I am no expert in physics so this is a bit of guessing on that end from experience in IT, servers and game engines / game dev, if anyone can correct or add information to this its welcome.

Scientific researchers have done particle simulations of the universe (or clusters), but they are based on physics models and equations that are interpretations of the universe to simulate how star clusters, galaxies etc would form, they are not simulating atoms and their properties, instead they simulate on a higher/simpler level by using particles that behave as how a masses of atoms, or planets or dust in space would behave to form star clusters / galaxies etc

Here's one https://www.youtube.com/watch?v=kndzioHG8Uc

A single mistake or missing part of that interpretation in the equations would output a different result compared to what we have in our real universe. So my personal opinion on these simulations is that they are more of guess as the equations are a simplification of our universe and an interpretation.

Also you would need a super computer, and even today's super computers, I am not informed enough to say, but I doubt we can simulate the scale of our universe at an atomic level.

Simulating everything at an atomic level requires tons of processing power, maybe we don't even know enough about how the universe works / physics for the simulation to generate an universe with galaxies/planets etc and life, very hard.

Either way it probably has to be simplified or a small region has to be simulated so its doable in terms of computing power and simplified so "life and the universe" can form itself.

And for video games it definitely needs to be over simplified, a desktop computer depending on the specs can only simulate between a few thousand or a few hundred thousand to a few million particles in real time (the scientific ones are generally pre-calculated then visualized once its done calculating).