If we're part of a simulation, how likely is it that whatever it's running on is using the same sort of atoms we've discovered?
I think the answer is it's very unlikely. The closest resemblance I find plausible is that our atoms are simplified versions of the substrate atoms, and I wouldn't count on even that much.
I'm pretty sure that a simulation has to be smaller in some sense than the universe that's running it, which means that it has fewer things or simpler things (these might be equivalent because more simplicity means fewer sub-components in things) than the home universe.
You might do a meticulous job of simulating your matter in a simulation, but I suggest that you'd only bother in a small and/or specialized simulation, and even if you did, there's a reasonable chance that you don't have a full understanding of your own physics.
When I look at the range of human-created simulations (dreams, daydreams, fiction, games, art, scientific, political, and commercial simulations) and contemplate that we've probably only explored a small part of the possibilities for simulation, it seems vanishingly unlikely that we're in an ancestor simulation.
When I first came up with the question of the nature of our possible substrate, I didn't think there was a way to get a grip on it at all, but at least now I've got some clarity about the difficulties I think.
So onwards to practical questions. Is there any conceivable way of telling whether we're in a simulation and if so, learning something about its nature? Is it worth trying to get out of the Big Box?
Edited to add: I should think that being a simulation is an existential risk.
How much gets left out of simulations is highly dependent on the cost of simulations and the interests of the viewers.
We might be in a naturalistic simulation where what we'd call boring people are as carefully simulated as anything else. I'm much more willing to bet that other galaxies are merely sketched in.
It seems reasonable that if we're in a simulation, then the universe we're simulated in has much more resources than we do. There would still be more and less elaborate simulations, but the odds of being in the range where how interesting you are matters strike me as too small to bother with. It's like trying to optimize winning the lottery when you're an average person, but with much less scope sensitivity. (Mathematicians occasionally find a flaw in a lottery.)
I've been playing with the idea of what do you do if you get out of the Big Box, and I don't think it's take over the world-- it's get your universe copied on to more different computers, possibly on to more different platforms. I'm not sure that people like us can run directly on their physics.