Rutherford needed to come up with an entirely new model of the atom in order to explain his results. Because the vast majority of the alpha particles had passed through the gold, he reasoned that most of the atom was empty space. In contrast, the particles that were highly deflected must have experienced a tremendously powerful force within the atom. He concluded that all of the positive charge and the majority of the mass of the atom must be concentrated in a very small space in the atom's interior, which he called the nucleus. The nucleus is the tiny, dense, central core of the atom and is composed of protons and neutrons.

Thomson assumed that an electron is two thousand times lighter than a proton and believed that an atom is made up of thousands of electrons. In this atomic structure model, he considered atoms surrounded by a cloud having positive as well as negative charges. The demonstration of the ionization of air by X-ray was also done by him together with Rutherford. They were the first to demonstrate it. Thomson’s model of an atom is similar to a plum pudding.