Goldman equation

Random walk with statistics - random angle movement - up down left or right - up down random but always left or right on alternating rows
Continuous random walk - up down left or right - up down random, randomized rows are single direction (resulting in "super-diffusive motion)

Pendulum - elastic collision - projectile - coupled
cycloid - variable cycloid

Poisson process
Gaussian process

Speed test - how many particles can flash/action script handle?

Guess-timate: How many dots are there? -- What is the fraction of red dots?
Mean and standard deviation in a line distribution
-- What is the mean and standard deviation of a two dimensional pattern of dots?

Chain reaction - Chain reaction with variable spacing between targets

An attempt at Ohm's Law

An attempt at a diode - holes and electrons diffuse in p and n materials, a red dot shows where they combine. Each red dot increases the charge difference between the p and n sides, which hinders diffusion of holes into the n side and electrons into the p side, so that eventually a "depletion zone" develops at the boundary between the p and m sides.

Non-programmed animations:
Centrioles during meiosis (from a journal club on Shirato, Tamura, Yoneda, and Nemoto, Development 133: 343 (2006).
Quantitative microinjection method

Cdc2 activation (accompaniment to Slepchenko, B.M., and Terasaki, M.  2003.  Cyclin aggregation and robustness of bio-switching.  Mol. Biol. Cell 14: 4695-4706)
Membrane traffic (animation of Heinrich, R., and Rapoport, T.A. Generation of nonidentical compartments in vesicular transport systems. J. Cell Biol. 168: 271-280 (2005)).
Nuclear transport (animation of Smith, A.E., Slepchenko, B.M., Schaff, J.C., Loew, L.M., and Macara, I.G. Systems analysis of Ran transport. Science 295: 488-491 (2002))