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Longitudinal diffusion

Posted: Sun Aug 20, 2006 8:37 pm
by ted
By default the only stuff that spreads down the length of a section is charge. If you want
longitudinal diffusion of any particular solute, the accumulation mechanism for that solute
must be specified with a KINETIC block that contains the LONGITUDINAL_DIFFUSION
keyword. For further discussion of implemeting models of diffusion with kinetic schemes,
and the use of LONGITUDINAL_DIFFUSION, see
9.10 Example 9.8: Calcium diffusion with buffering (pp. 245 et seq. in The NEURON Book).
For slightly different NMODL code see
c:/nrn59/examples/nrniv/nmodl/cadifusl.hoc (MSWin)
(in NEURON's source code).

Note that chemical signals tend to have a much shorter effective length constant than
electircal signals do. Therefore nseg will probably have to be much larger than if you were
interested only in electrical signals. As always, choose odd values for nseg, and test
for adequate spatial accuracy by following this protocol:

Code: Select all

run a simulation with nseg = 1 and note results
  triple nseg
  run a new simulation and compare with previous results
until no significant change is seen
divide nseg by 3

Re: Longitudinal diffusion

Posted: Thu Aug 02, 2007 9:58 am
by ted
What happens if adjacent compartments have different diameters?
hines wrote:The flux area is the average of the cross sectional areas of the centers
of the adjacent compartments.
For more information about this, see