You should play with particle effects. First learn how to do them, there is great module for you: orbit.
When you know a bit about particles play with GPU accelerated ones, you can create thousands of those. They have limits compared to CPU particles but for creating atoms it is all you need imo.
You probably could simulate those cloud shapes with bunch of cylinder spawning areas, then making them fuzzy with orbit modules.
However if shell of those shapes is what you need, you should look into custom meshes created by blueprints, but this will be a lot of work to properly model such surfaces from code.