Chen / Jonoska / Rozenberg Nanotechnology: Science and Computation

1. Auflage 2006
ISBN: 978-3-540-30296-4
Verlag: Springer Berlin Heidelberg
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 393 Seiten

Reihe: Natural Computing Series

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).

Autoren/Hrsg.

Chen, Junghuei

Jonoska, Natasha

Rozenberg, Grzegorz

Inhaltsverzeichnis

1;Preface;7
2;Contents;9
3;Part I DNA Nanotechnology – Algorithmic Self-assembly;12
3.1;Scaffolded DNA Origami: from Generalized Multicrossovers to Polygonal Networks;13
3.1.1;1 Sca.olded DNA Origami for Parallel Multicrossovers;14
3.1.2;2 DNA Origami for Polygonal Networks;19
3.1.3;Acknowledgments;30
3.1.4;References;30
3.2;A Fresh Look at DNA Nanotechnology;32
3.2.1;1 Two-Dimensional DNA Triangle Arrays Designed with;32
3.2.2;a Tensegrity Strategy;32
3.2.3;2 DNA Molecular Motors;33
3.2.4;3 DNA Encoded One-Dimensional Array of Nanogold;39
3.2.5;4 DNA as Templates for Nanofabrication;40
3.2.6;5 Final Remarks;42
3.2.7;References;42
3.3;DNA Nanotechnology: an Evolving Field;44
3.3.1;1 Introduction;44
3.3.2;2 Programmable Self-assembly of 2D DNA Lattices;47
3.3.3;3 DNA Lattices as Nanosca.olds for Templated;49
3.3.4;Self-assembly;49
3.3.5;4 DNA Nanomechanical Devices;54
3.3.6;5 Conclusions and Outlook;58
3.3.7;References;59
3.4;Self-healing Tile Sets;63
3.4.1;1 Algorithmic Crystal Growth;63
3.4.2;2 Self-healing Transformations for Quarter-Plane;71
3.4.3;Patterns;71
3.4.4;3 A General Self-healing Transformation;75
3.4.5;4 Self-healing for Polyomino Tile Sets;77
3.4.6;5 Open Questions;80
3.4.7;6 Discussion;83
3.4.8;References;85
3.5;Compact Error-Resilient Computational DNA Tilings;87
3.5.1;1 Introduction;87
3.5.2;2 Algorithmic Assembly Problems;88
3.5.3;3 Error-Resilient Assembly Using Two-Way Overlay;93
3.5.4;Redundancy;93
3.5.5;4 Error-Resilient Assembly Using Three-Way Overlay;100
3.5.6;Redundancy;100
3.5.7;5 Computer Simulation;107
3.5.8;6 Discussion;108
3.5.9;References;109
3.6;Forbidding-Enforcing Conditions in DNA Self-assembly of Graphs;112
3.6.1;1 Introduction;112
3.6.2;2 Forbidding–Enforcing Systems;113
3.6.3;3 A Model for DNA Self-assembly;115
3.6.4;4 Forbidding–Enforcing Systems for Graphs;118
3.6.5;5 Forbidding–Enforcing for DNA Nanostructures;119
3.6.6;6 Conclusion;123
3.6.7;References;124
4;Part II Codes for DNA Nanotechnology;126
4.1;Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set;127
4.1.1;1 Introduction;127
4.1.2;2 Review of Algorithm for the Optimal MFE;129
4.1.3;Combination Problem;129
4.1.4;3 An Algorithm for the;134
4.1.5;Suboptimal;134
4.1.6;MFE;134
4.1.7;Combinations Problem;134
4.1.8;4 Time and Space Complexity;137
4.1.9;5 Conclusions;141
4.1.10;References;141
4.2;Involution Solid Codes;142
4.2.1;1 Introduction;142
4.2.2;2 De.nitions;143
4.2.3;3 Properties of Involution Overlap-Free Codes;145
4.2.4;4 Properties of Involution Solid Codes;146
4.2.5;References;149
4.3;Test Tube Selection of Large Independent Sets of DNA Oligonucleotides;152
4.3.1;1 Introduction;152
4.3.2;2 Methods and Materials for the Selection Protocol;153
4.3.3;3 Gel Characterization;154
4.3.4;4 Sample Sequencing of Library Oligonucleotides;156
4.3.5;5 Spectroscopic Characterization;159
4.3.6;6 Potential Advantages and Applications;163
4.3.7;7 Conclusion;164
4.3.8;References;164
5;Part III DNA Nanodevices;167
5.1;DNA-Based Motor Work at Bell Laboratories;168
5.1.1;1 Moore’s Law;168
5.1.2;2 Bad Luck;168
5.1.3;3 Dealing with the Press;173
5.1.4;References;176
5.2;Nanoscale Molecular Transport by Synthetic DNA Machines*;178
5.2.1;1 Introduction;178
5.2.2;2 A DNA Walker with the Gait of Kinesin;179
5.2.3;3 Hauling Molecular Cargo on a DNA Conveyor;181
5.2.4;4 Discussion;184
5.2.5;5 Methods;186
5.2.6;Acknowledgment;189
5.2.7;References;189
6;Part IV Electronics, Nanowire and DNA;192
6.1;A Supramolecular Approach to Metal Array Programming Using Arti.cial DNA;193
6.1.1;1 Introduction;193
6.1.2;2 Metal-Mediated Base Pairing in DNA;193
6.1.3;3 Discrete Self-assembled Metal Arrays in DNA;197
6.1.4;4 Perspectives;197
6.1.5;References;199
6.2;Multicomponent Assemblies Including Long DNA and Nanoparticles – An Answer for the Integration Problem?;200
6.2.1;1 Introduction;200
6.2.2;2 Immobilization of DNA on Surfaces;201
6.2.3;3 Nanoparticle Binding on DNA;204
6.2.4;4 Metallization of DNA;205
6.2.5;5 Concluding Remarks;208
6.2.6;References;209
6.3;Molecular Electronics: from Physics to Computing;215
6.3.1;1 Introduction;215
6.3.2;2 Ultimate Physical Limits to Computation;217
6.3.3;3 Limits of Semiconductor Technology;220
6.3.4;4 Molecular Electronics: from Physics to Computing;225
6.3.5;5 Discussion and Conclusion;236
6.3.6;References;237
7;Part V Other Bio-molecules in Self-assembly;246
7.1;Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials;247
7.1.1;1 Introduction;247
7.1.2;2 A Crystal Surface Recognizes the T-Rich Face of;249
7.1.3;Curved DNA Chains;249
7.1.4;3 The Strategy of the Palindromic Dimers;250
7.1.5;4 Experimental Evidence of DNA Sequence Recognition;252
7.1.6;by Mica Surface;252
7.1.7;5 How E.ective Is This Recognition Process?;254
7.1.8;6 From Statistics to Determinism;256
7.1.9;References;257
7.2;Adding Functionality to DNA Arrays: the Development of Semisynthetic DNA–Protein Conjugates;259
7.2.1;1 Introduction;259
7.2.2;2 Immobilization of Proteins by Means of DNA Hybridization;261
7.2.3;3 Functional Multiprotein Assemblies;263
7.2.4;4 Synthesis of Semisynthetic DNA–Protein Conjugates;264
7.2.5;5 Conclusions;268
7.2.6;References;270
7.3;Bacterial Surface Layer Proteins: a Simple but Versatile Biological Self-assembly System in Nature;275
7.3.1;1 Introduction;275
7.3.2;2 Occurrence of S-Layers;275
7.3.3;3 Ultrastructure of S-Layers;276
7.3.4;4 Secondary Cell Wall Polymers (SCWPs);278
7.3.5;5 Genetic Engineering of S-Layer Proteins;278
7.3.6;6 Reassembly of Native and Recombinant S-Layer Proteins;280
7.3.7;7 Summary;284
8;Part VI Biomolecular Computational Models;289
8.1;Computing with Hairpins and Secondary Structures of DNA;290
8.1.1;1 Introduction;290
8.1.2;2 Computing by Hairpin Formation;290
8.1.3;3 Computing by Repeated Hairpin Formation and;292
8.1.4;Dissociation;292
8.1.5;4 Computing by Loop Dissociation;293
8.1.6;Acknowledgments;304
8.1.7;References;304
8.2;Bottom-up Approach to Complex Molecular Behavior;306
8.2.1;1 Introduction;306
8.2.2;2 Molecular-Scale Logic Gate as a Basic Computational;307
8.2.3;Unit;307
8.2.4;3 Initial Molecular Circuits;310
8.2.5;4 Molecular Automata;311
8.2.6;5 Molecular Cascades;312
8.2.7;6 Conclusions;315
8.2.8;References;316
8.3;Aqueous Computing: Writing on Molecules Dissolved in Water;318
8.3.1;1 Introduction: the Aqueous Concept;318
8.3.2;2 At Leiden University;319
8.3.3;3 At Binghamton University;320
8.3.4;4 At Tokyo Institute of Technology;322
8.3.5;5 At Hokkaido University;323
8.3.6;6 At Leiden Again: a Sample from Henkel’s Dissertation;324
8.3.7;7 The Future;326
8.3.8;References;327
9;Part VII Computations Inspired by Cells;329
9.1;Turing Machines with Cells on the Tape;330
9.1.1;1 Introduction;330
9.1.2;2 Prerequisites;331
9.1.3;3 Bio-Turing Machines;332
9.1.4;4 Some Examples;333
9.1.5;5 One-Letter Universality;336
9.1.6;6 Two Byzantine-Like Problems;340
9.1.7;7 Further Research Topics;342
9.1.8;References;343
9.2;Insights into a Biological Computer: Detangling Scrambled Genes in Ciliates;344
9.2.1;1 Introduction;344
9.2.2;2 Pointer Sequences;346
9.2.3;3 IES Excision in Oligohymenophorans;349
9.2.4;4 Gene Unscrambling in Spirotrichs;352
9.2.5;References;353
9.3;Modelling Simple Operations for Gene Assembly;355
9.3.1;1 Introduction;355
9.3.2;2 Mathematical Preliminaries;356
9.3.3;3 The Intramolecular Model;357
9.3.4;4 Formal Models for Simple Operations;360
9.3.5;5 Discussion;365
9.3.6;References;366
10;Part VIII Appendix;368
10.1;Publications by Nadrian C. Seeman;369