Who is the person called "professor" that is kept in the basement under Ichigaya?
It is revealed in the third part Grisaia no Rakuen that:


   Locked away in the basement was Yuuji's sister Kazuki Kazami, but it was her brain that was left and functioning. Ichigaya was the one who retrieved her body and built a super computer with her brain.


In the anime, the corresponding scene is at the end of episode 5, and further elaborated in episode 6 of Grisaia no Rakuen.