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Test Molecules and 3-D Electron Orbitals (Image 8)

Structures of seven test molecules calculated by a direct self-consistent-field algorithm

Structures of seven test molecules calculated by a direct self-consistent-field algorithm rewritten to run on a computer's graphical processing unit (GPU). The numbers indicate how much faster the GPU-run algorithm calculates the structure of molecules in comparison to a molecular design program called GAMESS running on a computer's central processing unit (CPU). Carbon atoms are aqua, nitrogen atoms are blue, oxygen atoms are red and hydrogen atoms are white. In this image, C60 is made of 60 carbon atoms and is commonly referred to as a "buckyball," valinomycin transports potassium ions in biological systems, taxol is a chemotherapy drug, and CLN025 is a recently reported artificial protein.

In 2009, Todd Martínez, a professor of chemistry at Stanford University, and graduate student Ivan S. Ufimtsev published information about their National Science Foundation (NSF)-supported study in which they'd rewritten algorithms to run on a computer's GPU rather than the CPU of a traditional desktop computer.

When designing and simulating molecules, computers can spend long periods of time--ranging from days to years--running the complex mathematical equations (or algorithms) used by scientists and engineers to develop more effective drugs, catalysts for fuel cells and other molecular-based materials and applications. The improved method for running algorithms calculated the structures of test molecules up to 650 times faster than the molecular design program called GAMESS running on a computer's CPU.

To learn more, see the NSF Discovery story Video Game Technology and Science? [The research on adapting quantum chemistry algorithms for video game architectures, specifically PlayStation2 and PlayStation3, was initially funded by NSF's Division of Materials Research (grant DMR 03-25939). Work aimed at NVIDIA architectures, informed by our PS2 and PS3 efforts, was supported by NSF's Division of Chemistry (grant CHE 06-26354).] (Date of Image: 2008-2009) [Image 8 of 9 related images. See Image 9.]

Credit: Ivan S. Ufimtsev, Stanford University; Image created using VMD

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