Edited by a renowned and much cited chemist, this book covers the whole span of molecular computers that are based on biomolecules. The contributions by all the major scientists in the field provide an excellent overview of the latest developments in this rapidly expanding area.
A must-have for all researchers working on this very hot topic.
TOC:
Preface XIII
List of Contributors XV
1 Biomolecular Computing: From Unconventional Computing to ‘‘Smart’’ Biosensors and Actuators – Editorial Introduction 1
Evgeny Katz
References 5
2 Peptide-Based Computation: Switches, Gates, and Simple Arithmetic 9
Zehavit Dadon, Manickasundaram Samiappan, Nathaniel Wagner, Nurit Ashkenasy, and Gonen Ashkenasy
2.1 Introduction 9
2.2 Peptide-Based Replication Networks 10
2.3 Logic Gates within Ternary Networks 13
2.4 Symmetry and Order Requirements for Constructing the Logic Gates 16
2.5 Taking the Steps toward More Complex Arithmetic 19
2.6 Experimental Logic Gates 21
2.7 Adaptive Networks 24
2.8 Peptide-Based Switches and Gates for Molecular Electronics 28
2.9 Summary and Conclusion 29
Acknowledgments 30
References 30
3 Biomolecular Electronics and Protein-Based Optical Computing 33
Jordan A. Greco, Nicole L. Wagner, Matthew J. Ranaghan, Sanguthevar Rajasekaran, and Robert R. Birge
3.1 Introduction 33
3.2 Biomolecular and Semiconductor Electronics 34
3.3 Bacteriorhodopsin as a Photonic and Holographic Material for Bioelectronics 40
3.4 Fourier Transform Holographic Associative Processors 42
3.5 Three-Dimensional Optical Memories 45
3.6 Genetic Engineering of Bacteriorhodopsin for Device Applications 51
3.7 Future Directions 53
Acknowledgments 54
References 54
4 Bioelectronic Devices Controlled by Enzyme-Based Information Processing Systems 61
Evgeny Katz
4.1 Introduction 61
4.2 Enzyme-Based Logic Systems Producing pH Changes as Output Signals 62
4.3 Interfacing of the Enzyme Logic Systems with Electrodes Modified with Signal-Responsive Polymers 64
4.4 Switchable Biofuel Cells Controlled by the Enzyme Logic Systems 68
4.5 Biomolecular Logic Systems Composed of Biocatalytic and Biorecognition Units and Their Integration with Biofuel Cells 70
4.6 Processing of Injury Biomarkers by Enzyme Logic Systems Associated with Switchable Electrodes 74
4.7 Summary and Outlook 77
Acknowledgments 78
References 78
5 Enzyme Logic Digital Biosensors for Biomedical Applications 81
Evgeny Katz and Joseph Wang
5.1 Introduction 81
5.2 Enzyme-Based Logic Systems for Identification of Injury Conditions 82
5.3 Multiplexing of Injury Codes for the Parallel Operation of Enzyme Logic Gates 85
5.4 Scaling Up the Complexity of the Biocomputing Systems for Biomedical Applications – Mimicking Biochemical Pathways 89
5.5 Application of Filter Systems for Improving Digitalization of the Output Signals Generated by Enzyme Logic Systems for Injury Analysis 94
5.6 Conclusions and Perspectives 96
Acknowledgments 98
Appendix 98
References 99
6 Information Security Applications Based on Biomolecular Systems 103
Guinevere Strack, Heather R. Luckarift, Glenn R. Johnson, and Evgeny Katz
6.1 Introduction 103
6.2 Molecular and Bio-molecular Keypad Locks 104
6.3 Antibody Encryption and Steganography 108
6.4 Bio-barcode 113
6.5 Conclusion 114
Acknowledgments 114
References 114
7 Biocomputing: Explore Its Realization and Intelligent Logic Detection 117
Ming Zhou and Shaojun Dong
7.1 Introduction 117
7.2 DNA Biocomputing 119
7.3 Aptamer Biocomputing 121
7.4 Enzyme Biocomputing 124
7.5 Conclusions and Perspectives 128
References 129
8 Some Experiments and Models in Molecular Computing and Robotics 133
Milan N. Stojanovic and Darko Stefanovic
8.1 Introduction 133
8.2 From Gates to Programmable Automata 133
8.3 From Random Walker to Molecular Robotics 139
8.4 Conclusions 142
Acknowledgments 143
References 143
9 Biomolecular Finite Automata 145
Tamar Ratner, Sivan Shoshani, Ron Piran, and Ehud Keinan
9.1 Introduction 145
9.2 Biomolecular Finite Automata 146
9.3 Biomolecular Finite Transducer 167
9.4 Applications in Developmental Biology 172
9.5 Outlook 176
References 178
10 In Vivo Information Processing Using RNA Interference 181
Yaakov Benenson
10.1 Introduction 181
10.2 RNA Interference-Based Logic 183
10.3 Building the Sensory Module 189
10.4 Outlook 195
References 197
11 Biomolecular Computing Systems 199
Harish Chandran, Sudhanshu Garg, Nikhil Gopalkrishnan, and John H. Reif
11.1 Introduction 199
11.2 DNA as a Tool for Molecular Programming 200
11.3 Birth of DNA Computing: Adleman’s Experiment and Extensions 203
11.4 Computation Using DNA Tiles 205
11.5 Experimental Advances in Purely Hybridization-Based Computation 209
11.6 Experimental Advances in Enzyme-Based DNA Computing 212
11.7 Biochemical DNA Reaction Networks 217
11.8 Conclusion: Challenges in DNA-Based Biomolecular Computation 218
Acknowledgments 221
References 221
12 Enumeration Approach to the Analysis of Interacting Nucleic Acid Strands 225
Satoshi Kobayashi and Takaya Kawakami
12.1 Introduction 225
12.2 Definitions and Notations for Set and Multiset 226
12.3 Chemical Equilibrium and Hybridization Reaction System 227
12.4 Symmetric Enumeration Method 230
12.5 Applying SEM to Nucleic Acid Strands Interaction 236
12.6 Conclusions 243
References 244
13 Restriction Enzymes in Language Generation and Plasmid Computing 245
Tom Head
13.1 Introduction 245
13.2 Wet Splicing Systems 246
13.3 Dry Splicing Systems 249
13.4 Splicing Theory: Its Original Motivation and Its Extensive Unforeseen Developments 252
13.5 Computing with Plasmids 253
13.6 Fluid Memory 254
13.7 Examples of Aqueous Computations 255
13.8 Final Comments about Computing with Biomolecules 260
References 261
14 Development of Bacteria-Based Cellular Computing Circuits for Sensing and Control in Biological Systems 265
Michaela A. TerAvest, Zhongjian Li, and Largus T. Angenent
14.1 Introduction 265
14.2 Cellular Computing Circuits 267
14.3 Conclusion 276
Acknowledgments 277
References 277
15 The Logic of Decision Making in Environmental Bacteria 279
Rafael Silva-Rocha, Javier Tamames, and Víctor de Lorenzo
15.1 Introduction 279
15.2 Building Models for Biological Networks 281
15.3 Formulation and Simulation of Regulatory Networks 283
15.4 Boolean Analysis of Regulatory Networks 285
15.5 Boolean Description of m-xylene Biodegradation by P. putida mt-2: the TOL logicome 289
15.6 Conclusion and Outlook 298
Acknowledgments 299
References 299
16 Qualitative and Quantitative Aspects of a Model for Processes Inspired by the Functioning of the Living Cell 303
Andrzej Ehrenfeucht, Jetty Kleijn, Maciej Koutny, and Grzegorz Rozenberg
16.1 Introduction 303
16.2 Reactions 304
16.3 Reaction Systems 305
16.4 Examples 307
16.5 Reaction Systems with Measurements 310
16.6 Generalized Reactions 312
16.7 A Generic Quantitative Model 315
16.8 Approximations of Gene Expression Systems 316
16.9 Simulating Approximations by Reaction Systems 318
16.10 Discussion 319
Acknowledgments 321
References 321
17 Computational Methods for Quantitative Submodel Comparison 323
Andrzej Mizera, Elena Czeizler, and Ion Petre
17.1 Introduction 323
17.2 Methods for Model Decomposition 324
17.3 Methods for Submodel Comparison 327
17.4 Case Study 332
17.5 Discussion 342
Acknowledgments 343
References 343
18 Conclusions and Perspectives 347
Evgeny Katz
References 349
Index 351