Longitudinal diffusion
Posted: Sun Aug 20, 2006 8:37 pm
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)
or
nrn-x.x/share/examples/nrniv/nmodl/cadifusl.mod
(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:
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)
or
nrn-x.x/share/examples/nrniv/nmodl/cadifusl.mod
(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
repeat
triple nseg
run a new simulation and compare with previous results
until no significant change is seen
divide nseg by 3