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baseline_values.txt
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baseline_values.txt
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/**** This is from the Wolf et al. (2005) modelDB entry.
** Copied here to the Rumbell optimization code.
**
** cmw 9/1/16
**
*****/
//****************************************************************************
// These are the default parameters for creation of the MSP cell. This file
// is usually called by hoc/nacb_main.hoc
cai0_ca_ion = 0.001 // mM, Churchill 1998
cao0_ca_ion = 5 // mM, Churchill 1998 - gives eca = 100 mV
cali0_cal_ion = 0.001 // mM, Churchill 1998
calo0_cal_ion = 5 // mM, Churchill 1998 - gives eca = 100 mV
celsius = 34 // degC
global_ra = 100 // not really sure what this is
RA = 100 // ohm-cm - constant for whole cell
CM = 1 // uF-cm2 - constant for whole cell
G_PAS = 1.15e-5 // S/cm2
E_PAS = -70 // mV
G_NAF = 1.574293733 // soma only
G_NAF0=1.5
G_NAFD = 0.0195 // all dends
G_NAP = 0.000442277// soma only
G_NAP0=4e-05
G_NAPD = 1.3802e-7 // all dends, according to Wolf et al. paper
//G_NAPD = 1.3802e-6 // all dends -- CHANGED in Wolf modelDB entry
G_KIR = 0.0078159677 // S/cm2
G_KAS = 0.001027479 // soma & prox dends; s/cm2
G_KAS0=0.0104
G_KAF0=0.0225
G_KASD = 0.00095142 // mid & distal dends; S/cm2
G_KAF = 0.076646754 // soma & prox dends; S/cm2
G_KAFD = 0.020584 // mid & dist dends; S/cm2
G_BKKCA = 0.000201663 //
G_SKKCA = 0.015110434
G_KDR = 0.002534187
G_KDR_AIS = 0.008686058
G_NAF_AIS = 0.638380868 // different values allowed in axon initial segment
G_KAS_AIS = 0.053928332
G_KAF_AIS = 0.046105939
G_NAP_AIS = 0.005511567
CAINF = 1e-5 // mM, steady state intracell ca conc.
TAUR = 43 // ms, time const of ca diffusion - Jackson 2003
CA_DRIVE = 10000
CA_PUMP = 0.02
caNMDA = 0.1
P_CAL = 0.000010697 // cm/s
P_CAL13 = 0.000006685 //1.7e-6 // cm/s
P_CAN = 0.000000673 // cm/s
P_CAQ = 0 // cm/s
P_CAR = 0.000021257 // cm/s
P_CAT = 0.000000439 // cm/s 4e-7
newEK = -94
ENA = 50
HSHIFT_NAP = -10
MSHIFT_NAP = -10
MSHIFT_KAS = 2
HSHIFT_KAS = -15
MSHIFT_KAF = 0
HSHIFT_KAF = 0
HTAUSHIFT_KAS = -88
M1HALF_BK = -10
M2HALF_BK = -65
M3HALF_BK = -44
CELSIUS_SK_SKKCA = 22
NET_N = 1e10
G_AMPA = 8.5e-4 //350e-6 //8.81e-4
G_NMDA = 12.2e-5 // 9.2e-5
G_GABA = 0.0021 //4300e-6 //0.0027
AMPA_WT = 1
NMDA_WT = 1
GABA_WT = 1
NOISE = 1
NGLU = 84
NGABA = 84
NSYN = NGABA + NGLU
// factors for adding the Hay axon
CM_MYELINFAC = 0.02 // Hay myelin had cm=0.02, cm=1 in AIS/soma
AXON_MSHIFT = 10
AXON_HSHIFT = 5
AXON_MSLOPEFAC = 1.29 // Hay NaT m_slope was 9/mV in axon, 7/mV in soma
SOMA_MVHALF_NAF = -23.9
SOMA_MSLOPE_NAF = -11.8
SOMA_MSHIFT_NAF = 0
SOMA_HVHALF_NAF = -62.9
SOMA_HSLOPE_NAF = 10.7
SOMA_HSHIFT_NAF = 0
/****************************************************************************
//
// These values were optimized by Hanbing's runs on 3/18/17 (and followed up by christina), including the -170 and -220 pA injections, and optimizing the KIR kinetics. The morphology (dend, soma, axon) is updated, as is the EK value.
//
// Results emailed to me from Hanbing, run on redrocks.
{set_n_params(0.0000119053, -76.9833632311, 1.0997180745, 0.0081315679, 3.2975411649, 82.3722247792, 8.9016691371) set_params() }
************************************/
G_PAS = 0.0000319077
E_PAS = -81.607398
CM = 0.9021622
G_KIR = 0.00592857
QKIR = 0.24109102
SHKIR = 89.439483
SLPKIR = 11.8723217
//dgkaf = 0.0012340247
V0 = -80
P_CAQ = 0 // cm/s - turn this off, Evans excluded it.
// note, we will include NaP in this optimization due to the axon inclusion.