1  5
1. Biomolecular feedback systems [2015]
 Del Vecchio, Domitilla, 1975 author.
 Princeton, New Jersey : Princeton University Press, [2015]
 Description
 Book — vi, 275 pages : illustrations ; 27 cm
 Summary

 Preface vii
 1 Introductory Concepts 1 1.1 Systems biology: Modeling, analysis and role of feedback 1 1.2 The cell as a system 8 1.3 Control and dynamical systems tools 11 1.4 Input/output modeling 18 1.5 From systems to synthetic biology 22 1.6 Further reading 28
 2 Dynamic Modeling of Core Processes 29 2.1 Modeling chemical reactions 29 2.2 Transcription and translation 44 2.3 Transcriptional regulation 55 2.4 Posttranscriptional regulation 70 2.5 Cellular subsystems 81 Exercises 86
 3 Analysis of Dynamic Behavior 89 3.1 Analysis near equilibria 89 3.2 Robustness 103 3.3 Oscillatory behavior 113 3.4 Bifurcations 124 3.5 Model reduction techniques 127 Exercises 133
 4 Stochastic Modeling and Analysis 139 4.1 Stochastic modeling of biochemical systems 139 4.2 Simulation of stochastic systems 154 4.3 Input/output linear stochastic systems 157 Exercises 164
 5 Biological Circuit Components 169 5.1 Introduction to biological circuit design 169 5.2 Negative autoregulation 171 5.3 The toggle switch 177 5.4 The repressilator 180 5.5 Activatorrepressor clock 184 5.6 An incoherent feedforward loop (IFFL) 189 5.7 Bacterial chemotaxis 191 Exercises 203
 6 Interconnecting Components 205 6.1 Input/output modeling and the modularity assumption 205 6.2 Introduction to retroactivity 206 6.3 Retroactivity in gene circuits 209 6.4 Retroactivity in signaling systems 214 6.5 Insulation devices: Retroactivity attenuation 219 6.6 A case study on the use of insulation devices 236 Exercises 239
 7 Design Tradeoffs 243 7.1 Competition for shared cellular resources 243 7.2 Stochastic effects: Design tradeoffs in systems with large gains 253 Exercises 257 Bibliography 259 Index 267.
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Engineering Library (Terman)
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QH508 .D45 2015  Unknown 1day loan 
BIOE305, ME30501
 Course
 BIOE305  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Course
 ME30501  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
2. Nonlinear dynamics and chaos : with applications to physics, biology, chemistry, and engineering [2015]
 Strogatz, Steven author.
 Second edition.  Boulder, CO : Westview Press, a member of the Perseus Books Group, [2015]
 Description
 Book — xiii, 513 pages, 4 unnumbered pages of plates : illustrations (some color) ; 23 cm
 Summary

 Preface 1. Overview 1.0 Chaos, Fractals, and Dynamics 1.1 Capsule History of Dynamics 1.2 The Importance of Being Nonlinear 1.3 A Dynamical View of the World PART I. ONEDIMENSIONAL FLOWS 2. Flows on the Line 2.0 Introduction 2.1 A Geometric Way of Thinking 2.2 Fixed Points and Stability 2.3 Population Growth 2.4 Linear Stability Analysis 2.5 Existence and Uniqueness 2.6 Impossibility of Oscillations 2.7 Potentials 2.8 Solving Equations on the Computer
 Exercises 3. Bifurcations 3.0 Introduction 3.1 SaddleNode Bifurcation 3.2 Transcritical Bifurcation 3.3 Laser Threshold 3.4 Pitchfork Bifurcation 3.5 Overdamped Bead on a Rotating Hoop 3.6 Imperfect Bifurcations and Catastrophes 3.7 Insect Outbreak
 Exercises 4. Flows on the Circle 4.0 Introduction 4.1 Examples and Definitions 4.2 Uniform Oscillator 4.3 Nonuniform Oscillator 4.4 Overdamped Pendulum 4.5 Fireflies 4.6 Superconducting Josephson Junctions
 Exercises PART II. TWODIMENSIONAL FLOWS 5. Linear Systems 5.0 Introduction 5.1 Definitions and Examples 5.2 Classification of Linear Systems 5.3 Love Affairs
 Exercises 6. Phase Plane 6.0 Introduction 6.1 Phase Portraits 6.2 Existence, Uniqueness, and Topological Consequences 6.3 Fixed Points and Linearization 6.4 Rabbits versus Sheep 6.5 Conservative Systems 6.6 Reversible Systems 6.7 Pendulum 6.8 Index Theory
 Exercises 7. Limit Cycles 7.0 Introduction 7.1 Examples 7.2 Ruling Out Closed Orbits 7.3 PoincareBendixson Theorem 7.4 Lienard Systems 7.5 Relaxation Oscillators 7.6 Weakly Nonlinear Oscillators
 Exercises 8. Bifurcations Revisited 8.0 Introduction 8.1 SaddleNode, Transcritical, and Pitchfork Bifurcations 8.2 Hopf Bifurcations 8.3 Oscillating Chemical Reactions 8.4 Global Bifurcations of Cycles 8.5 Hysteresis in the Driven Pendulum and Josephson Junction 8.6 Coupled Oscillators and Quasiperiodicity 8.7 Poincare Maps
 Exercises PART III. CHAOS 9. Lorenz Equations 9.0 Introduction 9.1 A Chaotic Waterwheel 9.2 Simple Properties of the Lorenz Equations 9.3 Chaos on a Strange Attractor 9.4 Lorenz Map 9.5 Exploring Parameter Space 9.6 Using Chaos to Send Secret Messages
 Exercises 10. OneDimensional Maps 10.0 Introduction 10.1 Fixed Points and Cobwebs 10.2 Logistic Map: Numerics 10.3 Logistic Map: Analysis 10.4 Periodic Windows 10.5 Liapunov Exponent 10.6 Universality and Experiments 10.7 Renormalization
 Exercises 11. Fractals 11.0 Introduction 11.1 Countable and Uncountable Sets 11.2 Cantor Set 11.3 Dimension of SelfSimilar Fractals 11.4 Box Dimension 11.5 Pointwise and Correlation Dimensions
 Exercises 12. Strange Attractors 12.0 Introductions 12.1 The Simplest Examples 12.2 Henon Map 12.3 Rossler System 12.4 Chemical Chaos and Attractor Reconstruction 12.5 Forced DoubleWell Oscillator
 Exercises Answers to Selected Exercises References Author Index Subject Index.
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Engineering Library (Terman)
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Q172.5 .C45 S767 2015  Unknown 1day loan 
BIOE305, ME30501
 Course
 BIOE305  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Course
 ME30501  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Åström, Karl J. (Karl Johan), 1934
 Princeton, N.J. : Princeton University Press, c2008.
 Description
 Book — xii, 396 p. : ill., map ; 27 cm.
 Summary

 Preface ix
 Chapter 1. Introduction 1 1.1 What Is Feedback? 1 1.2 What Is Control? 3 1.3 Feedback Examples 5 1.4 Feedback Properties 17 1.5 Simple Forms of Feedback 23 1.6 Further Reading 25 Exercises 25
 Chapter 2. System Modeling 27 2.1 Modeling Concepts 27 2.2 State Space Models 34 2.3 Modeling Methodology 44 2.4 Modeling Examples 51 2.5 Further Reading 61 Exercises 61
 Chapter 3. Examples 65 3.1 Cruise Control 65 3.2 Bicycle Dynamics 69 3.3 Operational Amplifier Circuits 71 3.4 Computing Systems and Networks 75 3.5 Atomic Force Microscopy 81 3.6 Drug Administration 84 3.7 Population Dynamics 89 Exercises 91
 Chapter 4. Dynamic Behavior 95 4.1 Solving Differential Equations 95 4.2 Qualitative Analysis 98 4.3 Stability 102 4.4 Lyapunov Stability Analysis 110 4.5 Parametric and Nonlocal Behavior 120 4.6 Further Reading 126 Exercises 126
 Chapter 5. Linear Systems 131 5.1 Basic Definitions 131 5.2 The Matrix Exponential 136 5.3 Input/Output Response 145 5.4 Linearization 158 5.5 Further Reading 163 Exercises 164
 Chapter 6. State Feedback 167 6.1 Reachability 167 6.2 Stabilization by State Feedback 175 6.3 State Feedback Design 183 6.4 Integral Action 195 6.5 Further Reading 197 Exercises 197
 Chapter 7. Output Feedback 201 7.1 Observability 201 7.2 State Estimation 206 7.3 Control Using Estimated State 211 7.4 Kalman Filtering 215 7.5 A General Controller Structure 219 7.6 Further Reading 226 Exercises 226
 Chapter 8. Transfer Functions 229 8.1 Frequency Domain Modeling 229 8.2 Derivation of the Transfer Function 231 8.3 Block Diagrams and Transfer Functions 242 8.4 The Bode Plot 250 8.5 Laplace Transforms 259 8.6 Further Reading 262 Exercises 262
 Chapter 9. Frequency Domain Analysis 267 9.1 The Loop Transfer Function 267 9.2 The Nyquist Criterion 270 9.3 Stability Margins 278 9.4 Bode's Relations and Minimum Phase Systems 283 9.5 Generalized Notions of Gain and Phase 285 9.6 Further Reading 290 Exercises 290
 Chapter 10. PID Control 293 10.1 Basic Control Functions 293 10.2 Simple Controllers for Complex Systems 298 10.3 PID Tuning 302 10.4 Integrator Windup 306 10.5 Implementation 308 10.6 Further Reading 312 Exercises 313
 Chapter 11. Frequency Domain Design 315 11.1 Sensitivity Functions 315 11.2 Feedforward Design 319 11.3 Performance Specifications 322 11.4 Feedback Design via Loop Shaping 326 11.5 Fundamental Limitations 331 11.6 Design Example 340 11.7 Further Reading 343 Exercises 344
 Chapter 12. Robust Performance 347 12.1 Modeling Uncertainty 347 12.2 Stability in the Presence of Uncertainty 352 12.3 Performance in the Presence of Uncertainty 358 12.4 Robust Pole Placement 361 12.5 Design for Robust Performance 369 12.6 Further Reading 374 Exercises 374
 Bibliography 377 Index 387.
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Engineering Library (Terman)
Engineering Library (Terman)  Status 

On reserve: Ask at Engineering circulation desk  
TJ216 .A78 2008  Unknown 1day loan 
BIOE305, ME30501
 Course
 BIOE305  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Course
 ME30501  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Alon, Uri, 1969
 Boca Raton, FL : Chapman & Hall/CRC, c2007.
 Description
 Book — xvi, 301 p., [4] p. of plates : ill. (some col.) ; 26 cm.
 Summary

 INTRODUCTION TRANSCRIPTION NETWORKS, BASIC CONCEPTS Introduction The Cognitive Problem of the Cell Elements of Transcription Networks Dynamics and Response Time of Simple Gene Circuits AUTOREGULATION, A NETWORK MOTIF Introduction Patterns, Randomized Networks and Network Motifs Autoregulation is a Network Motif Negative AutoRegulation Speeds the Response Time of Gene
 Circuits Negative AutoRegulation Promotes Robustness to Fluctuations
 in Production Positive autoregulation speeds responses and widens cellcell variability Summary THE FEEDFORWARD LOOP NETWORK MOTIF Introduction The Number of Appearances of a Subgraph in Random
 Networks The Feedforward Loop (FFL) is a Network Motif The Structure of the Feedforward Loop Circuit Dynamics of the Coherent FFL with ANDLogic The C1FFL is a SignSensitive Delay Element The Incoherent FFL: a pulse generator and response accelerator Why Are Some FFL Types Rare? Convergent Evolution of FFLs Summary TEMPORAL PROGRAMS AND THE GLOBAL STRUCTURE OF TRANSCRIPTION NETWORKS Introduction The SingleInput Module (SIM) Network Motif SIMs Can Generate Temporal Expression Programs Topological Generalizations of Network Motifs The MultiOutput FFL Can Generate FIFO Temporal Order Signal Integration and Combinatorial Control: BiFans and
 DenseOverlapping Regulons Network Motifs and the Global Structure of Sensory
 Transcription Networks NETWORK MOTIFS IN DEVELOPMENTAL, SIGNALTRANSDUCTION AND NEURONAL NETWORKS Introduction Network Motifs in Developmental Transcription Networks: Positive feedback loops and bistability Motifs in Signal Transduction Networks Information Processing Using MultiLayer Perceptrons Composite Network Motifs: Negative Feedback and Oscillator
 Motifs Network Motifs in the Neuronal Network of C. Elegans Summary ROBUSTNESS OF PROTEIN CIRCUITS, THE EXAMPLE OF BACTERIAL CHEMOTAXIS The Robustness Principle Bacterial Chemotaxis, or How Bacteria 'Think' The Chemotaxis Protein Circuit of E. coli Two Models Can Explain Exact Adaptation, One is Robust and
 the Other Fine Tuned The BarkaiLeibler model Individuality and Robustness in Bacterial Chemotaxis ROBUST PATTERNING IN DEVELOPMENT Introduction to Morphogen Gradients Exponential Gradients Are Not Robust Increased Robustness by SelfEnhanced Morphogen
 Degradation Network Motifs That Provide Robust Patterning The Robustness Principle Can Distinguish Between
 Mechanisms of Fruit Fly Patterning KINETIC PROOFREADING Introduction Kinetic Proofreading of the Genetic Code Can Reduce Error
 Rates of Molecular Recognition Recognition of Self and NonSelf by the Immune System Kinetic Proofreading May Occur in Diverse Recognition
 Processes in the Cell OPTIMAL GENE CIRCUIT DESIGN Introduction Cost and Benefit Analysis of Gene circuits Optimal Expression Level of a Protein Under Constant
 Conditions To Regulate or Not to Regulate: Optimal Regulation in Variable
 Environments Environmental Selection of the Feedforward Loop Network Motif Summary RULES FOR GENE REGULATION BASED ON ERROR MINIMIZATION Introduction The Savageau Demand Rules Rules for Gene Regulation Based on Minimal Error Load Demand Rules for Genes with Multiple Regulators Summary EPILOGUE: Simplicity in Biology APPENDIX A: The InputFunction of a Gene, MichaelisMenten and Hill Equations
 APPENDIX B: MultiDimensional InputFunctions APPENDIX C: Graph Properties of Transcription Networks APPENDIX D: CellCell Variability in Gene Expression GLOSSARY BIBLIOGRAPHY.
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Engineering Library (Terman)
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On reserve: Ask at Engineering circulation desk  
QH324.2 .A46 2007  Unknown 1day loan 
QH324.2 .A46 2007  Unknown 1day loan 
BIOE305, ME30501
 Course
 BIOE305  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Course
 ME30501  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Weinheim : WileyVCH, c2005.
 Description
 Book — xix, 465 p. : ill. ; 25 cm.
 Summary

 Preface. Foreword. Part I: General Introduction.
 1. Basic Principles.
 2. Biology in a Nutshell.
 3. Mathematics in a Nutshell.
 4. Experimental Techniques in a Nutshell. Part II: Standard Models and Approaches in Systems Biology.
 5. Metabolism.
 6. Signal Transduction.
 7. Selected Biological Processes.
 8. Modeling of Gene Expression.
 9. Analysis of Gene Expression Data.
 10. Evolution and Selforganization.
 11. Data Integration.
 12. What's Next? Part III: Computerbased Information Retrieval and Examination.
 13. Databases and Tools on the Internet.
 14. Modeling Tools. Subject Index.
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Engineering Library (Terman)
Engineering Library (Terman)  Status 

On reserve: Ask at Engineering circulation desk  
QH308.2 .S98 2005  Unknown 2day loan 
BIOE305, ME30501
 Course
 BIOE305  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu
 Course
 ME30501  Dynamics and Feedback Control of Living Systems
 Instructor(s)
 Michaelle Mayalu