I've been updating my lesson plans for atomic and nuclear physics and was looking into using Algodoo to simulate scattering experiments. One reason we know the nuclear force is so big is because it's difficult to knock the particles out of a nucleus. I tried varying the attractive force between particles and investigated the minimum speed needed for a projectile to knock them apart. By adding tracers you get some nice "cloud chamber" tracks. Could be some interesting investigations here.

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With Interactive physics you can add charge, magnetic field and air resistance.