AFM simulation references

This is a synthetic teaching model, not a calibrated instrument or a manufacturer operating procedure. The moving-probe view shows a laser source travelling with the cantilever, with a stationary sample and detector. This is one possible AFM arrangement, not a universal design. The light-collection path is an idealized illustration; it does not turn scan translation into a measured deflection signal. Tip size and vertical height are exaggerated for visibility.

Optical-layout reference: Digital Instruments, US6032518A. The description of Figure 3 documents a moving laser/cantilever and stationary detector, including possible scan-induced detector shifts. Later figures describe stationary-source alternatives.

What is calculated

The geometric envelope uses a sphere-capped 20-degree cone. Sphere and step samples use analytic physical-coordinate envelopes; the smooth polymer uses numerical optimization. A simplified PI controller and Z actuator generate trace and retrace. Output sampling is separate from tip interaction.

What is simplified

Mode presets share a height-feedback envelope. The scan view adds qualitative contact bending and slowed tapping motion, driven by the surface-minus-Z tracking residual. A clamped-beam shape determines the surface normal and local reflected ray; an ideal collection relay moves the stationary detector spot. This is not a calibrated deflection, amplitude or force measurement. The enlarged tip is constrained to the accessible surface envelope to keep the illustration readable; its vertical motion is not an extra acquired channel. Pausing acquisition freezes the motion; reduced motion initially hides tapping oscillation, with an explicit Show tapping motion control available. Off-resonance force cycles are omitted. Probe stiffness and resonance are nominal teaching values. Alignment voltages are offsets, not live cantilever deflection. Phase is an error-derived proxy, not material contrast. Continuous frames repeat deterministically when settings stay unchanged. Live rate, gain and tapping-setpoint adjustments affect the next acquired pixel and preserve earlier pixels. CSV records initial settings and each adjustment; controlled comparison lessons require complete frames with unchanged settings. The quadrant widget and 3D spot share relative diagram coordinates, not calibrated photodiode voltages. Horizontal torsion is not modeled.

All four surfaces are synthetic. The graphite-labelled surface uses a nominal 0.335 nm step; this is not a calibrated specimen. The image and CSV identify the app and numerical model version.

Primary references

These sources explain AFM principles; they do not endorse or validate this simulator. No source illustrations are reproduced.