DNA computing models:
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
New York, NY
Springer
2008
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIII, 288 S. Ill. |
| ISBN: | 9780387736358 0387736352 |
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Record in the Search Index
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| adam_text | Contents
1 Introduction.............................................. 1
References................................................. 7
2 Theoretical Computer Science............................ 9
2.1 Graphs................................................ 9
2.1.1 Basic Notions.................................... 9
2.1.2 Paths and Cycles................................. 11
2.1.3 Closures and Paths............................... 13
2.1.4 Trees........................................... 14
2.1.5 Bipartite Grapte................................. 16
2.2 Finite State Automata.................................. 16
2.2.1 Strings and Languages............................ 17
2.2.2 Deterministic Finite State Automata................ 18
2.2.3 Non-Deterministic Finite State Automata........... 19
2.2.4 Regular Expressions.............................. 21
2.2.5 Stochastic Finite State Automata.................. 23
2.3 Computability......................................... 25
2.3.1 Turing Machines................................. 25
2.3.2 Universal Turing Machines........................ 27
2.3.3 Church s Thesis.................................. 29
2.3.4 Register Machines................................ 31
2.3.5 Cellular Automata................................ 31
2.4 Formal Grammars...................................... 33
2.4.1 Grammars and Languages......................... 33
2.4.2 Chomsky s Hierarchy............................. 34
2.4.3 Grammars and Machines.......................... 35
2.4.4 Undecidability................................... 36
2.5 Combinatorial Logic.................................... 40
2.5.1 Boolean Circuits................................. 40
2.5.2 Compound Circuits............................... 42
2.5.3 Minterms and Maxterms.......................... 43
Contents
2.5.4 Canonical Circuits................................ 44
2.5.5 Adder Circuits................................... 46
2.6 Computational Complexity.............................. 48
2.6.1 Time Complexity................................. 48
2.6.2 Infinite Asymptotics.............................. 49
2.6.3 Decision Problems................................ 51
2.6.4 Optimization Problems............................ 54
References................................................. 54
Molecular Biology........................................ 57
3.1 DNA ................................................. 57
3.1.1 Molecular Structure .............................. 57
3.1.2 Manipulation of DNA............................. 60
3.2 Physical Chemistry..................................... 63
3.2.1 Thermodynamics................................. 63
3.2.2 Chemical Kinetics................................ 65
3.2.3 DNA Annealing Kinetics.......................... 68
3.2.4 Strand Displacement Kinetics...................... 68
3.2.5 Stochastic Chemical Kinetics ...................... 69
3.3 Genes................................................. 76
3.3.1 Structure and Biosynthesis........................ 77
3.3.2 DNA Recombination.............................. 80
3.3.3 Genomes........................................ 81
3.4 Gene Expression....................................... 82
3.4.1 Protein Biosynthesis.............................. 82
3.4.2 Proteins - Molecular Structure..................... 85
3.4.3 Enzymes........................................ 88
3.5 Cells and Organisms.................................... 92
3.5.1 Eukaryotes and Prokaryotes....................... 93
3.6 Viruses................................................ 94
3.6.1 General Structure and Classification................ 94
3.6.2 Applications..................................... 95
References................................................. 97
Word Design for DNA Computing........................ 99
4.1 Constraints............................................ 99
4.1.1 Free Energy and Melting Temperature.............. 99
4.1.2 Distance........................................ 100
4.1.3 Similarity ....................................... 101
4.2 DNA Languages........................................ 104
4.2.1 Bond-Free Languages............................. 104
4.2.2 Hybridization Properties.......................... 105
4.2.3 Small DNA Languages............................ 107
4.3 DNA Code Constructions and Bounds .................... 108
4.3.1 Reverse and Reverse-Complement Codes............ 108
Contents
4.3.2 Constant GC-Content Codes.......................111
4.3.3 Similarity-Based Codes............................113
4.4 In Vitro Random Selection ..............................117
4.4.1 General Selection Model...........................118
4.4.2 Selective Word Design............................118
Concluding Remarks........................................120
References.................................................120
Non-Autonomous DNA Models...........................123
5.1 Seminal Work..........................................123
5.1.1 Adleman s First Experiment.......................123
5.1.2 Lipton s First Paper..............................126
5.2 Filtering Models........................................127
5.2.1 Memory-Less Filtering............................127
5.2.2 Memory-Based Filtering...........................128
5.2.3 Mark-and-Destroy Filtering........................129
5.2.4 Split-and-Merge Filtering..........................131
5.2.5 Filtering by Blocking.............................133
5.2.6 Surface-Based Filtering ...........................135
5.3 Sticker Systems........................................138
5.3.1 Sticker Machines.................................138
5.3.2 Combinatorial Libraries...........................141
5.3.3 Useful Subroutines ...............................141
5.3.4 NP-Complete Problems...........................149
5.4 Splicing Systems.......................................169
5.4.1 Basic Splicing Systems............................169
5.4.2 Recursively Enumerable Splicing Systems............171
5.4.3 Universal Splicing Systems ........................173
5.4.4 Recombinant Systems.............................175
Concluding Remarks........................................178
References.................................................178
Autonomous DNA Models................................181
6.1 Algorithmic Self-Assembly...............................181
6.1.1 Self-Assembly....................................181
6.1.2 DNA Graphs....................................182
6.1.3 Linear Self-Assembly..............................184
6.1.4 Tile Assembly ...................................185
6.2 Finite State Automaton Models..........................194
6.2.1 Two-State Two-Symbol Automata..................194
6.2.2 Length-Encoding Automata .......................198
6.2.3 Sticker Automata ................................200
6.2.4 Stochastic Automata .............................207
6.3 DNA Hairpin Model....................................207
6.3.1 Whiplash PCR...................................207
x Contents
6.3.2 Satisfiability.....................................211
6.3.3 Hamiltonian Paths ...............................213
6.3.4 Maximum Cliques................................216
6.3.5 Hairpin Structures................................220
6.4 Computational Models..................................222
6.4.1 Neural Networks.................................222
6.4.2 Tic-Tac-Toe Networks ............................226
6.4.3 Logic Circuits....................................232
6.4.4 Turing Machines.................................235
Concluding Remarks........................................239
References.................................................239
7 Cellular DNA Computing ................................243
7.1 Ciliate Computing......................................243
7.1.1 Ciliates.........................................243
7.1.2 Models of Gene Assembly.........................246
7.1.3 Intramolecular String Model.......................249
7.1.4 Intramolecular Graph Model.......................252
7.1.5 Intermolecular String Model.......................256
7.2 Biomolecular Computing................................258
7.2.1 Gene Therapy ...................................258
7.2.2 Anti-Sense Technology............................259
7.3 Cell-Based Finite State Automata........................261
7.4 Anti-Sense Finite State Automata........................264
7.4.1 Basic Model.....................................265
7.4.2 Diagnostic Rules.................................266
7.4.3 Diagnosis and Therapy............................266
7.5 Computational Genes...................................269
7.5.1 Basic Model.....................................269
7.5.2 Diagnostic Rules.................................271
7.5.3 Diagnosis and Therapy............................273
Concluding Remarks........................................275
References.................................................276
Index.........................................................279
|
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| spelling | Ignatova, Zoya Verfasser (DE-588)133329828 aut DNA computing models Zoya Ignatova ; Israel Martínez-Pérez ; Karl-Heinz Zimmermann New York, NY Springer 2008 XIII, 288 S. Ill. txt rdacontent n rdamedia nc rdacarrier Biocomputer (DE-588)4270224-0 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content DNS (DE-588)4070512-2 s Biocomputer (DE-588)4270224-0 s DE-604 Martínez-Pérez, Israel Verfasser aut Zimmermann, Karl-Heinz 1956-2023 Verfasser (DE-588)132198975 aut HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=020112262&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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| subject_GND | (DE-588)4270224-0 (DE-588)4070512-2 (DE-588)4123623-3 |
| title | DNA computing models |
| title_auth | DNA computing models |
| title_exact_search | DNA computing models |
| title_full | DNA computing models Zoya Ignatova ; Israel Martínez-Pérez ; Karl-Heinz Zimmermann |
| title_fullStr | DNA computing models Zoya Ignatova ; Israel Martínez-Pérez ; Karl-Heinz Zimmermann |
| title_full_unstemmed | DNA computing models Zoya Ignatova ; Israel Martínez-Pérez ; Karl-Heinz Zimmermann |
| title_short | DNA computing models |
| title_sort | dna computing models |
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