geometry.mdl

/******************************************************/
/* A simple model of a single AZ at the calyx of Held */
/*                                                    */
/* Celft and Vesicle Geometry                         */
/*                                                    */
/* Matthias Hennig                                    */
/* mhennig@inf.ed.ac.uk                               */
/******************************************************/

DEFINE_SURFACE_CLASSES
{
  transp_Glu
  {
    TRANSPARENT = Glu
  }
}

/* the PSD with receptors */
psd BOX {
  CORNERS = [-Rex/2,-Rex/2,-cleft/2], [Rex/2,Rex/2,cleft/2]

  /* allow diffusion in/out of PSD */
  DEFINE_SURFACE_REGIONS
  {
    sr { INCLUDE_ELEMENTS = [LEFT, RIGHT, FRONT, BACK] }
    bottom { 
      INCLUDE_ELEMENTS = [BOTTOM]
      MOLECULE_DENSITY { AMPAR_C0, = AMPAR_density }
    }
  }

}

/* the vesicle */
vesicle BOX {
  CORNERS = [-vDiam/2,-vDiam/2,cleft/2+fpL], [vDiam/2,vDiam/2,cleft/2+fpL+vDiam]
}

/* fusion pore */
pore BOX {
  CORNERS = [-fpD/2,-fpD/2,cleft/2], [fpD/2,fpD/2,cleft/2+fpL]
  DEFINE_SURFACE_REGIONS
  {
    sr { INCLUDE_ELEMENTS = [TOP, BOTTOM] }
  }
  SCALE = [pore_scale,pore_scale,1.0]
}

/* template for a synaptic celft element */
synaptic_cleft_element BOX {
  CORNERS = [0,0,-cleft/2], [Rex,Rex,cleft/2]

  /* AMPA receptors */
  /*ADD_EFFECTOR {*/
  /*  STATE = AMPAR.C0*/
  /*  DENSITY = AMPAR_density_far*/
  /*  [>NUMBER = AMPAR_number_far<]*/
  /*  ELEMENT = BOTTOM*/
  /*  POLE_ORIENTATION = POSITIVE_BACK*/
  /*}*/

  /* allow diffusion in/out of celft */
  DEFINE_SURFACE_REGIONS
  {
    sr { INCLUDE_ELEMENTS = [LEFT, RIGHT, FRONT, BACK] }
    bottom { INCLUDE_ELEMENTS = [BOTTOM] }
  }
}

MODIFY_SURFACE_REGIONS
{
  psd[sr]
  {
    SURFACE_CLASS = transp_Glu
  }
  pore[sr]
  {
    SURFACE_CLASS = transp_Glu
  }
  synaptic_cleft_element[sr]
  {
    SURFACE_CLASS = transp_Glu
  }
}