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 */
/*                                                    */
/* Simulation parameters                              */
/*                                                    */
/* Matthias Hennig                                    */
/* mhennig@inf.ed.ac.uk                               */
/******************************************************/
/* source: https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=85981 */
/* Modified by D.Kufel on 08/08/2016 */
/* Some parameters corrected to be equal to the Postlethwaite et al. 2007 - there */
/* were some discrepancies originally (compare with the source) */

/* KINETICS *********************/

/* factors to translate rate constants for temperature 25C -> 35C */
tf  = 1.0                              /* AMPAR kinetics */
tfd = 1.0                              /* diffusion */

/* AMPA receptor rate constants */
Rb  = 10e6 * tf
Ru1 = 8e3 * tf
Ro1 = 20e3 * tf
Rc1 = 10e3 * tf
Rd0 = 4e3 * tf
Rd1 = 4e3 * tf
Rr1 = 0.015e3 * tf
Rd2 = 10e6 * tf
Rr2 = 8e3 * tf

/* glutamate diffusion */
/* [cm^2/s], Franks et al., 2002 */
D = tfd * 3.0e-6                       

/* GEOMETRY *********************/

/* vesicle diameter */
/* [\mu m], Sätzler et al., 2002, assuming membrane thickness 6nm */
/* 40nm => volume 133510nm^3 => box d=32nm */
vDiam = 0.032                          

/* fusion pore dimensions */
fpD = 0.009                           
fpL = 0.009                           /* approx 1.5 * membrane thickness */

/* synaptic cleft */
/* diameter of PSD in [\mu m], == area 0.1 \mu m^2, Sätzler et al., 2002  */
Rex = 0.317                           
/* separation in [\mu m] , volume 0.0028 \mu m^3, Sätzler et al., 2002 */
cleft = 0.028                         

/* assuming 80 AMPARs/AZ */
AMPAR_number = 80
/* extra-PSD AMPARs */
AMPAR_number_far = 0
/* the same expressed as density */
AMPAR_density = 796
AMPAR_density_far = 0

/* number of glu molecules/vesicle */
n = 6000

/* glu transporters */
GluT_density = 0                      /* no transporters in calyx reported (only glial) */
vesicle_pos = 0.0 

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