I have 2 approaches to this.

• Nuclear Manipulation allows manipulation of protons and neutrons, not electrons.

• Atomic Manipulation may refer to manipulating the specific elements of the periodic table (not fire or water, literal ELEMENTS) since the atom is the smallest unit with the characteristic property of it's respective element.

I have my own interpretation. With nuclear manipulation, you basically control the energy of atoms while atomic manipulation allows you to directly control the basic units of matter.