Theoretical and Experimental DNA Computation (Natural ...

More documents

Recommendations

Info

z z x w x w y y u (a) (b) u (c) Fig. 6.8. Excision/inversion z x w y 6.6 Summary 155 The model has been successfully applied to all known experimental data on the assembly of real genes, including the actin I gene of Urostyla grandis and Engelmanniella mobilis, the gene encoding α telomere binding protein in several stichotrich species, and assembly of the gene encoding DNA polymerase α in Sterkiella nova. Descriptions of these applications are presented in [124]. 6.6 Summary In this chapter we have introduced the notion of computing with and inside living cells and reviewed several models for the assembly of genes in ciliates. Although the fundamental molecular mechanisms underlying the operations within these models are still not well-understood, they do suggest possible areas of experimental enquiry. Looking further ahead, it may well be that in the future these mechanisms may even be exploited by using ciliates as prototype cellular computers. This engineering process has already begun, and we have cited several successful examples of the genetic modification of organisms for computational purposes. u
156 6 Cellular Computing 6.7 Bibliographical Notes A comprehensive review of the state of the art in cellular computing is [7]. The definitive text on computation in ciliates is [55], which covers both the biological and theoretical aspects of this area of research.
Page 2 and 3:
Natural Computing Series Series Edi
Page 4:
Martyn Amos Department of Computer
Page 8 and 9:
Preface DNA computation has emerged
Page 10:
Preface IX acknowledged. Finally, I
Page 13 and 14:
XII Contents 4 Complexity Issues ..
Page 16 and 17:
Introduction “Where a calculator
Page 18 and 19:
Introduction 3 Even though their un
Page 20 and 21:
1 DNA: The Molecule of Life “All
Page 22 and 23:
1.3 DNA as the Carrier of Genetic I
Page 24 and 25:
1.3 DNA as the Carrier of Genetic I
Page 26 and 27:
Synthesis 1.4 Operations on DNA 11
Page 28 and 29:
Gel electrophoresis 1.4 Operations
Page 30 and 31:
5’ 3’ A T A G A G T T 3’ TCA
Page 32 and 33:
1.4 Operations on DNA 17 Others may
Page 34 and 35:
Vector Strand to be inserted (targe
Page 36:
1.5 Summary 1.6 Bibliographical Not
Page 39 and 40:
24 2 Theoretical Computer Science:
Page 41 and 42:
Page 43 and 44:
Page 45 and 46:
Page 47 and 48:
Page 49 and 50:
Page 51 and 52:
Page 53 and 54:
Page 55 and 56:
Page 57 and 58:
Page 59 and 60:
Page 61 and 62:
46 3 Models of Molecular Computatio
Page 63 and 64:
Page 65 and 66:
Page 67 and 68:
Page 69 and 70:
Page 71 and 72:
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Page 79 and 80:
Page 81 and 82:
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
72 4 Complexity Issues is that, alt
Page 89 and 90:
74 4 Complexity Issues The weak par
Page 91 and 92:
76 4 Complexity Issues 4.3 A Strong
Page 93 and 94:
78 4 Complexity Issues Ω = {∧,
Page 95 and 96:
80 4 Complexity Issues 0 1 0 1 x1 x
Page 97 and 98:
82 4 Complexity Issues connecting a
Page 99 and 100:
84 4 Complexity Issues Level simula
Page 101 and 102:
86 4 Complexity Issues At level D(S
Page 103 and 104:
88 4 Complexity Issues xANDy)) and
Page 105 and 106:
90 4 Complexity Issues Input matrix
Page 107 and 108:
92 4 Complexity Issues memory acces
Page 109 and 110:
94 4 Complexity Issues denoted by P
Page 111 and 112:
96 4 Complexity Issues The final st
Page 113 and 114:
98 4 Complexity Issues 1)), ADDR[])
Page 115 and 116:
100 4 Complexity Issues Size(STI)=O
Page 117 and 118:
102 4 Complexity Issues best attain
Page 119 and 120: 104 4 Complexity Issues 10. LDC 0 1
Page 121 and 122: 106 4 Complexity Issues ACC[] := bi
Page 124 and 125: 5 Physical Implementations “No am
Page 126 and 127: 5.3 Initial Set Construction Within
Page 128 and 129: Vertex 1 Vertex 2 Vertex 3 ¡ ¡ ¡
Page 130 and 131: 5.5 Evaluation of Adleman’s Imple
Page 132 and 133: 5.6 Implementation of the Parallel
Page 134 and 135: 5.8 Experimental Investigations 119
Page 138 and 139: Create initial strand library Confi
Page 144 and 145: Experiment 25. New full-length chai
Page 150 and 151: 5.9 Other Laboratory Implementation
Page 160: 5.11 Bibliographical Notes 145 whic
Page 163 and 164: 148 6 Cellular Computing of truly i
Page 165 and 166: 150 6 Cellular Computing 6.2 Succes
Page 167 and 168: 152 6 Cellular Computing are “glu
Page 169: 154 6 Cellular Computing x y z x (a
Page 173 and 174: 158 References 14. Martyn Amos, Ste
Page 175 and 176: 160 References 53. Dónall A. Mac D
Page 177 and 178: 162 References 92. D. Knuth. The Ar
Page 179 and 180: 164 References 135. Kensaku Sakamot
Page 182 and 183: Index ALGOL, 102 AND, 23-24, 42, 87
Page 184 and 185: iological, 74, 114, 150 Feynman, R.
Page 186 and 187: Petrinet,63 phage, 18-20 phosphate,
Page 188: Natural Computing Series W.M. Spear
show all

Theoretical and Experimental DNA Computation (Natural ...

Create successful ePaper yourself

Delete template?

Save as template?