Skip to main content

A Clause String DNA Algorithm for SAT

  • Conference paper
  • First Online:

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2340))

Abstract

A DNA algorithm for SAT, the satisfiability of propositional formulae, is presented where the number of separation steps is given by the number of clauses of the instance. This represents a computational improvement for DNA algorithms based on Adleman and Lipton’s extraction model, where the number of separations equates the number of literals of the instance.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about 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, Vol. 266, pp. 1021–1024, November 11, 1994.

    Google Scholar 

  2. D. Boneh, C. Dunworth, R. J. Lipton, J. Sgall, Making DNA computers error resistant, in [18] pp. 163–170, 1999.

    Google Scholar 

  3. R. S. Brainch, C. Johnson, P.W.K. Rothemund, D. Hwang, N. Chelyapov, L. M. Adleman, Solutions of a Satisfiability Problem on a Gel-Based DNA Computer, Sixth International Meeting on DNA Based Computers, Leiden Center for Natural Computing, A. Condon G. Rozenberg (eds.), Leiden, 2000.

    Google Scholar 

  4. C. Calude, Gh. Păun, Computing with Cells and Atoms, Taylor and Francis, London, 2000.

    Google Scholar 

  5. K. Chen, E. Winfree, Error Correction in DNA Computing: Misclassification and Strand Loss, in [26] pp. 49–63, 2000.

    Google Scholar 

  6. M. R. Garey, D. S. Johnson, Computers and Intractability, Freeman, San Francisco, 1979.

    MATH  Google Scholar 

  7. C. P. Gomes, B. Selman, N. Crator, H. Kautz, Heavy-tailed phenomena in satisfiability and constraint satisfaction problems, J. of Automated Reasoning, Vol. 24(1/2), pp. 67–100, 1999.

    Article  Google Scholar 

  8. T. Head, X. Chen, M. J. Nichols, M. Yamamura, and S. Gal, Aqueous Solutions of Algorithmic Problems: emphasizing knights on a 3 × 3, in [10] pp. 219–230, 2001.

    Google Scholar 

  9. N. Jonoska, S. A. Karl, M. Saito, Three Dimensional DNA Structures in Computing, Biosystems, Vol. 52, 242–245, 1999.

    Article  Google Scholar 

  10. N. Jonoska, N. Seeman (eds.), 7th International Meeting on DNA Based Computers, Preliminary Proceedings, Tampa, FL (U.S.A.), 2001.

    Google Scholar 

  11. L. Landweber, E. Baum, DNA Based Computers II, DIMACS Series 44, American Math. Society, Providence, RI, 1999.

    Google Scholar 

  12. R. Lipton, DNA Solutions of hard computational problems, Science, Vol. 268, 242–245, 1995.

    Article  Google Scholar 

  13. V. Manca, Monoidal systems and membrane systems, in Pre-proc. Workshop on Multiset Processing, Curtea de Arges, Romania, TR 140, CDMTCS, Univ. Auckland (New Zealand), pp. 176–190, 2000.

    Google Scholar 

  14. V. Manca, and Di Gregorio S., Lizzari D., Vallini G., Zandron C., A DNA Algorithm for 3-SAT(11,20), in [10], pp. 167–178, 2001.

    Google Scholar 

  15. V. Manca, Membrane Algorithms for Propositional Satisfiability, in Pre-proc. Workshop on Membrane Computing, Curtea de Arges, Romania, TR 17, GRLMC, Univ. Rovira i Virgili, Tarragona (Spain), pp. 181–192, 2001.

    Google Scholar 

  16. Gh. Păun, G. Rozenberg, A. Salomaa, DNA Computing: New Computing Paradigms, Springer-Verlag, Berlin, 1998.

    MATH  Google Scholar 

  17. Gh. Păun, P Systems with Active Membranes: Attacking NP Complete Problems, J. Automata Languages and Combinatorics, 6, 1, 2001.

    Google Scholar 

  18. H. Rubin, D. Wood, DNA Based Computers III, DIMACS Series 48, American Math. Society, Providence, RI, 1999.

    MATH  Google Scholar 

  19. G. Rozenberg, A. Salomaa, eds., Handbook of Formal Languages, Springer-Verlag, Heidelberg, 1997.

    MATH  Google Scholar 

  20. K. Sakamoto, H. Gounzu, D. Kiga, K. Komiya, H. Gouzu, S. Yokoyama, T. Yoko-mori, S. Ikeda, H. Sugiyama, M. Hagiya, State transitions by molecules, Biosystems, Vol. 52, pp. 81–91, 1999.

    Article  Google Scholar 

  21. K. Sakamoto, H. Gounzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, M. Hagiya, Molecular Computation by DNA Hairpin Formation, Science, Vol. 288, pp. 1223–1226, May 19, 2000.

    Google Scholar 

  22. K. Selman, H. Kautz, B. Cohen, Local Search Strategies for Satisfiability Testing, in: Cliques, Coloring, and Satisfiability, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, D. S. Johnson, M. A. Trick, eds., vol. 26, AMS, 1996.

    Google Scholar 

  23. Y. Takenaka, A. Hashimoto, A proposal of DNA computing on beads and its application to SAT problems, in [10], pp. 331–339, 2001.

    Google Scholar 

  24. H. Yoshida and A. Suyama, Solutions to 3-SAT by breadth first search, in [26] pp. 9–22, 2000.

    Google Scholar 

  25. M. Yamamoto, J. Yamashita, T. Shiba, T. Hirayama, S. Takiya, K. Suzuki, M; Munekata, and A. Ohuchi, A study of hybridization process in DNA computing, in [26], pp. 101–110, 2000.

    Google Scholar 

  26. E. Winfree E., D. K. Gifford, DNA Based Computers V, DIMACS Series 54, American Math. Society, Providence, RI, 2000.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Manca, V., Zandron, C. (2002). A Clause String DNA Algorithm for SAT. In: Jonoska, N., Seeman, N.C. (eds) DNA Computing. DNA 2001. Lecture Notes in Computer Science, vol 2340. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48017-X_16

Download citation

  • DOI: https://doi.org/10.1007/3-540-48017-X_16

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-43775-8

  • Online ISBN: 978-3-540-48017-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics