/* Original model from Poirazi et al. 2003, "CA1 pyramidal neuron: as a 2-layer NN and subthreshold synaptic summation", model DB accession # 20212 at senselab.med.yale.edu. Modified by Fiona Muellner, MPI Neurobiology, March 2015 (email: fiona.muellner@gmail.com).
Modifications:
Removed all R-type Ca2+-channels (car) which behave very unphysiologically by opening at voltage-step OFFset, not ONset, due to a much faster inactivation than activation time constant (typo?). Compare dynamics e.g. to Randall & Tsien 1997, "Contrasting Biophysical and Pharmacological Properties of T-type and R-type Calcium Channels".
Modified the cad-mechanism to correct the surface-volume-ratio which should vary with dendrite diameter (see Anwar et. al. 2014, "Dendritic diameters affect the spatial variability of intracellular calcium dynamics in computer models"); has an effect on Ca2+-amplitudes, but not Ca2+-inhibition.
Modified the cat-mechanism (T-type channels) to replace the dummy-ion Ca by the ion ca, which updates cai.
Set ek = -80mV for all mechanisms (has been -77mV for some); minimally reduces Vrest.
Changed density of the LH-channels (calH) to linearly increase along the first 50um apical dendritic tree (conductance increased step-wise before).
Increased medium Ca2+-dependent K+-current density (mykca_init) 3x, to prevent Ca2+-spikes in terminal branches.
Modified the linear function increasing the Na+ spike attenuation variable ar2_hha_old with distance to remove abrupt steps in current density.
Switched off current-balance.hoc. It forces e_pas to arbitrarily negative potentials. E.g. when Ih density is increased, this results in a paradoxical hyperpolarizing net-effect of Ih.
Chose finer segmentation (maximum segment length 25um, minimum 3 segments.
*/
/* ----- PROCEDURES USED IN CELL SETUP -------*/
/* To make the distal membrane less conductive (comment FM: more conductive), vis-a-vis Stuart G. and Spruston N., J. Neuroscience 18(10) 3501-3510, 1998, we decay Rm from proximal to distal sigmoidally */
proc Rm_sigmoid() { local rm
$o1.defvar("channel:pas","Rm_soma", "Rm_default", "")
$o1.defvar("channel:pas","Rm_end", "12e3", "")
$o1.defvar("channel:pas","dhalf", "200", "")
$o1.defvar("channel:pas","steep", "50", "")
for (x) {
xdist = find_vector_distance_precise(secname(),x) // calc. perpedicular distance
rm = Rm_soma + (Rm_end - Rm_soma)/(1.0 + exp((dhalf-xdist)/steep))
g_pas(x) = 1.0/rm
}
}
/* Changing Ra sigmoidally along the apical trunk (obsolete in this case)*/
proc Ra_sigmoid() {
$o1.defvar("channel:pas","Ra_soma", "Ra_default", "")
$o1.defvar("channel:pas","Ra_end", "0.7*Ra_default", "")
$o1.defvar("channel:pas","dhalf", "210", "")
$o1.defvar("channel:pas","steep", "50", "")
for (x) {
xdist = find_vector_distance_precise(secname(),x) //calc. perpedicular distance
Ra = Ra_soma + (Ra_end - Ra_soma)/(1.0 + exp((dhalf-xdist)/steep))
}
}
/* To make the distal trunk h-current conductance, g_h, about 7
times higher (at 300 um) than the somatic value vis-a-vis Magee
J., J. of Neuroscience 18(19) 7613-7624, 1998, we vary I_h
conductance sigmoidally along the apical trunk.
*/
proc apical_h_insert_sig() {
$o1.defvar("channel:h","gh_soma", "soma_hbar", "")
$o1.defvar("channel:h","gh_end", "soma_hbar*9", "")
$o1.defvar("channel:h","dhalf", "280", "")
$o1.defvar("channel:h","steep", "50", "")
for (x) {
xdist = find_vector_distance_precise(secname(),x) //calc. perpedicular distance
insert h
gbar_h(x) = gh_soma + (gh_end - gh_soma)/(1.0 + exp((dhalf-xdist)/steep))
}
}
/* Inserting proximal (kap) and distal(kad) A-type channels
along the apical trunk. Proximal I_A is distributed in a fixed
conductance over the first 100 um from the cell
body. Distal-type I_A is distributed in a linearly increasing
manner for distances 100 < xdist < 350. For xdist < 100,
g_A_distal(x) = 0 and for xdist > 350 g_A_distal(x) = constant =
g_A_distal(350)
*/
proc A_insert() {
$o1.defvar("channel:kap","kap_distal_maxfactor", "1", "maximum cond. factor in dendrites")
$o1.defvar("channel:kap","kap_distal_distance", "100", "distance in dendrites for maximum cond.")
$o1.defvar("channel:kad","kad_distal_maxfactor", "6.5", "maximum cond. factor in dendrites")
$o1.defvar("channel:kad","kad_distal_distance", "350", "distance in dendrites for maximum cond.")
for (x) {
xdist=find_vector_distance_precise(secname(),x)
fr = xdist/kad_distal_distance
insert kap
insert kad
ek = -80
if (xdist < kap_distal_distance ) {
gkabar_kad(x) = 0
gkabar_kap(x) = soma_kap
} else if (xdist < kad_distal_distance ) {
gkabar_kap(x) = 0
gkabar_kad(x) = kad_distal_maxfactor*kad_init*fr
} else {
gkabar_kap(x) = 0
gkabar_kad(x) = kad_distal_maxfactor*kad_init
}
}
}
/* Inserting m-type potassium current with a fixed conductance along the apical trunk
*/
proc apical_km_insert() {
$o1.defvar("channel:km","km_distal_maxfactor", "1", "maximum cond. factor in dendrites")
$o1.defvar("channel:km","km_distal_distance", "350", "distance in dendrites for maximum cond.")
for (x) {
//xdist = find_vector_distance_precise(secname(),x)
//fr = xdist/km_distal_distance
insert km
gbar_km(x)=soma_km
}
}
/* Inserting K(Ca++)-type channels and calcium pumps along the
apical trunk with maximum conductances in 50 < xdist < 200
*/
proc apical_kca_insert() {
$o1.defvar("channel:kca","kca_distal_maxfactor", "1", "maximum cond. factor in dendrites")
$o1.defvar("channel:kca","kca_distal_distance", "200", "distance in dendrites for maximum cond.")
for (x) {
xdist = find_vector_distance_precise(secname(),x)
fr = xdist/kca_distal_distance
insert cad // calcium pump/buffering mechanism
insert kca // slow AHP K++ current
insert mykca // medium AHP K++ current
if (xdist < kca_distal_distance && xdist > 50) {
gbar_kca(x) = 5*soma_kca
gkbar_mykca = 2*mykca_init
} else {
gbar_kca(x) = 0.5*soma_kca
gkbar_mykca = 0.25*mykca_init
}
}
}
/* Inserting LVA (comment FM: HVA) Ca++ T-type channels along the apical trunk in a linearly increasing manner, for xdist > 100 um
*/
proc apical_caT_insert() {
$o1.defvar("channel:cat","caT_distal_maxfactor", "4", "maximum cond. factor in dendrites")
$o1.defvar("channel:cat","caT_distal_distance", "350", "distance in dendrites for maximum cond.")
for (x) {
xdist = find_vector_distance_precise(secname(),x)
fr = xdist/caT_distal_distance
insert cat
if (xdist < 100) {
gcatbar_cat(x) = 0
} else {
gcatbar_cat(x) = caT_distal_maxfactor*soma_caT*fr
}
}
}
/* Inserting HVA Ca++ R-type and HVA L-type channels along the apical trunk. The R-type current is distributed in a fixed conductance while the L-type current is distributed in a maximum fixed conductance for distances xdist > 50 um and in a very small (modification FM: linearly increasing) conductance for xdist < 50 um
*/
proc apical_caR_caLH_insert() {
for (x) {
xdist = find_vector_distance_precise(secname(),x)
//insert car
//gcabar_car(x) = 0.1*soma_car
insert calH
if (xdist > 50) {
gcalbar_calH(x) = 4.6*soma_caLH
} else {
//gcalbar_calH(x) = 0.1*soma_caLH
gcalbar_calH(x) = (0.1 + 4.5*xdist/50)*soma_caLH
}
}
}
/* Setting conductances in all apical oblique dendrites so that the values of all dedrites after an initial section
are the same (or a multiple) as the values in apical_dendrite[46]. The values in the initial section of 50 um from
the parent trunk are set equal to the parent trunk conductances. For dendrites located beyond 300 (or/and 350) um,
we increase the Na+-persistent current, the A current, the Ca++ and K(Ca++) conductances and reduce the spike
attenuation coefficent. */
strdef khsection
proc khoblique_peri_decay() { local i,x,d
$o1.defvar("channel:obliques", "khsection", "\"apical_dendrite[46]\"", "Trunk section used for oblique conductance values")
$o1.defvar("morphology:apical-non-trunk", "peri_trunkl", "50.0", "Length of the peri-trunk region")
// Holding the conductance values from apical_dendrite[46]
//sprint($o1.tmp_str,"%s { hold_cat=gcatbar_cat(1) hold_car=soma_car hold_calH=soma_caLH hold_nap=0.0004*gnabar_hha_old }", khsection)
sprint($o1.tmp_str,"%s { hold_cat=gcatbar_cat(1) hold_calH=soma_caLH hold_nap=0.0004*gnabar_hha_old }", khsection)
execute1($o1.tmp_str)
sprint($o1.tmp_str,"%s { hold_h=gbar_h(1) hold_ar2_hha_old=ar2_hha_old(1) hold_kdr=gkbar_hha_old(1) }", khsection)
execute1($o1.tmp_str)
sprint($o1.tmp_str,"%s { hold_g_pas=g_pas(1) hold_Ra=Ra hold_kap=gkabar_kap(1) hold_kad=gkabar_kad(1) }", khsection)
execute1($o1.tmp_str)
sprint($o1.tmp_str,"%s { hold_mykca=gkbar_mykca(1) hold_kca=gbar_kca(1) hold_km=gbar_km(1) }", khsection)
execute1($o1.tmp_str)
for i=0,plcount {
// set the origin to the currently accessed section
access opl[i].trunk_section.sec
xdist = find_vector_distance_precise(secname(),0)
distance(0,1)
trunk_kap = gkabar_kap(1) // holding the parent trunk values
trunk_kad = gkabar_kad(1)
trunk_h = gbar_h(1)
trunk_pas = g_pas(1)
trunk_Ra = Ra
//trunk_car = gcabar_car(1)
trunk_calH = gcalbar_calH(1)
trunk_cat = gcatbar_cat(1)
trunk_kca = gbar_kca(1)
trunk_mykca = gkbar_mykca(1)
trunk_km = gbar_km(1)
trunk_nap = 0.2*hold_nap // No persistent I_Na at the trunk => hold a small persent of hold_nap value
trunk_ar2_hha_old = ar2_hha_old(1) // spike attenuation variable
sec_count=0
forsec pl[i] {
if (!sec_count) { // skip all trunk sections
sec_count=sec_count+1
continue
}
insert kap
insert kad
insert h
insert pas
//insert car
insert calH
insert cat
insert kca
insert mykca
insert km
insert nap
insert cad
e_pas = v_init
ek = -80
for (x) {
if (x > 0 && x < 1) {
d = distance(1,x)
if (d < peri_trunkl) { // for distances close to the parent trunk section keep trunk values
Ra = Ra_default
gkabar_kap(x) = trunk_kap
gkabar_kad(x) = trunk_kad
gbar_h(x) = trunk_h
g_pas(x) = trunk_pas
//gcabar_car(x) = trunk_car
gcalbar_calH(x) = trunk_calH
gcatbar_cat(x) = trunk_cat
gbar_kca(x) = trunk_kca
gkbar_mykca = mykca_init
gbar_km(x) = trunk_km
gnabar_nap(x) = trunk_nap
ar2_hha_old(x) = trunk_ar2_hha_old
} else { // for further distances set conductances to apical_dendrite[46] values (or a multiple)
gkabar_kap(x) = hold_kap
gkabar_kad(x) = 1.25*hold_kad
gbar_h(x) = hold_h
g_pas(x) = hold_g_pas
Ra = Ra_default
//gcabar_car(x) = hold_car
gcalbar_calH(x) = hold_calH
gcatbar_cat(x) = hold_cat
ar2_hha_old(x) = 0.8*hold_ar2_hha_old // set to 80% of dend. 46 value
gbar_kca(x) = hold_kca
gkbar_mykca = 1.1*mykca_init
gnabar_nap(x) = hold_nap
gbar_km(x) = 2*hold_km // set to 2 times the dend 46 value
if (xdist > 300 ) { // for xdist > 300 um increase:
gkabar_kad(x) = 1.3*1.9*hold_kad // A-current,
//gcabar_car(x) = 13*hold_car // Ca++-R current,
gcalbar_calH(x) = 14*hold_calH // Ca++-L current,
gbar_kca(x) = 5*soma_kca // slow AHP current
gkbar_hha_old(x) = 1.07*hold_kdr // delayed rectifier
}
if (xdist > 350) { // for xdist > 350 um increase even more:
gcalbar_calH(x)=15*hold_calH // Ca++-L current,
//gcabar_car(x) = 13*hold_car // Ca++-R current,
ar2_hha_old(x) = 0.95 // less spike attenuation
gnabar_nap(x)=2*hold_nap // Na+ persistent
}
}
}
}
sec_count=sec_count+1
}
}
}
/* Setting conductance values in all basal dendrites to be the
same as the values in apical_dendrite[14], except for the A
current conductance which is 0.6 times higher.
*/
proc khbasal_fixed() { local i,x,d
$o1.defvar("channel:basal", "khsection", "\"apical_dendrite[14]\"", "Trunk section used for basal conductance values")
sprint($o1.tmp_str,"%s { hold_g_pas=g_pas(1) hold_kap=gkabar_kap(1) hold_kad=gkabar_kad(1) hold_h=gbar_h(1)}", khsection)
execute1($o1.tmp_str)
forsec basal_tree_list {
insert kap
insert kad
insert h
insert pas
for (x) {
gkabar_kap(x) = 1.6*hold_kap
gkabar_kad(x) = 1.6*hold_kad
gbar_h(x) = soma_hbar
g_pas(x) = hold_g_pas
Ra = Ra_default
e_pas = v_init
ek = -80
}
}
}
/* The Na channels developed Mel and modified by Brannon,
Poirazi (hha2 and hha_old) both reduce activation as function
of voltage. In other words, they show actvity-dependent
attenuation of conductance. Within both of these mechanisms,
ar2 ([0..1]) is used to inversely describe the intensity of
voltage-dependent attenuation. 0 is maximum attenuation, 1 is
no attenuation.
Within the cell model, we vary the amount of attenuation along
the apical trunk as a function of distance from the cell body
such that proximal sections show little attenuation and distal
sections show comparably more (with the exception of distal
obliques).
We typically decay ar2 linearly from proximal to distal with
the maximum and minimum values of decay as
parameters. Initialize these parameters:
*/
max_ar2=0
min_ar2=0
decay_start=0 /* The distance at which decay starts.
The distance at which decay ends.
*/
decay_end=0
strdef ar24_tmp_str
objref strobj, ar24_f
strobj=new StringFunctions()
ar2_firsttime=1
proc ar2_log() {
if (!ar2_firsttime) { return }
ar24_f=new File()
sprint($o3.tmp_str3, "%s/ar2_log", $o3.generic_dir)
ar24_f.wopen($o3.tmp_str3)
ar24_f.printf("%s:",$s1)
while (strobj.substr($s2, "*") > -1) {
//printf("substr:%d\n", strobj.substr($s2, "*"))
index=strobj.head($s2, "\\*", ar24_tmp_str)
//printf("index:%d\n", index)
strobj.right($s2, 1+index)
//printf("%s ... %s \n", ar24_tmp_str, $s2)
$o3.create_variable("ar24_val", ar24_tmp_str)
ar24_f.printf("%s:%g:", ar24_tmp_str, ar24_val)
//printf("%s:%g", ar24_tmp_str, ar24_val)
}
$o3.create_variable("ar24_val", $s2)
ar24_f.printf("%s:%g\n", $s2, ar24_val)
//printf("%s:%g\n", $s2, ar24_val)
ar24_f.close()
ar2_firsttime=0
}
/*______ END OF PROCEDURES ROUTINELY USED IN CELL SETUP______*/
/* ____________ CELL SET-UP PROCEDURE _____________ */
maximum_segment_length=25
strdef sectype
proc cell_setup() {
// Set passive membrane properties
$o1.defvar("passive", "Rm_default", "200000","Specific membrane resistance. ")
$o1.defvar("passive", "Rm_trunk", "Rm_default","Non-oblique dendritic specific membrane resistance.")
$o1.defvar("passive", "Rm_non_trunk", "Rm_default","Apical oblique specific membrane resistance.")
$o1.defvar("passive", "Rm_basal", "Rm_default","Basal specific membrane resistance.")
$o1.defvar("passive", "Rm_tip", "Rm_default","Tip specific membrane resistance.")
$o1.defvar("passive", "Rm_soma", "Rm_default", "Somatic specific membrane resistance.")
$o1.defvar("passive", "Rm_axon", "Rm_default", "Axonal specific membrane resistance. ")
$o1.defvar("passive", "Ra_default", "50","Specific axial resistance. ")
$o1.defvar("passive", "Ra_basal", "Ra_default","Basal specific axial resistance.")
$o1.defvar("passive", "Ra_trunk", "Ra_default","Somatic specific axial resistance.")
$o1.defvar("passive", "Ra_non_trunk","Ra_default","Somatic specific axial resistance.")
$o1.defvar("passive", "Ra_soma", "Ra_default","Somatic specific axial resistance.")
$o1.defvar("passive", "Ra_tip", "Ra_default","Apical tip specific axial resistance.")
$o1.defvar("passive", "Ra_axon", "Ra_default","Axonal specific axial resistance. ")
$o1.defvar("passive", "Cm_default", "1","Default specific capacitance.")
$o1.defvar("passive", "Cm_axon", "Cm_default","Axonal specific capacitance. ")
$o1.defvar("passive", "Cm_soma", "Cm_default","Somatic specific capacitance. ")
$o1.defvar("passive", "Cm_trunk", "Cm_default","Trunk specific capacitance.")
$o1.defvar("passive","Cm_non_trunk", "Cm_default","Oblique specific capacitance.")
$o1.defvar("passive", "Cm_basal", "Cm_default","Basal specific capacitance.")
$o1.defvar("passive", "Cm_tip", "Cm_default","Apical tip specific capacitance.")
$o1.defvar("general", "v_init", "-70","Initial voltage of sections.")
// SEVERELY affects experiment results
$o1.defvar("general", "celsius", "34","Temperature of slice.")
// Set HH Sodium - Potassium properties
$o1.defvar("channel:na", "gna_default", "0.007", "Default Na conductance.")
$o1.defvar("channel:na", "gna_trunk", "gna_default", "Trunk Na conductance. ")
$o1.defvar("channel:na", "trunk_non_trunk_ratio", "1.0", "Non-trunk Na conductance ratio")
$o1.defvar("channel:na", "gna_non_trunk", "trunk_non_trunk_ratio*gna_default", "Non-trunk Na conductance")
$o1.defvar("channel:na", "gna_tip", "gna_non_trunk", "Oblique Tip Na conductance.")
$o1.defvar("channel:na", "gna_basal", "gna_default", "Basal Na conductance.")
$o1.defvar("channel:na", "gna_axon", "0.1", "Axonal Na conductance. ")
$o1.defvar("channel:na", "gna_soma", "gna_default", "Somatic Na conductance. ")
// Set delayed rectifier properties as a percent of Na conductances
$o1.defvar("channel:na-kdr", "kdr_div", "10.0/1.24", "Default ratio of Na to kdr conductances")
$o1.defvar("channel:na-k", "kdr_div_soma", "10.0/2.0", " Soma Na-kdr divider")
$o1.defvar("channel:na-k", "kdr_div_axon", "kdr_div_soma", " Axon Na-kdr divider")
$o1.defvar("channel:na-k", "kdr_div_trunk", "kdr_div"," Trunk Na-kdr divider")
$o1.defvar("channel:na-k", "kdr_div_non_trunk", "kdr_div", "Non-trunk Na-kdr divider")
$o1.defvar("channel:na-k", "kdr_div_tip", "kdr_div", "Oblique Tips Na-kdr divider")
$o1.defvar("channel:na-k", "kdr_div_basal", "kdr_div", "Basal Na-kdr divider")
// Set delayed rectifier conductances
$o1.defvar("channel:kdr", "gkdrbar_default", "gna_default/kdr_div", "Default KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_axon", "gna_axon/kdr_div_axon", "Axonal KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_basal", "gna_basal/kdr_div_basal","Basal KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_soma", "gna_soma/kdr_div_soma", "Somatic KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_trunk", "gna_trunk/kdr_div_trunk", "Trunk KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_non_trunk", "gna_non_trunk/kdr_div_non_trunk", "Non-Trunk KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_tip", "gna_tip/kdr_div_tip", "Oblique Tip KDR conductance. ")
$o1.defvar("channel:kdr", "gkdrbar_basal", "gna_basal/kdr_div_basal", "Basal KDR conductance. ")
$o1.xopen_library("Terrence","cut-sections")
cut_sections(maximum_segment_length)
// make 3-d mapping of cell sections
$o1.xopen_library("Terrence","map-segments-to-3d")
map_segments_to_3d()
// prepare to make a graph with cell configuration
$o1.tmpo2=new Shape()
// Set initial conductance values
soma_caL = 0.014
//soma_car = 0.0003
//gsomacar = 0.003
soma_caLH =0.95*0.000333
soma_caT = 0.0001
soma_kca = 0.0001
soma_km = 0.06
mykca_init = 1.1*0.015*3
soma_hbar = 1.872e-5
soma_kap = 0.0075
kad_init = 1.04*0.0072
// Start inserting mechanisms in cell
sectype ="soma"
forsec "soma" {
insert hha2 // HH mechanism with low threshold for Na spikes (-57 mV)
gnabar_hha2 = gna_soma
gkbar_hha2 = gkdrbar_soma
gl_hha2 = 0
el_hha2 = v_init
ena = 50
insert pas // leak conductance
g_pas = 1/Rm_soma
e_pas = v_init
Ra = Ra_soma
insert h // h current
gbar_h = soma_hbar
K_h = 8.8
vhalf_h = -82
insert kap // proximal A current
gkabar_kap = soma_kap
ek = -80
insert km // m-type potassium current
gbar_km = soma_km
ek = -80
insert cal // HVA Ca++-L type current
gcalbar_cal = soma_caL/2
insert cat // LVA Ca++-T type current
gcatbar_cat = soma_caT/2
//insert somacar // HVAm Ca++-R type current
// gcabar_somacar = gsomacar
insert kca // K(Ca) sAHP potassium type current
gbar_kca = 5*soma_kca
insert mykca // K(Ca) mAHP potassium type current
gkbar_mykca = 5.5*mykca_init
insert cad // calcium pump/buffering mechanism
$o1.tmpo2.color(2)
}
// Configure Axon
sectype="axon"
forsec axon_sec_list {
insert hha2 // HH mechanism with low threshold for Na spikes (-57 mV)
gnabar_hha2 = gna_axon
gkbar_hha2 = gkdrbar_axon
gl_hha2 = 0
el_hha2 = v_init
ena = 50
insert pas // leak conductance
g_pas = 1/Rm_axon
e_pas = v_init
Ra = Ra_axon
cm = Cm_axon
insert km // m-type potassium current
gbar_km = 0.5*soma_km
ek = -80
$o1.tmpo2.color(1)
}
// Configure apical trunk
forsec apical_trunk_list {
apical_h_insert_sig($o1) // Inserting h-current
apical_caR_caLH_insert($o1) // Inserting Ca++ R-type and Ca++ L-type currents
apical_caT_insert($o1) // Inserting Ca++ T-type current
apical_kca_insert($o1) // Inserting K(Ca) sAHP and mAHP potassium currents
apical_km_insert($o1) // Inserting m-type potassium current
A_insert($o1) // Inserting A-current
insert hha_old // HH mechanism with high threshold for Na spikes (-50 mV)
gnabar_hha_old = gna_trunk
gkbar_hha_old = gkdrbar_trunk
ena = 50
insert pas // leak conductance
e_pas = v_init
el_hha_old = v_init
Ra = Ra_trunk
cm = Cm_trunk
Rm_sigmoid($o1) // configure Rm along apical trunk
Ra_sigmoid($o1) // configure Ra along apical trunk
$o1.tmpo2.color(4)
// Set the Na+ spike attenuation variable (linearly decreasing from soma to 300 um)
$o1.defvar("channel:na", "max_ar2", "0.95", "Somatic value of ar2")
$o1.defvar("channel:na", "min_ar2", "0.30", "Minimum value of ar2")
$o1.defvar("channel:na", "decay_end", "300.0", "Distance beyond which all values are min_ar2")
$o1.defvar("channel:na", "decay_start", "50.0", "Distance at which ar2 starts to decrease")
m_ar2 = (max_ar2 - min_ar2)/(decay_start - decay_end)
for (x) {
xdist = find_vector_distance_precise(secname(),x)
if (xdist < decay_start) {
ar2_hha_old(x) = max_ar2
} else if (xdist > decay_end) {
ar2_hha_old(x) = min_ar2
} else {
// ar2_hha_old(x) = max_ar2 + m_ar2*xdist
ar2_hha_old(x) = max_ar2 + m_ar2*(xdist - decay_start)
}
}
ar2_log("linear", "min_ar2*max_ar2*m_ar2*decay_start*decay_end",$o1)
}
// Configure the apical-non-trunk section: insert basic mechanisms
sectype = "apical non-trunk"
forsec apical_non_trunk_list {
insert hha_old // HH mechanism with high threshold for Na spikes (-50 mV)
gnabar_hha_old = gna_non_trunk
gkbar_hha_old = gkdrbar_non_trunk
el_hha_old = v_init
ena = 50
insert pas // passive properties
g_pas = 1/Rm_non_trunk
e_pas = v_init
Ra = Ra_non_trunk
cm = Cm_non_trunk
$o1.tmpo2.color(3)
}
khoblique_peri_decay($o1) // Configure the apical oblique dendrites
// Configure the basal dendrites
sectype = "basal tree"
forsec basal_tree_list {
insert hha_old // HH mechanism with high threshold for Na spikes (-50 mV)
gnabar_hha_old = gna_basal
gkbar_hha_old = gkdrbar_basal
el_hha_old = v_init
gl_hha_old = 0
insert pas // passive properties
g_pas = 1/Rm_basal
e_pas = v_init
Ra = Ra_basal
cm = Cm_basal
insert kap // Insert proximal A current
gkabar_kap = 2.5*soma_kap
Ra_sigmoid($o1) // configure Ra
$o1.tmpo2.color(5)
}
khbasal_fixed($o1) // Configure basal dendrites
forsec "soma" { g_pas=1/Rm_soma } // force Rm at all soma sections
forall if (ismembrane("hha_old")) { // zero out gl (leak conductance) since g_pass is taking its place
gl_hha_old = 0
ek = -80
}
forall if (ismembrane("hha2")) { // zero out gl (leak conductance) since g_pass is taking its place
gl_hha2 = 0
ek = -80
}
forall if(ismembrane("ca_ion")) {
eca = 140
ion_style("ca_ion",0,1,0,0,0)
vshift_ca = 0
}
// Account for spines (obsolete in this case)
forall {
for (x) {
if (x > 0 && x < 1) {
diam(x)=diam(x)*1.0
}
}
}
// Print a postcript file in the generic directory with the cell configuration
// sprint($o1.tmp_str2, "%s/configure_sections.eps", $o1.generic_dir)
// $o1.tmpo2.printfile($o1.tmp_str2)
// Comment FM: current-balance forces e_pas to arbitrarily low values, which produces paradoxical results e.g. if ih conductances are increased. Switched off for this simulation, resulting in a resting membrane potential of ~-68mV.
// $o1.xopen_library("Terrence","current-balance") // balance current to -70 mV
// current_balance(v_init)
}
proc init() {
finitialize(v_init)
fcurrent()
}