creating pin wheel structure

NMODL and the Channel Builder.
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kukkoo161
Posts: 4
Joined: Sun Feb 07, 2010 8:53 am

creating pin wheel structure

Post by kukkoo161 »

hi,
i am working on extracellular calcium diffusion in a pinwheel structure. The way i understand it, i have two choices. First is, after creating neural and glial cells, i ASSUME that they are placed in a pinwheel structure along with the extracellular elemements and then create the mod file to account for calcium concentrations and diffusion. Second is, i create the entire structure using the hoc code (including extracellular elements) and then write separate mod files for neural and extracellular cells. Which would be a better approach? Also, if it is the later one, then how do i go about it?
thanks a lot.
ted
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Re: creating pin wheel structure

Post by ted »

Current implementations of NEURON do not offer a "general" representation of diffusion in either intra- or extracellular space. The basic architectural element is a cable with rotational symmetry. Tapering diameter and deviation of the central axis from a straight line are represented with conical frusta. Effects of noncircular cross-section on electrical properties may be approximated by adjusting equivalent diameter and scaling specific membrane capacitance and ionic conductance densities; effects on "chemical accumulation mechanisms" are represented by scale factors that adjust surface areas, volumes, and surface/volume ratios as necessary.

Diffusion and chemical reactions are represented by using NMODL to embed families of ODEs or kinetic schemes within each segment (electrical compartment). In this way, each segment may contain multiple chemical compartments, which may include any combination of volumes and/or surfaces (the latter are handy for carrier-mediated transport mechanisms). Chemical species may be immobile or may move between compartments. Each compartment may contain any combination of chemical reactions. The NEURON book presents several examples, two of which are in chapter 9: extracellular K accumulation, and intracellular Ca accumulation.

Material exchange can be represented with ODEs, but kinetic schemes are better for conceptual clarity. The easiest diffusional architecture to implement is concentric shells with radial exchange between adjacent compartments, but there is no reason why you could not represent extracellular space as "spokes" radiating away from the surface of a neuron, such that
1. each spoke exchanges with the perineuronal space at its "central" end
2. there is ("radial") diffusion along the length of each spoke
and
3. there is ("transverse") exchange between adjacent spokes


Now back to the mundane . . .

Passive electrical properties of the extracellular medium may be represented by inserting the extracellular mechanism, which is equivalent to adding concentric layers with user-specifiable specific capacitance and radial and longitudinal conductance. Electrical coupling between cells can be represented by using special mechanisms that implement gap junctions, or by using the extracellular mechanism and the LinearCircuit class together: extracellular "exposes" the external surface of each segment, so that the LinearCircuit mechanism can be used to specify electrical coupling between nonadjacent segments.
kukkoo161
Posts: 4
Joined: Sun Feb 07, 2010 8:53 am

Re: creating pin wheel structure

Post by kukkoo161 »

sir,
thanks a lot for your help. i am working on your suggestions.
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