Tom Glynn, who just left his job as CEO of Massport, is moving over to Harvard University on Monday to run a subsidiary that will oversee the planning and development of a new, 36-acre neighborhood in Allston.

Glynn’s appointment gives the university a skilled inside player to deal with the real estate side of the project, neighborhood concerns, and the complex negotiations with state transportation officials over road and transit service in the area.

The Massachusetts Turnpike currently runs right through the middle of the empty Harvard property. The state is preparing to relocate the Turnpike to one side of the property and construct a new network of on and off ramps as well as a new transit station. It’s a very complicated project and the state and Harvard have often not seen eye to eye. Harvard has pledged $50 million toward the final transit station and $8 million for a possible interim station.

Glynn comes to the table with a resume full of top-level positions in government, health care, and academia. Since 2012, he has been CEO of Massport, which runs Logan International Airport and the port of Boston. He previously served as chief operating officer of Partners HealthCare and general manager of the MBTA. He also worked as deputy secretary of labor in Washington, served in the administration of former governor Michael Dukakis, and taught at Harvard’s Kennedy School of Government.

At Harvard, Glynn will be the CEO of an as-yet-unnamed subsidiary of the university in charge of building out a new neighborhood just south of Harvard Business School and adjacent to the new school of engineering and applied sciences, which is scheduled to open in 2020. Harvard officials envision the area as the next Kendall Square. In addition to residences, restaurants, and other amenities, Harvard officials hope to attract the research labs of all sorts of companies, from startups to large firms.

In a statement issued Thursday morning, Harvard President Larry Bacow said Allston will be “Greater Boston’s next epicenter of research, discovery, and innovation.” He predicted the new company Harvard is setting up with Glynn at the helm “will have a long-lasting impact on the development of our campus – and the broader community – and spark and shape future enterprises that will change the world in ways that none of us can predict.”

The new company will be managed by a governing board chaired by Harvard Business School Dean Nitin Nohria. In an interview with the Harvard Gazette, Nitin said once the Turnpike project is completed Harvard will abut Boston University and have access to both the Red Line in Harvard Square and the Green Line along Commonwealth Avenue. West Station is also expected to have a stop on the Worcester Line of the commuter rail system.

“I don’t know what the world looks like 20, 30 years from now, but there’s no other place with the same potential as Allston,” Nitin said.