Expectation and variance of self-assembled graph structures

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

Volumn 3892 LNCS, Issue , 2006, Pages 144-157

  Jonoska, Nataša ^a   McColm, Gregory L ^a   Staninska, Ana ^a  

^a UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

JUNCTION MOLECULES; PROBABILISTIC METHODS; SELF ASSEMBLED CYCLES; STATIC CONDITIONS;

GRAPH THEORY; LARGE SCALE SYSTEMS; MATHEMATICAL MODELS; MOLECULAR BIOLOGY; NANOTECHNOLOGY; PROBABILITY; STATISTICAL METHODS;

SELF ASSEMBLY;

EID: 33745760705     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11753681_11     Document Type: Conference Paper

References (22)

1. L.M. Adleman, Q. Cheng, A. Goel, M-D. Huang, D. Kempe, P. Moisset de Espanes, P.W.K. Rothemund. Combinatorial optimization problems in self-assembly, STOC'02 Proceedings, Montreal Quebec, Canada, 2002.
2. L.M. Adleamn, J. Kari, L. Kari, D. Reishus. On the decidability of self-assembly of infinite ribons Proceedings of FOCS 2002, IEEE Symposium on Foundations of Computer Science, Washington (2002) 530-537.
3. J.H. Chen, N.C. Seeman. Synthesis from DNA of a molecule with the connectivity of a cube, Nature 350 (1991) 631-633.
4. A. Dugaiczyk, H.W. Boyer, H.M. Goodman. Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures. Journal of Molecular Biology 96(1) (1975) 171-178.
5. S. Janson, T. Luczak, A. Rucinski. Random Graphs, New York : John Wiley, 2002.
6. N. Jonoska, S. Liao, N.C.Seeman, Transducers with Programmanle Input by DNA Self-Assembli, in: Aspects of Molecular Computing (N. Jonoska, Gh. Paun, G.Rozenberg eds.), Springer LNCS 2950 (2004) 219-240.
7. N. Jonoska, S. Karl, M. Saito. Three dimensional DNA structures in computing, BioSystems 52 (1999) 143-153.
8. N. Jonoska, P. Sa-Ardyen, N.C. Seeman. Computation by self-assembly of DNA graphs, Genetic Programming and Evolvable Machines 4 (2003) 123-137.
9. N. Jonoska, G.L. McColm. Self-assembly by DNA Junction Molecules: The Theoretical Model, Foundations of Nanoscience. J.Reif (edi) (2004).
10. M-Y. Kao, V. Ramachandran. DNA self-assembly for constructing 3D boxes. Algorithms and Computations, ISAC 2001 Preceedings, Springer LNCS 2223 (2001) 429-440.
11. C. Mao, W. Sun, N.C. Seeman. Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy, Journal of American Chemical Society 121(23) (1999) 5437-5443.
12. J. Qi, X. Li, X. Yang, N.C. Seeman. Ligation of Triangles Built from bulged 3-arm DNA Branched Junctions., Journal of American Chemical Society 120 (1996) 6121-6130.
13. S. M. Ross. A First Course in Probability, Prentice Hall, (2001).
14. th DNA Based Computers, Madison Wisconsin June 1-4 (2003).
15. P.W.K. Rothemund, E. Winfree. The Program-Size Complexity of Self-Assembled Squares, Proceedings of 33rd ACM meeting STOC 2001, Portland, Oregon, May 21-23 (2001) 459-468.
16. P. Sa-Ardyen, N. Jonoska, N.C. Seeman. Self-Assembly of graphs represented by DNA helix axis topology, Journal of American Chemical Society 126(21) (2004) 6648-6657.
17. Seeman, N.C., DNA junctions and lattices, Journal of theoretical biology 99 (1982) 237-247.
18. W.M. Shih, J.D. Quispe, G.F. Joyce., A 1.7-kilobase single stranded DNA folds into a nanoscale octahedron, Nature 427 (2004) 618-621.
19. J.H. Spencer. Ten lectures on the probabilistic method, SIAM, Philadelphia, PA (1987).
20. Y. Wang, J.E. Mueller, B. Kemper, N.C. Seeman. The assembly and characterization of 5 arm and 6 arm DNA junctions, Biochemistry 30 (1991) 5667-5674.
21. E. Winfree, F. Liu, L.A. Wenzler, N.C. Seeman. Design and self-assembly of two-dimentsional DNA crystals, Nature 394 (1998) 539-544.
22. Y. Zhang, N.C. Seeman. The construction of a DNA truncated octahedron, Journal of American Chemical Society 116(5) (1994) 1661-1669.