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Monte Carlo Methods for Simulating Realistic Synaptic Microphysiology Using MCell
Joel R. Stiles and Thomas M. Bartol
MCell Movies
There are two versions of each movie: a relatively small one (~10 Mb) in mpeg1 format and a high resolution one (~100Mb+) in mpeg2 format. The mpeg1 movies can be played with most mpeg decoders. Under Linux there are may be problems with mpeg_play or xanim but the free program gtv from the smpeg package (part of most Debian and Red Hat distributions) works fine. If this is not the default viewer for your web browser, you can view the movies by starting gtv independently and opening the .mpg files from there.
The large mpeg2 files are encoded the same way as DVD movies and require DVD software to view them.
The initial segment of each movie contains the legend and details of the reaction schemes. The third item in each movie list below is a link to images from the initial segment for reference while viewing the movie.
Section 4.5, Example Model: Acetylcholine exocytosis and miniature endplate current generation at a realistic neuromuscular junction.
Animation NMJ
Animation nmj shows the structure of the model junction 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, total of only 0.3 microseconds elapsed time), so that the movements of diffusing acetylcholine and choline molecules may be seen clearly. At this time-scale, state changes for the acetylcholine receptor, acetylcholinesterase, and choline reuptake effector sites are extremely rare, but several do occur. The color code for molecules and effector sites is the same as in the text Color Plates 4.1 - 4.3.
Animation MEPC
Animation mepc shows the postsynaptic muscle membrane from above the acetylcholine release site (nerve membrane and choline reuptake sites are not shown), and acetylcholine exocytosis begins as the movie begins. The time-step per frame is increased to 0.25 microseconds, so that acetylcholine receptor and acetylcholinesterase state changes can be visualized during the rising phase of the simulated mepc (total elapsed time of 300 microseconds).
Section 4.6, Example Model: Potential spatial and temporal interaction of neuronal glutamatergic currents.
Animation NEURON
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, glutamate release events can be seen as sudden jumps in the number of free molecules diffusing around the cell body (the magnification is low, however, and the small glutamate molecules may be difficult to see unless the high resolution movie can be played). The color code for the glutamate receptor effector sites is the same as in the text Color Plates 4.4 - 4.6. The color code for glutamate reuptake sites is: white, unbound; gray, reversibly bound; translucent, long-lived state prior to glutamate 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 glutamate receptor sites to be seen more clearly. Glutamate molecules that have been transported out of the intercellular diffusion space are not shown.
MCell Input Files
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. There is also a plain text version of these lists.
There are two versions of each file: the first (.htm) has the comments highlighted in red for readability; the second is the plain text .mdl file, which can be used to run the simulations with MCell version 2.50.
Files for Section 4.5, Example Model: Acetylcholine exocytosis and miniature endplate current generation at a realistic neuromuscular junction.
These files are complete except that the lengthy lists of polygon mesh vertices and elements (for nerve membrane, basal lamina, and muscle membrane surfaces) have been truncated.
- rat_nmj.main.mdl.htm; (plain mdl)
- reaction_mechanisms.mdl.htm; (plain mdl)
- release_sites.mdl.htm; (plain mdl)
- nerve_membrane.mdl.htm; (plain mdl)
- basal_lamina.mdl.htm; (plain mdl)
- muscle_membrane.mdl.htm; (plain mdl)
- ligand_sampling_boxes.mdl.htm; (plain mdl)
- visualization_output.mdl.htm; (plain mdl)
- reaction_output.mdl.htm; (plain mdl)
Files for Section 4.6, Example Model: Potential spatial and temporal interaction of neuronal glutamatergic currents.
These files are complete and can be used with MCell version 2.50 to run the simulation and generate reaction data and visualization output as shown in the text and animation neuron.
- neuronal_epscs.main.mdl.htm; (plain mdl)
- input_parameter_values.mdl.htm; (plain mdl)
- cell_membrane.mdl.htm; (plain mdl)
- diffusion_space_boundary.mdl.htm; (plain mdl)
OpenDX Files for Rendering MCell Visualization Output
After the second example simulation has been run, the visualization output data can be rendered using OpenDX. To do so, start OpenDX and then open the visual program render_neuron_model.net. The DX Visual Program Editor window should display a page labeled README, which contains additional instructions for executing the visual program to render frames. The other pages included in the visual program are annotated to explain how the MCell data is imported and processed to add colors, molecule glyphs, etc. Other files used by the visual program during execution are render_neuron_model.cfg and GluR_glyph.dx.