A self-assembly model of time-dependent glue strength

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3892 LNCS, Issue , 2006, Pages 290-304

  Sahu, Sudheer ^a   Yin, Peng ^a   Reif, John H ^a  

^a Duke University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL COMPLEXITY; COMPUTER SCIENCE; MATHEMATICAL MODELS; SELF ASSEMBLY; STRENGTH OF MATERIALS; TILE;

JUXTAPOSED TILES; NEIGHBORING POSITIONS; SELF-REPLICATION; THIN RECTANGLE;

GLUES;

EID: 33745759002     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11753681_23     Document Type: Conference Paper

References (43)

1. http://mrsec.wisc.edu/edetc/selfassembly/.
2. L. Adleman. Towards a mathematical theory of self-assembly. Technical Report 00-722, University of Southern California, 2000.
3. L. Adleman, Q. Cheng, A. Goel, and M.D. Huang. Running time and program size for self-assembled squares. In Proceedings of the thirty-third annual ACM symposium on Theory of computing, pages 740-748. ACM Press, 2001.
4. L. Adleman, Q. Cheng, A. Goel, M.D. Huang, D. Kempe, P.M. de Espans, and P.W.K. Rothemund. Combinatorial optimization problems in self-assembly. In Proceedings of the thirty-fourth annual ACM symposium on Theory of computing, pages 23-32. ACM Press, 2002.
5. L. Adleman, J. Kari, L. Kari, and D. Reishus. On the decidability of self-assembly of infinite ribbons. In Proceedings of the 43rd Symposium on Foundations of Computer Science, pages 530-537, 2002.
6. G. Aggarwal, M.H. Goldwasser, M.Y. Kao, and R.T. Schweller. Complexities for generalized models of self-assembly. In Proceedings of 15th annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 880-889. ACM Press, 2004.
7. N. Bowden, A. Terfort, J. Carbeck, and G.M. Whitesides. Self-assembly of mesoscale objects into ordered two-dimensional arrays. Science, 276(11):233-235, 1997.
8. R.F. Bruinsma, W.M. Gelbart, D. Reguera, J. Rudnick, and R. Zandi. Viral self-assembly as a thermodynamic process. Phys. Rev. Lett., 90(24):248101, 2003 June 20.
9. N. Chelyapov, Y. Brun, M. Gopalkrishnan, D. Reishus, B. Shaw, and L. Adleman. DNA triangles and self-assembled hexagonal tilings. J. Am. Chem. Soc., 126:13924-13925, 2004.
10. H.L. Chen, Q. Cheng, A. Goel, M.D. Huang, and P.M. de Espanes. Invadable self-assembly: Combining robustness with efficiency. In Proceedings of the 15th annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 890-899, 2004.
11. Q. Cheng and P.M. de Espanes. Resolving two open problems in the self-assembly of squares. Technical Report 03-793, University of Southern California, 2003.
12. Q. Cheng, A. Goel, and P. Moisset. Optimal self-assembly of counters at temperature two. In Proceedings of the first conference on Foundations of nanoscience: self-assembled architectures and devices, 2004.
13. M. Cook, P.W.K. Rothemund, and E. Winfree. Self-assembled circuit patterns. In DNA Based Computers 9, volume 2943 of LNCS, pages 91-107, 2004.
14. K. Fujibayashi and S. Murata. A method for error suppression for self-assembling DNA tiles. In DNA Based Computing 10, pages 284-293, 2004.
15. B.D. Hughes. Random Walks and Random Environments, Vol. I: Random Walks. New York: Oxford University Press, 1995.
16. M. Kao and R. Schweller. Reduce complexity for tile self-assembly through temperature programming. In Proceedings of 17th annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (to appear). ACM Press, 2006.
17. E. Klavins. Directed self-assembly using graph grammars. In Foundations of Nanoscience: Self Assembled Architectures and Devices, Snowbird, UT, 2004.
18. E. Klavins, R. Christ, and D. Lipsky. Graph grammars for self-assembling robotic systems. In Proceedings of the International Conference on Robotics and Automation, 2004.
19. T.H. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, J.H. 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.
20. M.G. Lagoudakis and T.H. LaBean. 2-D DNA self-assembly for satisfiability. In DNA Based Computers V, volume 54 of DIMACS, pages 141-154. American Mathematical Society, 2000.
21. D. Liu, M. Wang, Z. Deng, R. Walulu, and C. Mao. Tensegrity: Construction of rigid DNA triangles with flexible four-arm dna junctions. J. Am. Chem. Soc., 126:2324-2325, 2004.
22. C. Mao, W. Sun, and N.C. Seeman. Designed two-dimensional DNA holliday junction arrays visualized by atomic force microscopy. J. Am. Chem. Soc., 121:5437-5443, 1999.
23. J.H. Reif, S. Sahu, and P. Yin. Compact error-resilient computational DNA tiling assemblies. In Proc. 10th International Meeting on DNA Computing, pages 248-260, 2004.
24. J.H. Reif, S. Sahu, and P. Yin. Complexity of graph self-assembly in accretive systems and self-destructible systems. In Proc. 11th International Meeting on DNA Computing, pages 101-112, 2005.
25. R.M. Robinson. Undecidability and non periodicity of tilings of the plane. Inventiones Math, 12:177-209, 1971.
26. P.W.K. Rothemund. Using lateral capillary forces to compute by self-assembly. Proc. Natl. Acad. Sci. USA, 97(3):984-989, 2000.
27. P.W.K. Rothemund. Theory and Experiments in Algorithmic Self-Assembly. PhD thesis, University of Southern California, 2001.
28. P.W.K. Rothemund and E. Winfree. The program-size complexity of self-assembled squares (extended abstract). In Proceedings of the thirty-second annual ACM symposium on Theory of computing, pages 459-468. ACM Press, 2000.
29. P. Sa-Ardyen, N. Jonoska, and N.C. Seeman. Self-assembling DNA graphs. Lecture Notes in Computer Science, 2568:1-9, 2003.
30. S. Sahu, P. Yin, and J.H. Reif. A self-assembly model of DNA tiles with time-dependent glue strength. Technical Report CS-2005-04, Duke University, 2005.
31. R. Schulman, S. Lee, N. Papadakis, and E. Winfree. One dimensional boundaries for DNA tile self-assembly. In DNA Based Computers 9, volume 2943 of LNCS, pages 108-125, 2004.
32. R. Schulman and E. Winfree. Programmable control of nucleation for algorithmic self-assembly. In DNA Based Computers 10, LNCS, 2005.
33. R. Schulman and E. Winfree. Self-replication and evolution of DNA crystals. In The 13th European Conference on Artificial Life (ECAL), 2005.
34. D. Soloveichik and E. Winfree. Complexity of compact proofreading for self-assembled patterns. In Proc. 11th International Meeting on DNA Computing, pages 125-135, 2005.
35. D. Soloveichik and E. Winfree. Complexity of self-assembled shapes. In DNA Based Computers 10, LNCS, 2005.
36. H. Wang. Proving theorems by pattern recognition ii. Bell Systems Technical Journal, 40: 1-41, 1961.
37. E. Winfree. Simulation of computing by self-assembly. Technical Report 1998.22, Caltech, 1998.
38. E. Winfree. Self-healing tile sets (draft). 2005.
39. E. Winfree and R. Bekbolatov. Proofreading tile sets: Error correction for algorithmic self-assembly. In DNA Based Computers 9, volume 2943 of LNCS, pages 126-144, 2004.
40. E. Winfree, F. Liu, L.A. Wenzler, and N.C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394(6693):539-544, 1998.
41. E. Winfree, X. Yang, and N.C. Seeman. Universal computation via self-assembly of DNA: Some theory and experiments. In L.F. Landweber and E.B. Baum, editors, DNA Based Computers 11, volume 44 of DIMACS, pages 191-213. American Mathematical Society, 1999.
42. H. Yan, T.H. LaBean, L. Feng, and J.H. Reif. Directed nucleation assembly of DNA tile complexes for barcode patterned DNA lattices. Proc. Natl. Acad. Sci. USA, 100(14): 8103-8108, 2003.
43. H. Yan, S.H. Park, G. Finkelstein, J.H. Reif, and T.H. LaBean. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science, 301(5641):1882-1884, 2003.