PSICS Results for rcwvc.xml

cwvclamp (rcwvc.xml)

Chow and White (1996), Biophys J

Total CPU time 1.640 seconds; at 10:36:02 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timestep/ms	stochThreshold	CPU Time / s
1	780 / 1	0 / 0	3000 / 1	1.00e+03	0.01	1000000000	1.41
1	0 / 0	780 / 1	3000 / 1	1.00e+03	0.01	0	0.230

Morphology: cell

Predefined views

whole

mean= 0.08880, sd= 4.758e-08 st-0.txt, line 2
mean= 0.08730, sd= 0.04223 st-1000000000.txt, line 2

All files

Model	Preprocessed	Outupt data	Reference data etc
rcwvc.xml cell.xml membrane.xml environment.xml record-voltageclamp.xml NaHH.xml KHH.xml Leak.xml	st-1000000000.ppp st-0.ppp	log.txt st-1000000000.sum st-0.sum st-1000000000.dat st-1000000000.txt st-0.dat st-0.txt	whole.txt

Model

Archive file of the complete model: cwvclamp.jar

rcwvc.xml

<PSICSRun   timeStep="0.01ms" runTime="1s" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="record-voltageclamp"
        stochThreshold="1000000"
	quickChannels="true"
        repeats="1">

	<RunSet vary="stochThreshold" values="[1000000000 0]" filepattern="st-$"/>

	<info>Chow and White (1996), Biophys J</info>

	<ViewConfig>
		<LineGraph width="1000" height="400">
		<XAxis min="0" max="100" label="time / ms"/>
		<YAxis min="-5" max="5" label=""/>


		<LineSet file="st-0.txt" color="green" show="2">
			<Stats xmin="100ms"/>
		</LineSet>

		<LineSet file="st-1000000000.txt" color="yellow" show="2">
			<Stats xmin="100ms"/>
		</LineSet>


		<View id="whole" xmin="-10." xmax="400." ymin="-0." ymax="0.3"/>



		</LineGraph>
	</ViewConfig>
</PSICSRun>

cell.xml

<CellMorphology id="cell">
	<Point id="p0" x="0" y="0" z="0" r="0.89206"/>
</CellMorphology>

membrane.xml

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

	<ChannelPopulation channel="NaHH" density="60per_um2"/>
    <ChannelPopulation channel="KHH" density="18per_um2"/>
    <ChannelPopulation channel="Leak" density="300per_um2"/>

</CellProperties>

environment.xml

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="50mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-77mV"/>
	<Ion id="LEAK" name="Non-specific leak" reversalPotential="-54.4mV"/>
</CellEnvironment>

record-voltageclamp.xml

<Access id="record-voltageclamp" recordClamps="true">

    <VoltageClamp at="p0" hold="-60mV" record="false"/>
<!--
	<SmartRecorder at="p0" record="current" channel="NaHH"/>
	<SmartRecorder at="p0" record="current" channel="KHH"/>
	<SmartRecorder at="p0" record="conductance" channel="NaHH"/>
	-->
	<SmartRecorder at="p0" record="conductance" channel="KHH"/>
</Access>

NaHH.xml

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

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

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

</KSChannel>

KHH.xml

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

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


</KSChannel>

Leak.xml

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