Page 1 of 1

Ca Diffusion

Posted: Tue Feb 21, 2012 1:00 pm
by dzocchi
Hi,

In the code for Calcium ion accumulation with longitudinal and radial diffusion (Cadifusl.mod) there is a part under the Kinetic State section which says:

FROM i=0 TO NANN-2 {
~ k <-> k[i+1] (DFree*frat[i+1], DFree*frat[i+1])
}


I was wondering what the function frat is, and what the symbol <-> means.

Thanks,

-Dhruv Zocchi

Re: Ca Diffusion

Posted: Tue Feb 21, 2012 3:55 pm
by ted
Ah, good, digging into NMODL. Very useful.

Two questions, an answer, and two suggestions:

Have you examined the remainder of the file to look for code that defines frat? Try the INITIAL block.

A more general question: where did you find the file? (I ask because the fact that some file is called foo does not guarantee that its contents are the same as those of any other file with the same name)

<-> is part of NMODL's "kinetic scheme" syntax for declaring a transition between two states, or a reaction. Reactants would go on the left, and products on the right.

It would be a good idea to read chapter 9 of The NEURON Book. This will explain many of NMODL's peculiarities, including its notation for kinetic schemes. If you don't have that, read
Hines, M.L. and Carnevale, N.T.
Expanding NEURON's repertoire of mechanisms with NMODL.
Neural Computation 12:995-1007, 2000.
Be sure to get the "enhanced preprint" version from the link at http://www.neuron.yale.edu/neuron/nrnpubs