COMMENT
26 Ago 2002 Modification of original channel to allow variable time
step and to correct an initialization error.
Done by Michael Hines(michael.hines@yale.e) and Ruggero
Scorcioni(rscorcio@gmu.edu) at EU Advance Course in Computational
Neuroscience. Obidos, Portugal
11 Jan 2007
Glitch in trap where (v/th) was where (v-th)/q is. (thanks Ronald
van Elburg!)
na.mod
Sodium channel, Hodgkin-Huxley style kinetics.
Kinetics were fit to data from Huguenard et al. (1988) and Hamill et
al. (1991)
qi is not well constrained by the data, since there are no points
between -80 and -55. So this was fixed at 5 while the thi1,thi2,Rg,Rd
were optimized using a simplex least square proc
voltage dependencies are shifted approximately from the best
fit to give higher threshold
Author: Zach Mainen, Salk Institute, 1994, zach@salk.edu
20150512 NTC
Cleaned code up a bit.
Made threadsafe and replaced vtrap0 with efun,
which is a better approximation in the vicinity of a singularity.
See na.mod in ModelDB entry 2488.
Special comment:
This mechanism borrowed heavily from na.mod in ModelDB entry 2488.
That code, which was intended to be used only at 37 deg C
(see comments from 20120514 in that file),
calculated ionic conductance as the product
g = tadj*gbar*product_of_gating_variables
where
tadj = q10^((celsius - temp)/10)
temp is the "reference temperature" (at which the gating variable
time constants were originally determined)
celsius is the "operating temperature"
This deviates from the standard HH formula
g = gbar*product_of_gating_variables
and has the unfortunate consequence of not only making the
effective channel density differ from the nominal (i.e. user-assigned)
channel density, but it would also make the effective channel density
depend on temperature!
Sooner or later this is guaranteed to confound studies of the effects
of temperature on model operation.
It would also be a debugging nightmare, not least because
the ModelView tool--so handy for discovering the properties of a
model and verifying a close match between the computational model
and the conceptual model--would report the NOMINAL channel density,
not the effective channel density.
To eliminate this problem, every statement of the form
g = tadj*gbar*gating variables
has been replaced by
g = gbar*gating variables
Furthermore, the numerical value assigned to gbar,
whether by an assignment statement in the PARAMETER block
or by a hoc or Python statement,
must now use the actual conductance density.
For this particular mechanism, tadj at 37 deg C is 3.20936
so the actual conductance density is 3.20936 times
the nominal conductance density.
ENDCOMMENT
NEURON {
THREADSAFE
SUFFIX na
USEION na READ ena WRITE ina
RANGE m, h, gna, gbar
GLOBAL tha, thi1, thi2, qa, qi, qinf, thinf
RANGE minf, hinf, mtau, htau
GLOBAL Ra, Rb, Rd, Rg
GLOBAL q10, temp, tadj, vmin, vmax, vshift
}
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(pS) = (picosiemens)
(um) = (micron)
}
PARAMETER {
: this assignment doesn't matter
: if it is overridden by assignments in hoc or Python
gbar = 1000 (pS/um2) : 0.1 mho/cm2
vshift = -5 (mV) : voltage shift (affects all)
tha = -43 (mV) : v 1/2 for act (-42)
qa = 7 (mV) : act slope
Ra = 0.182 (/ms) : open (v)
Rb = 0.124 (/ms) : close (v)
thi1 = -50 (mV) : v 1/2 for inact
thi2 = -75 (mV) : v 1/2 for inact
qi = 5 (mV) : inact tau slope
thinf = -72 (mV) : inact inf slope
qinf = 6.2 (mV) : inact inf slope
Rg = 0.0091 (/ms) : inact (v)
Rd = 0.024 (/ms) : inact recov (v)
temp = 23 (degC) : original temp
q10 = 2.3 : temperature sensitivity
: v (mV)
: dt (ms)
: celsius (degC)
vmin = -120 (mV)
vmax = 100 (mV)
}
ASSIGNED {
v (mV)
celsius (degC)
a (/ms)
b (/ms)
ina (mA/cm2)
gna (pS/um2)
ena (mV)
minf hinf
mtau (ms) htau (ms)
tadj
}
STATE { m h }
INITIAL {
: since tadj is a per-thread GLOBAL
: all threads must calculate its value at initialization
tadj = q10^((celsius - temp)/(10 (degC)))
trates(v+vshift)
m = minf
h = hinf
}
BREAKPOINT {
SOLVE states METHOD cnexp
: gna = tadj*gbar*m*m*m*h
gna = gbar*m*m*m*h
ina = (1e-4) * gna * (v - ena)
}
: LOCAL mexp, hexp
DERIVATIVE states { :Computes state variables m and h
trates(v+vshift) : at the current v
m' = (minf-m)/mtau
h' = (hinf-h)/htau
: m = m + mexp*(minf-m)
: h = h + hexp*(hinf-h)
}
PROCEDURE trates(v (mV)) {
TABLE minf, hinf, mtau, htau
DEPEND celsius, temp, Ra, Rb, Rd, Rg, tha, thi1, thi2, qa, qi, qinf
FROM vmin TO vmax WITH 199
rates(v): not consistently executed from here if usetable == 1
: tadj = q10^((celsius - temp)/10)
: tinc = -dt * tadj
: mexp = 1 - exp(tinc/mtau)
: hexp = 1 - exp(tinc/htau)
}
UNITSOFF
PROCEDURE rates(vm (mV)) {
: LOCAL a, b
: a = trap0(vm,tha,Ra,qa)
: b = trap0(-vm,-tha,Rb,qa)
a = Ra*qa*efun((tha-vm)/qa)
b = Rb*qa*efun((vm-tha)/qa)
tadj = q10^((celsius - temp)/(10 (degC)))
mtau = 1/tadj/(a+b)
minf = a/(a+b)
: mtau = 1/(a+b)
: minf = a*mtau
:"h" inactivation
: a = trap0(vm,thi1,Rd,qi)
: b = trap0(-vm,-thi2,Rg,qi)
a = Rd*qi*efun((thi1-vm)/qi)
b = Rg*qi*efun((vm-thi2)/qi)
htau = 1/tadj/(a+b)
hinf = 1/(1+exp((vm-thinf)/qinf))
: htau = 1/(a+b)
: hinf = 1/(1+exp((vm-thinf)/qinf))
}
COMMENT
FUNCTION trap0(v,th,a,q) {
: if (fabs(v/th) > 1e-6) {
if (fabs((v-th)/q) > 1e-6) {
trap0 = a * (v - th) / (1 - exp(-(v - th)/q))
} else {
trap0 = a * q
}
}
ENDCOMMENT
FUNCTION efun(z) {
if (fabs(z) < 1e-6) {
efun = 1 - z/2
}else{
efun = z/(exp(z) - 1)
}
}
UNITSON