title: Parallelizing a DNA simulation code for the Cray MTA-2.
abstract: 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.
authors.affiliation: Department of Electrical Engineering, University of Engineering and Technology, Lahore, Pakistan. shb@acm.org
authors.forename: Shahid H
authors.initials: SH
authors.lastname: Bokhari
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Glaser
authors.forename: Harry F
authors.initials: HF
authors.lastname: Jordan
authors.forename: Yves
authors.initials: Y
authors.lastname: Lansac
authors.forename: Jon R
authors.initials: JR
authors.lastname: Sauer
authors.forename: Bart
authors.initials: B
authors.lastname: Van Zeghbroeck
mesh_terms: D000465:Algorithms; D015374:Biosensing Techniques / Q000379:methods*; D003205:Computing Methodologies; D004247:DNA / Q000032:analysis / Q000737:chemistry*; D004058:Diffusion; D008567:Membranes, Artificial; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D016062:Porosity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D008567:Membranes, Artificial; D004247:DNA