This is the readme for the mcell simulation associated with the paper
Keller D, Babai N, Kochubey O, Han Y, Markram H, Schürmann F,
Schneggenburger R (2015) An Exclusion Zone for Ca2+ Channels around
Docked Vesicles Explains Release Control by Multiple Channels at a CNS
Synapse. PLoS Comput Biol 11:e1004253
The directory is organized into supporting subsolders and main
simulations. The supporting subfolders are:
data_files : data waveforms used for driving reaction rates
molecules : the base molecules used in the simulations
rates : the rates used by the reactions
geometry_files : geometry of the system
mechanisms : reactions that the molecules undergo
parameters : common parameters used by the simulation
There are four main simulations in the following directories:
small_AZ_random
small_AZ_exclusion
small_AZ_exclusion_EGTA
large_AZ_exclusion
Each of these contains a subfolder with an mcell_top.mdl and
variables.mdl file. The main file is mcell_top.mdl and variables
contains variables particular to that simulation.
To run the simulation, change to the subdirectory/1.0 and execute:
mcell mcell_top.mdl
In general, many seeds must be run due to the stochasticity of the
simulation.
Questions can be addressed to: daniel.keller@epfl.ch
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