Temperature 1 self-assembly: Deterministic assembly in 3D and probabilistic assembly in 2D

Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

Volumn , Issue , 2011, Pages 570-589

  Cook, Matthew ^a   Fu, Yunhui ^b   Schweiler, Robert ^b  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b UNIVERSITY OF TEXAS PAN AMERICAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSEMBLY; MACHINERY; SELF ASSEMBLY; TURING MACHINES;

ASSEMBLY SYSTEMS; HIGH PROBABILITY; LOGARITHMIC SCALE; MACHINE SIMULATION; MOLECULAR COMPUTING; PROBABILITY OF ERRORS; TEMPERATURE SYSTEM; THRESHOLD-VALUE;

THERMAL LOGGING;

EID: 79955736737     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1137/1.9781611973082.45     Document Type: Conference Paper

References (36)

1. Zachary Abel, Nadia Benbernou, Mirela Damian, Erik D. Demaine, Martin L. Demaine, Robin Flatland, Scott Kominers, and Robert Schweller. Shape replication through self-assembly and RNase enzymes. In Proceedings of the 21st Annual ACM- S1AM Symposium on Discrete Algorithms (SODA 2010), pages 1045-1064, Austin, Texas, January 17-19 2010.
2. Leonard Adleman, Q. Cheng, A. Goel, and M. Huang. Running time and program size for self-assembled squares. In Proceedings of the 33nd Annual ACM Symposium on Theory of Computing, pages 740-748, 2001. (Pubitemid 32865792)
3. Gagan Aggarwal, Qi Cheng, Micheal H. Gold-wasser, Ming-Yang Kao, Pablo Moisset de Espanes, and Robert T. Schweller. Complexities for generalized models of self-assembly. SIAM Journal on Computing, 34:1493-1515, 2005. (Pubitemid 43003153)
4. Ho-Lin Chen Ashish, Ho lin Chen, and Ashish Goel. Error free self-assembly using error prone tiles. In In DNA Based Computers 10, pages 274-283, 2004.
5. Robert D. Barish, Rebecca Schulman, Paul W. Rothemund, and Erik Winfree. An information- bearing seed for nucleating algorithmic self-assembly. Proceedings of the National Academy of Sciences, 106(15):6054-6059, March 2009.
6. Yuriy Brun. Solving np-complete problems in the tile assembly model. Theor. Comput. Sci, 395(1):31-46, 2008. (Pubitemid 351434509)
7. Harish Chandran, Nikhil Gopalkrishnan, and John Reif. The tile complexity of linear assemblies. In ICALP'09: Proceedings of the 36th International Colloquium on Automata, Languages and Programming, pages 235-253, Berlin, Heidelberg, 2009. Springer-Verlag.
8. Ho-Lin Chen, Ashish Goel, and Chris Luhrs. Dimension augmentation and combinatorial criteria for efficient error-resistant dna self-assembly. In SODA'08: Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms, pages 409-418, Philadelphia, PA, USA, 2008. Society for Industrial and Applied Mathematics.
9. Ho-Lin Chen, Rebecca Schulman, Ashish Goel, and Erik Winfree. Reducing facet nucleation during algorithmic self-assembly. Nano Letters, 7(9):2913-2919, September 2007. (Pubitemid 47522459)
10. E. Demaine, M. Demaine, S. Fekete, M. Ishaque, E. Rafalin, R. Schweller, and D. Souvaine. Staged self-assembly: Nanomanufacture of arbitrary shapes with O(l) glues. In Proceedings of the 13th International Meeting on DNA Computing, 2007.
11. DNA and Natural Algorithms Group. Xgrow simulator. Homepage: http://www.dna.caltech.edu/Xgrow, 2009.
12. D. Doty, M. Patiz, and S. Summers. Limitations of self-assembly at temperature I. In Proceedings of the 15th D1MACS Workshop on DNA Based Computers, 2008.
13. David Doty. Randomized self-assembly for exact shapes. In FOCS'09: Proceedings of the 2009 50th Annual IEEE Symposium on Foundations of Computer Science, pages 85-94, Washington, DC, USA, 2009. IEEE Computer Society.
14. Tsu-Ju Fu and Nadrian C. Seeman. DNA double- crossover molecules. Biochemistry, 32:3211-3220, 1993. (Pubitemid 23126886)
15. Yunhui Fu. Self-assembly simulation system. Homepage: http://zope.cs.panam.edu/selfassembly/projects/sss-project/2009.
16. Kei Goto, Yoko Hinob, Takayuki Kawashima, Masahiro Kaminagab, Emiko Yanob, Gaku Yamamotob, Nozomi Takagic, and Shigeru Nagasec. Synthesis and crystal structure of a stable S- nitrosothiol bearing a novel steric protection group and of the corresponding S-nitrothiol. Tetrahedron Utters, 41(44): 8479-8483, 2000.
17. Wilfried Heller and Thomas L. Pugh. "Steric protection" of hydrophobic colloidal particles by adsorption of flexible macromolecules. Journal of Chemical Physics, 22(10): 1778, 1954.
18. Wilfried Heller and Thomas L. Pugh. "Steric" stabilization of colloidal solutions by adsorption of flexible macromolecules. Journal of Polymer Science, 47(149):203-217, 1960.
19. Ming-Yang Kao and Robert Schweller. Randomized self-assembly for approximate shapes. In ICALP'08: Proceedings of the 35th international colloquium on Automata, Languages and Programming, Part I, pages 370-384, Berlin, Heidelberg, 2008. Springer-Verlag.
20. T. H. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, H. J. Reif, and N. C. Seeman. The construction, analysis, ligation and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc., 122:1848- 1860, 2000. (Pubitemid 30143885)
21. M. Li and P. Vitanyi. An Introduction to Komogorov Complexity and Its Applications (Second Edition). Springer Verlag, New York, 1997.
22. Furong Liu, Ruojie Sha, and Nadrian C. Seeman. Modifying the surface features of two-dimensional DNA crystals. Journal of the American Chemical Society, 121 (5):917-922, 1999.
23. U. Majumder, T. H. Labean, and J. H. Reif. Activatable tiles: Compact, robust programmable assembly and other applications. In Proceedings of the 15th DIMACS Workshop on DNA Based Computers, pages 15-25, 2008.
24. Chengde Mao, Thomas H. LaBean, John H. Reif, and Nadrian C. Seeman. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature, 407(6803):493-6, 2000.
25. Chengde Mao, Weiqiong Sun, and Nadrian C. Seeman. Designed two-dimensional DNA holli- day junction arrays visualized by atomic force microscopy. Journal of the American Chemical Soci-ety, 121 (23):5437-5443, 1999.
26. Ján Mañuch, Ladislav Stacho, and Christine Stoll. Two lower bounds for self-assemblies at temperature I. In SAC'09: Proceedings of the 2009 ACM symposium on Applied Computing, pages 808-809, New York, NY, USA, 2009. ACM.
27. Matthew J. Patitz. ISU TAS. Homepage: http://www.cs.iastate.edu/~lnsa/ software.html, 2008.
28. Paul Rothemund and Erik Winfree. The program- size complexity of self-assembled squares. In Proceedings of the 32nd Annual ACM Symposium on Theory of Computing, pages 459-468, 2000.
29. Paul W.K. Rothemund, Nick Papadakis, and Erik Winfree. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biology, 2(12):2041-2053, 2004.
30. Rebecca Schulman and Erik Winfree. Self-replication and evolution of dna crystals. In In The 13th European Conference on Artificial Life (ECAL, pages 734-743. Springer-Verlag, 2005.
31. Michael Sipser. Introduction to the Theory of Computation, Second Edition. Course Technology, 2 edition, February 2005.
32. David Soloveichik and Erik Winfree. Complexity of self-assembled shapes. In Tenth International Meeting on DNA Computing, pages 344-354, 2005. (Pubitemid 41231409)
33. Leroy G. Wade. Organic Chemistry. Prentice Hall, 2nd edition, 1991.
34. Erik Winfree. Algorithmic Self-Assembly of DNA. PhD thesis, California Institute of Technology, Pasadena, 1998.
35. Erik Winfree and Renat Bekbolatov. Proofreading tile sets: Error correction for algorithmic self- assembly. In DNA Computers 9 LNCS, pages 126-144, 2004.
36. Erik Winfree, Xiaoping Yang, and Nadrian C. Seeman. Design and self-assembly of two-dimensional DNA crystals. In Proceedings of the 2nd International Meeting on DNA Based Computers, 1996.