3D Antibody-Antigen Binding Chamber

Binding Chamber

Association k_on 1.0e5

Dissociation k_off 1.0e-2

Antibody count 18

K_d (affinity)

–

Complexes

–

Neutralized

–

Collisions/s

–

How it works

Unlike a mean-field rate equation, this chamber is diffusion-limited: antigen (red) and antibody (blue) molecules physically drift through 3D space via Brownian motion, and a binding event can only happen when a pair actually collides. On contact, k_on sets the capture probability that the collision sticks; once bound, the complex (green) still separates at each step with a probability set by k_off. Effective on-rate therefore depends on both chemistry (kon) and physics (how often molecules meet) — exactly how real diffusion-limited immune reactions behave.

P(capture | collision) = 1 − e^(−kon·[Ab]local·dt)
P(release | bound)    = 1 − e^(−koff·dt)
Kd = koff / kon

k_on — capture probability per collision; low kon means antigen and antibody can bounce off each other many times before sticking.
k_off — how readily a formed complex falls back apart; watch complexes flicker green→red→green at high koff.
Antibody count — more antibody molecules in the chamber means more frequent collisions and a higher local encounter rate, mirroring a higher antibody dose.
Collisions/s — the raw encounter rate; compare it with the neutralized fraction to see how much of diffusion-limited binding is collision frequency versus sticking probability.

Real-world relevance: at high antibody potency (very low Kd), binding becomes diffusion-limited exactly like this — the reaction is capped not by chemistry but by how fast molecules can physically find each other in tissue or blood.

Free antigen Free antibody Bound complex

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