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Remarks about accumulation mechanisms

Posted: Thu Sep 14, 2006 11:05 am
by ted
Be sure to read either chapter 9 of The NEURON Book, or the "enhanced preprint" of
this paper
Hines, M.L. and Carnevale, N.T.
Expanding NEURON's repertoire of mechanisms with NMODL.
Neural Computation 12:995-1007, 2000
which you can get from a link at

Initialization of accumulation mechanisms presents a special challenge. Incorrect
initialization can lead to undesired results, such as slow shifts of concentrations that
require prolonged simulations for transients to die away. Chapter 8 of The NEURON
Book contains much useful information about initialization of accumulation mechanisms
that can make such models much easier to implement and debug.

Kinetic scheme representation is most natural, i.e. easiest to conceptualize and
implement. Anything that involves radial diffusion, multiple buffers, or organelles, will be
more readily expressed in terms of kinetic schemes rather than DEs. DEs should be
used only for the very simplest accumulation mechanisms.

A section can have multiple mechanisms that assert
USEION x . . . WRITE ix
(this ensures conservation of mass when there are multiple sources of transmembrane
ionic flux). However, a section can have only one mechanism that may WRITE the
corresponding concentration xi or xo.