Sidney Drell, a Stanford theoretical physicist who counseled government leaders for more than 50 years and who was an internationally prominent advocate of limits on nuclear weapons, died Dec. 21 at his home in Palo Alto, Calif. He was 90.

He had complications from pneumonia, said a daughter, Joanna Drell.

Dr. Drell, who received a prestigious MacArthur Foundation fellowship, or “genius grant,” made key advances in particle physics while occasionally stepping on the public stage as a writer and an adviser to military and intelligence leaders at the highest levels.

His career, he wrote, was “divided between pursuing the dream of discovery and working to avoid the nightmare of a nuclear holocaust.”

For many years, Dr. Drell was a key figure at the Stanford Linear Accelerator Center, a laboratory operated by the Energy Department. Now called the SLAC National Accelerator Laboratory, it is a leading research center and contains a particle accelerator in a building almost two miles long — the longest in the world.

Dr. Drell made several major advances in particle physics and quantum theory at SLAC. His specialties included quantum electrodynamics, which describes the interactions of matter and light, and quantum chromodynamics, a study of the behavior of subatomic particles.

He and a colleague, Tung-Mow Yan, developed the Drell-Yan Process, which describes the effects of a quark in one particle colliding with an antiquark in a second particle. It has become part of the framework of particle physics.

“Drell’s theoretical work was very critical in setting SLAC on the course that it took,” Stanford physicist and Nobel laureate Burton Richter said in a statement. “As head of the SLAC theory group, Drell brought to us a whole host of a younger generation of theoretical physicists who began creating the present picture we have of the structure of matter.”

In addition to his scientific work at SLAC, Dr. Drell was co-director of the Stanford Center for International Security and Arms Control (now the Center for International Security and Cooperation). It followed an interdisciplinary approach in proposing solutions to worldwide problems, through science, diplomacy, economics and other fields.

When Stanford refused to grant tenure to scholars in the program, Dr. Drell abruptly resigned in 1988, leading to the departure of several notable figures at the center, including astronaut and physicist Sally Ride.

Since 1960, Dr. Drell was a fixture in an elite group of scientists known as “Jason” (after Jason and the Argonauts of Greek myth), who act as advisers to military and intelligence experts on sensitive issues of national security. He had been a consultant to the U.S. Arms Control and Disarmament Agency since 1961.

“One gets a feeling, with a few people sitting around a table, that one is being heard,” Dr. Drell told the San Jose Mercury News in 1996, describing his interactions with high-echelon officials. “They come at you with all the questions and concerns and then have to go think about it.”

Long known as a proponent of arms control, Dr. Drell led a study that determined that the U.S. stockpile of nuclear weapons could be maintained without underground tests. He was a persuasive behind-the-scenes voice in high-level discussions that led to the 1996 signing of the Comprehensive Nuclear Test Ban Treaty, which prohibits global testing of nuclear devices.

In the 1970s and 1980s, Dr. Drell was a leading public supporter of Soviet physicist and dissident Andrei Sakharov, who received the Nobel Peace Prize in 1975 for his work on nuclear disarmament and human rights.

For years, Sakharov was forced to live in internal exile in the Soviet Union and was not allowed to leave the country. Dr. Drell’s efforts on Sakharov’s behalf were credited with helping win the activist’s freedom not long before his death in 1989.

Sidney David Drell was born Sept. 13, 1926, in Atlantic City. His father was a pharmacist, his mother a schoolteacher. Both were Jewish immigrants from Eastern Europe.

As a student at Princeton University during World War II, Dr. Drell was hospitalized for several months with a ruptured appendix and peritonitis that disqualified him from military service. He graduated from Princeton in 1946, then went to the University of Illinois at Urbana-Champaign for graduate work in physics, receiving a master’s degree in 1947 and a doctorate in 1949.

He had faculty assignments at Stanford and the Massachusetts Institute of Technology before settling permanently at Stanford in 1956.

He published several textbooks on physics and was the co-author of other books about Sakharov and nuclear deterrence. He received a MacArthur fellowship in 1984 and was elected to the National Academy of Sciences and the American Academy of Arts and Sciences. He was a past president of the American Physical Society. In 2013, he received the National Medal of Science at a White House ceremony.

Dr. Drell was prominently featured in “The Partnership: Five Cold Warriors and Their Quest to Ban the Bomb,” a 2012 book by journalist Philip Taubman.

In 2006, Dr. Drell teamed with former secretary of state George P. Shultz to launch a program at Stanford’s Hoover Institution dedicated to freeing the world of nuclear weapons. They published several books together.

Survivors include his wife of 64 years, Harriet Stainback Drell of Palo Alto; a son, Daniel Drell of Falls Church, Va.; two daughters, Persis Drell, a former SLAC director and the recently named provost of Stanford University, of Stanford, Calif., and Joanna Drell of Richmond; and three grandchildren.

Dr. Drell’s office at Stanford was filled with books and a blackboard on which he scrawled scientific equations. He was also a devoted reader of poetry and a skilled violinist who often played in informal chamber groups — sometimes with Condoleezza Rice, a pianist and former secretary of state who is a Stanford professor.

In the 1970s, Dr. Drell’s links to the defense industry led to occasional protests and disruptions of his scientific talks by antiwar activists, even though his stance was firmly in favor of limiting nuclear arms. A decade later, he faced criticism from the right because of his opposition to the Reagan administration’s Strategic Defense Initiative, commonly called “star wars.”

“You don’t play games,” he said in 1996, explaining his ability to steer his way through divisive policy debates. “You shouldn’t try to be a politician in Washington. You have to meet them on the grounds where you are comfortable: ‘These are the things I know. These are the things I don’t.’ ”