// nRTcell.p - Cell parameter file
// 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
*relative
*cartesian
*asymmetric
// Specifying constants
*set_compt_param RM 2.0 // (2.50)
*set_compt_param RA 2.50 // (2.00)
*set_compt_param CM 0.01 // (0.01)
*set_compt_param EREST_ACT -0.088 // -0.090
*set_compt_param ELEAK -0.0666
//SOMA *************************************************************
// For the soma, use the leakage potential (-0.07 + 0.0106) for Em
//*set_compt_param ELEAK -0.0594
// Actually, after Cunningham et al. PNAS 2004;101:7152-7157, will maintain
// leakage potential at ELEAK -0.07
soma none 0 0 20 16.68 Ca_s21 -1.18144994E15 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPs21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCs21 100
*set_compt_param ELEAK -0.0666 //-0.075
*set_compt_param RM 2.0 // (2.50)
*set_compt_param RA 2.5 // (2.00)
*set_compt_param CM 0.01 // (0.01)
//PROXIMAL DENDRITE COMPARTMENTS ***************************************
// proxdendN Cunningham et al., PNAS 2004;101:7152-7157
proxdendN soma 0 0 75 2.12 Ca_d21 -6.2460809E15 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// proxdendE Cunningham et al., PNAS 2004;101:7152-7157
proxdendE soma 75 0 -10 2.12 Ca_d21 -6.2460809E15 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// proxdendS Cunningham et al., PNAS 2004;101:7152-7157
proxdendS soma 0 0 -75 2.12 Ca_d21 -6.2460809E15 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// proxdendW Cunningham et al., PNAS 2004;101:7152-7157
proxdendW soma -75 0 -10 2.12 Ca_d21 -6.2460809E15 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
*set_compt_param RM 2.0 // (2.50)
*set_compt_param RA 2.5 // (2.00)
*set_compt_param CM 0.01 // (0.01)
*set_compt_param ELEAK -0.0725
//North DISTAL DENDRITE COMPARTMENTS ***************************************
// distdendNlonga Cunningham et al., PNAS 2004;101:7152-7157
distdendNlonga proxdendN -25.6 0 70.5 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendNlongb Cunningham et al., PNAS 2004;101:7152-7157
distdendNlongb distdendNlonga -25.6 0 70.5 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNlongc Cunningham et al., PNAS 2004;101:7152-7157
distdendNlongc distdendNlongb -25.6 0 70.5 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNlongd Cunningham et al., PNAS 2004;101:7152-7157
distdendNlongd distdendNlongc -25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNlonge Cunningham et al., PNAS 2004;101:7152-7157
distdendNlonge distdendNlongd -25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNlongf Cunningham et al., PNAS 2004;101:7152-7157
distdendNlongf distdendNlonge -25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNlongg Cunningham et al., PNAS 2004;101:7152-7157
distdendNlongg distdendNlongf -25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNmida Cunningham et al., PNAS 2004;101:7152-7157
distdendNmida proxdendN 25.6 0 70.5 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendNmidb Cunningham et al., PNAS 2004;101:7152-7157
distdendNmidb distdendNmida 25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNmidc Cunningham et al., PNAS 2004;101:7152-7157
distdendNmidc distdendNmidb 25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNshorta Cunningham et al., PNAS 2004;101:7152-7157
distdendNshorta distdendNlonga 25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendNshortb Cunningham et al., PNAS 2004;101:7152-7157
distdendNshortb distdendNshorta 25.6 0 70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
//East DISTAL DENDRITE COMPARTMENTS ***************************************
// distdendElonga Cunningham et al., PNAS 2004;101:7152-7157
distdendElonga proxdendE 70.5 25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendElongb Cunningham et al., PNAS 2004;101:7152-7157
distdendElongb distdendElonga 70.5 25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendElongc Cunningham et al., PNAS 2004;101:7152-7157
distdendElongc distdendElongb 70.5 25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendElongd Cunningham et al., PNAS 2004;101:7152-7157
distdendElongd distdendElongc 70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendElonge Cunningham et al., PNAS 2004;101:7152-7157
distdendElonge distdendElongd 70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendElongf Cunningham et al., PNAS 2004;101:7152-7157
distdendElongf distdendElonge 70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendElongg Cunningham et al., PNAS 2004;101:7152-7157
distdendElongg distdendElongf 70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendEmida Cunningham et al., PNAS 2004;101:7152-7157
distdendEmida proxdendE 70.5 -25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendEmidb Cunningham et al., PNAS 2004;101:7152-7157
distdendEmidb distdendEmida 70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendEmidc Cunningham et al., PNAS 2004;101:7152-7157
distdendEmidc distdendEmidb 70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendEshorta Cunningham et al., PNAS 2004;101:7152-7157
distdendEshorta distdendElonga 70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendEshortb Cunningham et al., PNAS 2004;101:7152-7157
distdendEshortb distdendEshorta 70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
//South DISTAL DENDRITE COMPARTMENTS ***************************************
// distdendSlonga Cunningham et al., PNAS 2004;101:7152-7157
distdendSlonga proxdendS 25.6 0 -70.5 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendSlongb Cunningham et al., PNAS 2004;101:7152-7157
distdendSlongb distdendSlonga 25.6 0 -70.5 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSlongc Cunningham et al., PNAS 2004;101:7152-7157
distdendSlongc distdendSlongb 25.6 0 -70.5 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSlongd Cunningham et al., PNAS 2004;101:7152-7157
distdendSlongd distdendSlongc 25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSlonge Cunningham et al., PNAS 2004;101:7152-7157
distdendSlonge distdendSlongd 25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSlongf Cunningham et al., PNAS 2004;101:7152-7157
distdendSlongf distdendSlonge 25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSlongg Cunningham et al., PNAS 2004;101:7152-7157
distdendSlongg distdendSlongf 25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSmida Cunningham et al., PNAS 2004;101:7152-7157
distdendSmida proxdendS -25.6 0 -70.5 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendSmidb Cunningham et al., PNAS 2004;101:7152-7157
distdendSmidb distdendSmida -25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSmidc Cunningham et al., PNAS 2004;101:7152-7157
distdendSmidc distdendSmidb -25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSshorta Cunningham et al., PNAS 2004;101:7152-7157
distdendSshorta distdendSlonga -25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendSshortb Cunningham et al., PNAS 2004;101:7152-7157
distdendSshortb distdendSshorta -25.6 0 -70.5 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
//West DISTAL DENDRITE COMPARTMENTS ***************************************
// distdendWlonga Cunningham et al., PNAS 2004;101:7152-7157
distdendWlonga proxdendW -70.5 -25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendWlongb Cunningham et al., PNAS 2004;101:7152-7157
distdendWlongb distdendWlonga -70.5 -25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWlongc Cunningham et al., PNAS 2004;101:7152-7157
distdendWlongc distdendWlongb -70.5 -25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWlongd Cunningham et al., PNAS 2004;101:7152-7157
distdendWlongd distdendWlongc -70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWlonge Cunningham et al., PNAS 2004;101:7152-7157
distdendWlonge distdendWlongd -70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWlongf Cunningham et al., PNAS 2004;101:7152-7157
distdendWlongf distdendWlonge -70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWlongg Cunningham et al., PNAS 2004;101:7152-7157
distdendWlongg distdendWlongf -70.5 -25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWmida Cunningham et al., PNAS 2004;101:7152-7157
distdendWmida proxdendW -70.5 25.6 0.0 1.34 Ca_d21 -1.32416728E18 NaF21 600 \
NaP21 6 KDR21 600 \
KA21 50 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 0.5 AR21 0.25\
CaH21 5 KCd21 100
// distdendWmidb Cunningham et al., PNAS 2004;101:7152-7157
distdendWmidb distdendWmida -70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWmidc Cunningham et al., PNAS 2004;101:7152-7157
distdendWmidc distdendWmidb -70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWshorta Cunningham et al., PNAS 2004;101:7152-7157
distdendWshorta distdendWlonga -70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// distdendWshortb Cunningham et al., PNAS 2004;101:7152-7157
distdendWshortb distdendWshorta -70.5 25.6 0.0 0.84 Ca_d21 -1.32417099E18 NaF21 100 \
NaP21 1 KDR21 100 \
KA21 10 KM21 5 \
K221 5 KAHPd21 1 \
CaL21 20 AR21 0.25\
CaH21 5 KCd21 100
// Specifying constants for axonal compartment
*set_compt_param RM 0.1 // (0.1)
*set_compt_param RA 1.0 // (1.0)
*set_compt_param CM 0.01 // (0.01) RC = 0.001
//*set_compt_param ELEAK -0.0666
// axona Fig 1. Traub et al., J Neurophysiol 2003;89:909-921
// Differs from Traub et al., in that axon is vertical
axona soma 0 0 -25 1.8 NaF21 4000 \
NaP21 0 \
KDR21 4000 \
KA21 10 \
K221 5
// axonb Fig 1. Traub et al., J Neurophysiol 2003;89:909-921
// Differs from Traub et al., in that axon is vertical
axonb axona 0 0 -75 1.4 NaF21 4000 \
NaP21 0 \
KDR21 4000 \
KA21 10 \
K221 5
// axonLa Fig 1. Traub et al., J Neurophysiol 2003;89:909-921
// Differs from Traub et al., in that axon is vertical
axonLa axonb -8.5 0 -124.0 1.2 NaF21 4000 \
NaP21 0 \
KDR21 4000 \
KA21 10 \
K221 5
// axonLb Fig 1. Traub et al., J Neurophysiol 2003;89:909-921
// Differs from Traub et al., in that axon is vertical
axonLb axonLa -17.0 0 -173.0 1.0 NaF21 4000 \
NaP21 0 \
KDR21 4000 \
KA21 10 \
K221 5
// axonRa Fig 1. Traub et al., J Neurophysiol 2003;89:909-921
// Differs from Traub et al., in that axon is vertical
axonRa axonb 8.5 0 -124.0 1.2 NaF21 4000 \
NaP21 0 \
KDR21 4000 \
KA21 10 \
K221 5
// axonRb Fig 1. Traub et al., J Neurophysiol 2003;89:909-921
// Differs from Traub et al., in that axon is vertical
axonRb axonRa 17.0 0 -173.0 1.0 NaF21 4000 \
NaP21 0 \
KDR21 4000 \
KA21 10 \
K221 5