By Jessi Hempel
August 15, 2012

FORTUNE — When Russian Investor Yuri Milner decided to put some of his fast-growing fortune to work in support of his greatest passion, physics, he had any number of options. He could have funded a university or started a scholarship fund. He could have followed Mark Zuckerberg’s philanthropic model by making a multi-million dollar challenge grant. (Zuckerberg’s $100 million challenge grant to the Newark Public School System required the school system to match the money with help from wealthy donors, doubling the gift’s economic value.) Instead, Milner chose a novel device: he launched the Fundamental Physics Prize, an annual $3 million award for physicists.

The prize is designed to draw attention. For one, the cash value is twice that of the famed Nobel. And though it will be awarded to just one physicist annually, Milner kicked it off by naming nine winners, which he selected personally, for a total payout of $27 million. These recipients will form a committee to select an annual winner each February or March.

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Even more striking, the award doesn’t recognize accomplishment, so much as aspiration — and a general attempt to make physics sexy for a mainstream audience. The Web site says the prize recognizes “scientific breakthroughs, as well as communicating the excitement of fundamental physics to the public.” Scientists become eligible not because they have proven the unproven, but because they are trying to do so. They’re encouraged to devote their efforts to problems so intractable the solutions may not arrive in an individual lifetime. Sometimes, their efforts may even fail. Each winner is required simply to give a lecture on his or her work to the general public sometime during the year. A smaller award of $100,000 will also be given to young physicists — grad students and the like — just embarking on their careers. The point is to restructure and broaden the field itself, to encourage many of the world’s youngest intellectual champions to eschew Wall Street or Silicon Valley in favor of academia.

It’s a classic Yuri Milner move. The soft-spoken physicist-turned-investor specializes in making bold, cash-heavy moves that disrupt markets and mindsets. When we first met back in 2009, he handed me a playbook for a new type of investment model. That was the year his firm Digital Sky Technologies dropped $200 million for a 2% stake in Facebook (FB). (In the years that followed, he increased that investment to a high of 9.5%, and then decreased it slowly, selling a significant number of his shares during the IPO.) The terms baffled many of Silicon Valley’s most established dealmakers: Milner’s original investment valued the company at $10 billion, a huge figure in 2009, and he planned to be hands off — not taking a board seat nor requesting a voting share in the company.

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I asked Zuckerberg about Milner for a 2010 profile of the investor, and he told me “I talked to a bunch of different [venture] firms and I spent time with [Milner] and I was like, this guy is clearly smarter and more insightful and has more experience in what we are doing.” Within a year, as Milner’s investment strategy landed him in many of the hottest consumer Internet companies in the United States, other firms began replicating his practice of giving massive cash infusions with generous terms to promising startups.

Two years later, Milner made another disruptive move. He partnered with one of Silicon Valley’s most connected angel investors, Ron Conway, to guarantee all of the graduates of YCombinator — the Harvard University of tech incubators — $150,000 in funding. His assumption was that another trusted institution had already selected the entrepreneurs and committed to helping them. Sure, many of them probably weren’t great deals. But if just one of them became a breakout star, he’d likely benefit. By penning a formal deal, Milner basically stepped in front of all the valley investors who line up at the incubator’s demo days to search out investment opportunities.

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So it was hardly surprising to hear his take on the prize when I spoke to him this week: he is hoping for disproportionate impact. In a world ever more focused on short-term commercial gains—when large companies look to apply research more quickly to new products and governments have less funding to offer academics for the sake of inquiry alone. Milner wants to coax the globe’s most sophisticated thinkers to spend their careers trying advance our knowledge of the universe. He wants more smart people to think simply for the sake of thinking.

But as with all prizes, the size of the purse alone won’t be enough to confer authority and respect over time. In fact, with its focus on preaching to a more mainstream audience, Milner will need to work harder to boost the award’s reputation in scientific communities. (Some academic bloggers are skeptical.) Milner invited theoretical physicist Steven Weinberg, a 1979 winner of the Nobel Prize in physics, to be on his board. The nine prize winners will serve on a selection committee to choose the 2013 winner; anyone can nominate a candidate online. Milner was able to win the trust and admiration of Silicon Valley’s skeptics; it’s likely he’ll be able to do the same among academia’s most prestigious scientists.

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