During his term in office Peña has promoted management reforms across the department and increased transparency at the national labs. Peña's involvement in promoting awareness of the greenhouse effect and climate change at the White House was considered crucial in obtaining US support for the Kyoto agreement on carbon dioxide emissions.

In a statement Peña pointed to the DOE's record in developing world class research, and spoke of how new facilities such as the National Ignition Facility and the National Spallation Neutron Source will maintain US prominence in physics.

President Clinton will have to appoint a replacement as soon as possible. Over the next few months, the DOE has to introduce increased competition to the US electricity market, ship nuclear weapon grade material from Russia to the US, and agree a procedure with the US nuclear electricity companies for the disposal of radioactive waste from nuclear power plants. Moler's experience with these programmes makes her appointment to the post very likely.