The answer to your question ultimately comes down to a showdown between dark energy and the fundamental forces.
Contrary to popular belief, each and every system (from the biggest scale to the smallest) is expanding (there are certain ideas that inside galaxies, where gravity is strong, matter is not expanding at all), the effects are just too little to measure.
There is no critical density, and all of the systems you mentioned are expanding, but the effect is much too small to measure.
How is expansion of universe seen locally?
The catch with dark energy is that it has a constant energy-density, despite the expansion of space1. To paint a simple picture, as space expands, more dark energy is "created" so that the energy-density of dark energy remains unchanged.
Is Dark Energy A Constant?
Now there are basically two cases:
- dark energy is going to eventually overcome the EM and the strong force, even at the smallest scales. In this case, what you mention will happen, and electrons will be separated from the nucleus, and even the nucleus itself will be separated into its constituents. This is where it is very important to understand what hadronization and confinement means. What is actually might happen is that as dark energy overcomes the confinement of the strong force, the color tube it creates will eventually break and create a new particle antiparticle pair.
The strong interaction has the property of confinement, which in the case of trying to separate a pair of quark qq¯ is adequately pictured by a colour tube stretching between the quarks until it breaks, producing new q′q¯′ pairs.
fate of a hadron in a big rip
- the fundamental forces will remain stronger then dark energy on the smallest scales. This might cause atoms to stay intact (though as you can see from the other answer they might fall apart due to thermodynamic reasons). Eventually most of the matter will fall to atoms and will be separated by space expansion and the only macro scale pieces of matter will be black holes.
The fate of black holes again depends on the showdown between dark energy and the forces.
An answer that got deleted linked to this paper:Babichev, Dokuchaev, Eroshenko, "The Accretion of Dark Energy onto a Black Hole," arxiv.org/abs/astro-ph/0505618
Will the Big Rip tear black holes apart?
And for gravity vs dark energy, to our current knowledge, gravity on the small scale does win over dark energy.
Is dark energy around a black hole locally curved?