Transforming XML file: NeuroMLFiles/Examples/ChannelML/NaF2_Chan.xml using XSL file: NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1_HTML.xsl

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Converting the file: NaF2_Chan.xml

General notes
Notes present in ChannelML file
ChannelML file based on Traub et al. 2003

Unit system of ChannelML file
This can be either SI Units or Physiological Units (milliseconds, centimeters, millivolts, etc.)
Physiological Units

Channel: naf2

Status of element in file
Comment: Verified equivalence of NEURON and GENESIS mapping to orig NEURON mod impl at 0.02ms dt with current pulse
Issue: In original mod, m is initialised to 0, as opposed to minf at t=0. ChannelML impl corrects this
Issue: Comment in original mod file: hinf, and htau are shifted 3.5 mV compared to the paper
Contributor: Padraig Gleeson
As described in the ChannelML file
Fast Sodium transient (inactivating) current. Channel used in Traub et al 2005, slight modification of naf from Traub et al 2003. This example is used to illustrate the use of parameters in the generic expressions for the rates
Authors of original model:
   Maciej Lazarewicz   (Conversion of FORTRAN model to NEURON. See Traub et al 2003 for detailed origin of channels)
   Roger D Traub   (Conversion of FORTRAN model to NEURON. See Traub et al 2003 for detailed origin of channels)
Translators of the model to NeuroML:
   Padraig Gleeson  (UCL)  p.gleeson - at -
   Yoana Dimitrova  (UCL)
Referenced publicationRoger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels J Neurophysiol 89: 909-921, 2003 Pubmed
Referenced publicationRoger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. J. Neurophysiol. 93, 2194-2232, 2005 Pubmed
Reference in NeuronDB Na channels
Reference in ModelDB Mechanisms of fast rhythmic bursting in a layer 2/3 cortical neuron (Traub et al 2003)
Reference in ModelDB A single column thalamocortical network model (Traub et al 2005)
Current voltage relationshipohmic
Ion involved in channel
The ion which is actually flowing through the channel and its default reversal potential. Note that the reversal potential will normally depend on the internal and external concentrations of the ion at the segment on which the channel is placed.
na (default Ena = 50 mV)
Default maximum conductance density
Note that the conductance density of the channel will be set when it is placed on the cell.
Gmax = 0.1 mS cm-2
Conductance expression
Expression giving the actual conductance as a function of time and voltage
Gna(v,t) = Gmax * m(v,t) 3 * h(v,t)
Current due to channel
Ionic current through the channel
Ina(v,t) = Gna(v,t) * (v - Ena)
A number of parameters which can be used in the rate expressions, etc. for the channels. These should be publicly accessible in the objects implementing the channel.
fastNa_shift = 0
a = 0
b = 0
c = 0
d = 0

Gate: m

The equations below determine the dynamics of gating state m

Instances of gating elements3
Closed statem0
Open statem
    Transition time course: tau from m0 to m
Generic expressiontau(v) = ( v + fastNa_shift ) < -30 ? 0.0125 + 0.1525 * ( exp ( ((v + fastNa_shift) + 30) / 10) ) : 0.02 + a + (0.145 + b) * ( exp ( -1 * ((v + fastNa_shift + d) + 30) / (10 + c)) )
    Transition steady state: inf from m0 to m
Generic expressioninf(v) = 1 / ( 1 + (exp ( ( -1 * (v + fastNa_shift) - 38) / 10)) )

Gate: h

The equations below determine the dynamics of gating state h

Instances of gating elements1
Closed stateh0
Open stateh
    Transition time course: tau from h0 to h
Generic expressiontau(v) = 0.225 + 1.125 / ( 1 + ( exp (( ( v + fastNa_shift * 0 ) + 37 ) / 15) ) )
    Transition steady state: inf from h0 to h
Generic expressioninf(v) = 1 / ( 1 + (exp (( ( v + fastNa_shift * 0 ) + 58.3 ) / 6.7)) )

Implementation Preferences

Information is provided to help produce the best implementation of the channel mechanism. Due to some parameters in the channel mechanism the default values used in the simulator mappings may not be sufficient, e.g. if the rate equations change rapidly, but the default table size isn't large enough.

Explanation taken from file
Note: increased max v past Na rev potential
Settings for rate equation tables
Recommended settings if a table of values is used to speed up calculation of the rate equation values.
Number of table divisions: 1041
Maximum voltage for tables: 140 mV
Minimum voltage for tables: -120 mV

Time to transform file: 0.118 secs