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Self-assembly of Patterns in the Abstract Tile Assembly Model

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Unconventional Computation and Natural Computation (UCNC 2024)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 14776))

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Abstract

In the abstract Tile Assembly Model, self-assembling systems consisting of tiles of different colors can form structures on which colored patterns are “painted.” We explore the complexity, in terms of the numbers of unique tile types required, of assembling various patterns. We first demonstrate how to efficiently self-assemble a set of simple patterns, then show tight bounds on the tile type complexity of self-assembling 2-colored patterns on the surfaces of square assemblies. Finally, we demonstrate an exponential gap in tile type complexity of self-assembling an infinite series of patterns between systems restricted to one plane versus those allowed two planes.

S. M. Summers—This author was supported in part by University of Wisconsin Oshkosh Research Sabbatical (S581) Fall 2023.

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References

  1. Adleman, L., Cheng, Q., Goel, A., Huang, M.D.: Running time and program size for self-assembled squares. In: Proceedings of the 33rd Annual ACM Symposium on Theory of Computing, pp. 740–748. Hersonissos, Greece (2001)

    Google Scholar 

  2. Czeizler, E., Popa, A.: Synthesizing minimal tile sets for complex patterns in the framework of patterned DNA self-assembly. In: Stefanovic, D., Turberfield, A. (eds.) DNA Computing and Molecular Programming. LNCS, vol. 7433, pp. 58–72. Springer, Heidelberg (2012)

    Google Scholar 

  3. Doty, D., Fleming, H., Hader, D., Patitz, M.J., Vaughan, L.A.: Accelerating self-assembly of crisscross slat systems. In: 29th International Conference on DNA Computing and Molecular Programming (DNA 29). Leibniz International Proceedings in Informatics (LIPIcs), vol. 276, pp. 7:1–7:23. Schloss Dagstuhl – Leibniz-Zentrum für Informatik, Dagstuhl (2023)

    Google Scholar 

  4. Drake, P., Patitz, M.J., Summers, S.M., Tracy, T.: Self-assembly of patterns in the abstract tile assembly model. Tech. Rep. arXiv preprint arXiv:2402.16284 (2024)

  5. Drake, P., Patitz, M.J., Tracy, T.: Pattern self-assembly software (2024). http://self-assembly.net/wiki/index.php/Pattern_Self-Assembly

  6. Evans, C.G.: Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly. Ph.D. thesis, California Institute of Technology (2014)

    Google Scholar 

  7. Hader, D., Koch, A., Patitz, M.J., Sharp, M.: The impacts of dimensionality, diffusion, and directedness on intrinsic universality in the abstract tile assembly model. In: Chawla, S. (ed.) Proceedings of the 2020 ACM-SIAM Symposium on Discrete Algorithms, SODA 2020, Salt Lake City, 5–8 January 2020, pp. 2607–2624. SIAM (2020)

    Google Scholar 

  8. Kari, L., Kopecki, S., Meunier, P., Patitz, M.J., Seki, S.: Binary pattern tile set synthesis is np-hard. Algorithmica 78(1), 1–46 (2017)

    Google Scholar 

  9. Lathrop, J.I., Lutz, J.H., Patitz, M.J., Summers, S.M.: Computability and complexity in self-assembly. Theory Comput. Syst. 48(3), 617–647 (2011)

    Article  MathSciNet  Google Scholar 

  10. Lathrop, J.I., Lutz, J.H., Summers, S.M.: Strict self-assembly of discrete Sierpinski triangles. Theoret. Comput. Sci. 410, 384–405 (2009)

    Article  MathSciNet  Google Scholar 

  11. Lempiäinen, T., Czeizler, E., Orponen, P.: Synthesizing small and reliable tile sets for patterned DNA self-assembly. In: Proceedings of the 17th International Conference on DNA Computing and Molecular Programming (DNA 2011), pp. 145–159. Springer, Heidelberg (2011). http://dl.acm.org/citation.cfm?id=2042033.2042048

  12. Ma, X., Lombardi, F.: Synthesis of tile sets for DNA self-assembly. IEEE Trans. CAD Integrat. Circuits Syst. 27(5), 963–967 (2008)

    Google Scholar 

  13. Patitz, M.J., Summers, S.M.: Self-assembly of decidable sets. Nat. Comput. 10(2), 853–877 (2011)

    Article  MathSciNet  Google Scholar 

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

    Google Scholar 

  15. Rothemund, P.W.K., Papadakis, N., Winfree, E.: Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2(12), e424 (2004)

    Google Scholar 

  16. Rothemund, P.W.K., Winfree, E.: The program-size complexity of self-assembled squares (extended abstract). In: Proceedings of the thirty-second annual ACM Symposium on Theory of Computing (STOC 2000), pp. 459–468. ACM, Portland (2000)

    Google Scholar 

  17. Soloveichik, D., Winfree, E.: Complexity of self-assembled shapes. SIAM J. Comput. 36(6), 1544–1569 (2007)

    Article  MathSciNet  Google Scholar 

  18. Tikhomirov, G., Petersen, P., Qian, L.: Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns. Nature 552(7683), 67–71 (2017)

    Article  Google Scholar 

  19. Winfree, E.: Algorithmic Self-Assembly of DNA. Ph.D. thesis, California Institute of Technology (1998)

    Google Scholar 

  20. Wintersinger, C.M., et al.: Multi-micron crisscross structures grown from DNA-origami slats. Nat. Nanotechnol. 1–9 (2022)

    Google Scholar 

  21. Woods, D., et al.: Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature 567(7748), 366–372 (2019)

    Google Scholar 

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Correspondence to Matthew J. Patitz .

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Drake, P., Patitz, M.J., Summers, S.M., Tracy, T. (2024). Self-assembly of Patterns in the Abstract Tile Assembly Model. In: Cho, DJ., Kim, J. (eds) Unconventional Computation and Natural Computation. UCNC 2024. Lecture Notes in Computer Science, vol 14776. Springer, Cham. https://doi.org/10.1007/978-3-031-63742-1_7

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  • DOI: https://doi.org/10.1007/978-3-031-63742-1_7

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  • Online ISBN: 978-3-031-63742-1

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