Nanotechnology: Science and Computation (eBook)

Junghuei Chen, Natasha Jonoska, Grzegorz Rozenberg (Herausgeber)

eBook Download: PDF

2006 | 2006
XI, 393 Seiten
Springer Berlin (Verlag)
978-3-540-30296-4 (ISBN)

Infos

Nanoscale science and computing is becoming a major research area as today's scientists try to understand the processes of natural and biomolecular computing. The field is concerned with the architectures and design of molecular self-assembly, nanostructures and molecular devices, and with understanding and exploiting the computational processes of biomolecules in nature.

This book offers a unique and authoritative perspective on current research in nanoscale science, engineering and computing. Leading researchers cover the topics of DNA self-assembly in two-dimensional arrays and three-dimensional structures, molecular motors, DNA word design, molecular electronics, gene assembly, surface layer protein assembly, and membrane computing.

The book is suitable for academic and industrial scientists and engineers working in nanoscale science, in particular researchers engaged with the idea of computing at a molecular level.

Junghei Chen received his Ph.D. in Chemistry from NYU, under the supervision of Ned Seeman. He has since worked at Berkeley and is now Associate Professor in the Department of Chemistry and Biochemistry at the University of Delaware. He has edited a Springer book: LNCS 2943, Int. Workshop on DNA Based Computers, DNA 9 (2003). He has authored dozens of papers in key journals areas of chemistry, biochemistry, physics, computing and nanoscience

Natascha Jonoska received her Ph.D. in Mathematical Science from SUNY Binghamton and is currently Associate Professor in the Mathematics Dept. at the University of South Florida. She has coedited a number of Springer books: LNCS 2723, Genetic and Evolutionary Computation Conf., GECCO 2003; LNCS 2950, Aspects of Molecular Computing, Essays Dedicated to Tom Head on the Occasion of His 70th Birthday (2004). Natasha has also contributed chapters in various Natural Computing books, and many journal and LNCS articles. Her journal publications cover her interests in both theoretical computer science and natural computing.

Grzegorz Rozenberg is the editor of the Springer Natural Computing series; is one of the series editors of the Springer EATCS Texts in Theoretical Computer Science series; was until this year the editor of the Springer journal Natural Computing; is the editor of the Elsevier Theoretical Computer Science journal Track C (Natural Computing). He has also edited or authored dozens of Springer books over the last 30 years. He has authored hundreds of publications in theoretical computer science and natural computing, and has been involved in the organization of dozens of conferences in both communities. He has authored and edited dozens of LNCS volumes and monographs, across a range of theoretical computer science fields and also in the area of natural computing. He has also recently edited some relevant Natural Computing series and EATCS series books, such as: Modelling in Molecular Biology (2004); Computation in Living Cells (2004); DNA Computing -- New Computing Paradigms (Reprint 2005). He also coedited LNCS 2950, Aspects of Molecular Computing, Essays Dedicated to Tom Head on the Occasion of His 70th Birthday (2004).

Inhalt

Preface 7
Contents 9
Part I DNA Nanotechnology – Algorithmic Self-assembly 12
Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks 13
1 Sca.olded DNA Origami for Parallel Multicrossovers 14
2 DNA Origami for Polygonal Networks 19
Acknowledgments 30
References 30
A Fresh Look at DNA Nanotechnology 32
1 Two-Dimensional DNA Triangle Arrays Designed with 32
a Tensegrity Strategy 32
2 DNA Molecular Motors 33
3 DNA Encoded One-Dimensional Array of Nanogold 39
4 DNA as Templates for Nanofabrication 40
5 Final Remarks 42
References 42
DNA Nanotechnology: an Evolving Field 44
1 Introduction 44
2 Programmable Self-assembly of 2D DNA Lattices 47
3 DNA Lattices as Nanosca.olds for Templated 49
Self-assembly 49
4 DNA Nanomechanical Devices 54
5 Conclusions and Outlook 58
References 59
Self-healing Tile Sets 63
1 Algorithmic Crystal Growth 63
2 Self-healing Transformations for Quarter-Plane 71
Patterns 71
3 A General Self-healing Transformation 75
4 Self-healing for Polyomino Tile Sets 77
5 Open Questions 80
6 Discussion 83
References 85
Compact Error-Resilient Computational DNA Tilings 87
1 Introduction 87
2 Algorithmic Assembly Problems 88
3 Error-Resilient Assembly Using Two-Way Overlay 93
Redundancy 93
4 Error-Resilient Assembly Using Three-Way Overlay 100
Redundancy 100
5 Computer Simulation 107
6 Discussion 108
References 109
Forbidding-Enforcing Conditions in DNA Self-assembly of Graphs 112
1 Introduction 112
2 Forbidding–Enforcing Systems 113
3 A Model for DNA Self-assembly 115
4 Forbidding–Enforcing Systems for Graphs 118
5 Forbidding–Enforcing for DNA Nanostructures 119
6 Conclusion 123
References 124
Part II Codes for DNA Nanotechnology 126
Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set 127
1 Introduction 127
2 Review of Algorithm for the Optimal MFE 129
Combination Problem 129
3 An Algorithm for the 134
Suboptimal 134
MFE 134
Combinations Problem 134
4 Time and Space Complexity 137
5 Conclusions 141
References 141
Involution Solid Codes 142
1 Introduction 142
2 De.nitions 143
3 Properties of Involution Overlap-Free Codes 145
4 Properties of Involution Solid Codes 146
References 149
Test Tube Selection of Large Independent Sets of DNA Oligonucleotides 152
1 Introduction 152
2 Methods and Materials for the Selection Protocol 153
3 Gel Characterization 154
4 Sample Sequencing of Library Oligonucleotides 156
5 Spectroscopic Characterization 159
6 Potential Advantages and Applications 163
7 Conclusion 164
References 164
Part III DNA Nanodevices 167
DNA-Based Motor Work at Bell Laboratories 168
1 Moore’s Law 168
2 Bad Luck 168
3 Dealing with the Press 173
References 176
Nanoscale Molecular Transport by Synthetic DNA Machines* 178
1 Introduction 178
2 A DNA Walker with the Gait of Kinesin 179
3 Hauling Molecular Cargo on a DNA Conveyor 181
4 Discussion 184
5 Methods 186
Acknowledgment 189
References 189
Part IV Electronics, Nanowire and DNA 192
A Supramolecular Approach to Metal Array Programming Using Arti.cial DNA 193
1 Introduction 193
2 Metal-Mediated Base Pairing in DNA 193
3 Discrete Self-assembled Metal Arrays in DNA 197
4 Perspectives 197
References 199
Multicomponent Assemblies Including Long DNA and Nanoparticles – An Answer for the Integration Problem? 200
1 Introduction 200
2 Immobilization of DNA on Surfaces 201
3 Nanoparticle Binding on DNA 204
4 Metallization of DNA 205
5 Concluding Remarks 208
References 209
Molecular Electronics: from Physics to Computing 215
1 Introduction 215
2 Ultimate Physical Limits to Computation 217
3 Limits of Semiconductor Technology 220
4 Molecular Electronics: from Physics to Computing 225
5 Discussion and Conclusion 236
References 237
Part V Other Bio-molecules in Self-assembly 246
Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials 247
1 Introduction 247
2 A Crystal Surface Recognizes the T-Rich Face of 249
Curved DNA Chains 249
3 The Strategy of the Palindromic Dimers 250
4 Experimental Evidence of DNA Sequence Recognition 252
by Mica Surface 252
5 How E.ective Is This Recognition Process? 254
6 From Statistics to Determinism 256
References 257
Adding Functionality to DNA Arrays: the Development of Semisynthetic DNA–Protein Conjugates 259
1 Introduction 259
2 Immobilization of Proteins by Means of DNA Hybridization 261
3 Functional Multiprotein Assemblies 263
4 Synthesis of Semisynthetic DNA–Protein Conjugates 264
5 Conclusions 268
References 270
Bacterial Surface Layer Proteins: a Simple but Versatile Biological Self-assembly System in Nature 275
1 Introduction 275
2 Occurrence of S-Layers 275
3 Ultrastructure of S-Layers 276
4 Secondary Cell Wall Polymers (SCWPs) 278
5 Genetic Engineering of S-Layer Proteins 278
6 Reassembly of Native and Recombinant S-Layer Proteins 280
7 Summary 284
Part VI Biomolecular Computational Models 289
Computing with Hairpins and Secondary Structures of DNA 290
1 Introduction 290
2 Computing by Hairpin Formation 290
3 Computing by Repeated Hairpin Formation and 292
Dissociation 292
4 Computing by Loop Dissociation 293
Acknowledgments 304
References 304
Bottom-up Approach to Complex Molecular Behavior 306
1 Introduction 306
2 Molecular-Scale Logic Gate as a Basic Computational 307
Unit 307
3 Initial Molecular Circuits 310
4 Molecular Automata 311
5 Molecular Cascades 312
6 Conclusions 315
References 316
Aqueous Computing: Writing on Molecules Dissolved in Water 318
1 Introduction: the Aqueous Concept 318
2 At Leiden University 319
3 At Binghamton University 320
4 At Tokyo Institute of Technology 322
5 At Hokkaido University 323
6 At Leiden Again: a Sample from Henkel’s Dissertation 324
7 The Future 326
References 327
Part VII Computations Inspired by Cells 329
Turing Machines with Cells on the Tape 330
1 Introduction 330
2 Prerequisites 331
3 Bio-Turing Machines 332
4 Some Examples 333
5 One-Letter Universality 336
6 Two Byzantine-Like Problems 340
7 Further Research Topics 342
References 343
Insights into a Biological Computer: Detangling Scrambled Genes in Ciliates 344
1 Introduction 344
2 Pointer Sequences 346
3 IES Excision in Oligohymenophorans 349
4 Gene Unscrambling in Spirotrichs 352
References 353
Modelling Simple Operations for Gene Assembly 355
1 Introduction 355
2 Mathematical Preliminaries 356
3 The Intramolecular Model 357
4 Formal Models for Simple Operations 360
5 Discussion 365
References 366
Part VIII Appendix 368
Publications by Nadrian C. Seeman 369

Produkt-Details

• Erscheint lt. Verlag: 29.6.2006
• Reihe/Serie: Natural Computing Series
• Reihe/Serie: Natural Computing Series
• Zusatzinfo: XI, 393 p.
• Verlagsort: Berlin
• Sprache: englisch
• Themenwelt: Informatik ► Theorie / Studium ► Künstliche Intelligenz / Robotik
• Themenwelt: Naturwissenschaften ► Biologie
• Themenwelt: Technik
• Schlagworte: algorithm • algorithms • Biomolecular computing • Computer • DNA • Electronics • genes • Modeling • Molecular motors • nanoelectronics • Nanoengineering • Nanoscience • nanotechnology • programming • Self-Assembly
• ISBN-10: 3-540-30296-4 / 3540302964
• ISBN-13: 978-3-540-30296-4 / 9783540302964