Is there such thing as well defined physics and math for atomic interactions?

We have a lot of good Newtonian physics simulation software out there (Bullet, PhysX, Havok, etc.), but I see none good for simulating atomic interactions (going deeper). I like to build one for educational and gaming purposes, but I need some good references (book, paper, …) to implement the logic. Any suggestions, critics, etc. are welcome. For now, I have been looking into dozens of WIKI papers, but all speak about the atomic structure and not about their interactions.