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    <title>Calyx of Held - Monte Carlo simulations</title>
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    <h1>MCell scripts for the simulation of mEPSCs at the Calyx of Held</h1>

    <p>Simulation Results are presented in:</p>

    <cite>
      Postlethwaite M, Hennig MH, Steinert JR, Graham BP, Forsythe ID
      (2007) <a
      href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17138605&query_hl=5&itool=pubmed_docsum">
      Acceleration of AMPA receptor kinetics underlies
      temperature-dependent changes in synaptic strength at the rat
      calyx of Held. </a> J Physiol. 579(Pt 1): 69-84
    </cite>
    <p><b>These simulations require MCell version 2 (specifically 2.76)</b></p>

    <p>The MCell simulations are controlled by the following set of
    scripts:</p>

    <p><a href="MCell_scripts/calyx.mdl">calyx.mdl</a>: the main simulation script.</p>

    <p><a href="MCell_scripts/geometry.mdl">geometry.mdl</a>: definition of the synaptic geometry.</p>


    <p><a href="MCell_scripts/effectors.mdl">effectors.mdl</a>: the postsynaptic AMPA receptors</p>

    <p><a href="MCell_scripts/parameters.mdl">parameters.mdl</a>: definition of simulation parameters.</p>

    <p><a href="MCell_scripts/output.mdl">output.mdl</a>: definition of simulation output.</p>

    <p><a href="MCell_scripts/3dout.mdl">3dout.mdl</a>: defines rules
    for the output of visualisation data for DREAMM.</p>

    <p>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:</p>

    <p><a
    href="MCell_scripts/prepare_simulation_script.pl">prepare_simulation_scripts.pl</a>:
    this script prepares one or multiple simulation with different
    parameter sets.</p>

    <p><a href="MCell_scripts/run.pl">run.pl</a>: this script runs a single simulation.</p>

    <h1>Movies generated with MCell and DREAMM</h1>

    <p>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.</p>

    <a href="http://www.cn.stir.ac.uk/~mhh1/Calyx/overview_movie_25fps.avi">Movie showing release site from top, playing at 20 frames per sec (1 frame = 1 \mu s).</a>

<br />

    <a href="http://www.cn.stir.ac.uk/~mhh1/Calyx/inside_movie_25fps.avi">A release from the perspective of someone sitting inside the synaptic cleft, 25 frames per sec (1 frame = 1 \mu s).</a>

    <h1>References</h1>
    <p><a href="http://www.mcell.cnl.salk.edu/">MCell at Salk Institute</a></p>
    <p><a href="http://www.mcell.psc.edu/">MCell at PSC</a></p>
    <p><a href="http://www.mcell.psc.edu/DReAMM/">DREAMM at PSC</a></p>

    <hr>
    <address>Mattias Hennig</a></address>
<!-- Created: Thu Jan 19 17:38:56 GMT 2006 -->
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Last modified: Fri Feb 16 16:01:48 GMT 2007
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