% All the codes have introductory explanations that could be accessed
% with the command "help" in Matlab
%
% The folders contain the following codes:
%
% ChR2 contains two subfolders: FitChR2_4StateModel and ChR2_3StateModel
%
% FitChr2_4StateModel folder contains all the codes necessary to employ 
% search & optimization algorithms to find the best 4-state parameters to 
% fit the empirical profile; it also provides examples of comparison between the 
% empirical profile and the photocurrent evaluated with the 4-state model 
% (differential equations) for the best parameters we have found for ChRwt and
% ChETA modeled based on the experimental data provided by Gunaydin et al. 2010
%
% ChR2_3StateModel comprises the coded to generate the response to
% optostimulation of 1s and 2 ms starting from ideal initial conditions (IIC)
% and special initial conditions (SIC); Nicolic3stateGr_2stimuli.m is
% investigating the recovery of ChR2 by evaluating the photocurrent in 
% response to two consective stimuli of 1s each; the code could be easily
% modified to generate the recovery curve for ChR2
%
% The WB folder contains codes used to address the response of an
% interneuron (with dynamics given by Wang-Buszaki neuron model) expressing
% ChRwt or ChETA to various optostimulation protocols when either the
% 3-state or the 4-state model is accounting for ChR2 kinetics
%
% The Gol folder contains codes used to address the response of a
% pyramidal neuron (with dynamics given by Golomb neuron model) expressing
% ChRwt or ChR ET/TC to various optostimulation protocols when either the
% 3-state or the 4-state model is accounting for ChR2 kinetics
%
% The folder ThSol contains the code employed to evaluate the
% semi-analythical solution for the 4-state model in Light On condition;
% the Light Off solution provided by Nikolic et al. 2009 is also evaluated