An atom is made up from a nucleus surrounded by shells of electrons. Under conditions of high energy, such as the conditions in supernovae explosions or at the centre of a quasar, the electrons of atoms can be ripped away by the forces involved. This leaves just the bare nucleus. If the forces that rip away the electrons eject these nuclei from the quasar or supernova, they travel across the universe. Those which hit the Earth are detected as cosmic rays.
The simplest atom of all is the hydrogen atom. This has only one electron. The bulk of cosmic rays are made from the nucleus of a hydrogen atom.
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