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New Generation Computing

, Volume 20, Issue 3, pp 217–236 | Cite as

The emerging discipline of biomolecular computation in the US

  • John H. Reif
Special Issue

Abstract

This paper provides a description of the recent evolution in the US of an emerging technology known asDNA Computation or more generally asBiomolecular Computation from its early stages to its development and extension into other areas such as nanotechnology, emerging as a viable sub-discipline of science and engineering.

Keywords

DNA Computing Molecular Biomolecular Nanostructure Biochemical 

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References

  1. 1).
    Adleman, L., “Molecular Computation of Solution to Combinatorial Problems,”Science, 266, pp. 1021–7pt24, 1994.CrossRefGoogle Scholar
  2. 2).
    Adleman, L.,On Constructing a Molecular Computer, Dept of CS, U.S.C., Available via anonymous ftp from ftp.usc.edu/pub/csinfo/papers/adleman/molecular_computer ps, (1995).Google Scholar
  3. 3).
    Adleman, L. M., Rothemund, P. W. K., Roweis, S. and Winfree, E., “On Applying Molecular Computation to The Data Encryption Standard,”2nd Annual DIMACS Meeting on DNA Based Computers, DIMACS Workshop, Princeton, June 10–12, 1996 (44 in DIMACS) (Landweber, L. F. and Baum, E. B., eds.), American Mathematical Society, pp. 31–44, 1998. Published as Adleman, L. M., Rothemund, P. W. K., Roweis, S. and Winfree, E., “On Applying Molecular Computation to the Data Encryption Standard.”Journal of Computational Biology, 6, 1, pp. 53–63, 1999.Google Scholar
  4. 4).
    Adleman, L., “Toward a Mathematical Theory of Self-assembly,”USC Tech Report, January 2000.Google Scholar
  5. 5).
    Adleman, L., Cheng, Q., Goel, A., Huang, M., Kempe, D., de Moisset, P. M. and Rothemund, P. W. K., “Combinatorial Optimization Problems in Self-Assembly,”Thirty-fourth Annual ACM Symposium on Theory of Computing, Montréal, Québec, Canada, May pp. 19–21, 2002.Google Scholar
  6. 6).
    Alivisatos, A. P., Johnsson, K. P., Peng, X., Wilson, T. E., Loweth, C. J., Bruchez, M. P., Jr. and Schultz, P. G., “Organization of ‘Nanocrystal Molecules’ Using DNA,”Nature, 382, pp. 609–611, August 1996.CrossRefGoogle Scholar
  7. 7).
    Baum, E. B., “How to Build an Associative Memory Vastly Larger than the Brain,”Science, 268, pp 583–585, April 28, 1995.CrossRefGoogle Scholar
  8. 8).
    Baum, E. B., “DNA Sequences Useful for Computation,”2nd Annual DIMACS Meeting on DNA Based Computers, Princeton University, June 1996.Google Scholar
  9. 9).
    Bear, G., “Blood Music,”Analog, June, 1983, also, appearing inNanodreams (Elliott, E., ed.), Baen Pub., 1995. Also, appearing as a full novel asBlood Music, Ace Pub., 1985. “Blood Music,”Analog, june, 1983.Google Scholar
  10. 10).
    Beaver, D., “Factoring: The DNA Solution,”Advances in Cryptology, in Proc. of Asia Crypt94, Lecure Notes in Computer Science, Springer Verlag, 1994.Google Scholar
  11. 11).
    Beaver, D., “Computing with DNA,”J. Comp. Biol., 2, pp. 1–7, 1995.CrossRefGoogle Scholar
  12. 12).
    Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z. and Shapiro, E., “Programmable and Autonomous Computing Machine Made of Biomolecules,”Nature, 414, pp. 430–434, 2001.CrossRefGoogle Scholar
  13. 13).
    Berger, R., “The Undecidability of the Domino Problem,”Memoirs of the American Mathematical Society, 66, 1966.Google Scholar
  14. 14).
    Boneh, D., Dunworth, C. and Lipton, R., “Breaking DES Using a Molecular Computer,”Princeton CS Tech-Report, CS-TR-489-95, 1995.Google Scholar
  15. 15).
    Boneh, D., Dunworth, C., Lipton, R. and Sgall, J., “On the Computational Power of DNA,”Discrete Applied Math, December, 1996.Google Scholar
  16. 16).
    Boneh, D. and Lipton, R., “Making, DNA Computers Error Resistant,”Princeton CS Tech-Report, CS-TR-491-95, also in 2nd Annual DIMACS Meeting on DNA Based Computers, Princeton University, June 1996.Google Scholar
  17. 17).
    Braich, R. S., Johnson, C., Rothemund, P. W. K., Hwang, D., Chelyapov, N. and Adleman, L. M., “Solution of a Satisfiability Problem on a Gel-Based DNA Computer,”in Proc. of the 6th International Conference on DNA Computation, Lecture Notes in Computer Science series, Springer-Verlag, 2000.Google Scholar
  18. 18).
    Braich, R. S. N., Chelyapov, N., Johnson, C., Rothemund, P. W. K. and Adleman, L., “Solution of a 20 Variable 3-SAT Problem on a Molecular Computer,”Science, to appear in 2002.Google Scholar
  19. 19).
    Cai, W., Condon, A., Corn, R. M., Fei, Z., Frutos, T., Glaser, E., Guo, Z., Lagally, M. G., Liu, Q., Smith, L. M. and Thiel, A., “The Power of Surfacebased Computation,”in Proc. of First International Conference on Computational Molecular Biology (RECOMB97), January, 1997.Google Scholar
  20. 20).
    Clelland, C. T., Risca, V. and Bancroft, C., “Hiding Messages in DNA Microdots,”Nature, 399, pp. 533–534, 1999.CrossRefGoogle Scholar
  21. 21).
    Cukras, A., Faulhammer, D., Lipton, R. and Landweber, L., “Chess Games: A Model for RNA-based Computation,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  22. 22).
    Chen, J., Reed, M. A., Rawlett, A. M. and Tour, J. M., “Observation of a Large On-off Ratio and Negative Differential Resistance in an Electronic Molecular Switch,”Science, 286, pp. 1550, 1999.CrossRefGoogle Scholar
  23. 23).
    Chen, K., Winfree, E., “Error Correction in DNA Computing: Misclassification and Strand Loss,”in Proc. of the Fifth Annual Meeting on DNA Based Computers, MIT, June 14–15, 1999.Google Scholar
  24. 24).
    Faulhammer, D., Cukras, A. R., Lipton, R. J. and Landweber, L. F., “Molecular Computation: RNA Solutions to Chess Problems,”in Proc. of Natl. Acad. Sci. USA., 97, pp. 1385–1389, 2000.CrossRefGoogle Scholar
  25. 25).
    Faulhammer, D., Lipton, R. J. and Landweber, L. F., “When the Knight Falls: on Constructing an RNA Computer,”in Proc. of DNA Based Computers V (Winfree, E. and Gifford, D. eds.), DIMACS Series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society,54, pp. 1–7, 2000.Google Scholar
  26. 26).
    Frutos, A. G., Thiel, A. J., Condon, A. E., Smith, L. M. and Corn, R. M., “DNA Computing at Surfaces: 4 Base Mismatch Word Design,”3rd DIMACS Meeting on DNA Based Computers, Univ. of Penns., June, 1997.Google Scholar
  27. 27).
    Fu, B. and Beigel, R., “Length Bounded Molecular Computing,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  28. 28).
    Fu, T.-J. and Seeman, N. C., “DNA Double Crossover Structures,”Biochemistry, 32, pp. 3211–3220, 1993.CrossRefGoogle Scholar
  29. 29).
    Gehani, A., LaBean, T. H. and Reif, J. H., “DNA-based Cryptography, 5th DIMACS Workshop on DNA Based Computers,” MIT, June, 1999, to appear in “DNA Based Computers, V,”DIMACS Series in Discrete Mathematics and Theoretical Computer Science (Winfree, E., ed.), American Mathematical Society, 2000.CrossRefGoogle Scholar
  30. 30).
    Guarnieri, F. and Bancroft, C., “Use of a Horizontal Chain Reaction for DNA-Based Addition,”in Proc. of the 2nd Annual DIMACS Meeting on DNA Based Computers., June 10–12, 1996, American Mathematical Society, Providence, RI (in press), 1996.Google Scholar
  31. 31).
    Guarnieri, F., Fliss, M. and Bancroft, C., “Making DNA add,”Add. Science, 273, pp. 220–223, 1996.Google Scholar
  32. 32).
    Hagiya, M., Arita, M., Kiga, D., Sakamoto, K. and Yokoyama, S., “Towards Parallel Evaluation and Learning of Boolean μ-Formulas with Molecules,”3rd DIMACS Meeting on DNA Based, Computers, Univ. of Penns., June, 1997.Google Scholar
  33. 33).
    Hartemink, A. J. and Gifford, D. K., “Thermodynamic Simulation of Deoxyoligonucleotide Hybridize for DNA Computation,”3rd DIMACS Meeting on DNA Based Computers, Univ. of Penns., June, 1997.Google Scholar
  34. 34).
    Hartemink, A., Gifford, D. and Khodor, J., “Automated Constraint-based Nucleotide Sequence Selection for DNA Computation,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  35. 35).
    Head, T., “Formal Language Theory and DNA: an Analysis of the Generative Capacity of Specific Recombinant Behaviors,”Bull. Math. Biology, 49, pp. 737–759, 1987.MathSciNetCrossRefGoogle Scholar
  36. 36).
    Head, T., “Splicing Schemes and DNA,”in Proc. of Lindenmayer Systems: Impacts on Theoretical Computer Science, Computer Graphics, and Developmental Biology (Rozenberg, G. and Salomaa, A., eds.), pp. 371–383, 1992, Springer-Verlag, also appears in:Nanobiology, 1, pp. 335–342, 1992.Google Scholar
  37. 37).
    Head, T., “Splicing System and Molecular Processes,”ICEC'97 Special Session on DNA Based Computation, Indiana, April, 1997.Google Scholar
  38. 38).
    Ji, S., “The Cell as a DNA-based Molecular Computer,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  39. 39).
    Jonoska, N., Karl, S. and Saito, M., “Three Dimensional DNA Structures in Computing,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  40. 40).
    Jonoska, N. and Karl, S. A., “A Molecular Computation of the Road Coloring Problem,”2nd Annual DIMACS Meeting on DNA Based Computers, Princeton University, June, 1996.Google Scholar
  41. 41).
    Jonoska, N. and Karl, S. A., “Creating 3-dimensional Graph Structures with DNA,”3nd Annual DIMACS Meeting on DNA Based Computers, University of Pens., June, 1997.Google Scholar
  42. 42).
    Kari, L., “DNA Computers: Tomorrow's Reality”,Tutorial in the Bulletin of EATCS, 59, pp. 256–266, 1996.zbMATHGoogle Scholar
  43. 43).
    Kari, L. and Landweber, L. F.,Computing with DNA. Methods in Molecular Biology, 1999.Google Scholar
  44. 44).
    Kari, L. and L. Landweber., “Computational Power of Gene Rearrangement,”in Proc. of the Fifth International Meeting on DNA Based Computers, Massachusetts Institute of Technology, 14, 15 (Winfree, E. and Gifford, D., eds.), Boston, pp. 203–213, June, 1999.Google Scholar
  45. 45).
    Kari, L., Kari, J., Landweber, L. F., “Reversible Molecular Computation in Ciliates,”Jewels are Forever, 1999 (Karhumäki, J., Maurer, H., Paun, G., Rozenberg, G., eds.), “Jewels are Forever, Contributions to Theoretical Computer Science in honor of Arto Salomaa,” pp. 353–363, 1999, Springer Verlag.CrossRefGoogle Scholar
  46. 46).
    Kari, L., Paun, G., Rozenberg, G., Salomaa, A. and Yu, S.,DNA Computing, Sticker Systems, and Universality, 35, Acta Informatica, pp. 401–420, 1998.Google Scholar
  47. 47).
    Kazic, T., “After the Turing Machine: A Metamodel for Molecular Computing”,4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  48. 48).
    Knight, T. F. and Sussman, G. J.,Cellular Gate Technology, MIT Artificial Intelligence Labratory, July, 1997.Google Scholar
  49. 49).
    LaBean, T. H., Yan, H., Kopatsch, J., Liu, F., Winfree, E., Reif, J. H. and Seeman, N. C., “The Construction, Analysis, Ligation and Self-assembly of DNA Triple Crossover Complexes”,Journal of American Chemestry Society 122, pp. 1848–1860, 2000.CrossRefGoogle Scholar
  50. 50).
    LaBean, T. H., Winfree, E. and Reif, J. H., “Experimental Progress in Computation by Self-Assembly of DNA Tilings”,5th International Meeting on DNA Based Computers (DNA5), MIT, Cambridge, MA, June, 1999, DIMACS Series in Discrete Mathematics and Theoretical Computer Science (Winfree, E., ed.), to appear in American Mathematical Society, 2000.Google Scholar
  51. 51).
    LaBean, C. M., Reif, T. H. and Seeman, J. H., “Logical Computation Using Algorithmic Self-assembly of DNA Triple-crossover Molecules”,Nature, 407, pp. 493–495, 2000, Erratum, C.,Nature, 408, pp. 750–750, 2000.CrossRefGoogle Scholar
  52. 52).
    Lagoudakis, M. G. and LaBean, T. H., “2D DNA Self-assembly for Satisfiability”,5th International Meeting on DNA Based Computers (DNA5), MIT, Cambridge, MA, June, 1999,DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 44 (Winfree, E., ed.), American Mathematical Society, 1999.Google Scholar
  53. 53).
    Landweber, L. and Kari, L., “The Evolution of Cellular Computing: Nature's Solution to a Computational Problem”,Late Breaking Papers at the Genetic Programming 1998 Conference, in Proc. of the 3rd Annual Genetic Programming Conference, 22, July, 1998, Koza, J. R., San Francisco, CA: Morgan Kaufmann Publishers, pp. 700–708, 1998.Google Scholar
  54. 54).
    Landweber, L. and Kari, L., “Universal Molecular Computation in Ciliates”,in Proc. of the DIMACS Workshop on Evolution as Computation, 11, Princeton University, January, 1999, Winfree, E., Lipton, R. and Freeland, S.,Evolution As Computation, pp. 51–60, Springer-Verlag, New York, 1999.Google Scholar
  55. 55).
    Li, X. J., Yang, X. P., Qi, J. and Seeman, N. C., “Antiparallel DNA Double Crossover Molecules as Components for Nanoconstruction”,J. Am. Chem. Soc., 118, pp. 6131–6140, 1996.CrossRefGoogle Scholar
  56. 56).
    Lipton, R. J., “DNA Solution of Hard Computational Problems”,Science, 268, pp. 542–845, 1995.CrossRefGoogle Scholar
  57. 57).
    Lipton, R., “Speeding up Computations via Molecular Biology,”Princeton University Draft, 1994.Google Scholar
  58. 58).
    Liu, Q. H., Frutos, A. G., Wang, L. M., Thiel, T. J., Gillmor, S. D., Strother, C. T., Condon, A. E., Corn, R. M., Lagally, M. G. and Smith, L. M., “Progress toward Demonstration of a Surface based DNA Computation a One Word Approach to Solve a Model Satisfiability Problem”,Biosystems, 52, pp. 25–33, 1999.CrossRefGoogle Scholar
  59. 59).
    Liu, Q. H., Wang, L. M., Frutos, A. G., Condon, A. E., Corn, R. M. and Smith, L. M., “DNA Computing on Surfaces”,Nature, 403, pp. 175–179, 2000.CrossRefGoogle Scholar
  60. 60).
    Mao, W. S. and Seeman, N. C., “Designed Two-dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy”,J. Am. Chem. Soc., 121, pp. 5437–5443, 1999.CrossRefGoogle Scholar
  61. 61).
    Mao, W. S., Shen, Z. and Seeman, N. C., “A DNA Nanomechanical Device Based on the B-Z Transition”,Nature, 397, pp. 144–146, 1999.CrossRefGoogle Scholar
  62. 62).
    Mirkin, C. A., Letsinger, R. L., Mucic, R. C. and Storhoff, J. J., “A DNA-based Method for Rationally Assembling Nanoparticles into Macroscopic Materials”,Nature, 382, pp. 607–611, August, 1996.CrossRefGoogle Scholar
  63. 63).
    Mirkin, C. A., “Programming the Assembly of Two- and Three-dimensional Architectures with DNA and Nanoscale Inorganic Building Blocks”,Inorg. Chem. 39, pp. 2258–2272, 2000.CrossRefGoogle Scholar
  64. 64).
    Morimoto, N. and Suyama, M. A. A., “Solid Phase DNA Solution to the Hamiltonian Path Problem”,3rd DIMACS Meeting on DNA Based Computers, Univ. of Penns., June, 1997.Google Scholar
  65. 65).
    Ogihara, M. and Ray, A., “Breadth First Search 3SAT Algorithms for DNA Computer”,Technical Report TR-629, Department of Computer Science, University of Rochester, July, 1996.Google Scholar
  66. 66).
    Ogihara, M. and Ray, A., “Simulating Boolean Circuits on a DNA Computer”,1st Annual International Conference On Computational Molecular Biology (RE-COMB97), Santa Fe, New Mexico, January, 1997.Google Scholar
  67. 67).
    Orlian, M., Guarnieri, F. and Bancroft, C., “Parallel Primer Extension Horizontal Chain Reactions as a Paradigm of Parallel DNA-based Computation”,3rd DIMACS Meeting on DNA Based Computers, Univ. of Penns., June, 1997.Google Scholar
  68. 68).
    Paun, G., Rozenberg, G. and Salomaa, A., “DNA Computing—New Computing Paradigms”,Texts in Theoretical Computer Science-An EATCS Series, Springer Verlag, 1998.Google Scholar
  69. 69).
    Pirrung, M. C., Connors, R. V., Montague-Smith, M. P., Odenbaugh, A. L., Walcott, N. G. and Tollett, J. J., “The Arrayed Primer Extension Method for DNA Microchip Analysis: Molecular Computation of Satisfaction Problems”,J. Am. Chem. Soc., 122, pp. 1873, 2000.CrossRefGoogle Scholar
  70. 70).
    Prescott, D. M., Ehrenfeucht, A. and Rozenberg, G., “Molecular Operations for DNA Processing in Hypotrichous Ciliates”,European Journal of Protistology 37, pp. 241–260, 2001.CrossRefGoogle Scholar
  71. 71).
    Reif, J., “Parallel Molecular Computation: Models and Simulations”,Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA95), pp. 213–223, ACM, Santa Barbara, June, 1995,Algorithmica, special issue onComputational Biology, 25, 2, pp. 142–176, 1999.Google Scholar
  72. 72).
    Reif, J. H., “Local Parallel Biomolecular Computation”,3rd DIMACS Meeting on DNA Based Computers, Univ. of Penns., June, 1997, DIMACS Series in Discrete Mathematics and Theoretical Computer Science (Rubin, H. and Wood, D. H., eds.),American Mathematical Society, Providence, RI, 48, pp. 217–254, 1999.Google Scholar
  73. 73).
    Reif, J. H., “Paradigms for Biomolecular Computation”,First International Conference on Unconventional Models of Computation, Auckland, New Zealand, January, 1998,Unconventional Models of Computation (Calude, C. S., Casti, J. and Dinneen, M. J., eds.), Springer-Verlag, New York, pp. 72–93, January, 1998.Google Scholar
  74. 74).
    Reif, J. H., LaBean, T. H. and Seeman, N. C., “Challenges and Applications for Self-assembled DNA Nanostructures, Invited paper”,in Proc. of Sixth International Workshop on DNA-Based Computers, Leiden, The Netherlands, June, 2000,DIMACS Series in Discrete Mathematics and Theoretical Computer Science (Condon, A. and Rozenberg, G., eds.),Computer Science, 2054, Springer-Verlag, Berlin Heidelberg, pp. 173–198, 2001.Google Scholar
  75. 75).
    Reif, J. H. and LaBean, T. H., “Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector-Quantization”,Sixth International Meeting on DNA Based Computers (DNA6), DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Leiden, The Netherlands, June, 2000 (Condon, A., ed.) Computer Science, Springer-Verlag, 2001.Google Scholar
  76. 76).
    Reif, J. H., LaBean, T. H., Pirrung, M., Rana, V., Guo, B., Kingsford, K. and Wickham, G., “Experimental Construction of Very Large Scale DNA Databases with Associative Search Capability”,Seventh International Meeting on DNA Based Computers (DNA7), DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Tampa, FL, June 11–13, 2001.Google Scholar
  77. 77).
    Reif, J. H., “DNA Lattices: A Programmable Method for Molecular Scale Patterning and Computation, Special issue on Bio-Computation”,Computer and Scientific Engineering Journal of the Computer Society, 2002.Google Scholar
  78. 78).
    Rothermund, P. W. K. and Winfree, E., “The Program-size Complexity of Self-Assembled Squares”,Thirty–Second Symposium on Theory of Computing, May 21–23, 2000.Google Scholar
  79. 79).
    Rozenberg, G. and Salomaa, A., “DNA Computing: New Ideas and Paradigms”,LNCS 1644, Springer Verlag, pp. 106–118, 1999.CrossRefGoogle Scholar
  80. 80).
    Roweis, S. and Winfree, E., “On the Reduction of Errors in DNA Computation”,Journal of Computational Biology, 6, 1, pp. 65–75, 1999.CrossRefGoogle Scholar
  81. 81).
    Rozenberg, G., “Gene Assembly in Ciliates: Computing by Folding and Recombination,”A Half-Century of Automata Theory — Celebration and Inspiration (Salomaa, A., Wood, D. and Yu, S., eds.), World Scientific, New Jersey, pp. 93–130, 2001.CrossRefGoogle Scholar
  82. 82).
    Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K. and Adleman, L. M., “A Sticker Based Architecture for DNA Computation,”2nd Annual DIMACS Meeting on DNA Based Computers, Princeton University, June 10–12, 1996,44, DIMACS (Landweber, L. F. and Baum, E. B., eds.), American Mathematical Society, pp. 1–29, 1998, Published as Roweis, S., Winfree, E., Burgoyne, R., Chelyapov, N. V., Goodman, M. F., Rothemund, P. W. K. and Adleman, L. M., “A Sticker-Based Model for DNA Computation,”Journal of Computational Biology, 5, 4, pp. 615–629, 1998.CrossRefGoogle Scholar
  83. 83).
    Rubin, H., Klein, J. and Leete, T., “A Biomolecular Implementation of Logically Reversible Computation with Minimal Energy Dissipation,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  84. 84).
    Sakamoto, K., Kiga, D., Komiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., Sugiyama, H. and Hagiya, M., “State Transitions by Molecules,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  85. 85).
    Seeman, N., Liu, F., Mao, C., Yang, X., Wenzler, L. and Winfree, E., “DNA Nanotechnology: Control of 1-D and 2-D Arrays and the Construction of a Nanomechanical Device,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  86. 86).
    Seeman, N. C., Liu, F., Mao, C., Yang, X., Wenzler, L. A., Sha, R., Sun, W., Shen, Z., Li, X., Qi, J., Zhang, Y., Fu, T.-J., Chen, J. and Winfree, E., “Two Dimensions and Two States in DNA Nanotechnology,”Journal of Biomolecular Structure and Dynamics, Conversation 11, 2, pp. 253–262, May 2000.CrossRefGoogle Scholar
  87. 87).
    Seeman, N. C., Zhang, Y. and Chen, J., “DNA Nanoconstructions,”J. Vac. Sci. Technol., 12, 4, pp. 1895–1905, 1994.CrossRefGoogle Scholar
  88. 88).
    Turberfield, A. J., Yurke, B. and Mills, A. P. Jr., “DNA Hybridization Catalysts and Molecular Tweezers in DNA Based Computers V,”DIMACS Series in Discrete Mathematics and Theoretical Computer Science 54 ed. (Winfree, E. and Gifford, D. K., eds.), pp. 171, American Mathematical Society, Providence, RI, U.S.A., 2000.zbMATHGoogle Scholar
  89. 89).
    Wang, L., Liu, Q., Frutos, A., Gillmor, S., Thiel, A., Strother, T., Condon, A., Corn, R., Lagally, M. and Smith, L., “Surface-based DNA Computing Operations: DESTROY and READOUT,”Biosystems, 52, pp. 189–191, 1999.CrossRefGoogle Scholar
  90. 90).
    Winfree, E., “Complexity of Restricted and Unrestricted Models of Molecular Computation,”DNA Based Computers: in Proc. of a DIMACS Workshop, 27, in DIMACS (Lipton, R. J. and Baum, E. B., eds.), pp. 199–221, American Mathematical Society, 1996.Google Scholar
  91. 91).
    Winfree, E., “On the Computational Power of DNA Annealing and Ligation,”DNA based computers (Lipton, R. J. and Baum, E. B., eds.),Am. Math. Soc., 27, in DIMACS, Providence, RI, 1996.Google Scholar
  92. 92).
    Winfree, E., “Simulations of Computing by Self-assembly,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  93. 93).
    Winfree, E., “Whiplash PCR for O(1) Computing,”4th Int. Meeting on DNA-Based Computing, Baltimore, Penns., June, 1998.Google Scholar
  94. 94).
    Winfree, E., Liu, F., Wenzler, L. A. and Seeman, N. C., “Design and Self-assembly of Two Dimensional DNA Crystals,”Nature, 394, pp. 539–544, 1998.CrossRefGoogle Scholar
  95. 95).
    Winfree, E., Yang, X. and Seeman, N. C., “Universal Computation via Self-assembly of DNA: Some Theory and Experiments,”2nd Annual DIMACS Meeting on DNA Based Computers (Landweber, L. F. and Baum, E. B., eds.), June 10–12, 1996,44 in DIMACS, pp. 191–213, American Mathematical Society, 1998.Google Scholar
  96. 96).
    Winfree, E., Eng, T. and Rozenberg, G., “String Tile Models for DNA Computing by Self-assembly,”in Proc. of the Sixth Annual Meeting on DNA Based Computers, Leiden University, June 13–17, 2000, LNCS 2054, pp. 63–88, Springer Verlag, 2001.CrossRefGoogle Scholar
  97. 97).
    Winfree, E., “Algorithmic Self-assembly of DNA: Theoretical Motivations and 2D Assembly Experiments,”Journal of Biomolecular Structure and Dynamics, 11, 2, pp. 263–270, May 2000.MathSciNetCrossRefGoogle Scholar
  98. 98).
    Yan, H., Zhang, X., Shen, Z. and Seeman, N. C., “A Robust DNA Mechanical Device Controlled by Hybridization Topology,”Nature, 415, pp. 62–65, 2002.CrossRefGoogle Scholar
  99. 99).
    Yurke, B., Turberfield, A. J., Mills, A. P. Jr., Simmel, F. C. and Neumann, J. L., “A DNA-fuelled Molecular Machine Made of DNA,”Nature, 406, pp. 605–608, 2000.CrossRefGoogle Scholar
  100. 100).
    Yurke, B., Mills, A. P. and Turberfield, A. J., “A Molecular Machine Made of and Powdered By DNA,”Biophys. J. 78, pp. 2629, 2000.Google Scholar

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© Ohmsha, Ltd. and Springer 2002

Authors and Affiliations

  1. 1.Department of Computer ScienceDuke UniversityDurhamUSA

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