Analytical modelling of temperature effects on an AMPA-type synapse (Kufel & Wojcik 2018)

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Accession:239072
This code was used in the construction of the model developed in the paper. It is a modified version of the simulation developed by Postlethwaite et al. 2007 - for details of modifications refer to the main body of Kufel & Wojcik (2018).
Reference:
1 . Kufel DS, Wojcik GM (2018) Analytical modelling of temperature effects on an AMPA-type synapse. J Comput Neurosci 44:379-391 [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): AMPA;
Gene(s):
Transmitter(s): Glutamate;
Simulation Environment: MCell; Python;
Model Concept(s): Methods; Temperature;
Implementer(s): Kufel, Dominik [dominic.kufel at gmail.com];
Search NeuronDB for information about:  AMPA; Glutamate;
/******************************************************/
/* A simple model of a single AZ at the calyx of Held */
/*                                                    */
/* Main simulation script                             */
/*                                                    */
/* Matthias Hennig                                    */
/* mhennig@inf.ed.ac.uk                               */
/******************************************************/
/* source: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=85981 */
/* Used by D.Kufel */


/* time step */
dt = 1.0e-6

/* number of iterations */
it = 3000

TIME_STEP = dt
ITERATIONS = it
EFFECTOR_GRID_DENSITY = 10000
RADIAL_SUBDIVISIONS = 2^10
RADIAL_DIRECTIONS = 2^14 /* FULLY_RANDOM would be 2^15 */

/* this file contains the relative diameter of the fusion pore */
/* it is constantly updated during the run time of the simulation */
INCLUDE_FILE = "pore_scale"

pore_scale = 1-EXP(-(abs_time/10)*0.1)

CHECKPOINT_INFILE = "chkpt_pos"
CHECKPOINT_OUTFILE = "chkpt_pos"
CHECKPOINT_ITERATIONS = check_time

/* load simulation parameters */
INCLUDE_FILE = "parameters.mdl"

/* SIMULATION *********************/

INCLUDE_FILE = "effectors.mdl"
INCLUDE_FILE = "geometry.mdl"

/**********************************/

/* the synapse, here one PSD */
INSTANTIATE coh OBJECT {

  /* relase site/point source of glutamate in the centre of the vesicle */
  transmitter_release_site SPHERICAL_RELEASE_SITE {
    LOCATION = [-Rex*vesicle_pos,0,cleft/2+fpL+vDiam/2]
    LIGAND = Glu
    NUMBER_TO_RELEASE = n
    SITE_DIAMETER = 0.0
  }

  /* insert objects that constitute the synaptic cleft */
  cleft1 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,Rex/2,0 ] }
  cleft2 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,-3*Rex/2,0 ] }
  cleft3 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,-Rex/2,0 ] }
  cleft4 OBJECT synaptic_cleft_element { TRANSLATE=[-Rex/2,-3*Rex/2,0 ] }
  cleft5 OBJECT synaptic_cleft_element { TRANSLATE=[-Rex/2,Rex/2,0 ] }
  cleft6 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,-3*Rex/2,0,0 ] }
  cleft7 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,Rex/2,0,0 ] }
  cleft8 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,-Rex/2,0,0 ] }

  cleft9 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,Rex/2,0 ] }
  cleft10 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,-3*Rex/2,0 ] }
  cleft11 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,-3*Rex/2,0,0 ] }
  cleft12 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,Rex/2,0,0 ] }
  cleft13 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,3*Rex/2,0 ] }
  cleft14 OBJECT synaptic_cleft_element { TRANSLATE=[-3*Rex/2,-5*Rex/2,0 ] }
  cleft15 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,3*Rex/2,0 ] }
  cleft16 OBJECT synaptic_cleft_element { TRANSLATE=[Rex/2,-5*Rex/2,0 ] }
  cleft17 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,3*Rex/2,0 ] }
  cleft18 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,-5*Rex/2,0 ] }
  cleft19 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,3*Rex/2,0 ] }
  cleft20 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,-5*Rex/2,0 ] }

  cleft25 OBJECT synaptic_cleft_element { 
    SCALE=[2,9,1]
    TRANSLATE=[-9*Rex/2,-9*Rex/2,0 ] 
  }
  cleft26 OBJECT synaptic_cleft_element { 
    SCALE=[2,9,1]
    TRANSLATE=[5*Rex/2,-9*Rex/2,0 ] 
  }
  cleft27 OBJECT synaptic_cleft_element { 
    SCALE=[5,2,1]
    TRANSLATE=[-5*Rex/2,-9*Rex/2,0 ] 
  }
  cleft28 OBJECT synaptic_cleft_element { 
    SCALE=[5,2,1]
    TRANSLATE=[-5*Rex/2,5*Rex/2,0 ] 
  }

  /* the postsynaptic densities */
  psd OBJECT psd {}

  /* if these are removed, only the central PSD is active */
  psd2 OBJECT psd {TRANSLATE=[-2*Rex, 0 ,0 ] }
  psd3 OBJECT psd {TRANSLATE=[2*Rex, 0 ,0 ] }
  psd4 OBJECT psd {TRANSLATE=[0, -2*Rex ,0 ] }
  psd5 OBJECT psd {TRANSLATE=[0, 2*Rex ,0 ] }

/* These replace the four PSDs psd2-psd5 if only one PSD is to be simulated:
  cleftp1 OBJECT synaptic_cleft_element { TRANSLATE=[-5*Rex/2,Rex/2,0 ] }
  cleftp2 OBJECT synaptic_cleft_element { TRANSLATE=[3*Rex/2,Rex/2,0 ] }
  cleftp3 OBJECT synaptic_cleft_element { TRANSLATE=[-1*Rex/2,-4*Rex/2,0 ] }
  cleftp4 OBJECT synaptic_cleft_element { TRANSLATE=[-1*Rex/2,5*Rex/2,0 ] }
*/


  vesicle OBJECT vesicle {TRANSLATE=[-Rex*vesicle_pos, 0 ,0 ] }
  pore OBJECT pore {TRANSLATE=[-Rex*vesicle_pos, 0 ,0 ] }

}

/* write simulation results to a file */
INCLUDE_FILE = "output.mdl"

/* uncomment to create a movie of the simulation */
/* INCLUDE_FILE = "3dout.mdl" */


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