You're going to have to be a lot more specific about the similarities between black holes and atoms in order for me to understand what you're referring to. The only similarity that I can think of between atoms and black holes is that they're both very small...
Regarding reconciling relativity and quantum mechanics, the problem isn't coming up with a theory that reconciles them, but finding out whether or not that theory is right. There is a school of thought known as "string theory" that has been around for years which has proposed a potential solution to this problem.
Unfortunately, string theory has not thus far generated any predictions that physicists have been able to test, so we have no way of knowing whether the theory is right, needs modification, or is simply wrong.
One of the theories of quantum gravity predicts the existence of something called "quantum foam", which includes undulations and correlations, even tiny wormholes, in space-time that exist at extremely small scales. Recently, a way to test this has been identified: high energy photons emitted by gamma ray bursts traveling billions of light years to reach Earth should be slightly slowed down by this foaminess so that higher energy gamma rays should arrive a few seconds before the lower energy gamma rays. I hear that a satellite is in orbit trying to test this right now, but I don't believe the results are in yet.
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