Macromolecular electron density averaging on distributed memory MIMD systems | Zendy

Marinescu Dan C. | Zendy; Rice John R. | Zendy; CorneaHasegan Marius A. | Zendy; Lynch Robert E. | Zendy; Rossmann Michael G. | Zendy

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Macromolecular electron density averaging on distributed memory MIMD systems

Author(s) -

Marinescu Dan C.,

Rice John R.,

CorneaHasegan Marius A.,

Lynch Robert E.,

Rossmann Michael G.

Publication year - 1993

Publication title -

concurrency: practice and experience

Language(s) - English

Resource type - Journals

eISSN - 1096-9128

pISSN - 1040-3108

DOI - 10.1002/cpe.4330050803

Subject(s) - mimd , computer science , parallel computing , computation , distributed memory , computational science , reduction (mathematics) , shared memory , distributed computing , algorithm , mathematics , geometry

The paper discusses algorithms and programs for electron density averaging using a distributed memory MIMD system. Electron density averaging is a computationally intensive step needed for phase refinement and extension in the computation of the 3‐D structure of macromolecules like proteins and viruses. The determination of a single structure may require thousands of hours of CPU time for traditional supercomputers. The approach discussed in this paper leads to a reduction by one to two orders of magnitude of the computing time. The program runs on an Intel iPSC/860 and on the Touchstone Delta system and uses a user controlled shared virtual memory and a dynamic load‐balancing mechanism.

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