UNIVERSITI PUTRA MALAYSIA

MOHAMAD ZAMIN BIN MOHAMAD JUSOH

FK 2015 31

BREAKWATER GEOMETRIC MODEL BASE ON MANGROVE ROOTS STRUCTURE

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BREAKWATER GEOMETRIC MODEL BASE ON MANGROVE ROOTS STRUCTURE

By

MOHAMAD ZAMIN BIN MOHAMAD JUSOH

Thesis Submitted to the School of Graduate Studies, Universiti Putra Malaysia, in Fulfilment of the Requirements for the Degree of Master of

Science

May 2015

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Abstract of thesis presented to the Senate of Universiti Putra Malaysia in fulfilment of the requirement for the degree of Master of Science

BREAKWATER GEOMETRIC MODEL BASE ON MANGROVE ROOTS STRUCTURE

By

MOHAMAD ZAMIN BIN MOHAMAD JUSOH

May 2015

Chair: Associate Professor Nuraini Bt Abdul Aziz, PhD Faculty: Engineering

In year 2013, the Department of Irrigation and Drainage Malaysia indicates that 29% or 1,394 km out of 4,809 km of the country’s coastline are facing erosion. The coastal erosion had caused 1% of mangrove forest area to continue decline each year. Although mangroves were affected by the erosion but the erosion rate was reduces in the area which mangroves inhabited. Hence, researchers had conducted studies on wave dissipation process in mangrove forest structure that concentrated at west coast of the Malaysia peninsular. Contrarily, this study had taken different approach by investigating on a sole mangrove trees structures at east coast of Malaysia peninsular. The study were focused in the geometrical properties of the mangrove roots and the water flow structure within the mangrove roots area of the Avicennia marina (A. marina) and Rhizophora apiculata (R. apiculata) mangrove species. The roots properties were investigated by conducting a field work at Pantai Marina, Kemaman where the geometrical coordinate of each roots of A. marina and R. apiculata species were collected using grids. Henceforth, a 2D model of the mangrove roots was constructed using meshing software. The simulations were conducted in Computational Fluid Dynamic software using unsteady Spalart-Allmaras turbulence model, water liquid material and by setting the velocity inlet in boundary condition to 6 m/s. From the investigation, it was found that the mangrove roots tend to grow around the mangrove primary trunk which facing the direction of the water traveled. It had been observed that there was large density of mangrove roots within the distance 100 cm to 150 cm from the primary trunk. The simulation result shows that mangrove roots were capable to decrease the initial velocity 6 m/s of water flow to almost 2 m/s. The breakwater model also shows that the geometrical coordinate and the distance between structures were related to the velocity deficit rate. Each structure was arranged in zigzag pattern and the distance of the structure was placed within the maximum range of three times of the structures cross section diameter to create optimum velocity dissipation rate. Thus, the study had found that both

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mangrove roots and the breakwater models were capable reducing the velocity to 60 %. The velocity deficit also was related to the roots density, structure and coordination. Henceforth, the finding could contribute to the future construction of breakwater along the coastline in order to overcome the current coastal erosion problem or in the near future.

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Abstrak tesis yang dikemukakan kepada Senat Universiti Putra Malaysia sebagai memenuhi keperluan untuk ijazah Master Sains

MODEL GEOMETRI PEMECAH OMBAK BERASASKAN STRUKTUR AKAR POKOK BAKAU

Oleh

MOHAMAD ZAMIN BIN MOHAMAD JUSOH

Mei 2015

Pengerusi: Profesor Madya Nuraini Bt Abdul Aziz, PhD Fakulti: Kejuruteraan

Pada tahun 2013, Jabatan Pengairan dan Saliran telah mendapati bahawa 29% atau pun 1,394 km daripada 4,809 km persisian pantai di negara ini menghadapi masalah hakisan diperingkat bahaya. Masalah hakisan ini telah mengakibatkan kemusnahan hutan bakau yang berterusan dimana hampir 1% daripada hutan bakau akan mengecil setiap tahun. Walaupun hutan bakau terkesan dengan masalah hakisan pantai, akan tetapi hakisan yang dialami hutan bakau dapat dikurangkan kerana kelebihan pokok bakau untuk memecah ombak. Oleh itu, penyelidik telah menjalankan kajian mengenai proses pelesapan ombak dalam struktur hutan bakau yang tertumpu di pantai barat Semenanjung Malaysia. Sebaliknya, kajian ini telah mengambil pendekatan yang berbeza dengan mengkaji struktur pokok bakau di pantai timur Semenanjung Malaysia. Kajian ini bertujuan untuk menganalisi proses mitigasi pokok bakau dengan mengkaji ciri akar pokok bakau dan struktur aliran air dalam kawasan akar pokok bakau dari spesies Avicennia marina (A. marina) dan Rhizophora apiculata (R. apiculata). Kajian telah dijalankan di Pantai Marina, Kemaman dengan melakar grid di sekeliling pokok A. marina dan R. apiculata bagi mendapatkan data akar pokok bakau tersebut. Seterusnya, model akar pokok bakau telah dilukis dalam bentuk 2D dengan menggunakan perisian pemodelan. Manakala simulasi pemecahan ombak dan struktur aliran air di dalam kawasan akar pokok bakau telah dijalankan dengan menggunakan model Spalart-Allmaras, model cecair dan halaju dalam sempadan 6 m/s. Daripada kajian yang dijalankan, didapati akar pokok bakau cenderung untuk tumbuh disekeliling batang pokok utama dan menghadap laluan air. Hasil kajian menunjukkan akar pokok bakau tumbuh dengan lebih padat pada jarak 100 cm hingga 150 cm dari batang utama pokok bakau tersebut. Keputusan simulasi ke atas akar pokok bakau pula mendapati bahawa pokok bakau secara individu mampu untuk mengurangkan kelajuan aliran air daripada 6 m/s kepada 2 m/s. Keputusan simulasi ke atas model pemecah ombak menunjukkan kadar pengurangan kelajuan aliran adalah

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bergantung kepada koordinat dan jarak diantara struktur model pemecah ombak. Kelajuan air dapat di kurangkan secara optima dengan mengaturkan struktur model dalam bentuk bersilang-seli dan dengan menjarakkan struktur model dalam linkungan jarak maksima tiga kali nilai keratan rentas struktur model tersebut. Oleh itu, kajian ini mendapati bahawa kedua-dua model akar bakau dan pemecah ombak mampu mengurangkan halaju hingga 60%. Defisit halaju juga berkaitan dengan ketumpatan, struktur dan koordinat akar pokok bakau. .Dengan adanya penemuan ini, ia dapat menyumbang kepada pembinaan struktur pemecah ombak yang lebih efisien untuk menangani maslah hakisan pantai yang sedang dialami sekarang atau pun dimasa akan datang.

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ACKNOWLEDGEMENTS

All praises be to the Mighty Allah S.W.T, the Merciful and the Beneficent for the strength, patience, determination and blessing in the completion of this study. It is impossible for me to finish this thesis all by myself without the guidance and help of many important people. Firstly, I wish to express my gratitude to my main supervisor Dr. Nuraini Bt Abdul Aziz who guide me continuously and patiently reviewed this thesis. I had receiving encouragement, invaluable guidance and constructive criticism from my supervisor. She has been my advisor and mentor throughout my graduate education. I also would like to thank my co-supervisor Dr.Othman Inayatullah who had contributes me the valuable information and ideas during completing this study. Last but not least, a special thanks to all my family members especially my beloved parents who always given me their physical and moral supports, encouragements, and motivation while completing this thesis. Not forgotten, my appreciation to my friends and colleagues especially Najihah for their co-operations and kindness. Your supports and encouragements mean word to me.

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I certify that a Thesis Examination Committee has met on 26 May 2015 to conduct the final examination of Mohamad Zamin bin Mohamad Jusoh on his thesis entitled ʺBreakwater Geometrical model Base on Mangrove Roots Structureʺ in accordance with the Universities and University Colleges Act 1971 and the Constitution of the Universiti Putra Malaysia [P.U.(A) 106] 15 March 1998. The Committee recommends that the student be awarded the Master of Science.

Members of the Thesis Examination Committee were as follows:

Nur Ismarrubie Zahari, PhD

Associate Professor Faculty of Engineering Universiti Putra Malaysia (Chairman) Nawal Aswan b. Abdul Jalil, PhD Associate Professor Ir. Faculty of Engineering Universiti Putra Malaysia (Internal Examiner) Hanim Salleh, PhD

Associate Professor Universiti Tenaga Nasional Malaysia (External Examiner)

________________________ Zulkarnain Zainal, PhD

Professor and Deputy Dean School of Graduate Studies Universiti Putra Malaysia Date: 22 September 2015

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This thesis was submitted to the Senate of Universiti Putra Malaysia and has been accepted as fulfilment of the requirement for the degree of Master of Science. The members of the Supervisory Committee were as follows:

Nuraini Abdul Aziz, PhD

Associate Professor Faculty of Engineering Universiti Putra Malaysia (Chairman) Othman Inayatullah, PhD

Capt (Rtd) Faculty of Engineering Universiti Putra Malaysia (Member)

________________________ BUJANG KIM HUAT, PhD Professor and Dean School of Graduate Studies Universiti Putra Malaysia Date:

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Declaration by graduate student

I hereby confirm that: this thesis is my original work; quotations, illustrations and citations have been duly referenced; this thesis has not been submitted previously or concurrently for any other

degree at any other institutions; intellectual property from the thesis and copyright of thesis are fully-owned

by Universiti Putra Malaysia, as according to the Universiti Putra Malaysia (Research) Rules 2012;

written permission must be obtained from supervisor and the office of Deputy Vice-Chancellor (Research and Innovation) before thesis is published (in the form of written, printed or in electronic form) including books, journals, modules, proceedings, popular writings, seminar papers, manuscripts, posters, reports, lecture notes, learning modules or any other materials as stated in the Universiti Putra Malaysia (Research) Rules 2012;

there is no plagiarism or data falsification/fabrication in the thesis, and scholarly integrity is upheld as according to the Universiti Putra Malaysia (Graduate Studies) Rules 2003 (Revision 2012-2013) and the Universiti Putra Malaysia (Research) Rules 2012. The thesis has undergone plagiarism detection software.

Signature: ________________________ Date: __________________

Name and Matric No.: Mohamad Zamin bin Mohamad Jusoh, GS30189

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Declaration by Members of Supervisory Committee

This is to confirm that: the research conducted and the writing of this thesis was under our

supervision; supervision responsibilities as stated in the Universiti Putra Malaysia

(Graduate Studies) Rules 2003 (Revision 2012-2013) are adhered to.

Signature: Name of Chairman of Supervisory Committee:

Signature:

Name of Member of Supervisory Committee:

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TABLE OF CONTENTS

Page

ABSTRACT i ABSTRAK iii ACKNOWLEDGEMENTS v APPROVAL vi DECLARATION viii LIST OF TABLES xiii LIST OF FIGURES xv LIST OF ABBREVIATIONS xx

CHAPTER

1 INTRODUCTION 1 1.1 Background 1 1.2 Problem statement 1 1.3 Recent research 2 1.4 Research objective 3 1.5 Scope and limitation 3 1.5.1 Research scope and limitation 3 1.5.2 Software limitation 4 1.6 Outline of the thesis 4

2 LITERATURE REVIEW 6 2.1 Mangrove distribution 6 2.2 Mangrove ecosystem 7 2.3 Mangrove forest structure 8 2.4 Mangrove zonation 9 2.5 Mangrove aerial roots system 10 2.6 Avicennia Marina (Forks.) Vierh (A.

Marina) 14

2.7 Rhizophora apiculata (R. Apiculata) 16 2.8 Mangrove roots attenuation wave

energy 18

2.9 Wave propagation numerical model in mangrove forest

18

2.9.1 Avicennia simulation model, TUNA-M2

18

2.9.2 Rhizophora numerical model 22 2.9.3 2-D depth intergrated

mathematical model 25

2.10 Breakwater 26 2.10.1 Type of breakwaters 26 2.10.2 Recent breakwater researches 29

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3 METHODOLOGY 35 3.1 Method and materials 35 3.2 Introduction 35 3.3 Material 35 3.4 Flow chart of research activities 36 3.5 Validation of CFD simulation 41 3.6 Field observation 42 3.6.1 Study area 42 3.6.2 Collection of mangrove roots

geometrical coordinate and perimeter

45

3.6.3 Collection of wind speed and wave period

47

3.7 Field data computer analysis 48 3.7.1 Mangrove roots mesh creation 48 3.7.2 Mangrove roots CFD

simulation preparation 49

3.7.3 Mangrove roots CFD simulation procedure

51

3.8 Mangrove roots based breakwater analysis

51

3.8.1 Breakwater design procedure 51 3.8.2 Breakwater mesh generation

and simulation process 54

4 PNEUMATOPHORES AND STILT ROOTS

GEOMETRICAL PROPERTIES AND STUDY AREA CONDITION

55

4.1 Introduction 55 4.2 Mangrove roots geometrical coordinate

and characteristic 55

4.2.1 Avicennia marina species 55 4.2.2 Rhizophora apiculata species 58 4.3 Study area wind speed and wave period 62 4.4 Discussion 64

5 SIMULATION OF PNEUMATOPHORES AND STILT ROOTS USING COMPUTATIONAL FLUID DYNAMIC

69

5.1 Introduction 69 5.2 Validation result of CFD simulation

procedure 69

5.3 Mangrove roots mesh 70 5.4 Simulation result using Computational

Fluid Dynamic software 73

5.4.1 Simulation on Pneumatophores Roots of Avicennia marina

73

5.4.2 Simulation on Stilt Roots of Rhizophora apiculata

79

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5.5 Discussion 84 5.5.1 The influence of roots

properties on the water flow velocity

84

5.5.2 The effect of turbulent region and the jet flow to the water flow

87

6 CFD SIMULATION OF MANGROVE ROOTS

BASED BREAKWATER 94

6.1 Introduction 94 6.2 Breakwater mesh 94 6.3 Simulation result of the breakwater

using CFD software 95

6.3.1 Simulation on Avicennia breakwater models

95

6.3.2 Simulation on Rhizophora A breakwater models

98

6.3.3 Simulation on Rhizophora B breakwater models

101

6.4 Discussion 103

7 CONCLUSION AND RECOMMENDATION 111 7.1 Conclusion of the study 111 7.1.1 Field work study 111 7.1.2 Mangrove roots CFD

simulation 111

7.1.3 Breakwater model CFD simulation

112

7.2 Recommendation 113

REFERENCES 114 APPENDICES 121 BIODATA OF STUDENT 138 PUBLICATION 139

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LIST OF TABLES

Table Page 2.1 The pneumatophores density of Avicennia

marina mangrove 15

3.1 The specification of digital anemometer wind

speed gauge 35

3.2 The characteristic of sample mangrove trees 43 4.1 Pneumatophores aerial roots density and

diameter for each section 58

4.2 Stilt roots density and range of cross section

diameters for each section 62

4.3 The range of wind speed and wave period at

field work location 64

4.4 The pneumatophores density of Avicennia

marina mangrove species 65

5.1 Comparison table of VORTEX model

simulation result 70

5.2 Summary of Equiangle skew of 2D elements

for pneumatophores mesh 72

5.3 Summary of Equiangle skew of 2D elements

for stilt roots mesh 73

5.4 Summary of mangrove trees velocity

dissipation rate 92

6.1 Summary of Equiangle skew of the

breakwaters 95

6.2 Summary of Avicennia breakwater model

velocity deficit 98

6.3 Summary of Rhizophora A breakwater model

velocity deficit 100

6.4 Summary of Rhizophora B breakwater model

velocity deficit 103

6.5 Summary of breakwater model velocity deficit with previous studies

106

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6.6 Comparison of flow structure in breakwater

models with Furukawa et al. (1996) VORTEX model

109

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LIST OF FIGURES

Figure Page 2.1 Distribution of the world’s mangrove forest

6

2.2 True Mangrove Species in Southeast Asia 7 2.3 Six types of mangrove forests of common

occurrence 9

2.4 Hypothetical schematization of zonation in

mangrove forest 10

2.5 Mangrove aerial roots (a) Pneumatophores

(b) Stilt roots c) Knee roots (d) Plank roots 13

2.6 Avicennia marina (a) Bark (b) Leaf (c) Flower

(d) Fruit/ Seed 15

2.7 Rhizophora apiculata (a) Bark (b) Leaf (c)

Flower (d) Fruit/ Seed 17

2.8 Reduction ratios of elevation rɳ (a) and

velocity ru (b) as a function of forest width relative to wavelength

21

2.9 (a) Study area and tsunami heights along the

west coast of Thailand. Image (b) and (c) were the satellite imagery of mangrove forest near Pakarang Cape before and after the 2004 Indian Ocean Tsunami respectivel

22

2.10 The reduction rate of tsunami height and

hydraulic pressure in presence of mangrove forest at Pekarang Cape

25

2.11 Detached and attached breakwaters 27 2.12 Cross-section of typical rubber-mound

breakwater 28

2.13 Special breakwaters (a) Curtain-walled (b)

Pile (c) Horizontal plate 29

2.14 Semicircular breakwater (SCB9) model (a)

Curtain-walled (b) Pile (c) Horizontal plate 30

2.15 Test models: (a) Semicircular breakwater SCB9 model, (b) SCB9 with front wave

32

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screen, (c) SCB9 with rear screen and (d) SCB9 with double wave screens

2.16 Artificial mangrove roots system (ArMs)

Submerged Breakwater Physical Model 33

2.17 Artificial mangrove roots system (ArMs)

Transformation from Physical to Numerical Geometry

34

3.1 The apparatus that were used for field work

study 36

3.2 The flow chart of field data collection and

analysis 37

3.3 The flow chart of mangrove roots and

breakwater model mesh creation 38

3.4 The flow chart of mangrove roots and

breakwater model simulation 40

3.5 The fine-scale of a single Rhizophora roots

matrix (VORTEX model) 41

3.6 The location of Pantai Marina at Kuala

Kemaman River Mouth 42

3.7 Habitat of Avicennia marina species and

Rhizophora apiculata mangrove species at Pantai Marina coastal area

44

3.8 The parameter of the grid constructed around

the mangrove trees 46

3.9 The grid construction surrounded the

Avicennia marina species 46

3.10 The grid construction surrounded the

Rhizophora apiculata species 47

3.11 The location of wind speed data collection

area at Kuala Kemaman estuary 48

3.12 The hybrid mesh of the mangrove roots

geometry in Gambit software 49

3.13 Geometrical coordinate roots selected for 52

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breakwater design of (a) A. marina and (b), (c) R. apiculata mangrove species

3.14 Breakwater design with 3 different geometry

where (a), (b), (c) Avicennia Breakwater models while (d), (e), (f) were Rhizophora A Breakwater models and (g), (h), (i) were Rhizophora B Breakwater models

53

4.1 The geometrical coordinate of Avicennia

marina mangrove roots 56

4.2 The density of Avicennia marina aerial roots

in 1 x 1m wide area 57

4.3 The geometrical coordinate of Rhizophora

apiculata mangrove species stilt roots 59

4.4 The geometrical coordinate of roots A, B, C

and D 60

4.5 The cross section diameter of the stilt roots 61 4.6 The density of Rhizophora apiculata stilt roots

in 1 x 1 m wide area 61

4.7 The location of wind speed data collected at

Kuala Kemaman estuary 63

4.8 The number of pneumatophores roots in

against the direction of water travel 67

4.9 The number of stilt roots in against the

direction of water travel 68

5.1 Hybrid mesh of (a) Avicennia marina and (b)

Rhizophora apiculata roots 71

5.2 Simulation result of pneumatophores roots of

Avicennia marina mangrove species 74

5.3 The coordinate of line surface of

pneumatophores roots 75

5.4 The velocity magnitude of line surfaces at every 50 m distance of pneumatophores roots

78

5.5 Simulation result of Rhizophora apiculata stilt

roots 79

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5.6 The coordinate of line surface of stilt roots 80 5.7 The velocity magnitude of line surfaces at

every 50 m distance of stilt roots 83

5.8 Summary of simulation result of A. marina

and R. apiculata mangrove species 85

5.9 Relation of velocity magnitude and spatial

distribution density at x-axis cross section 86

5.10 Velocity vector of individual mangrove roots

in turbulent region 87

5.11 Turbulent intensity [%] at x-axis cross section

area of A. marina and R. apiculata mangrove species

88

5.12 Summary of modified turbulent viscosity of A.

marina and R. apiculata mangrove species 89

5.13 Relation of jet flow and the stagnation region

with the water flow velocity changes 90

5.14 Summary of relation between velocity

magnitude and turbulent intensity 91

6.1 Simulation result of Avicennia breakwater

models of (a) circular, (b) triangular, (c) rectangular geometry

96

6.2 Simulation result of Avicennia breakwater

models of (a) circular, (b) triangular, and (c) rectangular models

97

6.3 Simulation result of Rhizophora A breakwater

models of (a) circular, (b) triangular, (c) rectangular geometry

98

6.4 Simulation result of Rhizophora A breakwater

models of (a) circular, (b) triangular, (c) rectangular models

100

6.5 Simulation result of Rhizophora B breakwater

models of (a) circular, (b) triangular, and (c) rectangular geometry

101

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6.6 Simulation result of Rhizophora B breakwater models of (a) circular, (b) triangular, (c) rectangular models

102

6.7 Summary of simulation result of breakwater

models at outlet of x-axis cross section data 105

6.8 The pattern of geometrical coordinate of

breakwater models based on mangrove roots geometrical coordinate

108

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LIST OF ABBREVIATIONS

°C Celcius

2D Two Dimensional

3D Three Dimensional

AEP Atlantic East Pacific

A.marina vicennia marina

ArMs Artificial Mangrove Roots System

cm Centimeter

Cb2 Moleculor viscosity

CL Energy dissipation coefficient

CR Reflection coefficient

CT Transmission coefficient

Crn Reflection coefficients

Ctn Wave transmission coefficients

CFD Computational Fluid Dynamic

CSD Cross Section Diameter

d Water depth

ds Structure height

D Diameter

FTCS Forward in Time Central in Space

f Angular frequency

Ft Feet

g Gravitational acceleration

Gv Production of turbulence viscosity

h Height

IWP Indo West Pacific

Km Kilometer

L Distance travel

m Meter

M Mach number

N Number of time step

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NCES National Coastal Erosion Study

NSWE Non-Linear Shallow Water Equation

r Radius

Re Reynolds number

R.apiculata Rhizophora apiculata

R.mangle Rhizophora mangle

R. stlylosa Rhizophora stlylosa

R.mucronata Rhizophora mucronata

s Second

S User define source term

SCB Semicircular Breakwater

SCB9 Semicircular Breakwater with 9%

Front Wall Porosity

SCB9-FS Semicircular Breakwater 9% with

Front wave Screen

SCB9-RS Semicircular Breakwater 9% with Rear

wave Screen

SCB9-DS Semicircular Breakwater 9% with

Double wave Screen

SCB9-DS25S Semicircular Breakwater 9% with

Double wave Screen 25% Porosity

t Time

u Velocity of flow travel

Dynamic viscosity

Ve Volume of Empty Space

Vt Total Model Volume

Kinematic viscosity of the sea water

Turbulence kinematic viscosity

I Velocity of wave

soundv Velocity of sound

W Width

vY Destruction of turbulence viscosity

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t Time step

ζn Porosity

Density

Constants

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CHAPTER 1

INTRODUCTION

1.1 Background

The most common mangrove species that can be found in Malaysia are Rhizophora, Avicennia, Bruguiera, Sonneratia, Xylocarpus and Nypaspecies. Those mangroves species are tend to colonize at five geomorphologic environments which are river-dominated deltas, tide-dominated deltas, wave–dominated barrier lagoon, drowned bedrock valley and combination-river and wave dominated lagoon (Jan de Vos, 2004; RRC.AP, 2011). Mangrove trees have special adaptation called aerial roots that facilitate the ventilation of the root systems and allow mangroves to fix themselves on muddy soil (Mitsch and Gosselink, 2000). The main types of aerial roots are Stilt Roots (Rhizophora), Pneumatophores (Avicennia, Sonneratia), Root Knees (Bruguiera) and Plank Roots (Xylocarpus) (Jan de Vos, 2004). Stems or roots of mangroves play a major role in protecting the coast by dissipate incoming wave energy and reduce the rate of coastal erosion, hence making the trees as a natural breakwater. 1.2 Problem statement

The development which occurred along the coastlines has led to the problems such as coastal erosion, siltation, loss of coastal resource and the destruction of the marine habitat. This had led the Malaysia Government to carry out National Coastal Erosion Study (NCES) to study the erosion rate in Malaysia. Based on the study, Malaysia shoreline erosion were cause by natural threat and man activities such as high tide due to major storm and port or harbor activities. The result shows that 29% or 1,380 km from of 4,809 km out of the country’s coastline are facing erosion (Department of Irrigation and Drainage Malaysia, 2011). Although mangroves were affected by the erosion but the erosion rate was reduces in the area which mangroves inhabited (Thampanya et al., 2006). Furthermore, the tragedy of Andaman tsunami occurred on December 26, 2004 had cause enormous casualties around the Asia region including Malaysia. But the damage received by Malaysia is small compared to other countries because of the Malaysia Straits of Malacca is protected by Sumatra island and the mangrove forest that grow in the shallow water along the west coast of Peninsular Malaysia. In this tsunami incident, the role of mangroves in reducing the tsunami waves has been credited and these indirectly raise awareness about the role of mangroves forest as a natural breakwater on the beach (Teh et al., 2008)

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1.3 Recent research

Furukawa et al. 1996 in their study stated that an individual mangrove tree was also capable of mitigating the incoming wave within it roots area by creating friction and obstacles to the flow. The study which was conducted using VORTEX models manage to estimate the wave flow structures in the roots area where the obstacles created by the roots generated jet flow and complex current with eddies behind the individual roots. Thus, the complex circulation created a flow that was friction-dominated and each region behind the Rhizophora roots generated low velocity stagnation areas (Furukawa et al., 1996). Consequently, tsunami runup simulation study was carried out by researchers from Malaysia and overseas in Penang beaches using non-linear equations of shallow water (NSWE) in order to analyze the breakwater properties of the mangrove species. Teh, et al. 2008 had conducted simulation of tsunami wave mitigation over the shallow coastline of mangrove forests by using TUNA-RP model. The model had similar simulation data of wave height and velocity with TUNA-M2 model that were used by Koh et al. 2008. From the research it was concluded that the ratio of wave height and velocity reduction may vary depending on factors such as wave height, wave period and wavelength and the features including the width of the mangrove forest and the density (Teh, Koh et al., 2008). In another study, researchers investigate the vulnerability of mangroves by using an integrated approach that includes analysis of satellite imagery, field surveys, and numerical model of coastal Pakarang Cape, Thailand. The study objective was to identify the damaged mangrove areas and to measure the rate of damage from tsunami. Based on the estimated probability of damage from the numerical model, show that the mangrove Rhizophora sp. with a density of 0.2 trees m-2 and stem diameter of 15 cm in the 400 m wide can reduce 30% of tsunami flooding depth (Yanagisawa et al., 2008). Hence, from the above study it can be observe that most researches had been conducted at west coast of the peninsular. The studies also were more focusing on the dissipation process of the wave in mangrove forest structure rather investigating on the mangrove trees in individually and most simulation processes were conducted using numerical models. Thus, this study had taken different approach by investigating on the mangrove trees structures at east coast of Malaysia peninsular. The study had focused o the roots structured of each mangrove species sample which then converted into data that appropriate for Computational Fluid Dynamic simulation process.

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1.4 Research objective

The aim of the study is to investigate the geometrical properties of the mangrove roots and flow structure within the mangrove roots area of the Avicennia marina and Rhizophora apiculata species for breakwater modeling. Thus, to achieve aim of the study, several objectives had been put forward which were: 1. To identify the mangrove roots geometrical properties of the Avicennia

marina and Rhizophora apiculata mangrove species.

2. To analyze the flow structure of Avicennia pneumatophores and Rhizophora stilt roots.

3. To construct a breakwater model that applied similar mitigation mechanism as the mangrove roots.

1.5 Scope and limitation 1.5.1 Research scope and limitation

The research had limited the scope of the study within two mangrove species which are Avicennia marina and Rhizophora apiculata. These species are commonly inhabited at Malaysia coastline especially in the mangrove forest at the study area location. Since the study was focusing on investigating the flow structure around a mangrove tree, the study had selected a sample of tree from each species. The sample was sufficient as similar study was conducted by Furukawa et al. at Middle Creek, Crains, Australia. Furukawa et al. in his study on vegetation-induced current also used a single model to produce the fine scale flow pattern around Rhizophora roots. He had observed that the roots had created two-dimensional currents, with jets, eddies and stagnation region. He also had created a VORTEX model which had produced similar flow features to the observation result. Hence, the study decided to take only a tree sample from each species since it was sufficient in observation of water flow pattern in mangrove roots area. Henceforth, the study had only investigated the mangrove roots geometrical properties which are the geometrical coordinate and the cross section diameters of the roots in 3x3 m wide area. An area of 3x3 m was chosen by referring to the previous study conducted by Furukawa et al. for Rhizophora species. Furukawa et al. in his study had used an area with 2.5x2.5 m wide to observe the flow pattern around mangrove roots and the result of the study was as stated above. Thus, the study had created an area of 3x3 m around the mangrove trees due it was sufficient to cover all the roots around the selected mangrove trees.

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Simulation process was conducted using Sparlart-Allmaras turbulence model with water liquid material provided in Fluent data base. Since the study was only focusing in computational simulation of water flow in the mangrove roots area, the data validation was conducted by comparing the simulation results with previous studies that were done by other researchers. 1.5.2 Software limitation 1.5.2.1 Gambit Gambit is software which is use to design mesh model whether in 2 Dimensional (2D) or 3 Dimensional (3D). It can generate various types of mesh such as structured, unstructured and hybrid mesh. Hybrid mesh is generally as a combination of unstructured mesh and boundary layers. A hybrid mesh was proved to produce more accurate calculation for a very complex mesh model (Gambit 2.2 Tutorial Guide, 2004; Fluent 6.3 Tutorial Guide, 2006; ANSYS Fluent User Guide, 2001). Thus, in this study a 2D hybrid mesh model had been created since the complex structure of the Avicennia marina Rhizophora apiculata roots geometrical coordinate. 1.5.2.2 Fluent ANSYS Fluent software is use in various fields to simulate the heat transfer, air flow over an aircraft wing, bubble columns and the blood flow. The software is capable to simulate model flow in both laminar or turbulence with whether in 2D and 3D models. Fluent database contains large number of material properties from gases to liquid or even solid. The study had conducted simulations using turbulence flow as the value of Reynolds number exceeds 500k. Water liquid properties from fluent data base had been used since the study will only simulate the water flow around the mangrove roots area. 1.6 Outline of the thesis

The introductory briefly review the habitat of mangrove species in Malaysia and the coastal erosion problem which are occurred along Malaysia coastline. Meanwhile, the literature review chapter had discussed the mangrove habitat and mangrove species distribution especially for Avicennia marina and Rhizophora apiculata species. This chapter also discusses the previous study on mangrove trees water wave velocity dissipation properties and the research of breakwater structures.

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Chapter 3 describes the method used to collect the geometrical coordinate of each mangrove roots and the roots simulation procedure in dissipating water flow velocity. Chapter 4 and 5 discussed the result of the study during the field work and on the simulation results of the A. marina and R. apiculata species roots. Chapter 6 will discusses the simulation results of breakwater models constructed based on the roots. Chapter 7 presents the conclusion of the study on field work study, mangrove roots simulations and breakwater simulations.

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