Abstract
In this work we propose a generalization of Winfree’s abstract Tile Assembly Model (aTAM) in which tile types are assigned rigid shapes, or geometries, along each tile face. We examine the number of distinct tile types needed to assemble shapes within this model, the temperature required for efficient assembly, and the problem of designing compact geometric faces to meet given compatibility specifications. We pose the following question: can complex geometric tile faces arbitrarily reduce the number of distinct tile types to assemble shapes? Within the most basic generalization of the aTAM, we show that the answer is no. For almost all n at least \(\Omega(\sqrt{\log n})\) tile types are required to uniquely assemble an n×n square, regardless of how much complexity is pumped into the face of each tile type. However, we show for all n we can achieve a matching \(O(\sqrt{\log n})\) tile types, beating the known lower bound of Θ(logn / loglogn) that holds for almost all n within the aTAM. Further, our result holds at temperature τ = 1. Our next result considers a geometric tile model that is a generalization of the 2-handed abstract tile assembly model in which tile aggregates must move together through obstacle free paths within the plane. Within this model we present a novel construction that harnesses the collision free path requirement to allow for the unique assembly of any n×n square with a sleek O(loglogn) distinct tile types. This construction is of interest in that it is the first tile self-assembly result to harness collision free planar translation to increase efficiency, whereas previous work has simply used the planarity restriction as a desireable quality that could be achieved at reduced efficiency. This surprisingly low tile type result further emphasizes a fundamental open question: Is it possible to assemble n×n squares with O(1) distinct tile types? Essentially, how far can the trade off between the number of distinct tile types required for an assembly and the complexity of each tile type itself be taken?
A full version of this paper can be found at [13].
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Adleman, L., Cheng, Q., Goel, A., Huang, M.-D.: Running time and program size for self-assembled squares. In: Proceedings of the Thirty-third Annual ACM Symposium on Theory of Computing, pp. 740–748. ACM, New York (2001)
Adleman, L., Cheng, Q., Goel, A., Huang, M.-D., Wasserman, H.: Linear self-assemblies: Equilibria, entropy and convergence rates. In: Sixth International Conference on Difference Equations and Applications. Taylor and Francis (2001)
Aggarwal, G., Goldwasser, M.H., Kao, M.-Y., Schweller, R.T.: Complexities for generalized models of self-assembly. In: Proceedings of ACM-SIAM Symposium on Discrete Algorithms (2004)
Barish, R.D., Schulman, R., Rothemund, P.W., Winfree, E.: An information-bearing seed for nucleating algorithmic self-assembly. Proceedings of the National Academy of Sciences 106(15), 6054–6059 (2009)
Chandran, H., Gopalkrishnan, N., Reif, J.: The Tile Complexity of Linear Assemblies. In: Albers, S., Marchetti-Spaccamela, A., Matias, Y., Nikoletseas, S., Thomas, W. (eds.) ICALP 2009. LNCS, vol. 5555, pp. 235–253. Springer, Heidelberg (2009)
Chen, H.-L., Schulman, R., Goel, A., Winfree, E.: Reducing facet nucleation during algorithmic self-assembly. Nano Letters 7(9), 2913–2919 (2007)
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)
Cook, M., Fu, Y., Schweller, R.T.: Temperature 1 self-assembly: Deterministic assembly in 3d and probabilistic assembly in 2d. In: Randall, D. (ed.) Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, SODA 2011, pp. 570–589. SIAM (2011)
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)
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)
Doty, D., Patitz, M.J., Reishus, D., Schweller, R.T., Summers, S.M.: Strong fault-tolerance for self-assembly with fuzzy temperature. In: Proceedings of the 51st Annual IEEE Symposium on Foundations of Computer Science (FOCS 2010), pp. 417–426 (2010)
Endo, M., Sugita, T., Katsuda, Y., Hidaka, K., Sugiyama, H.: Programmed-assembly system using DNA jigsaw pieces. Chemistry: A European Journal, 5362–5368 (2010)
Fu, B., Patitz, M.J., Schweller, R., Sheline, R.: Self-assembly with geometric tiles. Arxiv preprint arXiv:1104.2809 (2012)
LaBean, T.H., Winfree, E., Reif, J.H.: Experimental progress in computation by self-assembly of DNA tilings. DNA Based Computers 5, 123–140 (1999)
Luhrs, C.: Polyomino-Safe DNA Self-assembly via Block Replacement. In: Goel, A., Simmel, F.C., Sosík, P. (eds.) DNA. LNCS, vol. 5347, pp. 112–126. Springer, Heidelberg (2009)
Mao, C., LaBean, T.H., Relf, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407(6803), 493–496 (2000)
Reif, J.H., Sahu, S., Yin, P.: Compact Error-Resilient Computational DNA Tiling Assemblies. In: Ferretti, C., Mauri, G., Zandron, C. (eds.) DNA 2004. LNCS, vol. 3384, pp. 293–307. Springer, Heidelberg (2005)
Rothemund, P.W.K.: Folding DNA to create nanoscale shapes and patterns. Nature 440(7082), 297–302 (2006)
Rothemund, P.W.K., Winfree, E.: The program-size complexity of self-assembled squares (extended abstract). In: STOC 2000: Proceedings of the Thirty-Second Annual ACM Symposium on Theory of Computing, Portland, Oregon, United States, pp. 459–468. ACM Press (2000)
Schulman, R., Winfree, E.: Synthesis of crystals with a programmable kinetic barrier to nucleation. Proceedings of the National Academy of Sciences 104(39), 15236–15241 (2007)
Soloveichik, D., Winfree, E.: Complexity of self-assembled shapes. SIAM Journal on Computing 36(6), 1544–1569 (2007)
Winfree, E.: Algorithmic self-assembly of DNA. Ph.D. thesis, California Institute of Technology (June 1998)
Winfree, E.: Self-healing tile sets. In: Chen, J., Jonoska, N., Rozenberg, G. (eds.) Nanotechnology: Science and Computation. Natural Computing Series, pp. 55–78. Springer (2006)
Woo, S., Rothemund, P.W.K.: Stacking bonds: Programming molecular recognition based on the geometry of dna nanostructures. Nature Chemistry 3, 620–627 (2011)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Fu, B., Patitz, M.J., Schweller, R.T., Sheline, R. (2012). Self-assembly with Geometric Tiles. In: Czumaj, A., Mehlhorn, K., Pitts, A., Wattenhofer, R. (eds) Automata, Languages, and Programming. ICALP 2012. Lecture Notes in Computer Science, vol 7391. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31594-7_60
Download citation
DOI: https://doi.org/10.1007/978-3-642-31594-7_60
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-31593-0
Online ISBN: 978-3-642-31594-7
eBook Packages: Computer ScienceComputer Science (R0)