PSICS Results for run.xml

params (run.xml)

Total CPU time 0.3000 seconds; at 10:35:36 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timestep/ms	cell:q	CPU Time / s
246	0 / 0	12975 / 11	0 / 0	100.0	0.05	0.2	0.0800
246	0 / 0	12975 / 11	0 / 0	100.0	0.05	0.3	0.0700
246	0 / 0	12975 / 11	0 / 0	100.0	0.05	0.4	0.0700
246	0 / 0	12975 / 11	0 / 0	100.0	0.05	0.5	0.0800

Morphology: cell

Predefined views

whole

start

end

All files

Model	Preprocessed	Outupt data	Reference data etc
run.xml cell.xml membrane.xml environment.xml recording.xml na1.xml k1.xml	out-0.2.ppp out-0.3.ppp out-0.4.ppp out-0.5.ppp	log.txt out-0.2.sum out-0.3.sum out-0.4.sum out-0.5.sum out-0.2.dat out-0.2.txt out-0.3.dat out-0.3.txt out-0.4.dat out-0.4.txt out-0.5.dat out-0.5.txt

Model

Archive file of the complete model: params.jar

run.xml

<PSICSRun  timeStep="0.05ms" runTime="100ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="0">
	<StructureDiscretization baseElementSize="3um"/>


	<RunSet vary="cell:q" values="[0.2, 0.3, 0.4, 0.5]"
		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-100.txt" color="orange"/>
		 
		 <View id="whole" xmin="-10." xmax="260." ymin="-100." ymax="80."/>
		 <View id="start"   xmin="0." xmax="30." ymin="-100." ymax="80."/>
		 <View id="end"   xmin="210." xmax="255." ymin="-100." ymax="80."/>
		</LineGraph>
	</ViewConfig>


</PSICSRun>

cell.xml

<CellMorphology id="cell">
	<Parameter name="q" value="0.5"/>

	<Point id="p0" x="0" y="0" z="0" r="1.5"/>
	<Point parent="p0" id="p1" x="1000" y="0" z = "0" r="(q)"/>
</CellMorphology>

membrane.xml

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

	<ChannelPopulation channel="na1" density="8per_um2" distribution="start"/>
    <ChannelPopulation channel="k1" density="20per_um2" distribution="start"/>

    <DistributionRule id="start">
    	<RegionMask action="include" where="p .lt. 50"/>
    </DistributionRule>

</CellProperties>

environment.xml

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

recording.xml

<Access id="recording">

	<CurrentClamp at="p0" lineColor="red" hold="0.08nA">

	</CurrentClamp>

    <VoltageRecorder at="p1" lineColor="blue"/>

</Access>

na1.xml

<KSChannel id="na1" gSingle="30pS" permeantIon="Na">
	<ClosedState id="c1"/>
	<ClosedState id="c2"/>	
	<OpenState id="o1"/>
	<ClosedState id="c3"/>
	
	
	<VHalfTransition from="c1" to="c2" vHalf = "-35mV" z="2.5e" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>
    <VHalfTransition from="c2" to="o1" vHalf = "-35mV" z="2.5e" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>

	<VHalfTransition from="o1" to="c3" vHalf = "-70mV" z="1.1e" gamma="0.90" tau="8.0ms" tauMin="0.01ms"/>

</KSChannel>

k1.xml

<KSChannel id="k1" gSingle="30pS" permeantIon="K">
	<ClosedState id="c1"/>
	<OpenState id="o1"/>
	
	<VHalfTransition from="c1" to="o1" vHalf = "0mV" z="1.5e" gamma="0.75" tau="3.2ms" tauMin="0.3ms"/>

</KSChannel>