Hardware acceleration for thermodynamic constrained DNA code generation

Qinru Qiu, Prakash Mukre, Morgan Bishop, Daniel Burns, Qing Wu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

Abstract

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.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages201-210
Number of pages10
Volume4848 LNCS
DOIs
StatePublished - 2008
Externally publishedYes
Event13th International Meeting on DNA Computing, DNA13 - Memphis, TN, United States
Duration: Jun 4 2007Jun 8 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4848 LNCS
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other13th International Meeting on DNA Computing, DNA13
CountryUnited States
CityMemphis, TN
Period6/4/076/8/07

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ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Qiu, Q., Mukre, P., Bishop, M., Burns, D., & Wu, Q. (2008). Hardware acceleration for thermodynamic constrained DNA code generation. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4848 LNCS, pp. 201-210). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4848 LNCS). https://doi.org/10.1007/978-3-540-77962-9_21