Computational modelling of channelrhodopsin-2 photocurrent characteristics (Stefanescu et al. 2013)

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Accession:150804
The codes are directly related with the results presented in the manuscript; in brief, it is a computational investigation on the effects of optogenetic actuation on excitatory and inhibitory neurons when 3- and 4- state model is used to implement the ChR2 kinetics. Different parameters of optostimulation are investigated and the results compared with experimental data previously published by other research groups.
Reference:
1 . Stefanescu RA, Shivakeshavan RG, Khargonekar PP, Talathi SS (2013) Computational modeling of channelrhodopsin-2 photocurrent characteristics in relation to neural signaling. Bull Math Biol 75:2208-40 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Channel/Receptor;
Brain Region(s)/Organism:
Cell Type(s): Hippocampus CA1 pyramidal cell; Hippocampus CA1 interneuron oriens alveus cell;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: MATLAB;
Model Concept(s):
Implementer(s): Stefanescu, Roxana [roxanast75 at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; Hippocampus CA1 interneuron oriens alveus cell;
% 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

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