Even though it's important, you don't necessarily need a visual of it.
I would go so far as to say that just because it's thematically important, it doesn't need to be the title, either. Because I'd hazard a guess that the only one it's not confusing to is you. The point of a title is to interest or intrigue people enough that they come and read the blurb of your book. For me, at least, the cover doesn't interest me because the two elements (the atom and the cookie) are at extreme odds with one another. One says sci-fi, one says kid's book. And the title doesn't clarify anything. It doesn't interest or intrigue me, it just leaves me even more confused.
Is there some other thematic element that you could use for the title that would be more clear for your target audience?