The Effect of Freshwater Biofilms on

Turbulent Boundary Layers and the

Implications for Hydropower Canals

by

Jessica Maree Andrewartha

BE (Hons)(Civil) GradIEAust

Submitted in fulfilment of the requirements for the Degree of

Doctor of Philosophy

School of Engineering

University of Tasmania

May 2010

Declaration of Originality

This thesis contains no material which has been accepted for a degree or diploma by the

University or any other institution, except by way of background information and duly

acknowledged in the thesis, and to the best of my knowledge and belief no material previously

published or written by another person except where due acknowledgement is made in the text

of the thesis, nor does the thesis contain any material that infringes copyright.

Date:

Jessica Maree Andrewartha

Statement of Authority to Access

This thesis may be made available for loan and limited copying in accordance with the

Copyright Act 1968.

Date:

Jessica Maree Andrewartha

Abstract

i

ABSTRACT

The majority of the electricity supplied in Tasmania, Australia, is produced by hydropower.

Hydro Tasmania, the power generation utility, operates 29 hydropower stations incorporating

170 km of open channels. These open channels are susceptible to extensive biofilm growth

dominated by the freshwater diatoms Gomphonema tarraleahae and Tabellaria flocculosa,

which form a gelatinous biofilm several millimetres thick and cause reductions in flow capacity

of up to 10%.

This thesis presents results of a multidisciplinary study on the effects of freshwater biofilms on

hydropower canal capacity and turbulent boundary layer structure. The extent to which the

surface roughness affects the structure of the turbulent boundary layer was critically examined,

in the context of the wall similarity hypothesis.

A recirculating water tunnel, equipped with a floating element force balance and a two-

dimensional Laser Doppler Velocimetry system, was used to obtain detailed measurements on

test plates covered with flow-conditioned freshwater biofilms. Total drag measurements, mean

velocity profiles and turbulent Reynolds stresses were compared for smooth, sandgrain and

biofouled test plates. An artificial biofilm was developed to study the motion of algae streamers

under flow conditions. Each test surface was mapped using digital close-range photogrammetry

to provide a three-dimensional surface model. A logarithmic relationship was found between the

roughness function and the maximum peak-to-valley height from the photogrammetry

measurements for the low-form gelatinous biofilms.

Seven methods for determining the wall shear stress were investigated; however, none of the

methods examined were entirely satisfactory. A method which can be used for both smooth and

rough surfaces with reasonable measurement uncertainty is needed to allow objective

comparison of the structure of smooth and rough wall turbulent boundary layers.

The presence of biofouling caused a significant increase in the local skin friction coefficient and

overall drag coefficient with increases in skin friction of up to 210% measured over smooth plate

values. Results for low-form gelatinous biofilms provided support for the wall similarity

hypothesis. The biofilms modified the structure of the turbulent boundary layer in the near-wall

region. Velocity defect profiles, Reynolds stress profiles and quadrant analyses showed good

agreement for different test plate surfaces in the outer region of the boundary layer. The results

for an artificial filamentous biofilm were less conclusive, and may not support wall similarity.

Acknowledgements

iii

ACKNOWLEDGEMENTS

This project was funded by an Australian Research Council Linkage Grant (LP0667925), with

significant financial and in-kind support from Hydro Tasmania.

This thesis would not have been possible without the assistance of a great number of people. I

would like to particularly thank Dr Jane Sargison for her supervision, support, friendship, and

inspiration over the past five years, including during the honours year of my undergraduate

degree. My co-supervisors Dr Greg Walker and Dr Alan Henderson have shared their

knowledge and enthusiasm for fluid dynamics, and provided much guidance over the course of

this study. Prof Chris Letchford, the Head of the School of Engineering, has also provided

support.

This project was of a multidisciplinary nature, and involved two PhD programs: my own, and

that of Kathryn Perkins from the School of Plant Science. Kate and I shared many trips to

Tarraleah, and provided advice and input into each other’s projects. All of the species

identification and microscope photographs of the biofilms in this thesis are attributed to Kate.

My thanks goes to Tony Denne at Hydro Tasmania, now retired, who gave me the opportunity to

work on this project in the first place and was one of the driving forces behind it. Norm Cribbin,

Michael Sylvester, Joshua Kline and Angus Swindon have also been great supporters. Brian

Knowles and Stephen Kelly provided invaluable support in the field at Tarraleah. I worked for

Hydro Tasmania Consulting on a casual basis during the first 18 months of my study, and I

would like to thank Fraser White for allowing me to do this, as it expanded my knowledge of

hydroelectricity generation.

The technical support staff at the University of Tasmania have been invaluable throughout this

project. I would like to thank in particular Peter Seward for his patience, perseverance, and

determination in helping commission the Laser Doppler Velocimetry system; it truly was a team

effort. Ray le Fevre, Nathan Smith, David Morley, and Andrew Bylett provided much assistance

in the Engineering workshop; John McCulloch assisted setting up the data acquisition; and

Glenn Mayhew, Steve Avery, and Bernard Chenery provided advice for all things electrical.

Russell Twining and Heather Mitchell provided assistance with IT issues.

Acknowledgements

iv

I inherited the UTAS Water Tunnel from Dr Andrew Barton, who spent many hours teaching me

how to use it, and also provided research papers for background reading. Associate Professor

Paul Brandner and his team from the Australian Maritime College assisted with the

instrumentation.

The photogrammetry methods used in this study were developed by Dr Jon Osborn and Timothy

Bendall from the School of Geography and Environmental Studies. All of the photographs and

surface topography models presented in this thesis were obtained by Alex Leith.

My brother, Tristan, spent many hours proofreading this thesis, and I would like to thank him for

his thoughtful suggestions. The critical discussion provided by the two anonymous examiners

was appreciated. Dr Colin Terry also provided thoughtful comments on my thesis defence and

response to the examiner’s reports.

On a personal note I would like to acknowledge the love and support from my parents, James

and Helen, and my siblings Tristan and Melissa, who have always encouraged me to do my best,

and without whom I would have never reached this level. Wendy and Trevor Walker have also

provided much support over the past four years.

Finally, thanks to my partner Karl, who has been there for the whole journey, and supported me

all the way.

Contents

v

Table of Contents

ABSTRACT ________________________________________________________________________________I

ACKNOWLEDGEMENTS _____________________________________________________________ III

NOMENCLATURE _____________________________________________________________________ XI

1 INTRODUCTION ___________________________________________________________________ 1

2 LITERATURE REVIEW ___________________________________________________________ 5

2.1 Freshwater Biofilms ______________________________________________________________ 5

2.1.1 The Nature of Biofilms _________________________________________________________ 5

2.1.2 The Effect of Biofilms on Skin Friction ____________________________________________ 7

2.1.3 Biofilms in the Tarraleah Power Scheme __________________________________________ 10

2.1.4 Biofouling Mitigation _________________________________________________________ 12

2.2 The Structure of Turbulent Boundary Layers ________________________________________ 18

2.2.1 Turbulent Flow ______________________________________________________________ 18

2.2.2 The Boundary Layer __________________________________________________________ 19

2.2.3 Regions of the Smooth Wall Boundary Layer ______________________________________ 21

2.2.4 Effect of Roughness __________________________________________________________ 27

2.2.5 Turbulence Structure in the Boundary Layer _______________________________________ 35

2.2.6 Townsend’s Wall Similarity Hypothesis __________________________________________ 42

2.3 Open Channel Flow ______________________________________________________________ 50

2.4 Turbulence Measurement Techniques ______________________________________________ 54

2.5 Chapter Summary _______________________________________________________________ 57

3 FIELD STUDY – TARRALEAH NO.1 CANAL ________________________________ 59

3.1 The Tarraleah Power Scheme _____________________________________________________ 59

3.2 Introduction to Field Study _______________________________________________________ 61

Contents

vi

3.3 Small Test Plate Details ___________________________________________________________ 61

3.4 Field Installations for Biofilm Growth _______________________________________________ 64

3.4.1 Bridge 9 ____________________________________________________________________ 64

3.4.2 Transition 4 _________________________________________________________________ 64

3.4.3 Pond No.1 ___________________________________________________________________ 67

3.5 Methodology ____________________________________________________________________ 67

3.6 Results _________________________________________________________________________ 69

3.6.1 Sikagard 680s Smooth Test Plates ________________________________________________ 69

3.6.2 Sikagard 680s Rough Test Plates ________________________________________________ 70

3.6.3 Rough Test Plates _____________________________________________________________ 71

3.6.4 Jotamastic 87 Test Plates _______________________________________________________ 72

3.6.5 Comparison of Test Plates ______________________________________________________ 73

3.7 Conclusions _____________________________________________________________________ 74

4 EXPERIMENTAL FACILITIES ________________________________________________ 77

4.1 Description of the UTAS Water Tunnel _____________________________________________ 77

4.2 UTAS Water Tunnel Components __________________________________________________ 77

4.3 Test Plate Details ________________________________________________________________ 81

4.4 Measured Variables & Instrumentation _____________________________________________ 82

4.4.1 Temperature _________________________________________________________________ 82

4.4.2 Pressure ____________________________________________________________________ 83

4.4.3 Mean Velocity from Pressure Measurements _______________________________________ 84

4.4.4 Total Drag __________________________________________________________________ 86

4.4.5 Laser Doppler Velocimeter (LDV) _______________________________________________ 90

4.5 Data Acquisition and Control ______________________________________________________ 91

4.5.1 LabVIEW ___________________________________________________________________ 91

4.5.2 LDV Velocity Profiling Procedure _______________________________________________ 93

4.6 Photogrammetric Surface Characterisation __________________________________________ 93

4.6.1 Camera and Analysis Software __________________________________________________ 93

Contents

vii

4.6.2 Set-up for Photographs ________________________________________________________ 95

4.6.3 Data Analysis _______________________________________________________________ 98

4.6.4 Accuracy and Precision of Photogrammetry ______________________________________ 101

5 MEASURING TURBULENCE __________________________________________________ 105

5.1 Investigation of Turbulence Measurement Using Pitot Probes _________________________ 105

5.1.1 System Setup _______________________________________________________________ 105

5.1.2 Mathematical Model _________________________________________________________ 106

5.1.3 Boundary Layer Parameters ___________________________________________________ 108

5.1.4 Mean Velocity Profiles _______________________________________________________ 110

5.1.5 Turbulence Profiles __________________________________________________________ 113

5.1.6 Frequency Spectra ___________________________________________________________ 114

5.1.7 Conclusions ________________________________________________________________ 115

5.2 Laser Doppler Velocimetry ______________________________________________________ 115

5.2.1 Potential Sources of Error _____________________________________________________ 117

5.2.2 Commissioning the 2D LDV System ____________________________________________ 126

5.3 Chapter Summary ______________________________________________________________ 143

6 DATA ANALYSIS ________________________________________________________________ 145

6.1 Methods to Determine Skin Friction _______________________________________________ 145

6.1.1 Direct Force Methods ________________________________________________________ 145

6.1.2 Preston Tube Method ________________________________________________________ 149

6.1.3 Momentum Integral Methods __________________________________________________ 150

6.1.4 Wall Similarity Methods ______________________________________________________ 150

6.1.5 Total Stress Method _________________________________________________________ 157

6.1.6 Discussion of Methods _______________________________________________________ 158

6.2 Boundary Layer Velocity Profile Analysis __________________________________________ 158

6.2.1 Preston Tube Method ________________________________________________________ 159

6.2.2 Bradshaw’s Method _________________________________________________________ 159

6.2.3 Log Law Slope Method _______________________________________________________ 160

6.2.4 Perry & Li’s Method _________________________________________________________ 162

6.2.5 Hama’s Method _____________________________________________________________ 164

Contents

viii

6.2.6 Total Stress Method __________________________________________________________ 165

6.2.7 Comparison of Methods _______________________________________________________ 166

6.3 Total Drag Analysis _____________________________________________________________ 177

6.3.1 Drag Analysis Theory ________________________________________________________ 177

6.3.2 Assessment of Virtual Origin __________________________________________________ 180

6.3.3 Repeatability Tests ___________________________________________________________ 184

6.4 Chapter Summary ______________________________________________________________ 187

7 MEASUREMENTS ON LIVE BIOFILMS ____________________________________ 189

7.1 Description of Test Plates ________________________________________________________ 189

7.1.1 RP1 F1 ____________________________________________________________________ 191

7.1.2 SP1 F2 ____________________________________________________________________ 192

7.1.3 SP2 F3 ____________________________________________________________________ 193

7.1.4 RP1 F4 ____________________________________________________________________ 193

7.1.5 RP2 F5 ____________________________________________________________________ 194

7.1.6 SP1 F6 ____________________________________________________________________ 195

7.2 Roughness Characterisation ______________________________________________________ 196

7.3 Boundary Layer Profiles _________________________________________________________ 197

7.3.1 Measurement and Analysis Procedures ___________________________________________ 197

7.3.2 Boundary Layer Development __________________________________________________ 198

7.3.3 Boundary Layer Parameters ____________________________________________________ 207

7.3.4 Inner Coordinates ____________________________________________________________ 210

7.3.5 Outer Coordinates ___________________________________________________________ 214

7.3.6 Roughness Plots _____________________________________________________________ 216

7.3.7 Turbulence Intensity _________________________________________________________ 217

7.3.8 Reynolds Normal Stresses _____________________________________________________ 219

7.3.9 Reynolds Shear Stress ________________________________________________________ 227

7.3.10 Quadrant Analysis ___________________________________________________________ 231

7.4 Drag Measurements _____________________________________________________________ 237

7.5 Results Synthesis ________________________________________________________________ 240

Contents

ix

7.6 Chapter Summary ______________________________________________________________ 244

8 MEASUREMENTS ON AN ARTIFICIAL FILAMENTOUS BIOFILM ___ 245

8.1 Experimental Procedure _________________________________________________________ 245

8.2 Results and Discussion __________________________________________________________ 247

8.3 Chapter Summary ______________________________________________________________ 252

9 DISCUSSION _____________________________________________________________________ 253

9.1 General Comments on Biofilms ___________________________________________________ 253

9.2 Physical Characterisation of Biofilms ______________________________________________ 256

9.3 Relating Roughness to Drag ______________________________________________________ 259

9.4 Adherence to Wall Similarity and The Effect of BioFilms on Boundary Layer Structure __ 263

10 CONCLUSIONS AND RECOMMENDATIONS ______________________________ 269

10.1 Conclusions ____________________________________________________________________ 269

10.1.1 Field Study ________________________________________________________________ 269

10.1.2 Turbulence Measurement _____________________________________________________ 269

10.1.3 Data Analysis ______________________________________________________________ 270

10.1.4 The Effects of Biofilms on Skin Friction _________________________________________ 271

10.1.5 Relating Roughness to Drag ___________________________________________________ 272

10.1.6 Wall Similarity and the Structure of the Turbulent Boundary Layer ___________________ 273

10.2 Recommendations ______________________________________________________________ 274

10.2.1 Growth of Biofilms __________________________________________________________ 274

10.2.2 UTAS Water Tunnel and Photogrammetry Process _________________________________ 274

10.2.3 Data Analysis ______________________________________________________________ 275

10.2.4 Filamentous Biofilms ________________________________________________________ 275

REFERENCES _________________________________________________________________________ 277

Contents

x

APPENDICES _________________________________________________________________________ 291

A Supporting Data for Chapter 7 ____________________________________________________ 293

A1 Roughness Data from Photogrammetry Measurements ______________________________ 293

A2 Tabulated Boundary Layer Profile Data __________________________________________ 301

A3 Boundary Layer Profiles in Inner Coordinates _____________________________________ 307

A4 Boundary Layer Profiles in Outer Coordinates _____________________________________ 313

A5 Roughness Plots _____________________________________________________________ 317

A6 Turbulence Intensity _________________________________________________________ 319

A7 Reynolds Normal Stresses _____________________________________________________ 324

A8 Reynolds Shear Stress ________________________________________________________ 328

A9 Quadrant Analysis ___________________________________________________________ 329

B Hydro Tasmania Field Study – Tarraleah No.1 Canal Capacity ________________________ 333

B1 Methodology _______________________________________________________________ 333

B2 Pre- and Post-Clean Test Results ________________________________________________ 335

B3 Hydraulic Model Results ______________________________________________________ 340

B4 Discussion of Hydraulic Model Results __________________________________________ 345

B5 Conclusions ________________________________________________________________ 346

B6 Recommendations ___________________________________________________________ 347

C Matlab Programs _______________________________________________________________ 349

D Publications Arising from Thesis __________________________________________________ 351

Nomenclature

xi

NOMENCLATURE

Symbols

A Cross-sectional area [m2]

B Velocity defect law intercept

BN Rough wall Nikuradse log law constant (value depends on flow regime)

C Smooth wall log law constant = 5.0

CD Total drag coefficient

D Drag force [N]

Ed Young modulus for pressure transducer diaphragm [Pa]

G Velocity defect parameter = ( )Hc f 112 −

H Boundary layer shape factor = δ*/θ or Hyperbolic hole size for quadrant analysis

P Pressure [Pa]

Q Volumetric flow rate [m3/s]

Ra Mean of absolute deviation of roughness profile from mean line [mm]

Re Reynolds number

ReD Reynolds number based on a diameter = Ud/υ

Red Pitot probe Reynolds number = Udp/υ

Rek Roughness Reynolds number = u*ks/υ

Rek,rough Flows with Rek > Rek,rough are hydraulically rough

Rek,smooth Flows with Rek < Rek,smooth are hydraulically smooth

Nomenclature

xii

Rel Test plate Reynolds number = Ul/υ

Reθ Momentum thickness Reynolds number = Uθ/υ

RH Hydraulic radius [m]

Rp Max height of profile above mean line of sample length [mm]

Rq Root mean square parameter [mm]

Rt Max peak to valley height of profile of sample length [mm]

Rv Max depth of profile below mean line of sample length [mm]

So Slope of channel invert

St Strouhal number = fD/U

T Temperature [oC]

U Freestream streamwise velocity [m/s]

b Width of test plate [m]

cf Local skin friction coefficient

d Diameter [m]

dp Pitot probe diameter [m]

df Spacing of interference pattern for LDV [m]

f Frequency [Hz]

fd Natural frequency of pressure transducer diaphragm [Hz]

fD Doppler shift frequency [Hz]

h Water depth [m]

Nomenclature

xiii

hd Thickness of pressure transducer diaphragm [m]

k Roughness height [mm]

kentry Entry loss coefficient

kexit Exit loss coefficient

k+

Roughness Reynolds number = u*Rt/υ

ks Equivalent sandgrain roughness height [mm]

l Length [m]

l+ Length of LDV measuring volume in viscous units = lu*/ υ

n Manning’s n friction coefficient

nd Poisson’s ratio

r Radius [m]

rd Radius of pressure transducer diaphragm [m]

t Thickness of test plate [m]

ti Transit time of ith particle through LDV measuring volume [s]

u Local streamwise velocity [m/s]

u* Wall shear velocity = (τw/ρ)½ [m/s]

u+

Normalised velocity = u/u*

∆u+

Roughness function

v Local wall-normal velocity [m/s]

w Local spanwise velocity [m/s]

Nomenclature

xiv

w(y/δ) Wake function

x Horizontal distance from leading edge of test plate [m]

xp Laser penetration depth [m]

y Distance from wall [m]

y+ Normalised distance from the wall = yu*/ υ

α Rotation of LDV in xy plane (degrees)

β Rotation of LDV in yz plane (degrees)

γ Light extinction coefficient [m-1]

∆ Change in a variable

δ Boundary layer thickness at 99% of freestream velocity [mm]

δw Wall correction for Pitot probe [mm]

δ* Displacement thickness [mm]

ε Virtual origin error [mm]

ηi Transit time weighting factor (defined Equation 5.12)

θ Momentum thickness [mm] or angle

κ von Karman constant

λ Wavelength of laser [nm]

µ Dynamic viscosity [kg/ms]

υ Kinematic viscosity [m2/s]

Π Wake strength

Nomenclature

xv

ρ Density [kg/m3]

ρd Density of pressure transducer diaphragm [kg/m3]

τ Shear stress [Pa]

τw Wall shear stress [Pa]

+ Normalised by u* or u*/υ

Time mean value

‘ Instantaneous fluctuation about the time mean value

Abbreviations

ADV Acoustic Doppler Velocimetry

EPS Extracellular polymer substances

LDV Laser Doppler Velocimetry

PIV Particle image velocimetry

UTAS University of Tasmania

UVP Ultrasonic velocity profiling

1D One-dimensional

2D Two-dimensional

Nomenclature

xvi

Test Plate Nomenclature

SP Lab Clean reference plate that remained in the laboratory with a smooth, painted

substrate

RP Lab Clean reference plate that remained in the laboratory with a sandgrain

roughened substrate

RP1 F1 RP – indicates substrate type (RP = rough plate; SP = smooth plate)

1 – test plate number (two of each substrate type were deployed in the field)

F1 – fouled plate number (from 1 – 6, denoting the order in which they were

removed from the field)

Nomenclature

17