Good work on the layout, but do you really want a desk inside in the dark? How do you study typically? What is your major? I'd put any desk nearer the light as you are going to spend many hours there and being in a cave is not pleasant. You are lucky to have such a wonderful space as a grad student. You wouldn't believe the apartment I had in Tucson, really, you wouldn't.

I'd go with a daybed. If you are like me, you read in bed and then get up to do work at a desk. I work a lot with my laptop in bed. Reading for hours necessitates propping your head up or you get neck problems. A daybed means you don't need a separate sofa, and you then have room for a really nice reading chair. Make sure you don't get a daybed that sits too high or it doesn't feel right as a sofa. With a daybed as a sofa, you can afford the space for a real dining table to use when you need to spread your work out. This allows you to have people over for dinner and meetings and room for group studying.

You are going to be studying long hours and you don't want the hassle of pulling down a Murphy bed after hours and hours of work into the wee hours of the morning.

If a daybed seems too small, then get a full or a queen and push it sideways against the wall with lots and lots of pillows against some sort of headboard you construct yourself.

Fit in a nice bookshelf, maybe a combo tv unit with bookshelves.