Skip to main content

Efficiency and Reliability of DNA-Based Memories

  • Conference paper
  • First Online:
Genetic and Evolutionary Computation — GECCO 2003 (GECCO 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2723))

Included in the following conference series:

Abstract

Associative memories based on DNA-affinity have been proposed [2]. Here, the performance, efficiency, reliability of DNA-based memories is quantified through simulations in silico. Retrievals occur reliably (98%) within very short times (milliseconds) despite the randomness of the reactions and regardless of the number of queries. The capacity of these memories is also explored in practice and compared with previous theoretical estimates. Advantages of implementations of the same type of memory in special purpose chips in silico is proposed and discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 74.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. L.M. Adleman: Molecular Computation of Solutions to Combinatorial Problems. Science 266 (1994) 1021–1024

    Article  Google Scholar 

  2. E. Baum, Building An Associative Memory Vastly Larger Than The Brain. Science 268 (1995) 583–585.

    Article  Google Scholar 

  3. A. Condon, G. Rozenberg (eds.): DNA Computing (Revised Papers). In: Proc. of the 6th International Workshop on DNA-based Computers, 2000. Springer-Verlag Lecture Notes in Computer Science 2054 (2001)

    Google Scholar 

  4. R. Deaton, R., J. Chen, H. Bi, M. Garzon, H. Rubin, D.H. Wood. A PCR-Based Protocol for In-Vitro Selection of Non-Crosshybridizing Oligonucleotides (2002). In [11], 105–114

    Google Scholar 

  5. R.J. Deaton, J. Chen, H. Bi, J.A. Rose: A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides. In [11], pp. 211–220.

    Google Scholar 

  6. R. Deaton, M. Garzon, R. E. Murphy, J. A. Rose, D. R. Franceschetti, S.E. Stevens, Jr. The Reliability and Efficiency of a DNA Computation. Phys. Rev. Lett. 80 (1998) 417–420

    Article  Google Scholar 

  7. M. Garzon, D. Blain, K. Bobba, A. Neel, M. West: Self-Assembly of DNA-like structures in silico. Journal of Genetic Programming and Evolvable Machines 4:2 (2003), in press.

    Google Scholar 

  8. M. Garzon: Biomolecular Computation in silico. Bull. of the European Assoc. For Theoretical Computer Science EATCS (2003), in press.

    Google Scholar 

  9. M. Garzon, C. Oehmen: Biomolecular Computation on Virtual Test Tubes. In: N. Jonoska and N. Seeman (eds.): Proc. of the 7th International Workshop on DNA-based Computers, 2001. Springer-Verlag Lecture Notes in Computer Science 2340 (2002) 117–128

    Google Scholar 

  10. M. Garzon, R. Deaton, P. Neathery, R.C. Murphy, D.R. Franceschetti, E. Stevens Jr.: On the Encoding Problem for DNA Computing. In: Proc. of the Third DIMACS Workshop on DNA-based Computing, U of Pennsylvania. (1997) 230–237

    Google Scholar 

  11. M. Hagiya, A. Ohuchi (eds.): Proceedings of the 8th Int. Meeting on DNA Based Computers, Hokkaido University, 2002, Springer-Verlag Lecture Notes in Computer Science 2568 (2003)

    Google Scholar 

  12. J. Lee, S. Shin, S.J. Augh, T.H. Park, B. Zhang: Temperature Gradient-Based DNA Computing for Graph Problems with Weighted Edges. In [11], pp. 41–50.

    Google Scholar 

  13. R. Lipton: DNA Solutions of Hard Computational Problems. Science 268 (1995) 542–544

    Article  Google Scholar 

  14. A. Marathe, A. Condon, R. Corn: On Combinatorial Word Design. In: E. Winfree and D. Gifford (eds.): DNA Based Computers V, DIMACS Series in Discrete Mathematics and Theoretical Computer Science. 54 (1999) 75–89

    Google Scholar 

  15. J.H. Reif, T. LaBean. Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector Quantization In [3], pp. 145–172

    Google Scholar 

  16. K.A. Schmidt, C.V. Henkel, G. Rozenberg: DNA computing with single molecule detection. In [3], 336.

    Google Scholar 

  17. J.G. Wetmur: Physical Chemistry of Nucleic Acid Hybridization. In: H. Rubin and D.H. Wood (eds.): Proc. DNA-Based Computers III, U. of Pennsylvania, 1997. DIMACS series in Discrete Mathematics and Theoretical Computer Science 48 (1999) 1–23

    Google Scholar 

  18. E. Winfree, F. Liu, L.A. Wenzler, N.C. Seeman: Design and self-assembly of two-dimensional DNA crystals. Nature 394 (1998) 539–544

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Garzon, M.H., Neel, A., Chen, H. (2003). Efficiency and Reliability of DNA-Based Memories. In: Cantú-Paz, E., et al. Genetic and Evolutionary Computation — GECCO 2003. GECCO 2003. Lecture Notes in Computer Science, vol 2723. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45105-6_47

Download citation

  • DOI: https://doi.org/10.1007/3-540-45105-6_47

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-40602-0

  • Online ISBN: 978-3-540-45105-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics