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Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract)

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Abstract

We consider a model of algorithmic self-assembly of geometric shapes out of square Wang tiles studied in SODA 2010, in which there are two types of tiles (e.g., constructed out of DNA and RNA material) and one operation that destroys all tiles of a particular type (e.g., an RNAse enzyme destroys all RNA tiles). We show that a single use of this destruction operation enables much more efficient construction of arbitrary shapes. In particular, an arbitrary shape can be constructed using an asymptotically optimal number of distinct tile type (related to the shape's Kolmogorov complexity), after scaling the shape by only a logarithmic factor. By contrast, without the destruction operation, the best such result has a scale factor at least linear in the size of the shape and is connected only by a spanning tree of the scaled tiles. We also characterize a large collection of shapes that can be constructed efficiently without any scaling.

BibTeX - Entry

@InProceedings{demaine_et_al:LIPIcs:2011:3011,
  author =	{Erik D. Demaine and Matthew J. Patitz and Robert T. Schweller and Scott M. Summers},
  title =	{{Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (extended abstract)}},
  booktitle =	{28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011) },
  pages =	{201--212},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-25-5},
  ISSN =	{1868-8969},
  year =	{2011},
  volume =	{9},
  editor =	{Thomas Schwentick and Christoph D{\"u}rr},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2011/3011},
  URN =		{urn:nbn:de:0030-drops-30118},
  doi =		{http://dx.doi.org/10.4230/LIPIcs.STACS.2011.201},
  annote =	{Keywords: Biomolecular computation, RNAse enzyme self-assembly, algorithmic self-assembly, Komogorov complexity}
}

Keywords: Biomolecular computation, RNAse enzyme self-assembly, algorithmic self-assembly, Komogorov complexity
Seminar: 28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011)
Issue date: 2011
Date of publication: 2011


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