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RodionovPhysical Oceanography of Frontal Zones in the Subarctic SeasElsevier Oceanography series, 72INTRODUCTION TOTHE MODELLING OFMARINE ECOSYSTEMSyW. FennelandT NeumannBaltic Sea Research Institute Warnemunde, Rostock, Germany2004ELSEVIERAmsterdam -Boston-Heidelberg-London-New York-OXfordParis- San Diego- San Francisco- Singapore- Sydney- TokyoELSEVIER BELSEVIER IncELSEVIER LtdELSEVIER LtdSara Burgerhartstraat 25525 B Street. Suite 1900The boulevard, Langford LaneP.O. Box 211, 1000 AESan Diego, CA 92101-4495adlington, Oxford OX5 1GBLondon WClX 8RRAmsterdam, The NetherlandUSAUKUKc 2004 Elsevier B V. All rights reservedThis work is protected under copyright by Elsevier B,V, and the following terms and conditions apply to its usePhotocopyingSingle photocopies of single chapters may be made for personal use as allowed by national copyright laws. 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Permission of the Publisher is required for all other derivative works, including compilations and translationsElectronic Storage or UsagePermission of the Publisher is required to store or use electronically any material contained in this work, including any chapter or partof a chaptermeans,electronic, mechanical, photocopying, recordin reproduced, stored in a retrieval system or transmitted in any form or by anyAddress permissions requests to: Elsevier's Rights Department, at the fax and e-mail addresses noted aboveNoticeNo responsibility is assumed by the Publisher for any injury andor damage to persons or property as a matter ofnegligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in tIBecause of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drugFirst edition 2004Library of Congress Cataloging in Publication DataA catalog record is available from the Library of CongressBritish Library Cataloguing in Publication DataA catalogue record is available from the British LibraryISBN: 0-444-51702-2( Hardbound)IsBN: 0-1704-9(Paperback)ISBN:0-444-51723-5CD-rom)ISSN:0422-9896 The paper used in this publication meets the requirements of ANSI/NISO Z39.48-1992(Permanence of Paper)Printed in The netherlandsWorking together togroOWlibraries in developing countrieswww.elsevier.comIwww.bookaid.orgIwww.sabre.orgELSLV'IER B(K Sabre foundationPrefaceDuring the last few decades the theoretical research on marine systems, particularlyin numerical modelling, has developed rapidly. A number of biogeochemical models,population models and coupled physical chemical and biological models have beendeveloped and are used for research. Although this is a rapidly growing field, asdocumented by the large number of publications in the scientific journals, thereare very few textbooks dealing with modelling of marine ecosystems, Wedin particular that a textbook giving a systematic introduction to the modellingof marine ecosystem is not available and, therefore it is timely to write a bookthat focuses on model building and which helps interested scientists to familiarizethemselves with the technical aspects of modelling and start building their ownmodelsThe book begins with very simple first steps of modelling and develops more andmore complex models. It describes how to couple biological model components withthree dimensional circulation models. In principle one can continue to include moreprocesses into models, but this would lead to overly complex models as difficult tounderstand as nature itself. The step-by-step approach to increasing the complexityof the models is intended to allow students of biological oceanography and interestedscientists with only limited experience in mathematical modelling to explore thetheoretical framework. The book may also serve as an introduction to coupledmodels for physical oceanographers and marine chemistsWe, the authors, are physicists with some background in theory and modellingHowever, we had to learn ecological aspects of marine biology from the scientificliterature and discussions with marine biologists. Nevertheless, when physicists aredealing with biology, there is a danger that many aspects of biology or biogcochcmistry are not as well represented as experts in the field may expect. On the otherhand, the Inost inportant aim of this text is to show how model development can bedone. Therefore the textbook concentrates on the approach of model developmentillustrating the mathematical aspects and giving examples. This tutorial aspect issupported by a set of matlab programmes on the attached CD, which can be usedto reproduce many of the results described in the second, third and fourth chaptersFor many discussions, in particular for the coupling of circulation and biologicalmodels, we have to choose example systems. We used the Baltic Sea, which canserve as a testbed. Hence the models are not applicable to all systems, becausethere are always site-specific aspects. On the other hand, the models have alsosome universal aspects and the understanding of the approach can be a useful guidefor model development in other marine areas. The book was not intended to givea comprehensive overview of all existing models and only a subset of papers onmodelling was quotedWe owe thanks to many colleagues, in particular from our institute, the BalticSea Research Institute(IOW), for helpful discussions and invaluable support. Weare indebted to Prof. Oscar Schofield and Dr. Katja Fennel for valuable comments on a draft version of the manuscript, and we thank leon Tovey for his carefulproofreading of the English. We further thank Thomas Fennel for helping with theproduction of several of the figuresWarnemunde January 2004Wolfgang Fennel and Thomas NeumannContents1 Introduction1.1 Coupling of models1.2 Models from Nutrients to Fish1.2.1 Models of Individuals, Populationsand biomass1.2.2 Fisheries models61.2.3 Unifying Theoretical Concept2 Chemical Biological-Models132. 1 Chemical Biological Processes132.1.1 Biomass models142.1.2 Nutrient limitation182.1.3 Recycling212. 1.4 Zooplankton Grazing252.2 Simple Models272.2.1 Construction of a Simple NPzD-Model272.2.2 First Model runs342.2.3 A Simple npzd-Model with Variable rates352.2. 4 Eutrophication Experiments412.2.5 Discussion443 More Complex models493. 1 Competition493.2 Several Functional Groups533.2. 1 Succession of Phytoplankton·613.3 N2-Fixation653.4 Denitrification3.4. 1 Numerical Experiments783.4.2 Processes in Sediments924 Modelling Life Cycles954.1 Growth and Stage duratio964.2 Stage Resolving Models of Copepods994.2, 1 Population DensityCONTENTS4.2.2 Stage Resolving Population Models1034.2.3 Population Model and Individual growth1054.2. 4 Stage Resolving Biomass Model1124.3 Experimental Simulations1144.3.1 Choice of Parameters1154.3.2 Rearing Tanks4.3.3 Inclusion of Lower Trophic Levels,,1201224.3.4 Simulation of Biennial Cycles1244.4 Discussion1285 Physical Biological Interaction1295.1 Irradiance1295.1.1 Daily, Seasonal and Annual variation1295.1.2 Production-Irradiance Relationship1315. 1. 3 Light Limitation and Mixing Depth1335.2 Coastal Ocean dynamics1385.2.1 Basic equations1395.2.2 Coastal jets1435.2.3 Kelvin Waves and Undercurrents1465.2.4 Discussion1535.3 Advection-Diffusion Equation1555.3.1 Reynolds rules1555.3.2 Analytical E1575. 3. 3 Turbulent Diffusion in Collinear Flows1595.3.4 Patchiness and Critical Scales1685. 4 Up- and Down-Scaling1705.5 Resolution of processes1755.5.1 State Densities and their dynamics1755.5.2 Primary Production Operator1775.5.3 Predator-Prey Interaction1785.5. 4 Mortality Operator1805.5.5 Model classes1816 Coupled Models1836.1 Introduction1836.2 Regional to Global Models6.3 Circulation Models1866.4 Balt6.5 Description of the Model System1946.5.1 Baltic Sea Circulation Model1946.5.2 The biogeochemical Model ERGOM1976.6 Simulation of the Annual Cycle,,,,.2046.7 Simulation of the Decade 1980-902146.8 A Load Reduction Experiment224CONTENTS6.9 Discussion.2317 Circulation Model and Copepods2337.1 Recruitment(Match-Mismatch2347.2 Copepods in the Baltic Sea Model2347. 3 Three-Dimensional Simulations2357.3.1 Time Series of Basin Average2367.3.2 Spatial Distribution2387.4 Modelling of behavioral aspects2447.4.1 Vertical Motion2457.4.2 Visibility and Predation2477.4.3 IBM Versus Population Models2477.4.4 Water Column Models2498 a Brief introduction to matlaB2558.1 Fundamentals2558.1.1 Matrix and Array Operations2578.1.2 Figures.2598.1.3 Script Files and Functions2628.2 Ordinary Differential EquatiOns2648.3 Miscellaneous.267A Content of the CD269Bibliography273Index285List of Figures287