Skip to main content
Erschienen in: Natural Computing 2/2017

09.03.2017

Reflections on tiles (in self-assembly)

verfasst von: Jacob Hendricks, Matthew J. Patitz, Trent A. Rogers

Erschienen in: Natural Computing | Ausgabe 2/2017

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

We define the Reflexive Tile Assembly Model (RTAM), which is obtained from the abstract Tile Assembly Model (aTAM) by allowing tiles to reflect across their horizontal and/or vertical axes. We show that the class of directed temperature-1 RTAM systems is not computationally universal, which is conjectured but unproven for the aTAM, and like the aTAM, the RTAM is computationally universal at temperature 2. We then show that at temperature 1, when starting from a single tile seed, the RTAM is capable of assembling \(n \times n\) squares for n odd using only n tile types, but incapable of assembling \(n \times n\) squares for n even. Moreover, we show that n is a lower bound on the number of tile types needed to assemble \(n \times n\) squares for n odd in the temperature-1 RTAM. The conjectured lower bound for temperature-1 aTAM systems is \(2n-1\). Finally, we give preliminary results toward the classification of which finite connected shapes in \(\mathbb {Z}^2\) can be assembled (strictly or weakly) by a singly seeded (i.e. seed of size 1) RTAM system, including a complete classification of which finite connected shapes can be strictly assembled by mismatch-free singly seeded RTAM systems.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Fußnoten
1
It is interesting to note that there are interesting temperature-2 RTAM systems that assemble a single assembly even when individual tile orientations are taken into account. For example, rectilinear tile assembly systems in the RTAM at temperature-2 can produce a single terminal assembly (even when taking tile orientations into account) when the seed assembly of the system is L-shaped. Note that the terminal assembly cannot have width or height exceeding that of the seed. See Kari et al. (2015) for interesting examples of such rectilinear tile assembly systems with L-shaped seeds.
 
2
Essentially, a compact zig-zag system is one in which assembly proceeds along a single possible assembly sequence which grows one row completely from left-to-right, then immediately above that grows the next complete row right-to-left, and so on. Also, each row may grow to a length of one tile longer than the row below it.
 
Literatur
Zurück zum Zitat Barish RD, Schulman R, Rothemund PWK, Winfree E (2009) An information-bearing seed for nucleating algorithmic self-assembly. Proc Natl Acad Sci 106(15):6054–6059CrossRef Barish RD, Schulman R, Rothemund PWK, Winfree E (2009) An information-bearing seed for nucleating algorithmic self-assembly. Proc Natl Acad Sci 106(15):6054–6059CrossRef
Zurück zum Zitat Cook M, Fu Y, Schweller RT (2011) Temperature 1 self-assembly: deterministic assembly in 3D and probabilistic assembly in 2D. In: SODA 2011: proceedings of the 22nd annual ACM-SIAM symposium on discrete algorithms. SIAM Cook M, Fu Y, Schweller RT (2011) Temperature 1 self-assembly: deterministic assembly in 3D and probabilistic assembly in 2D. In: SODA 2011: proceedings of the 22nd annual ACM-SIAM symposium on discrete algorithms. SIAM
Zurück zum Zitat Santini CC, Bath J, Tyrrell AM, Turberfield AJ (2013) A clocked finite state machine built from DNA. Chem Commun 49:237–239CrossRef Santini CC, Bath J, Tyrrell AM, Turberfield AJ (2013) A clocked finite state machine built from DNA. Chem Commun 49:237–239CrossRef
Zurück zum Zitat Demaine ED, Demaine ML, Fekete SP, Patitz MJ, Schweller RT, Winslow A, Woods D (2014) One tile to rule them all: simulating any tile assembly system with a single universal tile. In: Esparza J, Fraigniaud P, Husfeldt T, Koutsoupias E (eds) Proceedings of the 41st international colloquium on automata., languages, and programming (ICALP 2014), IT University of Copenhagen, July 8–11, 2014, vol 8572 of LNCS, Springer, Berlin, pp 368–379 Demaine ED, Demaine ML, Fekete SP, Patitz MJ, Schweller RT, Winslow A, Woods D (2014) One tile to rule them all: simulating any tile assembly system with a single universal tile. In: Esparza J, Fraigniaud P, Husfeldt T, Koutsoupias E (eds) Proceedings of the 41st international colloquium on automata., languages, and programming (ICALP 2014), IT University of Copenhagen, July 8–11, 2014, vol 8572 of LNCS, Springer, Berlin, pp 368–379
Zurück zum Zitat Doty D (2012) Theory of algorithmic self-assembly. Commun ACM 55(12):78–88CrossRef Doty D (2012) Theory of algorithmic self-assembly. Commun ACM 55(12):78–88CrossRef
Zurück zum Zitat Fekete SP, Hendricks J, Patitz MJ, Rogers TA, Schweller RT (2015) Universal computation with arbitrary polyomino tiles in non-cooperative self-assembly. In: Proceedings of the twenty-sixth annual ACM-SIAM symposium on discrete algorithms (SODA 2015), San Diego, Jan 4–6, pp 148–167 Fekete SP, Hendricks J, Patitz MJ, Rogers TA, Schweller RT (2015) Universal computation with arbitrary polyomino tiles in non-cooperative self-assembly. In: Proceedings of the twenty-sixth annual ACM-SIAM symposium on discrete algorithms (SODA 2015), San Diego, Jan 4–6, pp 148–167
Zurück zum Zitat Fu B, Patitz MJ, Schweller RT, Sheline R (2012) Self-assembly with geometric tiles. In: Proceedings of the 39th international colloquium on automata, languages and programming, ICALP, pp 714–725 Fu B, Patitz MJ, Schweller RT, Sheline R (2012) Self-assembly with geometric tiles. In: Proceedings of the 39th international colloquium on automata, languages and programming, ICALP, pp 714–725
Zurück zum Zitat Han D, Pal S, Yang Y, Jiang S, Nangreave J, Liu Y, Yan H (2013) DNA gridiron nanostructures based on four-arm junctions. Science 339(6126):1412–1415CrossRef Han D, Pal S, Yang Y, Jiang S, Nangreave J, Liu Y, Yan H (2013) DNA gridiron nanostructures based on four-arm junctions. Science 339(6126):1412–1415CrossRef
Zurück zum Zitat Kari L, Kopecki S, Meunier PÉ, Patitz MJ, Seki S (2015) Binary pattern tile set synthesis is NP-hard. In: Automata, languages, and programming—42nd international colloquium, ICALP 2015, Kyoto, July 6–10, 2015, Proceedings, Part I, pp 1022–1034 Kari L, Kopecki S, Meunier PÉ, Patitz MJ, Seki S (2015) Binary pattern tile set synthesis is NP-hard. In: Automata, languages, and programming—42nd international colloquium, ICALP 2015, Kyoto, July 6–10, 2015, Proceedings, Part I, pp 1022–1034
Zurück zum Zitat Ke Y, Ong LL, Shih WM, Yin P (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338(6111):1177–1183CrossRef Ke Y, Ong LL, Shih WM, Yin P (2012) Three-dimensional structures self-assembled from DNA bricks. Science 338(6111):1177–1183CrossRef
Zurück zum Zitat Kim J-W, Kim J-H, Deaton R (2011) DNA-linked nanoparticle building blocks for programmable matter. Angew Chem Int Edit 50(39):9185–9190CrossRef Kim J-W, Kim J-H, Deaton R (2011) DNA-linked nanoparticle building blocks for programmable matter. Angew Chem Int Edit 50(39):9185–9190CrossRef
Zurück zum Zitat Mao C, LaBean TH, Relf JH, Seeman NC (2000) Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407(6803):493–496CrossRef Mao C, LaBean TH, Relf JH, Seeman NC (2000) Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407(6803):493–496CrossRef
Zurück zum Zitat Patitz MJ, Schweller RT, Summers SM (2011) Exact shapes and turing universality at temperature 1 with a single negative glue. In: Proceedings of the 17th international conference on DNA computing and molecular programming, DNA’11. Springer, Berlin, pp 175–189 Patitz MJ, Schweller RT, Summers SM (2011) Exact shapes and turing universality at temperature 1 with a single negative glue. In: Proceedings of the 17th international conference on DNA computing and molecular programming, DNA’11. Springer, Berlin, pp 175–189
Zurück zum Zitat Pinheiro AV, Han D, Shih WM, Yan H (2011) Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol 6(12):763–772CrossRef Pinheiro AV, Han D, Shih WM, Yan H (2011) Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol 6(12):763–772CrossRef
Zurück zum Zitat Rothemund PWK (2001) Theory and experiments in algorithmic self-assembly. PhD thesis, University of Southern California Rothemund PWK (2001) Theory and experiments in algorithmic self-assembly. PhD thesis, University of Southern California
Zurück zum Zitat Rothemund PWK, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol 2(12):e424CrossRef Rothemund PWK, Papadakis N, Winfree E (2004) Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol 2(12):e424CrossRef
Zurück zum Zitat Rothemund PWK, Winfree E (2000) The program-size complexity of self-assembled squares (extended abstract). In: STOC ’00: Proceedings of the thirty-second annual ACM symposium on theory of computing. ACM, Portland, pp 459–468 Rothemund PWK, Winfree E (2000) The program-size complexity of self-assembled squares (extended abstract). In: STOC ’00: Proceedings of the thirty-second annual ACM symposium on theory of computing. ACM, Portland, pp 459–468
Zurück zum Zitat Schulman R, Winfree E (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc Nat Acad Sci 104(39):15236–15241CrossRef Schulman R, Winfree E (2007) Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc Nat Acad Sci 104(39):15236–15241CrossRef
Zurück zum Zitat Winfree E (1998) Algorithmic self-assembly of DNA. PhD thesis, California Institute of Technology Winfree E (1998) Algorithmic self-assembly of DNA. PhD thesis, California Institute of Technology
Zurück zum Zitat Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394(6693):539–544CrossRef Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394(6693):539–544CrossRef
Metadaten
Titel
Reflections on tiles (in self-assembly)
verfasst von
Jacob Hendricks
Matthew J. Patitz
Trent A. Rogers
Publikationsdatum
09.03.2017
Verlag
Springer Netherlands
Erschienen in
Natural Computing / Ausgabe 2/2017
Print ISSN: 1567-7818
Elektronische ISSN: 1572-9796
DOI
https://doi.org/10.1007/s11047-017-9617-2

Weitere Artikel der Ausgabe 2/2017

Natural Computing 2/2017 Zur Ausgabe