TABLE OF CONTENTS

 

PREFACE

 

TABLE OF CONTENTS

 

NOMENCLATURE

 

ABSTRACT

 

CHAPTER 1. INTRODUCTION                                                                        

                       1.1 Motivation

                       1.2 Great Bay Estuary, NH

                       1.3 Objectives

                       1.4 Numerical Methods

                       1.5 Approach

                       1.6 Overview of Thesis

 

CHAPTER 2. FINITE ELEMENT METHOD AND MESH GENERATION

                        2.1 Basics of Finite Element Methods

                        2.2 Mesh Generation in the Great Bay Estuary System

                              2.2.1 FE Mesh Generation Tool, TRIANGLE

                              2.2.2 Extracting Data for the Mesh Generation

                              2.2.3 Preliminary Meshes for the Great Bay Estuary System

 

CHAPTER 3. HYDRODYNAMIC MODEL, ADAM

                       3.1 Modeling Efforts in the Great Bay Estuary

                       3.2 ADAM Model

                       3.3 Governing Equations

                       3.4 Handling the Porous Medium

                             3.4.1 Equations in the Wet (saturated) Region where H> h_o

                             3.4.2 Equations in the Dry (unsaturated) Region where H< h_o

                       3.5 The Program Structure

                             3.5.1 Standard Output Files

 

CHAPTER 4. EELGRASS (ZOSTERA MARINA L.)

                       4.1 Functions of Eelgrass in an Estuary

                       4.2 Effects of Eelgrass on Current Flow

                       4.3 Disturbance Sources of Eelgrass

                             4.3.1 Wasting Disease

                       4.4 Restoration and Mitigation Efforts of Seagrass Habitats

 

CHAPTER 5. TIDES AND TIDAL FORCING

                       5.1 Boundary Conditions

                       5.2 Observational Data

                       5.3 Sea Level Observations

                       5.4 Current Observations

 

 CHAPTER 6. MODELING THE M₂TIDAL FLOW FOR THE ENTIRE GREAT BAY ESTUARY

                       6.1 Computational Setup

                       6.2 Tidal Boundary Forcing at Portsmouth Harbor

                       6.3 Bottom Friction Coefficient Adjustment for the Great Bay Estuary

                       6.4 Statistical Analysis Methods

                       6.5 Results for M₂ Forcing

                             6.5.1 Simulation A

                             6.5.2 Simulation B

                             6.5.3 Simulation C

                       6.6 The gbes16 Mesh

                       6.7 Boundary Forcing for the gbes16 Mesh

 

 

CHAPTER 7. MODELING THE M₂TIDAL FLOW IN GREAT BAY

                       7.1 Results for the M₂ Tidal Forcing without Eelgrass

                       7.2 Eelgrass Effects on the M₂ Tidal Flow in Great Bay

 

CHAPTER 8. MODELING THE M₂S₂ TIDAL FLOW IN GREAT BAY

                       8.1 Results for the M₂S₂ Tidal Forcing without Eelgrass

                       8.2 Eelgrass Effects on the M₂S₂ Tidal Flow in Great Bay

                             8.2.1 Eelgrass Effects on the M₂S₂ Tidal Flow at Spring Tide                                  

                             8.2.2 Eelgrass Effects on the M₂S₂ Tidal Flow at NeapTide

 

CHAPTER 9. MODELING THE M₂S₂N₂ TIDAL FLOW IN GREAT BAY

                       9.1 Results for the M₂S₂N₂ Tidal Forcing without Eelgrass

                       9.2 Eelgrass Effects on the M₂S₂N₂ Tidal Flow in Great Bay

                             9.2.1 Eelgrass Effects on the M₂S₂N₂ Tidal Flow at Spring Tide

                             9.2.2 Eelgrass Effects on the M₂S₂N₂ Tidal Flow NeapTide

 

CHAPTER 10. CONCLUSIONS AND DISCUSSION

 

 

LIST OF REFERENCES

 

                        APPENDIX A: Darcian Flow

                        APPENDIX B: The Galerkin Method

APPENDIX C: Movies (only available online)