Channelrhodopsin Photocycle: Four-State Gating Kinetics

Blue-Light Pulse

Irradiance (light intensity) 2.0 mW/mm²

Membrane voltage V_m -70 mV

Simulation speed 1.0×

Channel Population (N = 400)

C1 dark-closed O1 open O2 open (desens.) C2 closed

Photocurrent I

0.0 pA

Open fraction

0.0%

Photon rate F

0.0 s⁻¹

Time since flash

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How it works

Channelrhodopsin-2 (ChR2) is a light-gated cation channel: absorbing a blue photon (~470 nm) isomerizes its retinal chromophore and drives the protein through a photocycle with (at least) four kinetic states, following the standard 4-state model of Nikolic et al. / Williams et al.:

C1 --(F)--> O1 --(e12)--> O2
O1 --(Gd1)--> C2   O2 --(Gd2)--> C2   O2 --(e21)--> O1
C2 --(Gr)--> C1

F   = photon absorption rate  ∝ irradiance × cross-section σ
Gd1,Gd2 = dark-state decay rates of the two open states
e12,e21 = light-independent inter-open-state transitions
Gr  = slow thermal recovery, closed-desensitized → dark-adapted

Each of the 400 rendered channels is an independent Markov chain: every simulated millisecond it draws against each outgoing rate (probability ≈ rate × dt) and may hop to the next state, exactly like single-molecule patch-clamp recordings of real ChR2. The whole-cell photocurrent is the classic Ohmic form:

I(t) = N · g · (pO1 + γ·pO2) · (Vm − Erev)

where pO1, pO2 are the open-state occupied fractions, γ is O2's reduced conductance relative to O1, g is single-channel conductance, and Erev ≈ 0 mV is the (non-selective cation) reversal potential — so current flips sign as Vm crosses it, matching real ChR2 electrophysiology.

Flash — a single 500 ms light pulse: you'll see the fast rise to peak O1, the sag as channels shift into desensitized O2, and the biexponential decay back to C1/C2 after light-off — the signature ChR2 current shape.
Hold Light / Light Off — continuous illumination vs. darkness, to explore steady-state desensitization.
Irradiance — sets the photon absorption rate F; higher light drives faster, more complete activation.
Membrane voltage — moves Vm relative to the ~0 mV reversal potential, changing photocurrent magnitude and sign, as in real voltage-clamp experiments.

Real-world relevance: this exact kinetic scheme is what lets neuroscientists predict how a given light pulse shape will drive spiking when ChR2 is expressed in neurons — the basis of essentially all optogenetic circuit-control experiments.

C1 / C2 closed O1 open O2 open (desens.)

Photocurrent trace

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