Skip to main content

The Complexity of Multiple Handed Self-assembly

  • Conference paper
  • First Online:
Unconventional Computation and Natural Computation (UCNC 2021)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12984))

  • 470 Accesses

Abstract

In this paper we study complexities for the multiple-handed tile self-assembly model, a generalization of the two-handed tile assembly model in which assembly proceeds by repeatedly combining up to h assemblies together into larger assemblies. We first show that there exist shapes that are self-assembled with provably lower tile type complexities given more hands: we construct a class of shapes \(S_k\) that requires \(\varOmega (\frac{k}{h})\) tile types to self-assemble with h or fewer hands, and yet is self-assembled in \(\mathcal {O}(1)\) tile types with k hands. We further examine the complexity of self-assembling the classic benchmark \(n\times n\) square shape, and show how this is self-assembled in \(\mathcal {O}(1)\) tile types with \(\mathcal {O}(n)\) hands. We next explore the complexity of established verification problems. We show the problem of determining if a given assembly is produced by an h-handed system is polynomial time solvable, whereas the problem of unique assembly verification is coNP-complete if the hand parameter h is encoded in unary, and coNEXP-complete if h is encoded in binary.

This research was supported in part by National Science Foundation Grant CCF-1817602.

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 44.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 59.99
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., et al.: Combinatorial optimization problems in self-assembly. In: Proceedings of the 34th Annual ACM Symposium on Theory of Computing, pp. 23–32 (2002)

    Google Scholar 

  2. Aggarwal, G., Cheng, Q., Goldwasser, M.H., Kao, M.Y., de Espanes, P.M., Schweller, R.T.: Complexities for generalized models of self-assembly. SIAM J. Comput. 34(6), 1493–1515 (2005). https://doi.org/10.1137/S0097539704445202

    Article  MathSciNet  MATH  Google Scholar 

  3. Alon, N., Yuster, R., Zwick, U.: Finding and counting given length cycles. Algorithmica 17, 209–223 (1997). https://doi.org/10.1007/BF02523189

    Article  MathSciNet  MATH  Google Scholar 

  4. Becker, F., Rapaport, I., Rémila, É.: Self-assemblying classes of shapes with a minimum number of tiles, and in optimal time. In: Arun-Kumar, S., Garg, N. (eds.) FSTTCS 2006. LNCS, vol. 4337, pp. 45–56. Springer, Heidelberg (2006). https://doi.org/10.1007/11944836_7

    Chapter  Google Scholar 

  5. Bryans, N., Chiniforooshan, E., Doty, D., Kari, L., Seki, S.: The power of nondeterminism in self-assembly. In: Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 590–602. SIAM (2011)

    Google Scholar 

  6. Cannon, S., et al.: Two hands are better than one (up to constant factors): self-assembly in the 2HAM vs. aTAM. In: 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013). Leibniz International Proceedings in Informatics (LIPIcs), vol. 20, pp. 172–184. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik (2013)

    Google Scholar 

  7. Chalk, C., Luchsinger, A., Schweller, R., Wylie, T.: Self-assembly of any shape with constant tile types using high temperature. In: Proceedings of the 26th Annual European Symposium on Algorithms, ESA 2018 (2018)

    Google Scholar 

  8. Chalk, C.T., Fernandez, D.A., Huerta, A., Maldonado, M.A., Schweller, R.T., Sweet, L.: Strict self-assembly of fractals using multiple hands. Algorithmica 76(1), 195–224 (2016). https://doi.org/10.1007/s00453-015-0022-x

    Article  MathSciNet  MATH  Google Scholar 

  9. Demaine, E.D., et al.: Staged self-assembly: nanomanufacture of arbitrary shapes with O(1) glues. Nat. Comput. 7(3), 347–370 (2008). https://doi.org/10.1007/s11047-008-9073-0

    Article  MathSciNet  MATH  Google Scholar 

  10. Doty, D.: Randomized self-assembly for exact shapes. SIAM J. Comput. 39(8), 3521–3552 (2010)

    Article  MathSciNet  Google Scholar 

  11. Doty, D.: Theory of algorithmic self-assembly. Commun. ACM 55(12), 78–88 (2012)

    Article  Google Scholar 

  12. Doty, D.: Producibility in hierarchical self-assembly. In: Ibarra, O.H., Kari, L., Kopecki, S. (eds.) UCNC 2014. LNCS, vol. 8553, pp. 142–154. Springer, Cham (2014). https://doi.org/10.1007/978-3-319-08123-6_12

    Chapter  Google Scholar 

  13. Eppstein, D.: Subgraph isomorphism in planar graphs and related problems. J. Graph Algorithms Appl. 3(3), 1–27 (1999). https://doi.org/10.7155/jgaa.00014

    Article  MathSciNet  MATH  Google Scholar 

  14. Fekete, S.P., Schweller, R.T., Winslow, A.: Size-dependent tile self-assembly: constant-height rectangles and stability. In: Elbassioni, K., Makino, K. (eds.) ISAAC 2015. LNCS, vol. 9472, pp. 296–306. Springer, Heidelberg (2015). https://doi.org/10.1007/978-3-662-48971-0_26

    Chapter  MATH  Google Scholar 

  15. Kao, M.Y., Schweller, R.: Reducing tile complexity for self-assembly through temperature programming. arXiv preprint cs/0602010 (2006)

    Google Scholar 

  16. Kao, M.-Y., Schweller, R.: Randomized self-assembly for approximate shapes. In: Aceto, L., Damgård, I., Goldberg, L.A., Halldórsson, M.M., Ingólfsdóttir, A., Walukiewicz, I. (eds.) ICALP 2008. LNCS, vol. 5125, pp. 370–384. Springer, Heidelberg (2008). https://doi.org/10.1007/978-3-540-70575-8_31

    Chapter  Google Scholar 

  17. Kowalik, Ł: Short cycles in planar graphs. In: Bodlaender, H.L. (ed.) WG 2003. LNCS, vol. 2880, pp. 284–296. Springer, Heidelberg (2003). https://doi.org/10.1007/978-3-540-39890-5_25

    Chapter  MATH  Google Scholar 

  18. Kundeti, V., Rajasekaran, S.: Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models. Nat. Comput. 11(2), 199–207 (2012). https://doi.org/10.1007/s11047-012-9313-1

    Article  MathSciNet  MATH  Google Scholar 

  19. Minev, D., Wintersinger, C.M., Ershova, A., Shih, W.M.: Robust nucleation control via crisscross polymerization of highly coordinated DNA slats. Nat. Commun. 12(1), 1–9 (2021)

    Article  Google Scholar 

  20. Patitz, M.J.: An introduction to tile-based self-assembly and a survey of recent results. Nat. Comput. 13(2), 195–224 (2013). https://doi.org/10.1007/s11047-013-9379-4

    Article  MathSciNet  MATH  Google Scholar 

  21. Rothemund, P.W., Winfree, E.: The program-size complexity of self-assembled squares. In: Proceedings of the Thirty-Second Annual ACM Symposium on Theory of Computing, pp. 459–468 (2000)

    Google Scholar 

  22. Schweller, R., Winslow, A., Wylie, T.: Complexities for high-temperature two-handed tile self-assembly. In: Brijder, R., Qian, L. (eds.) DNA 2017. LNCS, vol. 10467, pp. 98–109. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-66799-7_7

    Chapter  Google Scholar 

  23. Schweller, R., Winslow, A., Wylie, T.: Nearly constant tile complexity for any shape in two-handed tile assembly. Algorithmica 81(8), 3114–3135 (2019). https://doi.org/10.1007/s00453-019-00573-w

    Article  MathSciNet  MATH  Google Scholar 

  24. Schweller, R., Winslow, A., Wylie, T.: Verification in staged tile self-assembly. Nat. Comput. 18(1), 107–117 (2018). https://doi.org/10.1007/s11047-018-9701-2

    Article  MathSciNet  MATH  Google Scholar 

  25. Summers, S.M.: Reducing tile complexity for the self-assembly of scaled shapes through temperature programming. Algorithmica 63(1), 117–136 (2012). https://doi.org/10.1007/s00453-011-9522-5

    Article  MathSciNet  MATH  Google Scholar 

  26. Winfree, E.: Algorithmic self-assembly of DNA. Ph.D. thesis, California Institute of Technology, June 1998

    Google Scholar 

  27. Woods, D.: Intrinsic universality and the computational power of self-assembly. Philos. Trans. Roy. Soc. A Math. Phys. Eng. Sci. 373(2046), 20140214 (2015)

    Article  Google Scholar 

  28. Woods, D., et al.: Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature 567(7748), 366–372 (2019). https://doi.org/10.1038/s41586-019-1014-9

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Timothy Gomez .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Caballero, D., Gomez, T., Schweller, R., Wylie, T. (2021). The Complexity of Multiple Handed Self-assembly. In: Kostitsyna, I., Orponen, P. (eds) Unconventional Computation and Natural Computation. UCNC 2021. Lecture Notes in Computer Science(), vol 12984. Springer, Cham. https://doi.org/10.1007/978-3-030-87993-8_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-87993-8_1

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-87992-1

  • Online ISBN: 978-3-030-87993-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics