Research Associate: Z. Zhang
Research Assistants: M. Cornea-Hasegan, C. Costian
The goal of this research is to study parallel algorithms and methods for the computation related to the determination and analysis of biological structures, and to make possible the determination of structures larger than is possible with the best supercomputers of the 1980's. Specifically, we are concerned with viruses and their complexes with neutralizing antibodies, receptors, and other ligands.
The principal tool for structure determination of biological molecules is X-ray Crystallography. After useful crystalline material has been obtained, X-ray diffraction data are collected and processed extensively by computers.
The three spatial coordinates of each atom are to be determined, and the number of parameters that need to be determined for even a small virus is about 2x10 to the sixth power. That also means it is necessary to collect and analyze at least that amount of data. To account for experimental error a small virus structure requires about 20 million primary observations. Many more are needed for the study of numerous mutants and ligand complexes that give functional understanding to a structure.
The largest amount of computing is in the analysis of thesedata--specifically in the solution of the phase problem. This is the central problem of X-ray crystallography and the analysis breaks down into the following principal components:
The structure determination uses a methodology for phase refinement and extension pioneered by the Structural Studies Group at Purdue. The computation is based upon an iterative process summarized in Figure 1 on page 83.
The goal of the project is to reduce the processing time needed for phase refinement and extension by two orders of magnitude by developing parallel algorithms for each of the tasks shown in Figure 1 on page 83, and by implementing efficiently such algorithms for different architectures. Figure 2 on page 84 presents the execution time functions of the number of PEs for the electron density averaging, one of the most compute-intensive tasks in the structure determination.
CS Annual Report - 19 APR 1996