<PSICSRun timeStep="0.05ms" runTime="2000ms" startPotential="-65mV"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="10000">
	<MorphologySource format="swc" file="NM1.swc"/>

	<StructureDiscretization baseElementSize="15um"/>


	<RunSet vary="clamp:hold" values="[200, 300, 400, 450, 550, 650]pA"  filepattern="out-$"/>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="potential / mV"/>

		<LineSet file="out-200.txt" color="red"/>
		<LineSet file="out-300.txt" color="green"/>
		<LineSet file="out-400.txt" color="blue"/>
		<LineSet file="out-450.txt" color="orange"/>
		<LineSet file="out-550.txt" color="white"/>
		<LineSet file="out-650.txt" color="pink"/>

		 <View id="whole" xmin="-10." xmax="450." ymin="-85." ymax="30."/>
		  <View id="wholethreshold" xmin="-10." xmax="450." ymin="-65." ymax="-55."/>
		  <View id="enlarged" xmin="200." xmax="250." ymin="-65." ymax="-50."/>
		<View id="650" xmin="0." xmax="2000." ymin="-70." ymax="-50."/>
		</LineGraph>
	</ViewConfig>


</PSICSRun>

<CellProperties id="membrane"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1uF_per_cm2">


    <ChannelPopulation channel="leak-Na" density="0.1per_um2"/>
	<ChannelPopulation channel="leak-K" density="0.1per_um2"/>

	<ChannelPopulation channel="naz_nature" density="60per_um2" distribution="proximal"/>
    <ChannelPopulation channel="kvz_nature" density="18per_um2" distribution="proximal"/>

	<ChannelPopulation channel="km" density="0.1per_um2" distribution="proximal"/>


	<DistributionRule id="proximal">
		<RegionMask action="include" where="p .lt. 100"/>
	</DistributionRule>


    <DensityAdjustment maintain="-65mV" vary="leak-Na, leak-K"/>

</CellProperties>

<CellEnvironment id="environment" temperature="13Celsius">
	<Ion id="Na" name="Sodium" reversalPotential="40mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

<Access id="recording">

	<CellLocation id="p0" path="10" rankBy="radius" sequenceFraction="1."/>
	<CellLocation id="p1" path="120" rankBy="radius" sequenceFraction="0.5"/>
	<CellLocation id="p2" path="240" rankBy="radius" sequenceFraction="0.5"/>


	<CurrentClamp id="clamp" location="p0" lineColor="red" hold="0pA"/>

	<VoltageRecorder location="p2" lineColor="blue"/>



</Access>

<KSChannel id="leak-Na" gSingle="20pS" permeantIon="Na">
	<OpenState id="o1"/>
	<ClosedState id="c1"/>
	<FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/>
</KSChannel>

<KSChannel id="leak-K" gSingle="20pS" permeantIon="K">
	<OpenState id="o1"/>
	<ClosedState id="c1"/>
	<FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/>
</KSChannel>

<KSChannel id="naz_nature" permeantIon="Na" gSingle="20pS">

	<About>
		Converted from naz_nature.mod (Zack Mainen, 1994)
	</About>

	<KSComplex id="m" instances="3">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="1.64per_ms" midpoint ="-35.mV" scale="9mV"
			baseTemperature="23Celsius" q10="2.3"/>
		<ExpLinearTransition from="o" to="c" rate="1.12per_ms" midpoint="-35.mV" scale="-9mV"
		  baseTemperature="23Celsius" q10="2.3"/>
	</KSComplex>


	<CodedTransitionFunction name="trap0" returnVariable="rate" type="double">
		<Argument name="v" type="double"/>
		<Argument name="th" type="double"/>
		<Argument name="a" type="double"/>
		<Argument name="q" type="double"/>
		<![CDATA[
			if (Math.abs(v - th) > 1.e-6) {
				rate =  a * (v - th) / (1 - Math.exp(-(v - th)/q));
			} else {
				rate = a * q;
			}
		]]>
	</CodedTransitionFunction>



	<KSComplex id="h">
		<ClosedState id="c"/>
		<OpenState id="o"/>


 	<TauInfCodedTransition from="c" to="o" tauvar="htau" infvar="hinf"
        	baseTemperature="23Celsius" q10="2.3">
 		<Constant name="thi1" value="-50"/>
 		<Constant name="thi2" value="-75"/>
 		<Constant name ="rd" value="0.024"/>
 		<Constant name="rg" value="0.0091"/>
 		<Constant name="qi" value="5"/>

 		<Constant name="thinf" value="-65"/>
 		<Constant name="qinf" value="6.2"/>
 	<![CDATA[

        double a = trap0(v, thi1, rd, qi);
        double b = trap0(-v, -thi2, rg, qi);
        htau = 1/(a+b);
        hinf = 1. / (1 + Math.exp((v - thinf)/qinf));
	]]>
 	</TauInfCodedTransition>


	</KSComplex>

</KSChannel>

<KSChannel id="kvz_nature" permeantIon="K" gSingle="20pS">

	<About>
		Converted from kvz_nature.mod (Zach Mainen, 1995)
	</About>

	<KSComplex id="n" instances="1">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.18per_ms" midpoint ="25.mV" scale="9mV"
		baseTemperature="23Celsius" q10="2.3"/>
		 <ExpLinearTransition from="o" to="c" rate="0.018per_ms" midpoint ="25.mV" scale="-9mV"
		baseTemperature="23Celsius" q10="2.3"/>

	</KSComplex>


</KSChannel>

<KSChannel id="km" permeantIon="K" gSingle="20pS">

	<About>
		Converted from km.mod, slow non-inactivating potassium current
		based on I-M (Zach Mainen, 1995)
	</About>

	<KSComplex id="n" instances="1">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.009per_ms" midpoint ="-30.mV" scale="9mV"
		baseTemperature="23Celsius" q10="2.3"/>
		 <ExpLinearTransition from="o" to="c" rate="0.0009per_ms" midpoint ="-30.mV" scale="-9mV"
		baseTemperature="23Celsius" q10="2.3"/>

	</KSComplex>


</KSChannel>