PMID- 15838145
OWN - NLM
STAT- MEDLINE
DCOM- 20050513
LR  - 20161021
IS  - 1555-3930 (Print)
IS  - 1555-3930 (Linking)
VI  - 1
DP  - 2002
TI  - Parallelizing a DNA simulation code for the Cray MTA-2.
PG  - 291-302
AB  - 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.
FAU - Bokhari, Shahid H
AU  - Bokhari SH
AD  - Department of Electrical Engineering, University of Engineering and Technology, 
      Lahore, Pakistan. shb@acm.org
FAU - Glaser, Matthew A
AU  - Glaser MA
FAU - Jordan, Harry F
AU  - Jordan HF
FAU - Lansac, Yves
AU  - Lansac Y
FAU - Sauer, Jon R
AU  - Sauer JR
FAU - Van Zeghbroeck, Bart
AU  - Van Zeghbroeck B
LA  - eng
GR  - R21HG02167-01/HG/NHGRI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - United States
TA  - Proc IEEE Comput Soc Bioinform Conf
JT  - Proceedings. IEEE Computer Society Bioinformatics Conference
JID - 101223605
RN  - 0 (Membranes, Artificial)
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Algorithms
MH  - Biosensing Techniques/*methods
MH  - *Computing Methodologies
MH  - DNA/analysis/*chemistry
MH  - Diffusion
MH  - Membranes, Artificial
MH  - *Models, Chemical
MH  - *Models, Molecular
MH  - Motion
MH  - Nucleic Acid Conformation
MH  - Porosity
MH  - Sequence Analysis, DNA/*methods
MH  - *Software
MH  - Structure-Activity Relationship
EDAT- 2005/04/20 09:00
MHDA- 2005/05/14 09:00
CRDT- 2005/04/20 09:00
PHST- 2005/04/20 09:00 [pubmed]
PHST- 2005/05/14 09:00 [medline]
PHST- 2005/04/20 09:00 [entrez]
PST - ppublish
SO  - Proc IEEE Comput Soc Bioinform Conf. 2002;1:291-302.