PSICS Results for run.xml

onsurface (run.xml)

Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds

Total CPU time 0.02000 seconds; at 10:35:42 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timeStep	CPU Time / s
3	0 / 0	0 / 0	22387 / 3	250.0	20	0.0100
3	0 / 0	0 / 0	22387 / 3	250.0	50	0.0100
3	0 / 0	0 / 0	22387 / 3	250.0	100	0.0
3	0 / 0	0 / 0	22387 / 3	250.0	200	0.0
3	0 / 0	0 / 0	22387 / 3	250.0	500	0.0

Morphology: ballstick2

Predefined views

whole

end

midrange

start

All files

Model	Preprocessed	Outupt data	Reference data etc
run.xml ballstick2.xml membrane.xml environment.xml recording.xml leak.xml	ts-20.ppp ts-50.ppp ts-100.ppp ts-200.ppp ts-500.ppp	log.txt ts-20.sum ts-50.sum ts-100.sum ts-200.sum ts-500.sum ts-20.dat ts-20.txt ts-50.dat ts-50.txt ts-100.dat ts-100.txt ts-200.dat ts-200.txt ts-500.dat ts-500.txt

Model

Archive file of the complete model: onsurface.jar

run.xml

<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV"
	method="weighted_crank_nicolson"
	morphology="ballstick2"
	environment="environment"
	properties="membrane"
	access="recording"
	squareCaps="true">

	<StructureDiscretization baseElementSize="50um"/>

	<RunSet vary="timeStep" values="[20, 50, 100, 200, 500]us"
		filepattern="ts-$"/>
	 <info>Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds</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="ts-500.txt" color="orange" label="500">

		</LineSet>

		<LineSet file="ts-200.txt" color="yellow" label="200">
		</LineSet>

		<LineSet file="ts-100.txt" color="green" label="100">
		</LineSet>

		<LineSet file="ts-50.txt" color="cyan" label="50">
		</LineSet>

		<LineSet file="ts-20.txt" color="blue" label="20">
		</LineSet>




		<View id="whole" xmin="-10." xmax="260." ymin="-100." ymax="100."/>
		<View id="end" xmin="249" xmax="250.2" ymin="101.93" ymax="101.94"/>
		<View id="midrange" xmin="80" xmax="90" ymin="25" ymax="30"/>
		<View id="start" xmin="-0.1" xmax = "2.1" ymin="-70" ymax="-10"/>


		</LineGraph>
	</ViewConfig>

</PSICSRun>

ballstick2.xml

<CellMorphology id="ballstick2" squareCaps="true">
	<Point id="p0" x="0" y="0" z="0" r="8"/>
	<Point parent="p0" id="p1" x="10" y="0" z = "0" r="8"/>
	<Point parent="p1" id="p2" x="130" y="0" z = "0" minor="false" r="0.5" onSurface="true"/>	
	<Point parent="p2" id="p2a" x="140" y="30" z = "0" minor="false" r="0.5"/>


	<Point parent="p0" id="p3" x="0" y="0.0" z = "0" onSurface="true" minor="true" r="1.8"/>
	<Point parent="p3" id="p4" x="20" y="-20" z = "0" minor="false" r="1.5"/>
</CellMorphology>

membrane.xml

<CellProperties id="membrane"
    membraneCapacitance="1.0uF_per_cm2"
    cytoplasmResistivity="100.0ohm_cm">
   <ChannelPopulation id="population_1"
       channel="leak"
       density="25per_um2"/>
</CellProperties>

environment.xml

<CellEnvironment id="environment">
    <Ion id="K" name="Potassium" reversalPotential="-65mV"/>
</CellEnvironment>

recording.xml

<Access id="recording">
	
	<CurrentClamp at="p0" lineColor="red" hold="0.1nA">
		 	
	</CurrentClamp>
	
    <VoltageRecorder at="p1" lineColor="blue"/>  

</Access>

leak.xml

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