PSICS Results for run.xml

vcsteps (run.xml)

Total CPU time 0.5400 seconds; at 10:36:04 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timeStep	CPU Time / s
65	0 / 0	6861 / 65	0 / 0	300.0	0.02	0.310
65	0 / 0	6861 / 65	0 / 0	300.0	0.04	0.160
65	0 / 0	6861 / 65	0 / 0	300.0	0.09	0.0700

Morphology: cell

Predefined views

whole

step1

All files

Model	Preprocessed	Outupt data	Reference data etc
run.xml cell.xml membrane.xml environment.xml recording.xml na1.xml	out-0.02.ppp out-0.04.ppp out-0.09.ppp	log.txt out-0.02.sum out-0.04.sum out-0.09.sum out-0.02.dat out-0.02.txt out-0.04.dat out-0.04.txt out-0.09.dat out-0.09.txt

Model

Archive file of the complete model: vcsteps.jar

run.xml

<PSICSRun  timeStep="0.01ms" runTime="300ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="0"
	quickChannels="true">
	<StructureDiscretization baseElementSize="1um"/>


	<!--
	<RunSet vary="napop:density" values="[2, 8]per_um2"
                filepattern="out-$.txt">
	      <CommandSet vary="vstep:to" values="[-60, -40, -20, 0, 20]mV"/>
	</RunSet>
 	-->

	<RunSet vary="timeStep" values="[0.02, 0.04, 0.09]ms" filepattern="out-$"/>

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

		<LineSet file="out-0.04.txt" color="blue"/>

		<LineSet file="out-0.02.txt" color="red"/>
		<LineSet file="out-0.09.txt" color="green"/>


		 <View id="whole" xmin="-10." xmax="3005." ymin="-60." ymax="20."/>
		 <View id="step1" xmin="4." xmax="7." ymin="-90." ymax="90."/>
		</LineGraph>
	</ViewConfig>


</PSICSRun>

cell.xml

<CellMorphology id="cell">

    <Point id="p0" x="0" y="0" z="0" r="1."/>

	 <Point id="p1" parent="p0" x="90" y="0" z="0" r="1."/>


</CellMorphology>

membrane.xml

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

	<ChannelPopulation id="napop" channel="na1" density="12per_um2"/>


</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" saveInterval="0.01ms" recordClamps="true">

	<VoltageClamp at="p0" lineColor="red" hold="-80.0mV">
		<VoltagePulse id="vstep" start="5ms" to="0mV"
			      duration="1ms" repeatAfter="50ms"/>
	</VoltageClamp>


	<CurrentClamp at="p1" hold="0.1nA"/>



</Access>

na1.xml

<KSChannel id="na1" gSingle="30pS" permeantIon="Na">
	<ClosedState id="c1"/>
	<OpenState id="o1"/>
	<ClosedState id="c2"/>
	
	<VHalfTransition from="c1" to="o1" vHalf = "-35mV" z="4.5e" gamma="0.8" tau="0.15ms" tauMin="0.001ms"/>

	<VHalfTransition from="o1" to="c2" vHalf = "-70mV" z="1.1e" gamma="0.90" tau="4.0ms" tauMin="0.01ms"/>

</KSChannel>