The ability to do useful work pretty much falls off at the scale of molecules. Although an individual molecule can act as a cage or a frame for an individual atom to flop back and forth in. Which might provide the fundamentally smallest way to store a binary 0 or 1 possible.
Sub-atomic units are pretty much already doing all that they're going to do by the laws of physics, unless you shotgun them into each other at fair fractions of
c in particle colliders and then they fly around for a bit before recombining or fading out and that tells physicists interesting things about the way the universe works. So the idea of a sub-atomic "machine" or device is kind of a non-concept.
Good news is that there's TONS of room down at the molecular level to do all sorts of stuff we can't even imagine yet, assuming we don't destroy ourselves in the process.
Although it would be nice if we could somehow figure out a way to uncouple matter/mass from the Higgs Boson field, and not have said matter explode or otherwise lose it's other fundamental properties or structure. That would be handy. (you would only need to overcome air resistance to get into space for an example...)
Although the Higgs wasn't even postulated yet, E.E. Doc Smith had a lot of his handwavium tech. in his Lensman books based on that idea.