These scripts (written by Erik De Schutter) demonstrate the use of the
difshell, fixbuffer, and taupump objects to model the diffusion of
intracellular calcium ions in dendritic spines, and the effect of buffering
and ionic pumps.  (To fully understand the scripts, see the documentation
for these three objects.)

This is a slightly simplified version of the model of calcium influx
through a NMDA channel into a single spine, described in:

De Schutter, E. and Bower, J. M.: Sensitivity of synaptic plasticity to the
Ca2+-permeability of NMDA-channels: a model of long-term potentiation in
hippocampal neurons.  Neural Computation 5, 681-694, 1993.

For a general description of buffered calcium diffusion see:
De Schutter E., and Smolen P., "Calcium dynamics in large neuronal
models", in Methods in neuronal modeling: From ions to networks
(2nd edition), C. Koch and I. Segev editors, pp. 211-250 (1998).

The scripts are:

SPINEDEMO-one.g: simulates a single activation of a NMDA and an AMPA
channel on a spine.

SPINEDEMO-burst.g: simulates a 200Hz burst activation of a NMDA and an AMPA
channel on a spine.

makeshells.g: sets up the model that is used in both of the simulation
scripts

parameters.g: contains the values of the constants used in the model

The model consists of 6 compartments: a spine head, spine neck, dendritic
shaft, distal dendrite, proximal dentrite, and soma.  All of these are
passive compartments, except the spine head, which contains a NMDA channel
(modeled with a synchan and Mg_block element) and an AMPA channel.

The idea is to look at the diffusion of Ca arising from the Mg-blocked Ca
current through the NMDA channel.  As the space constant for Ca diffusion
is much less than the electrotonic space constant, it is necessary to divide
each compartment into a number of diffusion shells.  Thus, there is a chain
of coupled difshells that correspond to the head compartment (5 SLABs),
neck (7 SLABs), and dendrite shaft (10 SHELLs).

The calcium fraction of the NMDA current enters the first difshell of the
spine head.  As it diffuses axially down the spine, the head and neck
difshells use the SLAB (SLICE) geometry.  When calcium ions enter the
dendritic shaft, they diffuse radially inward, so the SHELL geometry is
used.  Each of the difshells is coupled with the appropriate messages to
a fixbuffer (to model binding and release of Ca ions to non-mobile buffer
molecules) and to a taupump (an ionic pump that removes Ca ions from
the cell).
