS modifications based on [KS14] FS)
% 'DS02RSNPjs' : Custom RSNP interneuron ('RSNP') (IN from [DS02] w/ JSS modifications based on [KS14] RS and experiments)
% isolated compartments from multicompartment cell models:
% 'DS02PYs' : pyramidal cell soma ('Es') (from [DS02])
% 'DS02PYd' : pyramidal cell dendrite ('Ed') (from [DS02])
% 'DS02PYsjs' : Custom pyramidal cell soma ('Es') ([DS02] + [TW03] dend ih)
% 'DS02PYdjs' : Custom pyramidal cell dendrite ('Ed') ([DS02] + [TW03] dend ih)
% non-PFC cell models:
% 'WB96FS' : Wang-Buzsaki IN model of Hippocampal FS cells ('FS') [WB96]
% 'HH' : Classic Hodgkin-Huxley model of giant squid axon ('HH') [HH52]
% N: number of cells (default: 1)
%
% References for models used:
% [DS00] Durstewitz, D., Seamans, J. K., & Sejnowski, T. J. (2000). Dopamine-mediated stabilization of delay-period activity in a network model of prefrontal cortex. Journal of neurophysiology, 83(3), 1733-1750.
% [DS02] Durstewitz, D., & Seamans, J. K. (2002). The computational role of dopamine D1 receptors in working memory. Neural Networks, 15(4), 561-572.
% [KS14] Konstantoudaki, X., Papoutsi, A., Chalkiadaki, K., Poirazi, P., & Sidiropoulou, K. (2014). Modulatory effects of inhibition on persistent activity in a cortical microcircuit model. Frontiers in neural circuits, 8, 1-15.
% [TW03] Traub, R. D., Buhl, E. H., Gloveli, T., & Whittington, M. A. (2003). Fast rhythmic bursting can be induced in layer 2/3 cortical neurons by enhancing persistent Na+ conductance or by blocking BK channels. Journal of neurophysiology, 89(2), 909-921.
% [WB96]: Wang, Xiao-Jing, and Gy??rgy Buzs??ki. "Gamma oscillation by synaptic inhibition in a hippocampal interneuronal network model." The journal of Neuroscience 16.20 (1996): 6402-6413.
%
% Examples:
%
% % Example 1: load two-compartment PY cell, increase Iapp to soma and plot V:
% spec=get_PFC_cell('DS02PYjs'); % load cell specification (two compartments: 'Es' and 'Ed')
% data=dsSimulate(spec,'tspan',[0 500],'vary',{'Es','Iapp',.1},'solver','rk1','verbose_flag',1);
% dsPlot(data);
%
% % Example 2: load and characterize single-compartment FS model (taum)
% % for different values of Rm (Rin)
% spec=get_PFC_cell('DS02FSjs'); % note: spec.populations.name = 'FS'
% model=dsGenerateModel(spec);
% amps=[-2 -1 0 5 10]; onset=50; offset=250; tspan=[0 300];
% data=ProbeCellProperties(model,'membrane_area',model.parameters.FS_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Rin=%gMOhm: taum=%gms (theory: taum=Rm*Cm, Rin=Rm/area)\n',1/model.parameters.FS_pas_gpas,stats.FS.tau_m);
% model=dsApplyModifications(model,{'FS','gpas',2*model.parameters.FS_pas_gpas});
% data=ProbeCellProperties(model,'membrane_area',model.parameters.FS_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Rin=%gMOhm: taum=%gms (theory: taum=Rm*Cm, Rin=Rm/area)\n',1/model.parameters.FS_pas_gpas,stats.FS.tau_m);
% % tip: other intrinsic property measures are stored in stats (e.g., RMP, Vthresh, spikewidth)
%
% % Example 3: load and characterize multicompartment PY model (taum) for
% % different values of Cm (adjusted in all compartments) with current applied to soma
% spec=get_PFC_cell('DS02PYjs');
% model=dsGenerateModel(spec);
% amps=[-2 -1 0 5 10]/5; onset=50; offset=250; tspan=[0 300];
% data=ProbeCellProperties(model,'remove_connections_flag',0,'membrane_area',model.parameters.Es_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Cm=%gnF: taum=%gms (theory: taum=Rm*Cm)\n',model.parameters.Es_Cm,stats.Es.tau_m);
% model=dsApplyModifications(model,{'Es','Cm',.5*model.parameters.Es_Cm;'Ed','Cm',.5*model.parameters.Ed_Cm});
% data=ProbeCellProperties(model,'remove_connections_flag',0,'membrane_area',model.parameters.Es_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Cm=%gnF: taum=%gms (theory: taum=Rm*Cm)\n',model.parameters.Es_Cm,stats.Es.tau_m);
%
% See script PFC_cells_explicit.m for more details on model constraints.
% See also: PFC_1layer, get_PFC_1layer, dsApplyModifications, ProbeCellProperties
% % Example: load and characterize FS model (taum) for different values of Cm
% spec=get_PFC_cell('DS02FSjs'); % note: spec.populations.name = 'FS'
% model=dsGenerateModel(spec);
% amps=[-2 -1 0 5 10]; onset=50; offset=250; tspan=[0 300];
% data=ProbeCellProperties(model,'membrane_area',model.parameters.FS_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Cm=%gnF: taum=%gms (theory: taum=Rm*Cm)\n',model.parameters.FS_Cm,stats.FS.tau_m);
% model=dsApplyModifications(model,{'FS','Cm',.5*model.parameters.FS_Cm});
% data=ProbeCellProperties(model,'membrane_area',model.parameters.FS_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Cm=%gnF: taum=%gms (theory: taum=Rm*Cm)\n',model.parameters.FS_Cm,stats.FS.tau_m);
% % Example: load and characterize multicompartment PY model (taum) for
% % different values of Rm (Rin) with current applied to soma
% spec=get_PFC_cell('DS02PYjs');
% model=dsGenerateModel(spec);
% amps=[-2 -1 0 5 10]/5; onset=50; offset=250; tspan=[0 300];
% data=ProbeCellProperties(model,'remove_connections_flag',0,'membrane_area',model.parameters.Es_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Rin(Es)=%gMOhm: taum(Es)=%gms (theory: taum=Rm*Cm, Rin=Rm/area)\n',1/model.parameters.Es_pas_gpas,stats.Es.tau_m);
% model=dsApplyModifications(model,{'Es','gpas',2*model.parameters.Es_pas_gpas;'Ed','gpas',2*model.parameters.Ed_pas_gpas});
% data=ProbeCellProperties(model,'remove_connections_flag',0,'membrane_area',model.parameters.Es_area,'amplitudes',amps,'onset',onset,'offset',offset,'tspan',tspan,'solver','rk1');
% stats=CalcCellProperties(data);
% dsPlot(data,'ylim',[-100 50]);
% fprintf('Rin(Es)=%gMOhm: taum(Es)=%gms (theory: taum=Rm*Cm, Rin=Rm/area)\n',1/model.parameters.Es_pas_gpas,stats.Es.tau_m);
% created by JSS on 11-Apr-2016, contact: [email protected]
if nargin<1, type='DS02PY'; end
if nargin<2, N=1; end % # of cells in population
switch type
case 'DS02PY'
% -------------------------------------------------------------------------
% [DS02PY] Pyramidal cell: two compartments (PYs soma, PYd dendrite) [DS02]
% -------------------------------------------------------------------------
% Note: This implementation is an exact match to the [DS02] PY model.
% cell morphology (cylindrical compartments)
% pyramidal soma (length and diameter chosen to match surface area and internal resistance with a sphere of diam 23 microns)
ls=28.618; % um, length
ds=21.840; % um, diameter
% pyramidal dendrite
ld=650; % um, length
dd=6.5; % um, diameter
% shared parameters
epas=-70; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3;% um, depth of extracellular shell for K+ diffusion
cao=2e3; % uM, extracellular calcium concentration
cainf=50e-3; % uM, steady-state intracellular calcium concentration
dshellCa=2e-4;% um, depth of intracellular shell for Ca2+ diffusion
faraday=96487;% s*A/mol, faraday constant (charge per mole of ions)
% ionic mechanisms and voltage dynamics present in both compartments (see [DS00] Methods for justification)
mechanism_list={'DS00iNa','DS00iNaP','DS00iDR','DS02iKS','DS02iHVA','DS00iKCa','DS00CaDyn','DS00KDyn','pas'};
state_equations='dV/dt=(@current+Iapp)./Cm; Iapp=0; Cm=1; V(0)=-65; area=0';
spec=[];
% soma
l=ls; d=ds; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/30e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm [uS/um2]
gnaf=117e-5; % 117 mS/cm2 = 117e-5 uS/um2
gkdr=50e-5; % 50 mS/cm2 = 50e-5 uS/um2
gnap=1.8e-5; % uS/um2, persistent sodium channel
gks=.08e-5; % uS/um2, slow potassium channel
ghva=.4e-5; % uS/um2, high-voltage-activated Ca2+ channel
gkc=2.1e-5; % uS/um2, V- and Ca2+-dependent potassium channel
tauCa=250; % ms, calcium decay time constant
CAF=600; % calcium accumulation factor
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion/accumulation
VshellCa=pi*dshellCa*l.*(d-dshellCa); % um3, volume of intracellular shell for Ca2+ diffusion/accumulation
spec.populations(1).name='Es';
spec.populations(1).size=N;
spec.populations(1).equations=state_equations;
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'area',A,...
'gnaf',gnaf*A,'gnap',gnap*A,'ghva',ghva*A,'gkdr',gkdr*A,'gks',gks*A,'gkc',gkc*A,...
'CAF',CAF,'VshellCa',VshellCa,'cainf',cainf,'tauCa',tauCa,'cao',cao,...
'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday};
% dendrite
l=ld; d=dd; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=Cm*1.92; % 2.304 uF/cm2
gpas=gpas*1.92; % 1/(Rm/1.92)
gnaf=20e-5; % 20 mS/cm2 = 20e-5 uS/um2
gkdr=14e-5; % 14 mS/cm2 = 14e-5 uS/um2
gnap=.8e-5; % uS/um2, persistent sodium channel
gks=.08e-5; % uS/um2, slow potassium channel
ghva=.8e-5; % uS/um2, high-voltage-activated Ca2+ channel
gkc=2.1e-5; % uS/um2, V- and Ca2+-dependent potassium channel
tauCa=120; % ms, calcium decay time constant
CAF=600; % calcium accumulation factor
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion/accumulation
VshellCa=pi*dshellCa*l.*(d-dshellCa); % um3, volume of intracellular shell for Ca2+ diffusion/accumulation
spec.populations(2).name='Ed';
spec.populations(2).size=N;
spec.populations(2).equations=state_equations;
spec.populations(2).mechanism_list=mechanism_list;
spec.populations(2).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'area',A,...
'gnaf',gnaf*A,'gnap',gnap*A,'ghva',ghva*A,'gkdr',gkdr*A,'gks',gks*A,'gkc',gkc*A,...
'CAF',CAF,'VshellCa',VshellCa,'cainf',cainf,'tauCa',tauCa,'cao',cao,...
'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday};
% intercompartmental connections
Ri=1.5; % axial resistance [MOhm-um], Ri=150 Ohm-cm
% collect relevant info
compartments={'Es' 'Ed'};
lengths =[ls ld];
diameters =[ds dd];
connections={[1 2],[2 1]};
% add connections to specification
for c=1:length(connections)
src=connections{c}(1);
dst=connections{c}(2);
spec.connections(c).direction=[compartments{src} '->' compartments{dst}];
spec.connections(c).mechanism_list={'iCOM'};
gCOM=1/mean(Ri*4*lengths./(pi*diameters.^2));
spec.connections(c).parameters={'gCOM',gCOM};
end
% equivalent gCOM calculation for coupling from 2 to 1:
% g12=@(r1,L1,r2,L2)(r1*r2^2)/(Ri*L1*(L1*r2^2+L2*r1^2));
% gCOM=g12*(surface area)=g12*(2*pi*r1*L1)
% d->s: g12(ds/2,ls,dd/2,ld)*(pi*ls*ds)
% s->d: g12(dd/2,ld,ds/2,ls)*(pi*ld*dd)
% Units: [Ri]=MOhm*um, [r]=[L]=um, then [g12]=uS/um2 and [gCOM]=uS. Ra=1/gCOM
% Reference: https://en.wikipedia.org/wiki/Compartmental_modelling_of_dendrites
case 'DS02PYs'
spec = get_PFC_cell('DS02PY',N);
spec.populations=spec.populations(1);
spec.connections=[];
case 'DS02PYd'
spec = get_PFC_cell('DS02PY',N);
spec.populations=spec.populations(2);
spec.connections=[];
case 'DS02PYjs'
% -------------------------------------------------------------------------
% [DS02PYjs] Custom 2-compartment Pyramidal cell (PYs,PYd) ([DS02] + [TW03] dend ih)
% -------------------------------------------------------------------------
% This is the same as model (1) and [DS02] PY with the addition of a
% dendritic h-current (ih model taken from [TW03]). The PY dendritic h-current
% may be important for explaining the reduction in network rhythm frequency
% from gamma to beta2 that occurs when h-channels are blocked (in vitro;
% unpublished result from LeBeau lab); it may also be relevant for
% understanding how RSNP inhibition controls PY activity.
% Experimental motivation: Day, M., Carr, D. B., Ulrich, S., Ilijic, E., Tkatch, T., & Surmeier, D. J. (2005). Dendritic excitability of mouse frontal cortex pyramidal neurons is shaped by the interaction among HCN, Kir2, and Kleak channels. The Journal of neuroscience, 25(38), 8776-8787.
% cell morphology (cylindrical compartments)
% pyramidal soma (length and diameter chosen to match surface area and internal resistance with a sphere of diam 23 microns)
ls=28.618; % um, length
ds=21.840; % um, diameter
% pyramidal dendrite
ld=650; % um, length
dd=6.5; % um, diameter
% shared parameters
epas=-70; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3;% um, depth of extracellular shell for K+ diffusion
cao=2e3; % uM, extracellular calcium concentration
cainf=50e-3; % uM, steady-state intracellular calcium concentration
dshellCa=2e-4;% um, depth of intracellular shell for Ca2+ diffusion
faraday=96487;% s*A/mol, faraday constant (charge per mole of ions)
% ionic mechanisms and voltage dynamics present in both compartments (see [DS00] Methods for justification)
mechanism_list={'DS00iNa','DS00iNaP','DS00iDR','DS02iKS','DS02iHVA','DS00iKCa','DS00CaDyn','DS00KDyn','TW03iH','pas'};
state_equations='dV/dt=(@current+Iapp)./Cm; Iapp=0; Cm=1; V(0)=-65; area=0';
spec=[];
% soma
l=ls; d=ds; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/30e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm [uS/um2]
gnaf=117e-5; % 117 mS/cm2 = 117e-5 uS/um2
gkdr=50e-5; % 50 mS/cm2 = 50e-5 uS/um2
gnap=1.8e-5; % uS/um2, persistent sodium channel
gks=.08e-5; % uS/um2, slow potassium channel
ghva=.4e-5; % uS/um2, high-voltage-activated Ca2+ channel
gkc=2.1e-5; % uS/um2, V- and Ca2+-dependent potassium channel
gH=0e-5; % max conductance of h-channel
tauCa=250; % ms, calcium decay time constant
CAF=600; % calcium accumulation factor
htaunap=.5; % JSS made this change to speed up adaptation and time to reach SS firing
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion/accumulation
VshellCa=pi*dshellCa*l.*(d-dshellCa); % um3, volume of intracellular shell for Ca2+ diffusion/accumulation
spec.populations(1).name='Es';
spec.populations(1).size=N;
spec.populations(1).equations=state_equations;
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'gH',gH*A,'area',A,...
'gnaf',gnaf*A,'gnap',gnap*A,'ghva',ghva*A,'gkdr',gkdr*A,'gks',gks*A,'gkc',gkc*A,...
'CAF',CAF,'VshellCa',VshellCa,'cainf',cainf,'tauCa',tauCa,'cao',cao,'htaunap',htaunap,...
'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday};
% dendrite
l=ld; d=dd; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=Cm*1.92; % 2.304 uF/cm2
gpas=gpas*1.92; % 1/(Rm/1.92)
gnaf=20e-5; % 20 mS/cm2 = 20e-5 uS/um2
gkdr=14e-5; % 14 mS/cm2 = 14e-5 uS/um2
gnap=.8e-5; % uS/um2, persistent sodium channel
gks=.08e-5; % uS/um2, slow potassium channel
ghva=.8e-5; % uS/um2, high-voltage-activated Ca2+ channel
gkc=2.1e-5; % uS/um2, V- and Ca2+-dependent potassium channel
gH=.01e-5; % max conductance of h-channel
tauCa=120; % ms, calcium decay time constant
CAF=600; % calcium accumulation factor
htaunap=.5; % JSS made this change to speed up adaptation and time to reach SS firing
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion/accumulation
VshellCa=pi*dshellCa*l.*(d-dshellCa); % um3, volume of intracellular shell for Ca2+ diffusion/accumulation
spec.populations(2).name='Ed';
spec.populations(2).size=N;
spec.populations(2).equations=state_equations;
spec.populations(2).mechanism_list=mechanism_list;
spec.populations(2).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'gH',gH*A,'area',A,...
'gnaf',gnaf*A,'gnap',gnap*A,'ghva',ghva*A,'gkdr',gkdr*A,'gks',gks*A,'gkc',gkc*A,...
'CAF',CAF,'VshellCa',VshellCa,'cainf',cainf,'tauCa',tauCa,'cao',cao,'htaunap',htaunap,...
'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday};
% intercompartmental connections
Ri=1.5; % axial resistance [MOhm-um], Ri=150 Ohm-cm
% collect relevant info
compartments={'Es' 'Ed'};
lengths =[ls ld];
diameters =[ds dd];
connections={[1 2],[2 1]};
% add connections to specification
for c=1:length(connections)
src=connections{c}(1);
dst=connections{c}(2);
spec.connections(c).direction=[compartments{src} '->' compartments{dst}];
spec.connections(c).mechanism_list={'iCOM'};
gCOM=1/mean(Ri*4*lengths./(pi*diameters.^2));
spec.connections(c).parameters={'gCOM',gCOM};
end
case 'DS02PYsjs'
spec = get_PFC_cell('DS02PYjs',N);
spec.populations=spec.populations(1);
spec.connections=[];
case 'DS02PYdjs'
spec = get_PFC_cell('DS02PYjs',N);
spec.populations=spec.populations(2);
spec.connections=[];
case 'DS02FS'
% -------------------------------------------------------------------------
% 2) [DS02FS] Fast-spiking GABAergic interneuron [DS02]
% -------------------------------------------------------------------------
% Note: This implementation is an exact match to the [DS02] FS model.
% cell morphology (cylindrical-approximation to spherical somatic compartment)
% FS soma
l=42; % um, length
d=42; % um, diameter
epas=-70; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3; % um, depth of extracellular shell for K+ diffusion
faraday=96487; % s*A/mol, faraday constant (charge per mole of ions)
% mechanisms and interneuron-specific modifications to their kinetics (see [DS02] Fig 2)
mechanism_list={'DS00iNa','DS00iDR','DS00KDyn','pas'};
anV0=13-10; % 10mV more hyperpolarized than pyramidal cell
bnV0=23-10; % 10mV more hyperpolarized than pyramidal cell
amV0=-28-10; % 10mV more hyperpolarized than pyramidal cell
bmV0=-1-12; % 12mV more hyperpolarized than pyramidal cell
ahV0=-43.1-10; % 10mV more hyperpolarized than pyramidal cell
bhV0=-13.1-10; % 10mV more hyperpolarized than pyramidal cell
hnascale=2; % sodium inactivation sped up 2x
% soma
A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/30e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm [uS/um2]
gnaf=45e-5; % 45 mS/cm2 = 45-5 uS/um2
gkdr=18e-5; % 18 mS/cm2 = 18-5 uS/um2
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion
spec=[];
spec.populations(1).name='FS';
spec.populations(1).size=N;
spec.populations(1).equations='dV/dt=(@current+Iapp)./Cm; Iapp=0; Cm=1; V(0)=-65; area=0';
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'area',A,...
'gnaf',gnaf*A,'gkdr',gkdr*A,'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday,...
'anV0',anV0,'bnV0',bnV0,'hnascale',hnascale,'amV0',amV0,'bmV0',bmV0,'ahV0',ahV0,'bhV0',bhV0};
case 'DS02KS14FS'
% -------------------------------------------------------------------------
% [DS02KS14FS] Fast-spiking GABAergic interneuron: (model (2) with modifications)
% [DS02] FS with [TW03] ih and [KS14] FS soma parameters
% -------------------------------------------------------------------------
% Differences wrt [KS14] FS: [KS14] FS also includes A-type K+ current,
% slow K+ current, and high-threshold N-type Ca2+ current. [KS14] FS has 3
% compartments (soma, dendrite, axon); the model here has a single soma.
% However, soma geometry, RMP, ~Vthresh, and electrophysiological regime (FS) are the same.
epas=-72; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3; % um, depth of extracellular shell for K+ diffusion
faraday=96487; % s*A/mol, faraday constant (charge per mole of ions)
% mechanisms and interneuron-specific modifications to their kinetics
mechanism_list={'DS00iNa','DS00iDR','DS00KDyn','TW03iH','pas'};
anV0=13-10; % 10mV more hyperpolarized than pyramidal cell
bnV0=23-10; % 10mV more hyperpolarized than pyramidal cell
amV0=-28-10; % 10mV more hyperpolarized than pyramidal cell
bmV0=-1-12; % 12mV more hyperpolarized than pyramidal cell
ahV0=-43.1-10; % 10mV more hyperpolarized than pyramidal cell
bhV0=-13.1-10; % 10mV more hyperpolarized than pyramidal cell
hnascale=2; % Na+ inactivation sped up 2x
% soma
l=27; d=29; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/10e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm
gnaf=135e-5; % 45 mS/cm2 = 45-5 uS/um2
gkdr=36e-5; % 18 mS/cm2 = 18-5 uS/um2
gH=.01e-5; % max conductance of h-channel
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of shell for extracellular K+ diffusion
spec=[];
spec.populations(1).name='FS';
spec.populations(1).size=N;
spec.populations(1).equations='dV/dt=(@current+Iapp)./Cm; Cm=1; V(0)=-65; Iapp=0; area=0';
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'gH',gH*A,'area',A,...
'gnaf',gnaf*A,'gkdr',gkdr*A,'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday,...
'anV0',anV0,'bnV0',bnV0,'hnascale',hnascale,'amV0',amV0,'bmV0',bmV0,'ahV0',ahV0,'bhV0',bhV0};
case 'DS02FSjs'
% -------------------------------------------------------------------------
% [DS02FSjs] Custom Fast-spiking GABAergic interneuron: (model (3) with modifications)
% [DS02] FS with [TW03] ih and [KS14] FS soma parameters
% -------------------------------------------------------------------------
% Modifications wrt model (3): morphological dimensions (geometry) was
% adjusted to account for the effect of removing dendrite and axon
% compartments from [KS14] FS on the input resistance. Consequence: this model
% (6) FS cell is a better match to the experimental data than model (3).
% Approach: modified Rm to achieve desired Rin and reasonable taum.
% Also, modified gkdr wrt [KS14]: increased from gkdr=36e-5 to 50e-5 to achieve
% slightly shorter spike-width and lower Vthresh. This change also produces a
% gkdr/gnaf ratio that more closely matches [DS02].
epas=-72; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3; % um, depth of extracellular shell for K+ diffusion
faraday=96487; % s*A/mol, faraday constant (charge per mole of ions)
% mechanisms and interneuron-specific modifications to their kinetics
mechanism_list={'DS00iNa','DS00iDR','DS00KDyn','TW03iH','pas'};
anV0=13-10; % 10mV more hyperpolarized than pyramidal cell
bnV0=23-10; % 10mV more hyperpolarized than pyramidal cell
amV0=-28-10; % 10mV more hyperpolarized than pyramidal cell
bmV0=-1-12; % 12mV more hyperpolarized than pyramidal cell
ahV0=-43.1-10; % 10mV more hyperpolarized than pyramidal cell
bhV0=-13.1-10; % 10mV more hyperpolarized than pyramidal cell
hnascale=2; % Na+ inactivation sped up 2x
% soma
l=27; d=29; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/8e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm
gnaf=135e-5; % 45 mS/cm2 = 45-5 uS/um2
gkdr=50e-5; % [KS14] 36e-5 % 18 mS/cm2 = 18-5 uS/um2
gH=.01e-5; % max conductance of h-channel
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of shell for extracellular K+ diffusion
spec=[];
spec.populations(1).name='FS';
spec.populations(1).size=N;
spec.populations(1).equations='dV/dt=(@current+Iapp)./Cm; Cm=1; V(0)=-65; Iapp=0; area=0';
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'gH',gH*A,'area',A,...
'gnaf',gnaf*A,'gkdr',gkdr*A,'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday,...
'anV0',anV0,'bnV0',bnV0,'hnascale',hnascale,'amV0',amV0,'bmV0',bmV0,'ahV0',ahV0,'bhV0',bhV0};
case 'WB96FS'
Cm=1; % uF/cm2
gleak=.1; % mS/cm2. Note: taum=Cm/gleak=10ms
Eleak=-65; % mV
gNa=35; % mS/cm2
gK=9; % mS/cm2
spec=[];
spec.populations.name=type;
spec.populations.size=N;
spec.populations.equations='dV/dt=(@current+Iapp)./Cm; Cm=1; Iapp=0; V(0)=-65';
spec.populations.mechanism_list={'WB96FSiNa','WB96FSiK','WB96FSileak'};
spec.populations.parameters={'Cm',Cm,'Eleak',Eleak,'gleak',gleak,'gNa',gNa,'gK',gK};
case 'DS02KS14RSNP'
% -------------------------------------------------------------------------
% [DS02KS14RSNP] Regular Spiking Non-Pyramidal GABAergic interneuron:
% [DS02] FS with [TW03] ih and [KS14] RSNP soma parameters
% -------------------------------------------------------------------------
% Differences wrt [KS14] RSNP: [KS14] RSNP also includes A-type K+ current
% and low-threshold T-type Ca2+ current. [KS14] RSNP has 3 compartments
% (soma, dendrite, axon); the model here has a single soma.
% However, soma geometry, RMP, ~Vthresh, and electrophysiological regime (RS) are the same.
epas=-63.5; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3; % um, depth of extracellular shell for K+ diffusion
faraday=96487; % s*A/mol, faraday constant (charge per mole of ions)
% mechanisms and interneuron-specific modifications to their kinetics
mechanism_list={'DS00iNa','DS00iDR','DS00KDyn','TW03iH','pas'};
anV0=13-10; % 10mV more hyperpolarized than pyramidal cell
bnV0=23-10; % 10mV more hyperpolarized than pyramidal cell
amV0=-28-10; % 10mV more hyperpolarized than pyramidal cell
bmV0=-1-12; % 12mV more hyperpolarized than pyramidal cell
ahV0=-43.1-10; % 10mV more hyperpolarized than pyramidal cell
bhV0=-13.1-10; % 10mV more hyperpolarized than pyramidal cell
hnascale=2; % Na+ inactivation sped up 2x
% soma
l=42; d=42; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/40e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm
gnaf=75e-5; % 45 mS/cm2 = 45-5 uS/um2
gkdr=18e-5; % 18 mS/cm2 = 18-5 uS/um2
gH=.002e-5;
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion
spec=[];
spec.populations(1).name='RSNP';
spec.populations(1).size=N;
spec.populations(1).equations='dV/dt=(@current+Iapp)./Cm; Cm=1; V(0)=-65; Iapp=0; area=0';
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'gH',gH*A,'area',A,...
'gnaf',gnaf*A,'gkdr',gkdr*A,'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday,...
'anV0',anV0,'bnV0',bnV0,'hnascale',hnascale,'amV0',amV0,'bmV0',bmV0,'ahV0',ahV0,'bhV0',bhV0};
case 'DS02RSNPjs'
% -------------------------------------------------------------------------
% [DS02RSNPjs] Custom Regular Spiking Non-Pyramidal GABAergic interneuron: (model (4) with modifications)
% [DS02] FS with [TW03] ih and [KS14] RSNP soma parameters
% -------------------------------------------------------------------------
% Modifications wrt model (4): morphological dimensions (geometry) was
% adjusted to account for the effect of removing dendrite and axon
% compartments from [KS14] RS on the input resistance. Consequence: this model
% (6) RSNP cell is a better match to the experimental data than model (4).
epas=-63.5; % mV, passive leak reversal potential
ki=140; % mM, intracellular potassium concentration
koinf=3.82; % mM, steady-state extracellular potassium concentration
KAF=2e6; % potassium accumulation factor
tauK=7; % ms, extracellular potassium decay time constant
dshellK=70e-3; % um, depth of extracellular shell for K+ diffusion
faraday=96487; % s*A/mol, faraday constant (charge per mole of ions)
% mechanisms and interneuron-specific modifications to their kinetics
mechanism_list={'DS00iNa','DS00iDR','DS00KDyn','TW03iH','pas'};
anV0=13-10; % 10mV more hyperpolarized than pyramidal cell
bnV0=23-10; % 10mV more hyperpolarized than pyramidal cell
amV0=-28-10; % 10mV more hyperpolarized than pyramidal cell
bmV0=-1-12; % 12mV more hyperpolarized than pyramidal cell
ahV0=-43.1-10; % 10mV more hyperpolarized than pyramidal cell
bhV0=-13.1-10; % 10mV more hyperpolarized than pyramidal cell
hnascale=2; % Na+ inactivation sped up 2x
% soma
l=42; d=42; A=d*l*pi; % um2, cylinder surface area without the ends
Cm=1.2e-5; % 1.2 uF/cm2 = 1.2e-5 nF/um2
gpas=1/30e5; % Rm=30kOhm-cm2 = 30e5 MOhm-um2, gpas=1/Rm
gnaf=75e-5; % 45 mS/cm2 = 45-5 uS/um2
gkdr=18e-5; % 18 mS/cm2 = 18-5 uS/um2
gH=.002e-5;
VshellK=pi*dshellK*l.*(d+dshellK); % um3, volume of extracellular shell for K+ diffusion
spec=[];
spec.populations(1).name='RSNP';
spec.populations(1).size=N;
spec.populations(1).equations='dV/dt=(@current+Iapp)./Cm; Cm=1; V(0)=-65; Iapp=0; area=0';
spec.populations(1).mechanism_list=mechanism_list;
spec.populations(1).parameters={'Iapp',0,'Cm',Cm*A,'gpas',gpas*A,'epas',epas,'gH',gH*A,'area',A,...
'gnaf',gnaf*A,'gkdr',gkdr*A,'KAF',KAF,'VshellK',VshellK,'koinf',koinf,'tauK',tauK,'ki',ki,'faraday',faraday,...
'anV0',anV0,'bnV0',bnV0,'hnascale',hnascale,'amV0',amV0,'bmV0',bmV0,'ahV0',ahV0,'bhV0',bhV0};
otherwise
% Classic Hodgkin-Huxley model of giant squid axon [1952]
spec=[];
spec.populations.name='HH';
spec.populations.size=N;
spec.populations.equations='dV/dt=(@current+Iapp)./Cm; Cm=1; Iapp=0; V(0)=-65';
spec.populations.mechanism_list={'iNa','iK','ileak'};
spec.populations.parameters={};
end
% Additional References (experiments):
% [ZK05] Zaitsev, A. V., Gonzalez-Burgos, G., Povysheva, N. V., Kr??ner, S., Lewis, D. A., & Krimer, L. S. (2005). Localization of calcium-binding proteins in physiologically and morphologically characterized interneurons of monkey dorsolateral prefrontal cortex. Cerebral Cortex, 15(8), 1178-1186.
% [ZL09] (DLPFC L2/3 INs) Zaitsev, A. V., Povysheva, N. V., Gonzalez-Burgos, G., Rotaru, D., Fish, K. N., Krimer, L. S., & Lewis, D. A. (2009). Interneuron diversity in layers 2???3 of monkey prefrontal cortex. Cerebral cortex, 19(7), 1597-1615.
% [K93] (rat PrL L5 FS vs LTS) Kawaguchi, Y. A. S. U. O. (1993). Groupings of nonpyramidal and pyramidal cells with specific physiological and morphological characteristics in rat frontal cortex. Journal of neurophysiology, 69(2), 416-431.
% [GG03] Gao, W. J., Wang, Y., & Goldman-Rakic, P. S. (2003). Dopamine modulation of perisomatic and peridendritic inhibition in prefrontal cortex. The Journal of neuroscience, 23(5), 1622-1630.
% [VM09] Van Aerde, K. I., Mann, E. O., Canto, C. B., Heistek, T. S., Linkenkaer???Hansen, K., Mulder, A. B., ... & Mansvelder, H. D. (2009). Flexible spike timing of layer 5 neurons during dynamic beta oscillation shifts in rat prefrontal cortex. The Journal of physiology, 587(21), 5177-5196. http://onlinelibrary.wiley.com/doi/10.1113/jphysiol.2009.178384/full
% Results:
% [ZK05]: Rin [MOhm]: FS (235+/-68), RSNP (582+/-195), IS (585+/-137)
% [K93]: LTS RMP: -64mV (same as CB RS in [KS14]) > FS RMP
% [GG03],[VM09]: FS spike-width < nonFS spike-width
% [ZL09]: longer AP observed in DLPFC CB+ than PV+ INs
%{
% Custom model summary (cell intrinsic properties):
[ tau_m RMP V_thresh AP_dur Ih_abssag AHP_time2trough]
PYs: [48.41 -59.96 -37.93 1.1400 0 4.1500
PYs+d:[ -66
FS: [8.16 -73.25 -49.3951 0.7800 0.9894 2.2700]
RSNP: [31.45 -66.00 -45.8906 0.8800 0 3.7400]
PY taum is slower in superficial layers (L2/3 25+/-20ms vs L5/6 14+/-7ms)
L2/3: http://www.neuroelectro.org/neuron/110/
L5/6: http://www.neuroelectro.org/neuron/111/
Tip: decrease Rm (or Cm) in deep layer wrt superficial layer
%}