It's scientifically certain that we
can abstract away from the physical system. In fact, we're already doing that today. We run simulations of molecular interactions all the time. We can even "do" a cortical column in incredible detail.
The problem is not that we don't know whether it's possible. There are two issues concerning this development: we need to know what the right detail/abstraction level is for simulating a mind, and once we do we need to actually get that information. Doing the simulation itself is comparatively easy, though certainly not trivial.
> What exactly are you going to save to that file? Positions of molecules? States of atoms?
To be useful, it can't be just a file, it needs to be a database that can be executed. Positions of molecules seems to be the right detail level according to our current understanding. That includes the spatial configuration of proteins and their exact position in relation to another. But there might not be that many unique molecules to store, just a few thousand maybe.
An interesting question then becomes how can we abstract these scans even further and still be able to have a high fidelity mind simulation?