4 Search Results for "Summers, Scott M."

Document
DOI: 10.4230/LIPIcs.DNA.27.4
Improved Lower and Upper Bounds on the Tile Complexity of Uniquely Self-Assembling a Thin Rectangle Non-Cooperatively in 3D

Authors: David Furcy, Scott M. Summers, and Logan Withers

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

Abstract
We investigate a fundamental question regarding a benchmark class of shapes in one of the simplest, yet most widely utilized abstract models of algorithmic tile self-assembly. More specifically, we study the directed tile complexity of a k × N thin rectangle in Winfree’s ubiquitous abstract Tile Assembly Model, assuming that cooperative binding cannot be enforced (temperature-1 self-assembly) and that tiles are allowed to be placed at most one step into the third dimension (just-barely 3D). While the directed tile complexities of a square and a scaled-up version of any algorithmically specified shape at temperature 1 in just-barely 3D are both asymptotically the same as they are (respectively) at temperature 2 in 2D, the (nearly tight) bounds on the directed tile complexity of a thin rectangle at temperature 2 in 2D are not currently known to hold at temperature 1 in just-barely 3D. Motivated by this discrepancy, we establish new lower and upper bounds on the directed tile complexity of a thin rectangle at temperature 1 in just-barely 3D. The proof of our upper bound is based on the construction of a novel, just-barely 3D temperature-1 self-assembling counter. Each value of the counter is comprised of k-2 digits, represented in a geometrically staggered fashion within k rows. This nearly optimal digit density, along with the base of the counter, which is proportional to N^{1/(k-1)}, results in an upper bound of O(N^{1/(k-1)} + log N), and is an asymptotic improvement over the previous state-of-the-art upper bound. On our way to proving our lower bound, we develop a new, more powerful type of specialized Window Movie Lemma that lets us bound the number of "sufficiently similar" ways to assign glues to a set (rather than a sequence) of fixed locations. Consequently, our lower bound, Ω(N^{1/k}), is also an asymptotic improvement over the previous state-of-the-art lower bound.
Cite as

David Furcy, Scott M. Summers, and Logan Withers. Improved Lower and Upper Bounds on the Tile Complexity of Uniquely Self-Assembling a Thin Rectangle Non-Cooperatively in 3D. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{furcy_et_al:LIPIcs.DNA.27.4,
  author =	{Furcy, David and Summers, Scott M. and Withers, Logan},
  title =	{{Improved Lower and Upper Bounds on the Tile Complexity of Uniquely Self-Assembling a Thin Rectangle Non-Cooperatively in 3D}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{4:1--4:18},
  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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.27.4},
  URN =		{urn:nbn:de:0030-drops-146716},
  doi =		{10.4230/LIPIcs.DNA.27.4},
  annote =	{Keywords: Self-assembly, algorithmic self-assembly, tile self-assembly}
}
Document
DOI: 10.4230/LIPIcs.STACS.2013.172
Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM

Authors: Sarah Cannon, Erik D. Demaine, Martin L. Demaine, Sarah Eisenstat, Matthew J. Patitz, Robert T. Schweller, Scott M Summers, and Andrew Winslow

Published in: LIPIcs, Volume 20, 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)

Abstract
We study the difference between the standard seeded model (aTAM) of tile self-assembly, and the "seedless" two-handed model of tile self-assembly (2HAM). Most of our results suggest that the two-handed model is more powerful. In particular, we show how to simulate any seeded system with a two-handed system that is essentially just a constant factor larger. We exhibit finite shapes with a busy-beaver separation in the number of distinct tiles required by seeded versus two-handed, and exhibit an infinite shape that can be constructed two-handed but not seeded. Finally, we show that verifying whether a given system uniquely assembles a desired supertile is co-NP-complete in the two-handed model, while it was known to be polynomially solvable in the seeded model.
Cite as

Sarah Cannon, Erik D. Demaine, Martin L. Demaine, Sarah Eisenstat, Matthew J. Patitz, Robert T. Schweller, Scott M Summers, and Andrew Winslow. Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM. In 30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013). Leibniz International Proceedings in Informatics (LIPIcs), Volume 20, pp. 172-184, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{cannon_et_al:LIPIcs.STACS.2013.172,
  author =	{Cannon, Sarah and Demaine, Erik D. and Demaine, Martin L. and Eisenstat, Sarah and Patitz, Matthew J. and Schweller, Robert T. and Summers, Scott M and Winslow, Andrew},
  title =	{{Two Hands Are Better Than One (up to constant factors): Self-Assembly In The 2HAM vs. aTAM}},
  booktitle =	{30th International Symposium on Theoretical Aspects of Computer Science (STACS 2013)},
  pages =	{172--184},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-50-7},
  ISSN =	{1868-8969},
  year =	{2013},
  volume =	{20},
  editor =	{Portier, Natacha and Wilke, Thomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2013.172},
  URN =		{urn:nbn:de:0030-drops-39321},
  doi =		{10.4230/LIPIcs.STACS.2013.172},
  annote =	{Keywords: abstract tile assembly model, hierarchical tile assembly model, two-handed tile assembly model, algorithmic self-assembly, DNA computing, biocomputing}
}
Document
Extended Abstract
DOI: 10.4230/LIPIcs.STACS.2011.201
Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (Extended Abstract)

Authors: Erik D. Demaine, Matthew J. Patitz, Robert T. Schweller, and Scott M. Summers

Published in: LIPIcs, Volume 9, 28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011)

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.
Cite as

Erik D. Demaine, Matthew J. Patitz, Robert T. Schweller, and Scott M. Summers. Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor (Extended Abstract). In 28th International Symposium on Theoretical Aspects of Computer Science (STACS 2011). Leibniz International Proceedings in Informatics (LIPIcs), Volume 9, pp. 201-212, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InProceedings{demaine_et_al:LIPIcs.STACS.2011.201,
  author =	{Demaine, Erik D. and Patitz, Matthew J. and Schweller, Robert T. and Summers, Scott M.},
  title =	{{Self-Assembly of Arbitrary Shapes Using RNAse Enzymes: Meeting the Kolmogorov Bound with Small Scale Factor}},
  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 =	{Schwentick, Thomas and D\"{u}rr, Christoph},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2011.201},
  URN =		{urn:nbn:de:0030-drops-30118},
  doi =		{10.4230/LIPIcs.STACS.2011.201},
  annote =	{Keywords: Biomolecular computation, RNAse enzyme self-assembly, algorithmic self-assembly, Komogorov complexity}
}
Document
DOI: 10.4230/LIPIcs.STACS.2010.2461
Intrinsic Universality in Self-Assembly

Authors: David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods

Published in: LIPIcs, Volume 5, 27th International Symposium on Theoretical Aspects of Computer Science (2010)

Abstract
We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is capable of simulating a very wide class of tile systems, including itself. Specifically, we give a tile set that simulates the assembly of any tile assembly system in a class of systems that we call \emph{locally consistent}: each tile binds with exactly the strength needed to stay attached, and that there are no glue mismatches between tiles in any produced assembly. Our construction is reminiscent of the studies of \emph{intrinsic universality} of cellular automata by Ollinger and others, in the sense that our simulation of a tile system $T$ by a tile system $U$ represents each tile in an assembly produced by $T$ by a $c \times c$ block of tiles in $U$, where $c$ is a constant depending on $T$ but not on the size of the assembly $T$ produces (which may in fact be infinite). Also, our construction improves on earlier simulations of tile assembly systems by other tile assembly systems (in particular, those of Soloveichik and Winfree, and of Demaine et al.) in that we simulate the actual process of self-assembly, not just the end result, as in Soloveichik and Winfree's construction, and we do not discriminate against infinite structures. Both previous results simulate only temperature 1 systems, whereas our construction simulates tile assembly systems operating at temperature 2.
Cite as

David Doty, Jack H. Lutz, Matthew J. Patitz, Scott M. Summers, and Damien Woods. Intrinsic Universality in Self-Assembly. In 27th International Symposium on Theoretical Aspects of Computer Science. Leibniz International Proceedings in Informatics (LIPIcs), Volume 5, pp. 275-286, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{doty_et_al:LIPIcs.STACS.2010.2461,
  author =	{Doty, David and Lutz, Jack H. and Patitz, Matthew J. and Summers, Scott M. and Woods, Damien},
  title =	{{Intrinsic Universality in Self-Assembly}},
  booktitle =	{27th International Symposium on Theoretical Aspects of Computer Science},
  pages =	{275--286},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-16-3},
  ISSN =	{1868-8969},
  year =	{2010},
  volume =	{5},
  editor =	{Marion, Jean-Yves and Schwentick, Thomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2010.2461},
  URN =		{urn:nbn:de:0030-drops-24619},
  doi =		{10.4230/LIPIcs.STACS.2010.2461},
  annote =	{Keywords: Biological computing, Molecular computation, intrinsic universality, self-assembly}
}
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