Skip to main content

Identifying Shapes Using Self-assembly

(Extended Abstract)

  • Conference paper
Algorithms and Computation (ISAAC 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6507))

Included in the following conference series:

Abstract

In this paper, we introduce the following problem in the theory of algorithmic self-assembly: given an input shape as the seed of a tile-based self-assembly system, design a finite tile set that can, in some sense, uniquely identify whether or not the given input shape–drawn from a very general class of shapes–matches a particular target shape. We first study the complexity of correctly identifying squares. Then we investigate the complexity associated with the identification of a considerably more general class of non-square, hole-free shapes.

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 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.00
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. Abel, Z., Benbernou, N., Damian, M., Demaine, E., Demaine, M., Flatland, R., Kominers, S., Schweller, R.: Shape replication through self-assembly and RNAse enzymes. In: SODA 2010: Proceedings of the Twentyfirst Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1045–1064 (2010)

    Google Scholar 

  2. Adleman, L.: Toward a mathematical theory of self-assembly (extended abstract), Tech. Report 00-722, University of Southern California (2000)

    Google Scholar 

  3. 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, Abington (2001)

    Google Scholar 

  4. Andersen, E.S., Dong, M., Nielsen, M.M., Jahn, K., Subramani, R., Mamdouh, W., Golas, M.M., Sander, B., Stark, H., Oliveira, C.L.P., Pedersen, J.S., Birkedal, V., Besenbacher, F., Gothelf, K.V., Kjems, J.: Self-assembly of a nanoscale dna box with a controllable lid. Nature 459(7243), 73–76 (2009)

    Article  Google Scholar 

  5. 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)

    Article  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. 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 

  8. Fu, Y., Schweller, R.: Temperature 1 self-assembly: Deterministic assembly in 3d and probabilistic assembly in 2d. In: Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA 2011) (to appear, 2011)

    Google Scholar 

  9. Gu, H., Chao, J., Xiao, S.-J., Seeman, N.C.: A proximity-based programmable dna nanoscale assembly line. Nature 465(7295), 202–205 (2010)

    Article  Google Scholar 

  10. Hartgerink, J.D., Beniash, E., Stupp, S.I.: Self-Assembly and Mineralization of Peptide-Amphiphile Nanofibers. Science 294(5547), 1684–1688 (2001)

    Article  Google Scholar 

  11. Kalsin, A.M., Fialkowski, M., Paszewski, M., Smoukov, S.K., Bishop, K.J.M., Grzybowski, B.A.: Electrostatic Self-Assembly of Binary Nanoparticle Crystals with a Diamond-Like Lattice. Science 312(5772), 420–424 (2006)

    Article  Google Scholar 

  12. Luhrs, C.: Polyomino-safe DNA self-assembly via block replacement. In: Goel, A., Simmel, F.C., Sosík, P. (eds.) DNA14. LNCS, vol. 5347, pp. 112–126. Springer, Heidelberg (2008)

    Google Scholar 

  13. Lund, K., Manzo, A.J., Dabby, N., Michelotti, 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(7295), 206–210 (2010)

    Article  Google Scholar 

  14. Majumder, U., LaBean, T.H., Reif, J.H.: Activatable tiles for compact error-resilient directional assembly. In: 13th International Meeting on DNA Computing (DNA 13), Memphis, Tennessee, June 4-8 (2007)

    Google Scholar 

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

    Article  Google Scholar 

  16. 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, pp. 459–468. ACM, New York (2000)

    Chapter  Google Scholar 

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

    Article  Google Scholar 

  18. Soloveichik, D., Winfree, E.: Complexity of self-assembled shapes. SIAM Journal on Computing 36(6), 1544–1569 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  19. Tang, Z., Zhang, Z., Wang, Y., Glotzer, S.C., Kotov, N.A.: Self-Assembly of CdTe Nanocrystals into Free-Floating Sheets. Science 314(5797), 274–278 (2006)

    Article  Google Scholar 

  20. Vitányi, P., Li, M.: An introduction to kolmogorov complexity and its applications. Springer, Heidelberg (1997)

    MATH  Google Scholar 

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

    Google Scholar 

  22. Winfree, E.: Simulations of computing by self-assembly, Tech. Report CaltechCSTR:1998.22, California Institute of Technology (1998)

    Google Scholar 

  23. 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, Heidelberg (2006)

    Chapter  Google Scholar 

  24. Winfree, E., Yang, X., Seeman, N.C.: Universal computation via self-assembly of dna: Some theory and experiments. In: DNA Based Computers II. DIMACS, vol. 44, pp. 191–213. American Mathematical Society, Providence (1996)

    Chapter  Google Scholar 

  25. Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires. Science 301(5641), 1882–1884 (2003)

    Article  Google Scholar 

  26. Zeng, H., Li, J., Liu, J.P., Wang, Z.L., Sun, S.: Exchange-coupled nanocomposite magnets by nanoparticle self-assembly. Nature 420(6914), 395–398 (2002)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Patitz, M.J., Summers, S.M. (2010). Identifying Shapes Using Self-assembly. In: Cheong, O., Chwa, KY., Park, K. (eds) Algorithms and Computation. ISAAC 2010. Lecture Notes in Computer Science, vol 6507. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17514-5_39

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-17514-5_39

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-17513-8

  • Online ISBN: 978-3-642-17514-5

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics