Rutherford inferred that the atom had a concentrated center, a nucleus, made up of positively charged particles. He believed that charges were deflected strongly because that they collided with the nuclei of atoms. The reality is that the protons, being positively charged, deflected the electrons (protons were not yet known at the time of the gold foil experiment).
The primary breakthrough of this experiment was that atoms can be said to have a center, a nucleus, around which electronics orbit. Before Rutherford's gold foil experiment, J. J. Thompson had proposed in his "plum pudding" model that atoms were simply made up of randomly distributed particles. Rutherford proposed a new model that included a nucleus. He later named the proton.
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