William Swope




Simulations of Protein Folding on the BlueGene Supercomputer at IBM
We have entered an interesting and important phase of computational science enabled by supercomputers. Supercomputers are reaching performance levels that enable atomistic simulations of biological processes on time scales that approach and begin to overlap with the fastest (most time-resolved) experimental techniques. The simulations, therefore, can be used to help guide the interpretation of the experiments. But, perhaps even more importantly, the simulations can be validated and further improved through collaboration between experimental and computational scientists. In this talk, I will discuss one such study. Using the BlueGene supercomputer at IBM Research we have performed extensive simulations on a mutant construct of lambda repressor. This protein consists of 80 amino acids structured as a five helix bundle in its folded state. The mutant was designed in the Gruebele lab at the University of Illinois, Urbana-Champagne, to exhibit sub-10 microsecond folding times in laser temperature jump experiments. Our simulations employed replica exchange as well as traditional molecular dynamics at a number of different temperatures. Our simulations clearly reveal very complex folding behavior. In particular, different structural elements exhibit different degrees of thermodynamic stability and melt at different temperatures. Some of the structural transitions appear to be relatively cooperative, whereas others are quite diffuse.




Dr. William Swope is a Research Staff Member in Science and Technology at the IBM Almaden Research Center. His research focuses on the development of methods for and applications of computational chemistry, the use of computer simulations and modeling to address issues related to molecular and materials properties. Dr. Swope has been heavily involved in helping to define and execute the protein folding science research components of the BlueGene research project. He maintains close contact with computational chemists in the pharmaceutical industry and with many academic scientists involved in the study of protein folding. Dr. Swope received his A.B. degree in chemistry and physics from Harvard University in 1975, and his Ph.D. in theoretical chemistry from the University of California at Berkeley in 1979. He also performed postdoctoral research at Stanford University on the statistical mechanics of liquids and solutions before coming to IBM in 1982. Since joining IBM, he has been involved in a wide range of activities including hardware and software development, microcode development, mathematical function and scientific subroutine library development, technical writing, technical marketing support for high performance computing, and scientific and engineering data management. In 1992, Dr. Swope entered the Research Division and lead the team that developed the classical statistical mechanical (molecular dynamics and Monte Carlo) capabilities of the Mulliken computational chemistry software package. He has most recently been involved in basic research related to protein conformational dynamics, including protein folding. Dr. Swope is a member of the American Chemical Society and the American Physical Society.


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