README for CD-ROM files that accompany Chapter 4, Stiles 
and Bartol.

MCell Model Description Language (MDL) files are provided 
for the example simulations.  The MDL features and syntax 
are explained by embedded comments.  The best approach for 
a detailed understanding is to read through the files in 
the order listed below.

Animation (mpeg) files are included from each example 
simulation, in regular (mpeg1) and high (mpeg2) resolution 
formats.  These animations were produced with IBM 
DataExplorer (OpenDX), Pixar RenderMan, Adobe Illustrator, 
Photoshop, and Premier, Apple Quicktime, and Heuris Mpeg 
Pro, and are designed to run at 30 frames per second.  The 
high resolution versions are very large and will likely 
require mpeg2 (i.e., DVD) playback hardware.



Files for Section 4.5, Example Model:  Acetylcholine 
exocytosis and miniature endplate current generation at a 
realistic neuromuscular junction.

MDL files (complete aside from truncated lists of polygon 
mesh vertices and elements):
rat_nmj.main.mdl
reaction_mechanisms.mdl
release_sites.mdl
nerve_membrane.mdl
basal_lamina.mdl
muscle_membrane.mdl
ligand_sampling_boxes.mdl
visualization_output.mdl
reaction_output.mdl

Animations:
nmj.mpg (mpeg1)
nmj_hi_res.mpg (mpeg2)
mepc.mpg (mpeg1)
mepc_hi_res.mpg (mpeg2)

Notes on animations:
Animation "nmj" shows the structure of the model nmj in 
detail, first circling and then flying inside the 
synaptic cleft space.  While inside, the simulation 
runs with a very short time-step per movie frame (~85 
picoseconds), so that the movements of diffusing ACh 
and Ch molecules may be seen clearly.  At this time-
scale, state changes for the effector sites are 
extremely rare (several do occur).  The color code for 
molecules and effector sites is as given in the legend 
to Color Plates 4.1 and 4.2.  Animation "mepc" shows 
the postsynaptic membrane from above the ACh release 
site (nerve membrane and effector sites are not shown), 
and ACh exocytosis begins as the movie begins.  The 
time-step per frame is increased to 0.25 microseconds, 
so that AChR and AChE state changes can be visualized 
during the rising phase of the simulated mepc.


Files for Section 4.6, Example Model:  Potential spatial 
and temporal interaction of neuronal glutamatergic 
currents.

MDL files (complete):
neuronal_epscs.main.mdl
input_parameter_values.mdl
cell_membrane.mdl
diffusion_space_boundary.mdl

OpenDX visual program to render visualization output from 
simulation run with MCell version 2.50.  Start OpenDX, 
open the visual program (render_neuron_model.net), and 
then follow the instructions on the README page in the DX 
Visual Program Editor.
render_neuron_model.net
render_neuron_model.cfg
GluR_glyph.dx

Animations:
neuron.mpg (mpeg1)
neuron_hi_res.mpg (mpeg2)

Notes on animations:
Animation "neuron" was produced from the entire 
simulation time course of 140 milliseconds.  The time 
between movie frames is 100 microseconds.  Especially 
at later times, Glu release events can be seen as 
sudden jumps in the number of free Glu molecules 
diffusing around the cell body (the magnification is 
low, however, and the small Glu molecules may be 
difficult to see unless the high resolution movie can 
be played).  The color code for the GluR effector sites 
is as given in the legends to Color Plates 4.4-4.6.  
The color code for Glu reuptake sites is: white, 
unbound; gray, reversibly bound; translucent, long-
lived state prior to Glu translocation and reversion of 
the effector site to the unbound state.  This color 
scheme for the transporter sites causes them to 
disappear partially as the movie progresses, allowing 
the underlying GluR sites to be seen more clearly.  Glu 
molecules that have been transported out of the 
intercellular diffusion space are not shown.