New ORNL algorithm shatters record for
Normal Coordinate Analysis of Chemical/Biological Molecules

Knowing vibrational modes of molecules provides important insight into their behavior

identifying vibrational modes of rhinovirus could lead to improved 
drug design

Normal Coordinate Analysis (NCA) yields vibrational modes (eigenmodes), but until recently was only feasible for small systems with only a few thousand atoms. By combining new large-scale eigensolver techniques developed by CSM's Chao Yang (1999 Householder Fellow) with new methods for calculation of the Hessian matrix (work with CASD), ORNL has raised the bar for Normal Coordinate Analysis from the previous record of about 3,000 atoms to a polymer system of 24,000 atoms. ORNL's new large-scale NCA capability will soon allow study of molecules of even greater size and complexity (~100,000 atoms).

Research applications include optimized drug design, fabrication of nanoscale devices, and better understanding of basic biological processes such as photosynthesis.

Identifying vibrational modes of rhinovirus
could lead to improved drug design

Force field model for polymer materials. Our current research on NCA has allowed computational chemists to perform routine NCA on molecular systems with tens of thousands of atoms. The calculations we have performed so far helped verify the force field model of the polyethylene type of polymer particles, the simplest polymer in terms of its chemical structure. For many other large-scale molecular systems, the theoretical understanding of the nature of molecular bonding is still preliminary. The development of efficient large-scale NCA will play a vital role in helping us to successively modify, test and improve the existing force field model. With a good understanding of the molecular bonding, we will be able to characterize the thermal properties of various materials by computing their heat capacities and entropies.

The use of NCA is not limited to polymer materials. We are currently investigating the possibility of using large-scale NCA to help design various nano-scale devices.

Energy and charge transfer in photosynthesis. Another important application area is structural biology. We are currently collaborating with researchers at Caltech on using NCA to study the energy and charge transfer process triggered by small amplitude vibration on a picosecond time scale. One structure of interest is photosystem II. Photosystem II uses light energy to drive two chemical reactions: the oxidation of water and the reduction of plastoquinone. Photosystem II is the only known protein complex that can oxidize water, which results in the release of O2 into the atmosphere.

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