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The last idea is the ability to expand the area the particles are in

Oh ya and another cool idea would be selective velocity dampening that targets certain particle types and not just every particle 

Hey I have a great idea to make the simulation far more interesting.  So my idea is the option for particles to have different collision force distances depending on the particle, for example lets say a proton has a radius of 2 so when any particle gets within that radius the collision force will push the particle away. But lets say you change a slider so that electrons treat protons like there radius is 4 instead of 2 and they get repelled at that distance. I don't know if it is possible for you to do put if you can please do