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Blue Waters Supercomputer Brings Subatomic Resolution to Computational Microscope


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A view through the computational microscope.

Researchers at the University of Illinois have built a computational microscope that can model the atomic and subatomic forces driving molecular interactions.

Credit: University of Illinois

University of Illinois scientists have built a "computational microscope" that can model the atomic and subatomic forces driving molecular interactions, which they think will simplify efforts to understand the chemistry of life, simulate large molecular systems, and develop new pharmaceutical and industrial agents.

The team used a nanoscale molecular-dynamics program called NAMD, which applies classical-mechanics methods to model the structure and simulate the behavior of hundreds of millions of individual atoms, in combination with a program that models the interactions of protons, neutrons, and electrons.

By implementing a technique for partitioning large molecules into classical- and quantum-mechanics regions, the researchers could concentrate their computational resources on small regions involved in critical interactions.

"We set it up so that researchers can easily choose how they will partition their own systems," says University of Illinois professor Zaida Luthey-Schulten.

From Scientific Computing
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