As Sharp explains, there is gravity pulling down on every single nut in the mix. The nuts also interact with each other, jostling around in the container to produce friction and mechanical energy lost as heat. Precisely how much friction depends on the size and shape of the nuts, among other factors. And as Esther Inglis-Arkell wrote at io9 several years ago:

If the large particles are much less dense than their surrounding particles, they rise to the top and stay. If they are much denser than their surrounding particles – they also rise to the top and stay. Those that have a small difference in density from the other particles tend to remain mixed. And all this density dependence stops if the particles are in a vacuum. It seems that the simple course that a Brazil nut takes through life is dependent not only on its surrounding nuts, and on its density, but on air pressure as well.

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It is possible to reverse this effect by using a conical container, however. And as Sharp says, it’s an advantage if your snack food of choice happens to be popcorn. Shaking the bowl will cause the hard kernels to sink to the bottom, leaving the fluffy white goodness on top.

[Fuck Yeah Fluid Dynamics]