In the atomic structure, the vast majority of the space between the nucleus and the cloud of electrons is indeed empty. This region is known as the electron cloud or electron shell. It is not filled with a physical substance like air or a matrix. Instead, it represents the probability distribution of finding an electron in a particular region around the nucleus.
According to the quantum mechanical model of the atom, electrons do not orbit the nucleus in a classical sense, but rather exist in energy levels or orbitals. These orbitals represent regions of space where there is a high probability of finding an electron. The specific shape and size of these orbitals depend on the energy level and angular momentum quantum numbers associated with the electron.
It is important to note that the concept of "empty space" in the atomic structure does not imply a complete absence of anything. The electron cloud contains the potential for the existence of an electron, and it is through interactions with electrons that atoms can form chemical bonds and exhibit various properties. However, the vast majority of the space between the nucleus and the electron cloud is devoid of any significant physical matter or substance.