First I want to start by saying that I think this is an interesting concept. However, there are some downfalls, the main one being that the game is over simplistic. A few changes here and there and this could be a really engaging game.
Really, the problems I have with the game are just two things, but coupled together they form a major problem. The first thing is when the particle hits an atom, the atom becomes a particle and speeds off. This works, and the randomish direction that the particles go once there is a collision adds a level of difficulty, but the problem is that from what I could tell each atom becomes a particle. Perhaps implementing a randomly generated value to determine if the atom becomes a particle, say 75-80% chance that it does. This will make it so the majority become particles, but leaves room for difficulty when some do not. Next, I would have liked to see level variety. Try introducing walls to form simple paths or mazes and let the atoms randomly generate through out the level.
I did enjoy the core concept of the game and would have really liked to see variety. The game was fun, but far too simplistic.