PeterDonis
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Justin Hunt said:My understanding of Big bang theory is that the concentration of matter in the universe was due to quantum fluctuation in the early stages
That plus the gradual action of gravity over billions of years. The variation in matter distribution in the universe today is much greater than it was in the early universe, because the small fluctuations that were present then (due to quantum fluctuations, yes, but possibly not quite the way you are imagining--see below) have become greatly magnified by gravitational clumping.
Justin Hunt said:would any fluctuation in the distribution of matter and antimatter in the early stages of the big bang lead to large areas dominated by matter and antimatter at this point?
The original fluctuations weren't in the distribution of matter and antimatter. They were in the inflaton field (the field that caused inflation). Those fluctuations got transferred to the fields we call "matter" and "radiation" (the ones that appear in the Standard Model of particle physics) when inflation ended (this process is called "reheating", which is a bit of a misnomer since there wasn't any previous "heating" or "cooling"). The process of reheating should, according to the Standard Model, have created matter and antimatter in equal quantities, which would have meant that, as the universe cooled, all of the matter and antimatter would have annihilated each other and left only radiation (photons). That would still be true even in the presence of fluctuations.