Optical sensing in a microfluidic device · “Optical sensing in a microﬂuidic device ... for a...

Optical sensing in a

microfluidic device

A thesis submitted for the degree of

Doctor of Philosophy

by

Stephen Karl-Alan Weber

Centre for Micro-Photonics

Faculty of Engineering and Industrial Sciences

Swinburne University of Technology

Melbourne, Australia

2012

Today is the Tomorrow that I feared Yesterday.

— Sir Anthony Hopkins

I want to live my life taking the risk that I don’t know nearly enough. That

I haven’t understood enough. That I can’t know enough. That I’m always

hungry, operating on the margins of a potentially great harvest of future

knowledge.

— Christopher Hitchens

Declaration

I, Stephen Karl-Alan Weber, declare that this thesis entitled :

“Optical sensing in a microfluidic device”

is my own work and has not been submitted previously, in whole or in part,in respect of any other academic award.


Centre for Micro-PhotonicsFaculty of Engineering and Industrial ScienceSwinburne University of TechnologyAustralia

Dated this day, October 29, 2012

Abstract

This thesis describes the realisation of a lab-on-a-chip optical sensor that

is based on surface plasmon resonance (SPR) trapped microspheres acting

as localised sensing elements for morphology dependent resonance (MDR)

sensing.

The microfluidic device is fabricated by a combination of direct laser

writing and hot embossing. This allows simple integration of SPR techniques

by the evaporative coating of a metal layer on the surface of the microfluidic

device. Trapping of 4, 10 and 15 µm polystyrene microspheres is demon-

strated using SPR in static and dynamic fluidic environments. Patterning of

the metal surface is demonstrated to increase the trapping potential of the

SPR technique as well as provide a method of further localising the position

of the optical trap within the device. Comparison between the trapping of

microspheres for both on and off resonance incident angles of the trapping

beam show strong difference in the strength of the optical trap allowing for

a on/off switching of the trapping force within the device. The integrated

SPR trapping technique provides a method for arbitrary trapping of a range

of microspheres within a microfluidic environment.

A theoretical investigation is performed in order to further understand

the effects of the patterning of the metal surface on the magnitude and

i

location of the electric field under the range of SPR coupling conditions.

The investigation of a range of aperture diameters, of diameters equal to,

greater than and less than the wavelength of the incident light and incident

angles matching specific coupling conditions. Enhancement to the electric

field is observed when the light source is incident on the patterned surface

at an angle matching the SPR angle, the introduction of a patterned region

even at diameters greater than the wavelength demonstrates an electric field

enhancement over the unpatterned case. This enhancement supports the

experimental results for patterned surfaces providing a stronger trapping

force then unpatterned surfaces.

The MDR optical sensing technique was selected as a non-invasive, multi-

variable sensing technique that can be performed on a range of optically

trapped microcavities. Coupling to the MDR of a spherical microcavity is

achieved via evanescent wave coupling under total internal reflection within

a static fluidic environment. Fluid refractive index detection is realised with

a sensitivity of 9.66 x 10−2 refractive index units by the characterisation of

the shift of the MDR positions. A Quality (Q) factor of 1.1 x 104 is observed

for a 90 µm glass microsphere with a stability of ∆λ = ± 0.04.

The coupling of light to the MDR mode is realised for a 90 µm glass

microsphere trapped in a dynamic microfluidic device via SPR based optical

trapping. The position of the trapped microsphere is defined by the location

of the patterned region of the metal surface as well as the position of the

location of the focal spot of the SPR incident light source. A Q-factor of

4,429.6 and a visibility of 0.16 is observed under these coupling conditions.

Detection of a change in the refractive index of the local fluidic environment

is observed via change in the MDR of a microcavity held under SPR trapping

conditions, a resolution of 7.75 x 10−2 R.I.U is observed under a flow rate of

20 µm/sec.

ii

The research in this thesis explores the integration of optical based

manipulation and localised sensing techniques into a microfluidic environ-

ment. From the work demonstrated it is anticipated that this research will

develop towards a optical based sensing system where localised sensing can

be performed in an arbitrary location within a fluidic environment.

iii

Acknowledgements

I would like to thank my supervisor, Dr Daniel Day, for all your guidance

and wisdom in leading me to the completion of this PhD thesis. For your

patience, assistance and knowledge you have my deepest thanks.

To my co-supervisor Professor Min Gu, for giving me the opportunity to

do my PhD within the Center for Micro-Photonics and for the critique and

advice given on my work over the years. Thanks are also given to Johanna

Lamborn and Barbara Gillespie for their countless assistances with all the

administrative matters that arose over the length of this PhD.

My strongest regards to Mr Mark Kivinen for his outstanding skill,

craftsmanship and conventional wisdom in the design and manufacturing of

all the custom components I have requested over the years. Our varied and

entertaining conversations have added more to the completion of this thesis

then I think you will know.

To Dr Michael Ventura, I do not believe I can ever convey enough thanks

and gratitude for all that you have done over the course of this PhD thesis.

Your knowledge and advice has always been fantastic, as well as your patience

in listening to all my issues both academic and personal over the years.

iv

Finally, to my wife Katherine and to my mother Paula Weber, I forever

extend my love and gratitude. You who gave me the power to dream and the

strength to make it happen.


Melbourne, Australia

October 29, 2012

v

Contents

Declaration

Abstract i

Acknowledgements iv

Contents vi

List of Figures x

List of Tables xx

1 Introduction 1

1.1 Microfluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.1.1 Introduction to microfluidics . . . . . . . . . . . . . . . 1

1.1.2 Forces on the micrometre scale . . . . . . . . . . . . . 3

1.1.3 Design and application of microfluidic devices . . . . . 4

1.2 Optical biosensors . . . . . . . . . . . . . . . . . . . . . . . . . 5

1.3 Thesis objectives . . . . . . . . . . . . . . . . . . . . . . . . . 9

1.4 Thesis preview . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2 Literature Review 14

2.1 Morphology Dependent Resonance sensors . . . . . . . . . . . 14

vi

2.1.1 Fundamentals of Morphology Dependent Resonance

sensors . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

2.1.2 Design of Morphology Dependent Resonance sensors . 17

2.1.3 Applications of Morphology Dependent Resonances

sensors . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

2.2 Surface plasmon optical sensors . . . . . . . . . . . . . . . . . 21

2.2.1 Fundamentals of Surface Plasmon Resonance optical

sensors . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

2.2.2 Design of SPR optical sensors . . . . . . . . . . . . . . 26

2.2.3 Applications of surface plasmon resonance . . . . . . . 27

2.3 Sensing via optical trapping techniques . . . . . . . . . . . . . 30

2.3.1 Fundamentals of optical trapping techniques . . . . . . 30

2.3.2 Design and application of optical tweezer systems . . . 32

3 Surface Plasmon Resonance trapping in a microfluidic device 34

3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

3.2 Experimental Setup . . . . . . . . . . . . . . . . . . . . . . . . 37

3.2.1 Development of microfluidic devices . . . . . . . . . . . 37

3.2.1.1 Gen 1 microfluidic device . . . . . . . . . . . 38

3.2.1.2 Gen 2 microfluidic device . . . . . . . . . . . 42

3.3 Surface Plasmon Resonance based optical manipulation . . . . 45

3.3.1 Manipulation in a static fluid environment . . . . . . . 51

3.3.2 Manipulation via Surface Plasmon Resonances in a

dynamic fluidic environment . . . . . . . . . . . . . . . 53

3.4 Surface Plasmon Resonance manipulation on a patterned

metallic surface . . . . . . . . . . . . . . . . . . . . . . . . . . 56

3.4.1 Laser etching a metallic surface . . . . . . . . . . . . . 57

3.4.2 Microsphere manipulation via a patterned surface . . . 60

vii

3.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

4 Theoretical investigation of SPR on a patterned surface 66

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

4.2 Simulation details . . . . . . . . . . . . . . . . . . . . . . . . . 67

4.3 Electric field behavior on a metallic surface . . . . . . . . . . . 68

4.4 Microhole plasmonic confinement . . . . . . . . . . . . . . . . 70

4.4.1 Surface plasmons in isolated microhole patterns . . . . 70

4.4.2 Angular dependence of plasmonic confinement . . . . . 73

4.4.3 Comparison of electric field between patterned and

unpatterned surfaces . . . . . . . . . . . . . . . . . . . 78

4.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

5 Morphology Dependent Resonance sensing 82

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82


5.2.1 Microsphere sample preparation . . . . . . . . . . . . . 86

5.3 Objective based detection system . . . . . . . . . . . . . . . . 87

5.4 Fibre based detection system . . . . . . . . . . . . . . . . . . . 89

5.5 MDR in a static fluidic system . . . . . . . . . . . . . . . . . . 95

5.5.1 Experimental setup . . . . . . . . . . . . . . . . . . . . 96

5.6 MDR sensing . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

5.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

6 Sensing in a microfluidic device 111

6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111


6.3 Distance based MDR detection . . . . . . . . . . . . . . . . . 117

6.4 MDR detection in an SPR trapped microsphere . . . . . . . . 121

viii

6.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

7 Conclusion 127

7.1 Thesis conclusions . . . . . . . . . . . . . . . . . . . . . . . . . 127

7.2 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

Bibliography 134

Author’s Publications 153

ix

List of Figures

1.1 Diagrams of functions of microfluidic devices including: a) Fo-

cusing of chemical reagents, b) Dilution of chemical reagents,

c) Sorting of micro-particles, and d) passive mixing of flu-

ids/regents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

1.2 Diagram of biosensors using the optical detection method; a)

Raman spectrometry, b) Photonic crystal, c) Resonant cavity,

and d) Interferometric. . . . . . . . . . . . . . . . . . . . . . . 7

1.3 Diagrams of waveguide structure confining a traveling evanes-

cent wave. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

2.1 Schematic diagram of light rays of different wavelengths

constructively interfering inside a microcavity when incident

under total internal reflection. . . . . . . . . . . . . . . . . . . 15

2.2 Example of MDR resonance spectrum with the black spectrum

showing the cavity modes in an initial state and the red

spectrum demonstrating a potential MDR spectrum response

to a molecular binding event. . . . . . . . . . . . . . . . . . . 16

2.3 Schematic representation of MDR coupling to a microcavity

via (a) prism geometry and (b) tapered optical fibre geometry. 18

2.4 Shift in the MDR signal of a resonant microcavity in response

to a target molecule binding to the biochemical receptor on

the surface of the cavity. . . . . . . . . . . . . . . . . . . . . . 20

x

2.5 Example of SPR resonance spectrum with the red spectrum

showing the cavity mode in an initial state and the black

spectrum demonstrating a potential MDR spectrum response

to a molecular binding event. . . . . . . . . . . . . . . . . . . 22

2.6 Dispersion curve where blue curve shows the light line (ω =

c.k0) and red is the surface plasmon curve. . . . . . . . . . . . 24

2.7 Illustration of a target molecule binding to a ‘receptor’, with

the event being detected via the wavelength shift of the SPR

angle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

2.8 Label-free optical sensing via SERS based detection system

using a) Au nanoparticles in a colloid solution and b) nanos-

tructured Au surface. . . . . . . . . . . . . . . . . . . . . . . . 29

2.9 Illustration showing the resultant force (FA) acting on a

particle as a result of refracted rays (A’) and surface reflections

(Rx). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

3.1 Diagram of a setup showing the generation of a multiple

optical trapping landscape generated via a computer controlled

SLM/Wavefront manipulator (Hologram) . . . . . . . . . . . . 35

3.2 Schematic diagram of experimental setup for SPR manipu-

lation experiments. VA: variable aperture, L: lens. Insert

showing close up of a multilayer microfluidic device placed

on the equilateral prism, showing the materials respective

dielectric permitivity for λ = 1,064 nm. . . . . . . . . . . . . . 38

3.3 Diagram of the first generation microfluidic device. . . . . . . 39

3.4 Plot of SPR vs thickness for a glass/Cr/Au/water interface at

λ = 1,064 nm. . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

xi

3.5 Calibration curve for evaporative coating parameters at base

plate and sample surface height. . . . . . . . . . . . . . . . . . 41

3.6 Schematic of hot embossing process for fabrication of PDMS

microfluidic device components. . . . . . . . . . . . . . . . . . 42

3.7 Images of various molds during the hot embossing stage of the

fabrication of the microfluidic device (a) PDMS/silicon master

after CO2 laser cutting (b) PMMA master and (c) PDMS mold. 44

3.8 A sample design of a microfluidic device. . . . . . . . . . . . . 45

3.9 Schematic diagram outlining the procedure for coating of the

microfluidic device substrate. . . . . . . . . . . . . . . . . . . 45

3.10 Plot showing Reflectance vs angle for a Au coated glass

slide with highlights showing location of on and off resonance

positions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

3.11 SPR plots for nprism = 1.785, λ = 1,064 nm with refractive

index of the medium being (a) n = 1.00 (air) and (b) n =

1.33 (water). Effect of thickness of gold layer on minimum

reflectance shown vs (c) value of reflectance and (d) angular

position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

3.12 SPR plots for nprism = 1.51, λ = 1,064 nm with refractive

index of the medium being (a) n = 1.00 (air) and (b) n =

1.33 (water). Effect of thickness of gold layer on miminum

reflectance shown vs (c) value of reflectance and (d) angular

position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

3.13 Images of convection trapping of 5 µm polystyrene micro-

spheres in a static microfluidic environment at times (a) t = 0

min (laser is turned on), (b) t = 1 min, (c) t = 10 min, (d) t

= 20 min, (e) t = 30 min (laser is turned off) and (f) t = 40

min. Scale Bar is 100 µm. . . . . . . . . . . . . . . . . . . . . 51

xii

3.14 Schematic showing manipulation of microspheres via SPR

induced convection flow, showing (a) microspheres randomly

distributed on surface of the chamber, (b) a convection flow

induced in the chamber via heating from illumination of light

under SPR coupling, (c) microspheres are drawn to center

of the convection flow as defined by the position of the

incident focal spot and (d) if the convection flow overcomes

the gravitational forces the microspheres are drawn upwards

and away from the focal region. . . . . . . . . . . . . . . . . . 52

3.15 Results of SPR manipulation of 10 µm polystyrene micro-

spheres under (a) On resonance and (b) Off resonance coupling

conditions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

3.16 Results of surface wave manipulation of 15 µm polystyrene

microspheres under a) On surface plasmon resonance and b)

Off resonance coupling conditions. . . . . . . . . . . . . . . . . 56

3.17 Experimental setup for multi-photon laser etching of microme-

tre sized holes in a Au coated glass substrates. . . . . . . . . . 57

3.18 Plot showing incident power vs hole diameter of a 40 nm thick

Au coated surface patterned using a NA = 0.5 objective lens. . 58

3.19 Plot showing incident power vs hole diameter of a 40 nm thick

Au coated surface patterned using a NA = 0.7 objective lens. . 58

3.20 (a) Schematic of the microhole array and (b) SEM image of

microhole array patterned on a Au surface, scale bar = 20 µm

(insert at 17k x magnification, scale bar = 4 µm). . . . . . . . 59

3.21 Plot showing Particle Trapped Efficiency over time for a 4.33

µm microsphere, on and off resonance. . . . . . . . . . . . . . 61

xiii

3.22 Image of 4.33 µm microspheres trapping in a patterned surface

under SPR illumination (P = 60 mW) at t = 40 sec. Red circles

highlight trapped microspheres. . . . . . . . . . . . . . . . . . 62

3.23 Image of 10 µm microspheres trapping in a patterned surface

under SPR illumination (P = 60 mW) at t = 40 sec. Red circles

highlight trapped microspheres and blue circles highlight the

untrapped microspheres. Scale is 40 µm. . . . . . . . . . . . . 63

3.24 Plot showing Particle Trapped Efficiency over time for a 10


3.25 Plot showing Particle Trapped Efficiency over time for a 15


3.26 Image of 15 µm microspheres trapping in a patterned surface

under SPR illumination (P = 60 mW) at t = 40 sec. Scale bar

is 40 µm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

4.1 Design of the model used in theoretical simulations for plane

waves of λ = 1,064 nm at angle (θ) incident at a dielec-

tric/metallic interface. The composition of the layers are; 1)

Glass slide, 2) Cr (5 nm), 3) Au (40nm) and 4) surrounding

medium for (a) unpatterned surface and (b) a patterned

surface with the left and right sides of the aperture highlighted. 68

4.2 Electric field intensity for a plane wave, with TE polarisation,

incident on a dielectric interface with perpendicular propagation. 69

4.3 Electric field intensity in a dielectric/metal structure vs inci-

dent angle for 1,064 nm plane wave with TE polarisation. . . . 69

xiv

4.4 Field profile plots for a water medium simulated for plane wave

source incident perpendicular to the surface of the interface

with aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm, (d)

2 µm and (e) 4 µm. . . . . . . . . . . . . . . . . . . . . . . . . 71

4.5 Field profile plots for a air medium simulated for plane wave

source incident perpendicular to the surface of the interface

with aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm, (d)

2 µm and (e) 4 µm. . . . . . . . . . . . . . . . . . . . . . . . . 72


source incident at 67◦ to the surface of the interface with

aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm, (d) 2

µm and (e) 4 µm. Silver outline highlights gold surface. . . . . 74

4.7 Field profile plots for a water medium simulated for plane

wave source incident at 67◦ to the surface of the interface with

aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm, (d) 2 µm

and (e) 4 µm. . . . . . . . . . . . . . . . . . . . . . . . . . . 75


source incident at 73◦ to the surface of the interface with

aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm, (d) 2

µm and (e) 4 µm. Silver outline highlights gold surface. . . . . 76

4.9 Field profile plots for a water medium simulated for plane

wave source incident at 73◦ to the surface of the interface with

aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm, (d) 2 µm

and (e) 4 µm. . . . . . . . . . . . . . . . . . . . . . . . . . . 77

4.10 The magnitude of the electric field at x = 0 µm at the

Au/medium interface for incident angles 0◦, 67◦, and 73◦ with

a medium solution of (a) air and (b) water. . . . . . . . . . . . 78

xv

4.11 The magnitude of the electric field at the edge of the left

aperture at the Au/medium interface for incident angles 0◦,

67◦, and 73◦ with a medium solution of (a) air and (b) water. 79

4.12 The magnitude of the electric field at the edge of the right

aperture at the Au/medium interface for incident angles 0◦,

67◦, and 73◦ with a medium solution of (a) air and (b) water. 79

4.13 The symmetry of the simulation of an incident source propa-

gating at angle ±73◦ with the center of the source being at (a)

x = 0.53 and (b) x = -0.53. . . . . . . . . . . . . . . . . . . . 80

5.1 Schematic diagram of MDR setup for investigation of coupling

parameters via evanescent wave coupling. . . . . . . . . . . . . 85

5.2 MDR spectrum from 90 µm glass microspheres in air. . . . . . 88

5.3 MDR spectrum from 90 µm glass microspheres in water

collected with a 10x/0.4 NA objective lens. . . . . . . . . . . . 89

5.4 MDR spectrum from 90 µm glass microspheres in water

collected with a 20x/0.7 NA objective lens. . . . . . . . . . . . 90

5.5 Schematic diagram of MDR setup with fibre based detection

system. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

5.6 Comparison of signal collection systems for (a) S-polarised and

(b) P-polarised incident light. . . . . . . . . . . . . . . . . . . 91

5.7 Change in the MDR spectrum vs distance of detection system. 93

5.8 Change in the visibility of MDR spectrum vs distance of

detection system. . . . . . . . . . . . . . . . . . . . . . . . . . 93

5.9 Change in the Q-factor of MDR spectrum vs distance of

detection system. . . . . . . . . . . . . . . . . . . . . . . . . . 94

5.10 Shift in the MDR spectra vs changes in the incident angle. . . 94

xvi

5.11 Diagram of the well chamber for MDR investigation in a liquid

medium. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

5.12 MDR spectra for a 90 µm glass microsphere in air, before

and after the addition of a cover slip to the well with single

thickness adhesion layer for (a) S-polarisation and (b) P-

polarisation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

5.13 MDR spectra for a 90 µm glass microsphere in air, before

and after the addition of a cover slip to the well with double

thickness adhesion layer for (a) S-polarisation and (b) P-

polarisation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

5.14 MDR spectrum for 90 µm glass microsphere in water. . . . . . 99

5.15 MDR spectrum for 90 µm glass microsphere in water under

continuous illumination. Insert showing higher magnification

of peak 4. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

5.16 Value of the wavelength for the peaks of the MDR spectrum

for a 90 µm glass microsphere in water under continuous

illumination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

5.17 MDR spectra for a 90 µm glass microsphere in a water

medium, insert showing magnified image of peak 1. . . . . . . 102

5.18 MDR spectra for a 90 µm polystyrene microsphere in a water

medium, insert showing magnified image of peak 1. . . . . . . 103

5.19 Stability of the MDR spectrum for a 90 µm glass microsphere

where (a) shows the identification of the peak positions at t

= 0 and (b) plots the shift in wavelength of the peak position

from time t = 0 to t = 60 min. . . . . . . . . . . . . . . . . . 104

xvii

5.20 Stability of the MDR spectrum for a 90 µm polystyrene

microsphere where (a) shows the identification of the peak

positions at t = 0 and (b) plots the shift in wavelength of

the peak position from time t = 0 to t = 60 min. . . . . . . . 105

5.21 Schematic of modified static well environment. . . . . . . . . . 106

5.22 Comparison of MDR spectrum between ethanol and water

surrounding medium for a single 90 µm glass microsphere. . . 107

5.23 MDR spectrum response to changes in local refractive index

via change in surrounding medium for a single 90 µm glass

microsphere. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

5.24 Plot showing position of the wavelength peaks from Fig. 5.23

vs refractive index. . . . . . . . . . . . . . . . . . . . . . . . . 109

6.1 Experimental setup showing the integrated SPR and MDR

optical paths. . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

6.2 SPR plots for nprism = 1.785, λ = 779 nm with refractive index

of the medium being (a) n = 1.00 and (b) n = 1.33. Effect

of thickness of gold layer on minimum reflectance shown vs c)

value of reflectance and d) angular position. . . . . . . . . . . 115

6.3 SPR plots for nprism = 1.51, λ = 779 nm with refractive index

of the medium being (a) n = 1.00 and (b) n = 1.33. Effect

of thickness of gold layer on minimum reflectance shown vs c)

value of reflectance and d) angular position. . . . . . . . . . . 116

6.4 MDR spectra for 90 µm glass microsphere for a prism/glass

slide/air interface. . . . . . . . . . . . . . . . . . . . . . . . . . 118


slide/water interface. . . . . . . . . . . . . . . . . . . . . . . . 119

xviii


slide/Au/air interface. . . . . . . . . . . . . . . . . . . . . . . 120


slide/Au/water interface. . . . . . . . . . . . . . . . . . . . . . 120

6.8 MDR spectra for 90 µm glass microsphere held via SPR optical

trap in a microfluidic device. . . . . . . . . . . . . . . . . . . . 121

6.9 Sequence of images showing (a) 200 x 200 µm patterned array

in a microfluidic device, (b) introduction of SPR trapping

beam, (c) trapping region under white light illumination, (d)

trapping of a 90 µm glass microsphere via SPR trapping, (e)

Light from SPR trapping beam blocked by band-pass filter and

(f) introduction of diode laser focal spot to interaction region. 122

6.10 MDR spectra for 90 µm glass microsphere illuminated via the

SPR trapping beam under a range of incident powers. . . . . . 123

6.11 MDR spectra for 90 µm glass microsphere illuminated via the

SPR trapping beam under a range of incident powers. . . . . . 124

6.12 MDR spectra for 90 µm glass microsphere held via 60 mW

SPR trapping beam under flow of 20 µm/sec for a surrounding

medium of refractive index 1.33 and 1.37. . . . . . . . . . . . . 124

6.13 Plot showing shift in the position of the wavelength of defined

spectral features from Fig. 6.12 vs refractive index. . . . . . . 125

xix

List of Tables

2.1 Different MDR microcavities with corresponding Q-factor values 19

3.1 Optimum Au thickness coating for SPR under experimental

parameters for λ = 1064 nm. . . . . . . . . . . . . . . . . . . . 48

5.1 Refractive index of Glycerin-water solutions at 200. . . . . . . 108

6.1 Optimum Au thickness coating for SPR under experimental

parameters for λ = 779 nm. . . . . . . . . . . . . . . . . . . . 117

xx

Chapter 1

Introduction

1.1 Microfluidics

1.1.1 Introduction to microfluidics

Microfluidics is a multidiscipline field of science which intersects branches of

physics, chemistry, biology and engineering, as well as pharmaceutical and

bio-engineering. The field focuses on the manipulation of minute amounts

of fluids primarily for biological and chemical investigations in channels

and capillaries which have at least a single dimension smaller than 1 mm

(generally on the scale of tens to hundreds of micrometers). There is also an

offshoot of the field which focuses on investigations on the scale of nanometers

[1–3].

The origin of the field of microfluidics can be traced back to the 1970’s

with the gas chromatograph research from Stanford University [4] and the

development of the ink jet printer nozzles at IBM [5]. However it is only

1

Chapter 1 2

in the last few decades that the field has really become a ‘hot’ topic. This

interest is driven significantly by the potential of microfluidics to miniaturise

and replace large scale and costly equipment/processes with cheaper, smaller

and thus potentially more portable and more efficient devices.

Microfluidic devices possess several advantages over macro-scale counter

parts in terms of response time, consumption of power and analytes, small

regions of dead volume, the ease of batch fabrication of the devices with a high

degree of reproducibility and the ability to integrate a range of functions into

such devices such as micromechanical or optical sensors, valves and pumps

[6, 7], as well as biological or chemical reagents.

Figure 1.1 Diagrams of functions of microfluidic devices including: a) Focusing of chemicalreagents, b) Dilution of chemical reagents, c) Sorting of micro-particles, and d) passive mixingof fluids/regents.

Microfluidics also has enormous potential in lab-on-a-chip devices which

have multiple functions and operations integrated into a single device, which

has particular appeal to drug discovery which often requires thousands of

individual assays to be conducted over the course of an investigation [8].

They also have a variety of applications in DNA-replication and testing [9–

Chapter 1 3

11], transportation, immobilisation, and manipulation of biological molecules

and cells [12, 13], as well as performing separation, mixing, and dilution of

chemical reagents [14–16], see Fig. 1.1.

1.1.2 Forces on the micrometre scale

Devices on the scale of micrometres tend to behave differently compared

to their macro-world counterparts. Friction, electrostatic forces, interfacial

forces and viscous effects due to the surrounding air or liquid gain increasing

dominance with decreasing device scale. While inertial and gravitational

forces play an increasingly smaller role in the dynamics of the system.

Fluid dynamics in a microfluidic device are strongly dependent on the

channel geometry, the properties of the fluid itself and the flow conditions.

The stability of the flow is determined by the combination of the inertial,

viscous and interfacial forces [17]. The characterisation of the flow dynamics

is done by a number of dimensionless values. Primarily the Reynolds number

(Re) which represents the ratio of inertial to viscous forces and is defined as

Re =ρLr

µ, (1.1)

where ρ is the fluid density (kg.m−3), r is the characteristic velocity

(m.s−1), L is the hydraulic diameter of the microchannel and µ is the dynamic

viscosity (Pa.s). The other characteristic values of a microfluidic system

include the Bond number (Bo) which expresses the ratio of the gravitation

to surface tension forces, the Capillary number (Ca) which is the relationship

between the viscous and interfacial forces, the Ohnsorge number (Oh) relates

Chapter 1 4

the viscous forces to inertial and interfacial tension forces and the Weber

number (We) which compares the inertial effects to surface tension forces.

For fluidic systems where the Reynolds number is below a critical value,

around 2,000 - 2,300 [6] the flow can be described as Laminar. A laminar

flow system is one where the fluid behaves in a non-chaotic, predictable

behavior. It has two important consequences, the first is that like turbulent

systems the flow under Laminar conditions can be modeled using computer

simulations such as computational fluid dynamics and the second is that

speed of diffusion at the interface between two fluids is completely defined by

the molecular diffusion rate. However as molecular diffusion is a very slow

process and with channel dimensions and path lengths of tens to hundreds

of micrometres it is reasonable for this effect to be ignored, which means

that in a microfluidic channel two fluids will not mix unless effected by an

‘active’ or ‘passive’ mixing system. This has important applications for such

techniques as Hydrodynamic focusing, which utilises the Laminar flow state

of two or more liquids to control the width of fluids inside a microchannel by

controlling the ratio of fluid velocity between solutions.

1.1.3 Design and application of microfluidic devices

One of the primary drivers of microfluidic technology is the interest in

developing point-of-care (POC) total analysis systems. These systems

allow for on site investigations of DNA, blood or biological samples for

fast turn-around analysis. Common configurations of microchannel devices

arise from the organised assembly of capillary tubes or the use of high

precision micromachining techniques, which are generally categorised into

either bulk or surface techniques. Bulk techniques involve direct modification

Chapter 1 5

of the substrate material which can be made of ceramic [18, 19], glass [20],

polymeric materials (i.e. polydimethylsiloxane (PDMS) and epoxy-polymer

SU-8) [21, 22], stainless steel [23, 24] and Teflon [25]. Surface techniques

entails selective deposition of multiple layers of different materials of various

thickness which are shaped by the required functions of the device.

Microfluidic fabrication techniques include: hot embossing [26, 27],

injection molding [28], soft lithography [22, 29], optical lithography [30, 31]

and X-ray lithography [32]. More recently there have been developments in

alternative fabrication techniques such as liquid photolithography [33] and

lipid film hydration [34]. Among them, hot embossing has strong promise

as a rapid and cost effective means of producing microfluidic devices with

ease of channel design and the ability to integrate with several optic sensing

techniques.

1.2 Optical biosensors

Optofluidics is a term which refers to devices that merge microfluidics with

optical components to manipulate or measure liquid, light and matter. The

development of new technologies from microsystems, optics and fluidics

is opening new possibilities for increased functionality and integration in

biosensor development.

Optical detection techniques have several advantages over other analysis

methods such as electrochemical [35] and electronic methods [36–38]. First

they require no direct contact with the target sample or molecule and

second they permit an array configuration which when used in conjunction

with specifically targeted immobilising chemistry, allows for multiplexed

investigation of biological samples.

Chapter 1 6

One of the more exciting futures that optofluidic systems will play is a

key role in point-of-care “blood-to-diagnosis” systems for genetic analysis [39].

Challenges that have arisen for the development of such systems are primarily

based on the requirements of the end users and include speed, cost, sensitivity,

ease of use, non-contamination, and portability. System cost (including

cost per experiment and total equipment costs), material and design will

depend on the balance of functionality between disposable components and

the instrument. Point-of-care systems must isolate, capture and amplify

target DNA for detection, while utilising on-chip pumping, valving, mixing

and reaction capabilities. The test must be performed in a robust, repeatable

and representative fashion while minimising the possibility of contamination.

One promising technique to overcome the challenges in POC systems is

to use optical detection techniques in conjunction with biological or chemical

receptors to detect concentration, interactions and the presence of analytes

(molecules) in a sample. Systems which integrate these techniques are often

called optical biosensors and typically include such methods as evanescent

wave [40,41], interferometric (resolution = 5x10−8 R.I.U) [42], resonant cavity

(resolution = 7.6x10−7 R.I.U) [43,44], photonic crystal (resolution = 7x10−5

R.I.U) [45, 46], Raman spectrometry (resolution = 10−11 M) [47, 48] and

surface plasmon resonance (resolution = 5x10−5 R.I.U) [49,50], see Fig. 1.2.

There is often over-lap between the techniques with surface plasmon

resonance being utilised to improve the resolution of Raman scattering

techniques [47] or to enhance the transmission of light into the evanescent

wave [51]. Optical biosensers are frequently separated into label and label-

free [33, 52] categories. Label based systems perform treatments such as

fluorescent dye staining [53] or radiometric element binding to assist in the

measurements of samples. However such a treatment can potentially result

Chapter 1 7

Figure 1.2 Diagram of biosensors using the optical detection method; a) Ramanspectrometry, b) Photonic crystal, c) Resonant cavity, and d) Interferometric.

in the death of the specimen, thus preventing repeated measurements of a

single population. There is also a limitation on the size of the molecules such

treatments are applicable to, extremely small molecules such as virus and

antibodies are often present in concentrations and sizes that are extremely

difficult to observe and thus require a different detection approach.

As such there has been a strong push for measurement techniques

which do not utilise labeling. Label-free biosensors [54], are systems that

generally involve the measurement of a physical property (i.e size, mass,

dielectric permitivity etc) of the sample under investigation. The sensor

component of the system converts the physical property into a quantifiable

signal that can be collected via an appropriate system/instrument (such

as the voltage/current shift that occurs in a thin film crystal monitor in

response to a deposited mass in an evaporative coating machine). Optical

biosensors work on the principle that all biological molecules have a dielectric

permitivity greater than that of air or water, thus their modification of

Chapter 1 8

an electric field that interacts with the molecule is distinguishable from

the background material of the sample. Therefore the design goal for an

optical biosensor is to provide a system where the sensing surface possesses

a measurable characteristic that is modified in response to changes in the

dielectric permitivity on its surface.

In many types of optical biosensors, a solid material medium confines an

electromagnetic (EM) wave in such a way that the wave has the opportunity

to interact with a test sample. The EM wave is generally in the form of a

standing or traveling wave. In order to interact with the analyte at the sensor

region the EM wave must propagate away from the surface of the sensor

into the testing region. Electromagnetic waves that are bound to an optical

component but extend into an external medium are called evanescent fields.

The evanescent field decays exponentially away from the sensor surface, with

a decay length of approximately λ/2π, where λ is the wavelength of the light,

see Fig. 1.3.

Figure 1.3 Diagrams of waveguide structure confining a traveling evanescent wave.

For a common wavelength range for optical biosensors of 600 - 1064

nm this means that the evanescent field only extends around 95 - 169 nm

into the test media. Thus most optical biosensors can only detect within

Chapter 1 9

direct proximity of the sensing region. There are many investigations [55–57]

currently underway into techniques which either extend the evanescent field

further into the sensing medium or focus the evanescent field to higher

intensities to enhance the sensitivity of the sensor.

There are several characteristics of optical biosensors that determines

their overall performance. Two fundamental properties of the device are

its sensitivity and its resolution. Sensitivity in this case is defined as the

magnitude of the change in the sensors signal in response to a given shift in

the surface-absorbed mass-density, and the resolution refers to the smallest

observable change in the effective mass density that can measured by the

device/system. The resolution of an optical biosensor is often referred to

as the “Quality factor” or “Q-factor”, which is defined as Q = λ0/∆λ for

a wavelength-based sensing system. Here, λ0 is the center wavelength of a

resonance peak, and ∆λ is the spectral width determined at half of the peaks

maximum value.

1.3 Thesis objectives

The motivation of this research is to design and develop an optical biosensor

which allows biological and chemical investigations fully isolated from

external contamination while allowing the introduction of chemical analytes

via microfluidic flow systems. This device is proposed to be achieve via

the combination of surface plasmon based optical trapping techniques with

the phenomena of morphology dependent resonance (MDR) inside a dynamic

microfluidic environment towards highly localised optical sensing. Combining

these two phenomena will allow the potential for high resolution localised

environmental sensing by the introduction of the microspherical sensing

Chapter 1 10

elements within the flow of the fluidic solutions, the semi-arbitrary trapping

of the microsphere by surface plasmon resonance (SPR) based optical traps,

and the evanescent excitation of the MDR of the microsphere. While being

held under these coupling conditions the MDR of the microsphere will be

highly sensitive to changes in the local environment. Additionally by releasing

the optical trap the microsphere will be overcome by the fluid dynamics

and be removed from the detection region of our device, thus removing any

potential contamination sites from potential experimental element, i.e. cells,

bacteria, chemical reagents. This design has several advantages over previous

sensing systems in that by introducing surface treated microspherical sensing

elements into the system, rather than having the surface treatment built into

the device, the targeting of different molecules, chemicals and environmental

properties is achieved without requiring the fabrication of a new system for

each individual test. Secondly the surface plasmon based optical trap has

a high degree of flexibility in the location of the trapping site, allowing the

sensor to be positioned in arbitrary locations within the device, this coupled

with the high sensor resolution of MDR microcavities and the low cost per

device makes this proposed design show enormous promise for biological and

chemical investigations.

Towards this goal the development of a surface plasmon based optical

trapping technique, capable of localised optical trapping of microspherical

particles, ranging from 5 to 90 µm in diameter, and moving under flow

dynamics will need to be investigated. The role of plasmons in this body

of work primarily focuses on the trapping and manipulation of particles

via evanescent optical forces. The enhancement to the electric field by the

surface plasmon wave arises from the confinement of the field due to selective

patterning and/or structuring of the metal layer. The implications of such

Chapter 1 11

a field enhancement towards the localised trapping of microspheres moving

under flow conditions has yet to be fully investigated.

Furthermore to the knowledge of this author no investigation has occurred

of MDR detection occurring in surface plasmon based optical traps. Such an

investigation would require the development of the effects of experimental

parameters on the MDR profile of a microcavity both outside and in a

microfluidic system. Therefore it is the intent of this thesis to undertake

an experimental investigation of surface plasmon trapping in a microfluidic

environment, including developing a theoretical understanding on the field

enhancement that occurs in a structured plasmonic environment, and the

investigation of the the effect of experimental parameters on the MDR of

a microsphere cavity. The final investigation in this body of work will be

the integration of the two techniques into a microfluidic device under flow

conditions and demonstrate the viability of such a device as a potential

sensing platform.

1.4 Thesis preview

The thesis is organised as follows: Chapter 2 provides an overview of

technologies for localised optical sensing relating to morphology dependent

resonance, surface plasmon resonance and optical trapping. A brief review of

each of these techniques is presented with an emphasis on their functionality

as an optical sensing technique, with emphasis on their capability to perform

detection and sensing in an arbitrary location within a device.

Chapter 3 describes the fabrication and demonstration of a surface

plasmon based trapping optical technique integrated into a microfluidic

Chapter 1 12

device. Details are provided on experimental setup (section 3.2), design

of microfluidic device (section 3.2.1), manipulation via surface plasmon

resonances both in a static and dynamic fluid environment (section 3.3).

The experimental design and process for patterning the metal surface are

discussed in section 3.4.1 and the effect of the patterned surface of the ability

of the system to trap is presented in section 3.4.2.

Chapter 4 presents a theoretical investigation into the effect of incident

angle onto the plasmonic coupling and confinement of the electric field in a

structured metal surface. The behavior in a unstructured surface is first

discussed in section 4.3 for both direct and angled propagation. Light

propagating parallel to the metal surface with apertures of diameter less than

to greater than the wavelength of the incident light is presented in section

4.4.1. The effect of changing the propagation angle is shown in section 4.4.2,

and then compared to the unstructured structure in section 4.4.3 in order to

develop a further understanding of the trapping forces utilised in Chapter 3.

The optimisation of the coupling conditions of light, coupling via total

internal reflection generated evanescent wave coupling into a micro-sized

cavity is reported in Chapter 5. Section 5.2 is dedicated to the design of the

fluidic system, the preparation of the samples and the experimental setup.

The investigation of the effect of the incident angle of the MDR spectrum

is presented in section 5.3. The effect of the separation between the MDR

microcavity and the collection element of the detector path is shown in section

5.4. Modification to the chamber design and the characterisation of the

stability of the sensing system is reported in section 5.5, while section 5.6

demonstrates the sensitivity and functionality of the MDR system via the

detection of changes in the refractive index of the local environment.

Chapter 1 13

Chapter 6 shows the integration of the MDR sensing system into a

dynamic microfluidic device. The integration of the SPR trapping and MDR

sensing optical beam paths are shown in section 6.2. Section 6.3 presents

the results of MDR coupling into a microcavity under changing interface

conditions in the new detection setup. A microcavity is shown to be trapped

in a patterned metal surface via SPR based techniques and coupling into

the MDR mode is presented in Chapter 6. Detection of the change in the

refractive index of the local environment is observed via change in the MDR

of the microcavity under these trapping conditions with a resolution of 7.75

x 10−2 R.I.U under a flow rate of 20 µm/sec. With the removal of the

microcavity under flow forces the system is demonstrated to introduce, detect,

and remove a sensing element into a specific location within a microfluidic

device.

The conclusion chapter (Chapter 7) summarises the achievements and

results of the dissertation and presents a view of potential future work that

may arise both from this body of work and in this field in general.

Chapter 2

Literature Review

2.1 Morphology Dependent Resonance sensors

2.1.1 Fundamentals of Morphology Dependent Resonance

sensors

Optical resonators have been gaining increasing focus as a basis not only

for standard laser devices, but as a system for high accuracy measurements

and for non-linear optics in many modern optical devices. The exploration

of whispering gallery modes (WGM) in optical microcavities has gained

significant momentum over the last few years as they provide a platform for

modal stability, high quality factor (Q) and small modal volumes. Whispering

gallery modes can be described as light rays that are confined and propagate

along the surface of the structure, where the confinement originates from the

total internal reflection of the light at the surface.

14

Chapter 2 15

The circular optical mode in such resonators can be understood to be

caused by the interference of a light beam propagating inside a dielectric

particle confined by total internal reflection, see Fig.2.1. As a beam of light

propagating inside the particle returns to its starting position in phase, the

constructive interference effect leads to a series of peaks in the scattered field

for given an appropriate particle size. When the reflecting beam has high

index contrast and the radius of curvature exceeds several wavelengths, the

radiative loses (by absorption or transmission) become very small and the

Q becomes limited only by material attenuation and scattering caused by

geometrical imperfections (e.g. surface roughness). As the optical resonances

are a function of their morphology and dielectric properties, they are often

referred to as morphology dependent resonances (MDR) [58,59].

Figure 2.1 Schematic diagram of light rays of different wavelengths constructively interferinginside a microcavity when incident under total internal reflection.

A spherical microcavity possesses natural internal modes of oscillation

at characteristic frequencies corresponding to the specific ratio of size to

wavelength, an example is shown in Fig. 2.2.

Chapter 2 16

777.0 777.5 778.0 778.5 779.0 779.5 780.0 780.50.0

0.5

1.0

1.5

2.0

Inte

nsity

(a.u

.)

Wavelength (nm)

Figure 2.2 Example of MDR resonance spectrum with the black spectrum showing the cavitymodes in an initial state and the red spectrum demonstrating a potential MDR spectrumresponse to a molecular binding event.

The wavelength at which these MDR can occur can be calculated from the

theoretical studies by Mie on the scattering of plane electromagnetic waves

by a sphere. They also arise from Debye’s derived equations for the resonant

eigenfrequencies for free dielectric and metallic spheres. These calculations

arise due to the independence of the MDR on the scattering process, elastic

or inelastic, but from its dependence on the boundary conditions of the

microsphere, including the refractive index mismatch between the between

the microsphere and the surrounding medium as well as the shape, size and

surface roughness of the cavity. For a given spherical microcavity, resonances

occur at specific values on qm,l. Here q is the the size parameter given in Eq.

2.1

qm,l =2aπ

λ( ~Em,l), (2.1)

Chapter 2 17

where a is the radius of the spherical cavity, λ( ~Em,l) is the emission

wavelength and m and l are integers. The mode number m indicates the

order of the spherical Bessel and Hankel functions (ζ) describing the radial

field distribution and the order l indicates the number of maxima in the

radial dependence of the internal field distribution ( ~Em,l which is a function

of ζm,l). m and l indicate that both the discrete transverse electric (TE) and

transverse magnetic (TM) resonances exist.

2.1.2 Design of Morphology Dependent Resonance

sensors

Excitation of high Q MDR requires light coupled into the microcavity at

angles greater than the critical angle. This is extremely difficult with direct

coupling methods, however efficient coupling of MDR via evanescent waves

generated by total internal reflection (TIR) has been observed. The most

common system for TIR excitation of an evanescent wave is the coupling of

light on the back surface of a high refractive index prism. While this is the

most common method other systems such as tapered optical fibres and high

numerical aperture (NA) objectives have been used to demonstrate coupling

of light into MDR of microcavities.

Confinement of light into the surface wave at a prism interface is a well

understood optical phenomenon. The prism allows light to be incident of the

interface at angles beyond the critical angle, as defined by Snell’s law. The

surface wave is classified as an evanescent wave (EW) due to its propagation

away from the interface surface into the surrounding medium, a microcavity

positioned within the decay length of the EW acts as a scattering source. If

the scattered waves complete a round trip and constructively interfere on the

cavity surface they are classified as an MDR mode.

Chapter 2 18

Figure 2.3 Schematic representation of MDR coupling to a microcavity via (a) prismgeometry and (b) tapered optical fibre geometry.

More efficient methods for coupling light into MDR of microcavities have

been observed in fibre coupling [60] and high NA objective coupling [61].

Optical fibres propagate light via the continuous internal reflection between

the core and the surrounding cladding of the fibre. By stripping the cladding

of the fibre an evanescent wave is observed in the exposed region. This

evanescent wave can be utilised to couple light into the MDR, a schematic

representation of the evanescent wave and optical fibre geometries are shown

in Fig. 2.3. This MDR can be observed in either the transmission spectra of

the microcavity or in the transmission loss from the optical fibre.

Microcavities are not limited to spherical nor symmetrical objects and

have been observed in with cavity designs (see Table 2.1) ranging from

polystyrene [61, 62] and glass microspheres [60], square microcavities [63],

asymmetric microparticles [64], ring resonators on glass or silicon substrates,

and silicon oxide toroid structures [65]. Provided that the microcavity

presents at least one path length in which light can complete constructive

‘round-trips’ a cavity can support an MDR mode.

Chapter 2 19

Table 2.1 Different MDR microcavities with corresponding Q-factor values

Cavity Q-factor Schematic

Prism [66] Q = 8

Fabry-Perot [67, 68] Q ≈ 104

Square microcavity [63] Q > 105

Photonic crystal [69, 70] Q > 104

Microsphere [60–62,71] Q = 1010

Toroid [65,72] Q ≈= 108

2.1.3 Applications of Morphology Dependent Resonances

sensors

The use of optical microcavities with MDR is a growing field with many

potential applications such as spectroscopy [73, 74], remote sensing [52],

microcavity lasing [75, 76] , second harmonic generation [77, 78] and Raman

scattering [79].

Integration of MDR microcavities into microfluidic based devices shows

enormous potential for the development of high resolution sensing systems.

These systems utilise MDRs dependence on the sensitivity of the modes to

changes in the surrounding dielectric permitivity or changes to the surface

of the microcavity via binding of molecules, with resolution such that single

molecule detection is possible [80–82]. The primary advantage of a MDR

sensor is that, the trapped photons are able to circulate on their orbit

several thousand times before exiting the MDR, provided that the losses

Chapter 2 20

from absorption of the cavity material is low and that losses arising from the

TIR scattering at the cavity boundary is minimal. This long optical path

length corresponds to a lengthy confined photon lifetime and results in the

very high sensitivity associated with MDR cavity systems with potential to

detect single nanoparticles or single molecules.

The binding of a biochemical receptor (antibody, DNA, etc) onto the

surface of a resonance cavity provides a platform for the cavity to act as a

biosensor. The primary requirements of a biosensor are a high signal-to-noise

ratio, a low limit of detection, capacity of integration and high sensitivity.

When a micro- or nano-metre object (even one of biological origin) is brought

into contact with the surface or target receptor there is a resulting change

in the effective radius and/or refractive index of the surface of the cavity,

through the interaction with the evanescent part of the MDR field, a resultant

shift in the MDR spectrum of the resonator occurs, see Fig. 2.4.

Figure 2.4 Shift in the MDR signal of a resonant microcavity in response to a target moleculebinding to the biochemical receptor on the surface of the cavity.

Chapter 2 21

2.2 Surface plasmon optical sensors

Surface plasmons (SP) are an optical phenomenon which is sensitive to

changes in the optical properties of the medium close to the metal surface

[83,84]. The detection component of an SP system, is typically composed of a

monochromatic light source which is linearly polarised (where the polarisation

orientation is parallel to the plane of incidence), a glass prism, a thin metal

film (in direct or close contact to the prism surface), and a photodetector. The

glass prism acts as a momentum coupler to incident light photons, allowing for

the generation of an evanescent wave at the prism/metal interface for angles

of incidence beyond the critical angle. If the evanescent wave couples to the

electric field in the metal surface an electromagnetic wave, also known as a

surface plasmon, can be generated at the metal/liquid (or air) interface. Light

coupling into the surface plasmon wave is achieved at very specific angles of

incidence, known as the surface plasmon resonance angle. At the SPR angle

a minimum is observed in the reflectance of the incident light. The SPR

angle is determined by the respective values of the dielectric permittivity of

the materials that make up the SPR sensors, as such the position of the SPR

angle is highly sensitive to changes in the refractive index at the surface of the

metal layer. Therefore changes in the dielectric permittivity are observable

by the changes in the position of the SPR angle, see Fig. 2.5.

These changes can be a result of a number of different stimuli such as;

First a direct substitution of the material under investigation would produce

an observable shift (provided there was a strong contrast in the respective

refractive indices). The temperature of the local environment could be altered

as the shift in temperature would result in a change in the local density thus

changing the effective refractive index of the medium. The direct binding of

Chapter 2 22

49 50 51 52 53 54 550.0

0.2

0.4

0.6

0.8

1.0

Ref

lect

ance

Angle (deg)

Figure 2.5 Example of SPR resonance spectrum with the red spectrum showing the cavitymode in an initial state and the black spectrum demonstrating a potential MDR spectrumresponse to a molecular binding event.

a molecule to the surface of a sensor, which is most commonly observed in

systems where the metal surface has been treated with a biological receptor

targeted to bind with specific molecules, proteins, or DNA ligands, when the

target ligands bind to the receptors both the thickness of the surface layer

and the density are altered which is observed by the shift in the position of

the SPR angle.

While the bulk-prism based [49] coupler configuration is one of the most

common techniques first demonstrated by Kretschmann [85] it is by no means

the only method of light coupling into an SPR wave. There are several designs

that utilise the SPR sensing principles; diffraction grating based [49, 86],

integrated optical waveguide-based [87] and optical fiber-based [88,89].

Chapter 2 23

2.2.1 Fundamentals of Surface Plasmon Resonance

optical sensors

Surface plasmons are a field of interest to a broad variety of scientists, due

to its unique ability to concentrate and channel light using subwavelength

structures [55, 90, 91]. Surface plasmons arise from the resonant interactions

between the surface charge oscillations and the electromagnetic field of the

light. By surrounding the metallic structure with a non-conducting media,

the difference in the relative permitivities, ǫ, leads to the confinement of the

propagating plasmon wave to the surface of the metal. Concentrating light in

this fashion can lead to extremely high enhancement to the electric field, as

well as confinement of the field beyond the diffraction limit of conventional

optics. These phenomena can be used for light-matter interactions, or in

the case of optical sensing, to boost the non-linear effects of the surface way

towards single molecule detection via Surface-Enhanced Raman Spectroscopy

(SERS).

The interaction between the electromagnetic field and the surface charge

density results in the momentum of the free space mode, ~kSP , being greater

than that of a free-space photon of the same frequency, ~k0. (k0 = ω/c, is the

free-space wavelength, where ω is the angular momentum of the photon and

c is the speed of light). In order to achieve the required coupling conditions

for light into SPs, it is first necessary to solve Maxwell’s equations under the

appropriate boundary conditions,

kz1ǫ1

+kz2ǫ2

= 0, (2.2)

Chapter 2 24

which leads to the SP dispersion relation, that is, the frequency-dependent

SP wave-vector (kSP )

kSP = k0

√

ǫ1ǫ2ǫ1 + ǫ2

. (2.3)

Assuming that ǫ1 is real and ǫ1 is greater than 0, then to satisfy the

boundary conditions (see Eq. 2.2) the permittivity of ǫ2, must have the

opposite sign to ǫ1. This situation is satisfied for metals because ǫm is both

negative and complex. This resulting momentum mismatch between the light

and the SPs of the same frequency must be overcome if the light is to be used

to generate SPs, shown in Fig. 2.6.

Figure 2.6 Dispersion curve where blue curve shows the light line (ω = c.k0) and red is thesurface plasmon curve.

There are several techniques used to provide the missing momentum to

the incident light. The first is to make use of the prism coupling to enhance to

momentum of the incident light [85]. The second is to utilise scattering from

defects, natural or artificial, on the coupling surface [29]. The third involves

the use a metallic diffraction grating fabricated by periodic corrugation in

the metal’s surface [92, 93].

Chapter 2 25

Surface plasmon polaritons (SPP) arise due to the incident field inducing

a collective oscillation of free electrons, which results in sustained resonant

electromagnetic modes in the metal-dielectric interface. The SPP field is said

to be evanescent in the perpendicular direction, showing an enhanced field

near the surface and an exponential decay with increasing distance in the z-

direction [84,91]. In order to couple light into an SPP mode an enhancement

to the momentum of the photon of the free-space lightwave is required,

there are several techniques that are capable of providing this momentum

enhancement, in these experiments the Krestchmann configuration is used.

In this method the incident light is totally reflected at the interface between

a prism and a thin metal layer, the incident light evanescently penetrates

through the metal layer and excites an SP wave at the outer boundary of the

metal layer [49]. The excitation of a SP wave is accompanied by a drop in

the intensity of the reflected light.

Once light has been coupled into an surface plasmon wave on a flat metal

surface its propagation in the metal plane will be attenuated due to losses

arising from the absorption in the metal (a result of the complex refractive

index of the metal). The strength of this attenuation depends on the dielectric

function of the metal at the oscillation frequency of the SP. The propagation

length, δSP , can be calculated by from the imaginary part, k′′SP , of the complex

surface plasmon wavevector, kSP = k′SP + ik′′SP , from the SP dispersion Eq.

2.4,

δSP =1

2k′′

SP

=c

ω(ǫ′m + ǫdǫ′mǫd

)3

2

(ǫ′m)2

ǫ′′m, (2.4)

where ǫ′m and ǫ′′m are the real and imaginary parts of the dielectric function

of the metal, that is, ǫm = ǫ′m + iǫ′′m. The SP wave is also observed to decay

exponentially away from the surface of the metallic layer.

Chapter 2 26

2.2.2 Design of SPR optical sensors

There are several designs that utilise the SPR sensing principles; bulk-prism

based [9], diffraction grating based [29], integrated optical waveguide-based

[87,94] and optical fiber-based [88,89,95].

Bulk-prism based systems are mainly designed to utilise the attenuated

total internal reflection method. A common system the Kretschmann

configuration, consists of a high refractive index glass prism, metal layer and

a dielectric (the sensed media under investigation). A change in the refractive

index of the sensed media is observed using one of three basic approaches to

SPR-based measurements, the first is SPR-induced intensity change, angular

response [96, 97] and wavelength (spectral) investigation [49] are the other

two methods. This optical arraignment is also utilised in bio-based sensing

application via the selective binding of receptor molecules/proteins to the

surface of the metal layer. These molecules act as binding sites, when a

target molecule comes into contact with the receptor they bond, changing

the local density at the site and in the immediate vicinity. The change in

density state is observable via a shift in the resonant wavelength of the SPR

system, see Fig. 2.5. The advantages of bulk-prism systems is the ease of

the excitation of the SPR and its relatively low cost, however the system has

limited potential for miniaturisation and when coated with target analytes

for biological analysis there is a lose in sensitivity arising from the changes

in the surface conditions. Several of these limitations can be overcome by

the structuring of the SPR structure with a diffraction-grating system, this

design allows for large number of simultaneous measurements via the SPR

excitation of multiple channels and have a resolution around 5x10−6 R.I.U.

Chapter 2 27

An optical waveguide-based system involves the structural confinement

of a propagating SP wave along the surface of a dielectric interface. The

propagating wave pass through a sensing region which consists of a metal layer

over which the analyte under investigation resides. At the transition point

between the single-mode waveguide region of the device to the sensing region

the propagating wave decompose into all the guided and radiative eigenmodes

of the region, the intensity distribution of the new modes is highly dependent

on the field profile and thus the physical structure of all the surrounding

mediums involved in the decomposition. The wave then encounters a second

transition point after which the guided wave is transfered to the output

section of the device. The information of the structural profile within the

guided wave can be determined using a transfer matrix approach [98]. A

common method is to observe shifts in the TM modes of the p-polarised SP

wave. Waveguide based systems have several advantages on the bulk-prism

design in that the excitation source can be guided to the sensing region

by the structure and the miniaturisation of the sensing region allows for low

concentration of analyte required and have a resolution around 5x10−5 R.I.U.

Recent focus has been on the integration of Fibre-based excitation systems

with waveguide structures, these systems allow for increased miniaturisation

due to the small excitation region generated by the optical fibres, with a

resolution around 4x10−5 R.I.U. However the integration of optical fibres

increases the complexity of the system and require extremely fine position

control of the fibre.

2.2.3 Applications of surface plasmon resonance

One limitation of the Kretschmann configuration is that the system can only

take measurements from the point at which the laser light is focused. The

Chapter 2 28

technique also is limited to specific interaction regions particularly in the

case of proteins and biomolecules which require surface treatments of specific

protein strand ‘receptors’ selected to bind to target molecules, see Fig. 2.7.

This limits both the functionality of the sensor as it is only valid for the

selected molecules as well as requiring that the target molecules be selectively

introduced to the treated region of the SPR device.

Figure 2.7 Illustration of a target molecule binding to a ‘receptor’, with the event beingdetected via the wavelength shift of the SPR angle.

Rather then measure the change in the SPR angle position for a

given surface binding, another SPR based technique is to illuminate the

metal/liquid interface with a wide area collimated monochromatic source

and to measure its reflectivity with a inexpensive CCD chip or camera at a

fixed angle. If the SPR coupling conditions are met then the reflected signal

observed will be dark, when a protein or molecule binds to the surface the

incident coupling conditions are no longer met and shift in the intensity of the

reflected signal is observed on the CCD as a bright spot. This technique has

been demonstrated with high sensitivity for a variety of techniques including

DNA arrays and RNA arrays.

Surface enhanced Raman scattering is another label-free analysis tech-

nique that is capable of molecular specific analyte detection with low

detection limits. A SERS system typically falls into one of two designs:

Chapter 2 29

1) an analyte solution is passed through a channel in which a colloid solution

of metal nanoparticles (gold or silver) acts as sights of local SP excitations,

2) the analyte solution is passed over a nanostructured metal surface residing

at the bottom of a channel or well, see Fig. 2.8.

Figure 2.8 Label-free optical sensing via SERS based detection system using a) Aunanoparticles in a colloid solution and b) nanostructured Au surface.

While highly sensitive SERS systems present several problems integrating

with microfluidic devices, first is the reduced area of active SERS sites due to

the limitation of available space within a microfluidic system has a negative

effect on the detection limit of the sensor, second is the increased difficulty

of transportation of the analyte to the active sites in sufficient volumes

for detection. There have been several methods proposed to solve these

limitations including flowing the analyte solution through or around hollow

cladded or photonic crystal fibres, though this does improve the detection

limit of the system it significantly reduces the design features available to the

system as well as limiting the size of the molecules available for investigations.

Chapter 2 30

2.3 Sensing via optical trapping techniques

2.3.1 Fundamentals of optical trapping techniques

Optical tweezers are a clear manifestation that light is able to exert a force on

matter. This concept, although unintuitive, can be understood from quantum

theory which quantitatively states the amount of momentum contained in a

photon. From Maxwell [99], it has been stated that “In a medium in which

the waves are propagated there is pressure in the direction normal to the

wave, and numerically equal to the energy contained in unit volume”. The

pressure refers to the prediction of some form of radiative pressure which

is exerted on the objects by the light, a theory which dates back to Kepler

(1619) and his development of the nature of comet tails. Confirmation of the

existence of the radiation pressure was demonstrated by Lebedev [100] and

by E. F. Nichols and G. F. Hull [101] in 1901 by observing the effect of light,

produced by an arc lamp, on a gas moving through thin valves.

The current form of optical manipulation was pioneered by Arthur Ashkin

at Bell Laboratories in the 1970’s. These traps were based on the upward-

pointing radiation pressure to “Levitate” a particle against the downward

gravitational force. The generation of a three-dimensional optical trap arose

when it was discovered that a tightly focused laser beam generated a gradient

force of sufficient magnitude to trap small objects [102]. Thus the first

example of an “optical tweezer” was generated.

Optical tweezers provide a useful tool for non-invasive manipulation of

microscopic objects. A tweezer system consists of a laser beam(s) tightly

focused into a very small region, this generates an extremely large electric

field gradient. When the focused laser beam interacts with a particle, forces

Chapter 2 31

are exerted on the particle and it is attracted towards the region of highest

intensity by the so named gradient force (see Fig. 2.9), while the radiation

force, also referred to as the scattering force, acts on the particle in the

direction of the light propagation. If the gradient component exceeds the

scattering component, the microsphere will be trapped at an equilibrium

position near the focal region.

Figure 2.9 Illustration showing the resultant force (FA) acting on a particle as a result ofrefracted rays (A’) and surface reflections (Rx).

The forces behind the trapping mechanism primarily arise due to the

momentum transfer resulting from the interaction between the light rays and

the particle. A light ray can be thought of as a bunch of photons propagating

in the same direction, each photon posses a momentum ~k, where ~ is defined

as Planck constant divided by 2π and k is the wave vector of the incident

light. When a ray is refracted through a dielectric particle a changes in its

direction occurs due to the refraction process. From Newtons conservation of

Chapter 2 32

momentum laws a change in direction implies that there must exist a force

associated with that change.

2.3.2 Design and application of optical tweezer systems

In 1977 Ashkin et. al. demonstrated the use of optical force techniques

in a method they called force spectroscopy [103]. Dielectric spheres are

levitated via optical forces and sharp resonances are observed in the measured

force due to the Mie-Debye scattering. Via characterisation of the resonance

profile of the sphere the size of the trapped object can be determined with

extremely high sensitivity. The integration of this technique with Raman

scattering provides an effective method for the determination of the size and

the composition of a particle [104,105].

Weakly focused optical trapping techniques are limited in their applica-

tions due to their requirements on two incident sources to provide counter-

propagating waves for the generation of an optical trap. The generation of a

single-beam trap via tightly focusing a laser beam through a high numerical

aperture (NA) objective provides a method of overcoming this limitation.

An object in such a trap is not only confined in the plane transverse to the

beams direction of propagation but also in the axial direction as well [102].

Under this configuration the laser beam could be orientated in any direction

and still trap a particle, with the system effectively trapping objects of size

25 nm to tens of micrometers this system expands the regime of the optical

trap into the realm of biological particles [106].

Optical trapping techniques have several applications in cell biology

[107] and single-molecule research [108]. Optical forces generated via such

methods are commonly in the piconewton range which is excellent for

Chapter 2 33

dealing with biological cells and molecules. These optical forces, which

are generally generated at low incident powers (≤ 100 mW), are strong

enough to overcome the comparatively weak forces such as gravity, Brownian

motion and low fluid velocities. This allows the manipulation of biological

cells and microorganisms, including viruses, bacteria, red blood cells and

DNA. Such manipulations have been demonstrated using optical trapping

systems integrated into microfluidic devices in order to ‘squeeze’ [109, 110],

rotate [111], cut [112] and move trapped objects have been demonstrated.

These techniques also provide information on the local environment where

the force applied to a trapped object is recorded and the position within

the trap is kept constant, this results in changes to the force applied to the

object (e.g. via fluid velocity) is observed in a shift in the force applied to

the system [113,114].

As the single beam trap requires that light be focused to the diffraction

limited spot (for a typical setup around 500 nm) care must be taken not to

exceed a certain intensity limit of the laser light as this may lead to cell death

or damage. Similarly care must be taken when selecting the wavelength of

the incident light as the absorption of specific wavelengths of light also has

the potential to lead to cellular damage or death.

Recent advances have looked at extending the optical trap to multiple

trapping sites in order to sort/manipulate simultaneously multiple cells for

example via holographic techniques [115,116].

Chapter 3

Surface Plasmon Resonance

trapping in a microfluidic

device

3.1 Introduction

The three primary factors to consider when developing optical techniques for

the manipulation and trapping of micro-objects are the gradient of the field

intensity, scattering forces and gravity. It is the control and interplay between

these forces which determines the strength, stability and functionality of

the manipulation technique. Computer generated holograms [117], spatial

light modulators (SLM) [118, 119], acoustic-optical devices [72, 120] and

diffractive optical elements [121, 122] have all been demonstrate to achieve

multiple simultaneous trapping of micro-objects, see Fig. 3.1. Holographic

manipulation techniques manipulate the objects via changing the gradient

intensity profile within the trapping region by cycling through a series of

34

Chapter 3 35

holograms. The technique while allowing the manipulation of trapped objects

in three-dimensions (3D) possesses limitations on the range and translational

movement that can be achieved. The SLM also has issues with translation of

individual traps due to the degradation of the trap arising from aberration

and scattering of local objects. Moreover, the majority of these techniques are

limited to the field of view of the microscope, determined by the numerical

aperture (NA) of the objective used in the system. Hence the appeal of

evanescent wave (EW) manipulation techniques. When a micro-sized object

interacts with an EW, the wave can be converted to a propagating wave

which results in the guiding of the object along the surface in the direction

of the longitudinal wave-vector of the electric field [123].

Figure 3.1 Diagram of a setup showing the generation of a multiple optical trappinglandscape generated via a computer controlled SLM/Wavefront manipulator (Hologram)

One of the major challenges of extending near-field optical trapping to

large area manipulation is that optical interactions involving evanescent

Chapter 3 36

waves are considerably weaker than in standard optical trapping techniques.

This limits both the extent in area over which particle arrays may be

created and the strength of the particle traps. One method to overcome this

limitation is to use surface plasmon polaritons [84,91,124] which are surface

waves produced by collective oscillation of free electrons at a metal-dielectric

interface [92, 125]. Recent work has shown that enhanced optical forces and

optically induced thermophoretic and convective forces produced by SPP

excitation can be used for large scale ordering and trapping of colloidal

aggregations [126–128].

However when conducting experiments in a fluidic system, there is the

potential for the disruption of the thermo-based forces and the breaking of

the optical trap via cooling or flow based forces. It has previously been

demonstrated [129–131] that light propagating in the z-axis incident on a

subwavelength aperture in a metallic surface can also be used to generate

SPPs, which results from the diffraction of the incident light from the edge of

the hole which decays into SPPs emanating from the hole in the plane of the

film [92]. This provides a structural confinement to the SPP wave and when

the diameter of the aperture is less then the wavelength of the incident light

there is a plasmonic coupling [132], both these effects lead to an enhancement

of the electric field at the metal-dielectric interface. This generates a gradient

force at the interface strong enough to trap microspheres without thermo

effects. There have been several investigations using nano-hole arrays to trap

particles [133,134], however the fabrication systems required to pattern nano-

hole arrays are expensive and the traps set a limit for the size of particles

that can be trapped, also there have been few investigations into how such

traps are effected when the particles move under flow conditions.

Chapter 3 37

3.2 Experimental Setup

Experiments were performed on a Kretschmann prism-coupling geometry [84,

135], see Fig. 3.2. The illumination light beam from a 1,064 nm Nd:YAG laser

beam is expanded to a parallel beam by the lenses L1 (microscope objective,

NA = 0.25) and L2 (Plano-convex, focal length = 200 mm). The beam width

is controlled by a variable aperture (VA) and the beam polarisation is set

using a 1

2waveplate (WP). A third lens L3 (Plano-convex, focal length = 400

mm) focuses the beam onto the back surface of a 35 mm equilateral glass

prism (BK7, n = 1.51). The sample chamber was placed on top of the prism

via index matching liquid (n = 1.516). P-polarised light from the incident

laser beam was coupled into the chamber surface at an angle of 70◦, set by

the geometric alignment of the prism - L3 combination and fine tuned by the

micrometer controlled rotation stage. The incident power is controlled using

a neutral density (ND) filter wheel. The interactions of the microspheres

with the illuminated region are observed via an UPlanFl 10x/0.3 microscope

objective, a CCD camera and illumination from a white light source. In order

to perform detailed analysis, video files of the interactions were captured

using the VirtualDub capture software for image processing and analysis

using particle tracking algorithms in ImageJ (NIH).

3.2.1 Development of microfluidic devices

The development of a method of producing microfluidic devices with low cost,

low construction time, strong stability under a range of pump rates and ease

of redesign of the channel system was a ongoing priority of this thesis.

Chapter 3 38

Figure 3.2 Schematic diagram of experimental setup for SPR manipulation experiments. VA:variable aperture, L: lens. Insert showing close up of a multilayer microfluidic device placed onthe equilateral prism, showing the materials respective dielectric permitivity for λ = 1,064 nm.

3.2.1.1 Gen 1 microfluidic device

The first microfluidic device investigated was a thin plastic film chamber

bonded directly to the surface of a glass prism, see Fig. 3.3.

The input and output ports were fabricated by first cutting donut shaped

port mounts out of a sheet of PMMA via the CO2 laser system, the plastic

sections had an external diameter of 5 mm and an internal diameter of 1.27

mm. Metal ports of approximately 10 mm in length where inserted into the

plastic mounts and sealed via commercially available super glue. Sections

of polymer sheets with dimension 20 x 70 mm were produced with 7 mm

diameter holes cut at either end via the CO2 laser system. The port mount

Chapter 3 39

Figure 3.3 Diagram of the first generation microfluidic device.

was then sealed over the corresponding hole in the polymer section with

super glue. The final top section was then bonded to the glass prism via

double-sided tape, the tape was cut to have an external dimension of 20 x 70

mm and an internal section of dimensions 10 x 50 mm was removed. Silicon

tubing was used to connect the ports to a peristaltic pump which pumped

the fluid solution with a flow rate between 0.001 and 0.0005 ml/min. For a

water solution (dynamic viscosity = 10−3 Pa.s, fluid density = 1000 kg.m−3

@ 200) at a flow rate of 2.57−4 m/s the Reynolds number of the system is

calculated to be Re = 0.257.

A 40 ± 5 nm gold layer was coated onto the surface of the glass prism

via evaporative coating to allow for investigation into the surface plasmon

based effects inside the fluidic device. This thickness was selected for our

experimental setup as the 40 nm thickness showed the second best minimum

in reflectance, see Fig. 3.4 and presented the most efficient minima vs

material usage of the thickness of the Au layer. A prism mount was custom

made to allow the prism surface to rest horizontally. The surface height was

Chapter 3 40

Figure 3.4 Plot of SPR vs thickness for a glass/Cr/Au/water interface at λ = 1,064 nm.

measured at 32 mm. In order to get an accurate thickness of the metal layer

the thin-film thickness monitor of the evaporative coating machine needed to

be recalibrated to the prism surface height. To recalibrate the surface coating

parameters, a glass slide was coated with a 40.2 nm Au layer at the height

of the base plate (z = 0 mm) and its transmission spectrum vs wavelength

was recorded using a UV-vis spectrophotometer. The results are shown in

Fig. 3.5, that shows the percentage of transmitted light for a change in

the wavelength of the light, over a wavelength range of 400 - 800 nm. The

position of the glass slide was adjusted so its surface was positioned at z =

32 mm. A series of glass slides where evaporatively coated with a range of

gold coating thicknesses as recorded via the thin film detection monitor. The

transmission vs wavelength was recorded for each of the samples as shown in

Fig. 3.5. The transmission spectrum for the varying thickness coatings at z

= 32 mm is compared to the slide coated at z = 0 mm and a recorded gold

coating of 10.9 nm at a height of 32 mm is shown to produce the spectrum

that is the closest match to the original coatings.

Chapter 3 41

Figure 3.5 Calibration curve for evaporative coating parameters at base plate and samplesurface height.

The advantages of this device were; first its low cost, with the materials

in its construction being all commercially available, also by careful removal of

the polymer top section the device could be readily recycled. Second was its

short construction time, with the construction time primarily reliant on the

bonding time of the super glue adhesive a full device could be constructed

within a time frame of one hour. However there arose several disadvantages

with this design; low maximum pump power, the strength of the double-sided

tape’s adhesive bond limited the pump rate inside the device to a maximum

of 0.004 ml/min before pressure overcame the structural strength of the bond

and leaking was observed. In several cases full decay of the device occurred

under pump rates greater than this. Modification to the metal surface coating

via etching was impractical, due to the high cost of the glass prism (SF11)

the possibility of damage to the glass surface during a laser etching process

was too great.

Chapter 3 42

3.2.1.2 Gen 2 microfluidic device

Polydimethylsiloxane (PDMS), a two-part silicone compound, is formed by

mixing at a 10:1 ratio base with curing agent, is a common material used in

the fabrication of micro-scale objects and devices. Its liquid state is easy to

use and manipulate and after curing into a solid but flexible material responds

well to pre and post lithographic techniques. A multistage hot-embossing

technique, see Fig. 3.6, is used to form the PDMS into microfluidic devices.

Figure 3.6 Schematic of hot embossing process for fabrication of PDMS microfluidic devicecomponents.

Chapter 3 43

First PDMS is spin coated at 1,500 RPM for a 50 µm thick coating onto

a silicon wafer. The PDMS is then cured on a hot plate at 85◦C for 30

min. After curing the microfluidic design is cut into the PDMS using a

CO2 laser, see Fig. 3.7 (a) forming a PDMS/silicon master. The inverse of

this PDMS/silicon master is then imprinted onto a polymethyl methacrylate

(PMMA) sheet (25 x 75 mm) by bringing the plastic sheet to a temperature

above the glass transition temperature where the plastic ‘softens’, when

placed under sufficient pressure the soft plastic molds into the cavities of

any master it is in direct contact with. The plastic is then rapidly cooled

while in contact with the mold so as to harden it, thus generating a PMMA

substrate with the inverse pattern of the PDMS/silicon master imprinted

onto the surface, see Fig. 3.7 (b). This process is achieved by aligning both

the PMMA sheet and the PDMS/silicon mater and placing them into a vice

clamp which has been heated to a temperature of 1800C via contact with a

hot plate. A torque, applied by a torque wrench, of 10 Nm is applied for

10 min, the vise clamp is custom designed to allow the introduction of cold

water throughout the whole clamp causing a rapid cooling of the system.

The embossed PMMA slide then forms the base for a mold, PDMS solution

is poured onto the mold and then cured for 1 hour at 850C.

Figure 3.8, shows a typical schematic of a microfluidic device fabricated

using this technique. The channels of the device are imprinted into the PDMS

during the curing process. The four ports (i - iv) are bored into the PDMS

before being sealed with metallic tubes, these act as input and output ports

for the introduction and extraction of solution from our device. The PDMS

chamber is sealed onto a glass substrate by activating both surfaces using an

O2 plasma and then bonding the surfaces together. The coating procedure for

the glass substrate is schematically shown in Fig. 3.9. A mask is patterned

Chapter 3 44

50 mm 50 mm

50 mm

Figure 3.7 Images of various molds during the hot embossing stage of the fabrication of themicrofluidic device (a) PDMS/silicon master after CO2 laser cutting (b) PMMA master and(c) PDMS mold.

out of double-sided tape using the CO2 laser and the adhesive section is

bonded to a glass slide, 40 nm thick Au layer was thermally evaporated onto

the glass slide. A (5 nm) Cr layer was evaporated onto the surface prior to

the Au layer to increase the adhesion strength of the Au to the glass. The

mask was then removed, leaving the gold coated glass substrate.

The design of the microfluidic device with three input ports allows for

the utilisation of the microfluidic technique called hydrodynamic focusing.

Hydrodynamic focusing manipulates the width of the inner fluid by adjusting

the ratio of flow rates between the inner and outer fluids with a higher

ratio resulting in a thinner inner width. This setup allows the increase

in concentration of microspheres by reducing the width of the microsphere

solution through the center of the device.

Chapter 3 45

Figure 3.8 A sample design of a microfluidic device.

Figure 3.9 Schematic diagram outlining the procedure for coating of the microfluidic devicesubstrate.

3.3 Surface Plasmon Resonance based optical

manipulation

Figure 3.10 shows a calculation for the magnitude of the reflected signal

vs the angle of incidence, for a light source incident under total internal

Chapter 3 46

reflection of a metallic-dielectric interface. The wavelength of the incident

light is 1,064 nm, with a transverse electric (TE) polarisation. A four layer

interface was simulated for the calculation with the first layer composing

of the glass slide substrate with a refractive index of n1 = 1.51. The second

layer is Chromium with a refractive index of n2 = 3.54 + 3.579i (at λ = 1,064

nm [136]) and a thickness of 5 nm. The third material in the calculation is

a 40 nm thick layer of gold (Au) with a refractive index of n3 = 0.285 +

7.35i (at λ = 1,064 nm [136]). The final layer simulates the solution within

the microfluidic device, primarily being water with an index of n4 = 1.33.

The figure highlights two points of interest on the curve. The first position

is the point of minimum reflectance, at an angle 660 it is the point where

the magnitude of the incident light coupled into the surface plasmon wave

is at its maximum. This angle is called the surface plasmon resonance angle

and hence forth in this thesis is referred to as the ‘on’ resonance position.

The second point of interest in Fig. 3.10 is an arbitrarily selected position on

the reflectance curve, defined as the ‘off’ resonance position it is at an angle

of 730 and equates to the point of maximum reflection within the angular

range of the experimental setup where the coupling to the SPR is minimised.

These two labeled positions are selected to allow us to compare the trapping

and manipulation effects of the incident wave for both on and off resonance

positions of the incident light.

The absorption of hydrophobic molecules such as polystyrene particles

[137] via the PDMS introduces error into the analysis of the efficiencies

of optical trapping techniques under investigation. Surface modification

of the PDMS material is required to reduce aggregation and adhesion of

microspheres to the chamber walls and substrate. Poly(ethylene oxide)

(PEO) is effectively used to inhibit the bonding on hydrophobic surface

Chapter 3 47

Figure 3.10 Plot showing Reflectance vs angle for a Au coated glass slide with highlightsshowing location of on and off resonance positions.

[138–140]. Bonding to the surface layers of the microfluidic chamber PEO

generates an exclusion layer, which is the area covered by the PEO material

and its immediate vicinity. Via molecular repulsion the PEO coating prevents

bonding to the surface in the areas in which it occupies. The physical

absorption of the PEO material onto the surface is one of the most common

coating methods, however it can be easily disrupted by the presence of

proteins or other material that have the potential to replace the PEO on the

surface. The Pluronic range of PEO-based copolymers has been synthesised

to contain hydrophobic blocks which ensures a stronger and more stable

coating of the surface [141]. The microfluidic channel is coated with Pluronic

F127 surfactant and left for a minimum period of 12 hrs to ensure a solid

uniform coating. The chamber is flushed with a phosphate buffered solution

(PBS), a buffer solution with a refractive index of n = 1.33 that is commonly

used in biological research. The solution helps maintain a constant pH and

is often used due to its similarity with the cell environment in the human

Chapter 3 48

body. The microspheres under investigation are suspended in a PBS solution

in order to bring the proposed microfluidic sensor more in-line with current

biological research practices.

Figures 3.11 and 3.12 show the calculations of the surface plasmon reso-

nance position under a range of experimental conditions. These conditions

match those to be investigated and show both prisms used, the SF11 (n =

1.785) and the BK7 (n =1.51). The calculations where performed over a range

of metal thicknesses and demonstrates that for a change in the thickness of

the metal layer the magnitude of the resonance dip is effected, however there

is less than a 20 shift in the angular position of the minimum reflection point.

The thickness and angle for the minimum reflection conditions are

summarised in Table 3.1, it can bee seen that across all parameters the

optimum thickness is around 60 - 70 nm. However in order to save material

costs the thickness of the metal layer for experiments was set to 40 nm.

Table 3.1 Optimum Au thickness coating for SPR under experimental parameters for λ =1064 nm.

nprism λ nm θr (deg) dθr (nm)

1.785 1,064 1.00 35.1 601.785 1,064 1.33 51.1 701.51 1,064 1.00 42.8 701.51 1,064 1.33 67 70

Chapter 3 49

10 nm

20 nm

30 nm

40 nm

50 nm

60 nm

70 nm

80 nm

90 nm

100 nm

10 nm

20 nm

30 nm

40 nm

50 nm

60 nm

70 nm

80 nm

90 nm

100 nm

Figure 3.11 SPR plots for nprism = 1.785, λ = 1,064 nm with refractive index of the mediumbeing (a) n = 1.00 (air) and (b) n = 1.33 (water). Effect of thickness of gold layer on minimumreflectance shown vs (c) value of reflectance and (d) angular position.

Chapter 3 50

10 nm

20 nm

30 nm

40 nm

50 nm

60 nm

70 nm

80 nm

90 nm

100 nm

10 nm

20 nm

30 nm

40 nm

50 nm

60 nm

70 nm

80 nm

90 nm

100 nm

Figure 3.12 SPR plots for nprism = 1.51, λ = 1,064 nm with refractive index of the mediumbeing (a) n = 1.00 (air) and (b) n = 1.33 (water). Effect of thickness of gold layer on miminumreflectance shown vs (c) value of reflectance and (d) angular position.

Chapter 3 51

3.3.1 Manipulation in a static fluid environment

In order to investigate the effect of SP waves in a microfluidic device

under dynamic conditions an understanding of the effects of SP in a static

environment first needs to be developed. 5 µm polystyrene microspheres were

placed in the detection region of a microfluidic device and allowed to settle to

the surface of the device over a period of 10 minutes. Residual internal flow

velocities are observed to decay to zero over this time period. The focal region

of an incident light source under SPR coupling conditions is illuminated in

the region of interest with a focal spot diameter of 350 µm at an intensity of

84.5 ± 2 mW.

Figure 3.13 Images of convection trapping of 5 µm polystyrene microspheres in a staticmicrofluidic environment at times (a) t = 0 min (laser is turned on), (b) t = 1 min, (c) t =10 min, (d) t = 20 min, (e) t = 30 min (laser is turned off) and (f) t = 40 min. Scale Bar is100 µm.

Figure 3.13 shows the effect on the microspheres in the region inside and

surrounding the focal volume of the incident light. At time t = 0 min,

the microspheres are diffused in a random arrangement. The incident light

source is turned on and the microspheres are observed to moved towards the

Chapter 3 52

center of the focal spot. The self organisation of the microspheres into a

hexagonal lattice is observable after a period of 30 min, see Fig. 3.13 (b).

As discussed by Garces-Chavez [142], this is a result of the intensity of the

incident beam under SPR coupling conditions inducing localised heating in

the metal surface, which generates a convection current in the fluid in the

region above the focal spot. If the velocity of the convection flow is balanced

via fine tuning of the incident intensity then the microspheres will be drawn

to the center of the focal spot without the flow have enough momentum

to remove them from the region, see Fig. 3.14. After the incident light is

removed, the convection flow dissipates and Brownian motion overtakes the

micropheres and particle diffusion occurs, as seen in Fig. 3.13.

Figure 3.14 Schematic showing manipulation of microspheres via SPR induced convectionflow, showing (a) microspheres randomly distributed on surface of the chamber, (b) aconvection flow induced in the chamber via heating from illumination of light under SPRcoupling, (c) microspheres are drawn to center of the convection flow as defined by the positionof the incident focal spot and (d) if the convection flow overcomes the gravitational forces themicrospheres are drawn upwards and away from the focal region.

Chapter 3 53

Figure 3.14 shows a schematic diagram of the potential effects of

convection flow based manipulation. Initial random states and induction

of the convection forces are shown in Fig. 3.14 (a) and (b) respectively.

When the velocity of the convection flow is slow enough (as controlled by

the intensity of the incident light) the microspheres are drawn to the center

of the focal region yet do not have enough energy to be drawn away from

the trap against gravity, see Fig. 3.14 (c). However in the state where the

flow velocity is fast enough the convection force is strong enough to overcome

gravitation forces are the microspheres are drawn upwards and away from the

trap as demonstrated by Fig. 3.14 (d).

This form of optical based manipulation is an excellent form of large area

multiple particle manipulation, with the position and dimensions of the trap

being dictated by the location and size of the focal spot of the light source.

3.3.2 Manipulation via Surface Plasmon Resonances in

a dynamic fluidic environment

The introduction of a flow velocity into a microchannel results in a change in

the mechanisms of optical manipulation systems. Under static conditions

thermal induced forces have a tendency to dominate over optical forces,

however the introduction of a flow allows for the removal of energy from

the system by transporting the heated fluid away from the focal region and

thus preventing the formation of thermal forces.

10 and 15 µm polystyrene microspheres were suspended in a PBS solution

and pumped through a microfluidic device. Hydrodynamic focusing resulted

in a solution width of 200 µm. Incident light is focused to the surface with

Chapter 3 54

a focal spot diameter of 100 µm. The ~k of the incident surface wave is

aligned to be in opposite direction to the flow inside the microfluidic channel.

The power of the incident light was varied between 20 and 70 mW in 10

mW intervals and the manipulation of the polystyrene microspheres flowing

through the interaction region at an average flow rate of 22 µm/sec was

recorded via image capture software. In order to compare the efficiency of

the microspherical trapping effect the variable, Particle Trapped Efficiency

(PTE) is defined as

PTE =NTr

NT

, (3.1)

where NTr is the number of microspheres that are observed to be trapped

within the patterned region over a set time interval and NT is the total number

of microspheres that pass through the patterned region over the same time

interval. The PTE is a representation of the efficiency of the optical trap

over a particular interval to allow investigation of the changes to the trapping

force over time. Each time interval was set at ten second over a period of 1

minute, where t = 0 defines the point in time when the incident light source

was turned on. The PTE of each parameter was determined based on the

interaction region being the whole 400 x 400 µm array viewable via the CCD

camera.

For the 10 µm polystyrene microspheres the PTE vs power is shown in

Fig. 3.15. Under a flow rate of 22 µm/s trapping of microspheres is only

observed to occur on resonance for powers above 50 mW, after which higher

incident power is observed to result in a higher PTE. This is intuitive based on

the theory of evanescent wave trapping, where the more energy the incident

photons can convey to the particle the more momentum transfer can occur,

Chapter 3 55

a higher number of trapping events also occur as there are more photons

which posses sufficient energy to trap a microsphere. In order to investigate

the effect of higher incident light coupling to the evanescent wave, trapping

for both the on and off resonant conditions of the experimental setup were

performed for all trapping experiments. It can be seen by comparing Fig 3.15

(a) and (b) that while the off resonance condition demonstrates trapping at a

lower power, 50 mW, the PTE is more unstable than that of the on resonance

condition.

Figure 3.15 Results of SPR manipulation of 10 µm polystyrene microspheres under (a) Onresonance and (b) Off resonance coupling conditions.

For 15 µm microsphere trapping the difference between on and off

resonance trapping is much more pronounced then for 10 µm microspheres.

The off resonance trapping is shown only for an incident intensity of 70 mW

with a maximum PTE of 25 % at time t = 20 sec, see Fig. 3.16 (b). After 1

minute the PTE is shown to drop to zero showing that even at its maximum

trapping potential the off resonance traps are still significantly weaker then

the on resonance counterpart, with a decrease in PTE an indication of

microspheres escaping the trapped region. A significant increase in the PTE

is observed in the 15 µm microsphere trapping when compared to the 10

Chapter 3 56

µm. This is a result of two factors; the first is the increase in surface area of

the microsphere increases the number of potential photon interactions, the

second is that the larger microsphere has a higher density and thus flows at

a lower height in the microchannel, as discussed earlier the magnitude of the

electric field decays exponentially into the solution thus a lower position in

the microchannel results in encountering a larger trapping force.

Figure 3.16 Results of surface wave manipulation of 15 µm polystyrene microspheres undera) On surface plasmon resonance and b) Off resonance coupling conditions.

3.4 Surface Plasmon Resonance manipulation

on a patterned metallic surface

The use of subwavelength apertures and structured surface components to

confine and enhance the electric field of a plasmon has been well investigated

in the literature [91,92,132,143]. This led to the theory of structured surface

components creating regions of high gradient intensity in order to create

localised optical trapping sites as independent from the surface plasmon wave

trapping whose dimensions are currently only confined to the size of the focal

Chapter 3 57

spot of the excitation light source. A full theoretical investigation of the

enhancement to the electric field for apertures of dimensions of λ20

≤ d ≤ 5λ,

where d is is size of the aperture, is conducted in Chapter 4. The reason for

investigating electric field confinement in greater than wavelength dimensions

is that a) a full study into the effects of such a structure was not discovered in

the literature review and b) the resolution limitations of fabrication systems

available to our research were limited to the wavelength scale.

3.4.1 Laser etching a metallic surface

Prior to bonding the Au coated glass substrate to the PDMS section, a series

of 200 x 200 µm array of holes was etched into the microfluidic devices Au

surface using an amplified femtosecond pulse laser (Spitfire, Spectra Physics,

800 nm, 1 kHz) and direct multiphoton laser etching, see Fig. 3.17.

Figure 3.17 Experimental setup for multi-photon laser etching of micrometre sized holes ina Au coated glass substrates.

Chapter 3 58

Figure 3.18 Plot showing incident power vs hole diameter of a 40 nm thick Au coated surfacepatterned using a NA = 0.5 objective lens.

Figure 3.19 Plot showing incident power vs hole diameter of a 40 nm thick Au coated surfacepatterned using a NA = 0.7 objective lens.

The limits of the resolution of the fabrication setup was investigated using

a 0.70 and a 0.5 NA near infrared (NIR) objective lens. A series of 4 x 4 hole

Chapter 3 59

arrays were fabricated under a range of power and shutter speed conditions

and an array of lines were also fabricated under a range of power, shutter

speed and scanning speed. The average diameter of the holes fabricated were

plotted for both objective lens in Fig. 3.18 and Fig. 3.19 for a range of

incident powers and exposure times. From this data we can see the limit of

resolution of our fabrication setup is 1 µm with a fabrication range of 1 to 5

µm. The NA = 0.7 objective lens was selected as it has the best fabrication

resolution.

(a) (b)

Figure 3.20 (a) Schematic of the microhole array and (b) SEM image of microhole arraypatterned on a Au surface, scale bar = 20 µm (insert at 17k x magnification, scale bar = 4µm).

Using the NA = 0.7 objective lens an microhole array was fabricated with

an average hole diameter of 4 µm. The array was generated with an x and

y lattice spacing of 8 µm, see Fig. 3.20 (a). The lattice spacing was set to

8 µm to prevent potential plasmonic coupling between two or more holes,

and thus generating an additional optical force in our experimental setup. A

diameter of 4 µm was fabricated to generate an aperture size several orders

of magnitude greater than the wavelength of the incident light (λ = 1,064

µm). This aperture dimension allowed the investigation of the effect on the

confinement of the electric field on the trapping efficiency of the microhole

Chapter 3 60

array while preventing interference effects from the plasmonic coupling of

light from subwavelength structural components. The secondary effect of

using this aperture dimension is that it is equal in size to the diameter of the

smallest microsphere under investigation, 4.33 µm polystyrene, the change

in the trapping effect of a structural design of equivalent magnitude to the

particle being trapped will be investigated.

3.4.2 Microsphere manipulation via a patterned surface

Incident light is focused to the glass/Au interface of a 200 x 200 µm hole

array via the Kretchmann configuration. The change in the SPR angle due

to the diffraction effect of the hole array structured was not accounted for

in our theoretical calculation of the SPR angle. However the SPR angle was

experimentally determined for each microfluidic device via the measurement

of the intensity of the reflected beam prior to each experiment. The ~k of

the incident surface wave is aligned to be in opposite direction to the flow

inside the microfluidic channel. The power of the incident light was varied

between 20 and 60 mW in 10 mW intervals. The manipulation of polystyrene

microspheres flowing through the interaction region at an average flow rate

of 22 µm/sec was recorded via image capture software for microspheres of

diameter 4.33, 10 and 15 µm. When calculating the PTE of the patterned

region the number of trapped microspheres, NTr, only takes into consideration

the microspheres trapped within the patterned region.

From Fig. 3.21 a fast increase is observed between the value of the PTE

and the incident power for the on resonance incident coupling condition,

the trend line of the 40 mW on resonance parameter gives indication that

saturation of the array occurs shortly after t = 40 sec. This saturation may be

Chapter 3 61

Figure 3.21 Plot showing Particle Trapped Efficiency over time for a 4.33 µm microsphere,on and off resonance.

a result of a ‘filling’ of the trapping region via microspheres thus preventing

further microspheres being trapped. The distance of the microsphere from

the surface of the microfluidic device is believed to play an important part in

the observed trapping results.

The results of the 4.33 µm manipulation via a patterned surface show

an enhancement to the PTE of the optical trap for all incident powers,

when compared to the unpatterned surface condition where there was no

observable trapping of 4.33 µm polystyrene microspheres. However there is

no discernible trend observed when comparing an increase in intensity of the

trapping beam to the PTE of the system. This lack of linear trend may arise

from several different reasons, the first being the flow rate of the fluid solution

in the device may vary over time, this would vary both the position (in the

z-axis) of the microspheres in the solution, and increase the velocity of the

microsphere resulting in a change on the required value of the trapping force.

Chapter 3 62

Another potential influence is the induced heating effect on the surface of the

microfluidic device. It has already been shown that the incident light induces

a local heating effect is strong enough to induce a convection force inside a

static solution, see Fig. 3.13.

There is no observed trapping of the 4.33 µm microspheres under off

resonance coupling conditions. This is a result of the significantly reduced

momentum of the photons of the ~k of the surface wave in the off resonance

case compared to the on resonance. This lower photon energy means that

the momentum shift imparted on the microspheres via the surface wave is

of lower magnitude, which corresponds to a lower PTE. Figure 3.22 shows

the trapping of 4.33 µm microspheres within the 200 x 200 µm patterned

region under SPR illumination, the position of microspheres are highlighted

for both trapped and non-trapped microspheres.

Figure 3.22 Image of 4.33 µm microspheres trapping in a patterned surface under SPRillumination (P = 60 mW) at t = 40 sec. Red circles highlight trapped microspheres.

Images of the trapping of the 10 µm microspheres are presented in Fig.

3.23. The figure shows for an increase in the power of the incident light there

is a decrease in the PTE of the optical trap. Compared with the unpatterned

trapping results, see Fig. 3.15, a modest enhancement is observed in the

PTE of the 60 mW power and a dramatic increase in the PTE of all other

Chapter 3 63

powers with the 20 mW showing the greatest enhancement to the PTE at

the 60 sec mark. No trapping was observed with either of the off resonance

powers. This demonstrates the enhancement effect to the PTE of the on

resonance coupling condition, leading to a potential on/off switch via angular

adjustment and that secondary light sources will provide no effect on the

motion of the microspheres if coupled into the microcavity under off resonance

conditions.

Figure 3.23 Image of 10 µm microspheres trapping in a patterned surface under SPRillumination (P = 60 mW) at t = 40 sec. Red circles highlight trapped microspheres andblue circles highlight the untrapped microspheres. Scale is 40 µm.

Figure 3.24 Plot showing Particle Trapped Efficiency over time for a 10 µm microsphere, onand off resonance.

From Fig. 3.25 we can see a fast increase between the value of the PTE

Chapter 3 64

Figure 3.25 Plot showing Particle Trapped Efficiency over time for a 15 µm microsphere, onand off resonance.

Figure 3.26 Image of 15 µm microspheres trapping in a patterned surface under SPRillumination (P = 60 mW) at t = 40 sec. Scale bar is 40 µm.

and the incident power for the on resonance incident coupling condition,

the trend line of the 40 mW on resonance parameter gives indication that

saturation of the array occurs shortly after t = 40 sec the same as observed

in the 4.33 and 10 µm cases. A example of the 15 µm trapping is presented

in Fig. 3.26.

The presented data sets were selected from multiple experiments as they

Chapter 3 65

showed the only data set that was collected which covered all experimental

parameters. A statistical representation could not be built up due to issues

with inconsistent flow rates and microsphere concentrations.

3.5 Summary

In this chapter the investigation of the trapping and manipulation of 4.33,

10 and 15 µm microspheres was conducted for SPR induced trapping in a

static flow environment, microspheres moving under flow and trapping via

a patterned metallic surface. It was demonstrated that the efficiency of the

trap could be increased by a factor of 30 - 40 % by the structuring of the

metal surface with apertures of diameter greater than the wavelength of the

incident light.

The structuring of the metal surface is shown to confine the region of

trapping by a factor of 4 when compared to the unstructured case. This

method shows strong promise of further confinement to single microsphere

trapping by the patterning of unit cells of total dimensions equal to the size

of the microspheres under investigation.

Chapter 4

Theoretical investigation of

SPR on a patterned surface

4.1 Introduction

There have been several studies on the extraordinary enhancement and

transmission of the incident field through subwavelength apertures and

array of apertures and their potential for subwavelength diffraction and

nanoparticle manipulation. These structural elements in the surface have

been demonstrated by circular, square and triangular holes as well as the

equivalent shapes in nano- and micro-islands. A secondary effect of the

patterning of the metallic surface is the added control of the position of

the field strength, balancing the field strength at the metal surface could

allow for the generation of selected trapping areas defined by the elements

placed on the surface. These elements are generally formed using electron-

beam or ion-beam deposition/etching which presents significant costs in both

equipment and materials. Fabrication of holes via an amplified femtosecond

66

Chapter 4 67

pulse laser system presents a significant reduction in cost at the expense of

resolution.

As discussed previously in Section 3.2 at specific incident angles light

at a metal/dielectric interface and TIR coupling setup, can couple into a

surface plasmon resonance mode. These modes show significant increase

in transmission of the light intensity into the surface wave. The effect of

the incident field of light coupled into a metal/dielectric interface under

SPR conditions with an aperture larger then the wavelength has yet

to be thoroughly investigated. As these coupling conditions match the

experimental conditions of the SPR manipulation experiments shown in

Chapter 3, a thorough understanding of the role patterning the metal surface

plays in the field strength is required in order to understand the forces

involved.

4.2 Simulation details

Two-dimensional finite difference time domain (FDTD) simulations were

performed using the program FDTD SOLUTIONS (Lumerical Solutions,

Inc., Vancouver, Canada). Figure 4.2 (a) shows a schematic of the simulated

geometry, a transverse electric (TE) polarised, 1,064 nm, plane wave beam is

propagated at selected angles through 1) a glass substrate (ng = 1.51) onto

2) a 5 nm Cr (ncr = 3.54 + 3.58i) layer, 3) a 40 nm Au (nau = 0.28 + 7.35i)

surface bounded by 4) a surrounding dielectric medium of either air (nA =

1.33) or water (nW = 1.33). The incident light is centered on a metal surface

patterned with apertures of varying diameter, with the angle of the incident

light set at 00, 670, or 730. The electric field at the Au-water interface along

the y-axis were monitored for y = 0 µm, the left edge of the aperture and

the right edge of the aperture.

Chapter 4 68

Figure 4.1 Design of the model used in theoretical simulations for plane waves of λ = 1,064nm at angle (θ) incident at a dielectric/metallic interface. The composition of the layers are;1) Glass slide, 2) Cr (5 nm), 3) Au (40nm) and 4) surrounding medium for (a) unpatternedsurface and (b) a patterned surface with the left and right sides of the aperture highlighted.

4.3 Electric field behavior on a metallic surface

Theoretical investigation into the strength of the evanescent wave at the

surface of an unpatterned metal layer inside a microfluidic device is per-

formed. Initial investigation on the enhancement and transmission of light

are conducted for an incident wave propagating perpendicular to the metal

surface.

The strength of the electric field in an unpatterned metal surface is shown

in Fig. 4.2. The maximum intensity value occurs with a value of 0.013 a.u.

at x = 0 µm. This demonstrates that a wave parallel at the metal interface

is more than 95% reflected.

The angle of the incident wave was varied between 30 and 800 for a

glass/Cr/Au/water interface and the field profile in the y direction (field

perpendicular to the metal surface) at x = 0 µm was plotted, see Fig. 4.3.

It can be seen there is a 35 times enhancement of the electric field of the

incident wave on the resonant angle of the setup which propagates away

from the surface with an exponential decay.

Chapter 4 69

Figure 4.2 Electric field intensity for a plane wave, with TE polarisation, incident on adielectric interface with perpendicular propagation.

Figure 4.3 Electric field intensity in a dielectric/metal structure vs incident angle for 1,064nm plane wave with TE polarisation.

Chapter 4 70

4.4 Microhole plasmonic confinement

4.4.1 Surface plasmons in isolated microhole patterns

Changes to the electric field via patterning of the metal surface was

investigated. The size of the apertures were set to 0.1, 0.5, 1, 2 and 4 µm in

diameter. These size parameters allowed for simulation of the three potential

hole-particle ratio; subwavelength, wavelength and greater than wavelength.

The field profiles of a 00 propagating wave for surrounding mediums water and

air are shown in Fig. 4.4 and 4.5 respectively. For aperture diameters 0.1, 0.5

and 1 µm there is an observed enhancement on the intensity of the incident

light at the edge of the apertures on the Au/medium side of the structure.

This enhancement is on the scale of tens to hundreds times the initial intensity

of the light, depending on the structural and coupling conditions, and is a

result of the plasmonic coupling between the confined plasmon waves at the

edge of the aperture structure. A small enhancement (a maximum two-fold

enhancement at the edge of the aperture) is observed for aperture dimensions

greater than the incident wavelength. At such dimensions the enhancement

of the electric field is a result of the structural confinement at the Au/medium

interface.

Chapter 4 71

Figure 4.4 Field profile plots for a water medium simulated for plane wave source incidentperpendicular to the surface of the interface with aperture diameter (a) 0.1 µm, (b) 0.5 µm,(c) 1 µm, (d) 2 µm and (e) 4 µm.

Chapter 4 72

Figure 4.5 Field profile plots for a air medium simulated for plane wave source incidentperpendicular to the surface of the interface with aperture diameter (a) 0.1 µm, (b) 0.5 µm,(c) 1 µm, (d) 2 µm and (e) 4 µm.

Chapter 4 73

4.4.2 Angular dependence of plasmonic confinement

The angles selected for investigation of 670 and 730, correspond to the on and

off resonance angles respectively for the experimental setup investigated in

Chapter 3 for a glass/Cr/Au/water interface. For the air interface case both

angles are sufficiently far from the SPR angle of 42.80 to allow investigation

of the changes to electric field enhancement due to shifts in incident angle

away from the resonance condition. The field profiles of the on resonance

angle are shown in Fig. 4.6 and 4.7. The off resonance plots are shown in

Fig. 4.8 and 4.9.

The electric field intensity is observed it be increased for a decreasing

aperture size with the electric field observed to be confined to the edge corners

of the aperture for diameters close to or less than the wavelength of the

incident light. The propagation of the incident light through the centre of

the aperture for diameters greater than the wavelength of the incident light

is of a magnitude less than or equal to 1. This means for these aperture

dimensions the light freely propagates through the space unchanged. A detail

comparison of the changes to the electric field throughout the structure for

the various incident parameters is presented in Section 4.4.3.

Chapter 4 74

Figure 4.6 Field profile plots for a air medium simulated for plane wave source incident at67◦ to the surface of the interface with aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm,(d) 2 µm and (e) 4 µm. Silver outline highlights gold surface.

Chapter 4 75

Figure 4.7 Field profile plots for a water medium simulated for plane wave source incidentat 67◦ to the surface of the interface with aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1µm, (d) 2 µm and (e) 4 µm.

Chapter 4 76

Figure 4.8 Field profile plots for a air medium simulated for plane wave source incident at73◦ to the surface of the interface with aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1 µm,(d) 2 µm and (e) 4 µm. Silver outline highlights gold surface.

Chapter 4 77

Figure 4.9 Field profile plots for a water medium simulated for plane wave source incidentat 73◦ to the surface of the interface with aperture diameter (a) 0.1 µm, (b) 0.5 µm, (c) 1µm, (d) 2 µm and (e) 4 µm.

Chapter 4 78

4.4.3 Comparison of electric field between patterned

and unpatterned surfaces

The electric field strength of the various aperture diameters is compared for

the three incident angles. The electric field intensity is plotted for the center

of the aperture/structure (see Fig. 4.10), the left edge of the aperture (see

Fig. 4.11) and the right edge of the aperture (see Fig. 4.12). For aperture

dimensions at or below that of the incident light source the 00 condition is

seen to have significant higher enhancement than the other conditions, though

there are observed enhancements in the 0.5 µm case for 730 water which

possess a stronger enhancement effect. This arises as the plasmon coupling

effect between the two aperture points is weakened as the confinement on the

side furthest away from the incident source only confines light incident at the

edge rather than from the back aperture.

(a) (b)

Figure 4.10 The magnitude of the electric field at x = 0 µm at the Au/medium interfacefor incident angles 0◦, 67◦, and 73◦ with a medium solution of (a) air and (b) water.

For apertures greater than the size of the wavelength the largest electric

field enhancement is observed to occur for the on resonance angle, with the

2 µm aperture showing a 3 to 4 fold enhancement at both left and right

edges. For the 4 µm case there was no observed enhancement at the aperture

Chapter 4 79

(a) (b)

Figure 4.11 The magnitude of the electric field at the edge of the left aperture at theAu/medium interface for incident angles 0◦, 67◦, and 73◦ with a medium solution of (a) airand (b) water.

(a) (b)

Figure 4.12 The magnitude of the electric field at the edge of the right aperture at theAu/medium interface for incident angles 0◦, 67◦, and 73◦ with a medium solution of (a) airand (b) water.

edges, a decrease in the intensity was observed arising due to the little or

no structural confinement of the propagating wave, most of the energy is

observed to pass through the aperture itself (see Fig. 4.10).

In order to confirm the symmetry of the simulation results, the position

of the light source was reflected about the x = 0 axis. The incident angle

was set to - 73◦, as shown in Fig. 4.13. By comparing Fig. 4.13 it can be

seen that the results of the simulations are identical intensity values reflected

around the position x = 0.

Chapter 4 80

(a) (b)

Figure 4.13 The symmetry of the simulation of an incident source propagating at angle ±73◦

with the center of the source being at (a) x = 0.53 and (b) x = -0.53.

4.5 Summary

In this Chapter it has been shown that the patterning of the metal surface

with aperture sizes equal to or less than the wavelength of the incident

light provides significant enhancement to the electric field at the edge of

the apertures at the metal/medium interface, a 41.5 times enhancement is

observed for a wave propagating perpendicular to the surface with a 0.5 µm

aperture when compared to an unstructured surface. At aperture diameters

greater than the wavelength the field is observed to propagate primarily

through the aperture with some enhancement observed at the edges due to

the structural confinement of the light.

The effect of an incident wave propagating at angles on and off the SPR

was observed. In both the air and water systems, structures with a 2 and

4 µm aperture demonstrated enhancement (1.1 to 4 times) of the electric

field compared to the values observed in the 00 propagating case. In almost

all aperture dimensions the on resonance angle demonstrated higher (up to

a 1.6 times enhancement) electric field intensity values resulting from the

Chapter 4 81

stronger coupling of light into the SPR mode, except for the 0.5 µm aperture

case where the off resonance condition demonstrated a larger electric field

strength then the on resonance.

Patterning of the metal surface can be seen to provide an excellent method

of enhancing the electric field intensity and thus the trapping force of light

as well as providing a method of controlling the location of the trapping sites

within a microfluidic device.

Chapter 5

Morphology Dependent

Resonance sensing

5.1 Introduction

The investigation of morphology dependent resonance (MDR) is of significant

interest to many fields of science. Resonance probes offer many advantages

over conventional detection systems, including extremely high sensitivity to

changes in the immediate vicinity of the probes and remote sensing capability

to allow for non-invasive sensing systems to be realised. The primary issue

arising from using such probes is the difficulty in coupling to and from

the modes of the probe under investigation, where in order to maximise

the absorption and scattering efficiency of the probe the wavelength of the

incident light needs to be tuned to the natural modes of oscillation of the

microcavity. Many different designs have been proposed that investigate

varying the microcavity, from square to circular, cylindrical and toroid. They

are all quite successful at producing strong local field enhancements and high

82

Chapter 5 83

Q-factor resonance spectrum however many have strong limitations when

required to integrate into practical devices. Several of these designs require

fabricating the microcavity in set locations and introducing the material

under investigation via fluidics or another methodology. Other techniques

require the isolation of the microcavities in specific locations to achieve the

MDR coupling, optical trapping techniques such as optical tweezers have

many desirable qualities towards this purpose, the use of a high NA lens to

generate the gradient force needed for such a trap however greatly restricts

both the design of the experimental system as well as the size of the effective

sensing area of the MDR system. The Surface Plasmon Resonance based

manipulation and trapping technique developed in Chapter 3 is investigated

as a methodology for isolating the microcavities for a MDR based sensing

system.

The coupling system is also of great importance, if the source only possess

a narrow linewidth such as a continuous wave excitation source, then it can

only satisfy a single modal condition of the microcavity. There are several

different coupling conditions that are under investigation today from tapered

fibre to high NA total internal reflection (TIR) objective systems as well

as TIR based evanescent wave coupling. The last method is the strongest

candidate due to ease of integration with the SPR manipulation technique

discussed in Chapter 3.

Although the MDR effect and its many applications have been investi-

gated for several microfluidic systems, there has yet to be work to investigate

the changes to the MDR profile of a microcavity as the system is changed

from an open direct detection base to an enclosed microfluidic system. The

effect of intervening material and the resultant change on the separation

of the detection system from the microcavity is an important aspect to be

understood as the move towards more complex fluidic systems occurs.

Chapter 5 84

In this Chapter the resonance of a spherical microcavity is investigated

for various coupling conditions, as well as for changes in the detection

conditions and systems. The use of MDR as a technique for localised sensing

is investigated by changing various parameters such as refractive index of

the surrounding medium and of the microcavity itself, inside a microfluidic

system.


The investigation of coupling into the MDR mode of various sized micro-

cavities was demonstrated in the experimental system shown in Fig. 5.1.

The illumination light beam from a Velocity tunable diode-laser system

(New Focus, 765-781 nm) is expanded to a parallel beam by the lenses L1

(microscope objective (Melles Griot) with NA = 0.25) and L2 (Plano-convex,

focal length = 175 mm). The beam width is controlled by a variable aperture

(VA) and the beam polarisation is set using a 1

2waveplate (WP). A third

lens L3 (Plano-convex, focal length = 400 mm) focuses the beam onto the

back surface of a 35 mm equilateral glass prism (SF11, n = 1.785) under TIR

conditions (θ = 620). The focal spot is further confined by the introduction

of an objective lens (NA = 0.26) in the beam path between the prism and L3,

the objective is mounted to an X-Y-Z stage (M1) to allow fine control of the

position of the focal spot on the surface of the prism. The prism is placed in

custom made mount and attached to a micrometer controlled rotation stage,

an adjustment plate was made so the prism, when rotated, would induce

minimum translation of the focal spot at the prism surface.

The scattered light is collected by a Fluor 40x/0.7 objective lens (Obj) and

expanded by a Plano-concave lens (focal length = 88 mm, L4) and the image

Chapter 5 85

Figure 5.1 Schematic diagram of MDR setup for investigation of coupling parameters viaevanescent wave coupling.

is observed via a CCD camera onto a monitor. A flip-mounted mirror allows

the beam path to be changed from the CCD camera to a photodetector which

is connected to an oscilloscope (CRO). This allows the focusing of the incident

beam onto a microcavity with the working distance of the detection objective

and then to switch beam paths to observe the changes in the scattering

intensity with respect to the changes in the wavelength of the incident beam.

The incident light source is tuned over a wavelength range of 776.5 nm ≤ λ

≤ 781.3 nm, with a wavelength scanning speed of 0.2 nm/sec.

Chapter 5 86

5.2.1 Microsphere sample preparation

Two primary microcavities were used in this work; the first are soda lime

microspheres (Duke Scientific)(n = 1.52 @ λ = 589 nm) with a diameter of

90.3 µm ± 2.8 µm (referred to as 90 µm glass in the rest of this thesis). The

second is 90 µm polystyrene microspheres (Polysciences, Inc.)(n = 1.59 @ λ

= 589 nm). The sample of 90 µm glass microspheres is prepared by mixing

the powdered microspheres into 7 ml of Methanol in a plastic measuring

cylinder, the solution is then mixed via a mechanical stirrer for 5 min before

being transfered to a glass vial for storage. The plastic cylinder is required

to prevent damage to the microspheres via impact with the surface of the

container.

The polystyrene microsphere solution is prepared by placing 2 - 3 drops of

the microsphere solution in a certrefuge tube along with 5 ml of Methanol and

mixed using a mechanical stirrer, the solution was then placed in a centrefuge

and run at 10,000 RPM for 2 min. The liquid is then extracted from the tube

leaving the microsphere residue. This process is repeated and the remaining

microspheres are diluted with 10 ml of Methanol before being placed in a

glass vial.

The microspheres are placed in an alcohol based solution to aid in

evaporation when preparing samples for experimentation. The solution was

pipetted onto the surface of the prism and allowed to evaporate. The

microsphere distribution was then observed via an optical microscope to

confirm single microsphere distribution within the translation range of the

objective based detection system before being placed in the prism mount of

the experimental setup (see Fig. 5.1).

Chapter 5 87

90 µm microspheres where used to investigate MDR coupling under our

experimental geometries due to the increased ease of locating and coupling

to diameters greater than those used in the trapping experiments shown in

Section 3.

5.3 Objective based detection system

Light is coupled into the MDR cavity mode of the microspheres via an

evanescent wave, generated by the Kretschmann TIR system. This system

requires the incident light to be at an angle greater than the critical angle

at the prism/microsphere interface. The critical angle can be determined by

calculating Fresnel’s’ reflection and transmission coefficients over a range of

incident angles, this was done for the combinations of refractive indicies that

would occur for our experiment. An example of a the MDR spectrum from

the microcavity under evanescent wave excitation is shown in Fig. 5.2, the

fluctuations in the intensity of the scattering signal reflect the constructive

and destructive coupling of the modes of the microcavity. The polarisation

of the incident light was changed by rotating the 1/2 waveplate by 900

which shifts the orientation from perpendicular to the prism surface (P-

polarisation state) to parallel (S-polarisation state), a corresponding shift

in the wavelength position of the resonance peaks is observed. By rotating

the position of the 1/2 waveplate by a further 900 the original spectral profile

is restored. This indicates the presence of differently polarised modes within

the MDR spectrum, resulting from the changed coupling conditions into the

MDR modes.

In order to compare the changes in the MDR spectrum in response to

changing conditions the measured quantity, visibility (V), which quantifies

Chapter 5 88

Figure 5.2 MDR spectrum from 90 µm glass microspheres in air.

the strength of the MDR spectral features from the scattering background

defined by Eq. 5.1 is introduced,

V =Ipeak − IbackgroundIpeak + Ibackground

. (5.1)

From Eq. 5.1 we can determine that the P-polarisation spectrum has a

visibility of 0.298 and the S-polarisation a value of 0.42. The cavity quality

factor Q, which can be estimated from the elastic-scattering line-width based

on Lorenz-Mie theory [144,145] is defined as

Q =λ

∆λ, (5.2)

where λ is the wavelength at the center of a spectral feature and ∆λ is

the FWHM of the spectral feature and for Fig. 5.2 is approximately 1,096

for S-polarisation and 1,497 for the P-polarisation.

Chapter 5 89

A comparison of two different NA objectives is presented in Fig. 5.3

and 5.4 with an NA of 0.4 and 0.7 respectively. The higher NA objective

demonstrates a significantly higher Q-factor value, 8,725.1 compared to the

lower NA case of 4,017.1. This arises from the higher NA collecting the

scattered light over a greater angle range thus showing a higher detection

efficiency than the lower NA case.

Figure 5.3 MDR spectrum from 90 µm glass microspheres in water collected with a 10x/0.4NA objective lens.

5.4 Fibre based detection system

Due to the fine tuning of the SPR angle required for our proposed microfluidc

sensing device, the effect on the MDR spectrum of changes to the incident

angle is required to be investigated. However this requires that the signal

detection system be allowed to be rotated in relation to the surface of the

prism, which an objective mounted system is unable to do. Thus investigation

into fibre based detection system was performed.

Chapter 5 90

Figure 5.4 MDR spectrum from 90 µm glass microspheres in water collected with a 20x/0.7NA objective lens.

The experimental setup for the fibre based detection system has the same

basic design as in Fig. 5.1 except the previous detection system is replaced

by an optical fibre (core size = 600 µ, without ball lens), mounted onto an

x-y-z stage (M2). When the rotation stage is adjusted the fibre moved with

the prism while maintaining the same focus conditions at the prism surface.

In order to compare the two detection systems the MDR spectrum for

the same experimental parameters was collected for both systems. The

MDR spectrum was collected for both polarisation states using the objective

system, the objective was then removed and the fibre was aligned to collect

the maximum signal intensity perpendicular to the surface of the prism. By

comparing the spectrum in Fig. 5.6 we can see that for each polarisation state

the MDR spectrum is nearly identical with the same mode profile being shown

and only slight changes in the visibility of the signal between the collection

signals. This means that comparisons can be made between signals collected

Chapter 5 91

Figure 5.5 Schematic diagram of MDR setup with fibre based detection system.

with either the fibre or the objective based detection systems.

Figure 5.6 Comparison of signal collection systems for (a) S-polarised and (b) P-polarisedincident light.

The visibility of the MDR signal vs the distance away from the microcav-

ity source was investigated to determine working distance of the sensing setup.

Chapter 5 92

The integration of the sensing system into the microfluidic device requires

the introduction of spacing elements between the detection system and the

microcavity in the form of a chamber roof as well as the change in height of

the channel. A maximised spectrum signal from a 90 µm glass microsphere

was collected via the fibre system, the distance between the surface of the

prism and the fibre was then adjusted and the signal was collected at each

distance. From Fig. 5.7 it can be seen that in the first increment of 3.56 mm

the intensity of the collected signal drops by 71 %, however it can be observed

that the visibility of the MDR spectrum does not significantly decrease until

a distance of 11.14 mm is reach (see Fig. 5.8), which is more than enough

working distance for standard microfluidic devices. A similar trend is shown

in Fig. 5.9 for the Q-factor of the MDR spectra vs detector distance resulting

in the resolution of the spectral features of the MDR profile over a significant

working distance. In figures 5.7 and 5.8 the line connecting the data points

is for visual clarity and to emphasise the general decreasing trend of the data

set.

As the SPR based trapping mechanism in Chapter 3 is highly sensitive

to the angle of incidence on the surface of the prism, the angular response of

the MDR spectrum is required to be determined, the incident angle was the

adjusted by adjusting the rotation stage by single increments. As both the

prism and the fibre detection system are mounted to the rotation stage both

position are change in equal amounts. In order to correct for changes to the

coupling condition of the MDR mode due to shifts in the focal position of the

incident light source, the scattering signal of the microcavity was maximised

at the wavelength λ = 779.2 nm, which corresponds to the position of one of

the peaks in the initial angle of the experimental setup.

Chapter 5 93

Figure 5.7 Change in the MDR spectrum vs distance of detection system.

Figure 5.8 Change in the visibility of MDR spectrum vs distance of detection system.

Chapter 5 94

Figure 5.9 Change in the Q-factor of MDR spectrum vs distance of detection system.

777 778 779 780 7810.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

Inte

nsity

(a.u

.)

Wavelength (nm)

65.6 deg 64.8 deg 64.1 deg 63.3 deg 62.6 deg 61.9 deg

Figure 5.10 Shift in the MDR spectra vs changes in the incident angle.

Chapter 5 95

From Fig. 5.10 is can be seen that as the incident angle is increased away

from the critical angle (θ = 620) there occurs a shift in the the intensity of

the MDR spectra. Primarily this shift is observed to occur in the central

peak, as the angle is further detuned from the critical angle the intensity

of the peak decrease till spectral features no longer appear in the profile.

This is a result of the reduced intensity of the evanescent wave from the TIR

coupling mechanism as well as shifts in the coupling position at the base

of the microsphere. From this data it can be seen that coupling light into

the cavity mode at or just beyond the critical angle generates the highest

visibility and strongest mode separation spectrum.

5.5 MDR in a static fluidic system

Morphology dependent resonance is highly sensitive to various changes in the

local environment of the microcavity, this is generally a result in a change

in one of two parameters. The first is a change in the surface quality of the

microcavity by the binding of an object to the surface of the cavity or via

the damaging of the surface by mechanical collision or chemical or optical

etching of the surface, these changes shift the effective cavity size of the

microsphere and and or remove potential modes. The second is a change in

the local refractive index, this can occur by the introduction of a different

solution or by a local heating/cooling effect changing the local density of the

solution the microcavity resides in, the change of index adjusts the coupling

conditions of the incident light source by adjusting the critical angle of the

light coupling into the microcavity. In order to develop MDR as a sensing

system in a microfluidic environment the cavity response to a large number

of variables must be investigated so that secondary responses to variables

Chapter 5 96

can be illuminated. Towards this aim the investigation of the MDR response

to several variables was investigated, the microcavity was placed in a static

fluidic well.

5.5.1 Experimental setup

The experimental system is the same as shown in Fig. 5.1 with the incident

angle set to θ = 62.60 as this angle was observed to highest visibility due to

coupling into the cavity mode (see Fig. 5.10), the well chamber is produced

by placing a u-shaped section of double-sided adhesive onto the surface of

the prism. Microspheres are then evaporatively dried onto the surface of

the prism as described in Section 5.2.1, the MDR spectrum of a 90 µm glass

microsphere is measured in air before and after the placement of the chamber

roof in order to observe the effect on the addition of a glass cover slip in

between the scattering source and the objective detector. A diagram of the

well chamber is shown if Fig. 5.11.

Figure 5.11 Diagram of the well chamber for MDR investigation in a liquid medium.

Figure 5.12 shows that with the addition of the chamber roof there is a

significant change to the MDR spectrum for both the S and P polarisation

modes of the microcavity, however the addition of an intervening material

Chapter 5 97

is not enough to explain the changes to the position and Q-factor values of

the MDR spectrum as observed. Further investigation revealed the thickness

of our double-sided adhesive is measured to be 90 µm, the same size as our

microspheres, suggesting the change to the MDR spectrum may be a result of

physical damage to the microcavity upon the addition of the chamber roof.

To confirm this idea the thickness of the double-sided adhesive layer was

doubled to 180 µm and the experiment was repeated, with the results being

shown in Fig. 5.13. In this experimental setup there is no change to the MDR

spectrum by the introduction of the cover slip, which confirms the hypothesis

that the original effect was due to the physical damage of the microcavity as

well as showing that there is no negative effects on the detection of the MDR

spectrum via the introduction of a thin glass layer.

Figure 5.12 MDR spectra for a 90 µm glass microsphere in air, before and after the additionof a cover slip to the well with single thickness adhesion layer for (a) S-polarisation and (b)P-polarisation.

Initial attempts were made to introduce liquid solutions via capillary

action into the already sealed well, however the low surface adhesion between

the microspheres and the prism surface meant the surface tension of many

liquids, i.e. water, were of sufficient strength to displace the position of the

Chapter 5 98

Figure 5.13 MDR spectra for a 90 µm glass microsphere in air, before and after the additionof a cover slip to the well with double thickness adhesion layer for (a) S-polarisation and (b)P-polarisation.

microsphere. The introduction of a liquid environment was thus achieved

by placing 4 drops of solution into the prism well before the addition of

the glass cover slip roof. Initial experiments were performed with distilled

water, with Fig. 5.14 showing a typical MDR spectrum for a 90 µm glass

microsphere. The Q-factor for this spectrum is estimated to be 11,124 for

the S-polarisation and 11,137 for the P-polarisation with a visibility of V =

0.8 for both polarisation states. This value is over 7 times the Q-factor

of 1,497 for the glass microsphere in Air with a P-polarisation. This is

counter-intuitive as the Air medium system should have a higher Q-factor

due to the greater difference in the prism-medium refractive index. There

are several potential factors which could result in this discrepancy, these

factors include the difference in the TIR angle between the Air and Water

systems and the difference in the position of the detection source in relation

to the microsphere.

The illumination of secondary shifts to the MDR spectrum will be of

prime concern when attempting to utilise an MDR based sensing system.

For example there exists a potential for the illumination source to induce

Chapter 5 99

Figure 5.14 MDR spectrum for 90 µm glass microsphere in water.

localised heating effects in the vicinity of the microcavity, which would induce

an effective change in the local refractive index observable by a shift in the

MDR spectrum. Figure 5.15 shows the plot of the MDR spectrum over a time

interval of 15 min with the microcavity under constant illumination, the diode

laser was set to maximum current of 80 mA and the shift in the wavelength of

the MDR peak features was recorded and plotted in Fig. 5.16 showing that

over the investigated time-frame the MDR cavity mode maintained strong

stability with a fluctuation of ± 0.03 nm observed.

It has been reported the the absorption of the liquid medium by a PMMA

substrate affects the position of the wavelength spectrum of a Fabry-Perot

cavity [146]. As the Fabry-Perot is effectively a microcavity this presents a

potential problem in the use of polymer or other material based microcavities

for long term sensing applications. In order to investigate this effect the MDR

spectrum was recorded over a period of one hour, in five minute intervals,

with the illumination only incident on the microcavity when measurements

Chapter 5 100

Figure 5.15 MDR spectrum for 90 µm glass microsphere in water under continuousillumination. Insert showing higher magnification of peak 4.

Figure 5.16 Value of the wavelength for the peaks of the MDR spectrum for a 90 µm glassmicrosphere in water under continuous illumination.

Chapter 5 101

of the spectrum were taken. The MDR spectrum for a glass microsphere

are shown in Fig. 5.17 and for a polymer microsphere in Fig. 5.18. The

peaks were defined and the changes in the wavelength position were plotted

for each time measurement (see Fig. 5.19). We observe minor fluctuations

in the wavelength position over a period of one hour, however the long term

stability of the MDR within microcavity is maintained. Similar observations

are made for the polystyrene microsphere (see Fig. 5.20) indicating that for

both materials the afformentioned swelling of the microcavity via absorption

of the surrounding medium is not observable and there is no significant effect

of long term stability for our MDR sensing system.

The MDR optical sensing technique has the potential to measure localised

temperature in several ways; First a change in temperature results in a change

in the fluid density which produces a change in the local refractive index of the

solution. Second energy absorbed by the microsphere from localised heating

results in a swelling of the microsphere. These changes are observable by a

shift in the MDR spectrum, similar to that observed in Figs 5.17 and 5.18.

Chapter 5 102

Figure 5.17 MDR spectra for a 90 µm glass microsphere in a water medium, insert showingmagnified image of peak 1.

Chapter 5 103

Figure 5.18 MDR spectra for a 90 µm polystyrene microsphere in a water medium, insertshowing magnified image of peak 1.

Chapter 5 104

Figure 5.19 Stability of the MDR spectrum for a 90 µm glass microsphere where (a) showsthe identification of the peak positions at t = 0 and (b) plots the shift in wavelength of thepeak position from time t = 0 to t = 60 min.

Chapter 5 105

Figure 5.20 Stability of the MDR spectrum for a 90 µm polystyrene microsphere where (a)shows the identification of the peak positions at t = 0 and (b) plots the shift in wavelength ofthe peak position from time t = 0 to t = 60 min.

Chapter 5 106

5.6 MDR sensing

The advantage of MDR as a sensing technique is its high Q-factor providing

highly sensitive response to a variety of local environmental variables. In

the previous sections of this Chapter we’ve investigated the effect of the

experimental parameters of our system that has a potential influence on the

MDR spectrum. In order to observe the response in the MDR spectrum for

changes in the refractive index of the surrounding solution the design of the

static microfluidic chamber had to be modified. A section of the double-

sided adhesive layer (thickness = 180 µm) was removed from the base of the

well, see Fig. 5.21. This output port allowed for the slow diffusion of the

solution from inside the well, by replacing the solution with a liquid of a

different refractive index the solution surrounding the microsphere could be

exchanged without risk of disrupting the position of the microsphere with

respect to the incident coupling conditions.

Figure 5.21 Schematic of modified static well environment.

Initial experiments were performed by measuring the MDR spectrum of

a 90 µm glass microsphere surrounded by distilled water (nW = 1.33 at λ

Chapter 5 107

= 589 nm) and slowly replacing the solution with ethanol (nE = 1.36 at

λ = 589 nm). The MDR spectrum was measured after the introduction of

every amount of ethanol and was recorded when no further shifts in the MDR

spectrum were observed indicating the surrounding medium had completely

transitioned from water to ethanol. The change in the MDR spectrum in

response to the change in the refractive index of the surrounding solution is

shown in Fig. 5.22, with an wavelength red shift of 0.07 ± 0.03 nm observed.

Figure 5.22 Comparison of MDR spectrum between ethanol and water surrounding mediumfor a single 90 µm glass microsphere.

In order to determine the resolution of the MDR sensing system a series

of liquids with a known refractive index needed to be tested. From Table

5.1 we can generate a glycerin-water solution with a refractive index ranging

from 1.33 to 1.474. Four solutions were prepared using this table, the first

had a glycerin concentration of 7 % (n = 1.341), the second had a glycerin

concentration of 15 % (n = 1.351), the third was 31.85 (n = 1.376) and the

fourth was water (n = 1.333).

The observations of the MDR spectrum were performed for a single 90

µm glass microsphere for each of the refractive index solutions. As with the

water to ethanol experiment, each solution is introduced in single drops and

Chapter 5 108

Table 5.1 Refractive index of Glycerin-water solutions at 200.

Water % by Weight Glycerin % by Weight Refractive Index nD

68.15 31.85 1.3733885 15 1.3510693 7 1.34118100 0 1.333

the MDR spectrum is observed on the CRO, this is repeated until no further

additions of solution result in an observable shift in the wavelength position

of the MDR spectrum which is then recorded. The MDR spectrum for each

solution is presented in Fig. 5.23. The corresponding shifts in the peak

position of the MDR spectrum is recorded and plotted in Fig. 5.24. The

trend-lines are a linear extrapolation both forward and backward to cover

the entire refractive index range that is reasonable for our setup.

Figure 5.23 MDR spectrum response to changes in local refractive index via change insurrounding medium for a single 90 µm glass microsphere.

The shifts in the MDR peaks correspond to a sensor sensitivity of 9.66 x

10−2 R.I.U, where the sensitivity of the sensor is defined as ∆n∆λ

which defines

the minimum detectable refractive index variation in this system as a function

of the shift in the MDR spectra.

Chapter 5 109

Figure 5.24 Plot showing position of the wavelength peaks from Fig. 5.23 vs refractiveindex.

5.7 Summary

In this Chapter the effect of the MDR spectrum on various experimental

parameters as well as its effectiveness as a localised environmental sensor has

been presented. Evanescent wave coupling under TIR conditions has been

used to couple light into the cavity mode of 90 µm soda lime and polystyrene

microspheres. The Q-factor has been measured for a glass microsphere to be

1,497 in air and 11,137 in water for a P-polarised incident light source.

By utilising a fibre based detection system it has been shown that the

intensity of the scattered light decreases by as much as 95 % by increasing

the seperation of the detector from the scattering source, the visiblity of the

MDR spectrum only significantly decrease after a distance of 11.14 mm. The

visibility of the MDR spectral features is also shown to decrease as the angle

of incidence of the coupling source is increased away from the critical angle.

A visiblity decrease of v = 0.087 is shown for an angle change of 1.5 deg.

Chapter 5 110

The investigation of the introduction of a fluidic well chamber revealed

the importance of design when utilising microcavity sensors with the physical

interaction of the chamber roof resulting in the complete loss of the high

quality MDR spectrum. The stability of our MDR microcavity was observed

for both illumination time and the effect of absorption of the microcavity of

the surrounding medium. It was found that under all investigated parameters

the microcavity maintained a high degree of stability, i.e. ∆λ = ± 0.04 over

t = 1 hour for glass microsphere in water.

The use of MDR in spherical microcavities as a sensing platform was

investigated, first by the observing the change in the MDR spectrum as

the surrounding medium was transitioned from water to ethanol. While

maintaining the same mode profile a shift towards the infrared of 0.07 ±

0.03 nm was observed. Specific concentrations of Glycerin-Water solutions

were used to create a range of known refractive index solutions. The MDR

response due to the introduction of each of these solutions was observed, with

a sensor sensitivity of 9.66 x 10−2 R.I.U and the trend line of wavelength vs

refractive index was calculated.

In summary we have demonstrated the stability of Morphology Dependent

Resonance based sensing system within the experimental parameters likely

to be encountered when integrated within a microfluidic device. We have also

shown that MDR asks as a highly sensitive local environmental sensor that

can be used to determine changes in the refractive index of its surrounding

medium to an accuracy of three decimal places within the error range of our

experiment.

Chapter 6

Sensing in a microfluidic device

6.1 Introduction

The integration of a SPR based optical manipulation technique and a MDR

sensing technique has strong potential as a non-invasive, non-destructive,

all optical based sensing system. This technique show particular promise

in extending the sensing regime away from the surface of the device by the

use of micrometer sized spheres which under MDR coupling act as sensing

elements for all regions within the near-field of the sphere. The use of a SPR

technique allows for the trapping of the microsphere within an arbitrarily

defined position within the microsphere provided illumination of the area is

achievable at angles greater than the critical angle, which would allow for the

technique to be performed within nearly any arbitrary designed microfluidic

device which presents a significant increase in freedom of design over other

integrated MDR sensing systems.

111

Chapter 6 112

In this chapter the investigation of the changes to the MDR sensing tech-

nique via integration into a dynamic microfluidic system is performed along

with characterisation of the detection system under the new experimental

setup.


The optical beam path shown in Section 5.2 is integrated into the SPR

experimental setup (see Section 3.2) in order to investigate the coupling to

the MDR mode of a SPR trapped microsphere . A schematic diagram of

the combined setup is presented in Fig. 6.1, there was no adjustments made

to the optical beam path of the SPR experimental setup (i.e all components

before the prism interface remained the same. The components of the MDR

setup were then incorporated into the SPR experimental system.

The illumination light beam from a Velocity tunable diode-laser system

(New Focus, 765-781 nm) is expanded to a parallel beam by the lenses L1

(microscope objective (Melles Griot) with NA = 0.25) and L2 (Plano-convex,

focal length = 175 mm). The beam width is controlled by a variable aperture

(VA) and the beam polarisation is set using a 1

2waveplate (WP). Two gold

mirrors are used in a telescopic mirror configuration to adjust the height of

the beam path to 20 cm, this allows the introduction of the beam path for the

MDR system to the same plane as the SPR setup. A third lens L3 (Plano-

convex, focal length = 400 mm) focuses the beam onto the back surface of a

35 mm equilateral glass prism (BK7, n = 1.51) under total internal reflection

conditions, with an incident power of 21.5 mW. The focal spot is further

confined by an objective lens (O1)(NA = 0.26) in the beam path between the

prism and L3, the objective is mounted to an X-Y-Z stage which is mounted

to a vertical plate.

Chapter 6 113

Figure 6.1 Experimental setup showing the integrated SPR and MDR optical paths.

Experiments were performed on a Kretschmann prism-coupling geometry

[84,135] (see Fig.3.2). The illumination light beam from a 1064 nm Nd:YAG

laser beam is expanded to a parallel beam by the lenses L4 (microscope

objective, NA = 0.25 (Newport)) and L5 (Plano-convex, focal length = 200

mm). The beam width is controlled by a variable aperture (VA) and the

beam polarisation is set for P-polarised incident light at the prism interface

using a 1

2waveplate (WP). A third lens L6 (Plano-convex, focal length =

400 mm) focuses the beam onto the back surface of a 35 mm equilateral

glass prism (BK7, n = 1.51). The sample chamber, fabricated as via Section

3.2.1.2, was placed on top of the prism via index matching liquid (n = 1.516).

The interactions of the microspheres with the illuminated region are

observed via an UPlanFl 10x/0.3 microscope objective, (O2) , a CCD camera

Chapter 6 114

and illumination from a white light source. A flip-mounted mirror is aligned

into the detection beam bath between O2 and the CCD camera, the mirror

shifts the beam path to a photodetector to allow detection of changes to the

intensity of the scattered light. The entire detection system is enclosed in a

light box to block stray light from being detected.

There exists the potential for interference in the coupling of light into the

MDR cavity mode under these experimental conditions due to the shift in

the microspheres position via SPR induced wave vector forces. As such the

determination of the SPR angle for λ = 779 nm (the central wavelength of

the scanning range of the variable diode laser) was performed for the range of

experimental conditions. Figures 6.2 and 6.3 show the theoretical calculations

of the SPR profile under the range of experimental conditions for our system

with the SPR angle for each prism-solution conditions summarised in Table

6.1. For our device with a 40 nm thick gold coating these angles are within

the maximum angles achievable by our system. At the prism/Au interface

the light from the MDR system is arbitrarily selected to incident at an angle

of 54.70, this angle was selected as it is far enough away from the SPR angle

of any of the experimental conditions to allow coupling to the MDR cavity

mode but prevent interference effects arising with respect to the manipulation

of the microspheres within the microfluidic device.

A summation of the lowest reflection Au coating thickness is presented

an Table 6.1, which shows the optimum coating thickness to be 50 nm for all

combinations of prism/medium refractive indecies.

Chapter 6 115

Figure 6.2 SPR plots for nprism = 1.785, λ = 779 nm with refractive index of the mediumbeing (a) n = 1.00 and (b) n = 1.33. Effect of thickness of gold layer on minimum reflectanceshown vs c) value of reflectance and d) angular position.

Chapter 6 116

Figure 6.3 SPR plots for nprism = 1.51, λ = 779 nm with refractive index of the mediumbeing (a) n = 1.00 and (b) n = 1.33. Effect of thickness of gold layer on minimum reflectanceshown vs c) value of reflectance and d) angular position.

Chapter 6 117

Table 6.1 Optimum Au thickness coating for SPR under experimental parameters for λ =779 nm.

nprism λ nm θr (deg) dθr (nm)

1.785 779 1.00 35 501.785 779 1.33 51 501.51 779 1.00 42.8 501.51 779 1.33 66.7 50

6.3 Distance based MDR detection

Prior to the integration of the experimental setups the detection of the

MDR scattering signal was performed using a Fluor 40x/0.85 objective.

When moving to the microfluidic system, the distance created by the PDMS

section of the device from the surface of the channel resulted in a change

of detection system being required. This detection resolution of the new

objective UPlanFl 10x/0.3 was required to be investigated under the range

of experimental conditions in order to understand the maximum resolution

of the system.

Initial experimental setup investigated was using 90 µm glass micro-

spheres dried onto the surface of a glass slide. The glass slide is placed

onto the surface of a BK7 (n=1.51) prism via index matching liquid (n =

1.52). The position of the glass slide is then positioned with the visual range

of the detector objective (UPlanFl 10x/0.3) via manual adjustment of the

position of the glass slide. Light is then coupled into the MDR cavity mode

with the strength of the scattered signal, as detected via the photodetector,

maximised for the wavelength λ = 776.5 nm. When the scattered signal is

maximised the wavelength is varied between 776.5 and 781.3 nm in 0.2 nm

increments and the intensity of the scattered light is recorded via on a CRO.

Chapter 6 118

Figure 6.4 shows the MDR spectrum from a 90 µm glass microsphere

under the above coupling conditions in an air medium. Analysis shows the

spectra has a Q = 1,148.8 and a v = 0.03, compared to the results shown in

Fig. 5.2 a significant loss of visibility in the MDR signal is observed. From

Fig. 5.8 we know that there is significant loss of visibility with increases

in distance from the signal source, also the potential for collection of stray

light is greater the larger the collection angle of the detection element, hence

the observable increase in the noise of the spectra. The noise is a result of

low signal-to-noise (SNR) meaning that the scattered signal is very small

compared to the optical and electrical noise of the detection system, which

is seen as the high-frequency fluctuations in the data.

Figure 6.4 MDR spectra for 90 µm glass microsphere for a prism/glass slide/air interface.

Distilled water is pipetted onto the surface of the slide and the MDR

spectrum is recorded, Fig. 6.5, demonstrating a Q = 1,187.9 and a v =

0.11. A shift in the wavelength of the resonance peaks is observed which is

consistent with the previous experimental results. A significant decrease in

the background noise of the system is observed most likely due to improved

coupling from the evanescent wave to the cavity mode. A reduction in

Chapter 6 119

the intensity of the scattered light is observed due to the introduction of

a secondary medium in the form of the water solution providing a damping

agent.

Figure 6.5 MDR spectra for 90 µm glass microsphere for a prism/glass slide/water interface.

The detection characterisation was then repeated using a metal coated

glass substrate. The metal coating was a 5 nm Cr and a 40 nm Au system,

coated as per Section 3.2. 90 µm glass microsphere were evaporatively dried

to the surface of the metal layer and the slide was placed onto the prism

via index matching liquid. The MDR spectra for light coupled through the

three interface system (effects from the Cr layer are ignored due to it being

optically thin) are shown for an external refractive index of n = 1.00 (air),

Fig. 6.6 (Q = 1,290.29 and v = 0.05) and n = 1.33 (water), Fig. 6.7 (Q

= 1,170.54 and v = 0.046). Both figures show a low visibility, low Q-factor

MDR spectra with a very low scattering intensity. However a shift in the

wavelength of the peak positions are clearly observed between the two plots,

showing the potential for this system to act as a refractive index sensor is

still valid.

The low Q-factor and visibility of the peaks of the MDR spectra in the

Chapter 6 120

Figure 6.6 MDR spectra for 90 µm glass microsphere for a prism/glass slide/Au/air interface.

Figure 6.7 MDR spectra for 90 µm glass microsphere for a prism/glass slide/Au/waterinterface.

combined experimental setups arises due to the un-optimised alignment of the

coupling of the MDR system. Particularly the optimisation of the incident

angle by taking into account the phase matching conditions of the TIR and

MDR, by aligning the MDR coupling angle to the SPR angle of the diode

laser to maximise coupling to the MDR cavity mode, by optimising the metal

Chapter 6 121

surface coating thickness and patterning design to maximise coupling to the

SPR generated evanescent wave are all options that would greatly improve

the sensing resolution of the system.

6.4 MDR detection in an SPR trapped microsphere

The 90 µm glass microsphere are pumped through the microfluidic device at

a flow rate of 22 µm/sec in a solution of distilled water. The intensity of

the SPR trapping beam is set to 70 mW and illuminates a 200 x 200 µm

array of 4 µm holes. The microspheres are observed to be trapped against

the flow via the SPR optical trap (see Fig. 6.9). The scattered light is then

blocked from observation by placing a narrow band-pass filter (1 µm) within

the detection path of the experimental system. The focal spot of the MDR

illumination source is then introduced to the interaction region and coupled

into the trapped microcavity.

Figure 6.8 MDR spectra for 90 µm glass microsphere held via SPR optical trap in amicrofluidic device.

The scattering signal is then maximised and the MDR spectra is recorded

Chapter 6 122

(see Fig. 6.8), with a Q = 1,456.35 and v = 0.071 the Q-factor of the system

is still lower than the static MDR system and the visibility of the system

is very low for this type of microcavity. After detection the beam from the

SPR trap is blocked and the microsphere is observed to be removed from the

interaction region via the flow velocity of the chamber solution.

Figure 6.9 Sequence of images showing (a) 200 x 200 µm patterned array in a microfluidicdevice, (b) introduction of SPR trapping beam, (c) trapping region under white lightillumination, (d) trapping of a 90 µm glass microsphere via SPR trapping, (e) Light fromSPR trapping beam blocked by band-pass filter and (f) introduction of diode laser focal spotto interaction region.

The introduction of the SPR trapping beam provides a potential source

of interference in the MDR spectrum collected via the detector. In order to

observe this effect the MDR signal from a microsphere was collected from a 90

µm glass microsphere, while the system is illuminated under a range of SPR

beam intensities (see Fig. 6.10) with no filter to block the background signal

Chapter 6 123

Figure 6.10 MDR spectra for 90 µm glass microsphere illuminated via the SPR trappingbeam under a range of incident powers.

of the SPR beam. It can be seen that while the intensity of the scattered

signal increases as a result of the increase in the background signal, it does

not effect the spectral profile of the MDR signal, however it can be seen that

at the 60 mW the SPR beam does increase the noise in the MDR signal.

Another potential source of error in the detected signal is the adjustment

of the position of the microsphere via the SPR beam. Figure 6.11 shows

the MDR spectrum for a 90 µm glass microsphere that has aggregated to

the surface of the microfluidic device before and after exposure to 30 and

60 mW SPR trapping beams. The wavelength of the MDR features are not

observed to shift indicating the coupling conditions are preserved even after

the exposure of the trapping beam

A 90 µm glass microsphere is trapped via the SPR trapping beam

with incident intensity of 60 mW against a flow rate of 22 µm/sec. The

surrounding medium was transitioned from water (n = 1.33) to a 29.56 %

glycerin-water solution with refractive index of 1.37. The MDR spectrum was

measured every 15 min and was recorded when no further shifts in the MDR

spectrum were observed. The change in the MDR spectrum in response to

Chapter 6 124

Figure 6.11 MDR spectra for 90 µm glass microsphere illuminated via the SPR trappingbeam under a range of incident powers.

the change in the refractive index of the surrounding solution is shown in Fig.

6.12.

Figure 6.12 MDR spectra for 90 µm glass microsphere held via 60 mW SPR trapping beamunder flow of 20 µm/sec for a surrounding medium of refractive index 1.33 and 1.37.

The shift in the peak position of the MDR spectrum is recorded and

plotted in Fig. 6.13, with an wavelength shift of 0.516 ± 0.032 nm observed.

The trend lines are shown in Fig. 6.13 to visually connect the points for the

reader, a straight trend line was selected based on the trend set in Figure

Chapter 6 125

5.24. The Q-factor of the spectrum was determined to be 2,924 and 4,424.6

for the refractive indicies 1.33 and 1.37. The visibility of the spectra was

observed to be 0.267 for the 1.33 refractive index and 0.16 for the 1.37 case.

Figure 6.13 Plot showing shift in the position of the wavelength of defined spectral featuresfrom Fig. 6.12 vs refractive index.

The resolution of the system was calculated to be 7.75 x 10−2 R.I.U, this

resolution is comparable to the resolution observed in the static fluidic system

with a value of 9.66 x 10−2 R.I.U.

6.5 Summary

In this chapter the trapping of a 90 µm glass microsphere under a 22

µm/sec flow rate via patterned surface plasmon resonance trapping has been

observed. Coupling of light into the MDR mode of the trapped microsphere

was observed under evanescent wave coupling conditions. A Q factor of 2,924

and a visibility of 0.267 was observed for this MDR mode. While smaller than

the values observed in the static MDR coupling demonstrated in Chapter 4

these values are typical for the additional detection path length and low NA

Chapter 6 126

objective of the current experimental system. Once released from the optical

trap the microsphere was removed from the detection region demonstrating

the feasibility of this design to add and remove sensing elements into specific

locations of a dynamic microfluidic device, with optical power intensities low

enough to prevent damage to biological reagents. The MDR response due to

the change in refractive index of the medium solution was observed with a

sensor sensitivity of 7.75 x 10−2 R.I.U which is of comparable resolution of

the static condition.

Chapter 7

Conclusion

7.1 Thesis conclusions

Integration of optical sensing techniques into mircofluidic devices shows

enormous promise in the development in cheap and effective biological

detection systems. However, most optofluidic sensing systems require the

transportation of the analyte, molecules or cells under investigation to the

detection region of the microfluidic device. This is untenable for several

systems and as such a technique which allows for the addition and removal of

the optical sensing elements to a specific location within a microfluidic device

is extremely appealing to several fields on science.

In the research presented in this thesis we provide evidence for the

potential for a Morphology Dependent Resonance based sensing system,

performed on glass microspheres which are trapped in an arbitrary location

within a microfluidic device. The microspheres are trapped via the evanescent

wave trapping of Surface Plasmon Resonance waves generated under TIR.

127

Chapter 7 128

In Chapter 3 the potential of a SPR based optical trap is investigated

inside a microfluidic device fabrication by direct laser cutting and hot

embossing in a PMMA polymer substrate. The surface plasmon technique

was selected for its ease in design, its ability to trap over a large (hundreds

of microns) area and for its compatibility with MDR coupling systems.

The particle trapping efficiency (PTE) of 4.33, 10, and 15 µm polystyrene

microspheres is characterised for both patterned and unpatterned gold

surfaces at both on and off resonance incident angles. On resonance a 40

% increase in the PTE of both 4.33 µm (0 → 40 %) and 15 µm (50 → 90

%) at 40 and 60 mW respectively via the patterning of the metal surface,

50 to 60 % increases in the PTE of 10 µm microspheres are observed for

lower intensity incident light (20 and 40 mW). Off resonace shows no PTE

for almost all incident intensities and microspheres offering the potential to

act as an on/off switch for a continuous illumination source. The patterning

of the metal surface was demonstrated to act as a method of localisation of

the optical trap, with the enhancement to the PTE being observed for only

particles trapped within the 100 x 100 µm patterned region of the detection

area, reducing the trapping volume via a factor of 4. As the location of

the patterning of the metal surface or the location of the incident focal

spot is arbitrary, SPR trapping is demonstrated to be an excellent trapping

technique for trapping of a particle anywhere within a microfluidic device.

A theoretical investigation is undertaken in Chapter 4 to develop a

more in depth understanding of the effect on the patterning of the metal

surface has on the electric field under the experimental conditions observed

in Chapter 3. For the 4 µm aperture diameter experimentally investigated

there is an small enhancement in the electric field observed resulting from

the structural confinement of the incident light at the edge of the aperture.

Chapter 7 129

This enhancement is greater for an light source incident at angles on the

resonance angle of the structure than off as the coupled surface plasmon

wave generates a higher transmission of the incident light at the interface

prior to structural confinement. Stronger field enhancements are observed

as the diameter of the aperture is decrease to less than the wavelength of

the incident light, arising from the plasmonic coupling between the confined

electric field. This is observed to be greater for a wave incident perpendicular

to the surface interface as the initial symmetry in the field confinement give

rise to a greater coupling. As angled incidence produces an asymmetry in the

electric field at the aperture edges the strength of the coupling is significantly

reduced, particularly observable for the λ/5 aperture diameter where there

is a ten to thousand factor difference between the perpendicular and angled

coupling field strengths.

Optimisation of the coupling of light into the morphology dependent

resonance modes of microspheres in a microfluidic device is presented in

Chapter 5. The strength of the scattered signal was observed for distance

increases between the detector and the microsphere and it was observed that

over a range of 11 mm a loss of 90 % of the scattering intensity occured

however the visibilty of the spectral features of the microsphere remained

stable, with a decrease of only 0.04. It was similarily observed that a shift

in the angle of the incident light at the prism/solution interface resulted

in a strong loss in spectral features for shifts away the critical angle of

the interface. A 30 % loss of scattered light intensity was shown for a

shift in angle of 30. It was shown that both polystyrene and soda-lime

based microspheres posses stable MDR mode profiles over long term use

as a maximum wavelength shift of 0.04 nm was observed for microspheres

resting in both water and ethanol solutions for a period of one hour. The

Chapter 7 130

investigation of the stability of the MDR modes of a glass microspheres under

continuous illumination was undertaken, no temperature induced wavelength

shift were observed with the microsphere. A very high Q-factor of 11,124 was

observed in a 90 µm glass microsphere in water solution and the resolution

of such a system was determined to be 9.66 x 10−2 RIU.

The integration of a SPR trap with an MDR sensing technique for

arbitrary localised sensing system is presented in Chapter 6. A single 90

µm glass microsphere is observed to be trapped within one of several 200

x 200 µm patterned regions in a microfluidic device. The MDR mode from

the microsphere is then collected with an observed Q value of 2,924 with a

visibility of 0.267. Environment sensing is observed in a microsphere held

against a 20 µm/sec flow rate via SPR trapping, a refractive index shift

of 0.04 is observed in the MDR spectra with a resolution of 7.75 x 10−2

R.I.U. To our knowledge this is the first MDR sensing performed under such

coupling and trapping conditions. When the SPR trap was turned off the

microsphere was observed to be removed via flow forces from the detection

region of the system. This demonstrates the potential of this technique to

position a sensing element within an arbitrary location within a microfluidic

device, perform high resolution sensing experiments, and then be able to

remove the sensing elements to prevent interference in the experiment under

investigation.

7.2 Future Work

The integration of optical sensing and manipulation techniques into microflu-

idic systems has enormous potential for future point-of-care devices, as well

as greatly improving a large variety of biological and chemical processes

Chapter 7 131

and experiments. For some of these experiments the transportation of the

sensing element to the sample is required in order to perform or maximise

the potential of these techniques. The demonstration of one such technique

is presented in this thesis.

It is anticipated that the next step in point-of-care research would focus

on the following areas.

1) Targeted biological sensing

The use of ligands and receptors as a methodology of observed the

presence of specific molecules and DNA stands is a common technique from

biology. The integration of these techniques into microfluidic systems is

gaining increasing popularity due to the ability of microfluidics to control

the analyte concentration is specific regions of the device. Thus the next

step could be the coating of optical microcavities with biological strands

and ligands to increase the cavities functionality. These microcavities

would ideally be functionalised external to the system and introduced

secondarily to its construction to allow for multiple targets to be investigated

without fabrication of multiple systems to reduce cost, time, and risk of

contamination.

2) Increased device functionality

The potential for the integration of multiple functions into a single mi-

crofluidic device is one of the greatest appeals of such systems. Introduction

of pumps, valves, mixing and splitting functions into a device greatly increases

the development towards a single function system.

Particularly the reduction in channel dimensions and the addition of

parallel flows would allow for the simultaneous excitation and sensing of

Chapter 7 132

multiple events. This would greatly reduce the time per experiment as well

as increase the versatility of the system.

3) Miniaturisation

While the forces at play in the microfluidic devices in this thesis follow the

Rabi dynamics for microfluidic systems, the dimensions of the system are yet

to achieve full microscale in all its components. This would have significant

impact on the control of the forces as well as the ease of integration of optical

techniques. Advancement in the pre- and post-processing sections of the

hot embossing technique are foreseen to produce high quality, repeatable

microfluidic devices with full microscale dimensions.

4) Optimisation

The low Q-factor and visibility of the peaks of the MDR spectra in the

combined experimental setups arises due to the un-optimised alignment of

the coupling of the MDR system. This system would be greatly improved

by the optimisation of visibility and Q-factor of the system which could be

achieved in several ways such as by taking into account the phase matching

conditions of the TIR and MDR, by aligning the MDR coupling angle to

the SPR angle of the diode laser to maximise coupling to the MDR cavity

mode, by optimising the metal surface coating thickness and patterning

design to maximise coupling to the SPR generated evanescent wave and by

optimising the detection of the MDR signal by increasing the signal collection,

optimising the alignment of the collection element to the detection source,

and by reducing the separation between the microsphere and the collection

element via engineering of the microfluidic device are all options that would

greatly improve the sensing resolution of the system.

Chapter 7 133

With the increasing availability of high resolution fabrication and de-

position techniques the integration of nanoscale metal surface structures

or defects would allow for the investigation of unique optical forces with

potential in nanoparticle trapping, surface plasmon sensing techniques and

potentially unique coupling effects into surface and cavity modes.

Bibliography

[1] Y. H. Cho, J. Park, H. Park, X. Cheng, B. J. Kim, and A. Han.

Fabrication of high-aspect-ratio polymer nanochannels using a novel

si nanoimprint mold and solvent-assisted sealing. Microfluidics and

Nanofluidics, 9(2-3):163–170, 2010.

[2] D. Erickson, S. Mandal, A. H. J. Yang, and B. Cordovez.

Nanobiosensors: Optofluidic, electrical and mechanical approaches

to biomolecular detection at the nanoscale. Microfluidics and

Nanofluidics, 4(1-2):33–52, 2008.

[3] T. M. Squires and S. R. Quake. Microfluidics: Fluid physics at the

nanoliter scale. Reviews of modern physics, 77(3):977–1026, 2005.

[4] S. C. Terry, J. H. Jerman, and J. B. Angell. A gas chromatographic air

analyzer fabricated on a silicon wafer. IEEE Transactions on Electron

Devices, 26(12):1880–1886, 1979.

[5] E. Bassous, H. H. Taub, and L. Kuhn. Ink jet printing nozzle arrays

etched in silicon. Applied Physics Letters, 31(2):135–137, 1977.

[6] P. Gravesen, J. Branebjerg, and O. Jensen. Microfluidics - a review.

Journal of Micromechanics and Microengineering, 3(4):168–182, 1993.

134

Bibliography 135

[7] M. Krishnan, J. Park, and D. Erickson. Optothermorheological flow

manipulation. Optics Letters, 34(13):1976–1978, 2009.

[8] D. Brennan, J. Justice, B. Corbett, T. McCarthy, and P. Galvin.

Emerging optofluidic technologies for point-of-care genetic analysis

systems: A review. Analytical and Bioanalytical Chemistry, 395(3):621–

636, 2009.

[9] D. Brennan, P. Lambkin, E. J. Moore, and P. Galvin. An integrated

optofluidic platform for dna hybridization and detection. IEEE Sensors

Journal, 8(5):536–542, 2008.

[10] G. T. Roman and R. T. Kennedy. Fully integrated microfluidic separa-

tions systems for biochemical analysis. Journal of Chromatography A,

1168(1-2):170–188, 2007.

[11] C. Yi, C. W. Li, S. Ji, and M. Yang. Microfluidics technology for

manipulation and analysis of biological cells. Analytica Chimica Acta,

560(1-2):1–23, 2006.

[12] A. J. Engler, S. Sen, H. L. Sweeney, and D. E. Discher. Matrix elasticity

directs stem cell lineage specification. Cell, 126(4):677–689, 2006.

[13] C. Rivet, H. Lee, A. Hirsch, S. Hamilton, and H. Lu. Microfluidics

for medical diagnostics and biosensors. Chemical Engineering Science,

66(7):1490–1507, 2011.

[14] G. M. Whitesides. The origins and the future of microfluidics. Nature,

442(7101):368–373, 2006.

[15] M. P. C. Marques and P. Fernandes. Microfluidic devices: Useful tools

for bioprocess intensification. Molecules, 16(10):8368–8401, 2011.

Bibliography 136

[16] H. A. Stone, A. D. Stroock, and A. Ajdari. Engineering flows in small

devices: Microfluidics toward a lab-on-a-chip. 36:381–411, 2004.

[17] G.E. Karniadakis and A. Beskok. Micro flows : fundamentals and

simulation. Springer, New York, 2002.

[18] K. Jain, C. Wu, S. V. Atre, G. Jovanovic, V. Narayanan, S. Kimura,

V. Sprenkle, N. Canfield, and S. Roy. Synthesis of nanoparticles in high

temperature ceramic microreactors: Design, fabrication and testing.

International Journal of Applied Ceramic Technology, 6(3):410–419,

2009.

[19] R. Knitter and M. A. Liauw. Ceramic microreactors for heterogeneously

catalysed gas-phase reactions. Lab on a Chip - Miniaturisation for

Chemistry and Biology, 4(4):378–383, 2004.

[20] J. P. McMullen, M. T. Stone, S. L. Buchwald, and K. F. Jensen.

An integrated microreactor system for self-optimization of a heck

reaction: From micro-to mesoscale flow systems. Angewandte Chemie

- International Edition, 49(39):7076–7080, 2010.

[21] M. Miyazaki, T. Honda, H. Yamaguchi, M. P. P. Briones, and

H. Maeda. Enzymatic processing in microfluidic reactors. Biotechnology

and Genetic Engineering Reviews, 25:405–428, 2008.

[22] J. C. McDonald, D. C. Duffy, J. R. Anderson, D. T. Chiu, H. Wu,

O. J. A. Schueller, and G. M. Whitesides. Fabrication of microfluidic

systems in poly(dimethylsiloxane). Electrophoresis, 21(1):27–40, 2000.

[23] G. Sharma, S. Svensson, S. Ogden, L. Klintberg, and K. Hjort.

High-pressure stainless steel active membrane microvalves. Journal of

Micromechanics and Microengineering, 21(7), 2011.

Bibliography 137

[24] L. Martnez-Latorre, P. Ruiz-Cebollada, A. Monzn, and E. Garca-

Bordej. Preparation of stainless steel microreactors coated with carbon

nanofiber layer: Impact of hydrocarbon and temperature. Catalysis

Today, 147(SUPPL.):S87–S93, 2009.

[25] K. Ren, W. Dai, J. Zhou, J. Su, and H. Wu. Whole-teflon microfluidic

chips. Proceedings of the National Academy of Sciences of the United

States of America, 108(20):8162–8166, 2011.

[26] Y. Sun and Y. C. Kwok. Polymeric microfluidic system for dna analysis.

Analytica Chimica Acta, 556(1):80–96, 2006.

[27] M. Rasponi, F. Piraino, N. Sadr, M. Lagan, A. Redaelli, and

M. Moretti. Reliable magnetic reversible assembly of complex

microfluidic devices: Fabrication, characterization, and biological

validation. Microfluidics and Nanofluidics, 10(5):1097–1107, 2011.

[28] P. E. Neerincx, R. P. J. Denteneer, and H. E. H. Meijer. A fully

polymeric mouldable microfluidic device. part 1: The process of design.

Macromolecular Materials and Engineering, 296(12):1081–1090, 2011.

[29] J. Dostlek, J. Homola, and M. Miler. Rich information format surface

plasmon resonance biosensor based on array of diffraction gratings.

Sensors and Actuators, B: Chemical, 107(1 SPEC. ISS.):154–161, 2005.

[30] H. Cao, J. O. Tegenfeldt, R. H. Austin, and S. Y. Chou. Gradient

nanostructures for interfacing microfluidics and nanofluidics. Applied

Physics Letters, 81(16):3058–3060, 2002.

[31] D. Amarie, N. D. Rawlinson, W. L. Schaich, B. Dragnea, and S. C.

Jacobson. Three-dimensional mapping of the light intensity transmitted

through nanoapertures. Nano Letters, 5(7):1227–1230, 2005.

Bibliography 138

[32] T. Mappes, S. Achenbach, and J. Mohr. X-ray lithography for devices

with high aspect ratio polymer submicron structures. Microelectronic

Engineering, 84(5-8):1235–1239, 2007.

[33] Q. Fang, D. P. Kim, X. Li, T. H. Yoon, and Y. Li. Facile fabrication of

a rigid and chemically resistant micromixer system from photocurable

inorganic polymer by static liquid photolithography (slp). Lab on a

Chip - Miniaturisation for Chemistry and Biology, 11(16):2779–2784,

2011.

[34] K. Kitazoe, J. Wang, N. Kaji, Y. Okamoto, M. Tokeshi, K. Kogure,

H. Harashima, and Y. Baba. A touch-and-go lipid wrapping technique

in microfluidic channels for rapid fabrication of multifunctional

envelope-type gene delivery nanodevices. Lab on a Chip -

Miniaturisation for Chemistry and Biology, 11(19):3256–3262, 2011.

[35] Mark M. Crain Thomas J. Roussel Jr. Douglas J. Jackson Richard

P. Baldwin Robert S. Keynton Rekha S. Pai, Kevin M. Walsh and

John F. Naber. Fully integrated three-dimensional electrodes for

electrochemical detection in microchips: Fabrication, characterization,

and applicationsr. Analytical Cemistry, 81(12):4762–4769, 2009.

[36] C. F. Mandenius. Electronic noses for bioreactor monitoring. Advances

in biochemical engineering/biotechnology, 66:65–82, 2000.

[37] M. Navrtil, A. Norberg, L. Lembrn, and C. F. Mandenius. On-line

multi-analyzer monitoring of biomass, glucose and acetate for growth

rate control of a vibrio cholerae fed-batch cultivation. Journal of

Biotechnology, 115(1):67–79, 2005.

[38] A. Rudnitskaya and A. Legin. Sensor systems, electronic tongues

and electronic noses, for the monitoring of biotechnological processes.

Bibliography 139

Journal of Industrial Microbiology and Biotechnology, 35(5):443–451,

2008.

[39] F. B. Myers and L. P. Lee. Innovations in optical microfluidic

technologies for point-of-care diagnostics. Lab on a Chip -

Miniaturisation for Chemistry and Biology, 8(12):2015–2031, 2008.

[40] R. Wannemacher, M. Quinten, and A. Pack. Evanescent-wave

scattering in near-field optical microscopy. Journal of Microscopy,

194(2-3):260–264, 1999.

[41] M. Gu, J. B. Haumonte, Y. Micheau, J. W. M. Chon, and X. Gan. Laser

trapping and manipulation under focused evanescent wave illumination.

Applied Physics Letters, 84(21):4236–4238, 2004.

[42] P. V. Lambeck. Remote opto-chemical sensing with extreme sensitivity:

Design, fabrication and performance of a pigtailed integrated optical

phase-modulated mach-zehnder interferometer system. Sensors and

Actuators, B: Chemical, 61(1):100–127, 1999.

[43] M. Tanyeri, M. Nichkova, B. D. Hammock, and I. M. Kennedy.

Chemical and biological sensing through optical resonances in

microcavities. volume 5699 of Imaging, Manipulation, and Analysis

of Biomolecules and Cells: Fundamentals and Applications III, pages

227–236, San Jose, CA, 2005.

[44] M. Iqbal, M.A. Gleeson, B. Spaugh, F. Tybor, W.G. Gunn,

M. Hochberg, T. Baehr-Jones, and L.C. Bailey, R.C. ; Gunn. Label-free

biosensor arrays based on silicon ring resonators and high-speed optical

scanning instumentation. IEEE Journal of Selected Topics in Quantum

Electronics, 16(3):654–661, 2010.

Bibliography 140

[45] S. Mandai, X. Serey, and D. Erickson. Nanomanipulation using silicon

photonic crystal resonators. Nano Letters, 10(1):99–104, 2010.

[46] S. Mandal and D. Erickson. Nanoscale optofluidic sensor arrays. Optics

Express, 16(3):1623–1631, 2008.

[47] Y. S. Huh, A. J. Chung, and D. Erickson. Surface enhanced raman

spectroscopy and its application to molecular and cellular analysis.

Microfluidics and Nanofluidics, 6(3):285–297, 2009.

[48] Park T. Fully integrated three-dimensional electrodes for electro-

chemical detection in microchips: Fabrication, characterization, and

applicationsr. Analytical Cemistry, 81(12):4762–4769, 2009.

[49] J. Homola, I. Koudela, and S. S. Yee. Surface plasmon resonance

sensors based on diffraction gratings and prism couplers: sensitivity

comparison. Sensors and Actuators, B: Chemical, 54(1):16–24, 1999.

[50] Y. Li, J. Sun, L. Wang, P. Zhan, Z. Cao, and Z. Wang. Surface plasmon

sensor with gold film deposited on a two-dimensional colloidal crystal.

Applied Physics A: Materials Science and Processing, 92(2):291–294,

2008.

[51] V. Garcs-Chvez, G. C. Spalding, and K. Dholakia. Near-

field optical manipulation by using evanescent waves and surface

plasmon polaritons. volume 5930 of Optical Trapping and Optical

Micromanipulation II, pages 1–10, San Diego, CA, 2005.

[52] S. Arnold and S. I. Shopova. Whispering gallery mode biosensor:

Fulfilling the promise of single virus detection without labels. pages

237–259, 2011.

Bibliography 141

[53] D. Ross, M. Gaitan, and L. E. Locascio. Temperature measurement

in microfluidic systems using a temperature-dependent fluorescent dye.

Analytical Chemistry, 73(17):4117–4123, 2001.

[54] M. A. Cooper. Label-free biosensors techniques and applications.

Cambridge University Press, New York, 2009.

[55] H. J. Lezec and T. Thio. Diffracted evanescent wave model for enhanced

and suppressed optical transmission through subwavelength hole arrays.

Optics Express, 12(16):3629–3651, 2004.

[56] J. Luo, X. Zhuang, and J. Yao. Enlarging the evanescent field scope by

nanoparticle scattering for nanoparticle sensing of optical fiber sensors.

Journal of Nanoengineering and Nanosystems, 2011.

[57] D. Sarid. Long-range surface-plasmon waves on a very thin metal films.

Journal of Nanoengineering and Nanosystems, 2011.

[58] A. Ashkin and J. M. Dziedzic. Observation of optical resonances of

dielectric spheres by light scattering. Applied Optics, 20(10):1803–1814,

1981.

[59] C. C. Lam, P. T. Leung, and K. Young. Explicit asymptotic formulas

for the positions, widths, and strengths of resonances in mie scattering.

J. Opt. Soc. Am. B, 9(9):1585–1592, 1992.

[60] P. Caldas, P. A. S. Jorge, F. M. Araujo, L. A. Ferreir, G. Rego, J. L.

Santos, S. Berneschi, F. Cosi, S. Soria, S. Pelli, and G. Nunzi Conti.

Interrogation of microresonators using multimode fibers. volume 7653

of 4th European Workshop on Optical Fibre Sensors, Porto, 2010.

Bibliography 142

[61] D. Morrish, X. Gan, and M. Gu. Morphology-dependent resonance

induced by two-photon excitation in a micro-sphere trapped by a

femtosecond pulsed laser. Optics Express, 12(18):4198–4202, 2004.

[62] A. Rahman. Temperature sensor based on dielectric optical

microresonator. Optical Fiber Technology, 17(6):536–540, 2011.

[63] A. W. Poon, F. Courvoisier, and R. K. Chang. Multimode resonances

in square-shaped optical microcavities. Optics Letters, 26(9):632–634,

2001.

[64] V. Zamora, A. Dez, M. V. Andrs, and B. Gimeno. Cylindrical optical

microcavities: Basic properties and sensor applications. Photonics and

Nanostructures - Fundamentals and Applications, 9(2):149–158, 2011.

[65] T. J. Kippenberg, S. M. Spillane, and K. J. Vahala. Demonstration of

ultra-high- q small mode volume toroid microcavities on a chip. Applied

Physics Letters, 85(25):6113–6115, 2004.

[66] J. Salvi and D. Courjon. Resonant optical cavity used as a nonradiating

source for optical near-field microscopy. Optics Letters, 24(24):1811–

1813, 1999.

[67] B. Y. Jung, N. Y. Kim, C. Lee, C. K. Hwangbo, and C. Seoul. Control

of resonant wavelength from organic light-emitting materials by use of

a fabry-perot microcavity structure. Applied Optics, 41(16):3312–3318,

2002.

[68] P. Velha, E. Picard, T. Charvolin, E. Hadji, J. C. Rodier, P. Laianne,

and D. Peyrade. Ultra-high q/v fabry-perot microcavity on soi

substrate. Optics Express, 15(24):16090–16096, 2007.

Bibliography 143

[69] E. Chow, A. Grot, L. W. Mirkarimi, M. Sigalas, and G. Girolami.

Ultracompact biochemical sensor built with two-dimensional photonic

crystal microcavity. Optics Letters, 29(10):1093–1095, 2004.

[70] C. L. C. Smith, U. Bog, S. Tomljenovic-Hanic, M. W. Lee, D. K. C. Wu,

L. O’Faolain, C. Monat, C. Grillet, T. F. Krauss, C. Karnutsch, R. C.

McPhedran, and B. J. Eggleton. Reconfigurable microfluidic photonic

crystal slab cavities. Optics Express, 16(20):15887–15896, 2008.

[71] M. L. Gorodetsky, A. A. Savchenkov, and V. S. Ilchenko. Ultimate q

of optical microsphere resonators. Optics Letters, 21(7):453–455, 1996.

[72] J. T. Zhang, H. Lin, J. P. Sun, X. J. Feng, K. A. Gillis, and M. R.

Moldover. Cylindrical acoustic resonator for the re-determination of

the boltzmann constant. International Journal of Thermophysics,

31(7):1273–1293, 2010.

[73] I. Teraoka and S. Arnold. Resonance shifts of counterpropagating

whispering-gallery modes: Degenerate perturbation theory and

application to resonator sensors with axial symmetry. Journal of the

Optical Society of America B: Optical Physics, 26(7):1321–1329, 2009.

[74] A. A. Savchenkov, A. B. Matsko, and L. Maleki. White-light whispering

gallery mode resonators. Optics Letters, 31(1):92–94, 2006.

[75] M. Cai, O. Painter, K. J. Vahala, and P. C. Sercel. Fiber-coupled

microsphere laser. Opt. Lett., 25(19):1430–1432, 2000.

[76] G. R. Elliott, G. S. Murugan, J. S. Wilkinson, M. N. Zervas, and

D. W. Hewak. Chalcogenide glass microsphere laser. Optics Express,

18(25):26720–26727, 2010.

Bibliography 144

[77] Yannick Dumeige and Patrice Fron. Whispering-gallery-mode analysis

of phase-matched doubly resonant second-harmonic generation.

Physical Review A, 74(6):063804, 2006.

[78] J. L. Dominguez-Juarez, G. Kozyreff, and J. Martorell. Whispering

gallery microresonators for second harmonic light generation from a

low number of small molecules. Nature Communications, 2(1), 2011.

[79] A. Serpengzel and A. Poon. Optical Processes in Microparticles and

Nanostructures. World Scientific Publishing, Singapore, 2011.

[80] F. Vollmer and S. Arnold. Whispering-gallery-mode biosensing: Label-

free detection down to single molecules. Nature Methods, 5(7):591–596,

2008.

[81] T. Yoshie, L. Tang, and S. Y. Su. Optical microcavity: Sensing down

to single molecules and atoms. Sensors, 11(2):1972–1991, 2011.

[82] J. Zhu, S. K. Ozdemir, Y. F. Xiao, L. Li, L. He, D. R. Chen, and

L. Yang. On-chip single nanoparticle detection and sizing by mode

splitting in an ultrahigh-q microresonator. Nature Photonics, 4(1):46–

49, 2010.

[83] I. Gryczynski, J. Malicka, Z. Gryczynski, and J. R. Lakowicz.

Surface plasmon-coupled emission with gold films. Journal of Physical

Chemistry B, 108(33):12568–12574, 2004.

[84] Raether. Surface Plasmons on smooth and rough surfaces and on

gratings. Springer, Berlin, 1988.

[85] E. Kretschmann and H. Raether. Radiative decay of nonradiative

surface plasmons excited by ligh. Z. Naturforsc. A., 23:2135–2136,

1968.

Bibliography 145

[86] T. Kan, K. Matsumoto, and I. Shimoyama. Tunable gold-coated

polymer gratings for surface plasmon resonance coupling and scanning.

Journal of Micromechanics and Microengineering, 20(9), 2010.

[87] J. Ctyroky, J. Homola, P. V. Lambeck, S. Musa, H. J. W. M. Hoekstra,

R. D. Harris, J. S. Wilkinson, B. Usievich, and N. M. Lyndin. Theory

and modelling of optical waveguide sensors utilising surface plasmon

resonance. Sensors and Actuators, B: Chemical, 54(1):66–73, 1999.

[88] I. Leite, M. C. Navarrete, N. Daz-Herrera, A. Gonzlez-Cano, and

O. Esteban. Selectivity of spr fiber sensors in absorptive media:

An experimental evaluation. Sensors and Actuators, B: Chemical,

160(1):592–597, 2011.

[89] A. Abdelghani, J. M. Chovelon, N. Jaffrezic-Renault, C. Ronot-Trioli,

C. Veillas, and H. Gagnaire. Surface plasmon resonance fibre-optic

sensor for gas detection. Sensors and Actuators, B: Chemical, 39(1-

3):407–410, 1997.

[90] V. Coello and S. I. Bozhevolnyi. Surface plasmon polariton excitation

and manipulation by nanoparticle arrays. Optics Communications,

282(14):3032–3036, 2009.

[91] W. L. Barnes, A. Dereux, and T. W. Ebbesen. Surface plasmon

subwavelength optics. Nature, 424(6950):824–830, 2003.

[92] S. H. Chang, S. K. Gray, and G. C. Schatz. Surface plasmon generation

and light transmission by isolated nanoholes and arrays of nanoholes

in thin metal films. Optics Express, 13(8):3150–3165, 2005.

Bibliography 146

[93] R. Mller, C. Ropers, and C. Lienau. Femtosecond light pulse

propagation through metallic nanohole arrays: The role of the dielectric

substrate. Optics Express, 12(21):5067–5081, 2004.

[94] C. E. H. Berger, T. A. M. Beumer, R. P. H. Kooyman, and

J. Greve. Surface plasmon resonance multisensing. Analytical

Chemistry, 70(4):703–706, 1998.

[95] R. Slavk, J. Homola, and J. tyrok. Miniaturization of fiber optic surface

plasmon resonance sensor. Sensors and Actuators, B: Chemical, 51(1-

3):311–315, 1998.

[96] B. Liedberg, I. Lundstrm, and E. Stenberg. Principles of biosensing

with an extended coupling matrix and surface plasmon resonance.

Sensors and Actuators: B. Chemical, 11(1-3):63–72, 1993.

[97] S. Lfs, M. Malmqvist, I. Rnnberg, E. Stenberg, B. Liedberg, and

I. Lundstrm. Bioanalysis with surface plasmon resonance. Sensors

and Actuators: B. Chemical, 5(1-4):79–84, 1991.

[98] John Chilwell and Ian Hodgkinson. Thin-films field-transfer matrix

theory of planar multilayer waveguides and reflection from prism-loaded

waveguides. Journal of the Optical Society of America A: Optics and

Image Science, and Vision, 1(7):742–753, 1984.

[99] J. C. Maxwell. A treatise on Electricity and Magnetism, volume 2.

Clarendon Press, Oxford, 1873.

[100] P. N. Lebedev. Experimental examination of light pressure. Annals of

Physics, 6(433), 1901.

[101] E. F. Nichols and G. F. Hull. A preliminary communication on the

pressure of heat and light radiation. Physics Review, 13(307-320), 1901.

Bibliography 147

[102] A. Ashkin, J. M. Dziedzic, J. E. Bjorkholm, and S. Chu. Observation of

a single-beam gradient force optical trap for dielectric particles. Optics

Letters, 11(5):288–290, 1986.

[103] A. Ashkin and J. M. Dziedzic. Observation of resonances in the

radiation pressure on dielectric spheres. Physical Review Letters,

38(23):1351–1354, 1977.

[104] C. Xie and Y. Q. Li. Confocal micro-raman spectroscopy of single

biological cells using optical trapping and shifted excitation difference

techniques. Journal of Applied Physics, 93(5):2982–2986, 2003.

[105] C. Xie, Chen De, and Y. Q. Li. Raman sorting and identification

of single living micro-organisms with optical tweezers. Optics Letters,

30(14):1800–1802, 2005.

[106] S. C. Kuo and M. P. Sheetz. Force of single kinesin molecules measured

with optical tweezers. Science, 260(5105):232–234, 1993.

[107] J. M. A. Mauritz, A. Esposito, T. Tiffert, J. N. Skepper, A. Warley,

Y. Z. Yoon, P. Cicuta, V. L. Lew, J. R. Guck, and C. F. Kaminski.

Biophotonic techniques for the study of malaria-infected red blood cells.

Medical and Biological Engineering and Computing, 48(10):1055–1063,

2010.

[108] A. D. Mehta, M. Rief, J. A. Spudich, D. A. Smith, and R. M.

Simmons. Single-molecule biomechanics with optical methods. Science,

283(5408):1689–1695, 1999.

[109] J. Guck, R. Ananthakrishnan, H. Mahmood, T. J. Moon, C. C.

Cunningham, and J. Ks. The optical stretcher: A novel laser tool

to micromanipulate cells. Biophysical Journal, 81(2):767–784, 2001.

Bibliography 148

[110] J. Guck, R. Ananthakrishnan, C. C. Cunningham, and J. Ks. Stretching

biological cells with light. Journal of Physics Condensed Matter,

14(19):4843–4856, 2002.

[111] K. Svoboda and S. M. Block. Biological applications of optical forces.

Annual Review of Biophysics and Biomolecular Structure, 23:247–285,

1994.

[112] Takatoki Yamamoto, Osamu Kurosawa, Hiroyuki Kabata, Nobuo

Shimamoto, and Masao Washizu. Molecular surgery of dna based on

electrostatic micromanipulation. volume 3, pages 1933–1940, 1998.

[113] R. M. Simmons, J. T. Finer, S. Chu, and J. A. Spudich. Quantitative

measurements of force and displacement using an optical trap.

Biophysical Journal, 70(4):1813–1822, 1996.

[114] T. P. Koehler, C. M. Brotherton, and A. M. Grillet. Comparison

of interparticle force measurement techniques using optical trapping.

Colloids and Surfaces A: Physicochemical and Engineering Aspects,

384(1-3):282–288, 2011.

[115] M. P. MacDonald, G. C. Spalding, and K. Dholakia. Microfluidic

sorting in an optical lattice. Nature, 426(6965):421–424, 2003.

[116] K. Visscher, S. P. Gross, and S. M. Block. Construction of multiple-

beam optical traps with nanometer-resolution position sensing. IEEE

Journal on Selected Topics in Quantum Electronics, 2(4):1066–1076,

1996.

[117] M. Dienerowitz, G. Gibson, R. Bowman, and M. Padgett. Holographic

tweezers: A platform for plasmonics. volume 8097 of Optical Trapping

and Optical Micromanipulation VIII, San Diego, CA, 2011.

Bibliography 149

[118] R. W. Bowman, A. J. Wright, and M. J. Padgett. An slm-based shack-

hartmann wavefront sensor for aberration correction in optical tweezers.

Journal of Optics, 12(12), 2010.

[119] M. Zheng, Y. Ogura, and J. Tanida. Three-dimensional dynamic optical

manipulation by combining a diffractive optical element and a spatial

light modulator. Optical Review, 15(2):105–109, 2008.

[120] B. Kanani. Sizing of microbubbles in the blood stream based on

ultrasound velocity. volume 5768 of Health Monitoring and Smart

Nondestructive Evaluation of Structural and Biological Systems IV,

pages 55–62, San Diego, CA, 2005.

[121] G. J. Brouhard, H. T. Schek Iii, and A. J. Hunt. Advanced optical

tweezers for the study of cellular and molecular biomechanics. Physical

Review Letters, 47(26):1927–1930, 1981.

[122] P. C. Mogensen and J. Glckstad. Dynamic array generation and pattern

formation for optical tweezers. Optics Communications, 175(1):75–81,

2000.

[123] Satoshi Kawata and Tadao Sugiura. Movement of micrometer-sized

particles in the evanescent field of a laser beam. Opt. Lett., 17(11):772–

774, 1992.

[124] J. M. Pitarke, V. M. Silkin, E. V. Chulkov, and P. M. Echenique.

Theory of surface plasmons and surface-plasmon polaritons. Reports

on Progress in Physics, 70(1):1–87, 2007.

[125] A. N. Grigorenko, N. W. Roberts, M. R. Dickinson, and Y. Zhang.

Nanometric optical tweezers based on nanostructured substrates.

Nature Photonics, 2(6):365–370, 2008.

Bibliography 150

[126] P. J. Reece, V. Gars-Chvez, and K. Dholakia. Near-field optical

micromanipulation with cavity enhanced evanescent waves. Applied

Physics Letters, 88(22), 2006.

[127] M. Righini, C. Girard, and R. Quidant. Light-induced manipulation

with surface plasmons. Journal of Optics A: Pure and Applied Optics,

10(9), 2008.

[128] M. Righini, G. Volpe, C. Girard, D. Petrov, and R. Quidant.

Surface plasmon optical tweezers: Tunable optical manipulation in the

femtonewton range. Physical Review Letters, 100(18), 2008.

[129] T. Rindzevicius, Y. Alaverdyan, B. Sepulveda, T. Pakizeh, M. Kll,

R. Hillenbrand, J. Aizpurua, and F. J. Garca De Abajo. Nanohole

plasmons in optically thin gold films. Journal of Physical Chemistry C,

111(3):1207–1212, 2007.

[130] P. Lalanne, J. C. Rodier, and J. P. Hugonin. Surface plasmons of

metallic surfaces perforated by nanohole arrays. Journal of Optics A:

Pure and Applied Optics, 7(8):422–426, 2005.

[131] E. X. Jin and X. Xu. Finitte-difference time-domain studies on optical

transmission through planar nano-apertures in a metal film. Japanese

Journal of Applied Physics, Part 1: Regular Papers and Short Notes

and Review Papers, 43(1):407–417, 2004.

[132] S. Collin, F. Pardo, and J. L. Pelouard. Waveguiding in nanoscale

metallic apertures. Optics Express, 15(7):4310–4320, 2007.

[133] R. Mller, V. Malyarchuk, and C. Lienau. Three-dimensional theory on

light-induced near-field dynamics in a metal film with a periodic array

Bibliography 151

of nanoholes. Physical Review B - Condensed Matter and Materials

Physics, 68(20):2054151–2054159, 2003.

[134] J. Cesario, R. Quidant, G. Badenes, and S. Enoch. Electromagnetic

coupling between a metal nanoparticle grating and a metallic surface.

Optics Letters, 30(24):3404–3406, 2005.

[135] G. Volpe, R. Quidant, D. V. Petrov, and G. Badenes. Measurement of

radiation forces generated by plasmon fields. volume 5930 of Optical

Trapping and Optical Micromanipulation II, pages 1–10, San Diego,

CA, 2005.

[136] P. B. Johnson and R. W. Christy. Optical constants of the noble metals.

Physical Review B, 6(12):4370–4379, 1972.

[137] E. Thormann, A. C. Simonsen, P. L. Hansen, and O. G. Mouritsen.

Interactions between a polystyrene particle and hydrophilic and

hydrophobic surfaces in aqueous solutions. Langmuir, 24(14):7278–

7284, 2008.

[138] R. J. Green, M. C. Davies, C. J. Roberts, and S. J. B. Tendler. A

surface plasmon resonance study of albumin adsorption to peo-ppo-

peo triblock copolymers. Journal of Biomedical Materials Research,

42(2):165–171, 1998.

[139] A. Higuchi, K. Sugiyama, B. O. Yoon, M. Sakurai, M. Hara, M. Sumita,

S. I. Sugawara, and T. Shirai. Serum protein adsorption and platelet

adhesion on pluronic-adsorbed polysulfone membranes. Biomaterials,

24(19):3235–3245, 2003.

Bibliography 152

[140] V. A. Liu, W. E. Jastromb, and S. N. Bhatia. Engineering protein

and cell adhesivity using peo-terminated triblock polymers. Journal of

Biomedical Materials Research, 60(1):126–134, 2002.

[141] K. Boxshall, M.H. Wu, Z. Cui, Z.F. Cui, J.F. Watts, and M.A.

Baker. Simple surface treatments to modify protein adsorption and

cell attachment properties within a poly(dimethylsiloxane) micro-

bioreactor. Surface and interface analysis, 38:198–201, 2006.

[142] V. Garcs-Chvez, R. Quidant, P. J. Reece, G. Badenes, L. Torner,

and K. Dholakia. Extended organization of colloidal microparticles by

surface plasmon polariton excitation. Physical Review B - Condensed

Matter and Materials Physics, 73(8):1–5, 2006.

[143] N. Garca and M. Bai. Theory of transmission of light by sub-wavelength

cylindrical holes in metallic films. Optics Express, 14(21), 2006.

[144] D. Ganic, X. Gan, and M. Gu. Three-dimensional evanescent wave

scattering by dielectric particles. Optik (Jena), 113(3):135–141, 2002.

[145] D. Ganic, X. Gan, and M. Gu. Parametric study of three-

dimensional near-field mie scattering by dielectric particles. Optics

Communications, 216(1-3):1–10, 2003.

[146] G. Gervinskas, D. Day, and S. Juodkazis. High-precision interferometric

monitoring of polymer swelling using a simple optofluidic sensor.

Sensors and Actuators, B: Chemical, 159(1):39–43, 2011.

Author’s Publications

Conference Papers

S. Weber, D. Day and M. Gu, Particle manipulation in a microfluidic device

via surface plasmon resonances. Nanophotonics Down Under, Melbourne,

Australia, January 1-4 th, 2009.

S. Weber, D. Day and M. Gu, Surface Plasmon Resonance Manipulation

Of Microparticles In A Microfluidic Device. Australasian Conference on

Optics, Lasers and Spectroscopy and Australian Conference on Optical Fibre

Technology, Melbourne, Australia, November 29 - December 3 rd, 2009.

S. Weber, D. Day and M. Gu, Manipulation of microparticles in a

microfluidic device via surface plasmon resonance on patterned and non-

patterned surfaces. 19th Australian Institute of Physics Congress, 35th

Australian conference on optical fibre , Melbourne, Australia, December 5-

9 th, 2010.

S. Weber, D. Day and M. Gu, Optical trapping in a microfluidic device

via surface plasmon resonance on patterned hole arrays. SPIE Optics and

Photonics, San Diego, U.S.A, August 21-25 th, 2011.

153

Bibliography 154

S. Weber, D. Day and M. Gu, Environmental sensing in a microfluidic

device via Morphology Dependent Resonance. SPIE Smart Nano + Micro

Materials and Devices, Melbourne, Australia, December 4-7 th, 2011.

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