The strong force has charges, just like electromagnetism. And just like electromagnetism, charges attract together to form a “neutral” structure.
One of the main differences is that the strong force has three charges instead of two, and their behaviour is far more complex.
Also unlike photons in electromagnetism, gluons (the force particles) actually carry a charge themselves, which means they interact with eachother. That both changes the behaviour of the force (why it has such a short range) and means there’s a lot of energy bound up between quarks.
As for how does binding energy generate mass… Well, it just does, ALL “confined” energy does. That’s from General Relativity, E = mc^2
Chemical bonds (electromagnetism) have mass too. Hell, a compressed spring technically has more mass, even though measuring that is tricky.
As for generating energy in nuclear reactions, it depends if you mean fusion or fission, since they’re opposite. In fusion, two nuclei have more energy separately than together, so when they fuse, they release the difference. In fission, the nucleus has more energy than the results of a split, so when ot does split, the difference is released.
The difference itself comes from the fact that the more protons you have in a nucleus, the more electromagnetic repulsion you have, but being bound by the Strong force is more energetically favourable than not. So in small nuclei, the Strong binding outweighs Electromagnetic repulsion, but in large nuclei it’s the opposite.
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