Notes on advanced topics in algorithmic tile self-assembly

1
Notes on advanced topics in algorithmic tile
self-assembly

• Day 39 of Comp Sci 480

2
Advanced topics

• In the following slides, some advanced topics in
  algorithmic tile self-assembly are mentioned
• A non-exhaustive list of notable references is
  given for each topic

3
Complexity of shapes and Turing machines

• James I. Lathrop, Jack H. Lutz, Matthew J.
  Patitz, Scott M. Summers Computability and
  Complexity in Self-assembly. Theory Comput. Syst.
  48(3) 617-647 (2011)
• David Soloveichik, Erik Winfree Complexity of
  Self-Assembled Shapes. SIAM J. Comput. 36(6)
  1544-1569 (2007)

4
Fractals

• Steven M. Kautz, Brad Shutters Self-Assembling
  Rulers for Approximating Generalized Sierpinski
  Carpets. Algorithmica 67(2) 207-233 (2013)
• Jack H. Lutz, Brad Shutters Approximate
  Self-Assembly of the Sierpinski Triangle. Theory
  Comput. Syst. 51(3) 372-400 (2012)
• Steven M. Kautz, James I. Lathrop Self-assembly
  of the Discrete Sierpinski Carpet and Related
  Fractals. DNA 2009 78-87

5
Error correction and fault-tolerance

• David Doty, Matthew J. Patitz, Dustin Reishus,
  Robert T. Schweller, Scott M. Summers Strong
  Fault-Tolerance for Self-Assembly with Fuzzy
  Temperature. FOCS 2010 417-426
• David Soloveichik, Matthew Cook, Erik Winfree
  Combining self-healing and proofreading in
  self-assembly. Natural Computing 7(2) 203-218
  (2008)
• Ho-Lin Chen, Ashish Goel, Chris Luhrs Dimension
  augmentation and combinatorial criteria for
  efficient error-resistant DNA self-assembly. SODA
  2008 409-418
• Urmi Majumder, Thomas H. LaBean, John H. Reif
  Activatable Tiles Compact, Robust Programmable
  Assembly and Other Applications. DNA 2007 15-25
• Erik Winfree Self-healing Tile Sets.
  Nanotechnology Science and Computation 2006
  55-78
• Sudheer Sahu, John H. Reif Capabilities and
  Limits of Compact Error Resilience Methods for
  Algorithmic Self-assembly in Two and Three
  Dimensions. DNA 2006 223-238
• John H. Reif, Sudheer Sahu, Peng Yin Compact
  Error-Resilient Computational DNA Tilings.
  Nanotechnology Science and Computation 2006
  79-103
• Ho-Lin Chen, Ashish Goel Error Free
  Self-assembly Using Error Prone Tiles. DNA 2004
  62-75
• Ho-Lin Chen, Qi Cheng, Ashish Goel, Ming-Deh A.
  Huang, Pablo Moisset de Espanés Invadable
  self-assembly combining robustness with
  efficiency. SODA 2004 890-899
• Erik Winfree, Renat Bekbolatov Proofreading Tile
  Sets Error Correction for Algorithmic
  Self-Assembly. DNA 2003 126-144

6
Randomized self-assembly

• Harish Chandran, Nikhil Gopalkrishnan, John H.
  Reif Tile Complexity of Linear Assemblies. SIAM
  J. Comput. 41(4) 1051-1073 (2012)
• David Doty Randomized Self-Assembly for Exact
  Shapes. SIAM J. Comput. 39(8) 3521-3552 (2010)
• Ming-Yang Kao, Robert T. Schweller Randomized
  Self-assembly for Approximate Shapes. ICALP (1)
  2008 370-384

7
Running-time in self-assembly

• Ho-Lin Chen, David Doty Parallelism and time in
  hierarchical self-assembly. SODA 2012 1163-1182
• Leonard M. Adleman, Qi Cheng, Ashish Goel,
  Ming-Deh A. Huang Running time and program size
  for self-assembled squares. STOC 2001 740-748

8
Intrinsic universality

• Pierre-Etienne Meunier, Matthew J. Patitz, Scott
  M. Summers, Guillaume Theyssier, Andrew Winslow,
  Damien Woods Intrinsic universality in tile
  self-assembly requires cooperation. SODA 2014 To
  appear
• Damien Woods Intrinsic universality and the
  computational power of self-assembly. MCU 2013
  16-22
• Erik D. Demaine, Matthew J. Patitz, Trent A.
  Rogers, Robert T. Schweller, Scott M. Summers,
  Damien Woods The Two-Handed Tile Assembly Model
  Is Not Intrinsically Universal. ICALP (1) 2013
  400-412
• David Doty, Jack H. Lutz, Matthew J. Patitz,
  Robert T. Schweller, Scott M. Summers, Damien
  Woods The Tile Assembly Model is Intrinsically
  Universal. FOCS 2012 302-310
• David Doty, Jack H. Lutz, Matthew J. Patitz,
  Scott M. Summers, Damien Woods Intrinsic
  Universality in Self-Assembly. STACS 2010
  275-286