We don't understand the universe, we interact with parts of it and dimly perceive the rest.

As for the "how can atoms think", it's late and I don't want to get Hyper-Cerebral Electrosis
My contention is that you're thinking of atoms in the brain on the wrong level of abstraction. Your question is a similar one to "How can silicon atoms play chess against a human?"

<font color="white">Hyper-Cerebral Electrosis is an urban legend by the way</font>