The statement that atoms are 99.9999999999996% empty is a common analogy used to describe the relative sizes of atomic particles. However, it's important to understand that this analogy refers to the space between the subatomic particles within an atom, rather than the size of the particles themselves.
Atoms consist of a nucleus at the center, which contains protons and neutrons, surrounded by electrons orbiting in energy levels or shells. The nucleus is extremely small compared to the overall size of the atom, and the electrons occupy a relatively large volume of space compared to the nucleus.
While it is possible to influence the size and structure of atoms through various means, such as ionization or excitation, the idea of "shrinking" an atom in the sense of compressing the particles closer together is not feasible. The size of the nucleus and the electron clouds are determined by fundamental physical properties and the laws of quantum mechanics.
In summary, the empty space analogy helps us understand the relative scales involved in atomic structures, but it does not imply that the particles within an atom can be compressed or shrunk further.