Introduction to the Modelling of Marine Ecosystems ：(with MATLAB programs on accompanying CD-ROM) ( 2 )

Publication subTitle ：(with MATLAB programs on accompanying CD-ROM)

Publication series ：2

Author： Fennel W.;Neumann T.

Publisher： Elsevier Science‎

Publication year： 2014

E-ISBN: 9780444634153

P-ISBN(Paperback): 9780444633637

P-ISBN(Hardback): 9780444633637

Subject： Q1 General Biology;Q14 Biological Ecology (Ecology)

Language： ENG

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Description

Introduction to the Modelling of Marine Ecosystems, Second Edition provides foundational information on the construction of chemical and biological models – from simple cases to more complex biogeochemical models and life cycle resolving model components. This step-by-step approach to increasing the complexity of the models allows readers to explore the theoretical framework and become familiar with the models even when they have limited experience in mathematical modeling. Introduction to the Modelling of Marine Ecosystems shows how biological model components can be integrated into three dimensional circulation models and how such models can be used for numerical experiments.

Covers the marine food web from nutrients, phytoplankton to higher trophic levels
Presents information on the response of marine systems to external pressures as seen in physical biological models
Provides an extended discussion of unifying theoretical concepts and of physical biological interaction
Covers higher trophic levels, in particular multi-species fish models and their interaction with the biogeochemical models
Offers MATLAB scripts on a companion website for many of the described example models to facilitate reproduction of the findings in the book and guide reader to writing own code

Chapter

Front Cover

Introduction to the Modelling of Marine Ecosystems

Contents

Preface

Chapter 1: Introduction

1.1 Models of Marine Ecosystems

1.2 Models from Nutrients to Fish

1.2.1 Models of Individuals, Populations and Biomass

1.2.2 Fisheries Models

1.2.3 Unifying Theoretical Concept

1.2.4 The Plan of the Book

Chapter 2: Chemical-Biological Models

2.1 Chemical-Biological Processes

2.1.1 Biomass Models

2.1.2 Nutrient Limitation

2.1.3 Recycling

2.1.4 Zooplankton Grazing

2.2 Simple Models

2.2.1 Construction of a Simple NPZD Model

2.2.2 First Model Runs

2.2.3 A Simple NPZD Model with Variable Rates

2.2.4 Eutrophication Experiments

2.2.5 Discussion

2.3 Simple Plankton Models for the Ocean

2.3.1 A Simple NPZ Model for the Ocean Mixed Layer

2.3.2 NPZ and NPZD Models for the Annual Cycle of the Oceanic Mixed Layer

Chapter 3: More Complex Models

3.1 Competition

3.2 Several Functional Groups

3.2.1 Succession of Phytoplankton

3.3 N2 Fixation

3.4 Denitrification

3.4.1 Numerical Experiments

3.4.1.1 Experiment 1

3.4.1.2 Experiment 2

3.4.1.3 Experiment 3

3.4.2 Processes in Sediments

Chapter 4: Modelling Life Cycles of Copepods and Fish

4.1 Growth and Stage Duration

4.2 Stage-Resolving Models of Copepods

4.2.1 Population Density

4.2.2 Stage-Resolving Population Models

4.2.3 Population Model and Individual Growth

4.2.4 Stage-Resolving Biomass Model

4.3 Experimental Simulations

4.3.1 Choice of Parameters

4.3.1.1 Grazing Rates

4.3.1.2 Loss Rates

4.3.1.3 Reproduction

4.3.1.4 Mortality and Overwintering

4.3.2 Rearing Tanks

4.3.3 Inclusion of Lower Trophic Levels

4.3.4 Simulation of Biennial Cycles

4.4 A Fish Model

4.4.1 Formulation of the Theory

4.4.2 Structure of the Fish Model Equations

4.4.3 Predator–Prey Interaction and Effective Growth

4.4.4 Modelling Reproduction and Mortality

4.4.5 Coupling Fish and Lower Trophic Levels

4.4.6 Example Scenarios

4.4.7 Discussion

Chapter 5: Physical–Biological Interaction

5.1 Irradiance

5.1.1 Daily, Seasonal and Annual Variation

5.1.2 Production–Irradiance Relationship

5.1.3 Light Limitation and Mixing Depth

5.2 Coastal Ocean Dynamics

5.2.1 Basic Equations

5.2.2 Large-Scale Winds and Coastal Jets

5.2.3 Kelvin Waves and Undercurrents

5.2.4 The Role of Wind-Stress Curls

5.2.5 Discussion

5.3 Advection–Diffusion Equation

5.3.1 Reynolds Rules

5.3.2 Analytical Examples

5.3.3 Turbulent Diffusion in Collinear Flows

5.3.3.1 Turbulent Diffusion in a Shear Flow

5.3.3.2 Turbulent Diffusion in Eddies

5.3.3.3 Turbulent Diffusion in Deformation Fields

5.3.3.4 Aggregation at Convergence Lines

5.3.4 Patchiness and Critical Scales

5.4 Upscaling and Downscaling

5.5 Resolution of Processes

5.5.1 State Densities and Their Dynamics

5.5.2 Primary Production Operator

5.5.3 Predator–Prey Interaction

5.5.4 Mortality Operators

5.5.5 Model Classes

Chapter 6: Coupled Models

6.1 Introduction

6.2 Regional to Global Models

6.3 Circulation Models

6.4 Baltic Sea

6.5 Description of the Model System

6.5.1 Baltic Sea Circulation Model

6.5.2 The Biogeochemical Model ERGOM

6.6 Simulation of the Annual Cycle

6.7 Simulation of the Decade 1980–1990

6.8 A Load Reduction Experiment

6.9 Projection of Future Changes

6.10 Tracking of Elements

6.11 Discussion

Chapter 7: Circulation Model, Copepods and Fish

7.1 Recruitment (Match–Mismatch)

7.2 Copepods in the Baltic Sea Model

7.3 Three-Dimensional Simulations

7.3.1 Time Series of Basin Averages

7.3.2 Spatial Distribution

7.4 Modelling of Behavioural Aspects

7.4.1 Vertical Motion

7.4.2 Visibility and Predation

7.4.3 Individual-Based Versus Population Models

7.4.4 Water-Column Models

7.5 Fish in a Three-Dimensional Model

7.5.1 Coupling Upper and Lower Food Webs

7.5.2 Horizontally Moving Fish

7.5.3 Initialization and First Simulation

7.5.4 Results and Discussion

7.5.5 Fish and Biogeochemistry

7.6 ERGOM: A Biogeochemical Model for Regional Seas

Chapter 8: A Brief Introduction to MATLAB

8.1 Fundamentals

8.1.1 Matrix and Array Operations

8.1.2 Figures

8.1.3 Script Files and Functions

8.2 Ordinary Differential Equations

8.3 Miscellaneous

Appendix: Content of the Booksite

Bibliography

Index

Color Plates

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