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Units specified by NEURON
Posted: Mon May 12, 2008 4:42 pm
by gabrielleg
If I've put calcium current in my ASSIGNED block with units of nA/cm2, does NEURON override my choice of units and calculate ica in terms of mA/cm2 anyway?
Code: Select all
ASSIGNED
{
ica (nA/cm2)
eca (mV)
F (mM/nA)
C0 (mM)
tauca (ms)
L (um)
diam (um)
}
-g
Posted: Tue May 13, 2008 2:41 am
by ted
"Go not there; that way lies error and confusion."
Currents that are declared in the WRITE clause of USEION statements must be in units
of mA/cm2. If you really truly need other units, then in addition to ica (which you declare
with a USEION ca . . . WRITE ica statement), declare a surrogate variable i in the
NEURON block, e.g.
give it the desired units in the ASSIGNED block, e.g.
and assign it the proper value in the BREAKPOINT block, with whatever scale factor is
needed to make units consistent., e.g.
Code: Select all
ica = expression that returns results in (mA/cm2)
i = ica*(1e6)
or alternatively
Code: Select all
i = expression that returns results in (nA/cm2)
ica = i*(1e-6)
And always check with modlunit to make sure that no units inconsistencies slip by.
Posted: Tue May 13, 2008 10:29 am
by gabrielleg
Hey, thanks for clearing that up. I didn't want to have to go back and write in scale factors everywhere until I was sure I'd have to. Also, modlunit was helpful. I'm starting to accumulate many scale factors in my mod files. Out of curiosity, why does NEURON use mA/cm2 instead of nA/um2? Biological currents are typically measured in nA and the dimensions diam and L are in terms of um. Is there an advantage to the system of units that NEURON uses that I haven't yet realized?
-g
Posted: Tue May 13, 2008 8:37 pm
by ted
NEURON has its roots in membrane biophysics, and its units are those that have long been
standard in that field.