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ALBANY — For eight of the nine defendants charged on Thursday in the wide-ranging bribery and bid-rigging scheme surrounding Gov. Andrew M. Cuomo’s economic development programs in upstate and Western New York, the motive for the alleged crime seemed to be simple, old-fashioned greed.

But for Alain E. Kaloyeros, a physicist who rose from a basement laboratory at the State University at Albany to oversee hundreds of millions of dollars in state economic development funds over a quarter-century, a more complex purpose seemed to be at work. Beyond money, the rewards he sought appeared to be power, prestige and, perhaps most of all, the fulfillment of a long-held dream: reinventing upstate New York as a Rust Belt Silicon Valley.

With an early zeal for nanotechnology, a taste for head-turning cars, a sardonic tongue and a talent for luring major corporations to with government financing, Dr. Kaloyeros, 60, is widely credited with transforming Albany from a drowsy government town into an unlikely center for high-tech research.

“It was pretty much a miracle,” said Lloyd Constantine, a top aide to Eliot Spitzer, the former governor. “From my standpoint, from the administration’s standpoint, he was doing a spectacular job. Revitalization of the upstate economy was Job No. 1. And he was doing it, and doing it really well.”

Now Dr. Kaloyeros is charged with secretly manipulating the process through which the State University of New York Polytechnic Institute, the university branch that he headed, awarded lucrative contracts to a select few developers in Buffalo, Albany and Syracuse, whose executives were also charged in the scheme. The university suspended him without pay on Thursday.

Often working with a lobbyist, Todd R. Howe, a former aide to Mr. Cuomo, D. Kaloyeros is accused of personally drafting and revising several requests for proposals to favor certain developers, including one for a SUNY Polytechnic dorm, another for a campus research building and two connected to huge economic development contracts in Syracuse and Buffalo.

Untethered from the usual government safeguards, the university all but supplanted the state’s economic development agency as the Cuomo administration’s chief economic engine in upstate New York.

The grants, rents and business he brought in to SUNY Polytechnic “all benefited him personally through his compensation package, and also added to his status as a kingmaker and an important person in state government,” said the New York attorney general, Eric T. Schneiderman, who charged Dr. Kaloyeros with three felony counts of bid-rigging at a news conference. Additional federal charges were brought by the United States attorney’s office in Manhattan.

Dr. Kaloyeros’s lawyer, Michael Miller, declined to comment.

Dr. Kaloyeros had bragged about his ability to “write an RFP in such a way that only one company could win it,” according to the state criminal complaint. Dr. Kaloyeros, referred to as “Dr. K” in the federal complaint, did so, according to prosecutors, to preserve his status as one of the state’s highest-paid employees, draw more research financing to SUNY Polytechnic and inflate his reputation as Albany’s most successful rainmaker.

“The job requires being a scientist, being a psychiatrist, being a priest, being a cop, being a negotiator, being a business developer or manager, being a teacher, being an adviser and being an ego-kisser,” Mr. Kaloyeros told the Albany Business Review in 2011. “I’d like to think I do all of them very well.”

Wheedling and wooing over sushi and Starbucks coffee, he made every college president, legislative leader and governor who supported him feel like a visionary, even as he outlasted, and out-earned, all of them. He consistently ranked among the state’s highest paid employees, earning a total of $1.17 million in salary and other performance-based payments last year.

“He worked the power, in a sense, and knew what buttons to push,” said Ronald Canestrari, the former majority leader of the State Assembly. “The more he produced, the more he received. He was king of the hill.”

Mr. Cuomo, a Democrat who frequently claims to have “invested more in upstate New York than any governor in history,” was perhaps Dr. Kaloyeros’s most ambitious partner yet, with plans to sprinkle Kaloyeros dust on Buffalo, Syracuse, Rochester and other areas in desperate need of new jobs.

In 2012, after Mr. Cuomo announced that the state would spend $50 million to open a medical research hub in Buffalo, modeled on what Dr. Kaloyeros had done at SUNY Polytechnic, Dr. Kaloyeros christened the Albany-Buffalo pipeline “the Andrew Cuomo 21st century high-tech innovation canal.”

Mr. Cuomo happily reciprocated: The state owed the scientist “a tremendous amount of gratitude,” the governor said last year.

In the sometimes drab world of state government, awash in power suits and committee hearings, Mr. Kaloyeros — with his elegant but hard-to-identify accent, his taste for John Varvatos and his wardrobe full of jeans frayed just so — openly flaunted his unconventionality.

Dr. Kaloyeros’s Facebook page pulsed with off-color jokes about women (“I bought a Ferrari for my girlfriend,” read one image he posted. “Best trade ever.”) and lighthearted Darth Vader memes.

If he was a geek, as he often said of himself, he was the kind of geek who made sure that the reporters who wrote about him, and there were quite a few, noticed the GEEK vanity license plate on his black Porsche Boxster. (Later iterations included NANOGEEK, on a black Range Rover, and DRNANO, on a black Ferrari.)

Any misgivings about his ego, style or centrality to the SUNY operation faded in the face of the private investment he had conjured. The Albany clean rooms, engineering programs and chip-fabrication plants he had a hand in eventually came to be worth about $14 billion.

Raised in East Beirut, Lebanon, Dr. Kaloyeros was a 19-year-old American University student when, he later told Albany acquaintances, he was attacked by members of the Palestine Liberation Organization in the early stages of Lebanon’s civil war. Later, he joined a small Christian militia before immigrating to the United States, where he earned a doctorate in physics from the University of Illinois.

By the early 2000s, as a State University at Albany professor, Dr. Kaloyeros was persuading state leaders to commit millions of dollars of state funds to high-tech equipment and laboratories, which he used to entice corporations and jobs to the area.

“We’re out to put Stanford out of business,” he told the Albany Times-Union in 2002.

Two of his most important political relationships were with Sheldon Silver, the former State Assembly speaker, and Joseph Bruno, the former State Senate majority leader. To keep the state money flowing, he often played the governor and the two legislative leaders off one another.

By the time Dr. Kaloyeros had amassed the clout to spin off the College of Nanoscale Science and Engineering at SUNY Albany into the independent campus known as SUNY Polytechnic, in 2013, the state’s top politicians were all but squabbling over who should receive credit for his work.

The two nonprofits that SUNY Polytechnic set up as its construction arms, Fort Schuyler Management Corporation and Fuller Road Management Corporation, had innocuous origins: They were formed to streamline the process of building the various laboratories, dormitories and research centers SUNY needed in order to expand, enabling the institution to quickly capitalize on partnerships with private companies. To that end, the Legislature in 2011 passed a law exempting both nonprofits from oversight by the state comptroller, who normally scrutinizes government contracts.

Whenever questions arose about the power and the money the state had concentrated in Dr. Kaloyeros, his bosses always concluded that he had earned it.

“His salary was a bargain,” Mr. Constantine said.

Mr. Cuomo apparently made the same calculation.

In 2010, an Albany Chamber of Commerce video dedicated to Dr. Kaloyeros’s exploits posed the question: What next?

The professor’s face spread into a corrugated smile.

“Stay tuned,” he said.

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