Active zone model of Ca2+ secretion coupling (Keller et al. 2015)

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Accession:182142
"... At a large model synapse, the calyx of Held, transmitter release is controlled by several Ca2+ channels in a "domain overlap" mode, at least in young animals. To study the geometrical constraints of Ca2+ channel placement in domain overlap control of release, we used stochastic MCell modelling, at active zones for which the position of docked vesicles was derived from electron microscopy (EM). ..."
Reference:
1 . 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 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Synapse;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: MCell;
Model Concept(s):
Implementer(s):
Search NeuronDB for information about:  Glutamate;
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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