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Except for elecrons, which can be viewed under an electron microscope, nuclei, protons, and neutrons, haven’t been seen. The proofs of their existence came from experiments, which by the different qualities of these particles, where able to differentiate them from one another. For elaborations of these experiments, which, if understood, may reveal the existence of these particles, you may go to the following links:
http://en.wikipedia.org/wiki/Atomic_theory
http://en.wikipedia.org/wiki/Neutron#Discovery
http://en.wikipedia.org/wiki/Atomic_nucleus#History
http://en.wikipedia.org/wiki/Proton#History
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