Modeling extracellular space and a plasma membrane
Posted: Tue Apr 04, 2017 5:34 pm
I have several questions regarding extracellular space and the plasma membrane using RxD. First of all, I've seen reference to extracellular space as a possible RxD conceptual region in the RxD documentation, but haven't seen an example of it actually defined. Is the best way to define it simply the following?
Secondly, the reason I want to define "ext" above is so that I can set up a calcium pump in the plasma membrane (using a MultiCompartmentReaction). This pump also requires the plasma membrane to be defined as a region:
My second question is with regards to the DistributedBoundary inputs, "area_per_vol" and "perim_per_area" (or similarly "scale" for ScalableBorder). Must these values be constant, or can they be variable? or reflect multiple constants? For example, in my code "h.allsec()" includes a dendrite, spine neck and spine head, each of which has a different diameter. I'd like for area_per_vol to depend on the diameter for each section (A = 2*V/r) = 4*V/diam for each compartment). I've been trying to iterate through the sections to call each diameter within the geometry definition but haven't gotten it to work. The clunky way to do this is to define three different membrane regions (i.e. membrane_dend, membrane_neck, membrane_head) and then the Distributed Boundary parameters can be entered as constants for each given membrane region. This would in turn require three separate pump definitions. Is there a smoother way to do this?
Lastly, the paper introducing RxD (McDougal, Hines, Lytton 2013) mentioned that there was limited support for extracellular diffusion at the time, but that this would hopefully be addressed in the future (pg. 4). Are there any updates on support for extracellular diffusion within RxD?
Thanks!
Code: Select all
ext = rxd.Region(h.allsec(), nrn_region='o')
Code: Select all
plasma_membrane = rxd.Region(h.allsec(), geometry=rxd.DistributedBoundary(??))
Lastly, the paper introducing RxD (McDougal, Hines, Lytton 2013) mentioned that there was limited support for extracellular diffusion at the time, but that this would hopefully be addressed in the future (pg. 4). Are there any updates on support for extracellular diffusion within RxD?
Thanks!