Skip to main content

Solving NP Hard Problems in the Framework of Gene Assembly in Ciliates

  • Conference paper
  • First Online:
Bio-inspired Computing: Theories and Applications (BIC-TA 2018)

Abstract

Molecular computing [1] is a field with a great potential and fastest growing area of Computer Science. Although some approaches to solve NP hard problems were successfully accomplished on DNA strand, only few results of practical use so far. A direction of molecular computing namely Gene assembly in ciliates has been studied actively [3] for a decade. In the present paper, we use a variant of gene assembly computing model of Guided recombination system with only two operations of insertion and deletion [7] as a decision problem solver. We present our results of parallel algorithms which solve computational hard problems HPP and CSP, in an efficient time.

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 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
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

Institutional subscriptions

References

  1. Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  2. Carmosino, M.L., Gao, J., Impagliazzo, R., Mihajlin, I., Paturi, R., Schneider, S.: Nondeterministic extensions of the strong exponential time hypothesis and consequences for non-reducibility. In: Proceedings of the 2016 ACM Conference on Innovations in Theoretical Computer Science, Cambridge, Massachusetts, USA, pp. 261–270 (2016)

    Google Scholar 

  3. Ehrenfeucht, A., Harju, T., Petre, I., Prescott, D.M., Rozenberg, G.: Computation in Living Cells: Gene Assembly in Ciliates. Springer, Heidelberg (2003). https://doi.org/10.1007/978-3-662-06371-2

    Book  MATH  Google Scholar 

  4. Ishdorj, T.-O., Petre, I.: Computing through gene assembly. In: Akl, S.G., Calude, C.S., Dinneen, M.J., Rozenberg, G., Wareham, H.T. (eds.) UC 2007. LNCS, vol. 4618, pp. 91–105. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-73554-0_10

    Chapter  Google Scholar 

  5. Ishdorj, T.-O., Loos, R., Petre, I.: Computational efficiency of intermolecular gene assembly. Fundam. Inform. 84(3–4), 363–373 (2008)

    MathSciNet  MATH  Google Scholar 

  6. Ishdorj, T.-O., Petre, I., Rogojin, V.: Computational power of intramolecular gene assembly. Int. J. Found. Comput. Sci. 18(5), 1123–1136 (2007)

    Article  MathSciNet  Google Scholar 

  7. Kari, L., Landweber, L.F.: Computational power of gene rearrangement. In: Winfree, E., Gifford, D.K. (eds.) Proceedings of DNA Based Computers, pp. 207–216. American Mathematical Society (1999)

    Google Scholar 

  8. Ma, B., Sun, X.: More efficient algorithms for closest string and substring problems. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS, vol. 4955, pp. 396–409. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-78839-3_33

    Chapter  Google Scholar 

  9. Moore, E.G.: Cramming more components onto integrated circuits. Electronics 38(8), 114–118 (1965)

    Google Scholar 

  10. Păun, G.: Membrane Computing - An Introduction. Springer, Berlin (2002). https://doi.org/10.1007/978-3-642-56196-2

    Book  MATH  Google Scholar 

  11. Rozenberg, G., Salomaa, A. (eds.): Handbook of Formal Languages. Springer, Berlin (1997). https://doi.org/10.1007/978-3-642-59126-6

    Book  MATH  Google Scholar 

  12. Zerjatke, T., Sturm, M.: Solving a PSPACE-complete problem by gene assembly. J. Log. Comput. 23(4), 897–908 (2013)

    Article  MathSciNet  Google Scholar 

Download references

Acknowledgments

This work has been supported by The Science and Technology Foundation of Mongolia, Research Grants ShUSS-2018/04 and MOST-MECSS2017001. Our thanks to Professor Erdenebaatar Altangerel for his continues support and three anonymous referees for all the suggestions which improved this paper.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Tseren-Onolt Ishdorj .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Ganbaatar, G., Altangerel, K., Ishdorj, TO. (2018). Solving NP Hard Problems in the Framework of Gene Assembly in Ciliates. In: Qiao, J., et al. Bio-inspired Computing: Theories and Applications. BIC-TA 2018. Communications in Computer and Information Science, vol 951. Springer, Singapore. https://doi.org/10.1007/978-981-13-2826-8_10

Download citation

  • DOI: https://doi.org/10.1007/978-981-13-2826-8_10

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-13-2825-1

  • Online ISBN: 978-981-13-2826-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics