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His departure had been widely expected, although as late as Thursday afternoon he was refusing to answer questions on the subject. The open slot at the Energy Department adds to a constellation of vacancies at the top of related agencies: the Environmental Protection Agency, the Transportation Department and the Interior Department.

President Obama said in a statement that Dr. Chu "brought to the Energy Department a unique understanding of both the urgent challenge presented by climate change and the tremendous opportunity that clean energy represents for our economy." The president said that in the four years of Dr. Chu's tenure, "we have doubled the use of renewable energy, dramatically reduced our dependence on foreign oil, and put our country on a path to win the global race for clean energy jobs."

He also praised Dr. Chu for expanded support for research into "groundbreaking innovations that could transform our energy future."

Dr. Chu presided over a $90 billion surge in expenditures in which the Obama administration tried to use the Energy Department to accomplish twin goals: stimulating the economy, and advancing energy efficiency and clean energy production. Dr. Chu said that some of the money would be used to "swing for the fences," promoting a variety of ventures, of which some were certain to fail. But the successes would more than compensate for the failures, he said, especially in the area of research and development, where key scientific breakthroughs could nurture whole new industries, he said.

The commercial verdict may not be delivered for some years to come on many of those investments. The initial outlook for the Obama administration's clean energy programs like wind and sun has been dimmed by the success of an Energy Department initiative of the 1990s, developing a method for drilling horizontally in shale formations and fracturing the rock to liberate natural gas, known as fracking, which cut the price of fossil energy just as the renewable technologies appeared poised to reach price parity.

Dr. Chu, a physicist, is the first cabinet secretary to come into office with a Nobel Prize (an honor he shared in 1997 for his work with supercooled atoms) and the first scientist to lead the department. His 15 predecessors as secretary included a dentist, an admiral from the nuclear navy, a former electric utility lobbyist and a variety of political figures.

But his scientific stature was such that he escaped the most severe criticism by Republicans when the department faced its biggest attack, over the bankruptcy of Solyndra, an innovative solar equipment company that got a $535 million loan guarantee from the department but declared bankruptcy because the market for its product had collapsed. Republicans accused the White House of cronyism, noting that among Solyndra's investors were some Obama campaign donors. But Dr. Chu was generally exempted by Republicans, or at worst, written off as outside his depth in financial matters.

While he had the political skills to manage the Lawrence Berkeley National Laboratory and its 4,000 employees, his job before he was chosen by Mr. Obama to be energy secretary, he also showed a physicist's penchant for speaking the truth plainly, in a way that people in politics generally avoid.

In September 2008, before Mr. Obama was elected, he told The Wall Street Journal, "Somehow we have to figure out how to boost the price of gasoline to the levels in Europe," a quote that Republicans in Congress have used to hammer him. Three months earlier, in a lecture he gave in Washington on energy, he said that new houses could be made energy-efficient with an investment of an extra $1,000, "but the American consumer would rather have a granite countertop."

And he demonstrated technical skill almost unheard-of for a cabinet secretary. He was dispatched by Mr. Obama to Houston to take control of some of the federal efforts after the Deepwater Horizon blowout of April 2010. He assembled a team of nuclear physicists to consider the options, and made some key decisions.

Also still uncertain is the fate of a giant infrastructure nurtured by Dr. Chu's Energy Department for manufacturing batteries for electric cars, because demand for the cars has not reached anticipated levels. Appearing on Thursday at the Washington Auto Show, he indicated that the administration was unlikely to reach its goal of one million electric vehicles on the roads by 2015.

And the more exotic research projects – in advanced batteries, or technologies for making gasoline from plants and trees, or improving on photosynthesis as a way to store the sun's energy – were always expected to take far longer to pay off.

Meanwhile, despite enthusiasm from Dr. Chu, the department's efforts to nurture the construction of new nuclear plants have mostly fallen flat; inheriting a $17.5 billion fund for loan guarantees for new nuclear energy plants, and proposing an additional $35 billion, the department never succeeded in making a loan. Following up on a campaign promise by Mr. Obama, his department closed down the effort to open a nuclear waste repository at Yucca Mountain, in Nevada, but did not reach the point of starting a process to find another site. And the department has lagged in its efforts to clean up radioactive wastes left over from decades of nuclear weapons production.

A vocal proponent of efforts to control greenhouse gas emissions, he served in an era when his party could not get a bill through Congress to institute a "cap-and-trade" system, or any other method, to limit such emissions.

Dr. Chu sent a letter to the department staff early on Friday, focusing on the department's work on climate change, clean energy and research. He said he and his wife were eager to return to California and that he would return to academic work.

Dr. Chu will turn 65 on Feb 28. He told colleagues he would stay in place until the end of the annual "summit" of the Advanced Research Projects Agency-Energy program, known as Arpa-e, an energy version of the better-known Darpa, the Defense Advanced Research Projects Agency.