PSICS Results for run.xml

raster (run.xml)

Cable with HH sodium and potassium channels, different timesteps

Total CPU time 46.26 seconds; at 17:11:19 Tue 8 Apr 2008

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	CPU Time / s
367	36763 / 367	0 / 0	23565 / 367	46.3

Morphology: cell

Predefined views

start

raster

All files

Model	Preprocessed	Outupt data	Reference data etc
run.xml cell.xml membrane.xml recording.xml leak.xml HH_Na.xml HH_K.xml environment.xml	psics-out.ppp	log.txt psics-out.sum psics-out.dat psics-out.txt

Model

Archive file of the complete model: raster.jar

run.xml

<PSICSRun  timeStep="0.1ms" runTime="250ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="10000"
	repeats="10">
	<StructureDiscretization baseElementSize="5um"/>

	<info>Cable with HH sodium and potassium channels, different timesteps</info>


	<ViewConfig>
		<LineGraph width="500" height="400">
			<XAxis min="0" max="250" label="time / ms"/>
			<YAxis min="-80" max="60" label="potential / mV"/>
			<LineSet file="psics-out.txt" color="blue"/>
			<View id="start"   xmin="0." xmax="30." ymin="-100." ymax="80."/>
		</LineGraph>

		<Raster id="raster" width="900" height="600" file="psics-out.txt" vmin="-100" vmax="60"
			threshold="0" colors="gray">
		</Raster>

	</ViewConfig>

</PSICSRun>

cell.xml

<CellMorphology id="cell">
	<Point id="p0" x="0" y="0" z="0" r="0.15"/>
	<Point parent="p0" id="p1" x="1000" y="0" z = "0" r="0.15"/>
</CellMorphology>

membrane.xml

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

	<ChannelPopulation channel="leak" density="25per_um2"/>

	<ChannelPopulation channel="HH_Na" density="30per_um2"/>
    <ChannelPopulation channel="HH_K" density="9per_um2"/>


</CellProperties>

recording.xml

<Access id="recording">

	<CurrentClamp at="p0" lineColor="red" hold="0.02nA">

	</CurrentClamp>

    <VoltageRecorder distance="100um"/>
    <VoltageRecorder distance="200um"/>
    <VoltageRecorder distance="300um"/>
    <VoltageRecorder distance="400um"/>
    <VoltageRecorder distance="500um"/>
    <VoltageRecorder distance="600um"/>
    <VoltageRecorder distance="700um"/>
    <VoltageRecorder distance="800um"/>
    <VoltageRecorder distance="900um"/>
    <VoltageRecorder at="p1"/>
</Access>

leak.xml

<KSChannel id="leak" gSingle="0.01pS" permeantIon="LEAK">
	<OpenState id="o1"/>
</KSChannel>

HH_Na.xml

<KSChannel id="HH_Na" permeantIon="Na" gSingle="40pS">

	<KSComplex id="m" instances="3">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="1.per_ms" midpoint ="-40.mV" scale="10mV"/>
		<ExpTransition from="o" to = "c" rate="4.per_ms" midpoint="-65.mV" scale="-18mV"/>
	</KSComplex>


	<KSComplex id="h">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpTransition from="c" to="o" rate="0.07per_ms" midpoint="-65.mV" scale="-20.mV"/>
		<SigmoidTransition from="o" to="c" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
	</KSComplex>

</KSChannel>

HH_K.xml

<KSChannel id="HH_K" permeantIon="K" gSingle="40pS">

	<KSComplex id="n" instances="4">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.1per_ms" midpoint ="-55.mV" scale="10mV"/>
		<ExpTransition from="o" to = "c" rate="0.125per_ms" midpoint="-65.mV" scale="-80mV"/>
	</KSComplex>


</KSChannel>

environment.xml

<CellEnvironment id="environment">
	<Ion id="LEAK" name="Non-specific leak" reversalPotential="-65mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-77mV"/>
	<Ion id="Na" name="Sodium" reversalPotential="50mV"/>
</CellEnvironment>