The nucleus was discovered in 1911 by Ernest Rutherford. Rutherford wanted to test Thomson's idea of the model. He had a very thin sheet of gold foil that he thought he would use for his experiment. He decided that he would send alpha particles, which are very tiny (smaller than an atom) particles that have a positive electric charge, at the gold foil. Now Rutherford expected these particles to go straight through the foil or come through at just a slight angle. If the atom looked like Thomson had said it did, with positive charges spread out everywhere, the particles should just go through the foil. If the particle got close to the one on the positive charges spread through the atom, it would be repelled slightly, since positive repels positive, but the particle would not be diverted from its path too much. One positive charge repelling another single positive charge would not make the particle change its path too much. So Rutherford set up his experiment, and he put his detecting paper around the room, only expecting the paper to detect the particles on the opposite side of the foil. Rutherford started his experiment, and low and behold, some of the alpha particles went right through the foil. The problem was, however, that some of the alpha particles, angled off of the foil at angles much much higher than Rutherford had expected. These angles were mush greater than what would have happened if the alpha particle was coming close to only a single positive charge. The only reason that the particles would angle off the foil at such large angles was if the particles were coming close to a large concentration of positive charge, i.e. a charge great than +1. Since Rutherford knew that one gold atom had 79 protons in it, Rutherford decided that all of these protons must be packed together, instead of spread out like Thomson had theorized. Rutherford used his alpha particle experiment to defend his idea that all the protons were bunched together in the center of the atom, which he called the nucleus. He did not know much about the electrons behavior or location, so he just said they were on the outside of the nucleus to make the atom neutral.
Today, we still call the center part of the atom the nucleus. Atoms are extremely small and so the nucleus must be even smaller. An atom is about 10-8 cm in diameter while the nucleus has a diameter of about 10-13 cm, 10,000 times smaller. Even though it is so small, the nucleus makes up most of the mass of an atom. This is because the nucleus holds the most massive parts of the atom, the protons and neutrons. Electrons make up the rest of the atom but weigh much much less than these to particles. The electrons whirl around the outside of the nucleus. The forces holding the protons and neutrons in the nucleus are still being studied today.