COMMENT
**************************************************
File generated by: neuroConstruct v1.7.1
**************************************************
This file holds the implementation in NEURON of the Cell Mechanism:
Gran_CaPool_98 (Type: Ion concentration, Model: ChannelML based process)
with parameters:
/channelml/@units = SI Units
/channelml/notes = A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the Cerebellar Granul ...
/channelml/ion/@name = ca
/channelml/ion/@charge = 2
/channelml/ion/@role = SignallingSubstance
/channelml/ion/notes = Signifies that the ion is involved in a process which alters its concentration
/channelml/ion_concentration/@name = Gran_CaPool_98
/channelml/ion_concentration/status/@value = stable
/channelml/ion_concentration/status/comment = This ChannelML file has been updated to reflect the preferred form of elements/attributes which will be required from v2.0. See info on Version 2 Req ...
/channelml/ion_concentration/status/contributor/name = Padraig Gleeson
/channelml/ion_concentration/notes = An expontially decaying pool of calcium
/channelml/ion_concentration/publication/fullTitle = Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a Detailed Network Model of the cerebellar Granule Cell Layer. J Neu ...
/channelml/ion_concentration/publication/pubmedRef = http://www.ncbi.nlm.nih.gov/pubmed/9819260
/channelml/ion_concentration/ion_species/@name = ca
/channelml/ion_concentration/decaying_pool_model/@resting_conc = 7.55e-5
/channelml/ion_concentration/decaying_pool_model/@decay_constant = 1e-2
/channelml/ion_concentration/decaying_pool_model/pool_volume_info/@shell_thickness = 8.4e-8
// File from which this was generated: /home/Simon/NML2_Test/AOB_MC_neuroConstruct/cellMechanisms/Gran_CaPool_98/CaPool.xml
// XSL file with mapping to simulator: /home/Simon/NML2_Test/AOB_MC_neuroConstruct/cellMechanisms/Gran_CaPool_98/ChannelML_v1.8.1_NEURONmod.xsl
ENDCOMMENT
? This is a NEURON mod file generated from a ChannelML file
? Unit system of original ChannelML file: SI Units
COMMENT
A channel from Maex, R and De Schutter, E. Synchronization of Golgi and Granule Cell Firing in a
Detailed Network Model of the Cerebellar Granule Cell Layer
ENDCOMMENT
? Creating ion concentration
TITLE Channel: Gran_CaPool_98
COMMENT
An expontially decaying pool of calcium
ENDCOMMENT
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(um) = (micrometer)
(l) = (liter)
(molar) = (1/liter)
(mM) = (millimolar)
}
NEURON {
SUFFIX Gran_CaPool_98
USEION ca READ ica WRITE cai VALENCE 2
RANGE cai
RANGE rest_conc
RANGE tau
RANGE thickness, F
RANGE total_current
RANGE volume_pool
}
ASSIGNED {
ica (mA/cm2)
diam (um)
area (um)
}
INITIAL {
LOCAL pi, shell_inner_diam, cylinderLen, circumference, circumference_shell, volumeOuter, volumeInner, volumeSph, volumeCyl
pi = 3.14159265
shell_inner_diam = diam - (2*thickness)
? Volume of the pool if it is a shell inside a sphere of diameter diam
volumeSph = (diam*diam*diam) * pi / 6 - (shell_inner_diam*shell_inner_diam*shell_inner_diam)* pi / 6
? Volume of the pool if it is a cylinder
circumference = diam * pi
circumference_shell = shell_inner_diam * pi
cylinderLen = area/circumference
volumeOuter = (diam * diam/4) * pi * cylinderLen
volumeInner = (shell_inner_diam * shell_inner_diam/4) * pi * cylinderLen
volumeCyl = volumeOuter - volumeInner
if ((area - (pi * diam * diam)) < 1e-3 && (area - (pi * diam * diam)) > -1e-3 ) {
? Assume the segment is a sphere
volume_pool = volumeSph
} else {
? assume segment is a cylinder
volume_pool = volumeCyl
}
cai = rest_conc
}
PARAMETER {
total_current
rest_conc = 0.0000755 (mM)
tau = 10 (ms)
F = 96494 (C)
thickness = 0.08399999999999999 (um)
volume_pool
}
STATE {
cai (mM)
}
BREAKPOINT {
SOLVE conc METHOD derivimplicit
}
DERIVATIVE conc {
LOCAL thickness_cm, surf_area_cm2, volume_cm3 ? Note, normally dimensions are in um, but curr dens is in mA/cm2, etc
thickness_cm = thickness *(1e-4)
surf_area_cm2 = area * 1e-8
volume_cm3 = volume_pool * 1e-12
total_current = ica * surf_area_cm2
cai' = ((-1 * total_current)/(2 * F * volume_cm3)) - ((cai - rest_conc)/tau)
}
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