TY - GEN
T1 - Hardware acceleration for thermodynamic constrained DNA code generation
AU - Qiu, Qinru
AU - Mukre, Prakash
AU - Bishop, Morgan
AU - Burns, Daniel
AU - Wu, Qing
PY - 2008
Y1 - 2008
N2 - Reliable DNA computing requires a large pool of oligonucleotides that do not cross-hybridize. In this paper, we present a transformed algorithm to calculate the maximum weight of the 2-stem common subsequence of two DNA oligonucleotides. The result is the key part of the Gibbs free energy of the DNA cross-hybridized duplexes based on the nearest-neighbor model. The transformed algorithm preserves the physical data locality and hence is suitable for implementation using a systolic array. A novel hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA under thermodynamic constraints is designed, implemented and tested. Experimental results show that the hardware system provides more than 250X speed-up compared to a software only implementation.
AB - Reliable DNA computing requires a large pool of oligonucleotides that do not cross-hybridize. In this paper, we present a transformed algorithm to calculate the maximum weight of the 2-stem common subsequence of two DNA oligonucleotides. The result is the key part of the Gibbs free energy of the DNA cross-hybridized duplexes based on the nearest-neighbor model. The transformed algorithm preserves the physical data locality and hence is suitable for implementation using a systolic array. A novel hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA under thermodynamic constraints is designed, implemented and tested. Experimental results show that the hardware system provides more than 250X speed-up compared to a software only implementation.
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U2 - 10.1007/978-3-540-77962-9_21
DO - 10.1007/978-3-540-77962-9_21
M3 - Conference contribution
AN - SCOPUS:49949110986
SN - 3540779612
SN - 9783540779612
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 201
EP - 210
BT - DNA Computing - 13th International Meeting on DNA Computing, DNA13, Revised Selected Papers
T2 - 13th International Meeting on DNA Computing, DNA13
Y2 - 4 June 2007 through 8 June 2007
ER -