Foreword xiii
1 Out-of-Equilibrium (Supra)molecular Systems and Materials: An Introduction 1
Nicolas Giuseppone and Andreas Walther
1.1 General Description of the Field 1
1.1.1 Background, Motivation, and Interdisciplinary Nature of the Topic 1
1.1.2 From Equilibrium Self-Assembly to Far-From-Equilibrium Self-Organization 5
1.1.3 From Responsive Materials to Adaptive and Interactive Materials Systems with Life like Behavior 7
1.1.4 An Outlook on Challenges Ahead 9
1.2 Description of the Book Content 10
Acknowledgments 14
References 14
2 Learning from Embryo Development to Engineer Self-organizing Materials 21
Anis Senoussi, Yuliia Vyborna, Hélène Berthoumieux, Jean-Christophe Galas, and André Estevez-Torres
2.1 The Embryo is a Material Capable of Chemical and Morphological Differentiation 22
2.2 Pattern Formation by a ReactionDiffusion Turing Instability 24
2.2.1 Short Mathematical Analysis of the Turing Instability in a Two-species System 26
2.2.2 Turing PatternsIn Vivo 27
2.2.3 Turing PatternsIn Vitro 28
2.2.4 Simpler than Turing: ReactionDiffusion WavesIn Vitro 29
2.2.4.1 Min Protein Waves 29
2.2.4.2 DNA/Enzyme Waves 31
2.3 Pattern Formation by Positional Information 32
2.3.1 Models of Positional Information 32
2.3.1.1 Equilibrium Model: Cooperativity 34
2.3.1.2 Reaction-only Mechanism: Temporal Bistability 34
2.3.1.3 ReactionDiffusion Mechanism: Spatial Bistability 35
2.3.2 Positional InformationIn Vivo: Patterning of the Drosophila blastoderm 35
2.3.3 Positional InformationIn Vitro 36
2.3.3.1 DNA Strand Displacement Patterns 36
2.3.3.2 PEN DNA/Enzyme Patterns 38
2.3.3.3 TranscriptionTranslation Patterns 39
2.4 Force Generation and Morphogenesis in Reconstituted Cytoskeletal Active Gels 40
2.4.1 Cytoskeletal Filaments and Molecular Motors, the Building Blocks of Active Gels 41
2.4.2 Active Gel Theory for a 1D System 42
2.4.3 Active Structures Generated by Cytoskeletal Systems In Vitro 45
2.4.3.1 Gliding Filaments 45
2.4.3.2 Aster Formation 45
2.4.3.3 Contractions 46
2.4.3.4 Active Flows 46
2.4.3.5 Corrugations 47
2.4.3.6 Vesicle and Droplet Deformation and Movement 47
2.5 Conclusion and Perspectives 48
Acknowledgment 49
References 50
3 From Clocks to Synchrony: The Design of Bioinspired Self-Regulation in Chemical Systems 61
Annette F. Taylor
3.1 Introduction 61
3.2 Bioinspired Behavior: Insight from Models 62
3.3 Feedback and Clocks 63
3.3.1 Clock Reactions 65
3.3.2 Autocatalysis in a Closed Reactor 66
3.4 Maintaining Systems Far from Equilibrium 69
3.5 Kinetic Switches 71
3.6 Design of Oscillators 72
3.7 Waves and Patterns 74
3.7.1 Fronts, Waves, and Spirals 74
3.7.2 Stationary Concentration Patterns 76
3.8 Synchronization and Collective Behavior 77
3.9 Materials Systems 78
3.9.1 Coupled Reactions and Materials 78
3.9.2 Feedback in Polymerization and Precipitation Processes 79
3.10 Conclusions 81
References 82
4 De novo Design of Chemical Reaction Networks and Oscillators and Their Relation to Emergent Properties 91
Sergey N. Semenov
4.1 Introduction 91
4.2 The Role of Out-of-Equilibrium Conditions in the Emergence of CRN Properties and Functions 94
4.3 The Role of Stoichiometry, Connectivity, and Kinetics for CRNs 96
4.4 Design Guidelines and Network Motifs 98
4.5 Examples ofDe novo Designed CRNs in Well-Mixed Solutions 107
4.6 Recent Advances in the Design of Flow Systems 112
4.7 Examples ofDe novo Designed ReactionDiffusion Networks 112
4.8 Autocatalysis as an Emergent Property of CRNs 116
4.9 Future Challenges and Directions in Designing CRNs 119
References 120
5 Kinetically Controlled Supramolecular Polymerization 131
Kazunori Sugiyasu
5.1 Introduction 131
5.2 Thermodynamic Models for Supramolecular Polymerization 134
5.3 Supramolecular Polymerization Under Kinetic Control 136
5.4 Living Supramolecular Polymerization 139
5.5 Seeded Supramolecular Polymerization Coupled with Chemical Reactions 147
5.6 Equipment-Controlled Supramolecular Polymerizations 151
5.7 Crystallization-Driven Self-Assembly and Other Systems 153
5.8 Conclusion 157
References 158
6 Chemically Fueled, Transient Supramolecular Polymers 165
Michelle P. van der Helm, Jan H. van Esch, and Rienk Eelkema
6.1 Introduction 165
6.2 Nonlinear Behavior: A Lesson from Biology 167
6.3 Walking Uphill in the Energy Landscape 169
6.4 The Nature of the Chemical Fuel 171
6.5 Chemically Fueled, Transient Supramolecular Polymerization Systems 172
6.6 Conclusion and Outlook 184
References 185
7 Design of Chemical Fuel-Driven Self-Assembly Processes 191
Krishnendu Das, Rui Chen, Sushmitha Chandrabhas, Luca Gabrielli, and Leonard J. Prins
7.1 Introduction 191
7.2 Chemically Fueled Self-Assembly 1917.3 Transient Signal Generation Using Gold Nanoparticles 197
7.4 Self-Assembly Under Dissipative Conditions 199
7.5 Out-of-Equilibrium Self-Assembly 201
7.6 Toward Chemical Fuel-Driven Self-Assembly 205
7.7 Outlook 209
References 210
8 Dynamic Combinatorial Chemistry Out of Equilibrium 215
Kai Liu and Sijbren Otto
8.1 Introduction 215
8.2 Kinetic Control in DCC 217
8.2.1 Introducing Irreversible Reactions into DCLs 217
8.2.1.1 Irreversible Reactions Acting on a Specific Library Member 218
8.2.1.2 Irreversible Reactions Acting on Multiple DCL Members 221
8.2.2 Kinetically Trapped Self-Assembly in DCC 223
8.2.3 Phase Changes in DCC 225
8.2.4 DCC Under Non-equilibrium Conditions 228
8.3 Dissipative DCC 230
8.3.1 Chemically Fueled DCC 231
8.3.2 Light-Driven DCC 231
8.4 Conclusions and Outlook 234
References 236
9 Controlling Self-Assembly of Nanoparticles Using Light 241
Tong Bian, Zonglin Chu, and Rafal Klajn
9.1 Introduction 241
9.2 Nanoparticle Surface-Functionalized with Photoswitchable Molecules 242
9.2.1 Azobenzene-Functionalized Nanoparticles 242
9.2.2 Spiropyran-Functionalized Nanoparticles 247
9.3 Assembling Nanoparticles Using Photodimerization Reactions 251
9.4 (De)protonation of Nanoparticle-Bound Ligands Using Photoacids/Photobases 253
9.5 Light-Induced Adsorption of Photoswitchable Molecules 256
9.5.1 Photoswitchable HostGuest Inclusion Complexes on Nanoparticle Surfaces 256
9.5.2 Nonselective Adsorption of Photoswitchable Molecules 259
9.6 Phase Transitions of Thermoresponsive Polymers Induced by Plasmonic Nanoparticles 261
9.7 Light-Induced Chemical Reduction of Nanoparticle-Bound Ligands 263
9.8 Irreversible Self-Assembly of Nanoparticles 265
9.9 Extension to Microparticles 266
9.10 Summary and Outlook 268
References 269
10 Photoswitchable Components to Drive Molecular Systems Away from Global Thermodynamic Minimum by Light 275
Michael Kathan and Stefan Hecht
10.1 Introduction 275
10.2 Thermodynamic vs. Photodynamic Equilibria 277
10.3 Manipulating Chemical Reactions and Equilibria with Light 281
10.4 From Shifting Equilibria to Continuous Work Powered by Light 287
10.5 Light to Control Assembly and Create Order 296
10.6 Conclusion: From Remote Controlling to Driving Processes 297
References 299
11 Out-of-Equilibrium Threaded and Interlocked Molecular Structures 305
Massimo Baroncini, Alberto Credi, and Serena Silvi
11.1 Introduction 305
11.1.1 Metastable, Kinetically Trapped, and Dissipative Non-equilibrium States 307
11.1.2 Energy Inputs 309
11.1.2.1 Chemical Energy 309
11.1.2.2 Electrical Energy 310
11.1.2.3 Light Energy 310
11.1.3 Mechanically Interlocked Molecules and Their Threaded Precursors 311
11.2 Pseudorotaxanes 312
11.2.1 Semirotaxane-Based Molecular Reservoirs 313
11.2.2 Supramolecular Pumps 315
11.3 Rotaxanes 319
11.3.1 Molecular Ratchets 319
11.3.2 Generation of Non-equilibrium States by Autonomous Energy Consumption 322
11.4 Catenanes 324
11.4.1 Molecular Switches and Energy Ratchets 325
11.4.2 Autonomous Chemically Fueled Catenane Rotary Motors 327
11.5 Conclusions 331
Acknowledgments 332
References 332
12 Light-driven Rotary Molecular Motors for Out-of-Equilibrium Systems 337
Anouk S. Lubbe, Cosima L.G. Stähler, and Ben L. Feringa
12.1 Introduction 337
12.2 Design and Synthesis of Light-driven Rotary Motors 339
12.3 Tuning the Properties of Molecular Motors 342
12.4 Molecular Motors as Out-of-Equilibrium Systems 346
12.5 Single Molecules Generating Work on the Nanoscale 348
12.5.1 Molecular Stirring 349
12.5.2 Amplifying Motor Function 350
12.6 Immobilization 352
12.6.1 Surface-Attached Molecular Motors 352
12.6.2 3D Networks 355
12.7 Liquid Crystals and Polymer Doping 358
12.7.1 Liquid Crystals 358
12.7.2 Polymer Doping 361
12.8 Self-assembled Systems 364
12.9 Conclusion 368
References 369
13 Design of Active Nanosystems Incorporating Biomolecular Motors 379
Stanislav Tsitkov and Henry Hess
13.1 Introduction 379
13.2 Active Nanosystem Design 381
13.3 Biological Components of Active Nanosystems 384
13.3.1 Microtubules 385
13.3.2 Kinesin 387
13.3.3 Dynein 388
13.3.4 Actin Filaments 388
13.3.5 Myosin 389
13.4 Interactions Between Components of Active Nanosystems 389
13.4.1 Filament Response to External Load 390
13.4.2 MotorFilament Interactions 390
13.4.3 FilamentFilament Interactions 392
13.4.4 FilamentCargo Interactions 392
13.4.5 MotorSurface Interactions 393
13.5 Implementations of Active Nanosystems 393
13.5.1 Delivering Cargo in Active Nanosystems 394
13.5.2 Sensing Using Active Nanosystems 396
13.5.2.1 Biosensors 396
13.5.2.2 Surface Characterization 396
13.5.2.3 Force Measurements 397
13.5.3 Controlling the Behavior of Active Nanosystems 397
13.5.3.1 Passive Control 397
13.5.3.2 Active Control 398
13.5.4 Extending the Lifetime of Active Nanosystems 398
13.5.5 Higher-Order Structure Generation 399
13.5.6 Simulating Active Nanosystems in the Inverted Motility Configuration 399
13.5.7 Active Nanosystems Employing the Native Motility Configuration 401
13.5.7.1 Biological Importance 401
13.5.7.2 Active Nanosystems 401
13.5.8 Active Nematic Gels 403
13.6 Conclusion 403
References 403
Index 423
