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

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

Name naf2

Status

Status of element in file

Stable
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

Description

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

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 - ucl.ac.uk

   Yoana Dimitrova (UCL)

Referenced publication Roger 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 publication Roger 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 relationship ohmic

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 E_na = 50 mV)

Default maximum conductance density

Note that the conductance density of the channel will be set when it is placed on the cell.

G_max = 0.1 mS cm^-2

Conductance expression

Expression giving the actual conductance as a function of time and voltage

G_na(v,t) = G_max * m(v,t) ³ * h(v,t)

Current due to channel

Ionic current through the channel

I_na(v,t) = G_na(v,t) * (v - E_na)

Parameters

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 elements 3

Closed state m0

Open state m

    Transition time course: tau from m0 to m

Generic expression tau(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 expression inf(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 elements 1

Closed state h0

Open state h

    Transition time course: tau from h0 to h

Generic expression tau(v) = 0.225 + 1.125 / ( 1 + ( exp (( ( v + fastNa_shift * 0 ) + 37 ) / 15) ) )

    Transition steady state: inf from h0 to h

Generic expression inf(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.

Comment

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: 0.447 secs