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I think the most prolific experiment to discover the atom and its general structure was the use of and electron gun firing a steady beam of electrons at a thin piece of metal.

the discovery was that electrons didn't pass straight through, or the beam didn't just stop when it hit the surface of the metal. This told us several things, one that this supposedly solid metal wasn't solid and was in fact mostly empty space, and it also proved due to reflections of some electrons that the center of an atom was charged so it would repel the negative electron.

Actually this experiment was not performed with electrons from an electron gun, but with alpha particles emitted from a sample of radium and collimated by a hole in a piece of lead. The alpha particles being positively charged are strongly repelled by the positive nucleus causing them to sometimes rebound directly backwards, electrons being negatively charged are attracted by the positive nucleus and thus only scatter in the forward direction.

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