Uploaded June 2010 | Updated September 2026, 2 weeks ago
Finally, it works! The strength of binding compared to the relative "heat" of the system puts the collection of charge-loaded shapes into dynamic equilibrium. When 3 shapes bind to one another, with a 3 fold axis (sharing adjacent faces), each shape is in contact with two other shapes and has 4 charge interaction points which is more stable and thus lasts longer than an interaction between just two shapes which has two contact points. With more shapes bound, the mass should increase and give the bulky object less tendency to be knocked around or to gain momentum before hitting a wall, but this effect seems pretty subtle, so the 3mers and 4mers and 5mers get smashed apart every now and then. In a 5mer, one shape has 4 faces and 8 charge contacts while the other 4 shapes have 3 faces and 6 charge contacts, reducing the overall free energy of this gravity-less system. If a 6mer forms, I would expect it to remain stable... I'll encourage this to happen by increasing the density of shapes in the system before moving on to generate a polio virus. You can see towards the end of this simulation that the excluded shape has roughly a 1/6 chance of bouncing into the last empty pocket, and a much lower chance of hitting said pocket at a productive orientation, so it could take a while for the last guy to bind before the 5mer falls apart (probability is low). I need to get a better grasp on how the turbulence acts on the objects, as the forces seem to affect massive objects more than I would expect, but first I'll just test with increased density and or a different random seed.
Finally, it works! The strength of binding compared to the relative "heat" of the system puts the collection of charge-loaded shapes into dynamic equilibrium. When 3 shapes bind to one another, with a 3 fold axis (sharing adjacent faces), each shape is in contact with two other shapes and has 4 charge interaction points which is more stable and thus lasts longer than an interaction between just two shapes which has two contact points. With more shapes bound, the mass should increase and give the bulky object less tendency to be knocked around or to gain momentum before hitting a wall, but this effect seems pretty subtle, so the 3mers and 4mers and 5mers get smashed apart every now and then. In a 5mer, one shape has 4 faces and 8 charge contacts while the other 4 shapes have 3 faces and 6 charge contacts, reducing the overall free energy of this gravity-less system. If a 6mer forms, I would expect it to remain stable... I'll encourage this to happen by increasing the density of shapes in the system before moving on to generate a polio virus. You can see towards the end of this simulation that the excluded shape has roughly a 1/6 chance of bouncing into the last empty pocket, and a much lower chance of hitting said pocket at a productive orientation, so it could take a while for the last guy to bind before the 5mer falls apart (probability is low). I need to get a better grasp on how the turbulence acts on the objects, as the forces seem to affect massive objects more than I would expect, but first I'll just test with increased density and or a different random seed.
