Visualization of neuron interaction in a fish.
Good for time scales.
Scale of the universe. More interactive powers of 10.
Virtual Particles and Higgs.(Made before the discovery of the Higgs)
Virtual Particle, Casmir Effect, and other such.
http://io9.com/5731463/are-virtual-particles-for-real
Odd video visualizing interactions of virtual particles.
Another odd video visualizing interactions of Higgs.
Quantum Computing. Because, why not?
Coastline Paradox and Fractals.
Turning a sphere inside out without cutting it.
Robot with a mouse brain
And a illy thing. Vacuum and the human body.
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For animations, there’s a good program called Source Film Maker:
http://www.sourcefilmmaker.com/
And if you’re interested in simulation data for it, here are some good programs to take a look at:
Clad Diagrams and evolution.
http://www.speciesgame.com/
Minimalist dynamic structure simulation.
http://sodaplay.com/
Human Populations and such
http://portaldev.rti.org/10_Midas_Docs/SynthPop/portal.html
Universe visualization and scale. Addons increase functionality tenfold.
http://www.shatters.net/celestia/
A few good short student projects for inspiration: