ISBN-10:
0387736352
ISBN-13:
9780387736358
Pub. Date:
07/02/2008
Publisher:
Springer US
DNA Computing Models / Edition 1

DNA Computing Models / Edition 1

Hardcover

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Product Details

ISBN-13: 9780387736358
Publisher: Springer US
Publication date: 07/02/2008
Edition description: 2008
Pages: 288
Product dimensions: 6.20(w) x 9.10(h) x 0.70(d)

Table of Contents


Introduction     1
References     7
Theoretical Computer Science     9
Graphs     9
Basic Notions     9
Paths and Cycles     11
Closures and Paths     13
Trees     14
Bipartite Graphs     16
Finite State Automata     16
Strings and Languages     17
Deterministic Finite State Automata     18
Non-Deterministic Finite State Automata     19
Regular Expressions     21
Stochastic Finite State Automata     23
Computability     25
Turing Machines     25
Universal Turing Machines     27
Church's Thesis     29
Register Machines     31
Cellular Automata     31
Formal Grammars     33
Grammars and Languages     33
Chomsky's Hierarchy     34
Grammars and Machines     35
Undecidability     36
Combinatorial Logic     40
Boolean Circuits     40
Compound Circuits     42
Minterms and Maxterms     43
Canonical Circuits     44
Adder Circuits     46
Computational Complexity     48
Time Complexity     48
Infinite Asymptotics     49
Decision Problems     51
Optimization Problems     54
References     54
Molecular Biology     57
DNA     57
Molecular Structure     57
Manipulation of DNA     60
Physical Chemistry     63
Thermodynamics     63
Chemical Kinetics     65
DNA Annealing Kinetics     68
Strand Displacement Kinetics     68
Stochastic Chemical Kinetics     69
Genes     76
Structure and Biosynthesis     77
DNA Recombination     80
Genomes     81
Gene Expression     82
Protein Biosynthesis     82
Proteins - Molecular Structure     85
Enzymes     88
Cells and Organisms     92
Eukaryotes and Prokaryotes     93
Viruses     94
General Structure and Classification     94
Applications     95
References     97
Word Design for DNA Computing     99
Constraints      99
Free Energy and Melting Temperature     99
Distance     100
Similarity     101
DNA Languages     104
Bond-Free Languages     104
Hybridization Properties     105
Small DNA Languages     107
DNA Code Constructions and Bounds     108
Reverse and Reverse-Complement Codes     108
Constant GC-Content Codes     111
Similarity-Based Codes     113
In Vitro Random Selection     117
General Selection Model     118
Selective Word Design     118
Concluding Remarks     120
References     120
Non-Autonomous DNA Models     123
Seminal Work     123
Adleman's First Experiment     123
Lipton's First Paper     126
Filtering Models     127
Memory-Less Filtering     127
Memory-Based Filtering     128
Mark-and-Destroy Filtering     129
Split-and-Merge Filtering     131
Filtering by Blocking     133
Surface-Based Filtering     135
Sticker Systems     138
Sticker Machines     138
Combinatorial Libraries      141
Useful Subroutines     141
NP-Complete Problems     149
Splicing Systems     169
Basic Splicing Systems     169
Recursively Enumerable Splicing Systems     171
Universal Splicing Systems     173
Recombinant Systems     175
Concluding Remarks     178
References     178
Autonomous DNA Models     181
Algorithmic Self-Assembly     181
Self-Assembly     181
DNA Graphs     182
Linear Self-Assembly     184
Tile Assembly     185
Finite State Automaton Models     194
Two-State Two-Symbol Automata     194
Length-Encoding Automata     198
Sticker Automata     200
Stochastic Automata     207
DNA Hairpin Model     207
Whiplash PCR     207
Satisfiability     211
Hamiltonian Paths     213
Maximum Cliques     216
Hairpin Structures     220
Computational Models     222
Neural Networks     222
Tic-Tac-Toe Networks     226
Logic Circuits     232
Turing Machines     235
Concluding Remarks     239
References     239
Cellular DNA Computing     243
Ciliate Computing     243
Ciliates     243
Models of Gene Assembly     246
Intramolecular String Model     249
Intramolecular Graph Model     252
Intermolecular String Model     256
Biomolecular Computing     258
Gene Therapy     258
Anti-Sense Technology     259
Cell-Based Finite State Automata     261
Anti-Sense Finite State Automata     264
Basic Model     265
Diagnostic Rules     266
Diagnosis and Therapy     266
Computational Genes     269
Basic Model     269
Diagnostic Rules     271
Diagnosis and Therapy     273
Concluding Remarks     275
References     276
Index     279

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