Insanity and genius
The plot plays on the idea that geniuses are tortured internally by their hyper intelligence. The plot structure can be seen as a metaphor for that basic idea (after all, the title is The Physicists, which points to intelligence. The three geniuses are subjected to von Sahnd because they are considered crazy by the society of their time, at least partially because they are so smart that they don't really perform well in social situations. Ultimately, this leads to this dilemma—they are constantly plagued by their minds, and von Sahnd and her army of nurses can be seen as a picture of the that dilemma.
Emotional loneliness
The men are kept in isolation, but they are not physically isolated at all times, because they are attended by female nurses, but that occasional female company drives them insane, because they are emotionally lonely. This novel shows what kinds of lengths a person will go to when they feel their emotional needs aren't being compromised. Mobius isn't exactly a happy camper, but someone is literally murdering people, so there's the spectrum of how people can react to loneliness.
Violence and the problem of malevolence
Two of the patients are delusional in that they believe they are literally people they are not. The first is Patient One, Herbert, who believes he is Sir Isaac Newton, one of the world's most elite geniuses of all time, and the second is Patient Two who believes he is Albert Einstein. Now, Mobius is also crazy, but he knows that one of the others is literally a murderer, and his delusions often help him to navigate their malevolence safely. Also, he must make decisions about violence, given that he isn't sure who is doing the killing.
