Stochastic ion channels and neuronal morphology (Cannon et al. 2010)

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Accession:128043
"... We introduce and validate new computational tools that enable efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. Comparison of five morphologically distinct neuronal cell types reveals that when all simulated neurons contain identical densities of stochastic ion channels, the amplitude of stochastic membrane potential fluctuations differs between cell types and depends on sub-cellular location. ..." The code is downloadable and more information is available at <a href="http://www.psics.org/">http://www.psics.org/</a>
Reference:
1 . Cannon RC, O'Donnell C, Nolan MF (2010) Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS Comput Biol [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Synapse; Channel/Receptor;
Brain Region(s)/Organism:
Cell Type(s): Dentate gyrus granule GLU cell; Hippocampus CA1 pyramidal GLU cell; Substantia nigra pars compacta DA cell; Neocortex L5/6 pyramidal GLU cell; Cerebellum Purkinje GABA cell;
Channel(s): I Na,t; I A; I K; I h;
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: PSICS;
Model Concept(s): Action Potential Initiation; Dendritic Action Potentials; Influence of Dendritic Geometry; Detailed Neuronal Models;
Implementer(s):
Search NeuronDB for information about:  Dentate gyrus granule GLU cell; Hippocampus CA1 pyramidal GLU cell; Substantia nigra pars compacta DA cell; Neocortex L5/6 pyramidal GLU cell; Cerebellum Purkinje GABA cell; I Na,t; I A; I K; I h;
<CellProperties id="membrane" membraneCapacitance="0.75uF_per_cm2"
    cytoplasmResistivity="200.0ohm_cm">

  	<PassiveProperties region="*_node*" cytoplasmResistivity="50.0ohm_cm"/>
	<PassiveProperties region="*inode*" membraneCapacitance="0.04uF_per_cm2"/>
	<PassiveProperties region="*dend*" membraneCapacitance="1.5uF_per_cm2"/>

	<CellRegion match="*soma*">
		<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20 per_um2"/>
		<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20 per_um2"/>
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24 per_um2"/>
		<ChannelPopulation id="Ih-Spru" channel="Ih-Spru" color="0x33ccff" density="1.5969 per_um2"/>
	</CellRegion>


	<CellRegion match="*dend*">
		<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20 per_um2"/>
		<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20 per_um2"/>
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24 per_um2">
			<RegionMask action="exclude" where="region=*dendA5*"/>
		</ChannelPopulation>
		<ChannelPopulation id="Ih-Spru" channel="Ih-Spru" color="0x33ccff" density="1.5969 + ((2.1582-1.5969)/(1+exp((p - 98.753)/50.07))) per_um2"/>
		<ChannelPopulation id="leak-na" channel="leak-na" color="0xffff00" density="0.02 per_um2"/>
		<ChannelPopulation id="leak-k" channel="leak-k" color="0xff33cc" density="0.02 per_um2"/>
	</CellRegion>

	<CellRegion match="*dendA5*">
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24 * (1 + p/100) per_um2">
			<RegionMask action="exclude" where="p .gt. 100"/>
        	</ChannelPopulation>

		<ChannelPopulation id="Kadist-Mig1" channel="Kadist-Mig" color="0x33ccff" density="24 * (1 + p/100) per_um2">
			<RegionMask action="exclude" where="p .lt. 100"/>
			<RegionMask action="exclude" where="p .gt. 500"/>
        	</ChannelPopulation>

		<ChannelPopulation id="Kadist-Mig2" channel="Kadist-Mig" color="0x33ccff" density="24 * 6 per_um2">
			<RegionMask action="exclude" where="p .lt. 500"/>
        	</ChannelPopulation>

	</CellRegion>

	<CellRegion match="*hill*">
		<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20 per_um2"/>
		<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20 per_um2"/>
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24 per_um2"/>
	</CellRegion>

	<CellRegion match="*iseg*">
		<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20 per_um2"/>
		<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20 per_um2"/>
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24 per_um2"/>
	</CellRegion>

	<CellRegion match="*inode*">
		<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20 per_um2"/>
		<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20 per_um2"/>
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="(24/5) per_um2"/>
	</CellRegion>

	<CellRegion match="*_node*">
		<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="1500 per_um2"/>
		<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20 per_um2"/>
		<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="(24/5) per_um2"/>
	</CellRegion>

	<ChannelPopulation id="leak-na" channel="leak-na" color="0xffff00" density="0.02per_um2">
		<RegionMask action="exclude" where="region=*node*"/>
	</ChannelPopulation>

	<ChannelPopulation id="leak-k" channel="leak-k" color="0xff33cc" density="0.02per_um2">
		<RegionMask action="exclude" where="region=*node*"/>
	</ChannelPopulation>

	<DensityAdjustment maintain="-70mV" vary="leak-na, leak-k"/>

	<SynapsePopulation id="synpop" synapse="syn1" density="0.1per_um2" seed="1010">
		<RegionMask action="include" where="region=*dend*"/>
		<RegionMask action="exclude" where="p .lt. 30"/>
		<NormalWeights min="0.9" max="1.1" sd="0.01"/>
		<!--<UniformWeights min="0.1" max="3"/>
		<LogUniformWeights min="0.1" max="3"/>
		<LogNormalWeights min="0.1" max="3" sd="0.5"/>-->
	</SynapsePopulation>


</CellProperties>