For new computer scientists that want to understand the interface between programs, operating systems, and hardware, I recommend Computer Systems, A Programmer'

For new computer scientists that want to understand the interface between programs, operating systems, and hardware, I recommend Computer Systems, A Programmer's Perspective, Third Edition by Bryant and O'Hallaron. It's detailed enough to use when trying to understand how a shell works or how to write a signal handler, but the writing couldn't be clearer.