Earlier this month, with mercifully little fanfare, scientists at Los Alamos National Laboratory in New Mexico witnessed a changing of the guard. For 63 years, the world's best-known nuclear-weapons laboratory had been under the management of the University of California. From 1 June, the university will run it in partnership with three commercial companies.

With luck, the change will conclude a period of turbulence at the laboratory, which began when Taiwanese-born scientist Wen Ho Lee was suspected of espionage in 1999 (see Nature 398, 96; 199910.1038/18079). Lee was never charged, and in the end pleaded guilty to mishandling classified data, but the lab has since been plagued by a series of security and procurement scandals. That encouraged the Department of Energy, which oversees the facility, to open its management contract up to bidding for the first time (see Nature 423, 104; 200310.1038/423104b).

Under a contract that runs until 2013, the university will run the laboratory jointly with San Francisco-based Bechtel National, an engineering contractor that already manages several US nuclear weapons facilities. Two other companies, BWX Technologies and Washington Group International, will also play roles in managing the laboratory's nuclear equipment and its hazardous waste.

The energy department and its congressional overseers hope the new arrangement will bring best business practice to the laboratory and draw its recent difficulties to a close. The laboratory's staff, who will retain their pension rights and status within the University of California, are also hoping that the change will quell public criticism of the laboratory.

But for scientists at the lab, this hope is tinged with concern that the new management will shift its focus away from basic research. Both BWX Technologies and Bechtel have a track record in engineering management, overseeing production facilities for US nuclear weapons. They are for-profit institutions, more interested in meeting government schedules than nurturing scientific excellence.

There are still grounds for optimism that science won't take a back seat at Los Alamos. The lab's new director, Michael Anastasio, is a physicist with a distinguished career in nuclear-weapons design. Other Department of Energy facilities under joint business and university management, such as Oak Ridge National Laboratory in Tennessee, have continued to do good science.

Scientists fear that a larger weapons-production role at Los Alamos will come at the expense of its research programmes.

None of these places enjoy Los Alamos's intellectual reputation, however, and fears persist of a shift in priorities at the New Mexico laboratory. The energy department is considering the construction of a multi-billion-dollar facility there to produce replacement plutonium triggers for existing nuclear weapons. In the zero-sum game that is the Department of Energy's budget process, scientists fear that a larger weapons-production role at Los Alamos will come at the expense of its research programmes — especially those not directly related to nuclear weapons.

The main strength of Los Alamos has always been its ability to attract good people by offering exceptional facilities dedicated to a range of scientific enquiry. It is home to some of the world's most powerful supercomputers, which are used for such purposes as simulating a possible bird-flu epidemic. The laboratory also houses acknowledged global leaders in neutron science, mathematics, computer science, nuclear non-proliferation, and more. The scientists and engineers who work on nuclear weapons there rely on the non-weapons work to retain links with the wider academic world. That interface is what makes Los Alamos special, and the laboratory's fresh management team should nurture it with care.