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

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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.
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 GLU cell; Hippocampus CA1 interneuron oriens alveus GABA cell;
Gap Junctions:
Simulation Environment: MATLAB;
Model Concept(s):
Implementer(s): Stefanescu, Roxana [roxanast75 at];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; Hippocampus CA1 interneuron oriens alveus GABA cell;
% This function is designed to integrate the WB model with ChR2 kinetics
% provided by the 4-state model;
% Last update: RAS 09/10/2012

function Vmdot = buszaki_chr(t,Vmh,P1,P2);

global Cm phi gNa ENa gK EK gL EL Idc
global Gd1 Gd2 Gr e12 e21 g1 gama tau_ChR

% WB model with ChR2
V = Vmh(1); h = Vmh(2); n = Vmh(3);
y(1) = Vmh(4); y(2) = Vmh(5); y(3) = Vmh(6); y(4) = Vmh(7);

            am = -0.1*(V+35)/(exp(-0.1*(V+35)) - 1);
            ah = 0.07*exp(-(V+58)/20);
            an = -0.01*(V+34)/(exp(-0.1*(V+34)) - 1);

            bm = 4*exp(-(V+60)/18);
            bh = 1/(exp(-0.1*(V+28)) + 1);
            bn = 0.125*exp(-(V+44)/80);

            minf = am/(am+bm);

                    % evaluating the currents
                    INa  = gNa*(minf^3)*h*(V-ENa);
                    IK   = gK*(n^4)*(V-EK);
                    IL   = gL*(V-EL);
                    %IChR = 0;
                    IChR = V*g1*(y(1)+gama*y(2));
                    Itot = -INa - IK - IL - IChR + Idc;

% integration
hdot = phi*(ah*(1-h) - bh*h);
ndot = phi*(an*(1-n) - bn*n);

% 4-state model
S0 = 0.5*(1+tanh(120*((P1>0) - 0.1))); 

 dy(1) = P1*y(4)*(1-y(1)-y(2)-y(3))-(Gd1+e12)*y(1) + e21*y(2);
 dy(2) = P2*y(4)*y(3) + e12*y(1) - (Gd2+e21)*y(2);
 dy(3) = Gd2*y(2) - (P2*y(4)+Gr)*y(3);
 dy(4) = (S0 - y(4))/tau_ChR;
 Vdot = (Itot/Cm);

 Vmdot = [Vdot hdot ndot dy(1) dy(2) dy(3) dy(4)];

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