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                               */
/******************************************************/
/* source: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=85981 */
/* Used by D.Kufel */

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

  /* AMPA receptors */
  ADD_EFFECTOR {
    STATE = AMPAR.C0
    DENSITY = AMPAR_density
    /*NUMBER = AMPAR_number*/
    ELEMENT = BOTTOM
    POLE_ORIENTATION = POSITIVE_BACK
  }

  /* glutamate transporters (not simulated here) */
  /*
  ADD_EFFECTOR {
    STATE = GluT.T
    DENSITY = GluT_density
    ELEMENT = BOTTOM
    POLE_ORIENTATION = POSITIVE_BACK
  }
  */

  /* allow diffusion in/out of PSD */
  TRANSPARENT {LIGAND = Glu  ELEMENT = LEFT}
  TRANSPARENT {LIGAND = Glu  ELEMENT = RIGHT}
  TRANSPARENT {LIGAND = Glu  ELEMENT = FRONT}
  TRANSPARENT {LIGAND = Glu  ELEMENT = BACK}

}

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

/* fusion pore */
pore BOX {
  CORNERS = [-fpD/2,-fpD/2,cleft/2], [fpD/2,fpD/2,cleft/2+fpL]
  FULLY_CLOSED = YES
  TRANSPARENT { LIGAND = Glu ELEMENT = TOP }
  TRANSPARENT { LIGAND = Glu ELEMENT = 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]

  FULLY_CLOSED = YES

  /* 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 */
  TRANSPARENT {LIGAND = Glu  ELEMENT = LEFT}
  TRANSPARENT {LIGAND = Glu  ELEMENT = RIGHT}
  TRANSPARENT {LIGAND = Glu  ELEMENT = FRONT}
  TRANSPARENT {LIGAND = Glu  ELEMENT = BACK}
}