Skip to main content

The Two-Handed Tile Assembly Model Is Not Intrinsically Universal

  • Conference paper
Automata, Languages, and Programming (ICALP 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7965))

Included in the following conference series:

Abstract

In this paper, we study the intrinsic universality of the well-studied Two-Handed Tile Assembly Model (2HAM), in which two “supertile” assemblies, each consisting of one or more unit-square tiles, can fuse together (self-assemble) whenever their total attachment strength is at least the global temperature τ. Our main result is that for all τ′ < τ, each temperature-τ′ 2HAM tile system cannot simulate at least one temperature-τ 2HAM tile system. This impossibility result proves that the 2HAM is not intrinsically universal, in stark contrast to the simpler abstract Tile Assembly Model which was shown to be intrinsically universal (The tile assembly model is intrinsically universal, FOCS 2012). On the positive side, we prove that, for every fixed temperature τ ≥ 2, temperature-τ 2HAM tile systems are intrinsically universal: for each τ there is a single universal 2HAM tile set U that, when appropriately initialized, is capable of simulating the behavior of any temperature τ 2HAM tile system. As a corollary of these results we find an infinite set of infinite hierarchies of 2HAM systems with strictly increasing power within each hierarchy. Finally, we show how to construct, for each τ, a temperature-τ 2HAM system that simultaneously simulates all temperature-τ 2HAM systems.

A full version of this paper will appear on the arXiv.

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 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.M., Cheng, Q., Goel, A., Huang, M.-D.A., Kempe, D., de Espanés, P.M., Rothemund, P.W.K.: Combinatorial optimization problems in self-assembly. In: Proceedings of the Thirty-Fourth Annual ACM Symposium on Theory of Computing, pp. 23–32 (2002)

    Google Scholar 

  2. Arrighi, P., Schabanel, N., Theyssier, G.: Intrinsic simulations between stochastic cellular automata. arXiv preprint arXiv:1208.2763 (2012)

    Google Scholar 

  3. Cannon, S., Demaine, E.D., Demaine, M.L., Eisenstat, S., Patitz, M.J., Schweller, R., Summers, S.M., Winslow, A.: Two hands are better than one (up to constant factors). In: Proceedings of the Thirtieth International Symposium on Theoretical Aspects of Computer Science (to appear, 2013)

    Google Scholar 

  4. Chacc, E.G., Meunier, P.-E., Rapaport, I., Theyssier, G.: Communication complexity and intrinsic universality in cellular automata. Theor. Comput. Sci. 412(1-2), 2–21 (2011)

    Article  Google Scholar 

  5. Chen, H.-L., Doty, D.: Parallelism and time in hierarchical self-assembly. In: SODA 2012: Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1163–1182. SIAM (2012)

    Google Scholar 

  6. Cheng, Q., Aggarwal, G., Goldwasser, M.H., Kao, M.-Y., Schweller, R.T., de Espanés, P.M.: Complexities for generalized models of self-assembly. SIAM Journal on Computing 34, 1493–1515 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  7. Delorme, M., Mazoyer, J., Ollinger, N., Theyssier, G.: Bulking I: an abstract theory of bulking. Theoretical Computer Science 412(30), 3866–3880 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  8. Delorme, M., Mazoyer, J., Ollinger, N., Theyssier, G.: Bulking II: Classifications of cellular automata. Theor. Comput. Sci. 412(30), 3881–3905 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  9. Demaine, E.D., Demaine, M.L., Fekete, S.P., Ishaque, M., Rafalin, E., Schweller, R.T., Souvaine, D.L.: Staged self-assembly: nanomanufacture of arbitrary shapes with O(1) glues. Natural Computing 7(3), 347–370 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  10. Doty, D., Lutz, J.H., Patitz, M.J., Schweller, R.T., Summers, S.M., Woods, D.: The tile assembly model is intrinsically universal. In: Proceedings of the 53rd Annual IEEE Symposium on Foundations of Computer Science, pp. 439–446 (October 2012)

    Google Scholar 

  11. Doty, D., Lutz, J.H., Patitz, M.J., Summers, S.M., Woods, D.: Intrinsic universality in self-assembly. In: Proceedings of the 27th International Symposium on Theoretical Aspects of Computer Science, pp. 275–286 (2009)

    Google Scholar 

  12. Durand, B., Róka, Z.: The game of life: universality revisited. In: Delorme, M., Mazoyer, J. (eds.) Cellular Automata. Kluwer (1999)

    Google Scholar 

  13. Fujibayashi, K., Hariadi, R., Park, S.H., Winfree, E., Murata, S.: Toward reliable algorithmic self-assembly of DNA tiles: A fixed-width cellular automaton pattern. Nano Letters 8(7), 1791–1797 (2007)

    Article  Google Scholar 

  14. Lafitte, G., Weiss, M.: Universal tilings. In: Thomas, W., Weil, P. (eds.) STACS 2007. LNCS, vol. 4393, pp. 367–380. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  15. Lafitte, G., Weiss, M.: Simulations between tilings. In: Conference on Computability in Europe (CiE 2008), Local Proceedings, pp. 264–273 (2008)

    Google Scholar 

  16. Lafitte, G., Weiss, M.: An almost totally universal tile set. In: Chen, J., Cooper, S.B. (eds.) TAMC 2009. LNCS, vol. 5532, pp. 271–280. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  17. Luhrs, C.: Polyomino-safe DNA self-assembly via block replacement. In: Goel, A., Simmel, F.C., Sosík, P. (eds.) DNA 14. LNCS, vol. 5347, pp. 112–126. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  18. Lund, K., Manzo, A.T., Dabby, N., Micholotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, R., Stojanovic, M.N., Walter, N.G., Winfree, E., Yan, H.: Molecular robots guided by prescriptive landscapes. Nature 465, 206–210 (2010)

    Article  Google Scholar 

  19. Ollinger, N.: Intrinsically universal cellular automata. In: The Complexity of Simple Programs, in Electronic Proceedings in Theoretical Computer Science, vol. 1, pp. 199–204 (2008)

    Google Scholar 

  20. Ollinger, N., Richard, G.: Four states are enough? Theoretical Computer Science 412(1), 22–32 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  21. Qian, L., Winfree, E.: Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034), 1196 (2011)

    Article  Google Scholar 

  22. Qian, L., Winfree, E., Bruck, J.: Neural network computation with DNA strand displacement cascades. Nature 475(7356), 368–372 (2011)

    Article  Google Scholar 

  23. Rothemund, P.: Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297–302 (2006)

    Article  Google Scholar 

  24. Rothemund, P.W., Papadakis, N., Winfree, E.: Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology 2(12), 2041–2053 (2004)

    Article  Google Scholar 

  25. Seeman, N.C.: Nucleic-acid junctions and lattices. Journal of Theoretical Biology 99, 237–247 (1982)

    Article  Google Scholar 

  26. Wang, H.: Proving theorems by pattern recognition – II. The Bell System Technical Journal XL(1), 1–41 (1961)

    Google Scholar 

  27. Winfree, E.: Algorithmic Self-Assembly of DNA. PhD thesis, California Institute of Technology (June 1998)

    Google Scholar 

  28. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394(6693), 539–544 (1998)

    Article  Google Scholar 

  29. Yurke, B., Turberfield, A., Mills Jr., A., Simmel, F., Neumann, J.: A DNA-fuelled molecular machine made of DNA. Nature 406(6796), 605–608 (2000)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Demaine, E.D., Patitz, M.J., Rogers, T.A., Schweller, R.T., Summers, S.M., Woods, D. (2013). The Two-Handed Tile Assembly Model Is Not Intrinsically Universal. In: Fomin, F.V., Freivalds, R., Kwiatkowska, M., Peleg, D. (eds) Automata, Languages, and Programming. ICALP 2013. Lecture Notes in Computer Science, vol 7965. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39206-1_34

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-39206-1_34

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-39205-4

  • Online ISBN: 978-3-642-39206-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics