3 Search Results for "Chalk, Cameron"

Document
DOI: 10.4230/LIPIcs.DNA.27.11
Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching

Authors: Tonglin Chen, Arnav Solanki, and Marc Riedel

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

Abstract
Prior research has introduced the Single-Instruction-Multiple-Data paradigm for DNA computing (SIMD DNA). It offers the potential for storing information and performing in-memory computations on DNA, with massive parallelism. This paper introduces three new SIMD DNA operations: sorting, shifting, and searching. Each is a fundamental operation in computer science. Our implementations demonstrate the effectiveness of parallel pairwise operations with this new paradigm.
Cite as

Tonglin Chen, Arnav Solanki, and Marc Riedel. Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching. In 27th International Conference on DNA Computing and Molecular Programming (DNA 27). Leibniz International Proceedings in Informatics (LIPIcs), Volume 205, pp. 11:1-11:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

Copy BibTex To Clipboard

@InProceedings{chen_et_al:LIPIcs.DNA.27.11,
  author =	{Chen, Tonglin and Solanki, Arnav and Riedel, Marc},
  title =	{{Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching}},
  booktitle =	{27th International Conference on DNA Computing and Molecular Programming (DNA 27)},
  pages =	{11:1--11:21},
  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.27.11},
  URN =		{urn:nbn:de:0030-drops-146780},
  doi =		{10.4230/LIPIcs.DNA.27.11},
  annote =	{Keywords: Molecular Computing, DNA Computing, DNA Storage, Parallel Computing, Strand Displacement}
}
Document
DOI: 10.4230/LIPIcs.ESA.2018.14
Self-Assembly of Any Shape with Constant Tile Types using High Temperature

Authors: Cameron Chalk, Austin Luchsinger, Robert Schweller, and Tim Wylie

Published in: LIPIcs, Volume 112, 26th Annual European Symposium on Algorithms (ESA 2018)

Abstract
Inspired by nature and motivated by a lack of top-down tools for precise nanoscale manufacture, self-assembly is a bottom-up process where simple, unorganized components autonomously combine to form larger more complex structures. Such systems hide rich algorithmic properties - notably, Turing universality - and a self-assembly system can be seen as both the object to be manufactured as well as the machine controlling the manufacturing process. Thus, a benchmark problem in self-assembly is the unique assembly of shapes: to design a set of simple agents which, based on aggregation rules and random movement, self-assemble into a particular shape and nothing else. We use a popular model of self-assembly, the 2-handed or hierarchical tile assembly model, and allow the existence of repulsive forces, which is a well-studied variant. The technique utilizes a finely-tuned temperature (the minimum required affinity required for aggregation of separate complexes). We show that calibrating the temperature and the strength of the aggregation between the tiles, one can encode the shape to be assembled without increasing the number of distinct tile types. Precisely, we show one tile set for which the following holds: for any finite connected shape S, there exists a setting of binding strengths between tiles and a temperature under which the system uniquely assembles S at some scale factor. Our tile system only uses one repulsive glue type and the system is growth-only (it produces no unstable assemblies). The best previous unique shape assembly results in tile assembly models use O(K(S)/(log K(S))) distinct tile types, where K(S) is the Kolmogorov (descriptional) complexity of the shape S.
Cite as

Cameron Chalk, Austin Luchsinger, Robert Schweller, and Tim Wylie. Self-Assembly of Any Shape with Constant Tile Types using High Temperature. In 26th Annual European Symposium on Algorithms (ESA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 112, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{chalk_et_al:LIPIcs.ESA.2018.14,
  author =	{Chalk, Cameron and Luchsinger, Austin and Schweller, Robert and Wylie, Tim},
  title =	{{Self-Assembly of Any Shape with Constant Tile Types using High Temperature}},
  booktitle =	{26th Annual European Symposium on Algorithms (ESA 2018)},
  pages =	{14:1--14:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-081-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{112},
  editor =	{Azar, Yossi and Bast, Hannah and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2018.14},
  URN =		{urn:nbn:de:0030-drops-94773},
  doi =		{10.4230/LIPIcs.ESA.2018.14},
  annote =	{Keywords: self-assembly, molecular computing, tiling, tile, shapes}
}
Document
DOI: 10.4230/LIPIcs.ESA.2016.26
Optimal Staged Self-Assembly of General Shapes

Authors: Cameron Chalk, Eric Martinez, Robert Schweller, Luis Vega, Andrew Winslow, and Tim Wylie

Published in: LIPIcs, Volume 57, 24th Annual European Symposium on Algorithms (ESA 2016)

Abstract
We analyze the number of stages, tiles, and bins needed to construct n * n squares and scaled shapes in the staged tile assembly model. In particular, we prove that there exists a staged system with b bins and t tile types assembling an n * n square using O((log n - tb - t log t)/b^2 + log log b/log t) stages and Omega((log n - tb - t log t)/b^2) are necessary for almost all n. For a shape S, we prove O((K(S) - tb - t log t)/b^2 + (log log b)/log t) stages suffice and Omega((K(S) - tb - t log t)/b^2) are necessary for the assembly of a scaled version of S, where K(S) denotes the Kolmogorov complexity of S. Similarly tight bounds are also obtained when more powerful flexible glue functions are permitted. These are the first staged results that hold for all choices of b and t and generalize prior results. The upper bound constructions use a new technique for efficiently converting each both sources of system complexity, namely the tile types and mixing graph, into a "bit string" assembly.
Cite as

Cameron Chalk, Eric Martinez, Robert Schweller, Luis Vega, Andrew Winslow, and Tim Wylie. Optimal Staged Self-Assembly of General Shapes. In 24th Annual European Symposium on Algorithms (ESA 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 57, pp. 26:1-26:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

Copy BibTex To Clipboard

@InProceedings{chalk_et_al:LIPIcs.ESA.2016.26,
  author =	{Chalk, Cameron and Martinez, Eric and Schweller, Robert and Vega, Luis and Winslow, Andrew and Wylie, Tim},
  title =	{{Optimal Staged Self-Assembly of General Shapes}},
  booktitle =	{24th Annual European Symposium on Algorithms (ESA 2016)},
  pages =	{26:1--26:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-015-6},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{57},
  editor =	{Sankowski, Piotr and Zaroliagis, Christos},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2016.26},
  URN =		{urn:nbn:de:0030-drops-63776},
  doi =		{10.4230/LIPIcs.ESA.2016.26},
  annote =	{Keywords: Tile self-assembly, 2HAM, aTAM, DNA computing, biocomputing}
}
  • Refine by Author
  • 2 Chalk, Cameron
  • 2 Schweller, Robert
  • 2 Wylie, Tim
  • 1 Chen, Tonglin
  • 1 Luchsinger, Austin
  • Show More...

  • Refine by Classification
  • 1 Applied computing → Computational biology
  • 1 Computing methodologies → Parallel computing methodologies
  • 1 Theory of computation → Self-organization

  • Refine by Keyword
  • 1 2HAM
  • 1 DNA Computing
  • 1 DNA Storage
  • 1 DNA computing
  • 1 Molecular Computing
  • Show More...

  • Refine by Type
  • 3 document

  • Refine by Publication Year
  • 1 2016
  • 1 2018
  • 1 2021

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH Imprint Privacy Contact