Inside atoms there are protons and neutrons. They are made up of quarks. In accordance with string theory, the quarks are made up of tiny loops of energy. Trillions of them. These loops of energy vibrate in 10500 different ways and the arrangement and number of specific loops are what create the properties of matter. There are many different theories involving a multiverse, but I like eternal inflation. With this theory there is a field of energy outside of the universe and every so often this energy discharges. These bursts of energy are what create universes. Our universe is doomed to a fate in which entropy will continue to increase (as it always does) until eventually all matter simply splits apart and we are left with a void containing something along the lines of 1 atom every parsec or some stuff like that. I do not see how it would be possible to have universes within atoms, but it is plausible I suppose. Although, there has been no scientific proof in regards to such a theory so until there is, this idea is in the garbage to me.