Remember the operative word 'simulate'. It's not 'recreate'.In order for any kind of computer to simulate our universe, the computer would have to exist in a "real" universe at least several times larger than our own. Well, it must be larger if we assume it takes more than one "real" atom to simulate a simulated atom, and also the computer would not occupy the entirety of the outer "real" universe... would it?
Combine the 'Simulation' conjecture with the 'Brain in a Jar' conjecture and you won't have to simulate atoms. You merely simulate the observation of atoms and feed it to the brain. In other words, all those atoms out there in the universe are not really there, they're a projection on our senses.
Interestingly, this creates the kind of reverse Holographic Principle: that the entire universe is merely a projection on the inside of spherical screen that surrounds us like a hollow shell.