In September 1950, Allen entered the University of Illinois for graduate study in nuclear physics. He completed his Master of Science degree in 1952. Allen continued his graduate study, and he earned his Ph.D. in physics in 1954. He had completed an experimental thesis on high-energy photonuclear reactions. Allen then was assigned to the U.S. Atomic Energy Commission's Los Alamos Scientific Laboratory in Los Alamos, New Mexico, as a physicist in the Test Division, where he became acquainted with the bomb designer Ted Taylor. Allen conducted experiments in several different nuclear test series. These experiments concerned the physics of thermonuclear weapons design and to the effects of high altitude nuclear explosions conceivably to be used for ballistic missile defense.