What's actually going on here?

Every assembly on this site is a simulated swarm of 500 identical particles, each shaped like a little hexagon with six "patches" around its rim — think of them as six sticky spots, each with its own strength. Two particles can only bond where a patch on one touches a patch on the other, and how strongly they stick depends on which pair of patches is in contact.

In this dataset, the strength of every one of the 21 distinct patch-pair combinations was drawn at random from a bell curve, rather than designed by hand. That bell curve has two dials: its average (how sticky patches are, on the whole) and its spread (how much patches disagree with each other — some pairs love sticking together, others repel). Turn those two dials and you get a completely different random rulebook for how particles interact — and a completely different structure grows out of it, from a lonely gas of monomers to a rigid crystal, a tangled gel, or a thin fiber.

The simulations themselves run with the Metropolis Monte Carlo method: particles are nudged and rotated one at a time, and a move is kept or discarded based on whether it lowers the system's energy (with some randomness so the system can escape dead ends). Left running long enough, particles settle into whatever arrangement is most favorable for that particular random rulebook.

How assemblies are sorted into families

Every simulated outcome was inspected and sorted into one of eight structural families — monomer, oligomer, gel, polycrystal, fiber, sponge, crystal, or liquid — based purely on its shape and connectivity, not on which dial settings produced it. Some of those calls were made and checked by a person; the rest were sorted automatically the same way and are flagged as such throughout the site.

What the "stability" view is showing

On each assembly's page, switching to the stability view colors every particle by how its local bonding compares to the assembly's average — not a real physical quantity with units, just a relative way to spot which particles sit in the most and least comfortable neighborhoods of a given structure.

The paper

This site visualizes simulation output from:

This site was built by the paper's first author as an independent visualization of that research, and is not an official publication of the journal or publisher.