He would undergo medical treatment in an effort to combat the condition, which was finally brought under limited control in 1960. However, he suffered flare ups that would last for the remainder of his life. Williams was instrumental in obtaining funding from the Atomic Energy Commission for the construction of a 50-MeV linear proton accelerator at the University, which became operational during the 1950s. During 1955–58 he served on the board of the Midwest Universities Research Association, and was the president in 1956–57. He was appointed Director of the Research Division for the Atomic Energy Commission in 1958. The following year he was appointed Atomic Energy Commissioner by U.S. President Dwight D. Eisenhower. From 1960–66, he was a member of the General Advisory Committee for the United States Atomic Energy Commission. He was elected to the National Academy of Sciences in 1961 and was president of the American Physical Society in 1963. In 1965, he was named as president of the Argonne Universities Association. Williams died of pneumonia in Minneapolis, Minnesota on April 18, 1966. During his career, he was awarded honorary doctorate of science by the University of British Columbia and an honorary doctorate of engineering from the Pennsylvania Military College.