Efficient Algorithms for Self Assembling Triangular and Other Nano Structures

  • Authors:
  • Vamsi Kundeti;Sanguthevar Rajasekaran

  • Affiliations:
  • Department of Computer Science and Engineering, University of Connecticut, Storrs, USA CT 06269;Department of Computer Science and Engineering, University of Connecticut, Storrs, USA CT 06269

  • Venue:
  • ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
  • Year:
  • 2009

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Abstract

Nano fabrication with biomolecular/DNA self assembly is a promising area of research. Building nano structures with self assembly is both efficient and inexpensive. Winfree [1] formalized a two dimensional (2D) tile assembly model based on Wang’s tiling technique. Algorithms with an optimal tile complexity of ($\Theta(\frac{\log(N)}{\log(\log(N))})$) were proposed earlier to uniquely self assemble an N×N square (with a temperature of α= 2) on this model. However efficient constructions to assemble arbitrary shapes are not known and have remained open. In this paper we present self assembling algorithms to assemble a triangle of base 2N − 1 (units) and height N with a tile complexity of Θ(log(N)). We also describe how this framework can be used to construct other shapes.