Super Computer for Molecular Mysteries

A privately financed team of scientists and engineers is nearing completion of a special-purpose supercomputer intended to offer more than a thousandfold increase in performance for complex molecular simulations. The machine, named Anton, in homage to Anton van Leeuwenhoek, a pioneer in microbiology, is a bold gamble to jump ahead of the most powerful general-purpose supercomputers by as much as a half decade. It could be used to investigate problems of great scientific interest, like the folding of protein molecules, and in the design of drugs based on the simulated biological activity of different molecules. Anton is massively parallel, with 512 specialized processors working simultaneously. The processors are called application-specific integrated circuits, and in this case their specialty is the calculation of the three-dimensional characteristics of molecules. Despite the publication of a detailed technical description of his computer, Mr. Shaw declined to be interviewed about the project. “At this stage of our research, though, we’ve been trying to communicate our results largely through academic talks and peer-reviewed publications in scientific journals,” he wrote in an e-mail message. Experimentation in the use of supercomputers to model molecular interactions has been going on for more than a decade, but the field is still largely in its infancy. Simulations of processes like the folding of proteins into three-dimensional structures or the interactions between proteins or between a protein and a drug molecule hold out the promise of advancing science and drug development.