// P6RSacell3D.p
// Format of file :
// x,y,z,dia are in microns, all other units are SI (Meter Kilogram Sec Amp)
// In polar mode 'r' is in microns, theta and phi in degrees
// Control line options start with a '*'
// The format for each compartment parameter line is :
//name parent r theta phi d ch dens ...
//in polar mode, and in cartesian mode :
//name parent x y z d ch dens ...
// For channels, "dens" = maximum conductance per unit area of compartment
// For spike elements, "dens" is the spike threshold
// Coordinate mode
*absolute
*relative
*cartesian
*asymmetric
*set_global RM 0.3333333
*set_global EREST_ACT -0.07
*set_compt_param ELEAK -0.0594
// Specifying constants
*set_compt_param RM 5.0 //0.33333
*set_compt_param RA 2.50 //0.3
*set_compt_param CM 0.009 //0.01
*set_compt_param ELEAK -0.0666 // -0.068
//SOMA *************************************************************
// For the soma, use the leakage potential (-0.07 + 0.0106) for Em
//*set_compt_param ELEAK -0.0594
// Actually, after Traub et al. J Neurophys 2003;89:909-921, will maintain
soma none 0 0 15 16 Ca_s13 -2.58626798e15 NaF13 2000 \
NaP13 0.8 KDR13 1700 \
KA13 1190 K213 1.0 \
KM13 42 CaL13 1.0 \
CaH13 2.0 KCs13 150 \
AR13 2.5 KAHPs13 2.0
*set_compt_param RA 2.5
*set_compt_param CM 0.018
*set_compt_param ELEAK -0.0666
*set_compt_param RM 2.5
//APICAL DENDRITE COMPARTMENTS ***************************************
// apdend1 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend1 soma 0 0 50 3 Ca_d13 -1.65521236e17 NaF13 3000 \
NaP13 1.2 KDR13 2400 \
KA13 2380 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apdend2 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend2 apdend1 0 0 50 2.8 Ca_d13 -1.88092836e17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 4 \
CaH13 2 KCd13 300 \
AR13 5 KAHPd13 4.0
// apdend3 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend3 apdend2 0 0 50 2.8 Ca_d13 -2.22818969E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend4 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend4 apdend3 0 0 50 2.6 Ca_d13 -2.22818969e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend5 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend5 apdend4 0 0 50 2.40 Ca_d13 -2.41385133e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend6 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend6 apdend5 0 0 50 2 Ca_d13 -3.31042301e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 40 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend7 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend7 apdend6 0 0 50 1.8 Ca_d13 -3.67824744e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 40 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend8 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend8 apdend7 0 0 50 1.6 Ca_d13 -4.1380285e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 40 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend9 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend9 apdend8 0 0 50 1.4 Ca_d13 -5.32033542e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 40 KCd13 0 \
AR13 5 KAHPd13 4.0
// apdend10 Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apdend10 apdend9 0 0 40 1.2 Ca_d13 -6.8967142e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 40 KCd13 0 \
AR13 5 KAHPd13 4.0
//APICAL OBLIQUE DENDRITE COMPARTMENTS ***************************************
// apobdistRa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobdistRa apdend3 42.4 42.4 0 1.24 Ca_d13 -6.1180627e17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apobdistRb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobdistRb apobdistRa 42.4 42.4 0 1.24 Ca_d13 -6.1180971e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobdistRc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobdistRc apobdistRb 42.4 42.4 0 1.24 Ca_d13 -6.1180994e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobdistLa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobdistLa apdend3 -42.4 -42.4 0 1.24 Ca_d13 -6.1180627e17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apobdistLb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobdistLb apobdistLa -42.4 -42.4 0 1.24 Ca_d13 -6.11809714e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobdistLc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobdistLc apobdistLb -42.4 -42.4 0 1.24 Ca_d13 -6.1180994e17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobmidRa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobmidRa apdend2 42.4 -42.4 0 1.24 Ca_d13 -6.1180483E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apobmidRb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobmidRb apobmidRa 42.4 -42.4 0 1.24 Ca_d13 -6.118106E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobmidRc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobmidRc apobmidRb 42.4 -42.4 0 1.24 Ca_d13 -6.1179686E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobmidLa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobmidLa apdend2 -42.4 42.4 0 1.24 Ca_d13 -6.1180483E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apobmidLb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobmidLb apobmidLa -42.4 42.4 0 1.24 Ca_d13 -6.118106E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobmidLc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobmidLc apobmidLb -42.4 42.4 0 1.24 Ca_d13 -6.1179686E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobproxRa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobproxRa apdend1 42.4 42.4 0 1.24 Ca_d13 -6.1180297E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apobproxRb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobproxRb apobproxRa 42.4 42.4 0 1.24 Ca_d13 -6.118106E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobproxRc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobproxRc apobproxRb 42.4 42.4 0 1.24 Ca_d13 -6.1181232E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobproxLa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobproxLa apdend1 -42.4 -42.4 0 1.24 Ca_d13 -6.1180297E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// apobproxLb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobproxLb apobproxLa -42.4 -42.4 0 1.24 Ca_d13 -6.118106E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// apobproxLc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
apobproxLc apobproxLb -42.4 -42.4 0 1.24 Ca_d13 -6.118106E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
*set_compt_param RA 2.5
*set_compt_param CM 0.018
*set_compt_param ELEAK -0.0666
*set_compt_param RM 2.5
//BASAL DENDRITE COMPARTMENTS ************************************************
// basalLsupera Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalLsupera soma -26.8 -46.4 -27.2 1.7 Ca_d13 -4.05689382E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// basalLsuperb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalLsuperb basalLsupera -26.8 -46.4 -27.2 1.7 Ca_d13 -4.05691135E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalLsuperc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalLsuperc basalLsuperb -26.8 -46.4 -27.2 1.7 Ca_d13 -4.05691135E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 136 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalLmida Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalLmida soma -19.3 33.4 -46.0 1.7 Ca_d13 -4.05689382E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// basalLmidb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalLmidb basalLmida -19.3 33.4 -46.0 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalLmidc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalLmidc basalLmidb -19.3 33.4 -46.0 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalRsupera Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalRsupera soma 26.8 46.4 -27.2 1.7 Ca_d13 -4.05689382E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 200 \
AR13 5 KAHPd13 4.0
// basalRsuperb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalRsuperb basalRsupera 26.8 46.4 -27.2 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalRsuperc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalRsuperc basalRsuperb 26.8 46.4 -27.2 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalRmida Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalRmida soma 19.3 -33.4 -46.0 1.7 Ca_d13 -4.05689382E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// basalRmidb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalRmidb basalRmida 19.3 -33.4 -46.0 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basalRmidc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basalRmidc basalRmidb 19.3 -33.4 -46.0 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basaldeepa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basaldeepa soma 0 0 -60.0 1.7 Ca_d13 -4.05689382E17 NaF13 1500 \
NaP13 0.6 KDR13 1500 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 300 \
AR13 5 KAHPd13 4.0
// basaldeepb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basaldeepb basaldeepa 0 0 -60.0 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// basaldeepc Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
basaldeepc basaldeepb 0 0 -60.0 1.7 Ca_d13 -4.05689382E17 NaF13 100 \
NaP13 0.04 KDR13 0 \
KA13 272 K213 2 \
KM13 84 CaL13 2 \
CaH13 4 KCd13 0 \
AR13 5 KAHPd13 4.0
// Specifying constants for axonal compartment RMCM=0.0024 (0.0009)
*set_compt_param RM 0.10 //(0.1)
*set_compt_param RA 1.00 //(1.00)
*set_compt_param CM 0.009 //(0.009)(0.024)
*set_compt_param ELEAK -0.0666
//AXONAL COMPARTMENTS ***************************************
// axona Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
// Differs from Traub et al., in that axon is vertical
axona soma 0 0 -25 1.8 NaF13 4500 \
KDR13 4500 \
KA13 40 K213 1
// axonb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
// Differs from Traub et al., in that axon is vertical
axonb axona 0 0 -50 1.8 NaF13 4500 \
KDR13 4500 \
KA13 40 K213 1
// axonLa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
// Differs from Traub et al., in that axon is vertical
axonLa axonb -8.7 0 -49.2 1.8 NaF13 4500 \
KDR13 4500 \
KA13 40 K213 1
// axonLb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
// Differs from Traub et al., in that axon is vertical
axonLb axonLa -8.7 0 -49.2 1.8 NaF13 4500 \
KDR13 4500 \
KA13 40 K213 1
// axonRa Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
// Differs from Traub et al., in that axon is vertical
axonRa axonb 8.7 0 -49.2 1.8 NaF13 4500 \
KDR13 4500 \
KA13 40 K213 1
// axonRb Fig A6 Traub et al. J. Neurophysiol 2005;93:2194-2232
// Differs from Traub et al., in that axon is vertical
axonRb axonRa 8.7 0 -49.2 1.8 NaF13 4500 \
KDR13 4500 \
KA13 40 K213 1