Different species parameters for different regions
Posted: Thu Feb 15, 2018 1:18 pm
What is the simplest way to allow a species to have different initial concentrations in different regions? Do I need to make two different "sub-species"?
For example, I am working with a buffer "buf" that has a higher buffering capacity in the dendrites than in spines. I want to try having either a larger total buffer concentration or different reaction rates in the dendrites than in spines, both yielding different initial concentrations (i.e. "b0_dend","b0_spine"). Do I need to write something like the following?:
I tried something like the above, but it doesn't seem to like two species having the same name "buf". However, I want it to know they are in fact the same species since the mobile buffer should be able to diffuse from dendrite to spine, and vice versa.
This question would also trickle down into defining the reactions I imagine (I am using "RxD.Rate" for all of mine). What is the best way to go about this? Thanks!
For example, I am working with a buffer "buf" that has a higher buffering capacity in the dendrites than in spines. I want to try having either a larger total buffer concentration or different reaction rates in the dendrites than in spines, both yielding different initial concentrations (i.e. "b0_dend","b0_spine"). Do I need to write something like the following?:
Code: Select all
spines = rxd.Region([head,neck],nrn_region='i')
dends = rxd.Region([dend,dend1,dend2],nrn_region='i')
ca = rxd.Species(r, initial=c0,name='ca',charge=2, d = dCa,atolscale = 10-9)
buf_dend = rxd.Species(dends, initial=b0_dend,name='buf', d = dB,atolscale = 10-6)
buf_spine = rxd.Species(spines, initial=b0_spine,name='buf', d = dB,atolscale = 10-6)
cabuf_dend = rxd.Species(dends, initial=bc0_dend,name='cabuf', d = dB,atolscale = 10-6)
cabuf_spine = rxd.Species(spines, initial=bc0_spine,name='cabuf', d = dB,atolscale = 10-6)
This question would also trickle down into defining the reactions I imagine (I am using "RxD.Rate" for all of mine). What is the best way to go about this? Thanks!