CONTENTS -- Preface -- PART I INTRODUCTION -- 1. Analysis, Design and Control of Complex Chemical Systems Alexander S. Mikhailov and Gerhard Ertl -- 1. Introduction -- 2. A Brief Historical Overview -- 3. Recent Developments and Open Perspectives -- References -- PART II SINGLE MOLECULES, NANOSCALE PHENOMENA AND ACTIVE PARTICLES -- 2. Imaging and Manipulation of Single Molecules by Scanning Tunneling Microscopy Leonhard Grill -- 1. Introduction -- 2. Imaging and Spectroscopy of Single Molecules -- 2.1. Imaging single molecules -- 2.2. Chemical identification by spectroscopy -- 2.3. Imaging of diffusion processes -- 3. Manipulation of Single Molecules -- 3.1. Manipulation without bias voltage -- 3.2. Electron-induced manipulation -- 3.3. Electric-field induced manipulation -- 3.4. Lateral manipulation: Hopping vs rolling -- 3.5. Vertical manipulation: Pulling single molecules from a surface -- Acknowledgments -- References -- 3. Self-Organization at the Nanoscale in Far-From- Equilibrium Surface Reactions and Copolymerizations Pierre Gaspard -- 1. Introduction -- 2. Fundamental Aspects of Nonequilibrium Nanosystems -- 2.1. Structure and function of nanosystems -- 2.2. Out-of-equilibrium directionality of fluctuating currents -- 2.3. Thermodynamic origins of dynamical order -- 3. Heterogeneous Catalytic Reactions in High Electric Fields -- 3.1. Surface conditions in FEM and FIM -- 3.2. Adsorption-desorption kinetics -- 3.3. Surface oxides of rhodium -- 3.4. The H2-O2/Rh system -- 3.4.1. Kinetic equations -- 3.4.2. Bistability -- 3.4.3. Oscillations -- 3.5. Self-organization at the nanoscale -- 4. Copolymerization processes -- 4.1. Information processing at the molecular scale -- 4.2. Thermodynamics of free copolymerization -- 4.3. Thermodynamics of copolymerization with a template -- 4.4. The case of DNA replication.

5. Conclusions and Perspectives -- Acknowledgments -- References -- 4. Single Molecule and Collective Dynamics of Motor Protein Coupled with Mechano-Sensitive Chemical Reaction Mitsuhiro Iwaki, Lorenzo Marcucci, Yuichi Togashi and Toshio Yanagida -- 1. What is a Motor Protein? -- 2. Measurement of Myosin at the Single Molecule Level -- 3. Mechanosensitivity of ATP Hydrolysis during the Unidirectional Motion of Dimeric Myosin -- 3.1. Mechanosensitive detachment of myosin-V from actin -- 3.2. Mechanosensitive attachment of myosin-VI to actin -- 4. Modeling and Simulating Mechanochemical Coupling and Motor Protein Motion -- 4.1. Molecular dynamics simulations -- 4.2. Coarse-grained models and dynamics -- 4.3. Quantum mechanics for chemical processes -- 5. Modeling and Simulations of the Collective Behaviour of Motor Proteins -- 5.1. Huxley's 1957 model -- 5.2. Huxley and Simmons' 1971 model -- 5.3. Diffusional model -- References -- 5. Nanomotors Propelled by Chemical Reactions Raymond Kapral -- 1. Introduction -- 2. Propulsion by Phoretic Mechanisms -- 3. Microscopic and Mesoscopic Dynamics of Nanomotors -- 4. Sphere Dimer Motors -- Motor efficiency -- Motor dynamics in chemically active media -- Motors can interact with chemical patterns -- Diffusion and mean square displacement -- 5. Collective Dynamics -- 6. Conclusion -- Acknowledgments -- References -- 6. Biology of Nanobots Wentao Duan, Ryan Pavlick and Ayusman Sen -- 1. Introduction -- 2. Mechanisms of Motility -- 2.1. Non-electrolyte diffusiophoresis -- 2.2. Electrolyte diffusiophoresis -- 2.3. Electrophoresis -- 2.4. Other phoretic mechanisms -- 2.5. Bubble propulsion -- 2.6. Non-reciprocal swimmers -- 2.7. Chemotaxis -- 3. Emergent Collective Behavior of Nanobots -- 3.1. Interaction between colloid particles based on self-diffusiophoresis.

3.1.1. Diffusiophoretic interaction between the central particle and nearby positive particles -- 3.1.2. Diffusiophoretic interaction between the central particle and nearby negative particles -- 3.2. Examples of diffusiophoresis-based emergent systems -- 3.3. Motion analysis of particles in collective emergent systems -- 4. Conclusion -- Acknowledgment -- References -- PART III REACTION-DIFFUSION SYSTEMS AND NONEQUILIBRIUM SOFT MATTER -- 7. Wave Phenomena in Reaction-Diffusion Systems Oliver Steinbock and Harald Engel -- 1. Introduction -- 2. The Belousov-Zhabotinsky Reaction -- 3. Anomalous Dispersion of Periodic Pulse -- 4. Pinned Two-dimensional Spiral Waves -- 5. Scroll Waves -- 6. Summary and Conclusions -- Acknowledgments -- References -- 8. Self-Oscillating Polymer Gels as Smart Materials Ryo Yoshida -- 1. Introduction -- 2. Chemomechanical Behavior of Self-Oscillating Polymer Gel -- 3. Application to Autonomous Mass Transport Systems -- 3.1. Mass transport surface utilizing peristaltic motion of gel -- 3.2. Modeling of mass transport on gel surface -- 3.3. Surface design of gel conveyer -- 3.4. Effect of physical interactions between loaded cargo and gel surface -- 3.5. Effect of surface roughness -- 4. Self-oscillation of Polymer Solution and Microgel Dispersion -- 4.1. Self-flocculating/dispersing oscillation of microgels -- 4.2. Viscosity oscillation of polymer solution and microgel dispersion -- 4.3. Autonomous viscosity oscillation by reversible complex formation of terpyridine-terminated poly(ethylene glycol) in the BZ reaction -- 5. Attempts of Self-oscillation under Physiological Conditions -- 6. Conclusions -- References -- 9. Stochastic Fluctuations and Spontaneous Symmetry Breaking in the Chemotaxis Signaling System of Dicyostelium Cells Tatsuo Shibata -- 1. Introduction -- 2. Eukaryotic Chemotaxis is Limited by Noise.

3. Signal Transduction and Spontaneous Cell Motility -- 4. Spontaneous Pattern Formation in Phosphatidylinositol Lipid Signaling Reaction -- 5. Conclusion -- References -- 10. Mechanochemical Pattern Formation in the Polarization of the One-Cell C. Elegans Embryo Justin S. Bois and Stephan W. Grill -- 1. Introduction -- 2. Polarization of the C. elegans zygote: The Basics -- 3. Mechanics -- 4. Biochemistry -- 5. Mechanochemistry -- 6. Conclusions -- References -- PART IV OSCILLATIONS AND SYNCRONIZATION -- 11. Synchronization of Electrochemical Oscillators Mahesh Wickramasinghe and Istvan Z. Kiss -- 1. Introduction -- 2. Methods -- 2.1. Experimental methodologies -- 2.2. Data processing -- 3. Synchronization with External Forcing -- 4. Coupled Electrochemical Oscillator Systems -- 4.1. Synchronization of two electrochemical oscillators -- 4.2. Synchronization in globally coupled oscillator populations -- 5. Synchronization Engineering -- 6. Electrochemical Oscillators in Networks -- 7. Conclusions -- Acknowledgment -- References -- 12. Turbulence and Synchrony in Spatially Extended Electrochemical Oscillators Vladimir Garcia-Morales and Katharina Krischer -- 1. Introduction -- 2. Electrochemical Oscillators Under Nonlocal (Migration) Coupling (NLC) -- 2.1. NLC in electrochemical systems -- 2.2. Electrochemical oscillations and the Nonlocal Complex Ginzburg-Landau Equation (NCGLE) -- 2.3. Electrochemical turbulence and the NCGLE -- 3. Electrochemical Oscillators Under Global Coupling (GC) -- 3.1. Physical origin of the global coupling -- 3.2. Global coupling induced pattern formation in experiments -- 3.3. Linear global coupling in electrochemical systems and the normal form approach -- 3.4. Nonlinear global coupling (NGC) and its normal form -- 4. Conclusions -- Acknowledgments -- References.

13. Quorum Sensing and Synchronization in Populations of Coupled Chemical Oscillators Annette F. Taylor, Mark R. Tinsley and Kenneth Showalter -- 1. Introduction -- 2. Model -- 3. Synchronization -- 4. Quorum Sensing -- 5. Spatially-Distributed Particles -- 6. Clusters -- 7. Oscillator Death and Multistability -- 8. Conclusions and Outlook -- Acknowledgments -- References -- 14. Collective Decision-Making and Oscillatory Behaviors in Cell Populations Koichi Fujimoto and Satoshi Sawai -- 1. Introduction -- 2. Collective Oscillations in Microbial Populations -- 2.1. Oscillatory and excitatory response in transcriptional regulation -- 2.2. Coupling synthetic circuits -- 2.3. Comparison with BZ reaction -- 2.4. Collective oscillations in budding yeast and Dictyostelium -- 3. Collective Decision Making -- 3.1. Generalization of the scheme and examples -- 3.2. Synchrony in decision making -- 3.3. Encoding cell density information -- 4. Conclusions -- References -- 15. Synchronization via Hydrodynamic Interactions Franziska Kendelbacher and Holger Stark -- 1. Introduction -- 1.1. Synchronization via hydrodynamic interactions in nature -- 1.2. Theoretical and experimental studies on model systems -- 2. Hydrodynamic Interactions -- 3. Synchronizing Helical Filaments -- 4. Metachronal Waves in a Chain of Driven Oscillators -- 5. Conclusions -- References -- PART V EVOLUTION, SYNTHETIC BIOLOGY, AND PROTOCELLS -- 16. Emergence and Selection of Biomodules: Steps in the Assembly of a Protocell Susanna C. Manrubia and Carlos Briones -- 1. Preamble -- 2. Introduction -- 2.1. The early Earth -- 2.2. Approaches to early life -- 3. Synthesis and Accumulation of Biomodules -- 3.1. Life's origin in the lab: Miller and Urey's experiment -- 3.2. Sugars and nucleotides -- 3.3. Chirality -- 3.4. Prebiotic polymerization of biomodules.

3.5. Chemical selection and compartmentalization.