Real structures. Explicit teaching simplifications.
The Clear view and all teaching activities run offline. Molecular view retrieves experimental coordinates from the Protein Data Bank. A fixed structure is not a movie of a functioning channel: the gate markers and ion paths are explanatory overlays.
Backbone traces join resolved Cα atoms; heavy-atom view shows deposited non-hydrogen coordinates. Unresolved stretches are left as gaps. Bound toxins, lipids and accessory proteins are omitted as described below. The snapshots are representative channel/pump structures, not a single experimentally reconstructed axon. Protein sizes, membrane placement and ion radii are adjusted for clarity. No structural transition is calculated.
An explicitly schematic time course uses −70 mV at rest, a −55 mV threshold example, a +30 mV peak and an −80 mV undershoot. Channel-opening and refractory-period graphics are illustrative and intentionally simplified. Individual neurones do not all have these exact values or timings.
A single-compartment Hodgkin–Huxley model calculates voltage-dependent Na⁺ activation, Na⁺ inactivation and delayed K⁺ activation. The classical voltage axis is shifted by −5 mV. Threshold emerges from the equations; the dashed −55 mV line is a reference, not a programmed trigger. Times retain the classical squid-model kinetics and are not human-axon measurements.
The 3 Na⁺ out / 2 K⁺ in pump cycle is a qualitative animation and runs in every phase. Neither the pump nor concentration changes are explicitly solved in the experiment. The model uses a lumped leak current: the displayed K⁺ leak protein is a separate biological teaching schematic, not a literal mapping of that term.
Particles show typical distributions and net transport directions, not a counted ion pool. Bulk Na⁺ and K⁺ concentrations do not swap during a spike. Only a tiny fraction of the ions needs to move to change membrane voltage. Other ions, water and fixed intracellular anions are omitted. Charges are shown only near membrane faces.
Physics & Maths Tutor — Communication and Homeostasis, section on nerve impulse conduction. Used to check teaching scope and UK terminology; explanations here are newly written, not copied.
Qualification content overview — neuronal communication.
Hodgkin & Huxley (1952), A quantitative description of membrane current and its application to conduction and excitation in nerve. Basis of the experiment, not a claim that these structural snapshots were used to fit the model.
Integration uses fourth-order Runge–Kutta with a 0.01 ms step. Cₘ = 1 µF cm⁻²; maximal gNa = 120, gK = 36 and gL = 0.3 mS cm⁻². Reversal potentials are +45, −82 and −59.387 mV. Classical rate equations are evaluated at V + 5 mV. Reduced K⁺ conductance sets gK = 9; Na⁺ block sets gNa = 0. The intervention starts at 2 ms from the normal initial resting state. No irreversible damage or depletion is modelled.
CSV exports contain model voltage, activation/inactivation variables, Na⁺ and K⁺ currents, and input current. They are simulated data, not recordings. The graph reports upward crossings of 0 mV as spikes; this is a detection convention, not the excitation threshold.
Play the guided journey once. Then turn on “Pause each step”. Ask students to predict the next ion movement before revealing it. Clicking a stage lands at a representative moment; clicking or dragging the graph lets you inspect the transitions.
In Experiment, run one pulse at 5, then 12, then 24. Pin each trace. The weak response is a local depolarisation, not a small action potential. The two full spikes have broadly similar peaks but different delays. Compare 12 and 24 under “Hold input” for frequency.
Use “Two pulses” at strength 16. Compare separations of 4 and 14 ms. Then explore intermediate separations and a doubled second pulse. Early Na⁺ inactivation prevents another spike; later, increased K⁺ permeability and incomplete recovery make excitation harder. No fixed refractory cutoff is imposed in the experiment.
Voltage means inside relative to outside, not the number of ions present. The guided trace is schematic. The experiment uses classical squid-model kinetics, so its exact timings and voltages are not values for students to memorise. Switching modes clears pinned comparisons.
Drag for unrestricted orbit, including underneath and behind the membrane. Shift-drag or right-drag to pan; scroll to zoom. On a touch screen, use one finger to orbit and two fingers to pan and pinch. Use View for front, back, outside or axoplasm perspectives; Focus centres a selected channel for closer inspection. Cutaway removes the facing half of the protein, revealing the ion route without moving it in front of the protein. Reset view restores the overview.
Normal takes about 85 seconds for the guided journey. Choose Slow or Very slow to follow individual ions, or Fast to review the sequence. Na⁺ influx remains denser and faster than the resting K⁺ leak. The time axis shows illustrative biological time; playback is slowed for observation. Pause freezes the animation.
Ion routes and gates share each channel’s central axis in 3D. Imported Na⁺ and K⁺ structures are rigidly oriented using their pore landmarks; pump placement is approximate. If those landmarks cannot be identified, the scene explicitly uses a schematic while the full coordinate model stays available in the protein explorer. Cutaway is a viewing tool, not a biological opening of half the protein. Ion paths, sizes and gate movements remain explanatory, not calculated molecular trajectories.
Space: play/pause. Left/right arrows: previous/next guided stage, or scrub the experiment. R: reset view. Escape: close a panel. The timeline slider also supports standard keyboard input. Shortcuts do not override focused form controls. All proteins have equivalent accessible buttons in the channel-state panel. Light projector view is available in the header.
Along an axon, local currents depolarise the next region and regenerate the action potential. The refractory region behind the advancing wave resists re-excitation. The same Na⁺ ions do not travel all the way along the axon. Propagation, synapses, myelin and saltatory conduction are not spatially simulated here.