Theoretical and Experimental DNA Computation (Natural ...

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Index ALGOL, 102 AND, 23–24, 42, 87–88, 93, 99, 149 accumulator, 30–31, 93, 97–99 actin I, 152, 155 active site, 8, 110 addition, 29, 93, 98, 143–144 adenine, 6, 131 adjacency matrix, 34, 89 agarose, 13, 114, 125, 131 algorithm, alphabet, 26, 47, 55, 60, 66–67, 73, 83 amino acid, 8 annealing, 6, 11, 16, 86, 111, 119, 126, 128, 131, 133, 134, 139 architecture, 1-3, 23, 44, 64, 102, 140 array, 33–34, 44, 64, 140, 144 automation, 15, 120, 138, 140 automata, see automaton automaton, 25–28, 44, 63, 145, 148 backbone, 6, 129, 145 bacteria, 4, 10, 15, 18–20, 125, 150 bacteriophage, see phage basis, 77 base, 6, 120, 128, 141, 143 base pair, 6, 14, 151 Batcher sorting network, see network, sorting Bennett, C., 109 big-oh notation, 41 binary, 23, 55, 62–63, 97–98, 142–144 bioinformatics, 8, 147 biology (as a discipline), 2–4, 147–148 biotechnology, 4 biotin, 12 biotinylation, 111, 121–122, 129–131, 135 bit, 23, 49, 55, 89, 97–99, 140, 142–144 blunt end, 16, 84, 86 bonding, see annealing Boolean algebra 24–25, 44, 148 circuit, see circuit, Boolean matrix 89 value 49, 89, 97 variable 55, 77, 82–83, 97 bubble sort, 41, 43 calcium, 18 capsid, 18 cardinality, 46, 110 catalyst, 7–8 cell (biological), 2, 17–19, 66, 150 cellular automaton, 63 central dogma of molecular biology, 7 central processing unit (CPU), 1–2 charge, 13, 68 CHemical Abstract Machine (CHAM), see model, CHAM chess game, 136 chromosome, 5, 153 Church’s Thesis, 29 circuit integrated, 1 Boolean 24–25, 41–42, 71, 73, 77–83, 86–91, 94–100, 102, 105–107, 145, 150 genetic 150
168 Index clause, 42, 49, 139–141, 144 clique, 39, 142–143 clock, 67, 148 cloning, 17–18, 21, 118, 125–126, 129–130, 134 coloring, 37, 46–48, 52, 120–122, 124–126, 130 combinatorial explosion, 42 complement arithmetic, 98 graph 142–143 complementarity (biological), 6–7, 10–12, 14, 17, 79, 83–84, 86, 110–111, 121, 134, 138–139, 144 complex system, 147 complexity 3, 5, 64, 71 complexity of Boolean circuit, 78, 83 computational, 39–41, 44–45, 73, 75–77, 93, 107 class, 43–44, 50–51, 60, 72, 94, 107, 115 computational problem, 3, 33, 73, 140 computer, 1–4, 23, 26, 30, 33, 40–41, 43–44, 141, 147–148 Brownian, 109 cellular, 155 DNA-based, 2, 140–141 computer science, 3–4, 23, 27, 43, 63, 147–148 concurrent programming, 64 conformation, 8, 110–111 connectivity, 36 Conrad, M., 109–110 control, 2, 32, 61, 64, 66, 68, 92, 110 experimental, 114, 116, 122, 124, 126–131, 133–134 genetic, 147–149 graph, 95–97 program, 92–95, 100, 103 Cook’s Theorem, 43 cytosine, 6 DNA charge, 13 cloning, see cloning as genetic material, 5, 7 operations on, 10–17 recombinant, 17 replication, see polymerase chain reaction structure, 5–6, 17 data, 1–2, 5, 34, 43, 97, 147, 155 input, 92–93 structure, 26, 33–34, 44 decision problem, 34, 43 denaturing, 11, 15, 85, 126–128 deoxyribonucleic acid, see DNA Descartes, R., 148 double helix, see DNA, structure E. coli, 18, 134, 139, 148, 150 electric field, 13 electroporation, 19 endonuclease, 16, 110 engineering (as a discipline), 4 genetic, 4, 21, 155 reverse, 4 enzyme, 7–8, 10, 110 allosteric, 110 hypothetical, 109 ligase, 7, 11, 85–86, 122, 124 polymerase, 2, 10 restriction, 16–17, 76, 80, 84–86, 110, 117–119, 127, 131, 133–134, 136, 143 effectiveness, 135 universal, 136 RsaI, 16 Sau3A, 17, 126–127, 130–131, 134–135 Taq, 15, 126–128, 131 error experimental, 3, 46, 81, 114–116, 118–120, 135 overflow, 98–99 sequence design, 120 ethidium bromide, 13 exonuclease, 116, 139 exponential curse, 72, 115 expression genetic, 10, 148 of algorithm, 31, 51, 55 factor 42, 45, 100 constant, 41, 81, 96 factoring algorithm, 40–41 feasibility 3, 88
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Natural Computing Series Series Edi
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Martyn Amos Department of Computer
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Preface DNA computation has emerged
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Preface IX acknowledged. Finally, I
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XII Contents 4 Complexity Issues ..
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Introduction “Where a calculator
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Introduction 3 Even though their un
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1 DNA: The Molecule of Life “All
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1.3 DNA as the Carrier of Genetic I
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1.3 DNA as the Carrier of Genetic I
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Synthesis 1.4 Operations on DNA 11
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Gel electrophoresis 1.4 Operations
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5’ 3’ A T A G A G T T 3’ TCA
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1.4 Operations on DNA 17 Others may
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Vector Strand to be inserted (targe
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1.5 Summary 1.6 Bibliographical Not
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24 2 Theoretical Computer Science:
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72 4 Complexity Issues is that, alt
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74 4 Complexity Issues The weak par
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76 4 Complexity Issues 4.3 A Strong
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78 4 Complexity Issues Ω = {∧,
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80 4 Complexity Issues 0 1 0 1 x1 x
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82 4 Complexity Issues connecting a
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84 4 Complexity Issues Level simula
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86 4 Complexity Issues At level D(S
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88 4 Complexity Issues xANDy)) and
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90 4 Complexity Issues Input matrix
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92 4 Complexity Issues memory acces
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94 4 Complexity Issues denoted by P
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96 4 Complexity Issues The final st
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98 4 Complexity Issues 1)), ADDR[])
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100 4 Complexity Issues Size(STI)=O
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102 4 Complexity Issues best attain
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104 4 Complexity Issues 10. LDC 0 1
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106 4 Complexity Issues ACC[] := bi
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5 Physical Implementations “No am
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5.3 Initial Set Construction Within
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Vertex 1 Vertex 2 Vertex 3 ¡ ¡ ¡
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Page 173 and 174: 158 References 14. Martyn Amos, Ste
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Page 179 and 180: 164 References 135. Kensaku Sakamot
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