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Ernest Rutherford used alpha particles to bombard a thin gold foil. In the early 1900's, particle accelerators were new and worked on the same principle as the old TV sets (before the plasma and LED ones we have now)

The alpha particle was emitted from radium bromide in to a vacuum tube with a large electric field applied. The alpha, with charge = +2 electrons, was accelerated in the electric field and made to hit the gold foil. By looking at the ways the alpha particles bounced off the foil, Rutherford formulated a model of the atomic structure more or less as we know it today - A dense nucleus and electrons floating around the outside. Basically, the vast majority of the atom volume is vacuum.

He didn't use protons because there is no radioactive substance which emits protons. Only alpha emiitters (2p + 2n), beta elecron/positron emitters and gamme (high energy light) emitters exist naturally.

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