CONTENTS -- Preface -- 1 Continuum Models for Interacting Machines Dieter Armbruster, Pierre Degond, Christian Ringhofer -- 1.1 Introduction -- 1.2 Heuristic Models -- 1.2.1 Quasistatic Models -- 1.2.2 Advection-Diffusion Equations -- 1.2.3 Policies and Bottlenecks -- 1.2.3.1 Dispatch Rules -- 1.2.3.2 Bottlenecks and Maximal Capacities -- 1.3 First Principle Models -- 1.3.1 Kinetic Models -- 1.3.2 Deterministic Kinetic Models -- Models with capacity constraints: -- The multi - phase model -- An example with bottlenecks: -- 1.3.3 Stochasticity and Diffusion -- Random velocity updates -- Asymptotics for many stage processes: -- A numerical comparison -- 1.4 Conclusions -- Acknowledgements -- References -- 2 Supply and Production Networks: From the Bullwhip Effect to Business Cycles Dirk Helbing, Stefan Lammer -- 2.1 Introduction -- 2.2 Input-Output Model of Supply Networks -- 2.2.1 Adaptation of Production Speeds -- 2.2.2 Modelling Sequential Supply Chains -- 2.2.3 More Detailed Derivation of the Production Dynamics -- 2.2.4 Dynamic Solution and Resonance Effects -- 2.2.5 The Bullwhip Effect -- 2.3 Network Effects -- 2.3.1 General Methods of Solution -- 2.3.2 Examples of Supply Networks -- 2.4 Network-Induced Business Cycles -- 2.4.1 Treating Producers Analogous to Consumers -- 2.5 Reproduction of Some Empirically Observed Features of Business Cycles -- 2.5.1 Dynamic Behaviors and Stability Thresholds -- 2.6 Summary -- 2.7 Future Research Directions -- 2.7.1 Network Engineering -- 2.7.2 Cyclic Dynamics in Biological Systems -- 2.7.3 Heterogeneity in Production Networks -- 2.7.4 Multi-Goal Control -- 2.7.5 Non-Linear Dynamics and Scarcity of Resources -- Acknowledgements -- Appendix A -- 2.8 Boundary between Damped and Growing Oscillations -- 2.9 Boundary between Damped Oscillations and Overdamped Behavior -- References.

3 Managing Supply-Demand Networks in Semiconductor Manufacturing Karl Kempf -- 3.1 Introduction to Supply-Demand Networks -- 3.2 Examples from the Semiconductor Manufacturing -- 3.2.1 A Product-Centric Perspective -- 3.2.2 A Facilities-Centric Perspective -- 3.2.3 Repetitive Decisions -- 3.2.4 Combinatorial Complexity -- 3.2.5 Complexity from Supply Stochasticity -- 3.2.6 Complexity from Demand Stochasticity -- 3.2.7 Complexity from Nonlinearity -- 3.2.8 Financial Complexity -- 3.3 Managing Supply-Demand Networks -- 3.3.1 A Capacity Planning Formulation -- 3.3.2 An Inventory Planning Formulation -- 3.3.3 Integrating Capacity and Inventory Planning -- 3.3.4 A Tactical Execution Formulation -- 3.3.5 Simulation Support -- 3.4 Conclusions -- Acknowledgments -- References -- 4 Modelling Manufacturing Systems for Control: A Validation Study Erjen Lefeber, Roel van den Berg, J.E. Rooda -- 4.1 Introduction -- 4.2 Preliminaries -- 4.3 Effective Process Times (EPT's) -- 4.4 Control Framework -- 4.4.1 Approximation Model -- 4.4.2 Model Predictive Control (MPC) -- 4.4.3 Control Framework (revisited) -- 4.5 Modelling Manufacturing Systems -- 4.6 Validation of PDE-Models -- 4.6.1 Manufacturing Systems -- 4.6.2 PDE-Models -- 4.6.3 Validation Study -- 4.7 Concluding Remarks -- References -- 5 Adaptive Networks of Production Processes Adam Ponzi -- 5.1 Introduction -- 5.2 Review of von-Neumann Model -- 5.3 Dynamical Production Model -- 5.4 Model Behaviour -- 5.4.1 Single Process in Fixed Environment -- 5.4.2 Multiple Timescales -- 5.4.3 Complex Dynamics -- 5.4.4 Network Structure -- 5.5 Discussion -- Acknowledgments -- References -- 6 Universal Statistics of Cells with Recursive Production Kunihiko Kanelco, Chikara Furusaura -- 6.1 Question to be Addressed -- 6.2 Logic -- 6.3 Model -- 6.4 Zipf Law -- 6.5 Log-Normal Distribution -- 6.6 Experiment.

6.6.1 Confirmation of Zipf Law -- 6.6.1.1 Confirmation of Laws on Fluctuations -- 6.7 Discussion -- References -- 7 Intracellular Networks of Interacting Molecular Machines Alexander S . Mikhailov -- 7.1 Introdution -- 7.2 Networks of Protein Machines -- 7.3 Coherent Molecular Dynamics -- 7.4 Mean-Field Approximation -- 7.5 Further Theoretical Developments -- 7.6 Coherence in Cross-Coupled Dynamical Networks -- 7.7 Discussion -- References -- 8 Cell is Noisy Tatsuo Shibata -- 8.1 Introduction -- 8.2 Origin of Molecular Noise -- 8.3 Stochastic Gene Expression -- 8.3.1 Noise in Single Gene Expression -- 8.3.2 Attenuating Gene Expression Noise by Autoregulation -- 8.4 Noisy Signal Amplification in Signal Transduction Reactions -- 8.5 Propagation of Noise in Reaction Networks -- 8.6 Outlook -- Acknowledgments -- References -- 9 An Intelligent Slime Mold: A Self-organizing System of Cell Shape and Information Tetsuo Ueda -- 9.1 Introduction -- 9.1.1 The True Slime Molds, Like Nothing on Earth -- 9.2 Cell Motility and Cell Behavior by the Plasmodium -- 9.2.1 Cell Motility -- 9.2.2 Chemotaxis -- 9.2.3 Sensing and Transduction -- 9.2.4 Search for Second Messengers -- 9.3 Integration of Sensed Information in Chemotaxis -- 9.3.1 A Model for Integration -- 9.4 Collective Dynamics of Coupled Oscillators in Cell Behavior -- 9.4.1 The Response to External Stimulation -- 9.4.2 Alteration of the Judgment by Oscillatory Stimulation through Entrainment -- 9.4.3 Correspondence of Tactic Behavior with Contractility -- 9.4.4 Bifurcation of Dynamic States in the Feeding Behavior by the Placozoan -- 9.5 Chemical Oscillations as a Basis for the Rhythmic Contraction -- 9.6 Transition of Chemical Patterns Accompanying the Selection of Cell Behavior -- 9.6.1 Theory of Cell Behavior in Terms of Dissipative Structure.

9.6.2 Link to the Organization of Cytoskeleton and Chemical Pattern -- 9.7 Computing by Changing Cell Shape -- 9.7.1 Solving a Maze Problem -- 9.7.2 Solving the Steiner Problem -- 9.7.3 Formation of Veins by External Oscillation -- 9.8 Fragmentation of the Plasmodium: Control of Cell Size -- 9.8.1 Thermo-Fragmentation -- 9.8.2 Photofragmentation and its Photosystem -- 9.9 Memory Effects and Morphogen: Phytochrome as Morphogen in the Fragmentation -- 9.10 Locomotion -- 9.10.1 Allometry in Locomotion Velocity -- 9.10.2 Correlation of Oscillations During Directional Movement -- 9.11 The Emergence of the Rhythmic Streaming -- 9.12 Time Order Among Multiple Rhythms in the Plasmodium -- 9.12.1 Long-Term Changes in Cell Shape of the Plasmodium -- 9.12.2 Multiple Oscillations -- 9.13 Concluding Remarks as Future Prospects -- Acknowledgments -- References -- 10 Communication and Structure within Networks Kim Sneppen, Martin Rosvall, Ala Trusina -- 10.1 Introduction -- 10.2 An Economy for Exchange of Social Contacts -- 10.3 Limited Information Horizons in Complex Networks -- 10.4 Conclusion -- Acknowledgments -- References.