Your Search Results

Use this resource - and many more! - in your textbook!

AcademicPub holds over eight million pieces of educational content for you to mix-and-match your way.

Experience the freedom of customizing your course pack with AcademicPub!
Not an educator but still interested in using this content? No problem! Visit our provider's page to contact the publisher and get permission directly.

Parallelizing a DNA simulation code for the Cray MTA-2

By: Glaser, M.A.; Bokhari, S.H.; Van Zeghbroeck, B.; Sauer, J.R.; Lansac, Y.; Jordan, H.F.;

2002 / IEEE / 0-7695-1653-X

Description

This item was taken from the IEEE Conference ' Parallelizing a DNA simulation code for the Cray MTA-2 ' 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. 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. 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.