It does say in the tutorial that the connections gets destroyed when an atom hits it, I thought about having seperate cutting particles, but I considered the gameplay to be more interesting when having a single atom to do everything (both adding an cutting.)
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Ah I see. Not sure if it quite worked because if the player is attempting to connect to the atom but ends up destroying a connection by accident, it isn't as satisfying. Whereas if you had a antiparticle or "delete atom" it would be clearer and more consistent in terms of what to expect in each collision.