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Molecular and Supramolecular Information Processing: From Molecular Switches to Logic Systems

Evgeny Katz (Editor)
ISBN: 978-3-527-33195-6
382 pages
August 2012
Molecular and Supramolecular Information Processing: From Molecular Switches to Logic Systems (3527331956) cover image
Edited by a renowned and much cited chemist, this book covers the whole span of molecular computers that are based on non-biological systems. 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 Biomolecular Information Processing, also by Prof. Katz, and available as a two-volume set.
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Preface XIII

List of Contributors XV

1 Molecular Information Processing: from Single Molecules to Supramolecular Systems and Interfaces – from Algorithms to Devices – Editorial Introduction 1
Evgeny Katz and Vera Bocharova

References 7

2 From Sensors to Molecular Logic: A Journey 11
A. Prasanna de Silva

2.1 Introduction 11

2.2 Designing Luminescent Switching Systems 11

2.3 Converting Sensing/Switching into Logic 13

2.4 Generalizing Logic 15

2.5 Expanding Logic 16

2.6 Utilizing Logic 17

2.7 Bringing in Physical Inputs 20

2.8 Summary and Outlook 21

Acknowledgments 21

References 21

3 Binary Logic with Synthetic Molecular and Supramolecular Species 25
Monica Semeraro, Massimo Baroncini, and Alberto Credi

3.1 Introduction 25

3.2 Combinational Logic Gates and Circuits 27

3.3 Sequential Logic Circuits 41

3.4 Summary and Outlook 48

Acknowledgments 49

References 49

4 Photonically Switched Molecular Logic Devices 53
Joakim Andréasson and Devens Gust

4.1 Introduction 53

4.2 Photochromic Molecules 54

4.3 Photonic Control of Energy and Electron Transfer Reactions 55

4.4 Boolean Logic Gates 61

4.5 Advanced Logic Functions 64

4.6 Conclusion 75

References 76

5 Engineering Luminescent Molecules with Sensing and Logic Capabilities 79
David C. Magri

5.1 Introduction 79

5.2 Engineering Luminescent Molecules 80

5.3 Logic Gates with the Same Modules in Different Arrangements 83

5.4 Consolidating AND Logic 84

5.5 ‘‘Lab-on-a-Molecule’’ Systems 87

5.6 Redox-Fluorescent Logic Gates 90

5.7 Summary and Perspectives 95

References 96

6 Supramolecular Assemblies for Information Processing 99
Cátia Parente Carvalho and Uwe Pischel

6.1 Introduction 99

6.2 Recognition of Metal Ion Inputs by Crown Ethers 100

6.3 Hydrogen-Bonded Supramolecular Assemblies as Logic Devices 102

6.4 Molecular Logic Gates with [2]Pseudorotaxane- and [2]Rotaxane-Based Switches 103

6.5 Supramolecular Host-Guest Complexes with Cyclodextrins and Cucurbiturils 110

6.6 Summary 116

Acknowledgments 117

References 117

7 Hybrid Semiconducting Materials: New Perspectives for Molecular-Scale Information Processing 121
Sylwia Gaw¸eda, Remigiusz Kowalik, Przemysław Kwolek, Wojciech Macyk, Justyna Mech, Marek Oszajca, Agnieszka Podborska, and Konrad Szaciłowski

7.1 Introduction 121

7.2 Synthesis of Semiconducting Thin Layers and Nanoparticles 122

7.3 Electrochemical Deposition 125

7.4 Organic Semiconductors–toward Hybrid Organic/Inorganic Materials 136

7.5 Mechanisms of Photocurrent Switching Phenomena 142

7.6 Digital Devices Based on PEPS Effect 161

7.7 Concluding Remarks 167

Acknowledgments 168

References 168

8 Toward Arithmetic Circuits in Subexcitable Chemical Media 175
Andrew Adamatzky, Ben De Lacy Costello, and Julian Holley

8.1 Awakening Gates in Chemical Media 175

8.2 Collision-Based Computing 176

8.3 Localizations in Subexcitable BZ Medium 176

8.4 BZ Vesicles 180

8.5 Interaction Between Wave Fragments 181

8.6 Universality and Polymorphism 183

8.7 Binary Adder 186

8.8 Regular and Irregular BZ Disc Networks 193

8.9 Memory Cells with BZ Discs 201

8.10 Conclusion 204

Acknowledgments 204

References 205

9 High-Concentration Chemical Computing Techniques for Solving Hard-To-Solve Problems, and their Relation to Numerical Optimization, Neural Computing, Reasoning under Uncertainty, and Freedom of Choice 209
Vladik Kreinovich and Olac Fuentes

9.1 What are Hard-To-Solve Problems and Why Solving Even One of Them is Important 209

9.2 How Chemical Computing Can Solve a Hard-To-Solve Problem of Propositional Satisfiability 218

9.3 The Resulting Method for Solving Hard Problems is Related to Numerical Optimization, Neural Computing, Reasoning under Uncertainty, and Freedom of Choice 228

Acknowledgments 234

References 234

10 All Kinds of Behavior are Possible in Chemical Kinetics: A Theorem and its Potential Applications to Chemical Computing 237
Vladik Kreinovich

10.1 Introduction 237

10.2 Main Result 239

10.3 Proof 246

Acknowledgments 256

References 257

11 Kabbalistic–Leibnizian Automata for Simulating the Universe 259
Andrew Schumann

11.1 Introduction 259

11.2 Historical Background of Kabbalistic–Leibnizian Automata 259

11.3 Proof-Theoretic Cellular Automata 264

11.4 The Proof-Theoretic Cellular Automaton for Belousov–Zhabotinsky Reaction 268

11.5 The Proof-Theoretic Cellular Automaton for Dynamics of Plasmodium of Physarum polycephalum 271

11.6 Unconventional Computing as a Novel Paradigm in Natural Sciences 276

11.7 Conclusion 278

Acknowledgments 278

References 278

12 Approaches to Control of Noise in Chemical and Biochemical Information and Signal Processing 281
Vladimir Privman

12.1 Introduction 281

12.2 From Chemical Information-Processing Gates to Networks 283

12.3 Noise Handling at the Gate Level and Beyond 286

12.4 Optimization of AND Gates 290

12.5 Networking of Gates 294

12.6 Conclusions and Challenges 296

Acknowledgments 297

References 297

13 Electrochemistry, Emergent Patterns, and Inorganic Intelligent Response 305
Saman Sadeghi and Michael Thompson

13.1 Introduction 305

13.2 Patten Formation in Complex Systems 306

13.3 Intelligent Response and Pattern Formation 308

13.4 Artificial Cognitive Materials 314

13.5 An Intelligent Electrochemical Platform 315

13.6 From Chemistry to Brain Dynamics 321

13.7 Final Remarks 327

References 328

14 Electrode Interfaces Switchable by Physical and Chemical Signals Operating as a Platform for Information Processing 333
Evgeny Katz

14.1 Introduction 333

14.2 Light-Switchable Modified Electrodes Based on Photoisomerizable Materials 334

14.3 Magnetoswitchable Electrodes Utilizing Functionalized Magnetic Nanoparticles or Nanowires 336

14.4 Potential-Switchable Modified Electrodes Based on Electrochemical Transformations of Functional Interfaces 339

14.5 Chemically/Biochemically Switchable Electrodes and Their Coupling with Biomolecular Computing Systems 343

14.6 Summary and Outlook 350

Acknowledgments 351

References 352

15 Conclusions and Perspectives 355
Evgeny Katz

References 357

Index 359

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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 Universität München (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.
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