Optogenetics

Excitation and silencing of neurons with light-gated proteins, and the limits of each tool.

Guided experiment: Controlling a neuron with light in a brain slice.

Optogenetics makes chosen neurons sensitive to light by giving them the gene for a light-gated microbial protein, an opsin. Channelrhodopsin-2 opens a cation channel in blue light and excites the cell; the halorhodopsin eNpHR3.0 pumps chloride ions into the cell in yellow light and inhibits it. Boyden and colleagues showed that channelrhodopsin-2 can drive spikes in mammalian neurons with millisecond precision (Boyden et al., 2005).

Design the experiment

Questions to investigate

Drive the neuron with channelrhodopsin-2 at increasing pulse frequencies. At what frequency does it stop following every pulse?
Repeat with Chronos, a faster channelrhodopsin. How far can the frequency now be pushed?
Find the lowest light intensity that still evokes a spike for every pulse.
Use eNpHR3.0 to silence a spontaneously active neuron. What happens when the light goes off?
Run the opsin-negative control. Why must every real optogenetic experiment include it?

In a real laboratory

Opsins are delivered with a viral vector or a genetically modified line so that only the chosen cell type expresses them, and light reaches the brain through an implanted optical fibre. Expression is confirmed in tissue after the experiment. Control animals receive the same light without an opsin, because light can heat tissue and can be seen by the animal. All procedures require approval by an Institutional Animal Ethics Committee (in India, under the CCSEA and the Prevention of Cruelty to Animals Act 1960; elsewhere, the equivalent national body).

How the simulation works

The neuron is a Hodgkin–Huxley model with accelerated kinetics, so that action potentials are about 0.5 ms wide at half amplitude, as in many fast-spiking mammalian neurons. A fluctuating background input can make it fire spontaneously. Each opsin is a kinetic model with opening and closing time constants and a light sensitivity, with approximate values based on published comparisons (Gradinaru et al., 2010; Mattis et al., 2011; Klapoetke et al., 2014). Channelrhodopsins pass a depolarising current; eNpHR3.0 produces a hyperpolarising pump current. Tissue heating, light scattering and differences in expression between cells are not simulated.

Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., & Deisseroth, K. (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nature Neuroscience, 8(9), 1263–1268. https://doi.org/10.1038/nn1525
Gradinaru, V., Zhang, F., Ramakrishnan, C., et al. (2010). Molecular and cellular approaches for diversifying and extending optogenetics. Cell, 141(1), 154–165. https://doi.org/10.1016/j.cell.2010.02.037
Mattis, J., Tye, K. M., Ferenczi, E. A., et al. (2011). Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins. Nature Methods, 9(2), 159–172. https://doi.org/10.1038/nmeth.1808
Klapoetke, N. C., Murata, Y., Kim, S. S., et al. (2014). Independent optical excitation of distinct neural populations. Nature Methods, 11(3), 338–346. https://doi.org/10.1038/nmeth.2836

About the simulations

Each simulator is a simplified version of a published model of cells, signals, instruments or behaviour, and runs in the web browser. The simulations show how the techniques work and how design choices change the results; they do not replace training in a laboratory.

All data are simulated and generated afresh on each run, so results vary between runs, as in real experiments. Nothing is stored or sent: designs and results are lost when the page is closed, unless the protocol is copied or the data file is downloaded.

Last updated 20 October 2026