Ciliary Clearance Visualizer

Controls

Preset

Examples vary: coverage (sparse↔dense), alignment (aligned↔misaligned), patches (regular↔disordered).

Modifier (human benchmark)

State

Ciliated coverage

Patch size / domain size

Patch disorder

Beat Orientational order (OOP)

Beat amplitude [×L0]

Cilia length/height [×L0]

Focal plane z [×L0]

Diffusion coefficient [×L0^2/T0]

Step size [×T0]

Trail length [×step]

Tracer count

Periodic domain size (X) [×L0]

Periodic domain size (Y) [×L0]

This ciliary clearance visualizer is based on a semi-infinite domain regularized Stokeslet formulation where a no-slip wall represents cell surface, and the average flow generated by each ciliated cell is each approximated by a single Stokeslet placed at one cilia length above the cell center with some regularization constant.
Characteristic scales of the simulation are average cell size L0~10μm, cilia beat period T0, and fluid viscosity μ0.
For experimental background and explanations to the preset data, see our Nature Communications article.

Navigation tips

Play/Pause button to halt or resume simulation; Reset tracers reseeds particles uniformly randomly.
Pan the view by dragging pointers; on mobile use pinch to zoom and two-finger pan.
Toggle top bar buttons to switch on/off cilia animation, 3D tracer movement, and periodic boundary conditions.
Edit cell fate — single tap or click then hold paints ciliated cells; double tap / click erase ciliation.
Edit beat direction — tap / click then drag to set local beat direction for ciliated cells.

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