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Biophysical Models


Optogenetics has been a revolution in the way we communicate with the nervous system. It derives from the 2003 PNAS paper by Nagel and co-workers which described the genetic insertion of channelrhodopsin-2 into cells to make them light sensitive. Channelrhodopsin-2 is an optically active channel protein from an alga that allows for transmission of cations across cell membranes. As cations such as sodium are key to neuroelectronic function, inserting this optically active channel unto cell membranes render them light sensitive.

The ability to use gene therapy techniques to photosensitize specific cells is what makes this technique so powerful. can be used to target specific cells types. For example, specifically photosensitizing inhibitory excitory cells allows for much more powerful neural control. Furthermore, the technique has been demonstrated in animals from invertebrates to non-human primates, and is now undergoing clinical trials in humans.

In recent years there has been considerable focus to develop new variants of channelrhodopsin – different light sensitivity as well both inhibitory and excitory variants. However, one of the key challenges is that Channelrhodopsin-2 has a very high light requirement for activation – typically defined as 0.7mW/mm2 on the cell. This generates both technical and regulatory challenges.


  1. What is the optimal stimulus method from an engineering perspective?

  2. What is the light requirement at different Tissue depth?

  3. Will intense light creation by implantables lead to unacceptable tissue heating?

  4. Will the blue light cause photochemical damage to the tissue?

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Figure 1: Results from biophysical modelling. (Left) The 4-state model of channelrhodopsin (Middle) Optical penetration of light into tissue (Right) Thermal modelling of LED probes

Optimal stimulus: In our papers by Nikolic et al. and Grossman et al., we combined a 4-state model of channelrhodopsin with a Hodgkin Huxley model of Channelrhodopsin-2. There are some detailed conclusions that can be drawn for any specific system. But a key conclusion is that as there is a low-efficiency light-adapted state for channelrhodopsin; short, high-intensity pulses prove most efficient for stimulus. Models available upon request.


Light transmission through tissue: Channelrhodopsin-2 encoded cells are considered to have a threshold of 0.7mW/mm2. This “threshold” is defined as what is required to achieve 50% stimulus in dissociated cells. So there is still some effect even below this level. In order to achieve this, light must traverse through tissue, which will tend to be backscattered. Furthermore, for non-collimated emitters such as LEDs, the emitted light will have an emission angle thus spreading light over a wide space. Na et all, therefore, developed a Monte Carlo model to explore the 3D decay profile. Models available upon request

Tissue heating effects: Light can be created externally and guided to the target tissue via optic fibres, or it can be generated locally. The latter allows for electronic multiplexing, but although best-in-class LEDs can be up to 80% efficient, micro LEDs used in optical probes have varied in wall plug efficiencies from 1%-30% efficiency. As the rest of the energy gets converted to heat, there is a possibility of local hot spots. Using a COMSOL finite element model of brain probes, we found that the thermal emission of the LEDs over a short duration should not exceed 5.2mW. Models available upon request

Photochemical degradation: In the 2009 study by Degenaar et al. and the 2018 study by Soltan et al., we explored the limits to blue light excitation of tissue from the regulatory perspective. Specific stimuli regimes need to be put in place to ensure that for 470nm light, the average irradiance in any 10,000 s period should not exceed 0.05mW/mm2. Calculations are available upon request.


Ahmed Soltan, John Martin Barrett, Pleun Maaskant, Niall Armstrong, Walid Al-Atabany, Lionel Chaudet, Mark Neil, Evelyne Sernagor and Patrick A head mounted device stimulator for optogenetic retinal prosthesis Journal of Neural Engineering, Volume 15, Number 6 Oct 2018

Na Dong, Ahmed Soltan, Rolando Berlinguer Palmini Nikhil Ponon, Anthony O’Neil, Andrew Trevelyan, Patrick Degenaar, Xiaohan Sun, "Opto-electro-thermal optimisation of optoelectronic probes for optogenetic neural stimulation" Submitted to Journal of Biophotonics – accepted and in revision with minor corrections to grammar DOI:10.1002/jbio.201700358

Grossman N, et al. Modeling Study of the Light Stimulation of a Neuron Cell With Channelrhodopsin-2 Mutants. IEEE T. on Biomedical Engineering 2011, 58(6), 1742-1751.

Nikolic K, Loizu J, Degenaar P, Toumazou C. A stochastic model of the single photon response in Drosophila photoreceptors. Integrative Biology 2010, 2, 354-370.

Nikolic K, et al. Photocycles of channelrhodopsin-2. Photochemistry and Photobiology 2009, 85(1), 400-411.

Degenaar P., Optobionic vision: a new genetically enhanced light on retinal prosthesis. Journal of Neural Engineering 2009, 6(3), 035007.

Nikolic K, et al. Noise reduction in analogue computation of Drosophila photoreceptors. Journal of Computational Electronics 2008, 7(3), 458-461.

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