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Using Parallel Computers To Solve the Phase Problem of X-Ray Crystallography

DEPARTMENT OF COMPUTER SCIENCE UNIVERSITY AT BUFFALO BUFFALO, NEW YORK 14260 MEDICAL FOUNDATION OF BUFFALO 73 HIGH STREET BUFFALO, NEW YORK 14203

G. DeTitta

DEPARTMENT OF COMPUTER SCIENCE UNIVERSITY AT BUFFALO BUFFALO, NEW YORK 14260 MEDICAL FOUNDATION OF BUFFALO 73 HIGH STREET BUFFALO, NEW YORK 14203

H. Hauptman

DEPARTMENT OF COMPUTER SCIENCE UNIVERSITY AT BUFFALO BUFFALO, NEW YORK 14260 MEDICAL FOUNDATION OF BUFFALO 73 HIGH STREET BUFFALO, NEW YORK 14203

R. Miller

DEPARTMENT OF COMPUTER SCIENCE UNIVERSITY AT BUFFALO BUFFALO, NEW YORK 14260 MEDICAL FOUNDATION OF BUFFALO 73 HIGH STREET BUFFALO, NEW YORK 14203

P. Thuman

DEPARTMENT OF COMPUTER SCIENCE UNIVERSITY AT BUFFALO BUFFALO, NEW YORK 14260 MEDICAL FOUNDATION OF BUFFALO 73 HIGH STREET BUFFALO, NEW YORK 14203

C. Weeks

DEPARTMENT OF COMPUTER SCIENCE UNIVERSITY AT BUFFALO BUFFALO, NEW YORK 14260 MEDICAL FOUNDATION OF BUFFALO 73 HIGH STREET BUFFALO, NEW YORK 14203

Direct methods are commonly used by crystallogra phers to determine relatively small crystal structures. However, existing techniques do not appear to be ex tensible to larger structures. The recent development of a solution strategy called Shake-and-Bake, aimed at determining structures via local minimization and re peated Fourier transformations, allows for implicit con straints to be included. In this article, a description of the Shake-and-Bake algorithm is given, along with a detailed description of master/slave MIMD implemen tations on a network of Sun workstations, an Intel iPSC/860 Hypercube, and a Connection Machine CM-5. Our experimental results on known structures, includ ing gramicidin A, are extremely encouraging. For ex ample, based on efficient implementations of Shake- and-Bake on the iPSC/860 and CM-5, for known struc tures of 28, 84, and 127 nonhydrogen atoms, we obtain success rates of 19%, 1%, and 0.2%, as opposed to existing methods, which yield success rates of ap proximately 6%, 0.006%, and 0.0002%, respectively.

International Journal of High Performance Computing Applications, Vol. 7, No. 1, 25-49 (1993)
DOI: 10.1177/109434209300700103


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