There's probably no need to go that low-level for modeling a mind, but of course the aggregate effects of biochemistry has to be taken into account (and it's full of non-linearities).

None of that means we don't understand the principles. I'd say it's pretty much like fusion. Yes, we know how the Sun works, but putting it into a bottle is a bit of a pickle, similarly with brains. (Except brains have a lot more complexity.)