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Small Tile Sets That Compute While Solving Mazes

Authors: Matthew Cook, Tristan Stérin, and Damien Woods

Published in: LIPIcs, Volume 205, 27th International Conference on DNA Computing and Molecular Programming (DNA 27) (2021)

Abstract

We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we call it the Maze-Walking Tile Assembly Model. The model has a number of implementation prospects, one being DNA strands that attach to a DNA origami substrate. Intuitively, the model suggests a separation of signal routing and computation: the input structure (maze) supplies a routing diagram, and the programmer’s tile set provides the computational ability. We ask how simple the computational part can be. We give two tiny tile sets that are computationally universal in the Maze-Walking Tile Assembly Model. The first has four tiles and simulates Boolean circuits by directly implementing NAND, NXOR and NOT gates. Our second tile set has 6 tiles and is called the Collatz tile set as it produces patterns found in binary/ternary representations of iterations of the Collatz function. Using computer search we find that the Collatz tile set is expressive enough to encode Boolean circuits using blocks of these patterns. These two tile sets give two different methods to find simple universal tile sets, and provide motivation for using pre-assembled maze structures as circuit wiring diagrams in molecular self-assembly based computing.

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Matthew Cook, Tristan Stérin, and Damien Woods. Small Tile Sets That Compute While Solving Mazes. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 8:1-8:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{cook_et_al:LIPIcs.DNA.27.8,
  author =	{Cook, Matthew and St\'{e}rin, Tristan and Woods, Damien},
  title =	{{Small Tile Sets That Compute While Solving Mazes}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{8:1--8:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-205-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{205},
  editor =	{Lakin, Matthew R. and \v{S}ulc, Petr},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.8},
  URN =		{urn:nbn:de:0030-drops-146758},
  doi =		{10.4230/LIPIcs.DNA.27.8},
  annote =	{Keywords: model of computation, self-assembly, small universal tile set, Boolean circuits, maze-solving}
}

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DOI: 10.4230/LIPIcs.STACS.2019.20

Average-Case Completeness in Tag Systems

Authors: Matthew Cook and Turlough Neary

Published in: LIPIcs, Volume 126, 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)

Abstract

To prove average-case NP-completeness for a problem, we must choose a known average-case complete problem and reduce it to that problem. Unfortunately, the set of options to choose from is far smaller than for standard (worst-case) NP-completeness. In an effort to help remedy this we focus on tag systems, which due to their extreme simplicity have been a target for other types of reductions for many problems including the matrix mortality problem, the Post correspondence problem, the universality of cellular automaton Rule 110, and all of the smallest universal single-tape Turing machines. Here we show that a tag system can efficiently simulate a Turing machine even when the input is provided in an extremely simple encoding which adds just log n carefully set bits to encode an arbitrary Turing machine input of length n. As a result we show that the bounded halting problem for nondeterministic tag systems is average-case NP-complete. This result is unexpected when one considers that in the current state of the art for simple universal systems it had appeared that there was a trade-off whereby simpler systems required more complicated input encodings. In other words, although simple systems can compute interesting things, they had appeared to require very carefully encoded inputs in order to do so. Our result surprisingly goes in the opposite direction by giving the first average-case completeness result for such a simple model of computation. In ongoing work we have already found applications of our result having used it to give average-case NP-completeness results for a 2D generalization of the Collatz function, a nondeterministic version of the 2D elementary functions studied by Koiran and Moore, 3D piecewise affine maps, and bounded Post correspondence problem instances that use simpler word pairs than previous results.

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Matthew Cook and Turlough Neary. Average-Case Completeness in Tag Systems. In 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 126, pp. 20:1-20:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{cook_et_al:LIPIcs.STACS.2019.20,
  author =	{Cook, Matthew and Neary, Turlough},
  title =	{{Average-Case Completeness in Tag Systems}},
  booktitle =	{36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)},
  pages =	{20:1--20:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-100-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{126},
  editor =	{Niedermeier, Rolf and Paul, Christophe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2019.20},
  URN =		{urn:nbn:de:0030-drops-102590},
  doi =		{10.4230/LIPIcs.STACS.2019.20},
  annote =	{Keywords: average-case NP-completeness, encoding complexity, tag system, bounded halting problem}
}

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Documents authored by Cook, Matthew

Small Tile Sets That Compute While Solving Mazes

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Average-Case Completeness in Tag Systems

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