Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012)

 Download zip file 
Help downloading and running models
A computational tool to explore the underlying principles of optogenetic neural stimulation. This "light-neuron" model consists of theoretical representations of the light dynamics generated by a fiber optic in brain tissue, coupled to a multicompartment cable model of a cortical pyramidal neuron (Hu et al. 2009, ModelDB #123897) embedded with channelrhodopsin-2 (ChR2) membrane dynamics. Simulations predict that the activation threshold is sensitive to many of the properties of ChR2 (density, conductivity, and kinetics), tissue medium (scattering and absorbance), and the fiber-optic light source (diameter and numerical aperture). This model system represents a scientific instrument to characterize the effects of optogenetic neuromodulation, as well as an engineering design tool to help guide future development of optogenetic technology.
1 . Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron. J Neurophysiol 107:3235-45 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon; Channel/Receptor; Dendrite;
Brain Region(s)/Organism:
Cell Type(s): Neocortex L5/6 pyramidal GLU cell;
Channel(s): I K; I M; I K,Ca; I Sodium; I Calcium; Channelrhodopsin (ChR);
Gap Junctions:
Simulation Environment: NEURON; Python;
Model Concept(s): Detailed Neuronal Models; Action Potentials; Parameter sensitivity; Intracortical Microstimulation; Neuromodulation;
Implementer(s): MacIntyre, CC [ccm4 at case.edu]; Foutz, Thomas J [tfoutz at uw.edu]; Arlow, Richard L [richard.arlow at case.edu];
Search NeuronDB for information about:  Neocortex L5/6 pyramidal GLU cell; I K; I M; I K,Ca; I Sodium; I Calcium; Channelrhodopsin (ChR);
:26 Ago 2002 Modification of original channel to allow
: variable time step and to correct an initialization error.
:    Done by Michael Hines(michael.hines@yale.edu) and Ruggero Scorcioni(rscorcio@gmu.edu)
: at EU Advance Course in Computational Neuroscience. Obidos, Portugal

TITLE decay of internal calcium concentration
: Internal calcium concentration due to calcium currents and pump.
: Differential equations.
: Simple model of ATPase pump with 3 kinetic constants (Destexhe 92)
:     Cai + P <-> CaP -> Cao + P  (k1,k2,k3)
: A Michaelis-Menten approximation is assumed, which reduces the complexity
: of the system to 2 parameters:
:       kt = <tot enzyme concentration> * k3  -> TIME CONSTANT OF THE PUMP
:	kd = k2/k1 (dissociation constant)    -> EQUILIBRIUM CALCIUM VALUE
: The values of these parameters are chosen assuming a high affinity of
: the pump to calcium and a low transport capacity (cfr. Blaustein,
: TINS, 11: 438, 1988, and references therein).
: Units checked using "modlunit" -> factor 10000 needed in ca entry
: VERSION OF PUMP + DECAY (decay can be viewed as simplified buffering)
: All variables are range variables
: This mechanism was published in:  Destexhe, A. Babloyantz, A. and
: Sejnowski, TJ.  Ionic mechanisms for intrinsic slow oscillations in
: thalamic relay neurons. Biophys. J. 65: 1538-1552, 1993)
: Written by Alain Destexhe, Salk Institute, Nov 12, 1992
: 20150524 NTC
: Changed integration method from euler to derivimplicit
: which is appropriate for simple ion accumulation mechanisms.
: See
: Integration methods for SOLVE statements
: http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592

	USEION ca READ ica, cai WRITE cai
	GLOBAL depth,cainf,taur

	(molar) = (1/liter)			: moles do not appear in units
	(mM)	= (millimolar)
	(um)	= (micron)
	(mA)	= (milliamp)
	(msM)	= (ms mM)
	FARADAY = (faraday) (coulomb)

	depth	= 0.1	(um)		: depth of shell
	taur	= 200	(ms)		: rate of calcium removal
	cainf	= 100e-6(mM)
	cai		(mM)

	ca		(mM) <1e-5>

	ca = cainf
	cai = ca

	ica		(mA/cm2)
	drive_channel	(mM/ms)

	SOLVE state METHOD derivimplicit : not euler
    : see http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592

	drive_channel =  - (10000) * ica / (2 * FARADAY * depth)
	if (drive_channel <= 0.) { drive_channel = 0. }	: cannot pump inward

	ca' = drive_channel + (cainf-ca)/taur
	cai = ca

Loading data, please wait...