Biomolecular Information Processing: From Logic Systems to Smart Sensors and Actuators

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. Perfectly complements Molecular and Supramolecular Information Processing, also by Prof. Katz, and available as a two-volume set.

Table of Contents:
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 Victor 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

About the Author :
Evgeny Katz received his Ph.D. in Chemistry from Frumkin Institute of Electrochemistry (Moscow) in 1983. He was a senior researcher in the Institute of Photosynthesis (Pushchino), Russian Academy of Sciences (1983-1991), a Humboldt fellow at Technische Universitat Munchen (Germany) (1992-1993), and a research associate professor at the Hebrew University of Jerusalem (1993-2006). Since 2006 he is Milton Kerker Chaired Professor at the Department of Chemistry and Biomolecular Science, Clarkson University, NY (USA). He has (co)authored over 300 papers in the areas of biocomputing, bioelectronics, biosensors and biofuel cells (Hirsch-index 65). Professor Katz serves as Editor-in-Chief for IEEE Sensors Journal and a member of editorial boards of many other journals.