Scientific Theory About Academy City

In this world of physics almost based on atomic theory, what kind of story would there be about a person with the ability to manipulate atoms? Achieve all currently known physical phenomena and miracles? This is the author's first work, and I hope readers can criticize and correct it if they see obvious illogicalities with the original work. This novel and its characters are purely fictitious. Any similarity is purely coincidental and should not be imitated.