I think you should realize that we already do that. In fact, that's one of the reasons computers were invented in the first place! It turns out that science is about unknown unknowns, and by definition simulations can't answer that.
replyBut agents are really useful for doing some of the really boring stuff, like convergence checks or setting up meshes or whatever.
If you're talking about things at the equivalent level of say, finding out if positrons maintain symmetry with electrons for their magnetic moment, then yeah - I hear you. Or if you wanted to research some unknown behaviour of hot plasma at 15 million C, you can't do that in a simulation.
reply..or can we?
Humour me for a moment. Maybe simulating to the degree that was necessary for cutting edge work was not possible earlier, when humans had to program each and every thing in the system that could affect the result. But with current gen petaflop-on-your-desk level compute + swarms of agents that can work tirelessly to account for every known thing to humanity, maybe the threshold has been pushed far enough to produce some more meaningful discovery work in simulation?