The list was announced this week during the International Supercomputing Conference in Dresden, Germany.
IBM's Blue Gene/P, known as 'Intrepid', is located at the Argonne Leadership Computing Facility and is also ranked third fastest overall.
The supercomputer has a peak performance of 557 teraflops and achieved a speed of 450.3 teraflops on the Linpack application used to measure speed for the Top 500 rankings.
"Intrepid's speed and power reflect the DoE Office of Science's effort to provide the R&D community with powerful tools to make innovative and high-impact science and engineering breakthroughs," said Rick Stevens, associate laboratory director for computing, environmental and life sciences at Argonne.
Eighty per cent of Intrepid's computing time has been set aside for open science research through the DoE Office of Science's highly select Innovative and Novel Computational Impact on Theory and Experiment (Incite) programme.
There are currently 20 Incite projects at Argonne that will use 111 million hours of computing time this year.
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