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DNA computation

By Martyn Amos

Abstract

This is the first ever doctoral thesis in the field of DNA computation. The field has its roots\ud in the late 1950s, when the Nobel laureate Richard Feynman first introduced the concept of\ud computing at a molecular level. Feynman's visionary idea was only realised in 1994, when\ud Leonard Adleman performed the first ever truly molecular-level computation using DNA\ud combined with the tools and techniques of molecular biology. Since Adleman reported the\ud results of his seminal experiment, there has been a flurry\ud of interest in the idea of using DNA\ud to perform computations. The potential benefits of using this particular molecule are enormous:\ud by harnessing the massive inherent parallelism of performing concurrent operations\ud on trillions of strands, we may one day be able to compress the power of today's supercomputer\ud into a single test tube. However, if we compare the development of DNA-based\ud computers to that of their silicon counterparts, it is clear that molecular computers are still\ud in their infancy. Current work in this area is concerned mainly with abstract models of\ud computation and simple proof-of-principle experiments. The goal of this thesis is to present\ud our contribution to the field, placing it in the context of the existing body of work. Our\ud new results concern a general model of DNA computation, an error-resistant implementation\ud of the model, experimental investigation of the implementation and an assessment of\ud the complexity and viability of DNA computations. We begin by recounting the historical\ud background to the search for the structure of DNA. By providing a detailed description of\ud this molecule and the operations we may perform on it, we lay down the foundations for subsequent\ud chapters. We then describe the basic models of DNA computation that have been\ud proposed to date. In particular, we describe our parallel filtering model, which is the first\ud to provide a general framework for the elegant expression of algorithms for NP-complete\ud problems. The implementation of such abstract models is crucial to their success. Previous\ud experiments that have been carried out suffer from their reliance on various error-prone laboratory\ud techniques. We show for the first time how one particular operation, hybridisation\ud extraction, may be replaced by an error-resistant enzymatic separation technique. We also\ud describe a novel solution read-out procedure that utilizes cloning, and is sufficiently general\ud to allow it to be used in any experimental implementation. The results of preliminary\ud tests\ud of these techniques are then reported. Several important conclusions are to be drawn from these investigations, and we report these in the hope that they will provide useful experimental\ud guidance in the future. The final contribution of this thesis is a rigorous consideration\ud of the complexity and viability of DNA computations. We argue that existing analyses of\ud models of DNA computation are flawed and unrealistic. In order to obtain more realistic\ud measures of the time and space complexity of DNA computations we describe a new strong\ud model, and reassess previously described algorithms within it. We review the search for\ud "killer applications": applications of DNA computing that will establish the superiority\ud of\ud this paradigm within a certain domain. We conclude the thesis with a description of several\ud open problems in the field of DNA computation

Topics: QA76
OAI identifier: oai:wrap.warwick.ac.uk:4238

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  1. A boom in plans for DNA computing. doi
  2. A comprehensive sequence analysis programme for the IBM personal computer. doi
  3. (1995). A DNA and restriction enzyme implementation of Turing Machines.
  4. A procedure for the isolation of deoxyribonucleic acid from microorganisms. doi
  5. A restricted genetic alphabet for DNA computing.
  6. A sticker based architecture for DNA computation. doi
  7. A surface-based approach to DNA computation. doi
  8. (1992). Active transport in biological computing.
  9. (1985). Algorithmtc Graph Theory.
  10. Biochemical method for inserting new genetic information into DNA of simian virus 40: circular SV40 DNA molecules containing lambda phage genes and the galactose operon of escherichia coli. doi
  11. (1990). Denovo design of sequences for nucleic- acid- structuralengineering.
  12. Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. doi
  13. DNA based molecular computation: template- template interactions in PCR.
  14. DNA double- crossover molecules. doi
  15. (1996). DNA Models and Algorithms for NP-complete Problems, doi
  16. DNA sequences useful for computation.
  17. DNA solution of hard computational problems. doi
  18. (1988). Effictent Parallel Algor%thms.
  19. Enzymatic end-to-end joining of DINA molecules. doi
  20. (1996). Error-resilient DNA computation. doi
  21. Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. doi
  22. (1990). Gene cloning: an introduchon. Chapman and Hall,
  23. (1989). Genetic algorithms in search, optimization, and machine learning. doi
  24. (1993). Genetic Engineering. Oios Scientific Publishers,
  25. (1953). Genetical implications of the structure of deoxyribose nuclew acid. doi
  26. (1993). Genetics: A molecular approach. doi
  27. (1972). History of genef., ics - from pre-historic tbocs to the rc(liscovery of Mendel's laws.
  28. Holliday junction crossover topology. doi
  29. Improved m13 phage cloning vectors and host strains: nucleotide sequences of the ml3mpl8 and pucl9 vectors. doi
  30. (1965). Introduction to switching and automata theory.
  31. (1996). Lila Kari, and Gheorghe P6un. DNA computation based on splicing: universality results. In
  32. (1986). Making DNA computers error resistant. doi
  33. (1996). Models of DNA computation. doi
  34. (1996). Molecular computation and splicing systems.
  35. Molecular computation of solutions to combinatorial problems. doi
  36. (1995). Molecular computation: Adleman's experiment repeated.
  37. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. doi
  38. Nucleic acid junctions and lattices. doi
  39. On constructing a molecular computer. doi
  40. (1979). On simultaneous resource bounds. doi
  41. (1994). On the path to computation with DNA. doi
  42. (1995). On the potential of molecular computing. doi
  43. (1995). On the potential of molecular coniplifilig. doi
  44. (1996). On the scalability of molecular computational solutions to NP problems.
  45. On the weight of computations. doi
  46. (1995). Parallel molecular computation: Models and simulations. doi
  47. (1994). Principles of gene manipulation, an introduction to genetic eng%neerZng. Blackwell Scientific Publications, fifth edition,
  48. (1992). Recombinant DNA. doi
  49. (1978). Relations among complexity measures. doi
  50. Running dynamic programming algorithms on a DNA computer.
  51. (1996). Simulating Boolean circuits on a DNA computer. doi
  52. (1992). Splicing schemes and DNA. doi
  53. (1986). The Biochemistry of the Nucleic AcZds. Chapman and Hall, tenth edition, doi
  54. (1988). The Complex%ty of Boolean Networks.
  55. (1996). The complexity and viability of DNA computations.
  56. The construction of a DNA truncated octahedron. doi
  57. The construction of a trefoil knot from a DNA branched junction motif. doi
  58. (1974). The design and analysts of computer algorithms. doi
  59. The network complexity and Turing machine complexity of finite functions. doi
  60. The thermodynamics of computation -a review. doi
  61. The unusual origin of the polymerase chain reaction. doi
  62. Universal computation via self-assembly of DNA: some theory and experiments.
  63. (1992). Xiaojun Li, Xiaoping Yang, Furong Liu, Weiqiong Sun, Zhiyong Shen, Ruojie Sha, Chengde Mao, Yinli Wang, Siwei Zhang, Tsu-Ju Fu, Shouming Du, doi

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