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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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)
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
Alon, N., Yuster, R., Zwick, U.: Finding and counting given length cycles. Algorithmica 17, 209–223 (1997). https://doi.org/10.1007/BF02523189
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
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)
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)
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)
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
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
Doty, D.: Randomized self-assembly for exact shapes. SIAM J. Comput. 39(8), 3521–3552 (2010)
Doty, D.: Theory of algorithmic self-assembly. Commun. ACM 55(12), 78–88 (2012)
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
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
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
Kao, M.Y., Schweller, R.: Reducing tile complexity for self-assembly through temperature programming. arXiv preprint cs/0602010 (2006)
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
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
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
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)
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
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)
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
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
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
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
Winfree, E.: Algorithmic self-assembly of DNA. Ph.D. thesis, California Institute of Technology, June 1998
Woods, D.: Intrinsic universality and the computational power of self-assembly. Philos. Trans. Roy. Soc. A Math. Phys. Eng. Sci. 373(2046), 20140214 (2015)
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
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this paper
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)