It's pretty much conventional wisdom that Org Mode is the killer app for Emacs. Even people who don't use Emacs seem to be aware of that and, of course, there are various efforts underway to port Org to other editors.
Matthieu Caneill considers how Org Mode can be leveraged by PhD students to organize their work and research. He discusses his file setup and how he uses each one in his workflow. It's a nice way of organizing things and exactly what you'd expect an Org mode beginner to have. Lots of people, including me, use similar organizations but it's not the only strategy available. Another possibility—and one that is arguably more Org like—is to have a single file for all your long term activities. The use of tags and advanced searching functionality make this an ideal solution.
My journal file is pretty much like that but I have a few others for things like managing my blog and recording medical/exercise data. If I were starting over, I'd consider combining everything—or almost everything—into a single journal file. In any event, if you're starting your PhD—regardless of your area—you should consider organizing things in Org. It's all plain text so you're not stuck and can move to something else if you find it suits your needs better.
Over and over again, you hear people saying how much Org mode increased their efficiency and productivity. If you're starting work on a PhD, your going to need all the help you can get so it's worth spending a little time coming up to speed with Emacs and Org mode.