What happens when a proton collide with an atom? How does the ionization occurs, assuming the proton has enough kinetic energy? How much energy is required for the proton to enter the atomic nucleus, resulting a higher chemical element ion?
What happens when a proton collide with an atom?
When we are talking of atoms and protons etc, we are in the quantum mechanical framework. Generally there will be an electromagnetic interaction, dependent on the energy of the proton. These interactions can be written down mathematically and the probability of the interaction taking place can be computed using Feynman diagrams. . The proton, to interact with an atom will be exchanging a virtual photon.
How does the ionization occurs, assuming the proton has enough kinetic energy?
The virtual photon exchange with an electron on the last filled energy level has to transfer enough energy for the electron to get out of the potential well where it is bound in a quantized energy level.
How much energy is required for the proton to enter the atomic nucleus, resulting a higher chemical element ion?
The chemical energies between atoms are of the order of electron volts. The energies involved in the nuclei of the atoms are of the order of million electron volts. A proton with million electron volts energy in head on collision on ,an atom will sweep a lot of the electrons away (by virtual photon exchange) until it is repulsed by the positive field of the nucleus. One cannot change atomic structure by using protons. It needs special quantum mechanical conditions to change the nucleon content of a nucleus, and protons, due to their charge are not good candidates . Neutrons which can get near the nucleus and be captured or scattered by the strong nuclear forces are what contribute to fission processes.
I'll answer your question in a very general scenario. I hope your confusion is regarding how the proton enters the atom without interacting with other particles. The same confusion was faced by many scientists when they were observing the $\beta$ decay process. How does a fast moving electron leave the atom without facing sufficient repulsion from orbital electrons? Well, the answer is quantum mechanical. To answer this succintly, the $\beta$ particle tunnels through the nucleus and appears out of the atom! It is like looking at the repulsion as a potential barrier and the electron as a particle in front of it. The $\beta$ particle simply tunnels through the barrier(and has a probability for this).