Physics and Chemistry Animations in After Effects Are there any plugins/physics simulation engines other than Newton that will be useful for creating Physics and Chemistry content in After Effects?? 
For example, if I have a requirement to create the motion of electrons in an atom, how do I go about it?
There are a number of physics engines and related scripts available in the Physics Simulation category at AEScripts.

However, without a more specific question about what kind of animation you're looking for (that is to say, I don't know how the electrons in an atom are supposed to move), it's hard to point you to a specific answer.