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Mitsunori Ogihara

Molecular Computation

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References

  1. M. Amos, P.E. Dunne, and A. Gibbons. DNA simulation of boolean circuits. In J. R. Koza, W. Banzhaf, K. Chellapilla, K. D. Deb, D. B. Fogel, M. H. Garzon, D. E. Goldberg, H. Iba, and R. L. Riolo, editors, Proceedings of 3rd Annual Genetic Programming Conference, pages 679-683, San Francisco, CA, 1998. Morgan Kaufmann.

    Google Scholar 

  2. L. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266:1021-1024, 1994.

    Article  Google Scholar 

  3. L. Adleman. On constructing a molecular computer. In R. Lipton and E. Baum, editors, DNA Based Computers, pages 1-21. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 27, 1996.

    Google Scholar 

  4. M. Amos, A. Gibbons, and D. Hodgson. Error-resistant implementation of DNA computations. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 151-162. The American Mathematical Society DIMACS Series in Dis- crete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  5. M. Arita, M. Hagiya, and A. Suyama. Joining and rotating data with molecules. In Proceedings of International Conference on Evolutionary Computing, pages 243-248. IEEE Computer Society Press, Los Alamitos, CA, 1997.

    Google Scholar 

  6. L. Adleman, P. Rothemund, S. Roweis, and E. Winfree. On applying molecular computation to the Data Encryption Standard. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 31-44. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  7. E. Baum and D. Boneh. Running dynamic programming algorithms on a DNA computer. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 77-80. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  8. E. Bach, A. Condon, E. Glaser, and C. Tanguay. DNA models and algorithms for NP-complete problems. In Proceedings of 11th Conference on Computational Complexity, pages 290-299. IEEE Computer Society Press, Los Alamitos, CA, 1996.

    Google Scholar 

  9. R. S. Braich, N. Chelapov, C. Johnson, P. W. K. Rothemund, and L. Adleman. Solution of a 20-variable 3-SAT problem on a DNA computer. Science, 296:499-502,2002.

    Article  Google Scholar 

  10. D. Boneh, C. Dunworth, and R. Lipton. Breaking DES using a molecular computer. In R. Lipton and E. Baum, editors, DNA Based Computers, pages 37-65. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 27, 1996.

    Google Scholar 

  11. D. Boneh, C. Dunworth, R. Lipton, and J. Sgall. On the computational power of DNA. Discrete Applied Mathematics, 71:79-94, 1996.

    Article  MATH  MathSciNet  Google Scholar 

  12. D. Beaver. Computing with DNA. Journal of Computational Biology, 2(1):1-8, 1995.

    Article  Google Scholar 

  13. R. Beigel and B. Fu. Molecular computing, bounded nondeterminism, and efficient recursion. Algorithmica, 25:222-238, 1999.

    Article  MATH  MathSciNet  Google Scholar 

  14. R. S. Braich, C. Johnson, P. W. K. Rothemund, D. Hwang, N. Chelapov, and L. Adleman. Solution of a satisfiability problem on a gel-based DNA computer. In A. Condon and G. Rozenberg, editors, DNA Computing, 6th International Workshop on DNA-Based Computers, pages 27-42. Springer-Verlag Lecture Notes in Computer Science 2054, 2000.

    Google Scholar 

  15. D. Boneh and R. Lipton. Batching DNA computations. manuscript.

    Google Scholar 

  16. D. Boneh and R. Lipton. A divide and conquer approach to sequencing. man- uscript.

    Google Scholar 

  17. W. Cai, A. Condon, R. Corn, E. Glaser, Z. Fei, T. Frutos, Z. Guo, M. Lagally, Q. Liu, L. Smith, and A. Thiel. The power of surface-based DNA computation. In Proceedings of 1st International Conference on Computational Molecular Biology, pages 67-74. ACM Press, 1997.

    Google Scholar 

  18. A. Cukras, D. Faulhammer, R. Lipton, and L. Landweber. Chess game: a model for RNA-based computation. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 27-37, 1998.

    Google Scholar 

  19. S. Díaz, J. L. Esteban, and M. Ogihara. A DNA-based random walk method for solving k-SAT. In A. Condon, editor, Proceedings of 6th Workshop on DNAbased Computers, pages 209-219. Springer-Verlag Lecture Notes in Computer Science 2054, 2000.

    Google Scholar 

  20. R. Deaton, M. Garzon, R. Murphy, J. Rose, D. Franceschetti Jr., and S. Stevens. Genetic search of reliable encodings for DNA-based computation. In Proceedings of 1st Annual Genetic Programming Conference, San Francisco, CA, 1996. Morgan Kaufmann.

    Google Scholar 

  21. R. Deaton, R. Murphy, M. Garzon, D. Franceschetti, and Jr. S. Stevens. Good encodings for DNA-based solutions to combinatorial problems. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 247-258. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  22. A. D. Ellington, M. P. Robertson, K. D. James, and J. Colin Cox. Strategies for DNA computing. In H. Rubin and D. H. Wood, editors, DNA Based Computers III, pages 173-184, 1997.

    Google Scholar 

  23. D. Faulhammer, A. Cukras, R. Lipton, and L. Landweber. Molecular compu- tation: DNA solutions to chess problems. Proceedings of the National Academy of Science, 97:1385-1389, 2000.

    Google Scholar 

  24. D. Faulhammer, R. Lipton, and L. Landweber. Counting DNA: estimating the complexity of a test tube of DNA. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 249-250, 1998.

    Google Scholar 

  25. A. G. Frutos, Q. Liu, A. J. Thiel, A. M. W. Sanner, A. E. Condon, L. M. Smith, and R. M. Corn. Demonstration of a word design strategy for DNA computation on surfaces. Nucleic Acids Research, 25:4748-4757, 1997.

    Article  Google Scholar 

  26. F. Guarnieri, M. Fliss, and C. Bancroft. Making DNA add. Science, 273:220-223,1995.

    Google Scholar 

  27. A. Gehani and J. Reif. Microflow bio-molecular computation. Biosystems, 52(1-3):197-216, 1999.

    Article  Google Scholar 

  28. M. Hagiya. Towards autonomous molecular computers. In J. R. Koza, W. Banzhaf, K. Chellapilla, K. D. Deb, D. B. Fogel, M. H. Garzon, D. E. Gold- berg, H. Iba, and R. L. Riolo, editors, Proceedings of 3rd Annual Genetic Pro- gramming Conference, pages 691-699, San Francisco, CA, 1998. Morgan Kauf- mann.

    Google Scholar 

  29. M. Hagiya, M. Arita, D. Kiga, K. Sakamoto, and S. Yokoyama. Towards parallel evaluation and learning of Boolean µ-formulas with molecules. In H. Rubin and D. H. Wood, editors, DNA Based Computers III, pages 57-72, 1997.

    Google Scholar 

  30. T. Head. Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. Bulletin of Mathematics Biology, 49 (6):737-759, 1987.

    MATH  MathSciNet  Google Scholar 

  31. A. J. Hartemink and D. K. Gifford. Theormodynamic simulatin of deoxyoligonucleotide hybridization for DNA computation. In DNA Based Computers III, pages 25-37, 1997.

    Google Scholar 

  32. A. Hartemink, D. Gifford, and J. Khodor. Automated constraint-based nu- cleotide sequence selection for DNA computation. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 287-297, 1998.

    Google Scholar 

  33. P. Kaplan, G. Cecchi, and A. Libchaber. DNA-based molecular computation: template-template interactions in PCR. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 97-104. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  34. J. Khodor and D. Gifford. Design and implementation of computational systems based on programmed mutagenesis. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 101-108, 1998.

    Google Scholar 

  35. R. Karp, C. Kenyon, and O. Waarts. Error-resilient DNA computation. In Proceedings of 7th ACM-SIAM Symposium on Discrete Algorithms, pages 458- 467. ACM Press/SIAM, 1996.

    Google Scholar 

  36. L. Kari and L. Landweber. The evolution of DNA computing: nature’s solution to a computational problem. In J. R. Koza, W. Banzhaf, K. Chellapilla, K. D. Deb, D. B. Fogel, M. H. Garzon, D. E. Goldberg, H. Iba, and R. L. Riolo, editors, Proceedings of 3rd Annual Genetic Programming Conference, pages 700-708, San Francisco, CA, 1998. Morgan Kaufmann.

    Google Scholar 

  37. S. Kurtz, S. Mahaney, J. Royer, and J. Simon. Biological computing. In L. Hemaspaandra and A. Selman, editors, Complexity Theory Retrospective II, pages 179-195. Springer-Verlag, New York, NY, 1997.

    Google Scholar 

  38. L. Kari, Gh. Paŭn, G. Rozenberg, A. Salomaa, and S. Yu. DNA computing, sticker sustems and universality. Acta Informatica, 35:401-420, 1998.

    Article  MATH  MathSciNet  Google Scholar 

  39. P. D. Kaplan, D. S. Thaler, and A. Libchaber. Parallel overlap assembly of paths through a directed graph. In Preliminary Proceedings of 3rd DIMACS Workshop on DNA Based Computers, pages 127-141, 1997.

    Google Scholar 

  40. S. Kobayashi, T. Yokomori, G. Sanpei, and K. Mizobuchi. DNA implementation of simple Horn clause comptuation. In Proceedings of International Conference on Evolutionary Computing, pages 213–217. IEEE Computer Society Press, Los Alamitos, CA, 1997.

    Google Scholar 

  41. R. Lipton. DNA solutions of hard computational problems. Science, 268:542- 545, 1995.

    Article  Google Scholar 

  42. R. Lipton. A memory based attack on cryptosystems with application to DNA computing. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 267-272, 1998.

    Google Scholar 

  43. L. F. Landweber, T.-C. Kuo, and E. A. Curtis. Evolution and assembly of an extremely scrambled gene. Proceedings of the National Academy of Science, 97:3298-3303, 2000.

    Article  Google Scholar 

  44. L. Landweber and R. Lipton. DNA2 DNA computations: a potential ‘killer app’ ? In Preliminary Proceedings of 3rd DIMACS Workshop on DNA Based Comput- ers, pages 59-68, 1997.

    Google Scholar 

  45. Q. Liu, L. Wang, A. G. Frutos, R. M. Corn, and L. M. Smith. DNA computing on surfaces. Nature, 403:175-178, 2000. January, 13.

    Article  Google Scholar 

  46. G. G. Owensen, M. Amos, D. A. Hodgson, and A. Gibbons. Dna-based logic. Soft Computing, 5(2):102-105, 2001.

    Article  Google Scholar 

  47. M. Ogihara. Breadth first search 3SAT algorithms for DNA computers. Techni- cal Report TR-629, Department of Computer Science, University of Rochester, Rochester, NY, July 1996.

    Google Scholar 

  48. M. Ogihara. Relating the minimum model for DNA computation and Boolean circuits. In W. Banzhaf, J. Daida, A. E. Eiben, M. H. Garzon, V. Honavar, M. Jakiela, and R. E. Smith, editors, Genetic and Evolutionary Computation Conference, pages 1817-1822. Morgan Kaufmann Publishers, San Francisco, CA, 1999.

    Google Scholar 

  49. Q. Ouyang, P. D. Kaplana, S. Liu, and A. Libchaber. DNA solution of the maximal clique problem. Science, 278:446-449, 1997.

    Article  Google Scholar 

  50. M. Ogihara and A. Ray. DNA-based parallel computation by counting. In H. Rubin and D. H. Wood, editors, DNA Based Computers III, pages 255-264, 1997.

    Google Scholar 

  51. M. Ogihara and A. Ray. Simulating boolean circuits on DNA computers. In Pro- ceedings of 1st International Conference on Computational Molecular Biology, pages 326-331. ACM Press, 1997.

    Google Scholar 

  52. M. Ogihara and A. Ray. The minimum DNA model and its computational power. In Unconventional Models of Computation, pages 309-322. Springer, Singapore, 1998.

    Google Scholar 

  53. G. Păun. The splicing as an operation on formal languages. In Proceedings of International Symposium on Intelligence in Neural and Biological Systems, pages 176-180. IEEE Computer Society Press, Los Alamitos, CA, 1995.

    Google Scholar 

  54. J. Reif. Parallel molecular computation. In Proceedings of 7th ACM Symposium on Parallel Algorithms and Architecture, pages 213-223. ACM Press, 1995.

    Google Scholar 

  55. P. Rothemund. A DNA and restriction enzyme implementation of Turing ma- chines. In R. Lipton and E. Baum, editors, DNA Based Computers, pages 75-119. The American Mathematical Society DIMACS Series in Discrete Math- ematics and Theoretical Computer Science Volume 27, 1996.

    Google Scholar 

  56. D. Rooß and K. Wagner. On the power of DNA computing. Information and Computation, 131:95-109, 1996.

    Article  MATH  MathSciNet  Google Scholar 

  57. S. Roweis, E. Winfree, R. Burgoyne, N. Chelapov, M. Goodman, P. Rothemund, and L. Adleman. A sticker based model for DNA computation. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 1-30. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  58. Y. Sakakibara. Solving computational learning problems of boolean formulae on DNA computers. In A. Condon and G. Rozenberg, editors, DNA Computing, 6th International Workshop on DNA-Based Computers, pages 220-230. Springer- Verlag Lecture Notes in Computer Science 2054, 2000.

    Google Scholar 

  59. J. Sakamoto, H. Gouzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, and M. Hagiya. Molecular computation by DNA hairpin formation. Science, 288:1223-1226, 2000.

    Article  Google Scholar 

  60. N. Seeman, F. Liu, C. Mao, X. Yang, L. Wenzler, and E. Winfree. DNA nan- otechnology: control of 1-D and 2-D arrays and the construction of a nanome- chanical device. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 241-242, 1998.

    Google Scholar 

  61. N. Seeman, H. Wang, B. Liu, J. Qi, X. Li, X. Yang, F. Liu, W. Sun, Z. Shen, R. Sha, C. Mao, Y. Wang, S. Zhang, T. Fu, S. Du, J. Mueller, Y. Zhang, and J. Chen. The perils of polynucleotides: the experimental gap between the design and assembly of unusual DNA structures. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 215-234. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  62. E. Winfree. Complexity of restricted and unrestricted models of molecular com- putation. In R. Lipton and E. Baum, editors, DNA Based Computers, pages 187-198. The American Mathematical Society DIMACS Series in Discrete Math- ematics and Theoretical Computer Science Volume 27, 1996.

    Google Scholar 

  63. E. Winfree. On the computational power of DNA annealing and ligation. In R. Lipton and E. Baum, editors, DNA Based Computers, pages 199-221. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 27, 1996.

    Google Scholar 

  64. E. Winfree. Whiplash PCR for O(1) computing. In Preliminary Proceedings of 4th DIMACS Workshop on DNA Based Computers, pages 175-188, 1998.

    Google Scholar 

  65. E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman. Design and self-assembly of two-dimensional DNA crystals. Nature, 394:539-544, 1998.

    Article  Google Scholar 

  66. E. Winfree, X. Yang, and N. Seeman. Universal comptuation via self-assembly of DNA: some theory and experiments. In L. Landweber and E. Baum, editors, DNA Based Computers II, pages 191-214. The American Mathematical Society DIMACS Series in Discrete Mathematics and Theoretical Computer Science Volume 44, 1999.

    Google Scholar 

  67. T. Yokomori and S. Kobayashi. DNA evolutionary linguistics and RNA struc- ture modeling: a computational approach. In Proceedings of International Sym- posium on Intelligence in Neural and Biological Systems, pages 38-45. IEEE Computer Society Press, Los Alamitos, CA, 1995.

    Google Scholar 

  68. T. Yokomori, S. Kobayashi, and C. Ferretti. On the power of circular splicing systems and DNA computability. In Proceedings of International Conference on Evolutionary Computing, pages 219-224. IEEE Computer Society Press, Los Alamitos, CA, 1997.

    Google Scholar 

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(2006). Mitsunori Ogihara. In: Esik, Z., Martín-Vide, C., Mitrana, V. (eds) Recent Advances in Formal Languages and Applications. Studies in Computational Intelligence, vol 25. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-33461-3_10

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