Calyx of Held - Monte Carlo simulations
MCell scripts for the simulation of mEPSCs at the Calyx of Held
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): 69-84
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.
Movies generated with MCell and DREAMM
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).
A release from the perspective of someone sitting inside the synaptic cleft, 25 frames per sec (1 frame = 1 \mu s).
References
MCell at Salk Institute
MCell at PSC
DREAMM at PSC
Mattias Hennig
Last modified: Fri Feb 16 16:01:48 GMT 2007
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