Japan offers many cultural and natural experiences. For starters, you may consult the Japan National Tourist Organization.
From Kavli IPMU, it takes about 40 minute to Akihabara/Asakusa on the Tsukuba Express. And much of downtown Tokyo is within an hour on Tsukuba Express and other trains. Also you can visit Nikko for one (two) -day trip. "Shrines and Temples of Nikko" is a UNESCO world heritage site where three of the Tokugawa shoguns from the 1600s are enshrined with incredible architecture.