I've read the intro. of the paper, but I'm not a physicist, so this question might seem dumb, but here goes:
The paper describes the "ultimate laptop" as being a computer that can use one atom to store 1 bit of information. Why is an atom the smallest unit of matter a computer can store a bit in?
(It does seem implausible for 1 bit per atom to be right. I mean, atoms themselves vary in hundreds of ways - # of protons, # of electrons, etc. Just using each element to represent a byte would seem to get you more than 1 bit per atom.)
But they also vary in size significantly, so it wouldn't be practical to store 8 different types of atoms. I think adjusting the spin state of one atom for one bit might be the limit.
This is a discussion of the theoretical limits. They may be substantially higher than the actual engineering limits we can attain with real configuration of real atoms. (Or relevant other building blocks as appropriate.)
However, the theoretical limits turn out not be entirely useless even if we can never attain them in practice; they offer some insight about the nature of the universe, and it may yet be some thoughts on how the universe can process information that cracks open the problem of what happens in black holes, rather than what you might think of as conventional physics. There's been a lot of interesting work done in that area; for instance, read http://en.wikipedia.org/wiki/Holographic_principle and observe how many times the word "information" comes up.
