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Computational Systems Bioinformatics Conference, International IEEE Computer Society (2002)
Stanford, California
Aug. 14, 2002 to Aug. 16, 2002
ISBN: 0-7695-1653-X
pp: 291
Shahid H. Bokhari , University of Engineering & Technology
Matthew A. Glaser , University of Colorado
Harry F. Jordan , University of Colorado
Yves Lansac , University of Colorado
Jon R. Sauer , Eagle Research & Development
Bart Van Zeghbroeck , Eagle Research & Development
<p>The Cray MTA-2 (Multithreaded Architecture) is an unusual parallel supercomputer that promises ease of use and high performance. We describe our experience on the MTA-2 with a molecular dynamics code, SIMU-MD, that we are using to simulate the translocation of DNA through a nanopore in a silicon based ultrafast sequencer.</p> <p>Our sequencer is constructed using standard VLSI technology and consists of a nanopore surrounded by Field Effect Transistors (FETs). We propose to use the FETs to sense variations in charge as a DNA molecule translocates through the pore and thus differentiate between the four building block nucleotides of DNA.</p> <p>We were able to port SIMU-MD, a serial C code, to the MTA with only a modest effort and with good performance. Our porting process needed neither a parallelism support platform nor attention to the intimate details of parallel programming and interprocessor communication, as would have been the case with more conventional supercomputers.</p>

J. R. Sauer, M. A. Glaser, S. H. Bokhari, Y. Lansac, B. Van Zeghbroeck and H. F. Jordan, "Parallelizing a DNA Simulation Code for the Cray MTA-2," Computational Systems Bioinformatics Conference, International IEEE Computer Society(CSB), Stanford, California, 2002, pp. 291.
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