This is pretty deep. We know a lot about what atoms _do_, but not really how they form. They just ‘are’.
Short answer is I don’t know, I tried Wikipedia (really!), and you got me thinking…
What you’ve asked is an important question, because there should be the same amount of matter and antimatter. However, there’s more matter than we expect, and no one really knows why. You put down Stephen Hawking on your profile, which makes me think you like physics. Check out this post on the CERN website because it’s a huge unanswered question: http://press.web.cern.ch/backgrounders/matterantimatter-asymmetry
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