Simulation Results are presented in:
Postlethwaite M, Hennig MH, Steinert JR, Graham BP, Forsythe ID (2007) Acceleration of AMPA receptor kinetics underlies temperature-dependent changes in synaptic strength at the rat calyx of Held. J Physiol. 579(Pt 1): 69-84These simulations require MCell version 2 (specifically 2.76)
The MCell simulations are controlled by the following set of scripts:
calyx.mdl: the main simulation script.
geometry.mdl: definition of the synaptic geometry.
effectors.mdl: the postsynaptic AMPA receptors
parameters.mdl: definition of simulation parameters.
output.mdl: definition of simulation output.
3dout.mdl: defines rules for the output of visualisation data for DREAMM.
The simulations use the checkpointing mechanism of MCell to modify the diameter of the fusion pore that connects the vesicle with the extracellular space. Therefore, each simulation is controlled by a perl script. A whole set of simulations is controlled by the following perl scripts, which can be used to run multiple simulations in parallel on clusters:
prepare_simulation_scripts.pl: this script prepares one or multiple simulation with different parameter sets.
run.pl: this script runs a single simulation.
In these movies, glutamate molecules are shown in yellow, closed receptors in grey (light grey indicate unbound receptors, dark grey bound receptors), open receptors in red (the darker, the higher the associated conductance), and desensitised receptors in blue.
Movie showing release site from top, playing at 20 frames per sec (1 frame = 1 \mu s).