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Within the massive federal stimulus bill is funding for a small but influential government agency: ARPA-E, or Advanced Research Projects Agency-Energy.

Modeled after DARPA, the Defense Department program credited with creating the Internet, stealth fighter and M16 assault rifle, ARPA-E was formed to fund transformational clean-energy research and technology.

ARPA-E operates with a staff of just 20 people and aims to be nimble and quick. The agency funds “pie in the sky” and “moonshot” clean-energy technologies that venture capitalists typically steer clear of.

“We’re funding projects that are too risky for the private sector,” said Arun Majumdar, who left his job at the Lawrence Berkeley National Laboratory to direct ARPA-E. “When it’s hard to shop it around Sand Hill Road,” he added, ARPA-E will often step in and bet on unproven technologies that venture capitalists won’t touch.

ARPA-E grants are small in size — the average is about $3 million. But they are highly prized in Silicon Valley.

Makani Power in Alameda was awarded a $3 million ARPA-E grant to continue its work on an “airborne wind turbine.” Makani, which is backed by Google, is working on wind “kites” that would be tethered to the Earth and capture the wind that blows at higher altitudes.

“Makani is taking a totally unconventional approach to wind power. It’s a very clever idea and it’s also very risky,” said Majumdar, whose childhood hobbies included making model airplanes. “The kite has to take off and land on its own, and it can’t crash.”

The Bay Area got about $50 million total in ARPA-E funds; other grantees in the region include Applied Materials, Codexis, NanOasis, Primus Power, Stanford University and the University of California.

The ARPA-E awards are highly competitive. The first ARPA-E solicitation was flooded with more than 3,600 preliminary applications; only 37 made the final cut.

The agency will host its second annual ARPA-E Energy Innovation Summit, designed to showcase ARPA-E grantees as well as finalists, Feb. 28 to March 2 in Washington, D.C. It’s easily one of the most significant cleantech conferences of the year, drawing venture capitalists, clean technology entrepreneurs and policymakers.

DARPA’s budget for 2010 is approximately $3 billion. By contrast, ARPA-E received just $400 million through the Recovery Act and has basically run out of money. President Barack Obama requested $300 million for ARPA-E in 2011, but it’s not certain that Congress will appropriate that much.

“The energy economy is a $1 trillion market, and our budget is just a small slice,” Majumdar said. “We have a risk portfolio, and my job is to manage it holistically. We want to change the ballgame, and we’re willing to take a shot when no one else is willing to take a shot.”

Contact Dana Hull at 408-920-2706. Follow her at Twitter.com/danahull.

For more information about ARPA-E, go to http://arpa-e.energy.gov