Skip to main content
SpringerLink
Log in

Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion

  • Conference paper
DNA Computing (DNA 2004)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3384))

Included in the following conference series:

Abstract

Intelligent nanomechanical devices that operate in an autonomous fashion are of great theoretical and practical interest. Recent successes in building large scale DNA nano-structures, in constructing DNA mechanical devices, and in DNA computing provide a solid foundation for the next step forward: designing autonomous DNA mechanical devices capable of arbitrarily complex behavior. One prototype system towards this goal can be an autonomous DNA mechanical device capable of universal computation, by mimicking the operation of a universal Turing machine. Building on our prior theoretical design and prototype experimental construction of an autonomous unidirectional DNA walking device moving along a linear track, we present here the design of a nanomechanical DNA device that autonomously mimics the operation of a 2-state 5-color universal Turing machine. Our autonomous nanomechanical device, called an Autonomous DNA Turing Machine (ADTM), is thus capable of universal computation and hence complex translational motion, which we define as universal translational motion.

Extended abstract. For full version, see [41].

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

Access this chapter

Log in via an institution
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

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

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

    Article  Google Scholar 

  2. Alberti, P., Mergny, J.L.: DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc. Natl. Acad. Sci. USA 100, 1569–1573 (2003)

    Article  Google Scholar 

  3. Benenson, Y., Adar, R., Paz-Elizur, T., Livneh, Z., Shapiro, E.: DNA molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA 100, 2191–2196 (2003)

    Article  Google Scholar 

  4. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nature 429, 423–429 (2004)

    Article  Google Scholar 

  5. Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414, 430–434 (2001)

    Article  Google Scholar 

  6. Chen, Y., Wang, M., Mao, C.: An autonomous DNA nanomotor powered by a DNA enzyme. Angew. Chem. Int. Ed. 43, 3554–3557 (2004)

    Article  Google Scholar 

  7. Faulhammer, D., Cukras, A.R., Lipton, R.J., Landweber, L.F.: Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA 97, 1385–1389 (2000)

    Article  Google Scholar 

  8. Feng, L., Park, S.H., Reif, J.H., Yan, H.: A two-state DNA lattice switched by DNA nanoactuator. Angew. Chem. Int. Ed. 42, 4342–4346 (2003)

    Article  Google Scholar 

  9. Henry, A.A., Romesberg, F.E.: Beyond A, C, G, and T: augmenting nature’s alphabet. Curr. Opin. Chem. Biol. 7, 727–733 (2003)

    Article  Google Scholar 

  10. LaBean, T.H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., Seeman, N.C.: The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000)

    Article  Google Scholar 

  11. Landweber, L.F., Lipton, R.J., Rabin, M.O.: DNA2 DNA computations: A potential ’Killer App’? In: Rubin, H., Wood, D.H. (eds.) DNA Based Computers III: DIMACS Workshop, University of Pennsylvania, June 23-27, pp. 161–172. American Mathematical Society, Providence, Rhode Island (1997)

    Google Scholar 

  12. Li, J., Tan, W.: A single DNA molecule nanomotor. Nano Lett. 2, 315–318 (2002)

    Article  Google Scholar 

  13. Lipton, R.J.: DNA solution of hard computational problem. Science 268, 542–545 (1995)

    Article  Google Scholar 

  14. Liu, D., Balasubramanian, S.: A proton fuelled DNA nanomachine. Angew. Chem. Int. Ed. 42, 5734–5736 (2003)

    Article  Google Scholar 

  15. Liu, Q., Wang, L., Frutos, A.G., Condon, A.E., Corn, R.M., Smith, L.M.: DNA computing on surfaces. Nature 403, 175–179 (2000)

    Article  Google Scholar 

  16. Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)

    Article  Google Scholar 

  17. Mao, C., Sun, W., Seeman, N.C.: Designed two-dimensional DNA holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc. 121, 5437–5443 (1999)

    Article  Google Scholar 

  18. Mao, C., Sun, W., Shen, Z., Seeman, N.C.: A DNA nanomechanical device based on the B-Z transition. Nature 397, 144–146 (1999)

    Article  Google Scholar 

  19. Ouyang, Q., Kaplan, P.D., Liu, S., Libchaber, A.: DNA solution of the maximal clique problem. Science 278, 446–449 (1997)

    Article  Google Scholar 

  20. Reif, J.H.: Parallel molecular computation: Models and simulations. In: Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA 1995), Santa Barbara,CA, pp. 213–223 (1995)

    Google Scholar 

  21. Reif, J.H.: Paradigms for biomolecular computation. In: Calude, C.S., Casti, J., Dinneen, M.J. (eds.) First International Conference on Unconventional Models of Computation, Auckland, New Zealand, pp. 72–93. Springer, Heidelberg (1998)

    Google Scholar 

  22. Reif, J.H.: Local parallel biomolecular computation. In: Rubin, H., Wood, D.H. (eds.) DNA-Based Computers 3. DIMACS, vol. 48, pp. 217–254. American Mathematical Society (1999)

    Google Scholar 

  23. Reif, J.H.: The design of autonomous DNA nanomechanical devices: Walking and rolling DNA. In: Hagiya, M., Ohuchi, A. (eds.) DNA 2002. LNCS, vol. 2568, pp. 22–37. Springer, Heidelberg (2003); Published in Natural Computing, DNA8 special issue, Vol. 2, p 439-461 (2003)

    Chapter  Google Scholar 

  24. Rothemund, P.W.K.: A DNA and restriction enzyme implementation of Turing machines. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers: Proceedings of the DIMACS Workshop, April 4 (1995); vol. 27, pp. 75–119. Princeton University, American Mathematical Society (1996)

    Google Scholar 

  25. Ruben, A.J., Landweber, L.F.: The past, present and future of molecular computing. Nature Rev. Mol. Cell Biol. 1, 69–72 (2000)

    Article  Google Scholar 

  26. Seeman, N.C.: DNA in a material world. Nature 421, 427–431 (2003)

    Article  MathSciNet  Google Scholar 

  27. Sherman, W.B., Seeman, N.C.: A precisely controlled DNA biped walking device. Nano Lett. 4, 1203–1207 (2004)

    Article  Google Scholar 

  28. Simmel, F.C., Yurke, B.: Using DNA to construct and power a nanoactuator. Phys. Rev. E 63, 41913 (2001)

    Article  Google Scholar 

  29. Simmel, F.C., Yurke, B.: A DNA-based molecular device switchable between three distinct mechanical states. Appl. Phys. Lett. 80, 883–885 (2002)

    Article  Google Scholar 

  30. Smith, W.D.: DNA computers in vitro and in vivo. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers: Proceedings of the DIMACS Workshop, April 4 (1995); pp. 121–186. Princeton University, American Mathematical Society, Providence, Rhode Island (1996):

    Google Scholar 

  31. Turberfield, A.J., Mitchell, J.C., Yurke Jr., B., Mills, A.P., Blakey, M.I., Simmel, F.C.: DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003)

    Article  Google Scholar 

  32. Turing, A.M.: On computable numbers, with an application to the Entscheidungs problem. Proc. London Math. Society Ser. II 42(2), 230–265 (1936)

    MATH  Google Scholar 

  33. Turing, A.M.: On computable numbers, with an application to the entscheidungsproblem. Proc. London Math. Society Ser. II 43, 544–546 (1937)

    Article  MATH  Google Scholar 

  34. Winfree, E.: On the computational power of DNA annealing and ligation. In: Lipton, R.J., Baum, E.B. (eds.) DNA Based Computers 1. DIMACS, vol. 27, pp. 199–221. American Mathematical Society (1996)

    Google Scholar 

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

    Article  Google Scholar 

  36. Wolfram, S.: A new kind of science. Wolfram Media, Inc., Champaign (2002)

    MATH  Google Scholar 

  37. Yan, H., LaBean, T.H., Feng, L., Reif, J.H.: Directed nucleation assembly of DNA tile complexes for barcode patterned DNA lattices. Proc. Natl. Acad. Sci. USA 100, 8103–8108 (2003)

    Article  Google Scholar 

  38. Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003)

    Article  Google Scholar 

  39. Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002)

    Article  Google Scholar 

  40. Yin, P., Turberfield, A.J., Reif, J.H.: Designs of autonomous unidirectional walking DNA devices. DNA Based Computers 10 (2004)

    Google Scholar 

  41. Yin, P., Turberfield, A.J., Sahu, S., Reif, J.H.: Design of an autonomous DNA nanomechanical device capable of universal computation and universal translational motion. Technical Report CS-2004-07, Duke University, Computer Science Department (2004)

    Google Scholar 

  42. Yin, P., Yan, H., Daniell, X.G., Turberfield, A.J., Reif, J.H.: A unidirectional DNA walker moving autonomously along a linear track. Angew. Chem. Int. Ed. (2004) (in press)

    Google Scholar 

  43. Yurke, B., Turberfield Jr., A.J., Mills, A.P., Simmel, F.C., Neumann, J.L.: A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, Duke University, Box 90129, Durham, NC 27708-0129, USA

    Peng Yin, Sudheer Sahu & John H. Reif

  2. Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, OX 1 3PU, UK

    Andrew J. Turberfield

Authors
  1. Peng Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrew J. Turberfield
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sudheer Sahu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. John H. Reif
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano – Bicocca, Via Bicocca degli Arcimboldi 8, 20126, Milano, Italy

    Claudio Ferretti  & Claudio Zandron  & 

  2. Complex Systems and Artificial Intelligence Research Center, University of Milan–Bicocca, Italy

    Giancarlo Mauri

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Yin, P., Turberfield, A.J., Sahu, S., Reif, J.H. (2005). Design of an Autonomous DNA Nanomechanical Device Capable of Universal Computation and Universal Translational Motion. In: Ferretti, C., Mauri, G., Zandron, C. (eds) DNA Computing. DNA 2004. Lecture Notes in Computer Science, vol 3384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11493785_37

Download citation

  • DOI: https://doi.org/10.1007/11493785_37

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-26174-2

  • Online ISBN: 978-3-540-31844-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation