Nicolas Giuseppone is Distinguished Professor of Chemistry (PREX2) at the University of Strasbourg, France.Andreas Walther is a Gutenberg Research Professor in the Department of Chemistry at the Johannes Gutenberg University of Mainz, Germany.

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• Foreword xiii1 Out-of-Equilibrium (Supra)molecular Systems and Materials: An Introduction 1Nicolas Giuseppone and Andreas Walther1.1 General Description of the Field 11.1.1 Background, Motivation, and Interdisciplinary Nature of the Topic 11.1.2 From Equilibrium Self-Assembly to Far-From-Equilibrium Self-Organization 51.1.3 From Responsive Materials to Adaptive and Interactive Materials Systems with Life like Behavior 71.1.4 An Outlook on Challenges Ahead 91.2 Description of the Book Content 10Acknowledgments 14References 142 Learning from Embryo Development to Engineer Self-organizing Materials 21Anis Senoussi, Yuliia Vyborna, Hélène Berthoumieux, Jean-Christophe Galas, and André Estevez-Torres2.1 The Embryo is a Material Capable of Chemical and Morphological Differentiation 222.2 Pattern Formation by a Reaction–Diffusion Turing Instability 242.2.1 Short Mathematical Analysis of the Turing Instability in a Two-species System 262.2.2 Turing Patterns In Vivo 272.2.3 Turing Patterns In Vitro 282.2.4 Simpler than Turing: Reaction–Diffusion Waves In Vitro 292.2.4.1 Min Protein Waves 292.2.4.2 DNA/Enzyme Waves 312.3 Pattern Formation by Positional Information 322.3.1 Models of Positional Information 322.3.1.1 Equilibrium Model: Cooperativity 342.3.1.2 Reaction-only Mechanism: Temporal Bistability 342.3.1.3 Reaction–Diffusion Mechanism: Spatial Bistability 352.3.2 Positional Information In Vivo: Patterning of the Drosophila blastoderm 352.3.3 Positional Information In Vitro 362.3.3.1 DNA Strand Displacement Patterns 362.3.3.2 PEN DNA/Enzyme Patterns 382.3.3.3 Transcription–Translation Patterns 392.4 Force Generation and Morphogenesis in Reconstituted Cytoskeletal Active Gels 402.4.1 Cytoskeletal Filaments and Molecular Motors, the Building Blocks of Active Gels 412.4.2 Active Gel Theory for a 1D System 422.4.3 Active Structures Generated by Cytoskeletal Systems In Vitro 452.4.3.1 Gliding Filaments 452.4.3.2 Aster Formation 452.4.3.3 Contractions 462.4.3.4 Active Flows 462.4.3.5 Corrugations 472.4.3.6 Vesicle and Droplet Deformation and Movement 472.5 Conclusion and Perspectives 48Acknowledgment 49References 503 From Clocks to Synchrony: The Design of Bioinspired Self-Regulation in Chemical Systems 61Annette F. Taylor3.1 Introduction 613.2 Bioinspired Behavior: Insight from Models 623.3 Feedback and Clocks 633.3.1 Clock Reactions 653.3.2 Autocatalysis in a Closed Reactor 663.4 Maintaining Systems Far from Equilibrium 693.5 Kinetic Switches 713.6 Design of Oscillators 723.7 Waves and Patterns 743.7.1 Fronts, Waves, and Spirals 743.7.2 Stationary Concentration Patterns 763.8 Synchronization and Collective Behavior 773.9 Materials Systems 783.9.1 Coupled Reactions and Materials 783.9.2 Feedback in Polymerization and Precipitation Processes 793.10 Conclusions 81References 824 De novo Design of Chemical Reaction Networks and Oscillators and Their Relation to Emergent Properties 91Sergey N. Semenov4.1 Introduction 914.2 The Role of Out-of-Equilibrium Conditions in the Emergence of CRN Properties and Functions 944.3 The Role of Stoichiometry, Connectivity, and Kinetics for CRNs 964.4 Design Guidelines and Network Motifs 984.5 Examples of De novo Designed CRNs in Well-Mixed Solutions 1074.6 Recent Advances in the Design of Flow Systems 1124.7 Examples of De novo Designed Reaction–Diffusion Networks 1124.8 Autocatalysis as an Emergent Property of CRNs 1164.9 Future Challenges and Directions in Designing CRNs 119References 1205 Kinetically Controlled Supramolecular Polymerization 131Kazunori Sugiyasu5.1 Introduction 1315.2 Thermodynamic Models for Supramolecular Polymerization 1345.3 Supramolecular Polymerization Under Kinetic Control 1365.4 Living Supramolecular Polymerization 1395.5 Seeded Supramolecular Polymerization Coupled with Chemical Reactions 1475.6 Equipment-Controlled Supramolecular Polymerizations 1515.7 Crystallization-Driven Self-Assembly and Other Systems 1535.8 Conclusion 157References 1586 Chemically Fueled, Transient Supramolecular Polymers 165Michelle P. van der Helm, Jan H. van Esch, and Rienk Eelkema6.1 Introduction 1656.2 Nonlinear Behavior: A Lesson from Biology 1676.3 Walking Uphill in the Energy Landscape 1696.4 The Nature of the Chemical Fuel 1716.5 Chemically Fueled, Transient Supramolecular Polymerization Systems 1726.6 Conclusion and Outlook 184References 1857 Design of Chemical Fuel-Driven Self-Assembly Processes 191Krishnendu Das, Rui Chen, Sushmitha Chandrabhas, Luca Gabrielli, and Leonard J. Prins7.1 Introduction 1917.2 Chemically Fueled Self-Assembly 1917.3 Transient Signal Generation Using Gold Nanoparticles 1977.4 Self-Assembly Under Dissipative Conditions 1997.5 Out-of-Equilibrium Self-Assembly 2017.6 Toward Chemical Fuel-Driven Self-Assembly 2057.7 Outlook 209References 2108 Dynamic Combinatorial Chemistry Out of Equilibrium 215Kai Liu and Sijbren Otto8.1 Introduction 2158.2 Kinetic Control in DCC 2178.2.1 Introducing Irreversible Reactions into DCLs 2178.2.1.1 Irreversible Reactions Acting on a Specific Library Member 2188.2.1.2 Irreversible Reactions Acting on Multiple DCL Members 2218.2.2 Kinetically Trapped Self-Assembly in DCC 2238.2.3 Phase Changes in DCC 2258.2.4 DCC Under Non-equilibrium Conditions 2288.3 Dissipative DCC 2308.3.1 Chemically Fueled DCC 2318.3.2 Light-Driven DCC 2318.4 Conclusions and Outlook 234References 2369 Controlling Self-Assembly of Nanoparticles Using Light 241Tong Bian, Zonglin Chu, and Rafal Klajn9.1 Introduction 2419.2 Nanoparticle Surface-Functionalized with Photoswitchable Molecules 2429.2.1 Azobenzene-Functionalized Nanoparticles 2429.2.2 Spiropyran-Functionalized Nanoparticles 2479.3 Assembling Nanoparticles Using Photodimerization Reactions 2519.4 (De)protonation of Nanoparticle-Bound Ligands Using Photoacids/Photobases 2539.5 Light-Induced Adsorption of Photoswitchable Molecules 2569.5.1 Photoswitchable Host–Guest Inclusion Complexes on Nanoparticle Surfaces 2569.5.2 Nonselective Adsorption of Photoswitchable Molecules 2599.6 Phase Transitions of Thermoresponsive Polymers Induced by Plasmonic Nanoparticles 2619.7 Light-Induced Chemical Reduction of Nanoparticle-Bound Ligands 2639.8 Irreversible Self-Assembly of Nanoparticles 2659.9 Extension to Microparticles 2669.10 Summary and Outlook 268References 26910 Photoswitchable Components to Drive Molecular Systems Away from Global Thermodynamic Minimum by Light 275Michael Kathan and Stefan Hecht10.1 Introduction 27510.2 Thermodynamic vs. Photodynamic Equilibria 27710.3 Manipulating Chemical Reactions and Equilibria with Light 28110.4 From Shifting Equilibria to Continuous Work Powered by Light 28710.5 Light to Control Assembly and Create Order 29610.6 Conclusion: From Remote Controlling to Driving Processes 297References 29911 Out-of-Equilibrium Threaded and Interlocked Molecular Structures 305Massimo Baroncini, Alberto Credi, and Serena Silvi11.1 Introduction 30511.1.1 Metastable, Kinetically Trapped, and Dissipative Non-equilibrium States 30711.1.2 Energy Inputs 30911.1.2.1 Chemical Energy 30911.1.2.2 Electrical Energy 31011.1.2.3 Light Energy 31011.1.3 Mechanically Interlocked Molecules and Their Threaded Precursors 31111.2 Pseudorotaxanes 31211.2.1 Semirotaxane-Based Molecular Reservoirs 31311.2.2 Supramolecular Pumps 31511.3 Rotaxanes 31911.3.1 Molecular Ratchets 31911.3.2 Generation of Non-equilibrium States by Autonomous Energy Consumption 32211.4 Catenanes 32411.4.1 Molecular Switches and Energy Ratchets 32511.4.2 Autonomous Chemically Fueled Catenane Rotary Motors 32711.5 Conclusions 331Acknowledgments 332References 33212 Light-driven Rotary Molecular Motors for Out-of-Equilibrium Systems 337Anouk S. Lubbe, Cosima L.G. Stähler, and Ben L. Feringa12.1 Introduction 33712.2 Design and Synthesis of Light-driven Rotary Motors 33912.3 Tuning the Properties of Molecular Motors 34212.4 Molecular Motors as Out-of-Equilibrium Systems 34612.5 Single Molecules Generating Work on the Nanoscale 34812.5.1 Molecular Stirring 34912.5.2 Amplifying Motor Function 35012.6 Immobilization 35212.6.1 Surface-Attached Molecular Motors 35212.6.2 3D Networks 35512.7 Liquid Crystals and Polymer Doping 35812.7.1 Liquid Crystals 35812.7.2 Polymer Doping 36112.8 Self-assembled Systems 36412.9 Conclusion 368References 36913 Design of Active Nanosystems Incorporating Biomolecular Motors 379Stanislav Tsitkov and Henry Hess13.1 Introduction 37913.2 Active Nanosystem Design 38113.3 Biological Components of Active Nanosystems 38413.3.1 Microtubules 38513.3.2 Kinesin 38713.3.3 Dynein 38813.3.4 Actin Filaments 38813.3.5 Myosin 38913.4 Interactions Between Components of Active Nanosystems 38913.4.1 Filament Response to External Load 39013.4.2 Motor–Filament Interactions 39013.4.3 Filament–Filament Interactions 39213.4.4 Filament–Cargo Interactions 39213.4.5 Motor–Surface Interactions 39313.5 Implementations of Active Nanosystems 39313.5.1 Delivering Cargo in Active Nanosystems 39413.5.2 Sensing Using Active Nanosystems 39613.5.2.1 Biosensors 39613.5.2.2 Surface Characterization 39613.5.2.3 Force Measurements 39713.5.3 Controlling the Behavior of Active Nanosystems 39713.5.3.1 Passive Control 39713.5.3.2 Active Control 39813.5.4 Extending the Lifetime of Active Nanosystems 39813.5.5 Higher-Order Structure Generation 39913.5.6 Simulating Active Nanosystems in the Inverted Motility Configuration 39913.5.7 Active Nanosystems Employing the Native Motility Configuration 40113.5.7.1 Biological Importance 40113.5.7.2 Active Nanosystems 40113.5.8 Active Nematic Gels 40313.6 Conclusion 403References 403Index 423

Nicolas Giuseppone is Distinguished Professor of Chemistry (PREX2) at the University of Strasbourg, France.Andreas Walther is a Gutenberg Research Professor in the Department of Chemistry at the Johannes Gutenberg University of Mainz, Germany.

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• Foreword xiii1 Out-of-Equilibrium (Supra)molecular Systems and Materials: An Introduction 1Nicolas Giuseppone and Andreas Walther1.1 General Description of the Field 11.1.1 Background, Motivation, and Interdisciplinary Nature of the Topic 11.1.2 From Equilibrium Self-Assembly to Far-From-Equilibrium Self-Organization 51.1.3 From Responsive Materials to Adaptive and Interactive Materials Systems with Life like Behavior 71.1.4 An Outlook on Challenges Ahead 91.2 Description of the Book Content 10Acknowledgments 14References 142 Learning from Embryo Development to Engineer Self-organizing Materials 21Anis Senoussi, Yuliia Vyborna, Hélène Berthoumieux, Jean-Christophe Galas, and André Estevez-Torres2.1 The Embryo is a Material Capable of Chemical and Morphological Differentiation 222.2 Pattern Formation by a Reaction–Diffusion Turing Instability 242.2.1 Short Mathematical Analysis of the Turing Instability in a Two-species System 262.2.2 Turing Patterns In Vivo 272.2.3 Turing Patterns In Vitro 282.2.4 Simpler than Turing: Reaction–Diffusion Waves In Vitro 292.2.4.1 Min Protein Waves 292.2.4.2 DNA/Enzyme Waves 312.3 Pattern Formation by Positional Information 322.3.1 Models of Positional Information 322.3.1.1 Equilibrium Model: Cooperativity 342.3.1.2 Reaction-only Mechanism: Temporal Bistability 342.3.1.3 Reaction–Diffusion Mechanism: Spatial Bistability 352.3.2 Positional Information In Vivo: Patterning of the Drosophila blastoderm 352.3.3 Positional Information In Vitro 362.3.3.1 DNA Strand Displacement Patterns 362.3.3.2 PEN DNA/Enzyme Patterns 382.3.3.3 Transcription–Translation Patterns 392.4 Force Generation and Morphogenesis in Reconstituted Cytoskeletal Active Gels 402.4.1 Cytoskeletal Filaments and Molecular Motors, the Building Blocks of Active Gels 412.4.2 Active Gel Theory for a 1D System 422.4.3 Active Structures Generated by Cytoskeletal Systems In Vitro 452.4.3.1 Gliding Filaments 452.4.3.2 Aster Formation 452.4.3.3 Contractions 462.4.3.4 Active Flows 462.4.3.5 Corrugations 472.4.3.6 Vesicle and Droplet Deformation and Movement 472.5 Conclusion and Perspectives 48Acknowledgment 49References 503 From Clocks to Synchrony: The Design of Bioinspired Self-Regulation in Chemical Systems 61Annette F. Taylor3.1 Introduction 613.2 Bioinspired Behavior: Insight from Models 623.3 Feedback and Clocks 633.3.1 Clock Reactions 653.3.2 Autocatalysis in a Closed Reactor 663.4 Maintaining Systems Far from Equilibrium 693.5 Kinetic Switches 713.6 Design of Oscillators 723.7 Waves and Patterns 743.7.1 Fronts, Waves, and Spirals 743.7.2 Stationary Concentration Patterns 763.8 Synchronization and Collective Behavior 773.9 Materials Systems 783.9.1 Coupled Reactions and Materials 783.9.2 Feedback in Polymerization and Precipitation Processes 793.10 Conclusions 81References 824 De novo Design of Chemical Reaction Networks and Oscillators and Their Relation to Emergent Properties 91Sergey N. Semenov4.1 Introduction 914.2 The Role of Out-of-Equilibrium Conditions in the Emergence of CRN Properties and Functions 944.3 The Role of Stoichiometry, Connectivity, and Kinetics for CRNs 964.4 Design Guidelines and Network Motifs 984.5 Examples of De novo Designed CRNs in Well-Mixed Solutions 1074.6 Recent Advances in the Design of Flow Systems 1124.7 Examples of De novo Designed Reaction–Diffusion Networks 1124.8 Autocatalysis as an Emergent Property of CRNs 1164.9 Future Challenges and Directions in Designing CRNs 119References 1205 Kinetically Controlled Supramolecular Polymerization 131Kazunori Sugiyasu5.1 Introduction 1315.2 Thermodynamic Models for Supramolecular Polymerization 1345.3 Supramolecular Polymerization Under Kinetic Control 1365.4 Living Supramolecular Polymerization 1395.5 Seeded Supramolecular Polymerization Coupled with Chemical Reactions 1475.6 Equipment-Controlled Supramolecular Polymerizations 1515.7 Crystallization-Driven Self-Assembly and Other Systems 1535.8 Conclusion 157References 1586 Chemically Fueled, Transient Supramolecular Polymers 165Michelle P. van der Helm, Jan H. van Esch, and Rienk Eelkema6.1 Introduction 1656.2 Nonlinear Behavior: A Lesson from Biology 1676.3 Walking Uphill in the Energy Landscape 1696.4 The Nature of the Chemical Fuel 1716.5 Chemically Fueled, Transient Supramolecular Polymerization Systems 1726.6 Conclusion and Outlook 184References 1857 Design of Chemical Fuel-Driven Self-Assembly Processes 191Krishnendu Das, Rui Chen, Sushmitha Chandrabhas, Luca Gabrielli, and Leonard J. Prins7.1 Introduction 1917.2 Chemically Fueled Self-Assembly 1917.3 Transient Signal Generation Using Gold Nanoparticles 1977.4 Self-Assembly Under Dissipative Conditions 1997.5 Out-of-Equilibrium Self-Assembly 2017.6 Toward Chemical Fuel-Driven Self-Assembly 2057.7 Outlook 209References 2108 Dynamic Combinatorial Chemistry Out of Equilibrium 215Kai Liu and Sijbren Otto8.1 Introduction 2158.2 Kinetic Control in DCC 2178.2.1 Introducing Irreversible Reactions into DCLs 2178.2.1.1 Irreversible Reactions Acting on a Specific Library Member 2188.2.1.2 Irreversible Reactions Acting on Multiple DCL Members 2218.2.2 Kinetically Trapped Self-Assembly in DCC 2238.2.3 Phase Changes in DCC 2258.2.4 DCC Under Non-equilibrium Conditions 2288.3 Dissipative DCC 2308.3.1 Chemically Fueled DCC 2318.3.2 Light-Driven DCC 2318.4 Conclusions and Outlook 234References 2369 Controlling Self-Assembly of Nanoparticles Using Light 241Tong Bian, Zonglin Chu, and Rafal Klajn9.1 Introduction 2419.2 Nanoparticle Surface-Functionalized with Photoswitchable Molecules 2429.2.1 Azobenzene-Functionalized Nanoparticles 2429.2.2 Spiropyran-Functionalized Nanoparticles 2479.3 Assembling Nanoparticles Using Photodimerization Reactions 2519.4 (De)protonation of Nanoparticle-Bound Ligands Using Photoacids/Photobases 2539.5 Light-Induced Adsorption of Photoswitchable Molecules 2569.5.1 Photoswitchable Host–Guest Inclusion Complexes on Nanoparticle Surfaces 2569.5.2 Nonselective Adsorption of Photoswitchable Molecules 2599.6 Phase Transitions of Thermoresponsive Polymers Induced by Plasmonic Nanoparticles 2619.7 Light-Induced Chemical Reduction of Nanoparticle-Bound Ligands 2639.8 Irreversible Self-Assembly of Nanoparticles 2659.9 Extension to Microparticles 2669.10 Summary and Outlook 268References 26910 Photoswitchable Components to Drive Molecular Systems Away from Global Thermodynamic Minimum by Light 275Michael Kathan and Stefan Hecht10.1 Introduction 27510.2 Thermodynamic vs. Photodynamic Equilibria 27710.3 Manipulating Chemical Reactions and Equilibria with Light 28110.4 From Shifting Equilibria to Continuous Work Powered by Light 28710.5 Light to Control Assembly and Create Order 29610.6 Conclusion: From Remote Controlling to Driving Processes 297References 29911 Out-of-Equilibrium Threaded and Interlocked Molecular Structures 305Massimo Baroncini, Alberto Credi, and Serena Silvi11.1 Introduction 30511.1.1 Metastable, Kinetically Trapped, and Dissipative Non-equilibrium States 30711.1.2 Energy Inputs 30911.1.2.1 Chemical Energy 30911.1.2.2 Electrical Energy 31011.1.2.3 Light Energy 31011.1.3 Mechanically Interlocked Molecules and Their Threaded Precursors 31111.2 Pseudorotaxanes 31211.2.1 Semirotaxane-Based Molecular Reservoirs 31311.2.2 Supramolecular Pumps 31511.3 Rotaxanes 31911.3.1 Molecular Ratchets 31911.3.2 Generation of Non-equilibrium States by Autonomous Energy Consumption 32211.4 Catenanes 32411.4.1 Molecular Switches and Energy Ratchets 32511.4.2 Autonomous Chemically Fueled Catenane Rotary Motors 32711.5 Conclusions 331Acknowledgments 332References 33212 Light-driven Rotary Molecular Motors for Out-of-Equilibrium Systems 337Anouk S. Lubbe, Cosima L.G. Stähler, and Ben L. Feringa12.1 Introduction 33712.2 Design and Synthesis of Light-driven Rotary Motors 33912.3 Tuning the Properties of Molecular Motors 34212.4 Molecular Motors as Out-of-Equilibrium Systems 34612.5 Single Molecules Generating Work on the Nanoscale 34812.5.1 Molecular Stirring 34912.5.2 Amplifying Motor Function 35012.6 Immobilization 35212.6.1 Surface-Attached Molecular Motors 35212.6.2 3D Networks 35512.7 Liquid Crystals and Polymer Doping 35812.7.1 Liquid Crystals 35812.7.2 Polymer Doping 36112.8 Self-assembled Systems 36412.9 Conclusion 368References 36913 Design of Active Nanosystems Incorporating Biomolecular Motors 379Stanislav Tsitkov and Henry Hess13.1 Introduction 37913.2 Active Nanosystem Design 38113.3 Biological Components of Active Nanosystems 38413.3.1 Microtubules 38513.3.2 Kinesin 38713.3.3 Dynein 38813.3.4 Actin Filaments 38813.3.5 Myosin 38913.4 Interactions Between Components of Active Nanosystems 38913.4.1 Filament Response to External Load 39013.4.2 Motor–Filament Interactions 39013.4.3 Filament–Filament Interactions 39213.4.4 Filament–Cargo Interactions 39213.4.5 Motor–Surface Interactions 39313.5 Implementations of Active Nanosystems 39313.5.1 Delivering Cargo in Active Nanosystems 39413.5.2 Sensing Using Active Nanosystems 39613.5.2.1 Biosensors 39613.5.2.2 Surface Characterization 39613.5.2.3 Force Measurements 39713.5.3 Controlling the Behavior of Active Nanosystems 39713.5.3.1 Passive Control 39713.5.3.2 Active Control 39813.5.4 Extending the Lifetime of Active Nanosystems 39813.5.5 Higher-Order Structure Generation 39913.5.6 Simulating Active Nanosystems in the Inverted Motility Configuration 39913.5.7 Active Nanosystems Employing the Native Motility Configuration 40113.5.7.1 Biological Importance 40113.5.7.2 Active Nanosystems 40113.5.8 Active Nematic Gels 40313.6 Conclusion 403References 403Index 423