This is the readme for the models associated with the paper:
Rahul Gupta, Melissa Reneaux, Karmeshu (2016) Role of Macromolecular
Crowding and Geometrical Irregularity at Central Excitatory Synapses
in Shaping Synaptic Transmission. PLOS ONE
MATLAB Scripts for the Numerical Simulation of Glutamate Diffusion,
Stochastic AMPA Receptor Activation and EPSC generation
This code was contributed by Rahul Gupta.
There are three folders:
It contains scripts for two seperate situations of glutamate
diffusion viz. (a) Standard diffusion with zero sigma_Dglut and
(b) Diffusion with non-zero sigma_Dglut. Both these scripts
perform simulation of the Brownian dynamics of glutamate diffusion
within the cleft space under the prescribed absorbing and
reflecting boundary conditions.
It contains scripts for the stochastic activation of AMPA
receptors located in the PSD in response to the temporal profile
of the local glutamate concentration obtained from the numerical
simulation of glutamate diffusion. The script
"AMPAR_activation_GillspiAlgorithm.m" perform the stochastic
activation of AMPA receptors using modified Gillespie algorithm
proposed by Skaugen and Walloe (1979). During simulation, it
repeatedly calls another script "AMPAR_activation_MNscheme.m",
which contains kinetic parameters of transition among the various
states of AMPA receptor under the Milstein-Nicoll scheme.
It contains a single script to compute the resultant profile of
EPSC generated due to stochastic AMPA receptor activation.