www.neuron.yale.edu

Dear All,

any suggestions for how can I insert channels in a given length density (hot spots) without increasing the number of segments of the section?

Best regards,
Eleftheria

Spatial resolution in any section is controlled by (section length)/nseg. If you want to represent a "hot spot" of a particular size at a particular location in a neurite, you have a choice:
1. represent the entire neurite by a single section, but make nseg big enough to approximate the size of the hot spot
OR
2. represent the neurite with two or more sections, whose lengths and nseg values are exactly what you want. For example, a 10 um long hot spot near the 1 end of a neurite that is 430 um long could be implemented by representing the neurite with two sections:If the hot spot is not near either end of a neurite, represent the neurite with three sections Those examples assume geometry is specified using the stylized method. If geometry uses the pt3d method, you'll have to figure out how to revise the sequence of pt3dadd statements to get the section lengths that you need.

You could also simply decide that the extra spatial resolution isn't worth the effort--just use a single section to represent the neurite, with whatever nseg is needed for adequate voltage resolution, and make sure to adjust the density parameter for the "hot spot mechanism" is correct. For example, to take into account a hot spot that consists of a cluster of ion channels, make sure that
(conductance density in the segment that contains the hot spot)*(area of that segment)
equals
(hot spot conductance density)*(hot spot area)

Thanks for the reply. Things are getting complicated and I don't think add to the big picture. Hot spots are very dense for the case of my model (0.8 per / um^2). Furthermore I am using the pt3d method. Instead, I am testing this: Having an estimation for the peak conductance density of the channel of interest for the hot spot (gbar_hotspot), multiplying by the number of hot spots per section (HS) and then divide by the section Area (A): (gbar_hotspot*HS)/A

I don't have clustered effects this way but at least I have ion influx of the desired quantity, right?
Please let me know if something is redundant.

Many thanks once again,
Eleftheria

ps: actually what I just wrote it is redundant, right?

tcp wrote:Hot spots are very dense for the case of my model (0.8 per / um^2). . . . Having an estimation for the peak conductance density of the channel of interest for the hot spot (gbar_hotspot)

A more appropriate name for that parameter would be gmaxhotspot or gpeakhotspot (gmaxhs or gpkhs if you want to avoid typing).

multiplying by the number of hot spots per section (HS) and then divide by the section Area (A): (gbar_hotspot*HS)/A

This is how to think about it. Suppose peak hs conductance is called gpkhs, and hs density is celled N. gpkhs has units of conductance/hotspot, and N has units of hotspot/area. hs conductance density gbar_hs must have units of conductance of area, so gbar_hs must equal the product gpkhs*N, times a scale factor to resolve any magnitude inconsistency between the units of gbar_hs and the units of gpkhs*N.

Concrete example: suppose gpkhs = 100 pS/hotspot, and N = 0.8 hotspot/um2, and you want gbar_hs to be in units of S/cm2. The product gpkhs*N has units of pS/um2. 1 pS = 1e-12 S and 1 um2 = 1e-8 um2, so gbar_hs in S/cm2 = 1e-4*gpkhs*N = 1e-4*100*0.8 = 0.008 S/cm2

I don't have clustered effects this way but at least I have ion influx of the desired quantity, right?

True.

Thanks a lot for untangling my misunderstanding
Eleftheria