[DennisP]

By asserting that the simulated brain is "experiencing" something, you're assuming it does have qualia.

We actually have no idea how a bunch of atoms interacting create qualia, or even whether they do. There's no math to tell us that a configuration of atoms makes qualia, or what qualia it makes. We have no way of distinguishing between a conscious being who experiences, and a philosophical zombie with the same behavior but no internal experience.

Therefore we can't know whether a simulation of atoms actually does capture what's necessary for qualia.