I believe the future of such simulation is to start from the lowest level - ie. schrodinger's equation, and get the simulator to derive all higher level stuff.
Obviously the higher level models are imperfect, but then it's the AI's job to decide if a pile of soil needs to be simulated as a load of grains of sand, or as crystals of quartz, or as atoms of silicon, or as quarks...
The AI can always check its answer by redoing a lower level simulation of a tiny part of the result, and check it is consistent with a higher level/cheaper simulation.