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.
Three tips for reasoning about the real world, for people who might be "living in a simulation" or otherwise inhabiting a systematic illusion:
(1) If: every world in some ensemble of possible worlds exists, and you know enough about this ensemble; then you can reason about the properties of the real world, by applying standard probabilistic inference to the set of all entities, occurring in this multiverse, which are subjectively identical to you. For example, if half of your subjective duplicates across the multiverse inhabit worlds made of superstrings, then the probability is 50% that your real world is made of superstrings.
This is both a no-brainer and arguably useless advice, since you just may not be in a position to know the full nature of the multiverse, or to calculate the demography of simulations and false realities throughout it. However, it is worth understanding that if we could know enough, then answering these questions really would be a matter of deduction and calculation.
(2) In the absence of a justified, top-down way of answering questions about the real world, you can at least aim for a systematic approach by collecting and generalizing hypotheses. Nancy has a small list above ("dreams, daydreams,..."); this could be expanded.
There are lists of proposed answers to the Fermi paradox (1, 2), perhaps it's time to start work on assembling comparably comprehensive lists of simulation scenarios.
(3) One might also wish to discreetly make a list of ways that making a list of simulation hypotheses could induce feedback from the laws or the lords of the matrix. There are simulation scenarios in which you are not supposed to know, or in which trying to learn the nature of the simulation has prearranged consequences. These could be called "simulation-fights-back" scenarios.