You need to clearly define what constitutes "real" before we can meaningfully talk about the distinction between "real" atoms and simulated ones.
As far as physics go, it's all just numbers in the end. Indeed, the more we keep digging into the nature of reality, the more information theory keeps popping up - see e.g. the holographic principle.
> "As far as physics go, it's all just numbers in the end."
No it isn't; numbers are a map, maps are not the territory. You are asking me to define how a map is different from a city, but you are not accepting that the city is made of concrete and is square kilometers large and the map is made of paper and is square centimeters large as a meaningful difference, when I think it's such an obvious difference it's difficult to put any more clearly.
What constitutes a real atom: a Hydrogen atom capable of combining with Oxygen to make water, capable of being affected by the magnetic field of an MRI scanner, etc.
What constitutes a simulated atom: a pattern of bits/ink/numbers which you say "this is a representation of a Hydrogen atom", capable of nothing, except you putting some more bits/ink/numbers near it and speaking the words "this is it interacting to make simulated water".
Ok, you are saying that a map is different than the territory. That a simulation is meaningfully different.
Do you deny that you could be in a simulation right now, in the matrix? What you actually think are are molecules of oxygen are actually simulated molecules. That there is no way for you to every tell the difference.
As far as physics go, it's all just numbers in the end. Indeed, the more we keep digging into the nature of reality, the more information theory keeps popping up - see e.g. the holographic principle.