Diffusion-Limited Molecular Self-Assembly Simulator

Molecular self-assembly is driven by two real physical processes working together: thermal (Brownian) diffusion that brings building blocks together, and selective binding that only succeeds when the blocks meet in the right position and the right orientation. This simulator models both directly. A population of three complementary "part" species undergoes real random-walk diffusion and rotational tumbling across the canvas. A target lattice grows outward from a single seed site, one binding event at a time — a free part locks into an open site only when it wanders within the bonding radius and its orientation falls inside the tolerance window around that site's required angle. Raise the temperature and parts diffuse faster but also shake loose more easily; raise the concentration and encounters happen more often; tighten the tolerance and correct alignment becomes rarer. The assembly yield you see is a genuine emergent outcome of these three dials, not a scripted animation.