ALBERT

Note: Contents 1 Introduction References Part I Molecular Stress Physiology 2 General Themes of Molecular Stress Physiology 2.1 Definitions and Concepts 2.1.1 Stress 2.1.2 Quantification of Stress 2.1.3 Escape–Resistance–Avoidance–Tolerance 2.1.4 Stress Responses–Acclimation–Adaptation 2.1.5 Filters Determining Species Distribution 2.2 Activation of Stress Tolerance and Avoidance Mechanisms 2.2.1 Stress Sensing and Signal Transduction 2.2.2 Transcriptional Control 2.2.3 Oxidative Stress 2.2.4 Long-Distance Stress Signalling 2.2.5 The Model System Arabidopsis thaliana 2.3 Stress and Growth Regulation 2.4 Molecular Basis of Escape and Anticipation of Stress 2.4.1 Circadian Rhythms 2.4.2 Anticipation of Seasonal Changes in Environmental Conditions 2.4.3 Developmental Switches Triggered by Favourable Conditions 2.4.4 Trans-Generational Stress Memory Summary References 3 Light 3.1 The Dual Significance of Light 3.2 Visible Light 3.2.1 Avoidance of Light Stress and Permanent or Dynamic Acclimation 3.2.2 Overexcitation and Damage to Photosynthetic Membranes. 3.2.3 Flexible Acclimation to Changes in Light Intensity 3.2.4 Continuous Light 3.2.5 Light Triggers Plant Adaptation and Acclimation to the Environment 3.3 UV-B Radiation 3.3.1 Ranges of Ultraviolet Radiation and Biological Activity 3.3.2 Ultraviolet-B Damage and Repair Mechanisms 3.3.3 Avoidance of Ultraviolet-B-Induced Stress 3.3.4 Ultraviolet-B Perception and Signalling 3.3.5 Crosstalk Between Ultraviolet-B and Visible Light Responses Summary References 4 Temperature 4.1 The Temperature Challenge 4.1.1 Temperature Dependence of Life 4.1.2 Plants as Poikilothermic Organisms 4.1.3 Variations in Temperature Range 4.1.4 Strategies to Cope with Temperature Fluctuations and Temperature Extremes 4.2 Cold Acclimation and Freezing Tolerance 4.2.1 Adjustment of Membrane Fluidity 4.2.2 Prevention of Photoinhibition 4.2.3 Cryoprotective Proteins 4.2.4 Control of Ice Formation 4.2.5 Signalling Networks Involved in Cold Acclimation 4.2.6 Freezing Avoidance and Freezing Tolerance in Tropical High Mountain Plants 4.3 Heat Stress 4.3.1 Heat Stress Avoidance 4.3.2 Acquired Thermotolerance 4.3.3 The Heat Shock Response 4.4 Temperature Sensing 4.4.1 Sensing of Extreme Temperatures 4.4.2 Sensing of Ambient Temperature Changes Summary References 5 Oxygen Deficiency 5.1 Conditions of Flooded Soil 5.2 Hypoxia-Induced Damage: Energy Metabolism of Plants Under Oxygen Deficiency 5.3 Natural Variation in the Ability to Endure Inundation by Water 5.4 Adaptations to Flooding-Prone Habitats 5.4.1 Anatomical–Morphological Adaptations and Modifications 5.4.2 Biochemical Modifications 5.5 Sensing of Flooding and Ensuing Signal Transduction 5.5.1 Ethylene Signal Transduction 5.5.2 Oxygen Sensing 5.6 Regulation of Avoidance and Tolerance Strategies Summary References 6 Water Deficiency (Drought) 6.1 The Properties of Water 6.2 Water Acquisition and Movement: Cellular Aspects 6.2.1 The Water Potential 6.2.2 Facilitation of Intercellular and Intracellular Water Flow: Aquaporins 6.3 Drought Stress Responses: Avoidance and Tolerance 6.3.1 Control of the Osmotic Potential 6.3.2 Protective Proteins 6.3.3 Regulation of the Stomatal Aperture 6.4 Acclimation of Growth 6.4.1 Inhibition of Shoot Growth 6.4.2 Stimulation of Root Growth 6.5 Sensing of Water Status and Signal Transduction 6.5.1 Sensing of Water Status 6.5.2 ABA Signal Transduction 6.5.3 ABA-Independent Signalling 6.6 Photosynthesis Variants with Improved Water Use Efficiency 6.6.1 C4 Photosynthesis 6.6.2 Evolution of C 4 Photosynthesis 6.6.3 Crassulacean Acid Metabolism 6.6.4 Evolution of Crassulacean Acid Metabolism Photosynthesis Summary References 7 Adverse Soil Mineral Availability 7.1 Mineral Nutrients 7.2 The Mineral Nutrition Challenge 7.2.1 Elements in the Soil 7.2.2 Element Toxicity 7.3 Nutrient Acquisition and Responses to Nutrient Scarcity 7.3.1 Modulation of Nutrient Availability 7.3.2 Cellular Ion Transport Mechanisms 7.3.3 Modulation of Nutrient Uptake in Response to Deficiency 7.3.4 Intracellular Transport and Cellular Aspects of Long-Distance Transport 7.3.5 Plasticity of Root Architecture and Responses to Nutrient Deficiency 7.3.6 Sensing of Nutrient Availability and Nutrient Status . 7.4 Nutrient Acquisition Symbioses 7.4.1 Mycorrhizae 7.4.2 Nitrogen Fixation 7.4.3 The Common Sym Pathway 7.5 Responses to Element Toxicity and Tolerance Mechanisms 7.5.1 Essential Metal Toxicity and Tolerance 7.5.2 Metal Hyperaccumulators as Models for Adaptation to Extreme Environments 7.5.3 Sodium Toxicity 7.5.4 Aluminium Toxicity and Tolerance 7.5.5 Non-Essential Toxic Metals Summary References 8 Biotic Stress 8.1 Plant Disease Caused by Pathogens 8.1.1 Types of Pathogens: Viruses, Bacteria, Fungi, Oomycetes and Nematodes 8.1.2 Pathogenicity Mechanisms 8.2 Plant Defences Against Microbial Pathogens and Viruses 8.2.1 Preformed Defences Against Bacteria, Fungi and Oomycetes 8.2.2 Inducible Local Defences 8.2.3 Inducible Systemic Resistance 8.2.4 Defence Against Viruses via Gene Silencing 8.3 Herbivory 8.3.1 Constitutive Defences 8.3.2 Inducible Defences Against Herbivores 8.3.3 How Plant–Herbivore Interactions Drive Genetic Diversity 8.4 Parasitic Plants 8.5 Allelopathy Summary References Part II Physiological and Biophysical Plant Ecology 9 Thermal Balance of Plants and Plant Communities 9.1 Energy Balance of the Atmospheric Boundary Layer 9.2 Microclimate Near the Ground Surface 9.2.1 Daily Changes in Temperature Near the Ground 9.2.2 Modification of Environmental Radiation and Temperature by Abiotic Factors 9.2.3 Modification of the Radiation Budget and Temperature by Biotic Factors 9.3 Energy Balance of Leaves 9.4 Acclimation and Adaptation to Temperature Extremes 9.4.1 Acclimation and Adaptation to High Temperatures 9.4.2 Acclimation and Adaptation to Low Temperatures Summary References 10 Water Relations 10.1 Water as an Environmental Factor 10.1.1 Water Use by Plants and Animals 10.1.2 Availability of Water on Earth 10.1.3 Drivers of Water Flow Between the Soil and the Atmosphere 10.2 Water Transport from the Soil to the Plant 10.2.1 Water Uptake 10.2.2 Xylem Water Transport 10.2.3 Phloem Water Transport 10.3 Transpiration 10.3.1 Stomatal Responses to Plant-Internal Factors 10.3.2 Stomatal Responses to Environmental Factors Summary References 11 Nutrient Relations 11.1 Availability of Soil Nutrients and Ion Use 11.1.1 Plant Nutrients 11.1.2 Availability of Nutrients in Soil 11.1.3 General Aspects of Plant Nutrition 11.1.4 Nutrient Deficiency and Excess 11.2 Nitrogen Nutrition 11.2.1 Nitrogen in Plant Metabolism 11.2.2 Nitrogen Uptake and Nutrition 11.2.3 Nitrogen Requirements for Growth 11.2.4 Nitrogen Storage 11.2.5 Insectivorous Plants 11.2.6 Nitrogen Deficiency and Excess 11.3 Sulphur Nutrition 11.3.1 Sulphur in Plant Metabolism 11.3.2 Sulphur Uptake and Plant Requirements 11.3.3 Indicators of Sulphur Deficiency and Excess 11.4 Phosphate Nutrition 11.4.1 Phosphorus in Plant Metabolism 11.4.2 Phosphate Uptake and Plant Requirements 11.4.3 Indicators of Phosphorus Deficiency and Excess 11.5 Alkaline Cation Nutrition 11.5.1 Magnesium 11.5.2 Calcium 11.5.3 Potassium Summary References 12 Carbon Relations 12.1 Photosynthetic CO2 Uptake: Physiological and Physical Basis 12.1.1 Photosynthesis as a Diffusion Process 12.1.2 Evolution of C 3, C4 and Crassulacean Acid Metabolism Plant Species 12.2 Photosynthesis Models and Calculation of 13C/12C Fluxes (Contribution by A. Arneth) 12.2.1 RubisCO-Limited or RuBP-Saturated Rate (Av) 12.2.2 RuBP Regeneration–Dependent and Electron Transport–Limiting Rate (Aj) 12.2.3 Supply of CO 2 Through Stomata 12.2.4 13C/12C Discrimination 12.3 Specific Leaf Area, Nitrogen Concentrations and Photosynthetic Capacity 12.3.1 Specific Leaf Area 12.3.2 Maximum Rates of CO2 Assimilation 12.4 Response of Photosynthesis to Environmental Variables 12.4.1 Light Response of CO 2 Assimilation 12.4.2 Temperature Response of CO2 Assimilation 12.4.3 Relative Air Humidi

Note: Contents 1 An Observational Overview of the Equatorial Ocean 1.1 The Thermocline: The Tropical Ocean as a Two-Layer Model 1.2 Equatorial Currents 1.3 The Somali Current and the Monsoon 1.4 Deep Internal Jets 1.5 The El Niño/Southern Oscillation (ENSO) 1.6 Upwelling in the Gulf of Guinea 1.7 Seasonal Variations of the Thermocline 1.8 Summary References 2 Basic Equations and Normal Modes 2.1 Model 2.2 Boundary Conditions 2.3 Separation of Variables 2.4 Lamb’s Parameter, Equivalent Depths, Kelvin Phase Speeds and All that 2.5 Vertical Modes and Layer Models 2.6 Nondimensionalization References 3 Kelvin, Yanai, Rossby and Gravity Waves 3.1 Latitudinal Wave Modes: An Overview 3.2 Latitudinal Wave Modes: Structure and Spatial Symmetries 3.3 Dispersion Relations: Exact and Approximate Frequencies 3.4 Analytic Approximations to Equatorial Wave Frequencies 3.4.1 Explicit Formulas 3.4.2 Long Wave Series 3.5 Separation of Time Scales 3.6 Forced Waves 3.7 How the Mixed-Rossby Gravity Wave Earned Its Name 3.8 Hough-Hermite Vector Basis 3.8.1 Introduction 3.8.2 Inner Product and Orthogonality 3.8.3 Orthonormal Basis Functions 3.9 Applications of the Hough-Hermite Basis: Linear Initial-Value Problems 3.10 Initialization Through Hough-Hermite Expansion 3.11 Energy Relationships 3.12 The Equatorial Beta-Plane as the Thin Limit of the Nonlinear Shallow Water Equations on the Sphere References 4 The “Long Wave” Approximation & Geostrophy 4.1 Introduction 4.2 Quasi-Geostrophy 4.3 The “Meridional Geostrophy”, “Low Frequency” or “Long Wave” Approximation 4.4 Boundary Conditions 4.5 Frequency Separation of Slow [Rossby/Kelvin] and Fast [Gravity] Waves 4.6 Initial Value Problems in an Unbounded Ocean, Linearized About a State of Rest, in the Long Wave Approximation 4.7 Reflection from an Eastern Boundary in the Long Wave Approximation 4.7.1 The Method of Images 4.7.2 Dilated Images 4.7.3 Zonal Velocity 4.8 Forced Problems in the Long Wave Approximation References 5 The Equator as Wall: Coastally Trapped Waves and Ray-Tracing 5.1 Introduction 5.2 Coastally-Trapped Waves 5.3 Ray-Tracing For Coastal Waves 5.4 Ray-Tracing on the Equatorial Beta-Plane 5.5 Coastal and Equatorial Kelvin Waves 5.6 Topographic and Rotational Rossby Waves and Potential Vorticity References 6 Reflections and Boundaries 6.1 Introduction 6.2 Reflection of Midlatitude Rossby Waves from a Zonal Boundary 6.3 Reflection of Equatorial Waves from a Western Boundary 6.4 Reflection from an Eastern Boundary 6.5 The Meridional Geostrophy/Long Wave Approximation and Boundaries 6.6 Quasi-normal Modes: Definition and Other Weakly Non-existent Phenomena 6.7 Quasi-normal Modes in the Long Wave Approximation: Derivation 6.8 Quasi-normal Modes in the Long Wave Approximation: Discussion 6.9 High Frequency Quasi-free Equatorial Oscillations 6.10 Scattering and Reflection from Islands References 7 Response of the Equatorial Ocean to Periodic Forcing 7.1 Introduction 7.2 A Hierarchy of Models for Time-Periodic Forcing 7.3 Description of the Model and the Problem 7.4 Numerical Models: Reflections and “Ringing” 7.5 Atlantic Versus Pacific 7.6 Summary References 8 Impulsive Forcing and Spin-Up 8.1 Introduction 8.2 The Reflection of the Switched-On Kelvin Wave 8.3 Spin-Up of a Zonally-Bounded Ocean: Overview 8.4 The Interior (Yoshida) Solution 8.5 Inertial-Gravity Waves 8.6 Western Boundary Response 8.7 Sverdrup Flow on the Equatorial Beta-Plane 8.8 Spin-Up: General Considerations 8.9 Equatorial Spin-Up: Details 8.10 Equatorial Spin-Up: Summary References 9 Yoshida Jet and Theories of the Undercurrent 9.1 Introduction 9.2 Wind-Driven Circulation in an Unbounded Ocean: f-Plane 9.3 The Yoshida Jet 9.4 An Interlude: Solving Inhomogeneous Differential Equations at Low Latitudes 9.4.1 Forced Eigenoperators: Hermite Series 9.4.2 Hutton–Euler Acceleration of Slowly Converging Hermite Series 9.4.3 Regularized Forcing 9.4.4 Bessel Function Explicit Solution for the Yoshida Jet 9.4.5 Rational Approximations: Two-Point Padé Approximants and Rational Chebyshev Galerkin Methods 9.5 Unstratified Models of the Undercurrent 9.5.1 Theory of Fofonoff and Montgomery (1955) 9.5.2 Model of Stommel (1960) 9.5.3 Gill (1971) and Hidaka (1961) References 10 Stratified Models of Mean Currents 10.1 Introduction 10.2 Modal Decompositions for Linear, Stratified Flow 10.3 Different Balances of Forces 10.3.1 Bjerknes Balance 10.4 Forced Baroclinic Flow in the “Bjerknes” Approximation 10.4.1 Other Balances 10.5 The Sensitivity of the Undercurrent to Parameters 10.6 Observations of Subsurface Countercurrents (Tsuchiya Jets) 10.7 Alternate Methods for Vertical Structure with Viscosity 10.8 McPhaden’s Model of the EUC and SSCC’s: Results 10.9 A Critique of Linear Models of the Continuously-Stratified, Wind-Driven Ocean References 11 Waves and Beams in the Continuously Stratified Ocean 11.1 Introduction 11.1.1 Equatorial Beams: A Theoretical Inevitability 11.1.2 Slinky Physics and Impedance Mismatch, or How Water Can Be as Reflective as Silvered Glass 11.1.3 Shallow Barriers to Downward Beams 11.1.4 Equatorial Methodology 11.2 Alternate Form of the Vertical Structure Equation 11.3 The Thermocline as a Mirror 11.4 The Mirror-Thermocline Concept: A Critique 11.5 The Zonal Wavenumber Condition for Strong Excitation of a Mode 11.6 Kelvin Beams: Background 11.7 Equatorial Kelvin Beams: Results References 12 Stable Linearized Waves in a Shear Flow 12.1 Introduction 12.2 UðyÞ: Pure Latitudinal Shear 12.3 Neutral Waves in Flow Varying with Both Latitude and Height: Numerical Studies 12.4 Vertical Shear and the Method of Multiple Scales References 13 Inertial Instability, Pancakes and Deep Internal Jets 13.1 Introduction: Stratospheric Pancakes and Equatorial Deep Jets 13.2 Particle Argument 13.2.1 Linear Inertial Instability 13.3 Centrifugal Instability: Rayleigh’s Parcel Argument 13.4 Equatorial Gamma-Plane Approximation 13.5 Dynamical Equator 13.6 Gamma-Plane Instability 13.7 Mixed Kelvin-Inertial Instability 13.8 Summary References 14 Kelvin Wave Instability: Critical Latitudes and Exponentially Small Effects 14.1 Proxies and the Optical Theorem 14.2 Six Ways to Calculate Kelvin Instability 14.2.1 Power Series for the Eigenvalue 14.2.2 Hermite-Padé Approximants 14.2.3 Numerical Methods 14.3 Instability for the Equatorial Kelvin Wave in the Small Wavenumber Limit 14.3.1 Beyond-All-Orders Rossby Wave Instability 14.3.2 Beyond-All-Orders Kelvin Wave Instability in Weak Shear in the Long Wave Approximation 14.4 Kelvin Instability in Shear: The General Case References 15 Nonmodal Instability 15.1 Introduction 15.2 Couette and Poiseuille Flow and Subcritical Bifurcation 15.3 The Fundamental Orr Solution 15.4 Interpretation: The “Venetian Blind Effect” 15.5 Refinements to the Orr Solution 15.6 The “Checkerboard” and Bessel Solution 15.6.1 The “Checkerboard” Solution 15.7 The Dandelion Strategy 15.8 Three-Dimensional Transients 15.9 ODE Models and Nonnormal Matrices 15.10 Nonmodal Instability in the Tropics 15.11 Summary References 16 Nonlinear Equatorial Waves 16.1 Introduction 16.2 Weakly Nonlinear Multiple Scale Perturbation Theory 16.2.1 Reduction from Three Space Dimensions to One 16.2.2 Three Dimensions and Baroclinic Modes 16.3 Solitary and Cnoidal Waves 16.4 Dispersion and Waves 16.4.1 Derivation of the Group Velocity Through the Method of Multiple Scales 16.5 Integrability, Chaos and the Inverse Scattering Method 16.6 Low Order Spectral Truncation (LOST) 16.7 Nonlinear Equatorial Kelvin Waves 16.7.1 Physics of the One-Dimensional Advection (ODA) Equation: ut + cux + buux = 0 16.7.2 Post-Breaking: Overturning, Taylor Shock or “Soliton Clusters”? 16.7.3 Viscous Regularization of Kelvin Fronts: Burgers’ Equation And Matched Asymptotic Perturbation Theory 16.8 Kelvin-Gravity Wave Shortwave Resonance: Curving Fronts and Undulations 16.9 Kelvin Solitary and Cnoidal Waves 16.10 Corner Waves and the Cnoidal-Corner-Breaking Scenario 16.11 Rossby Solitary Waves 16.12 Antisymmetr

Note: Contents: 1 Computing with Formulas. - 1.1 The First Programming Encounter: a Formula. - 1.1.1 Using a Program as a Calculator. - 1.1.2 About Programs and Programming. - 1.1.3 Tools for Writing Programs. - 1.1.4 Writing and Running Your First Python Program. - 1.1.5 Warning About Typing Program Text. - 1.1.6 Verifying the Result. - 1.1.7 Using Variables. - 1.1.8 Names of Variables. - 1.1.9 Reserved Words in Python. - 1.1.10 Comments. - 1.1.11 Formatting Text and Numbers. - 1.2 Computer Science Glossary. - 1.3 Another Formula: Celsius-Fahrenheit Conversion. - 1.3.1 Potential Error: Integer Division. - 1.3.2 Objects in Python. - 1.3.3 Avoiding Integer Division. - 1.3.4 Arithmetic Operators and Precedence. - 1.4 Evaluating Standard Mathematical Functions. - 1.4.1 Example: Using the Square Root Function. - 1.4.2 Example: Computing with sinh x. - 1.4.3 A First Glimpse of Rounding Errors. - 1.5 Interactive Computing. - 1.5.1 Using the Python Shell. - 1.5.2 Type Conversion. - 1.5.3 IPython. - 1.6 Complex Numbers. - 1.6.1 Complex Arithmetics in Python. - 1.6.2 Complex Functions in Python. - 1.6.3 Unified Treatment of Complex and Real Functions. - 1.7 Symbolic Computing. - 1.7.1 Basic Differentiation and Integration. - 1.7.2 Equation Solving. - 1.7.3 Taylor Series and More. - 1.8 Summary. - 1.8.1 Chapter Topics. - 1.8.2 Example: Trajectory of a Ball. - 1.8.3 About Typesetting Conventions in This Book. - 1.9 Exercises. - 2 Loops and Lists. - 2.1 While Loops. - 2.1.1 A Naive Solution. - 2.1.2 While Loops. - 2.1.3 Boolean Expressions. - 2.1.4 Loop Implementation of a Sum. - 2.2 Lists. - 2.2.1 Basic List Operations. - 2.2.2 For Loops. - 2.3 Alternative Implementations with Lists and Loops. - 2.3.1 While Loop Implementation of a for Loop. - 2.3.2 The Range Construction. - 2.3.3 For Loops with List Indices. - 2.3.4 Changing List Elements. - 2.3.5 List Comprehension. - 2.3.6 Traversing Multiple Lists Simultaneously. - 2.4 Nested Lists. - 2.4.1 A table as a List of Rows or Columns. - 2.4.2 Printing Objects. - 2.4.3 Extracting Sublists. - 2.4.4 Traversing Nested Lists. - 2.5 Tuples. - 2.6 Summary. - 2.6.1 Chapter Topics. - 2.6.2 Example: Analyzing List Data. - 2.6.3 How to Find More Python Information. - 2.7 Exercises. - 3 Functions and Branching. - 3.1 Functions. - 3.1.1 Mathematical Functions as Python Functions. - 3.1.2 Understanding the Program Flow. - 3.1.3 Local and Global Variables. - 3.1.4 Multiple Arguments. - 3.1.5 Function Argument or Global Variable?. - 3.1.6 Beyond Mathematical Functions. - 3.1.7 Multiple Return Values. - 3.1.8 Computing Sums. - 3.1.9 Functions with No Return Values. - 3.1.10 Keyword Arguments. - 3.1.11 Doc Strings. - 3.1.12 Functions as Arguments to Functions. - 3.1.13 The Main Program. - 3.1.14 Lambda Functions. - 3.2 Branching. - 3.2.1 If-else Blocks. - 3.2.2 Inline if Tests. - 3.3 Mixing Loops, Branching, and Functions in Bioinformatics Examples. - 3.3.1 Counting Letters in DNA Strings. - 3.3.2 Efficiency Assessment. - 3.3.3 Verifying the Implementations. - 3.4 Summary. - 3.4.1 Chapter Topics. - 3.4.2 Example: Numerical Integration. - 3.5 Exercises. - 4 User Input and Error Handling. - 4.1 Asking Questions and Reading Answers. - 4.1.1 Reading Keyboard Input. - 4.2 Reading from the Command Line. - 4.2.1 Providing Input on the Command Line. - 4.2.2 A Variable Number of Command-Line Arguments. - 4.2.3 More on Command-Line Arguments. - 4.3 Turning User Text into Live Objects. - 4.3.1 The Magic Eval Function. - 4.3.2 The Magic Exec Function. - 4.3.3 Turning String Expressions into Functions. - 4.4 Option-Value Pairs on the Command Line. - 4.4.1 Basic Usage of the Argparse Module. - 4.4.2 Mathematical Expressions as Values. - 4.5 Reading Data from File. - 4.5.1 Reading a File Line by Line. - 4.5.2 Alternative Ways of Reading a File. - 4.5.3 Reading a Mixture of Text and Numbers. - 4.6 Writing Data to File. - 4.6.1 Example: Writing a Table to File. - 4.6.2 Standard Input and Output as File Objects. - 4.6.3 What is a File, Really?. - 4.7 Handling Errors. - 4.7.1 Exception Handling. - 4.7.2 Raising Exceptions. - 4.8 A Glimpse of Graphical User Interfaces. - 4.9 Making Modules. - 4.9.1 Example: Interest on Bank Deposits. - 4.9.2 Collecting Functions in a Module File. - 4.9.3 Test Block. - 4.9.4 Verification of the Module Code. - 4.9.5 Getting Input Data. - 4.9.6 Doc Strings in Modules. - 4.9.7 Using Modules. - 4.9.8 Distributing Modules. - 4.9.9 Making Software Available on the Internet. - 4.10 Making Code for Python 2 and 3. - 4.10.1 Basic Differences Between Python 2 and 3. - 4.10.2 Turning Python 2 Code into Python 3 Code. - 4.11 Summary. - 4.11.1 Chapter Topics. - 4.11.2 Example: Bisection Root Finding. - 4.12 Exercises. - 5 Array Computing and Curve Plotting. - 5.1 Vectors. - 5.1.1 The Vector Concept. - 5.1.2 Mathematical Operations on Vectors. - 5.1.3 Vector Arithmetics and Vector Functions. - 5.2 Arrays in Python Programs. - 5.2.1 Using Lists for Collecting Function Data. - 5.2.2 Basics of Numerical Python Arrays. - 5.2.3 Computing Coordinates and Function Values. - 5.2.4 Vectorization. - 5.3 Curve Plotting. - 5.3.1 MATLAB-Style Plotting with Matplotlib. - 5.3.2 Matplotlib; Pyplot Prefix. - 5.3.3 SciTools and Easyviz. - 5.3.4 Making Animations. - 5.3.5 Making Videos. - 5.3.6 Curve Plots in Pure Text. - 5.4 Plotting Difficulties. - 5.4.1 Piecewisely Defined Functions. - 5.4.2 Rapidly Varying Functions. - 5.5 More Advanced Vectorization of Functions. - 5.5.1 Vectorization of StringFunction Objects. - 5.5.2 Vectorization of the Heaviside Function. - 5.5.3 Vectorization of a Hat Function. - 5.6 More on Numerical Python Arrays. - 5.6.1 Copying Arrays. - 5.6.2 In-Place Arithmetics. - 5.6.3 Allocating Arrays. - 5.6.4 Generalized Indexing. - 5.6.5 Testing for the Array Type. - 5.6.6 Compact Syntax for Array Generation. - 5.6.7 Shape Manipulation. - 5.7 High-Performance Computing with Arrays. - 5.7.1 Scalar Implementation. - 5.7.2 Vectorized Implementation. - 5.7.3 Memory-Saving Implementation. - 5.7.4 Analysis of Memory Usage. - 5.7.5 Analysis of the CPU Time. - 5.8 Higher-Dimensional Arrays. - 5.8.1 Matrices and Arrays. - 5.8.2 Two-Dimensional Numerical Python Arrays. - 5.8.3 Array Computing. - 5.8.4 Matrix Objects. - 5.9 Some Common Linear Algebra Operations. - 5.9.1 Inverse, Determinant, and Eigenvalues. - 5.9.2 Products. - 5.9.3 Norms. - 5.9.4 Sum and Extreme Values. - 5.9.5 Indexing. - 5.9.6 Transpose and Upper/Lower Triangular Parts. - 5.9.7 Solving Linear Systems. - 5.9.8 Matrix Row and Column Operations. - 5.9.9 Computing the Rank of a Matrix. - 5.9.10 Symbolic Linear Algebra. - 5.10 Plotting of Scalar and Vector Fields. - 5.10.1 Installation. - 5.10.2 Surface Plots. - 5.10.3 Parameterized Curve. - 5.10.4 Contour Lines. - 5.10.5 The Gradient Vector Field. - 5.11 Matplotlib. - 5.11.1 Surface Plots. - 5.11.2 Contour Plots. - 5.11.3 Vector Field Plots. - 5.12 Mayavi. - 5.12.1 Surface Plots. - 5.12.2 Contour Plots. - 5.12.3 Vector Field Plots. - 5.12.4 A 3D Scalar Field and Its Gradient Field. - 5.12.5 Animations. - 5.13 Summary. - 5.13.1 Chapter Topics. - 5.13.2 Example: Animating a Function. - 5.14 Exercises. - 6 Dictionaries and Strings. - 6.1 Dictionaries. - 6.1.1 Making Dictionaries. - 6.1.2 Dictionary Operations. - 6.1.3 Example: Polynomials as Dictionaries. - 6.1.4 Dictionaries with Default Values and Ordering. - 6.1.5 Example: Storing File Data in Dictionaries. - 6.1.6 Example: Storing File Data in Nested Dictionaries. - 6.1.7 Example: Reading and Plotting Data Recorded at Specific Dates. - 6.2 Strings. - 6.2.1 Common Operations on Strings. - 6.2.2 Example: Reading Pairs of Numbers. - 6.2.3 Example: Reading Coordinates. - 6.3 Reading Data fromWeb Pages. - 6.3.1 About Web Pages. - 6.3.2 How to Access Web Pages