Gold foil was chosen for the experiment due to its malleability and the ability to make it extremely thin. A thin foil was essential to allow the alpha particles to penetrate the atomic structure, enabling the scientists to observe their deflection patterns accurately. Gold’s atomic structure is also well-understood, offering a reliable medium for the experiment. Moreover, its inert nature ensured that the foil would not react chemically during the experiment, eliminating potential variables and ensuring that the observations were solely due to the physical interactions between the alpha particles and gold atoms.

The discovery of a dense, positively charged nucleus in the atom by the Geiger–Marsden–Rutherford experiment laid the groundwork for the subsequent identification of protons. The experiment demonstrated that a concentrated core of positive charge existed, but it didn’t identify the specific constituents of the nucleus. Later, scientists, building on this revelation, conducted further experiments and theoretical work that led to the discovery of protons as the carriers of positive charge within the nucleus, thereby offering a more detailed and comprehensive understanding of atomic structure.

The nuclear model rectified the plum pudding model’s limitations by introducing a central, dense, and positively charged nucleus within the atom. The plum pudding model couldn’t explain the significant deflection of some alpha particles observed in the Geiger–Marsden–Rutherford experiment. The nuclear model, however, with a nucleus containing most of the atom’s mass and positive charge, offered a coherent explanation for this phenomenon. Electrons orbiting the nucleus at relatively large distances explained why most alpha particles passed through with minimal deflection, as the atom was mostly empty space, resolving the inconsistencies highlighted by the experiment.

The fraction of alpha particles deflected at large angles was small but significant. Although the majority of the particles passed through the gold foil with minimal deflection, showcasing that atoms are largely empty space, the deflection of a noticeable minority at substantial angles was critical. This phenomenon couldn’t be explained by the prevailing plum pudding model and indicated a concentrated positive charge within the atom. Thus, while numerically minor, the impact of these deflected particles was monumental, leading directly to the proposal and acceptance of Rutherford’s nuclear model of the atom.

Rutherford, Geiger, and Marsden employed a systematic approach to ensure the accuracy of their observations. The use of a fluorescent zinc sulfide screen was instrumental in detecting the alpha particles’ deflection angles with precision. Each time an alpha particle struck the screen, it emitted a flash of light, allowing for exact recording of the particles' paths post-collision with the gold foil. Moreover, the experiment was repeated multiple times to confirm the consistency of the observed patterns of deflection, ensuring that the results were not anomalous but indicative of an underlying atomic structure contrary to the plum pudding model.