Voltage and light-sensitive Channelrhodopsin-2 model (ChR2-H134R) (Williams et al. 2013) (NEURON)

 Download zip file 
Help downloading and running models
Accession:244414
" ... Focusing on one of the most widely used ChR2 mutants (H134R) with enhanced current, we collected a comprehensive experimental data set of the response of this ion channel to different irradiances and voltages, and used these data to develop a model of ChR2 with empirically-derived voltage- and irradiance- dependence, where parameters were fine-tuned via simulated annealing optimization. This ChR2 model offers: 1) accurate inward rectification in the current-voltage response across irradiances; 2) empirically-derived voltage- and light-dependent kinetics (activation, deactivation and recovery from inactivation); and 3) accurate amplitude and morphology of the response across voltage and irradiance settings. Temperature-scaling factors (Q10) were derived and model kinetics was adjusted to physiological temperatures. ... "
Reference:
1 . Williams JC, Xu J, Lu Z, Klimas A, Chen X, Ambrosi CM, Cohen IS, Entcheva E (2013) Computational optogenetics: empirically-derived voltage- and light-sensitive channelrhodopsin-2 model. PLoS Comput Biol 9:e1003220 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Channel/Receptor;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s): Channelrhodopsin (ChR);
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Ion Channel Kinetics;
Implementer(s): Giugliano, Michele [mgiugliano at gmail.com];
Search NeuronDB for information about:  Channelrhodopsin (ChR);
//
// Demo
// by Michele Giugliano, 7/8/2018 Trieste
//

load_file("nrngui.hoc")                   // Loading of the standard GUI controls...
load_file("graphs.hoc")            // Loading some ad-hoc proc for displaying live traces...

print "Demonstration of the ChR2-H134R model under voltage-clamp"
print "from:"
print "Williams JC, Xu J, Lu Z, Klimas A, Chen X, et al. (2013) Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin- 2 Model."
print "PLoS Comput Biol 9(9): e1003220. doi:10.1371/journal.pcbi.1003220"
print ""
print "Original (MATLAB) code by: John C. Williams"
print "Implemented by: Michele Giugliano, SISSA Trieste, 6/8/2018, mgiugliano@gmail.com"

celsius = 22

objref vc1, vc2

create soma1
access soma1
insert ChR2
light_delay_ChR2 = 10.
pulse_width_ChR2 = 1000.
insert pas
vc1 = new VClamp(0.5)
vc1.dur[0] = 10000.

create soma2
access soma2
insert ChR2
light_delay_ChR2 = 10.
pulse_width_ChR2 = 1000.
insert pas
vc2 = new VClamp(0.5)
vc2.dur[0] = 10000.

print "Figure 4B"
// Figure 4B
access soma1
light_intensity_ChR2 = 1.6
vc1.amp[0] = -40.

access soma2
light_intensity_ChR2 = 1.6
vc2.amp[0] = -80.

t = 0. 							// ms - initial simulation time
tstart = 0. 					// ms - initial simulation time
tstop = 1500 					// ms - final simulation time

addgraph("soma1.i_ChR2(0.5)", -.025, 0)
g[0].addvar("soma2.i_ChR2(0.5)", -2, 0)
run()



Loading data, please wait...