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Commit a89e9da9 authored by Benjamin Cumming's avatar Benjamin Cumming Committed by Sam Yates
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Remove unused data/ directory (#712)

* Remove data/ directory, contents as they are not used now in Arbor.
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TITLE hh.mod squid sodium, potassium, and leak channels
: COMMENT
: This is the original Hodgkin-Huxley treatment for the set of sodium,
: potassium, and leakage channels found in the squid giant axon membrane.
: ("A quantitative description of membrane current and its application
: conduction and excitation in nerve" J.Physiol. (Lond.) 117:500-544 (1952).)
: Membrane voltage is in absolute mV and has been reversed in polarity
: from the original HH convention and shifted to reflect a resting potential
: of -65 mV.
: Remember to set celsius=6.3 (or whatever) in your HOC file.
: See squid.hoc for an example of a simulation using this model.
: SW Jaslove 6 March, 1992
: ENDCOMMENT
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(S) = (siemens)
}
NEURON {
SUFFIX hh
USEION na READ ena WRITE ina
USEION k READ ek WRITE ik
NONSPECIFIC_CURRENT il
RANGE gnabar, gkbar, gl, el, gna, gk
GLOBAL minf, hinf, ninf, mtau, htau, ntau
}
PARAMETER {
gnabar = .12 (S/cm2) : <0,1e9>
gkbar = .036 (S/cm2) : <0,1e9>
gl = .0003 (S/cm2) : <0,1e9>
el = -54.3 (mV)
celsius = 37 (degC)
}
STATE {
m h n
}
ASSIGNED {
v (mV)
gna (S/cm2)
gk (S/cm2)
minf
hinf
ninf
mtau (ms)
htau (ms)
ntau (ms)
}
BREAKPOINT {
SOLVE states METHOD cnexp
gna = gnabar*m*m*m*h
ina = gna*(v - ena)
gk = gkbar*n*n*n*n
ik = gk*(v - ek)
il = gl*(v - el)
}
INITIAL {
rates(v)
m = minf
h = hinf
n = ninf
}
DERIVATIVE states {
rates(v)
m' = (minf-m)/mtau
h' = (hinf-h)/htau
n' = (ninf-n)/ntau
}
PROCEDURE rates(v) :(mV))
{
LOCAL alpha, beta, sum, q10
q10 = 3^((celsius - 6.3)/10)
:"m" sodium activation system
alpha = .1 * vtrap(-(v+40),10)
beta = 4 * exp(-(v+65)/18)
sum = alpha + beta
mtau = 1/(q10*sum)
minf = alpha/sum
:"h" sodium inactivation system
alpha = .07 * exp(-(v+65)/20)
beta = 1 / (exp(-(v+35)/10) + 1)
sum = alpha + beta
htau = 1/(q10*sum)
hinf = alpha/sum
:"n" potassium activation system
alpha = .01*vtrap(-(v+55),10)
beta = .125*exp(-(v+65)/80)
sum = alpha + beta
ntau = 1/(q10*sum)
ninf = alpha/sum
}
FUNCTION vtrap(x,y) {
: Traps for 0 in denominator of rate eqns.
: Disabled for function inlining...
: there is a very good case for making vtrap a builtin function for the language
: - it is ubiquitous: used in so many models of ion channels
: - platform specific optimizations written in assembly/intrinsics
: required to facilitate vectorization/minimize branch misses
:if (fabs(x/y) < 1e-6) {
: vtrap = y*(1 - x/y/2)
:}else{
: vtrap = x/(exp(x/y) - 1)
:}
vtrap = x/(exp(x/y) - 1)
}
TITLE passive membrane channel
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(S) = (siemens)
}
NEURON {
SUFFIX pas
NONSPECIFIC_CURRENT i
RANGE g, e
}
INITIAL {}
PARAMETER {
g = .001 (S/cm2) :<0,1e9>
e = -70 (mV)
}
ASSIGNED {
v (mV)
}
BREAKPOINT {
i = g*(v - e)
}
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