Skip to main content

Step-Assembly with a Constant Number of Tile Types

  • Conference paper
Algorithms and Computation (ISAAC 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5878))

Included in the following conference series:

Abstract

Demaine et. al. [1] have introduced a model for staged assembly for constructing self-assembled shapes as an extension to the multiple tile model [2]. In their model the assembly proceeds in several bins and several stages with different sets of tiles and supertiles applied on each bin and in each stage. Taking advantage of all these features they showed that a constant number of tile types is sufficient to self-assemble any given shape.

In this paper, we consider a simplified model of staged assembly, called the step assembly model, in which we only have one bin in each step and assembly happens by attaching tiles one by one to the growing structure as in the standard assembly model. We show that in this simplified model a constant number of tile types (24) is sufficient to assemble a large class of shapes. This class includes all shapes obtained from any shape by scaling by a factor of 2. For general shapes, we note that the tile complexity of this model has connections to the monotone connected node search number of a spanning tree of the shape.

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 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 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  MATH  MathSciNet  Google Scholar 

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

    Article  MATH  MathSciNet  Google Scholar 

  3. Winfree, E., Yang, X., Seeman, N.: Universal computation via self-assembly of DNA: Some theory and experiments. In: Proceedings of the Second Annual Meeting on DNA Based Computers, pp. 191–214 (1996)

    Google Scholar 

  4. Reif, J.H.: Local parallel biomolecular computation. In: Proc. DNA-Based Computers, pp. 217–254 (1997)

    Google Scholar 

  5. Gomez-Lopez, M., Preece, J., Stoddart, J.: The art and science of self-assembling molecular machines. Nanotechnology 7, 183–192 (1996)

    Article  Google Scholar 

  6. Abelson, H., Allen, D., Coore, D., Hanson, C., Homsy, G., Knight, T.F., Nagpal, R., Rauch, E., Sussman, G.J., Weiss, R.: Amorphous computing. Communications of the ACM 43, 74–82 (2000)

    Article  Google Scholar 

  7. Rothemund, P.W.K., Winfree, E.: The program-size complexity of self-assembled squares. In: Proceedings of STOC, pp. 459–468 (2000)

    Google Scholar 

  8. Seeman, N.: DNA nanotechnology: novel DNA constructions. Annual Review of Biophysics and Biomolecular Structure 27, 225–248 (1998)

    Article  Google Scholar 

  9. Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two dimensional DNA crystals. Nature 394, 539–544 (1998)

    Article  Google Scholar 

  10. Mao, C., LaBean, T.H., Reif, J., Seeman, N.: Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000)

    Article  Google Scholar 

  11. LaBean, T., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J.H., Seeman, N.: Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. Journal of the American Chemical Society 122, 1848–1860 (2000)

    Article  Google Scholar 

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

    Article  Google Scholar 

  13. Kirousis, L.M., Papadimitriou, C.H.: Interval graphs and searching. Discrete Mathematics 55(1), 181–184 (1985)

    Article  MATH  MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Maňuch, J., Stacho, L., Stoll, C. (2009). Step-Assembly with a Constant Number of Tile Types. In: Dong, Y., Du, DZ., Ibarra, O. (eds) Algorithms and Computation. ISAAC 2009. Lecture Notes in Computer Science, vol 5878. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10631-6_96

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-10631-6_96

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-10630-9

  • Online ISBN: 978-3-642-10631-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics