Nanochemistry and Sensing in Photonic Crystal Fibers fileNanochemistry and Sensing in Photonic Crystal Fibers

Nanochemistry and Sensing

in Photonic Crystal Fibers

Photochemie und Spektroskopie im Nanoliter-Bereich

in Photonischen Kristallfasern

Der Naturwissenschaftlichen Fakultat

der Friedrich-Alexander-Universitat Erlangen-Nurnberg

zur

Erlangung des Doktorgrades Dr. rer. nat.

vorgelegt von

Jocelyn Ssu-Yin Chen

aus Taichung

Als Dissertation genehmigt von der Naturwissenschaftlichen Fakultat

der Friedrich-Alexander Universitat Erlangen-Nurnberg

Tag der mundlichen Prufung: 23 November 2010

Vorsitzender der Promotionskommission: Prof. Dr. Rainer Fink

Erstberichterstatter: Prof. Dr. Philip St.J. Russell

Zweitberichterstatter: Dr. Clemens F. Kaminski

For my family.

Zusammenfassung

Diese Arbeit handelt von Anwendungsmoglichkeiten photonischer Kristallfasern (PCF) im

Bereich der Photochemie und Spektroskopie im Nanoliter-Bereich. Photonische Kristall-

fasern haben die Fahigkeit, eine bestimmte Lichtmode uber sehr große Distanzen in

einem sehr kleinen Probe-Volumen zu fuhren. Diese einzigartige Eigenschaft photonischer

Kristallfasern erlaubt eine drastische Steigerung der erzielbaren Licht-Materie-Wechsel-

wirkung und ist Grundlage dieser Arbeit. Die Parameter, von denen optimale Bedingun-

gen fur Nachweisreaktionen sowie die Ausbeute photochemischer Reaktoren abhangen,

werden diskutiert. Außerdem werden verschiedene Verfahren zur Verwendung von PCF-

Sensoren in mikrofluidischen Systemen untersucht. Weiterhin wird ein hochgradig kon-

trollierbares photochemisches Reaktionsgefaß vorgestellt. Als prinzipieller Beweis seiner

Anwendbarkeit zur aktiven Herbeifuhrung und Beobachtung photochemischer Reaktionen

wird die Photolyse wassriger Cobalaminlosung im Kern einer PCF quantitativ gemessen.

Wegen der - fur diese Reaktion typischen - maßigen Quantenausbeute ware dies mit kon-

ventionellen Methoden schwierig oder unmoglich. Die dynamischen Vorgange wahrend

der aktiv herbeigefuhrten Reaktion konnten mittels Breitband-Absorptionsspektroskopie

in der Faser in Echtzeit aufgezeichnet werden. Die Ergebnisse wurden mit denen einer

herkommlichen Kuvettenmessung verglichen. Durch das verwendete Reaktionsgefaß kon-

nte das benotigte Probevolumen gegenuber konventionellen Techniken stark verkleinert

werden (in die Großenordnung von nL/cm). Die starke Licht-Materie-Wechselwirkung in

den mikrostrukturierten Fasern ermoglicht es, bei sehr niedrigen Lichtleistungen, kurzere

Reaktionszeiten zu erreichen. Weiterhin konnte das schnelle und reversible photoin-

duzierte Schalten eines Azobenzol-Derivats nachgewiesen und dadurch die Effizienz und

Reproduzierbarkeit des Reaktors bestatigt werden. Neben dem photochemischen Reaktor

wurde ein quantitativer breitbandiger Fasersensor entwickelt, basierend auf der Uberlap-

v

vi ZUSAMMENFASSUNG

pung evaneszenter Felder in den Mantellochern einer Vollkernfaser. Dabei wurde, trotz

des wesentlich verringerten Probevolumens, hervorragende ubereinstimmung mit dem

unter Verwendung einer gewohnlichen Kuvette erhaltenen Referenzspektrum festgestellt.

Zuletzt bieten PCF, neben großerer Licht-Materie-Wechselwirkung, auch ein großes Ober-

flachen-Volumen-Verhaltnis (∼ 105 m−1) fur Anwendungen, in denen Reaktionen mit

Oberflachengebundenen Probentypen von Interesse sind. Zu diesem Zweck wurden die

Selbstaggregation und das Photobleichen eines Thiazin-Farbstoffs in einer Index-leitenden

Faser mit “Mercedesstern”-Querschnitt untersucht. Durch Absorptionsspektroskopie an-

hand der evaneszenten Welle, die von der im Kern geleiteten Lichtmode in die Man-

tellocher der Faser ausstrahlt, konnte die Anzahl der, an der Oberflache der Faseradsor-

bierten, Molekule ermitteln werden.

Abstract

The work described in this thesis demonstrates the application of photonic crystal fibers

in nanochemistry and sensing. In the photonic crystal fiber, a well-defined optical mode

can propagate through a sample volume confined within the fiber’s microstructure over

very long distances. This property, unique to the photonic crystal fiber, offers greatly

enhanced figure of merit for light-matter interactions, and is the basis of this thesis. The

parameters governing the optimum sensing conditions and the figure of merit for photo-

chemical reactors are discussed and several fabrication techniques with the objective of

combining photonic crystal fiber sensors with microfluidics have also been investigated. A

highly-controlled photochemical reactor was proposed and demonstrated. As a proof-of-

principle for its application in actively inducing and monitoring photochemical reactions,

the photolysis of an aqueous cobalamin was quantitatively measured in a liquid-filled

hollow-core photonic crystal fiber. The reaction is characterized by modest quantum

yields which would otherwise be difficult or impossible to induce and monitor using con-

ventional methods. The dynamics of the actively induced reaction were monitored in

real-time by broadband absorption spectroscopy in the fiber. Results were compared to

those obtained using standard techniques in a cuvette. The reactor has greatly reduced

the sample volume requirement (in the order of nL/cm) compared to conventional tech-

niques. The strong light-matter interactions in the fiber microstructure allowed shorter

reaction times to be achieved at very low optical powers. Additionally, the fast and re-

versible photoswitching of an azobenzene derivative was demonstrated and confirmed the

effectiveness and reproducibility of the photochemical reactor. In addition to the photo-

chemical reactors, a quantitative broadband fiber sensor based on evanescent-field sensing

in the cladding holes of a suspended solid-core fiber was demonstrated. Excellent agree-

ment with the reference spectrum measured in a standard cuvette was obtained despite

vii

viii ABSTRACT

the much reduced sample volume used. Finally, in addition to enhancement in light-

matter interactions, the photonic crystal fiber also offers large surface-to-volume ratios

(∼ 105 m−1) for experiments in which reactions of surface-bound sample species are of

interest. To this end the self-aggregation and photobleaching of a thiazine dye was studied

in an index-guiding fiber with suspended solid core. It was shown that the amount of

molecules adsorbed onto the inner surfaces of the fiber could be obtained and monitored

by absorption spectroscopy via the evanescent wave of the core-guided mode that extends

into the cladding holes of the fiber.

Acknowledgments

This thesis would not have been possible without the scientific, technical and friendly

support from the following people:

Alexander Nazarkin Greg Pearce Myeong Soo Kang

Alexander Podlipensky Gustavo Wiederhecker Nicola Farrer

Amir Abdolvand Helga Hussy Nicolai Granzow

Amy Wan Hemant Tyagi Nicolas Joly

Andre Brenn Howard Lee Patrick Uebel

Andreas Walser Jerry Chen Pavel Marchenko

Aniruddha Ray Johannes Nold Peter Banzer

Anita Jones Konrad Heberlein Peter Sadler

Anna Butsch Lam Lee Philip Russell

Bastian Etzold Leonhard Heberlein Philipp Hoelzer

Bernhard Thomann Leyun Zang Ralf Keding

Bettina Schwender Luis Lorenzo Sanchez Soto Robert Fisher

Chris Poulton Luis Prill Sempere Robert Gall

Christine Kreuzer Marianne Heberlein Sarah Unterkofler

Christoph Heberlein Markus Schmidt Sebastian Stark

Daniel Ploß Marta Ziemienczuk Silke Rammler

Friedrich Heberlein Martin Butryn Stanislaw Dorschner

Gareth Williams Martin Garbos Thomas Spona

George Kakarantzas Matthias Schmidt Tijmen Euser

Gordon Wong Michael Scharrer Xin Jiang

Cheers, guys!

ix

Contents

Zusammenfassung v

Abstract vii

Acknowledgments ix

List of Figures xv

List of Tables xix

Abbreviations xxi

Preface xxiii

1 Photonic Crystal Fibers 1

1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1.2 Historical Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

1.3 Classification and Guidance Mechanisms . . . . . . . . . . . . . . . . . . . 4

1.3.1 Index-Guiding PCF . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

1.3.2 Hollow-Core PCF . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.4 Fabrication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1.5 Optical Sensing with PCF . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

1.5.1 Index-Guiding PCF Sensors . . . . . . . . . . . . . . . . . . . . . . 11

1.5.2 Hollow-Core PCF Sensors . . . . . . . . . . . . . . . . . . . . . . . 13

2 Experimental Considerations and Techniques 15

2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

xi

xii CONTENTS

2.2 Detection Strategies and Ideal Conditions . . . . . . . . . . . . . . . . . . 17

2.2.1 Ideal Conditions for Absorption-Based Sensors . . . . . . . . . . . . 17

2.2.2 Figure of Merit for Photochemistry . . . . . . . . . . . . . . . . . . 20

2.3 Experimental Setup and Instrumentation . . . . . . . . . . . . . . . . . . . 22

2.3.1 Transmission Properties of Liquid-Filled PCF . . . . . . . . . . . . 22

2.3.2 Microfluidic Flow in Confined Channels . . . . . . . . . . . . . . . . 25

2.3.3 Optical Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

2.3.4 LabVIEW Automation . . . . . . . . . . . . . . . . . . . . . . . . . 32

2.4 Fabrication Techniques for PCF Devices . . . . . . . . . . . . . . . . . . . 32

2.4.1 Femtosecond Laser Ablation . . . . . . . . . . . . . . . . . . . . . . 32

2.4.2 Two-Photon Polymerization . . . . . . . . . . . . . . . . . . . . . . 38

2.4.3 Focused Ion Beam Micromachining . . . . . . . . . . . . . . . . . . 40

3 Photochemistry in PCF 43

3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

3.2 Fiber Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

3.3 Photolysis of Metal Complexes . . . . . . . . . . . . . . . . . . . . . . . . 49

3.3.1 Photoaquation of Cyanocobalamin . . . . . . . . . . . . . . . . . . 50

3.3.2 Experimental Results . . . . . . . . . . . . . . . . . . . . . . . . . . 51

3.3.3 Reaction Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

3.3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

3.4 Photoswitching of Azobenzene Molecules . . . . . . . . . . . . . . . . . . . 57

3.4.1 Isomerization of Azo Dyes . . . . . . . . . . . . . . . . . . . . . . . 58

3.4.2 Reversible Isomerization in PCF . . . . . . . . . . . . . . . . . . . . 62

3.4.3 Reaction Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

3.4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

4 Spectroscopy in PCF 69

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

4.2 Evanescent-Wave Sensing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

4.2.1 Fiber Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . 70

4.2.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

CONTENTS xiii

4.2.3 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

4.3 Microscale Surface Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . 79

4.3.1 Self-Aggregation and Photobleaching of Methylene Blue . . . . . . . 79

4.3.2 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

5 Conclusions and Outlook 89

5.1 Optical Tweezers and Photodynamic Therapy . . . . . . . . . . . . . . . . 89

5.2 Microfluidic Flow Reactor . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

5.3 Mass Spectrometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

5.4 Surface Chemistry Using Higher-Order Modes . . . . . . . . . . . . . . . . 90

5.5 Final Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

A Counter-Propagating Pump-Probe Setup 93

List of Publications 97

Curriculum Vitae 121

List of Figures

1.1 Images showing the iridescence in the butterfly Morpho rhetenor and the

iridescent setae from polychaete worms. . . . . . . . . . . . . . . . . . . . . 3

1.2 Schematic illustration of the cross-section and the refractive index profile

for an index-guiding photonic crystal fiber. . . . . . . . . . . . . . . . . . . 5

1.3 Schematic illustrations of a hollow-core PBG-PCF, a kagome-lattice PCF

and a Bragg fiber. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

1.4 Images of the cross-section of the cane for a hollow-core PBG-PCF and the

fabricated fiber. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

1.5 Schematic illustration of the active sensing regions around the core of an

index-guiding PCF and a hollow-core PBG-PCF. . . . . . . . . . . . . . . 11

2.1 Operational principles of optical sensors in the non-resonant and resonant

regimes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

2.2 Ideal sensing parameter diagram for constant absorbance, defining regions

in which optimum sensing conditions can be achieved. . . . . . . . . . . . . 19

2.3 Schematics illustrating and comparing the geometries and sample volumes

in a conventional cuvette and a kagome PCF. . . . . . . . . . . . . . . . . 21

2.4 Shift in the central wavelength of the PBG as a result of infiltrating the

PBG-PCF with various solvents. . . . . . . . . . . . . . . . . . . . . . . . . 25

2.5 Cross-section of a capillary tube infiltrated with liquid. . . . . . . . . . . . 26

2.6 Simulated water filling time for silica microchannels of bore radii 1, 5 and

10 µm, with an applied pressure head of 1 bar. . . . . . . . . . . . . . . . . 28

2.7 Schematic diagram showing the experimental setup for sensing and photo-

chemistry experiments in PCF. . . . . . . . . . . . . . . . . . . . . . . . . 29

xv

xvi LIST OF FIGURES

2.8 Schematic diagram illustrating the increase in the effective N.A. as a result

of change in the interface medium of the objective (air) to that for the fiber

(liquid). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

2.9 Schematic diagram of photoionization regimes at low and high frequencies. 33

2.10 Schematic diagram of avalanche ionization. . . . . . . . . . . . . . . . . . . 34

2.11 Schematic diagram showing the experimental setup for femtosecond laser

ablation of side channels in PCF and the two-photon polymerization tech-

nique for selective blockage of microstructure holes. . . . . . . . . . . . . . 35

2.12 Diameter of ablated entry hole in the silica fiber as a function of pulse

energy incident on the fiber and the number of pulses. . . . . . . . . . . . . 36

2.13 Schematic showing the dependence of the diameter of laser-ablated entry

hole size on the peak irradiance, assuming a Gaussian irradiance distribution. 37

2.14 Examples of ablated side microchannel allowing access to one of the three

cladding holes in a suspended-core fiber and a damaged side microchannel

after applying 30 bar of water pressure. . . . . . . . . . . . . . . . . . . . . 38

2.15 Measured transmission losses as a function of the number of drilled side

channels in an ESM-PCF. . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

2.16 Images of a HC-PCF infiltrated with acrylic resin, a SC-PCF with selec-

tively photopolymerized cladding holes, and a gold nanowire embedded

into the cladding hole of a PCF using TPP as the hole-collapsing technique. 39

2.17 SEM of the cross-section of the nanoweb fiber prior to FIB milling and

after a hole was milled through the silica jacket of a nanoweb fiber. . . . . 41

3.1 Images showing the cross-section of a kagome HC-PCF. . . . . . . . . . . . 45

3.2 Transmission and loss spectra of the kagome HC-PCF. . . . . . . . . . . . 46

3.3 Transmission and loss spectra of the kagome HC-PCF filled with de-ionized

water. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

3.4 Transmission spectrum of the index-guiding kagome HC-PCF filled with

toluene. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

3.5 The photochemical conversion of CNCbl to [H2OCbl]+. . . . . . . . . . . . 50

LIST OF FIGURES xvii

3.6 Changes in the absorption spectrum as a result of the photochemical con-

version of CNCbl to [H2OCbl]+. . . . . . . . . . . . . . . . . . . . . . . . . 51

3.7 Spectral and temporal data for the photolysis of CNCbl in a kagome HC-PCF. 53

3.8 Comparison of the temporal evolution of molar absorptivity measured in a

kagome HC-PCF and a cuvette. . . . . . . . . . . . . . . . . . . . . . . . . 54

3.9 Configuration diagram depicting the photoaquation of CNCbl. . . . . . . . 55

3.10 Quantum yields for the photolysis of CNCbl obtained from measurements

in a kagome HC-PCF. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

3.11 Reversible isomerization between the trans (left) and the cis (right) geo-

metric isomers of azobenzene. . . . . . . . . . . . . . . . . . . . . . . . . . 58

3.12 Spectral and temporal data for the thermal back reaction of disperse orange

1 in toluene. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

3.13 Temporal evolution of molar absorptivity for the forward and back reaction

of disperse red 1 in cyclohexane. . . . . . . . . . . . . . . . . . . . . . . . . 61

3.14 Spectral and temporal data for the forward and back isomerization of dis-

perse orange 1 in toluene measured in a kagome HC-PCF. . . . . . . . . . 62

3.15 Temporal evolution of trans-DO1 in toluene irradiated with broadband

xenon lamp. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

3.16 Configuration diagram depicting the isomerization paths of trans ⇀↽ cis. . . 66

4.1 High resolution SEM of the core region of four different air-suspended solid-

core fibers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

4.2 Transmission and loss spectra for air-suspended SC-PCF with air- and

water-cladding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

4.3 Normalized mode profiles of an air-suspended SC-PCF with water-filled

cladding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

4.4 Dependence of calculated cladding power fraction on the effective core di-

ameter, wavelength and cladding medium. . . . . . . . . . . . . . . . . . . 75

4.5 Measured and calculated dispersion of air-suspended SC-PCFs. . . . . . . . 76

4.6 Absorption and molar absorptivity spectra of an aqueous NiCl2 solution. . 78

xviii LIST OF FIGURES

4.7 Molar absorptivity spectra of methylene blue in water, and photobleach-

ing of MB in suspended solid-core fiber induced by irradiation using the

broadband PCF SC source. . . . . . . . . . . . . . . . . . . . . . . . . . . 81

4.8 The calculated total surface density of MB along the inner surface of the

air-suspended SC-PCF cladding holes. . . . . . . . . . . . . . . . . . . . . 83

4.9 Photobleaching and surface adsorption of MB in kagome HC-PCF. . . . . . 85

A.1 Schematic diagram of the modified pump-probe setup with counter-propagating

beams for PCF photochemical reactors. . . . . . . . . . . . . . . . . . . . . 94

A.2 Schematic diagram showing the effect of refraction due to the tilted liquid

cell window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

List of Tables

1.1 Overview of photonic crystal fiber development. . . . . . . . . . . . . . . . 4

2.1 Comparison between various sample cell configurations. . . . . . . . . . . . 23

3.1 Quantum yields for the photolysis of CNCbl at various pH values. . . . . . 56

xix

Abbreviations

CCD Charge coupled device

CNCbl Cyanocobalamin

CW Continuous wave

DBI Dimethylbenzimidazole

DO1 Disperse orange 1

DR1 Disperse red 1

FC Franck Condon

FIB Focused ion beam

HC-PCF Hollow-core photonic crystal fiber

HPLC High performance liquid chromatography

[H2OCbl]+ Hydroxocobalamin, aquacobalamin

LMB leuco methylene blue

MB Methylene blue

MMF Multimode fiber

OSA Optical spectrum analyzer

PBG Photonic bandgap

PCF Photonic crystal fiber

SC Supercontinuum

SC-PCF Solid-core photonic crystal fiber

SEM Scanning electron micrograph

TS Transition state

UV Ultraviolet

ZDW Zero dispersion wavelength

xxi

Preface

From artificial eyes [1] and ears [2] to electronic noses [3] and tongues [4], devices with

sensing capabilities mimicking the organs of the most sophisticated living creatures on

Earth are paving the ways to improve the living quality of many and simplify routine

analyses in industries as well as our daily lives. Such “senses of electronics”, or sensors,

are able not only to “feel” the materials but even to distinguish their chemical composition

beyond the range of human perception.

A substantial amount of effort has been made in the research and development of chem-

ical sensors in recent years [5], incorporating research fields such as electronics, optics,

biochemistry, material science, analytical, inorganic and organic chemistry. With tech-

nological applications to industrial, medical and environmental needs, this continuously

evolving field is pushing for better sensor designs featuring selectivity, low detection lim-

its, reversibility, robustness and portability. However, most of the existing configurations

still exhibit clear limitations.

Among the world of sensors, a host of sensing modalities exist and are currently being

investigated. In particular, sensing devices using optics and photonics have undergone

extensive research during the last two decades [6-8] due to the wide variety of optical

phenomena that one can exploit as sensing mechanisms. Luminescence, fluorescence,

phosphorescence, absorbance, elastic scattering, Raman scattering, surface plasmon res-

onance, guided-wave resonance, interference, and reflection/transmission microscopy ex-

emplify such phenomena. Different detection techniques and setup configurations are

constantly being developed and optimized to increase the detection sensitivity. An exam-

ple is cavity enhanced absorption spectroscopy (CEAS), whereby the probe light makes

multiple passes through the same sample, effectively increasing the absorption path by

orders of magnitude. While CEAS has proven to be effective in measuring trace samples

xxiii

xxiv PREFACE

[9], its intrinsically narrow bandwidth and the requirement for calibration measurements

pose limitations on the range of applications for this technique [10]. Furthermore, the

conventional monitoring methods based on free-space interferometry and spectroscopy

are effective only for the line of sight, and are therefore prone to undesirable misalign-

ments and external perturbations.

Over the last years, increasing research efforts in fiber- and integrated-optics tech-

nologies, which were primarily developed for the telecommunication industry, have been

injected into optical sensors research. With advances in the development of high quality

fiber-optic components at reasonable costs, the prospect of fiber-optic sensors to replace

conventional ones has been realized. Unlike standard communication fibers which act as

passive media for signals, the function of a sensing fiber is to produce sensitive responses

to various chemical and physical changes that take place in the vicinity of the fiber. Such

novel sensing devices are used for routine analyses, with applications in chemical [11-14],

biochemical [15-18], biomedical and environmental [18-21] sensing.

These fiber-optic chemical and biosensors have shown the potential of a promising

technological platform characterized by numerous intrinsic advantages over their conven-

tional electronic counterparts. The principal single attractive feature of fiber-optic sensors

is undoubtedly the intrinsic immunity to electromagnetic interferences and the absence

of electrical risks which is important for safety in explosive environments. Optical fibers

are capable of guiding the light beam in a confined and inaccessible medium over large

distances, allowing for more versatile and less perturbed in situ or remote monitoring of

environmental or medical parameters. In addition, they also offer the capability for long-

range distributed sensing and the ability to be multiplexed, as optical waves of different

frequencies do not interfere with one another. The optical fiber is lightweight and its

compact geometry implies small volume of analyte consumption, such that low-cost mea-

surements can be achieved with high specificity and sensitivity; its great flexibility also

offers the ability to be embedded into various structures and materials, including textiles

and fabrics [22]. Fiber-optic sensors have major advantages in many chemically aggres-

sive and ionizing environments, and can withstand large physical strain and substantial

temperature excursions. They also have the potential to be integrated in rapid, real-time

high-throughput analysis and be easily interfaced with optical data communication sys-

xxv

tems whereby high information density can be achieved. Furthermore, various system

configurations demonstrate the accessibility of the fiber sensors for flow cells or pipetting

devices, facilitating measurement in the presence of the sample without any rinsing.

Emerging technologies in the field of waveguide-based chemical and biosensors are con-

tinuously evolving, with new focuses on higher sensitivity and stability. This key demand

is stimulating further advancement in the exploration of new material and structural

concepts as alternative platforms for standard sensing technologies, which provide better

performance with the prospect for novel devices.

This thesis focuses on the demonstration of one such novelty in which the concept of

optical fiber sensing is further developed to accommodate active in-fiber (photo)chemical

reactor employing absorption spectrometry in photonic crystal fibers (PCFs) [23, 24].

These microstructured fibers have revolutionized optical fiber technology by enabling

light to be guided and manipulated within the fiber in ways not previously possible; the

new degrees of freedom in the fiber design and fabrication have been extensively exploited

to considerably improve the sensor performance in terms of accuracy and precision.

Outline of the Thesis

Chapter 1 provides a historical perspective on the progress in the field of photonic crystal

fibers, and discusses the classification of PCFs based on their waveguiding mechanisms.

Particular attention is paid to the strong light-matter interaction within the fiber’s mi-

crostructure because of its importance in the photochemical reactions and sensing exper-

iments performed in this thesis. A short overview of the novel sensing applications based

on various types of PCFs and sensing mechanisms to date is also presented.

Chapter 2 introduces the various modes of operation for optical snesors and presents

the concept of detection sensitivity for a fiber-optic sensor. The parameters dictating the

effectiveness of PCF-based sensors are discussed and a diagram relating these parameters

is constructed to facilitate the determination of optimum sensing conditions. In addition

to passive sensing in PCF, the strong light-matter interaction provided by the PCF can

also be utilized as a photochemical reactor to simultaneously induce and monitor reaction

kinetics. The figure of merit for photochemical reactors is therefore discussed in detail.

xxvi PREFACE

The transmission properties and microfluidic flow through the liquid-filled PCF, together

with the main components making up the experimental setup, are also described. The

chapter concludes with a presentation of the preliminary results from several fabrication

techniques investigated with the objective of combining PCF sensors with microfluidics.

Chapter 3 demonstrates the use of a liquid-filled hollow-core PCF (HC-PCF) as a

highly-controlled photochemical reactor. Photochemical reactions with very low quantum

yields are efficiently induced and monitored within the hollow core of the PCF reactor in

real-time. Quantitative absorption spectroscopy of the photo-excited chemical species can

be obtained within seconds. Orders of magnitude enhancement in the reaction kinetics

is obtained with strongly reduced sample volumes compared to conventional techniques.

The second part of the chapter demonstrates the effectiveness of the PCF reactor in

monitoring fast, reversible photochemical reactions. The reactions are monitored in real-

time and show complete reversibility of the system.

Chapter 4 presents quantitative broadband sensing based on the evanescent interaction

of the guided core mode in a solid-core PCF (SC-PCF) with the analyte in the fiber

cladding. Excellent agreements are obtained between the experimentally measured and

numerically calculated fiber sensor characteristics without the use of free parameters.

More importantly, the PCF sensor provides stronger signals and excellent agreement with

the reference spectrum measured using standard techniques, despite using three orders of

magnitude lower sample volume. The second part of the chapter focuses on the interaction

between the sample molecules with the inner surfaces of the PCF microchannels. Results

from both SC- and HC-PCFs demonstrate the affinity of the molecules to adsorb onto

the silica surfaces and self-aggregate, an effect which would otherwise be unobservable in

bulk under the same experimental conditions. The high surface-to-volume ratio provided

by the microchannels in PCF promises a novel platform for surface chemistry.

Chapter 5 concludes this thesis with a discussion on the prospective extensions to the

current work.

Chapter 1

Photonic Crystal Fibers

1.1 Introduction

Over the past four decades, optical fibers have revolutionized the field of telecommuni-

cations [25]. However, despite their excellent performance in the transmission of optical

signals, the advances made in fiber optic technology have been driven towards its ulti-

mate limit as the intrinsic properties of silica have imposed fundamental restrictions on

the performance of conventional optical fibers. Firstly, standard optical fibers have strict

design rules to fulfill, such as limited core diameter for single-mode operation, modal

cut-off wavelength, and limitation on material selection as the core and cladding materi-

als must have matching thermal properties. Secondly, restrictions on the geometry and

refractive index profile of optical fibers hinder the flexibility in engineering fiber proper-

ties such as dispersion, nonlinearity and birefringence for better performance and more

specialized applications. Finally, light propagating in an optical fiber suffers from losses.

Several factors contribute to the attenuation in optical fibers, with material absorption

and Rayleigh scattering being the major contributing sources. Material absorption arises

from electronic and vibrational resonances of silica glass or impurities such as the OH−

ions in the fiber. Rayleigh scattering refers to the scattering of light from local fluctua-

tions in the refractive index introduced by inhomogeneities in the fiber that are on a scale

much smaller than the optical wavelength.

These limitations stimulated the development of a new class of optical waveguides

known as the photonic crystal fiber (PCF). In a PCF the fiber core is surrounded by a

1

2 CHAPTER 1. PHOTONIC CRYSTAL FIBERS

microstructured cladding based on a two-dimensional periodic lattice consisting of air-

filled capillaries running parallel to the fiber axis along the entire length of the fiber [26,

27]. Unlike conventional optical fibers, the PCF is usually made of a single material (sil-

ica), eliminating the need for two thermally, chemically and optically compatible glasses

to form its core and cladding. In addition, the PCF has several structural parameters one

can manipulate, offering great design flexibility and a wealth of physical properties for

many interesting applications. For example, the PCF allows highly-engineerable refrac-

tive index profiles to develop fibers of desirable nonlinearity, birefringence and chromatic

dispersion. The possibility for light to be guided in a hollow core also implies that it is

possible to fabricate fibers with losses lower than that achievable in conventional fibers

at wavelengths limited by high material absorption.

In this chapter, a brief historical overview of the development of PCF is given in

Section 1.2, followed by the classification and guidance mechanisms of various classes of

PCF in Section 1.3. A description of the general fabrication process is outlined in Section

1.4. The chapter concludes with an overview of optical sensing applications in PCF in

Section 1.5.

1.2 Historical Overview

Like many scientific inventions which are either inspired by or akin to living beings found

in nature, the photonic crystals of PCF also find similarities in the photonic stopband-

based nanostructures in the wings of butterflies (Figure 1.1(a)) and the iridescent setae

from polychaete worms (Figure 1.1(b)) [28]. The periodic variations in dielectric constant

in PCF also find analogy in semiconductor band structures in which electrons interact

with the periodic variation in the potential created by the atomic crystal lattice.

The idea of using periodic, one-dimensional variations in the dielectric constant to trap

light was first presented by Melekhin and Manenkov in 1968 [29] and Yeh et al. in 1978

[30], where it was proposed to clad a fiber core with a multilayer coating similar to that in

planar Bragg stacks. Light guidance in the Bragg fiber is therefore the result of a radial

stopband. The work by Yablonovitch [31, 32] predicted that certain three-dimensional

periodic dielectric structures can have a frequency band in which all propagation modes

1.2. HISTORICAL OVERVIEW 3

(a) (b)

Figure 1.1: (a) Iridescence in the butterfly Morpho rhetenor and transmission electronmicrograph (TEM) images showing wing-scale cross-sections. Scale bars: 1.8 µm, 1.3 µm.(b) Iridescent setae from polychaete worms: scanning electron micrograph (SEM) andTEM images of transverse sections through a single iridescent seta. Scale bars: 2 µm,5 µm, 1 µm, 120 nm [28].

are forbidden, termed the photonic bandgap (PBG). Within the forbidden bandgap range,

light can only exist and propagate along defects [33]. This mechanism completely inhibits

spontaneous emission (photonic states) in the lattice by having a three-dimensional pho-

tonic crystal. In comparison, the Bragg fiber still has photonic states in the cladding and

its guidance mechanism can therefore not be classified as that due to the PBG effect.

Similar to the three-dimensional photonic crystals, defects can be introduced into

photonic crystal slabs consisting of two-dimensional periodicities to form waveguides. The

guidance mechanism is based on the photonic bandgap effect in the plane of periodicity,

while light in the direction perpendicular to this plane is confined via the index guidance

mechanism. In comparison, guided propagation of the electromagnetic field in the PCF

is also achieved by the introduction of defects in the two-dimensional microstructured

morphology of the fiber. However, unlike the photonic crystal slab, light enters the PCF

waveguide normal to the plane of the periodicity. The difference between the photonic

crystal slab and the PCF can be understood via a simplified picture involving Bragg’s

law for constructive interference:

mλ = 2Λ cos θ, (1.1)


Year PCF Development

1996 First solid-core PCF [26, 27]

1997 Endlessly single-mode PCF [34]

1998 Ultra-large mode area [35]

1999 PCF with photonic bandgap and air core [36]

2000 Supercontinuum generation with PCF [37]

2001 Four-wave mixing [38]

2002 Laser-tweezer guidance of particles in HC-PCF [39]

2003 Tellurite glass PCF [40]

2005 All-solid photonic bandgap fiber at 1% index contrast [41]

Table 1.1: Overview of photonic crystal fiber development.

wherem is an integer, λ is the wavelength of the incoming light, Λ is the pitch of periodicity

and θ is the incident angle the incoming wave. It follows that for θ = 0 (as in the case

of the photonic crystal slab), Λ is of the order of λ; while for grazing incidence (as in

the case of the PCF), Λ is much larger than the wavelength of the incoming light. The

small pitch requirement of the photonic crystal slab waveguides leads to relatively high

losses and therefore makes the PCF the superior waveguide. The first PCF reported in

1996 was an index-guiding PCF and utilized a two-dimensional photonic crystal where

the structure is periodic in the plane perpendicular to the fiber axis but invariant along

the fiber length [26, 27]. A short overview of PCF development is presented in Table 1.1.

1.3 Classification and Guidance Mechanisms

Light guidance in the conventional fiber is based on the slight refractive index difference

between the two concentric regions of core and cladding with different doping levels.

Photonic crystal fibers, however, can be categorized into different classes, depending on

whether the mechanism of optical confinement is based on index guiding or photonic

bandgap effects, and whether the periodicity of the structure is one-dimensional or two-

dimensional.

1.3. CLASSIFICATION AND GUIDANCE MECHANISMS 5

d

�

nair

neff

ncore

Rad

ial

dis

tance

Index

jacket

core

cladding�

d

(a) (b)

Figure 1.2: Schematic illustration of (a) the cross-section and (b) the refractive indexprofile for an index-guiding photonic crystal fiber.

1.3.1 Index-Guiding PCF

Index-guiding PCF represents the simplest type of PCF, with its basic cross-sectional

structure being that of a solid core surrounded by a two-dimensional photonic crystal

consisting of a periodic array of air holes arranged in a hexagonal pattern on a silica back-

ground, extending invariantly along the length of the fiber, as illustrated in Figure 1.2(a).

In this case the two-dimensional photonic crystal is not utilized for its bandgap, but rather

to form a fiber cladding of lower effective index given that the solid core is made up of

the same material as the photonic crystal background. Figure 1.2(b) shows a schematic

demonstrating the subtle variations in the fiber’s refractive index profile. As a result,

light guidance is based on modified total internal reflection, akin to that in a conventional

fiber.

Due to the range of structures and air-filling fractions one can realize in the microstruc-

tured photonic crystal cladding, the PCF offers a number of unique properties that are

not attainable in conventional fibers. For example, the index-guiding PCF can be fabri-

cated to exhibit endlessly single-mode behavior. Here, the single lobe of the fundamental

mode with a diameter roughly equal to 2Λ is trapped in the core of the index-guiding

PCF while the lobes of higher-order modes are smaller and can leak out through the sil-

ica gaps between the cladding holes encircling the core. The fiber maintains its endlessly

single-mode behavior provided the relative hole size, d/Λ, is small enough; as the air holes


are made larger, successive higher order modes also become trapped in the fiber core.

State-of-the-art optical fibers constitute a careful trade-off between optical losses, opti-

cal nonlinearity, group velocity dispersion and polarization effects. During the last decade,

intense research and fabrication has led to precise control of the PCF characteristics com-

parable to that of standard fibers. Index-guiding PCF having loss of 0.18 dB/km at 1.55

µm has recently been obtained by reducing the OH− absorption loss and improving the

air hole surfaces [42].

By omitting more air holes in the core region of an index-guiding PCF, large mode

area single-mode PCF has been fabricated which supports a core diameter of 50 free-

space wavelengths [35], a property advantageous for the development of fiber lasers and

amplifiers.

The birefringence in PCFs can be attributed to either elasto-optical effect induced by

the anisotropy of the refractive index in the core due to internal stress, as in conventional

PANDA and bowtie fibers, leading to the demonstration of polarization-maintaining PCF

with large mode area [43, 44]; or the geometrical asymmetry in the fiber cross-section, as

in standard elliptical core fibers. The latter results in fibers with strong form birefringence

that are resilient to environmental factors such as temperature, strain and pressure, and

can be achieved by using holes with different radii or shape, or by local elongation of

the core region. Highly birefringent PCF with birefringence ten times larger than that of

conventional fibers has been fabricated [45].

The possibility to engineer the PCF structural parameters such as the cladding air hole

size and pitch, and the core diameter, allows one to efficiently manage the fiber chromatic

dispersion by changing its waveguide dispersion. Index-guiding PCFs having zero, low

or anomalous dispersion at visible wavelengths have been fabricated [37, 45, 46], while

ultra-flattened dispersion over a very large wavelength range has been demonstrated by

mirroring the PCF waveguide dispersion to the material dispersion [47-50].

The large core-cladding refractive index difference in SC-PCFs can lead to tight modal

confinement in the fiber and hence low effective mode area, giving rise to nonlinearities

one to two orders of magnitude higher than one can obtain in conventional fibers. This

high nonlinearity generally allows reduced interaction length and power requirement for

applications based on nonlinear optics, such as four-wave mixing [51, 52], multimode phase

1.3. CLASSIFICATION AND GUIDANCE MECHANISMS 7

matching [53], pulse compression [54] and generation of ultra-broadband supercontinuum

(SC) [55]. In addition to strong confinement of the guided mode, PCF nonlinearity can

also be enhanced by fabricating fibers from a single material constituent with high intrinsic

nonlinearity such as chalcogenide [56], tellurite [57], bismuth silicate [58] and lead silicate

[59] glasses.

1.3.2 Hollow-Core PCF

Standard hollow waveguides confine light either by total internal reflection (attenuated

total reflection guides) [60, 61] or by reflection off a metallic surface (leaky guides) [62].

These waveguides are inherently weak and highly multimode, allowing the use of only

relatively short lengths [63]. In contrast, hollow-core PCFs (HC-PCFs) [36] offer quasi

single-mode operation despite supporting multiple optical modes, including guided and

surface modes, at any given wavelength, provided careful launching conditions are applied

to selectively excite the fundamental mode. Furthermore, higher-order modes usually have

much higher confinement and scattering losses compared to the fundamental mode [64],

allowing one to effectively achieve single-mode output at the desired wavelength by em-

ploying long length of fiber [65] or by bending the fiber. Finally, HC-PCFs facilitate the

delivery of light with low attenuation over kilometer length scales, an attribute unachiev-

able in conventional hollow waveguides. Losses as low as 1.2 dB/km in HC-PCF has

been achieved by enlarging the core from 7 to 19 unit cells to reduce the overlap of the

fundamental core mode with the glass-air surface modes [66].

1.3.2.1 Photonic Bandgap PCF

An index-guiding PCF cannot be formed with a hollow core, as total internal reflection

requires the effective cladding index to be lower than that of the core index. Light guidance

in this case, however, can be realized by coherent Bragg scattering, in which light within

finite frequency regions is prohibited from propagating in the photonic crystal cladding

and is confined to a defect at the fiber core. Each of these frequency regions corresponds to

the existence of a full two-dimensional PBG in the fiber cladding; low-loss guided modes

can therefore be formed where a core resonance coincides with a bandgap. These fibers


(a) (b) (c)

Figure 1.3: Schematic illustrations of (a) a hollow-core PBG-PCF, with a two-dimensionally periodic cladding of air holes, (b) a kagome-lattice PCF, with a periodiccladding structure consisting of fine silica webs forming a kagome lattice and (c) a Braggfiber, with a one-dimensionally periodic cladding of concentric high and low index layers.

are called photonic bandgap PCFs (PBG-PCFs), as depicted in the schematic shown in

Figure 1.3(a). The PBG-PCF cladding generally comprises of a honeycomb lattice of air

holes and silica struts, with a large air-filling fraction of typically > 80%. In these fibers,

losses as low as 1.7 dB/km have been reported [67].

1.3.2.2 Kagome-Lattice PCF

In contrast to guidance via the existence of PBGs in PBG-PCF, another type of HC-PCF

has been demonstrated to allow guidance in the air core despite the lack of photonic

bandgaps. The cladding microstructure of these fibers consists of an array of thin silica

strands that form the kagome lattice, as depicted in Figure 1.3(b). The kagome fiber

exhibits much broader optical transmission bandwidth and lower dispersion compared to

the PBG-PCF. Several studies have been made towards understanding of the guidance

mechanism in the kagome fiber, such as low cladding density of states [68], reduced cou-

pling between the core and cladding mode fields [69, 70] and high-order bandgaps [71].

However complete understanding of the nature of guidance in these fibers is yet to be

established. In principle, the kagome fiber is a leaky waveguide in that there are always

real photonic states (i.e., propagating fields) in the cladding, consequently Fabry-Perot-

like resonances appear in the cladding. As a result, the leakage rate of the core “mode”

depends in a complicated oscillatory manner on the cladding thickness as well as the

1.4. FABRICATION 9

properties of the external medium, making the leaky core mode look more like a Mie res-

onance than a bound mode [64]. The kagome fibers typically have larger core diameters

than the PBG-PCFs, hence allowing them to support several such leaky resonances or

“modes”, resulting in higher losses than the PBG-PCFs, with the lowest loss achieved

thus far being 0.25 dB/m [72].

1.3.2.3 Bragg Fiber

Instead of employing two-dimensional periodicity in the fiber cladding, a one-dimensional

periodicity comprising of alternating multilayer of high and low index glasses (see Figure

1.3(c)) can also be used to confine light within a hollow core, resulting in what is known as

Bragg fibers, which were first proposed by Melekhin and Manenkov in 1968 [29] and Yeh

et al. in 1978 [30]. Bragg fibers based on omnidirectional mirrors have been demonstrated

[73] and utilized for delivery of high power lasers in endoscopic surgeries [74]. Note that

although strictly speaking the Bragg fiber cannot be categorized under PCF, it is included

here for reference.

1.4 Fabrication

The stack-and-draw technique is the most commonly used process in PCF fabrication.

Initially, the stack is manually built on a macroscopic scale using capillaries with a ratio

of inner diameter to outer diameter (ID/OD) closely matching the air-filling fraction (d/Λ)

of the desired fiber microstructure. The completed stack (typically 1 meter long and a

few centimeters in diameter) is then inserted into a jacket tube and drawn into preforms

of a few millimeters in diameter. Subsequently, the preform is either drawn directly

into fibers using a conventional fiber drawing tower, or drawn into canes before being

drawn into fibers in case a large scale reduction factor is required, as shown in Figure 1.4

for a hollow-core PBG-PCF. The newly-drawn optical fibers are then coated with high

performance polymers cured by ultraviolet (UV) exposure to improve their mechanical

properties. Techniques such as extrusion [59], built-in-casting [75] and drilling [76] for

preform production allow fabrication of PCFs using materials with lower melting points.


(a) (b)

Figure 1.4: (a) Optical micrograph showing the cross-section of the cane for a hollow-corePBG-PCF. (b) SEM showing the cross-section of a hollow-core PBG-PCF. The cane wasinserted into a separate silica jacket tube before being drawn into fibers to allow for largescale reduction during drawing. The cladding diameters were 2.6 mm for the cane and60 µm for the fiber.

1.5 Optical Sensing with PCF

The innovation of PCF has proven to be highly valuable for the design of advanced fiber-

optic components, enabling new optical phenomena and applications. In the realm of

optical fiber sensing, PCF offers a high degree of freedom in design flexibility, facilitating

the development of new sensing configurations. Photonic crystal fiber has proven to be

effective in enhancing light-matter interactions, offering interaction lengths much longer

than those available using conventional techniques, thus dramatically increasing its sensi-

tivity. The possibility for gases and fluids to occupy the holes in the PCF microstructure,

thereby utilizing them as a microfluidic channel or gas cell, offers a host of advantages.

A well-defined optical mode propagating through the micron-sized sample cell presents

a unique approach of monitoring the interaction between the propagating light and the

measurand. Furthermore, the micron-sized holes in the PCF microstructure strongly re-

duce the sample volume required for sensing. The follow sections detail the development

of fiber sensors based on index-guiding and HC-PCFs to date.

1.5. OPTICAL SENSING WITH PCF 11

(a) (b)

Figure 1.5: Schematic illustration of the active sensing regions around the core of (a) anindex-guiding PCF and (b) a hollow-core PBG-PCF.

1.5.1 Index-Guiding PCF Sensors

Most of the existing optical sensing techniques are based on the evanescent spectroscopic

sensor design, whereby the evanescent field associated with the light propagating in the

confinement region of the device extends into the region where the analyte to be sensed

is located. In the case of optical fiber sensors, this tailing optical field can transfer energy

out of the fiber core to the absorbing species in the surrounding medium. Additionally,

the evanescent field can also be used to create fluorescence in the surrounding medium, or

couple fluorescence into the fiber core. The change in the optical transmission properties

of the fiber due to the evanescent absorption of the analyte is then monitored, or “sensed”.

This sensor design therefore requires the chemical fingerprint region of the electromagnetic

spectrum to lie within the wavelength range of the light guided in the optical fiber core.

In order to access the evanescent wave near the boundary of the core and cladding of

a conventional fiber, standard evanescent-wave fiber sensors necessitate the complete or

partial removal of the fiber cladding by chemical etching [77], precise flame control [78], or

polishing [79, 80] to form a D-shape fiber. Alternatively, the evanescent wave of a tapered

fiber [81] can also be used to enhance the interaction between the guided light and the

sample [82].


The sensing mechanism of index-guiding PCF sensors is also based on the evanescent

interaction between the guided optical field and the sample, akin to that in the conven-

tional sensors (as shown in Figure 1.5(a)). However, they do not require cumbersome

post-processing procedures, since the presence of air-holes in the cladding microstructure

allows the accommodation of biological and chemical samples in gaseous or liquid forms

in the immediate vicinity of the fiber core. In addition, PCFs naturally integrate opti-

cal detection with microfluidics, allowing for continuous on-line monitoring of samples in

real-time. The infiltration of sample into the PCF cladding holes also allows the fiber to

maintain its original structure, without the need to even remove the polymer coating of

the fiber. Consequently the index-guiding PCF provides superior structural robustness

compared to the conventional fiber sensors.

The evanescent-wave PCF sensor configuration was first theoretically and numerically

studied by Monro et al. [83, 84]. In principle, strong light-matter interaction requires a

significant modal power overlap with the fiber holes within the wavelength range of the

sample absorption spectrum. The power overlap decreases with core size and increases

with wavelength, as light of longer wavelength is less tightly confined in the solid core of

the index-guiding PCF. Therefore, a larger fraction of the guided mode extends into the

cladding holes. The first experimental demonstration of evanescent-wave gas detection

with PCF used an index-guiding PCF with a length of 75 cm for the detection of acetylene

[85, 86]. The fiber used had a relatively low power overlap (∼ 5.5 % at 1530 nm) of the

optical field with the sample; nevertheless the long interaction length provided by the

PCF was able to compensate for weak light-matter interaction. Several approaches have

been reported in order to improve sensitivity of PCF sensors. For example, dual-cladding

PCF in which the solid fiber core was fabricated with additional holes to increase the

interaction of the optical field with the sample (e.g. from 0.041% to 4.22% at 633 nm for

a water-filled fiber [87]). The relatively simple concept of suspended-core fiber in which

a small core is held in air by three thin silica struts was introduced by ref. [83]. These

fibers have demonstrated large modal overlap of 29% at 1550 nm, which can find useful

applications in gas sensing [88].

In addition to chemical sensing, the evanescent-wave configuration has also been ap-

plied to biosensing, whereby fluorescently labeled antibodies in aqueous solution were

1.5. OPTICAL SENSING WITH PCF 13

detected via absorption spectroscopy [89]. Furthermore, SC-PCF has demonstrated su-

perior performance in surface-specific spectroscopy, whereby fluorescence sensing can be

optimized with improved detection efficiency of biomolecules compared to conventional

single-mode fibers [90, 91]. Additionally, it is worth noting that an axially periodic re-

fractive index variation can be inscribed in the solid core of PCFs, known as long-period

gratings (LPGs). These LPGs written in PCF are highly sensitive to refractive index vari-

ations of the external medium [92], and have been demonstrated as a label-free technique

for detection of biomolecules [93], as well as for temperature and strain measurements [94].

Finally, structural rocking filters can be fabricated by periodically twisting birefringent

PCFs [95]. Measurements of the sensitivity of the resonance wavelengths of the rocking

filters to temperature, strain and hydrostatic pressure have demonstrated application in

hydrostatic pressure sensing with very low cross-sensitivity to temperature [96].

1.5.2 Hollow-Core PCF Sensors

In addition to the various advantages mentioned in the previous sections, HC-PCFs exhibit

a significant advantage for sensing applications over evanescent wave PCF sensors in that

the modal overlap with the sample is considerably improved, guiding more than 90% of

the power in the core defect of the fiber. The direct interaction of the light and the sample

within the hollow fiber core is depicted in Figure 1.5(b). Consequently, the strong light

confinement provided by the PBG and the possibility of tuning the PBG by tailoring the

structural parameters have attracted much attention in the field of fiber sensors.

It has been shown that the hollow core of the PBG-PCF selectively filled with a dye

solution achieved an almost 100% modal overlap with the sample material, surpassing the

performance of index-guiding PCFs [97]. In particular, the detection limit of fluorescence

sensing was demonstrated to improve by four orders of magnitude. The study of gas

characteristics using PBG-PCF has been performed using a light-emitting diode (LED)

to measure the absorption spectra of hazardous gases [98]. The results obtained demon-

strated that gas sensing in PCF is feasible using low-power, cost-effective light sources to

realize miniaturization of the system setup.

In terms of biosensing applications, HC-PCF Bragg fiber has been demonstrated for

the detection of single-stranded deoxyribonucleic acid (DNA) by monitoring the changes


in the confinement loss of the Bragg fiber [99]. A Fabry-Perot strain sensor based on HC-

PCF has also been demonstrated to feature multiplexing capability, wide free-spectral

range, and insensitivity to temperature and fiber bending [100].

Chapter 2

Experimental Considerations and

Techniques

2.1 Introduction

Photonic crystal fiber sensors offer two modes of operation, namely, the resonant and non-

resonant regimes of sensing. In the non-resonant regime, one takes advantage of the large

optical modal overlap with the sample. Sensing is realized by monitoring changes in the

imaginary part of the sample’s refractive index, i.e., analyte absorption, by detecting the

presence and strength of the absorption bands within the fiber transmission spectrum, as

depicted in Figure 2.1(a). In this case, the absorption signal strength and sensor sensitivity

are directly proportional to the fiber sensor length, as will be shown in Section 2.2.

The second mode of operation of PCF-based sensor operates in the resonant regime

and can be categorized into two types. The first type relies on monitoring the changes in

the real part of the sample’s refractive index, by detecting the variations in the optical

confinement of a mode propagating inside a resonant fiber structure such as the PBG-PCF.

As the real part of the sample’s refractive index changes, the resonant condition for modal

confinement will also change, resulting in a strong variation of the fiber transmission loss,

as depicted in Figure 2.1(b). Such sensors can also operate in the non-resonant mode for

detection of changes in the imaginary part of the sample’s refractive index. The second

type of resonant sensors operate in the vicinity of a phase-matching wavelength between

a core-guided mode and a second mode which is sensitive to changes in the real part of

15

16 CHAPTER 2. EXPERIMENTAL CONSIDERATIONS AND TECHNIQUES

na

n i na+ Im{ }�

n na+Re{ }�

na

n

n

a -Re{

}�

(a)

Mo

dal

lo

ss

Mo

dal

lo

ss

�

(b)

�

Figure 2.1: Operational principles of optical sensors in the (a) non-resonant and (b)resonant regimes, whereby changes in the sensor transmission loss due to variations in the(a) imaginary and (b) real part of the analyte’s refractive index are monitored [8].

the sample’s refractive index, such as an absorbing plasmon mode propagating at the

interface between the analyte and the metal-coated fiber surface. As the real part of the

sample’s refractive index changes, the phase-matching condition between the core and

plasmon mode also changes, resulting in strong optical loss of the core mode at a specific

resonant wavelength [101, 102].

In this chapter, the figures-of-merit for sensing and photochemical reactions are intro-

duced in Section 2.2 to determine the ideal experimental conditions in PCF. The setup

and instrumentation considerations, including the transmission properties of liquid-filled

PCF, various components of the optical setup, microfluidic flow through the fiber and

computer automation of data acquisition, are summarized in Section 2.3. Finally, various

fabrication techniques for PCF devices, especially for sensors and photochemical reactors,

are described in Section 2.4.

2.2. DETECTION STRATEGIES AND IDEAL CONDITIONS 17

2.2 Detection Strategies and Ideal Conditions

2.2.1 Ideal Conditions for Absorption-Based Sensors

There are four major optical transduction mechanisms used in fiber-optic sensors, by

which the presence of a target analyte induces changes in the transmission of light through

the optical fiber, namely, absorbance, fluorescence or chemical luminescence, Raman scat-

tering, and surface plasmon resonance. The PCF sensors described in this thesis are based

on the exploitation of changes in the fiber transmission losses as a result of absorption by

the sample. The absorption-based sensing methodology can be based on both amplitude

and spectral interrogation.

In amplitude-based detection methodology, changes in the amplitude of an optical

signal at a given wavelength λ are used to deduce the changes in the analyte’s refractive

index. An amplitude sensitivity function S(λ, L) can be employed to characterize the

sensitivity of a fiber-optic sensor of length L [8]. S(λ, L) represents the relative change in

the irradiance P (δ, λ, L) of the transmitted light for an infinitesimal change in the measur-

and, δ, which can be any parameter capable of influencing the transmission properties of

a fiber sensor, such as the concentration and the real or imaginary parts of the refractive

index of the sample, and is defined as

S(λ, L) = limδ→0

P (δ, λ, L)− P (0, λ, L)

δ · P (0, λ, L)=∂P (δ, λ, L)/∂δ|δ=0

P (0, λ, L). (2.1)

The irradiance of light at the fiber output can be written as

P (δ, λ, L) = Pin(λ) exp[−α(δ, λ)L], (2.2)

where Pin(λ) is the light irradiance at the fiber input and α(δ, λ) is the fiber propaga-

tion loss. By substituting Equation (2.2) into Equation (2.1), the amplitude sensitivity

function can be rewritten as

S(λ, L) = − ∂α(δ, λ)

∂δ

∣∣∣∣δ=0

· L. (2.3)

According to classic perturbation theory, changes in the effective refractive index ∆neff

of a guided mode are related to the changes in the refractive index ∆na of the analyte

infiltrating the fiber,

∆neff = ∆na · φ = Re(∆na) · φ+ iIm(∆na) · φ, (2.4)


where φ is the fraction of power overlap in the analyte.

An important goal for non-resonant absorption-based sensors is the identification of

sample materials by the spectral shape of their absorption. Furthermore, the concentra-

tion of certain chemical compounds in the sample can be deduced from the magnitude of

the corresponding absorption peak. Defining N to be the number density of the absorbing

particles in the analyte, so that δ = N , it follows from Equation (2.4) that the total fiber

loss in the presence of absorbing sample can be written as

α(N, λ) = αf (λ) + σ(λ)Nφ, (2.5)

based on α(N, λ) ∼ Im(neff) and Im(∆na) ∼ σ(λ)N , where αf (λ) is the fiber loss in

the absence of the absorbing sample and σ(λ) is the absorption cross-section of a single

particle. Substituting Equation (2.5) into Equation (2.3) yields an expression for the

amplitude sensitivity function based on the experimental variables,

S(λ, L) = −σ(λ)φL. (2.6)

It follows from Equation (2.6) that the sensitivity of the fiber sensor is proportional to its

length and the fractional modal overlap of the guided mode with the sample analyte.

In fact, the absorption of light by a sample described in Equation (2.2) is the commonly

used Beer-Lambert law which relates the absorption of light to the properties of the

material through which it is traveling. Here, the conventional law is slightly modified to

take into account the fraction of the light φ that travels through the sample. The resulting

absorbance is

A(λ) = σ(λ)Nφ(λ)L = ln(10)ε(λ)cφ(λ)L, (2.7)

where ε(λ) is the molar absorptivity of the sample in Lmol−1cm−1, c is the molar concen-

tration of the sample in molL−1 (or simply in molar, M, as will be used interchangeably

throughout the thesis), and the mode-field overlap φ is wavelength dependent as will be

shown in Chapter 4. The convention of expressing the absorbance in dB, defined as

AdB(λ) = 10ε(λ)cφ(λ)L = 10 log10(e)σ(λ)Nφ(λ)L (2.8)

will be used throughout the thesis.

From Equations (2.6) and (2.7) one sees that the sensitivity is directly linked to the

absorbance signal amplitude, while Equation (2.2) signifies that the upper limit of the


1 10 1000.01

0.1

1

10

100

φ [%]

Fib

er

length

[m

]

1 cm cuvette

1.1 m SC-PCF

39 cm HC-PCFεc = 1 cm-1

εc = 0.1 cm-1

εc = 0.01 cm-1εc = 0.001 cm-1

Figure 2.2: Ideal sensing parameter diagram for constant absorbance of 5 dB, plottedin the φ-L plane, defining regions in which optimum sensing conditions can be achieved.The contour lines are of fixed εc. For a given εc, any combination of φ and L that lieson the corresponding line will result in a 5 dB absorbance signal. The fine dashed line at20 m indicates the fiber length above which the fiber loss becomes too high for sensitivemeasurement due to the power budget (ηdet is assumed to be 20 dB in this case). Thesolid circle, square and diamond symbols represent the experimental conditions for thesensing and photochemistry experiments in a 1 cm cuvette, 1.1 m of suspended SC-PCFand 39 cm of kagome HC-PCF described in Chapters 3 and 4.

sensor length is defined by the loss of the fiber. Assuming Pdet(λ) to be the lowest output

irradiance level of light at which changes can still be detected reliably, the maximum

sensor length allowed by the power detection limit can be calculated from Equation (2.2)

as

L =ηdet(λ)

αf (λ), (2.9)

where ηdet = ln[Pin(λ)/Pdet(λ)] is related to the power budget. Assuming that ηdet(λ) = 1

to allow for the characterization of the inherent sensitivity of the sensor, irrespective of any

additional power-dependent sensitivity enhancement, the maximum sensitivity allowed by

the power detection limit can be obtained by substituting Equation (2.9) into Equation

(2.6):

S(λ) = −φ σ(λ)

αf (λ). (2.10)

Note that as the absorption cross-section (similarly, the molar absorptivity) is completely

independent of the fiber loss, the sensitivity of the fiber sensor can therefore be increased

by using longer fibers with low propagation loss.

A general parameter diagram is shown in Figure 2.2 to provide further insight into


the optimum design parameters for fiber sensors. The absorbance signal (and hence the

sensitivity) is kept constant at AdB = 5 dB, which is sufficiently large to be detected by

any spectrometer of adequate signal-to-noise ratio and dynamic range. The lines in the

φ-L plane indicate contours of constant εc obtained from Equation (2.8). For a given

εc, any combination of φ and L that lies on the corresponding line will result in a 5 dB

absorbance signal. The lines thus define regions in which optimum sensing conditions can

be achieved. The intrinsic fiber loss in the absence of the absorbing particles is assumed

to be 1 dBm−1 in the calculations, while the power budget ηdB is assumed to be 20 dB.

The figure clearly demonstrates that the minimum value of a measurand, in this case the

concentration of the absorbing particles in the analyte, that can be detected by such a

fiber sensor is limited by the fiber loss, as indicated by the fine dashed line (at 20 m of fiber

length), since the sensitivity is limited by αf (λ) as shown in Equation (2.10). Depending

on the characteristics of the fiber used, the maximum fractional power overlap with the

sample can also be limited by the slope dφ(λ)/dλ for large values of φ(λ), resulting in a

sensitivity gradient in the measured absorption spectra. While the gradient in φ(λ) can

be compensated for, it is preferable to operate at lower values of φ, where it does not vary

much with wavelength.

2.2.2 Figure of Merit for Photochemistry

Photonic crystal fibers also provide a platform for performing photochemical reactions

within the holes of its microstructure. It is useful to examine critically the advantages

that PCF offers over a conventional cuvette-based sample cell (see Figure 2.3). Two im-

portant parameters determine the effectiveness of a photochemical experiment. Firstly,

the effective path length of the probe light (defined as the length at which the irradiance

drops to 1/e of the initial value in the pure liquid host, that is, in the absence of any

absorbing particle) should be long enough to allow detection of low concentrations. Sec-

ondly, the cross-sectional area of the sample cell should be as small as possible, so as to

maximize the irrdiance of the optical pump field; high intensities are required to achieve

rapid conversion, in particular for reactions with low quantum yields. Assuming that the

objective is to achieve complete photolytic conversion of all the chemicals in the sample,


1 cm

1 cm 1 cm19 µm

Figure 2.3: Schematics (not to scale) illustrating and comparing the geometries and sam-ple volumes in a conventional cuvette and a kagome PCF.

a suitable dimensionless figure of merit (FOM), is

FOM =Leffacuv

aeffLcuv

, (2.11)

where the ratio between the effective interaction length, Leff, and the effective cross-

sectional area, aeff, of the sample cell, is normalized to the respective depth, Lcuv, and

cross-sectional area, aeff, of a standard sample cuvette. The standard sample cuvette

is taken to be a 1 cm2 cross-section filled to a depth of 1 cm with the sample, with a

collimated pump beam illuminating the entire cross-section of the sample volume. The

FOM can be increased by a factor of 100 by reducing the cross-section of the cuvette from

1 cm × 1 cm to 1 mm × 1 mm, which is close to the smallest practical cuvette size.

For a free-space Gaussian beam tightly focused into a sample volume, the small ef-

fective area at the focus gives rise to high irradiance of the pump field, but is however

counter-balanced by the limitation in the effective interaction length as a result of strong

diffraction of the tightly focused beam, which is twice the Rayleigh range, zR,

Leff,Gaussian = 2zR =2πω2

0

λ, (2.12)

where ω0 is the radius of the beam waist and λ is the wavelength of operation. From the


definition for FOM in Equation (2.11), the FOM for a tightly-focused Gaussian beam in

free space is therefore inversely proportional to the wavelength of operation.

Hollow capillaries could be used to further decrease the cross-section, allowing FOM

to be increased by a further three orders of magnitude. However, the effective length of

such a sample cell is limited by optical leakage losses. With the conventional notations for

the electric field and irradiance of the EHnm mode (n 6= 0) as Enm(z) = E0 exp(−αnmz)

and Inm(z) = I0 exp(−2αnmz), respectively, the attenuation coefficient αnm for a perfectly

straight hollow capillary is [103]

αnm =(unm

2π

)2 λ2

r3

ν2 + 1

2√ν2 − 1

, (2.13)

where r is the bore radius, ν = n2/n1 is the ratio of the refractive indices of the capillary

cladding to the material in the hollow bore, and unm is the mth root of the equation

Jn−1(unm) = 0. With unm = 2.405 for the EH11 mode, the 1/e decay length is therefore

given by

Leff,capillary = 6.83r3

λ2

√ν2 − 1

ν2 + 1. (2.14)

The HC-PCF provides a near-ideal sample cell for photochemical reactions in that it

allows for single-mode guidance in a hollow core and the FOM is only limited by the fiber

loss rate, which dictates Leff. Table 2.1 shows the comparison between hollow capillaries

and the kagome HC-PCF used in the experiments. It is worth noting that the losses in

hollow capillary waveguides are very sensitive to even slight bends, making the use of long

capillaries very difficult. In contrast, hollow-core PCFs are almost completely insensitive

to bend losses, and the measured waveguide loss of the PCF used in the experiments is

175 times lower than the calculated loss of a hollow capillary with the same core diameter.

As a result, FOM for the kagome PCF is 175 times higher than a capillary with similar

dimensions, and more than seven orders of magnitude higher than a standard cuvette.

2.3 Experimental Setup and Instrumentation

2.3.1 Transmission Properties of Liquid-Filled PCF

Liquids play a prominent role in the fields of chemistry and biology, and since the emer-

gence of PCF, it has been suggested to utilize these fibers for the miniaturization of

2.3. EXPERIMENTAL SETUP AND INSTRUMENTATION 23

Sample cell configuration a [cm2] Leff [cm] Volume [mL] FOM

Cuvette 1 cm × 1 cm × 1 cm 1 1 1 1

Cuvette 1 mm × 1 mm × 1 mm 10−2 1 10−2 102

Focused Gaussian beam[a] 4.1× 104

Straight 19 µm glass capillary 2.8× 10−6 0.49[b] 1.4× 10−6 1.8× 105

Straight 100 µm glass capillary 7.9× 10−5 71[b] 5.6× 10−3 9.0× 105

19 µm core kagome PCF 2.8× 10−6 86[b] 2.4× 10−4 3.1× 107

Table 2.1: Comparison between various sample cell configurations and the kagome PCF.

[a] Free-space beam at 488 nm. [b] 1/e length, determined from waveguide losses.

chemical and biosensors, simplifying and enhancing the detection of the presence, ab-

sence, or properties of liquids and their constituents. Traditionally, the design for liquid-

core waveguides is limited by the nature of the waveguiding mechanism. Liquid-core

waveguides relying on the principle of total internal reflection allow only certain mate-

rial combinations, as the refractive indices of solid materials available for making up the

cladding are typically higher than most liquids. This design limitation presents a par-

ticular challenge for biosensors in which water is typically the basis for most biological

analytes, as it has a lower index than most solids used for making hollow capillaries.

One way to circumvent the index contrast problem is to use SC-PCF. By infiltrat-

ing its cladding air holes with materials of higher refractive indices, the index contrast

between the core and the cladding reduces, effectively weakening the strength of optical

confinement within the solid core. However, as the core mode remains index-guided within

the same silica core, the transmission spectrum of the liquid-filled fiber remains similar

to that of the unfilled fiber, with additional absorption dips in the transmission spectrum

due to the presence of the infiltrated material in the cladding holes. As the decrease in

index contrast also decreases the strength of confinement, the losses for the infiltrated

SC-PCF will be higher than the unfilled counterpart, with light at longer wavelengths

seeing more effect from the decreased confinement strength.

In order to increase the overlap between the probe light and the sample, a liquid-

filled hollow core is still the most desirable configuration. Several approaches have been

developed to combat the limitations imposed on the analyte index, such as applying a


layer of fluorinated polymer (e.g. Teflon AF, with an index of 1.29) on the inside of

a hollow capillary made of a rigid, higher index material. However, due to technical

limitations only large core diameters of 200-500 µm could be fabricated with relatively

large fluctuations in the thicknesses of the Teflon AF coating [104]. Furthermore, the

large core dimensions imply that the capillary is highly multimode.

Alternatively, non-TIR-based waveguides such as capillaries [103] (where the cladding

index is higher than the index of the liquid core) and metal-clad waveguides [105] (where

the inside of the cladding is coated with a highly reflective metal material) have been

used. Nevertheless, these waveguides suffer from attenuation issues (the source of which

is intrinsic in the case of capillaries, and surface imperfections in the case of metal-clad

waveguides) and are highly sensitive to bending losses.

The third and optimal approach would be to use interference-based waveguides such

as Bragg fibers and HC-PCFs. When the air holes in HC-PCF are filled with a material of

higher refractive index, the change in the refractive index contrast will inevitably change

the transmission properties of the fiber. The transmission spectra of the liquid-filled

HC-PCFs were found to be shifted in frequency according to the index scaling law for

PBG-PCFs which is derived from the scalar approximation of the vector wave equation

for the transverse field distribution [106]. When the low index material n2 of the PBG-

PCF is varied while the high index n1 remains unchanged, so that the index contrast of

the PCF changes from N0 = n1/n2 to N = n1/n′2, the wavelength λ0 of a photonic state

(bandgap) will shift to a new wavelength λ given by

λ = λ0

(1−N−2

1−N−20

)1/2

. (2.15)

Strictly speaking, Equation 2.15 is only valid for very small index contrasts, but can

still provide qualitative results for larger contrasts as the photonic states in PCFs result

from interference away from the interfaces where the effect of the vectorial term in the

wave equation can be neglected. Additionally, even though the kagome HC-PCF does

not guide via the PBG effect, this equation can still give qualitative indication of the

shift in the transmission band of the fiber when infiltrated with another material. This

equation becomes extremely useful when designing a PBG- or kagome HC-PCF for light

transmission that coincides with the absorption spectra of the chemicals to be studied in


0.8 1.2 1.6 2 2.4 2.8

0.5

0.6

0.7

0.8

λ0

[μm]

λ[μ

m]

Water

Acetone

Cyclohexane

Figure 2.4: Shift in the central wavelength of bandgap, from λ0 to λ, as a result ofinfiltrating the PBG-PCF with water, acetone and cyclohexane. The variation in therefractive indices in the range between 476.5 nm to 830 nm are nwater = 1.3380 to 1.3281,nacetone = 1.3644 to 1.3544 and ncyclohexane = 1.4325 to 1.4209.

the PCF sensor or reactor. Figure 2.4 shows the shift in the central wavelength of the PBG

as a result of infiltrating the PBG-PCF with various solvents used in the experiments,

including water, acetone and cyclohexane. The variation in the refractive indices in the

wavelength range between 476.5 nm to 830 nm are nwater = 1.3380 to 1.3281, nacetone =

1.3644 to 1.3544 and ncyclohexane = 1.4325 to 1.4209. The PBG of the fiber to be used for

experiments in various solvents can thus be determined. For example, for an experiment

where the absorption peak of the sample in water lies at λ = 650 nm, an unfilled PBG-PCF

with PBG at around λ0 = 1.2 µm is required for the experiment. Clearly, the spectral

position of the transmission window of the PBG-PCF is extremely susceptible to changes

in the local environmental conditions such as the refractive index, and can therefore be

utilized as the transduction signal in PCF sensors.

2.3.2 Microfluidic Flow in Confined Channels

Understanding the fiber filling process is important to PCF sensor design. Different

geometry of liquid flow pathway may result in different fiber filling behavior such as

infiltration time, possibility of entrapping an air bubble, etc. Knowledge of the infiltration

process allows for the optimization of liquid cell design and the arrangement of components

such as splits and valves to avoid potential filling problem and achieve high filling speed.

Consider a capillary immersed in a liquid, as depicted in Figure 2.5, there are four


Air

Liquid

�c

Figure 2.5: Cross-section of a capillary tube infiltrated with liquid. For θc < 90◦, theforce will pull the liquid into the capillary; for θc > 90◦, the force will push the liquid outof the capillary.

forces acting on the column of liquid inside the capillary, namely the capillary force, the

friction force (which is related to the viscosity of the liquid), the force from an applied

overhead pressure and the gravitational force [107]. The capillary force for a circular

capillary is given by

Fc = 2πaσ cos θc, (2.16)

where a is the radius of the capillary, σ is the surface tension and θc is the contact angle

between the liquid and the inner wall of the capillary. For θc below 90◦, the force will pull

the liquid into the capillary, while for contact angles larger than 90◦ the force will push

the liquid out of the capillary. The small dimensions of the fiber holes lead to very small

Reynold’s numbers which imply that the liquid flow inside the capillaries will be laminar.

The frictional force which results from the Poiseuille flow is

Ff = −8πµxv, (2.17)

where µ is the dynamic viscosity of the liquid, x is the length of the liquid column and

v is the average velocity of the liquid flow. The force of an applied overhead pressure is

given by

Fp = ∆Pπa2, (2.18)


where ∆P is the pressure difference between the liquid in the capillary and the open end

of the fiber. Finally, the gravitational force acting on the liquid column is

Fg = −ρgπa2x, (2.19)

where ρ is the density of the liquid and g is the gravitational constant. Balancing all four

forces acting on the liquid column yields

d

dt

(ρπa2xv

)= 2πaσ cos θc − 8πµxv + ∆Pπa2 − ρgπa2x. (2.20)

Noting that v = dx/dt and neglecting the gravitational term for a horizontally oriented

fiber, the equation can be expressed as

d2

dt2(x2)

+Bd

dt

(x2)

= A, (2.21)

where the constants A and B are

A =4σ cos θc + 2∆Pa

ρa, (2.22)

B =8µ

ρa2. (2.23)

The differential equation in Equation (2.21) has the solution

x(t) =

[A

B2exp(−Bt) +

A

Bt− A

B2

]1/2

. (2.24)

Figure 2.6 shows the simulated infiltration length as a function of filling time for water

in capillaries with bore radii of 1, 5 and 10 µm, with an applied pressure head of 1 bar.

The results clearly shows the strong dependence of the filling time on the size of the fiber

holes, with the larger core in the case of a HC-PCF being filled before the smaller holes

in the microstructured fiber cladding. In the case where the hollow core is completely

filled for the entire length of the fiber while the cladding holes are empty or only partially

filled, the fiber becomes index-guided as the core now has a higher index than the effective

index of the unfilled PCF cladding. The large index contrast and core size of the liquid-

filled fiber would lead to highly multimode guidance (∼ 103 for operation in the visible

wavelength region), resulting in difficult, if not impossible, coupling to the fundamental

mode, which is an undesirable effect especially if the measurements are phase-sensitive.


0 1 2 3 4 50

0.25

0.5

0.75

1

Infiltration time [min.]

Infiltra

tio

n le

ng

th [

m]

a = 1 µm

a = 5 µm

a = 10 µm

Figure 2.6: Simulated water filling time for silica microchannels of bore radii 1, 5 and 10µm, with an applied pressure head of 1 bar. The physical constants for water at 20◦Cused were: θc = 0◦, σ = 72.88 mN/m, ρ = 998 kgm−3 and µ = 0.001 Pa·s.

Calculations and design of specific PCF cladding structures for the single-mode guidance

of liquid-core PCF have been performed and suggested [108]; however the wavelength

and index contrast dependence of the cladding design make the proposed approach an

impractical one. It is therefore essential to continue the infiltration process for a longer

period of time until all the holes in the cladding have been filled with the liquid so as

to maintain single-mode guidance of the HC-PCF, with shift in the transmission window

according to the index scaling law discussed in Section 2.3.1.

2.3.3 Optical Setup

The general configuration of the optical setup used in the sensing and photochemical

experiments is depicted in the schematic shown in Figure 2.7. The main components

constituting the setup are described in the following sections.

2.3.3.1 Broadband Light Sources

A broadband light source is a crucial part of the setup used for broadband absorption

spectroscopy. Depending on the wavelength range of interest, either a PCF SC source

or a fiber-coupled xenon lamp is used. Supercontinuum with emission in the wavelength

range from 480 nm to beyond 1750 nm was generated from an ESM-PCF pumped by a

Q-switched Nd:YAG (yttrium aluminum garnet) microchip laser at λ = 1064 nm [52].


10x4x

10x 20xBroad-band

10xSpectro-

meterComputer

Excitation

CCD

Sample fiber

ESM PCF

MMF

BS1 BS2

Figure 2.7: Schematic diagram showing the experimental setup for sensing and pho-tochemistry experiments in PCF. The broadband light source and excitation laser areco-aligned using a 50:50 beam splitter (BS1) and coupled into 15 cm of ESM-PCF forspatial filtering before being coupled into the fiber filled with the sample chemical. Thetransmitted light is collected by the spectrometer via a multimode fiber (MMF) and 8%of the output beam is coupled out via a 92:8 beam splitter (BS2) and imaged on a CCDbeam profiler. Both light sources and the spectrometer are controlled electronically toautomate the data collection process (for the measurement of photochemical reactionkinetics).

The single-mode output of the SC allows for easy coupling into most sample fibers, but

has a disadvantage in that it does not provide sufficient output for wavelengths below

480 nm. In this case, a xenon lamp which provides usable wavelength from 380 nm to

1000 nm was used in experiments where the absorption spectrum of the sample lies at

the shorter wavelengths in the visible. However, the spatial incoherent nature of the lamp

implies that spatial filtering is required. This was achieved by coupling the output of

the xenon lamp through 15 cm of ESM-PCF. The coupling efficiency of the xenon lamp

through the ESM-PCF was less than 10%, however, the filtered light remained in a single

optical mode, allowing coupling to single fiber modes in the sample fiber.


2.3.3.2 Excitation Light Sources

Additional excitation sources were required in the photochemical experiments in order to

induce photochemical conversions of the chemical samples studied in the PCF nanoreac-

tors, as will be described in Chapter 3. A 20 mW pulsed microchip laser emitting 532 nm

pulses at 6 kHz and a 20 mW continuous wave diode laser emitting at 488 nm were used to

drive the photochemical reactions. As the samples have wavelength-dependent molar ab-

sorptivitiy coefficients, the rate of photochemical conversion would vary depending on the

wavelength of excitation. Both excitation sources were coupled into the same ESM-PCF

used as a spatial filter for the broadband light source so that excitation lasers of different

beam quality and divergence can be coupled into the sample fiber via the same setup.

Furthermore, the combination of all the light sources through the ESM-PCF spatial filter

simplifies the in-coupling of the light sources into the sample fiber and ensures that they

are all launched into the same fiber mode.

2.3.3.3 Liquid Cells

Both ends of the PCF were connected to custom-made liquid cells having thin sapphire

windows for in- and out-coupling of light. The aqueous sample was introduced into the

PCF by using a single-syringe infusion pump connected to one of the ports of the liquid

cells. The dead volume in the liquid cells was limited to 50 µL and the liquid cells could

withstand water pressures up to 10 to 500 bars, depending on the thickness of the glass

windows used (0.08 to 1 mm).

2.3.3.4 Numerical Aperture

Both the broadband and excitation sources (for photochemical experiments) were com-

bined through the ESM-PCF and coupled into the sample fiber via an objective, allowing

more freedom over coupling parameters than fiber butt coupling. The coupling of light

into the fibers was optimized by matching the numerical aperture (N.A.) of the coupling

objective to that of the fiber. The N.A. of the index-guiding fiber can be approximated

by

N.A. =√n2

1 − n22, (2.25)


n2

n2

n1

nliquid

nwindow

nair

Figure 2.8: Schematic diagram (not to scale) illustrating the increase in the effective N.A.as a result of change in the interface medium of the objective (air) to that for the fiber(liquid). The actual fiber N.A. and the effective N.A. are related via Snell’s law.

where n1 and n2 are the refractive indices of the core and cladding material, respectively.

The N.A. of the HC-PCF can be approximated by

N.A. =λ

2D, (2.26)

where λ is the wavelength of operation and D is the diameter of the hollow fiber core. It

is worth noting here that HC-PCF generally have very low N.A. in the order of 0.01.

The change in the interface medium of the objective (air) to that for the fiber (liquid)

will result in a higher effective N.A. (see Figure 2.8) given by

N.A.eff =nliquid

nair

N.A.. (2.27)

An objective with N.A. in accord with N.A.eff for the fiber/liquid-cell combination should

therefore be chosen for efficient coupling of light into the fiber.

2.3.3.5 Spectrum and Mode Profile

The transmitted light at the output facet of the fiber was collected and collimated by a

10×0.25NA objective. A 92:8 beam splitter imaged a small portion (8%) of the trans-

mitted light via a lens onto a charge coupled device (CCD) beam profiler to measure the

irradiance profile of the guided mode to ensure coupling to the fundamental core mode,

while the rest (92%) of the light was coupled to a multimode fiber (MMF) connected to

either an optical spectrum analyzer (OSA) or a USB spectrometer.


2.3.4 LabVIEW Automation

A stepwise measurement approach was implemented in the photochemistry experiments

described in Chapter 3. This was done to avoid signal saturation in the spectrometer

caused by the excitation sources, which had much higher irradiances than the broadband

probe light used to measure the absorption spectra. Furthermore, the wavelengths of

the excitation sources coincided with the absorption features of interest in the sample

absorption spectra, thereby making the use of optical bandpass filters inappropriate. The

broadband and excitation light sources, as well as the spectrometer, have electronic shut-

ters which were controlled by a LabVIEW program to allow for automated exposure of

the photochemical sample under study and collection of spectra for signal processing.

During one iteration of the program, the excitation source is switched on to irradiate the

sample for a predefined exposure time, and the broadband light source is then switched

on to enable the spectrometer to acquire a spectrum. The whole cycle repeats until the

photoreaction is complete or the photostationary state of the reaction is reached.

2.4 Fabrication Techniques for PCF Devices

Several techniques have been developed for the fabrication of PCF devices with applica-

tions spanning beyond the field of fiber optic sensors. The techniques described in the

following sections have been developed and studied with the main objective of combining

PCF sensors with microfluidics.

2.4.1 Femtosecond Laser Ablation

When a pure transparent material is exposed to high laser irradiance, nonlinear material

responses can lead to the promotion of electrons from the valence band to the conduction

band (photoionization), depositing laser energy into the material in the process (free-

carrier absorption by plasma) and ultimately causing damages in the material [110-112].

There are two different regimes of photoionization, namely the multipohoton ion-

ization regime and the tunneling ionization regime. For low laser frequencies, nonlinear

photoionization is a tunneling process, as depicted in Figure 2.9(a), whereby the Coulomb

2.4. FABRICATION TECHNIQUES FOR PCF DEVICES 33

(a) (b)

Figure 2.9: Schematic diagram of photoionization regimes. (a) At low frequencies, pho-toionization occurs via tunneling of the valance electron through the suppressed Coulombwell. (b) At high frequencies, photoionization occurs via excitation of the valence electronas a result of multiphoton absorption [109].

well that binds a valance electron to its parent atom is suppressed by the strong applied

electric field to a level which allows the bound electron to tunnel through and become

free. For higher laser frequencies, nonlinear photoionization is a process involving the

simultaneous absorption of multiple photons to reach energy higher than the bandgap of

the material and excite the electron from the valence to the conduction band, as shown

in Figure 2.9(b).

For a seed electron already in the conduction band, which can be provided either

by thermal excitation, ionization of impurity states, or by multiphoton or tunnelling

ionization, it can linearly absorb more photons through free-carrier absorption (see Figure

2.10(a)) and move to an even higher energy state in the conduction band. Once the

electron has enough energy it can impact ionize another electron in the valence band,

resulting in two electrons near the conduction band minimum, as depicted in Figure

2.10(b). This avalanche process can then continue to impact ionize more valence band

electrons.

Once the electron plasma density becomes high enough such that the plasma frequency

reaches the laser frequency, the absorption of laser energy becomes very efficient and as

a result a large fraction of the laser pulse energy will be deposited in the focal volume.

It is this deposition of laser energy that leads to permanent damage of the material. For


(a) (b)

Figure 2.10: Schematic diagram of avalanche ionization. (a) A seed electron in the con-duction band linearly absorbs more photons through free-carrier absorption and movesto a higher energy state in the conduction band. (b) Once the free election has enoughenergy it impact ionizes another electron in the valence band, resulting in two electronsnear the conduction band minimum [109].

longer pulses (> 10’s of ps), the damage mechanism is achieved via thermal diffusion of

the energy build-up at the focal volume. Once the temperature becomes high enough the

material begins to melt. For pulses shorter than a few picoseconds, the pulse duration

is shorter than the time scale for thermal diffusion, and material breakdown is achieved

via the build-up of plasma density through self-seeded electrons (via photoionization at

the leading edge of the laser pulse) for avalanche ionization. The damage mechanism for

short pulses is much less dependent on material defects (for seed electrons) than for longer

pulses, and therefore has more determinist damage threshold; as less energy is required

for reaching the damage threshold irradiance, less energy is deposited in the material,

effectively allowing more precise ablation of the material, which is ideal for controlled

micromachinging of PCF devices.

Figure 2.11 shows a schematic for the setup used for femtosecond laser ablation of

PCF. The goal was to fabricate microfluidic side channels into the PCF cladding holes,

through which liquid or gas can be infiltrated to reach the core region of the fiber for

detection or reaction. The system used for micromachining is a regeneratively amplified


BS

HeNe

Ti:S

CCD

50x

50x

Figure 2.11: Schematic diagram showing the experimental setup for femtosecond laserablation of side channels in PCF and the two-photon polymerization technique for selectiveblockage of microstructure holes. The system used for both experiments is a regenerativelyamplified Ti:Sapphire laser producing 150 fs pulses at 800 nm, with a maximum pulseenergy of 8 µJ at a repetition rate of 100 kHz.

Ti:Sapphire laser producing 150 fs pulses at 800 nm, with a maximum pulse energy of 8 µJ

at a repetition rate of 100 kHz. The laser pulses are co-aligned with a He-Ne laser used for

alignment and illumination, and focused through a 50×0.55N.A. Mitutoyo objective lens

with a working distance of 13 mm. The backscattered light re-enters the objective lens

and passes through a telescope for imaging on a CCD camera, allowing on-line monitoring

of the ablation process. Spatial characterization of the pump beam was performed by a

knife-edge measurement at the focus of the lens and the focal size of the laser beam was

measured to be 2.5 µm. The objective was measured to transmit 30% of the input power

for average power levels below 50 mW.

In order to determine the threshold energy required to achieve optical breakdown

in fused silica, varying laser powers were focused on the surface of bare capillary fiber

made of fused silica, the same glass as that used in the PCF. The formation of surface

void was monitored using the CCD camera. The damage threshold for fused silica was

determined to be 50 nJ, corresponding to a peak power of 0.3 MW and an irradiance of

1.7× 1012 W/cm2.


0 2.5 5 7.5 100

5

10

Number of pulses [×103]

Ep

= 0.36 µJ

Ep

= 0.75 µJ

(b)

0 0.2 0.4 0.6 0.80

5

10

En

try h

ole

dia

me

ter

[µm

]

Measured

Analytical

(a)

Pulse energy [µJ]

Figure 2.12: (a) Diameter of ablated entry hole in the silica fiber as a function of pulseenergy incident on the fiber. The solid curve shows the analytically calculated hole di-ameter for a constant damage threshold of Eth = 50 nJ and a Gaussian beam waist ofω0 = 2.5 µm. (b) Diameter of ablated entry hole in the silica fiber as a function of thenumber of pulses incident on the fiber for constant pulse energies of 0.36 and 0.75 µJ. Forexposure exceeding 2000 pulses (20 ms) the hole diameter saturates at 9 µm.

The diameters of the entry holes were subsequently characterized as a function of

pulse energy by focusing the laser beam onto the surface of the bare fibers and varying

the laser pulse energy while keeping the exposure time constant at 30 s. Figure 2.12(a)

shows the measured entry hole diameter as a function of pulse energy incident on the

fiber surface. The solid curve shows the analytical estimate of hole diameter calculated

assuming a Gaussian irradiance distribution of the beam waist (see Figure 2.13),

D = 2ω0

√ln(Ep/Eth)

2, (2.28)

where D is the ablated entry hole diameter, ω0 is the beam waist, and Ep and Eth are

the pulse energy and the threshold energy (50 nJ). The error bars indicate the standard

deviation of the measurements taken at the respective pulse energies. The higher measured

values are due to the edges of the entry hole being blown away by the material in the

center of the focus which is ablated by the laser.

The diameters of the entry holes were then measured as a function of exposure time

while keeping the pulse energy constant. Arrays of holes were made with varying exposure

time and pulse, and examined post-mortem using an optical microscope. Figure 2.12(b)

shows the diameter of the entry holes as a function of the number of pulses for pulse

energies at 0.36 and 0.75 µJ. No notable difference was observed for irradiation with 0.36


Figure 2.13: Schematic showing the dependence of the diameter of laser-ablated entryhole size on the peak irradiance, assuming a Gaussian irradiance distribution.

and 0.75 µJ pulses. Interestingly, for exposure exceeding 2000 pulses, the hole diameter

saturates at 9 µm, which is larger than the values measured in Figure 2.12(a).

Long microchannels from the surface of the fiber to the core were drilled by translating

the fiber through the laser focus using a piezo-controlled stage. Figure 2.14(a) shows SEM

of a microchannel drilled on the side of a suspended-core fiber used for evanescent-wave

sensing, allowing the lateral access of the cladding hole for introducing gas or liquid

samples without influencing the incoupling of light. The resulting microchannel had a

diameter of less than 2 µm.

In order to verify the robustness of the microchannels, water was pumped through

the microchannels (with core diameters of ∼ 1 µm) from the core of the capillary fibers

using a liquid pump for high performance liquid chromatography (HPLC) at pump pres-

sures ranging from 6 to 30 bar (corresponding to maximum fluid flow of vmax = 0.67 to

3.33 ms−1). The channels remained unmodified for pressures below 8 bars. At higher

pressures, the side walls of the channels were damaged, as shown in Figure 2.14(b).

Loss measurements were performed for an ESM-PCF with multiple drilled microchan-

nels. The loss due to individual microchannels drilled through the cladding region (down

to the core) was determined to be about 1.1 dB per channel at around λ = 800 nm, and

0.65 dB per channel at around λ = 1550 nm (see Figure 2.15). The loss scales with ω2,


(a) (b)

Figure 2.14: (a) Example of ablated side microchannel allowing access to one of thethree cladding holes in a suspended-core fiber. (b) Ablated side microchannel in a 40 µmcapillary fiber damaged after applying 30 bar of water pressure using a HPLC pump.

0 2 4 6

0

4

8

Number of drilled microchannels

α(7

50 to 8

50 n

m)

[dB

]

Measured

αfit

= 1.1 dB/channel

0 2 4 6

0

4

8

Number of drilled microchannels

α(1

.5 to 1

.6μ

m)

[dB

]

Measured

αfit

= 0.65 dB/channel

(a) (b)

Figure 2.15: Measured transmission losses (α) as a function of the number of drilled sidechannels in an ESM-PCF. The losses are averaged losses in (a) the 750-850 nm wavelengthrange and (b) the 1500-1600 nm range.

and can be attributed to Rayleigh-Gans scattering, which is applicable for scatterers with

dimensions approaching that of the incident light and have scattering cross-sections that

scale with ω2 [113].

2.4.2 Two-Photon Polymerization

Microfabrication technology utilizing two-photon polymerization (TPP) [114] has been

intensively studied towards the development of micromachines [115] and photonic devices

[116]. As the probability of n-photon absorption is proportional to the nth power of the

photon flux density, high photon flux densities are required to observe this phenomenon


(a) (b) (c)

Figure 2.16: (a) Side view of an HC-PCF with all of the cladding holes infiltrated withthe acrylic resin via capillary effect (depth of infiltration ≈ 120 µm. (b) TPP-fabricatedstructure with 10 photopolymerized cladding holes (1 µm diameter) in a SC-PCF. (c) Agold nanowire embedded into one of the sub-micron holes next to the core of a polarization-maintaining PCF using TPP as the hole-collapsing post-processing procedure [118]. Imagecourtesy of Howard Lee.

[117]. This requirement for high irradiance can again be provided by short-pulse lasers

with high pulse peak powers. In two-photon absorption (TPA) a molecule can absorb

two photons simultaneously to allow electron transition to the states not attainable with

single photon absorption. An UV photopolymerizing material is photo-solidified in a

small volume within the depth of focus of a pulsed near-IR laser, while the resin, which is

usually transparent in the IR, remain unpolymerized in regions where the laser beam is

out of focus due to the optical density being lower than the threshold required for TPA.

The polymerization is a process in which monomers or oligomers interconnect to form

polymers. Photoinitiators with low photodissociation energies are often added to increase

the photosensitivity of the material. Upon absorption of two NIR photons, radicalized

photoinitiator is formed via bond cleavage (photodissociation). The radicals break the

C=C double bonds in the acrylyl groups of the monomers and oligomers, resulting in

radicalized monomers and oligomers. The radicals then combine with other monomers

and oligomers and this chain reaction of radical polymerization eventually terminates

when a chained radical combines with another chained radical.

In our experiments we made use of TPP for the selective collapsing of PCF cladding

holes with applications in the fabrication of microfluidic circuits within the PCF as well

as in other novel PCF devices. Selective collapsing of PCF cladding holes was initially

investigated using the approach of direct mechanical insertion of photosensitive resin into

the target holes. A femto-tip and a micromanipulator were used to insert the resin into


individual holes with the aid of a CCD camera attached to a microscope. In spite of

the high accuracy of the micromanipulator and the small size of the tip, the results were

however unsatisfactory due to the time-consuming nature of the process, problems with

hardening of the glue on the tip, and destruction of the microstructured cladding caused

by the mechanical contact of the tip with the fiber. Using a similar setup configuration as

for the femtosecond micromachining process described in the previous section, with the

replacement of the fiber holder (by rotating it by 90◦ to that depicted in Figure 2.11),

the laser beam now replaces the mechanical tip. A photosensitive acrylic resin fills all the

cladding holes of the fiber via capillary effect. Figure 2.16(a) shows an image of the side

view of an HC-PCF with all of its cladding holes infiltrated with the acrylic resin. With

the laser beam focused on the cleaved facet of the fiber, the individual target holes were

selectively exposed to irradiation with an average power of 3 mW and an exposure time of

1 s. The unpolymerized resin in the unexposed holes was then rinsed away with acetone,

revealing the fabricated structure as shown in Figure 2.16(b). The polymer-blocked holes

were tested to withstand water pressures up to 20 bar. With some further post-processing

such as the inflation or collapse of holes using a flame on a fiber tapering rig, the technique

presented here has allowed metallic [118] and semiconductor nanowires [119] in the PCF

microstructure to be fabricated. Figure 2.16(c) shows an example of the above-mentioned

hole-collapsing procedure in which a single gold nanowire is embedded into one of the

sub-micron holes next to the core of a polarization-maintaining PCF [118]. As symmetry

is not necessary in post-processed fibers, this technique allows for flexible designs of fiber

devices. Similar techniques have been used to fabricate an all-fiber mode converter [120].

2.4.3 Focused Ion Beam Micromachining

Another method investigated to allow side access of the longitudinal holes of PCF is

via focused ion beam (FIB) micromachining [121, 122]. The use of FIB for the routine

fabrication of micro- and nano-structures and devices is based on a sputtering process in

which the collision of an energetic ion beam with the target material overcomes its binding

energy, resulting in the ejection of the material. Figure 2.17(a) shows a 45× 45 µm2 hole

milled in the silica jacket (approximately 35 µm in thickness) of a nanoweb fiber1 [123]

1Fiber fabricated by Michael Scharrer and Alexander Podlipensky.


(a) (b)

Figure 2.17: (a) A 45×45 µm2 hole milled through the silica jacket (approximately 35 µmin thickness) of a nanoweb fiber. (b) SEM of the cross-section of the nanoweb fiber priorto FIB milling.

(Figure 2.17(b)), exposing the nanoweb structure in the fiber. The exposed nanoweb

allows for a wide range of experiments to be performed on the in-fiber planar waveguide.

In terms of sensing, the fiber geometry offers improved surface-to-volume ratio advantage

especially useful for surface enhanced reactions.

Chapter 3

Photochemistry in PCF

3.1 Introduction

There is rapid growth in the applications of photochemistry in many areas, including

medicine [124-127], chemical synthesis [128, 129], and the conversion and storage of solar

energy [130, 131]. Two important constraints currently limit many photochemical exper-

iments. As discussed in Section 2.2, if spectroscopy (e.g., in the UV/Vis) is to be used to

monitor reactions, the product of molar absorptivity and concentration, integrated over

the optical path length, must be above a certain value which is limited by the detection

limit of the system. For weakly absorbing or sparingly soluble samples, the only way to

satisfy this condition is to increase the optical path length; in a conventional cuvette this

implies large sample volumes, which is a major drawback for valuable samples such as

biological constructs or multistep synthetic products. Furthermore, high pump intensities

are required for rapid photochemical conversion, in particular for reactions with low quan-

tum yields. If modest laser powers are to be used, this means that the cross-sectional

area of the excitation beam should be as small as possible, and comparable with the

cross-sectional area of the sample cell. In systems with low quantum yields and weakly

absorbing or sparingly soluble samples, the ideal photochemical cell is therefore one that

combines long optical path length with small cross-sectional area which is comparable to

the size of the excitation beam.

There is no obvious way to satisfy these conditions in existing microfluidic and lab-

on-chip systems, in which fluid flow is manipulated and chemical reactions monitored in

43

44 CHAPTER 3. PHOTOCHEMISTRY IN PCF

sub-millimeter scale channels [132-135]. Some progress has been made in this direction

using SC-PCF, in which the sample is probed by the evanescent tailing field of the guided

mode [86, 87, 136, 137]. A more revolutionary approach exploits HC-PCFs for their ability

to maximize the interaction between the optical field and the low refractive index sample

at path lengths that are much longer than achievable in conventional single-pass sample

cells [98, 138]. Hollow-core PCFs have several major advantages over conventional sample

cells: the sample volume per optical path length is very small, long optical path lengths

are possible as a result of very low intrinsic waveguide loss, and furthermore the light can

travel in a diffractionless single mode with a constant transverse irradiance profile.

In this chapter, the demonstration of a liquid-filled HC-PCF as a highly-controlled

photochemical reactor is reported. In Section 3.2 the fiber characteristics of the HC-PCF

used in the experiments are presented. Two photochemical experiments were performed

to demonstrate the effectiveness of the PCF reactor in monitoring both irreversible and

reversible photochemical reactions, exemplified here by the photolysis of a cobalamin in

Section 3.3 and the photoswitching of an azo dye derivative in Section 3.4.

3.2 Fiber Characteristics

In HC-PCFs, guidance is achieved through two mechanisms, as described in Section 1.3.

In PBG-PCF, a core resonance coincides with a photonic bandgap in the microstructured

cladding, resulting in the formation of ultra-low loss (∼1 dBkm−1 in the best cases)

guided modes over restricted bandwidths of typically a few hundred nanometers. In

contrast, the guidance mechanism of kagome HC-PCF is based on the reduced coupling

between the core mode and the cladding modes [69, 70], resulting in higher losses in the

order of 1 dBm−1, nevertheless still better than in a capillary. The kagome HC-PCF

has a spectrally much broader guidance band than the PBG-PCF, making it the fiber

of choice for broadband spectral measurements. A scanning electron micrograph (SEM)

of the kagome HC-PCF used in the experiments is shown in Figure 3.1(a). The fiber

was made from fused silica, with a hollow core of 19 µm in diameter, surrounded by a

kagome lattice of thin silica webs with a cladding pitch of 10 µm that runs along the entire

length of the fiber. The structural parameters of the fiber correspond to an approximate

3.2. FIBER CHARACTERISTICS 45

50 µm 50 µm

(a) (b)

Figure 3.1: (a) Scanning electron micrograph showing the cross-section of the kagome HC-PCF used in the experiments. The fiber was made from fused silica, with a hollow coreof 19 µm in diameter, surrounded by a kagome lattice of thin silica webs with a claddingpitch of 10 µm that runs along the entire length of the fiber. (b) Optical micrograph of thelight emerging from 3 cm length of the fiber illuminated from below with a halogen lamp.The colors observed in the cladding holes are caused by long-lived Mie-like resonancesand are related to the slight nonuniformity in the air hole diameters.

sample cell cross-section of 284 µm2, giving an ultra low sample volume of 2.8 nLcm−1.

The enhanced sensitivity and pumping efficiency means that even systems with very

small quantum yields can be measured much faster than in conventional cuvettes, as will

be shown in the later sections. Figure 3.1(b) shows an optical micrograph of the light

emerging from 3 cm length of the fiber illuminated from below with a halogen lamp. The

colors observed in the cladding holes are caused by long-lived Mie-like resonances and are

related to the slight nonuniformity in the air hole diameters [64].

The transmission and attenuation spectra are important in the characterization of the

fiber as they provide guidelines for the the wavelength range and maximum fiber length

that can be used in the experiments. The spectral attenuation of the fiber was determined

via the conventional cut-back technique [139], in which the power transmitted through

a long length of fiber is measured and normalized to the power transmitted through a

shorter length of the same fiber without changing the incoupling condition. Figure 3.2

shows the transmission spectrum of the fiber, normalized to the spectrum of the SC

source described in Section 2.3, showing a transmission band of the fiber extending from

the visible to 960 nm. The inset shows the transverse irradiance profiles measured at the

46 CHAPTER 3. PHOTOCHEMISTRY IN PCFN

orm

aliz

ed

tra

nsm

issio

n [

dB

]

-60

-40

-20

0

600 nm 800 nm

600 800 1000 1200 1400 16000

5

10

15

Wavelength [nm]

Lo

ss [

dB

/m]

Figure 3.2: Transmission (normalized to the supercontinuum source) and loss spectra ofthe kagome HC-PCF. Inset: measured transverse irradiance profiles after 4 m of the fiberat λ = 600 and 800 nm.

output of 4 m of the fiber at λ = 600 and 800 nm to confirm that single-mode guidance

within the guidance band of the fiber was achieved. The measured loss spectrum of the

fiber based on a cut-back from 4 m to 1.1 m indicates a 2 dBm−1 loss region from λ = 510

to 710 nm, while the loss peaks between λ = 800 and 1210 nm correspond to coupling to

surface states and resonances in the cladding struts.

The kagome HC-PCF was designed and fabricated to have a guidance band in the

wavelength range around 450 to 500 nm when filled with water to allow for spectroscopic

measurements to be performed on the sample chemicals used in the experiments. As light

guidance in the kagome HC-PCF is not via the PBG mechanism, the index scaling law

described in Section 2.3 cannot be applied here to quantitatively estimate the guidance

band of the unfilled fiber. However, the guidance band of an unfilled kagome HC-PCF is

still expected to shift to lower wavelengths upon filling of the air holes. The fabrication of

a kagome HC-PCF with guidance band in the required wavelength range can be achieved

3.2. FIBER CHARACTERISTICS 47

-75

-50

-25

No

rma

lize

d t

ran

sm

issio

n [

dB

]0

400 nm 450 nm 488 nm 500 nm 550 nm 600 nm 700 nm

400 500 600 700 800 9000

10

20

30

Wavelength [nm]

Lo

ss [

dB

/m]

Figure 3.3: Transmission (normalized to the supercontinuum source) and loss spectra ofthe kagome HC-PCF filled with de-ionized water. The transmission spectra were measuredusing two supercontinuum sources (solid and dashed curves). Inset: measured transverseirradiance profiles after 60 cm of the fiber filled with de-ionized water, at λ = 400, 450,488, 500, 550, 600 and 700 nm.

by appropriate scaling of the structural parameters of a fiber with known guidance band

during fabrication. The fiber shown above, when completely infiltrated with de-ionized

water, has broadband guidance in the visible up to 700 nm as shown in Figure 3.3. Two

PCF SC sources were used in the measurement of the transmission spectra; the solid

curve was measured with the conventional PCF SC source while the dashed curve was

measured using a SC source generated using a tapered conventional fiber1 pumped by

a frequency-doubled microchip laser emitting sub-nanosecond pulses at 532 nm. The

inset of the figure shows the transverse irradiance profiles measured at the output of

60 cm of the fiber infiltrated with de-ionized water. All the beam profiles were measured

using the SC sources in combination with interference filters at the output of the fiber,

1Tapered fiber courtesy of Marta Ziemienczuk.


400 500 600 700 800 900 1000-25

-15

-5

Wavelength [nm]

No

rma

lize

d t

ran

sm

isssio

n [

dB

]

5

488 nm

Figure 3.4: Transmission (normalized to the supercontinuum source) spectrum of theindex-guiding kagome HC-PCF filled with toluene. Inset: measured transverse irradianceprofile after 39 cm of the fiber filled with toluene at λ = 488 nm.

except for the beam profile at 488 nm which was measured using the CW excitation laser

described in Section 2.3. The measured irradiance profiles confirmed that the fundamental

mode is guided over the whole wavelength range of interest from 450 to 600 nm. The

higher-order core mode and light in the cladding region at 400 nm can be attributed to

chromatic aberrations in the coupling objective as the optimization wavelength for the

loss measurement was at 550 nm. Optimization of the core mode at 400 nm confirmed

guidance of the fundamental mode (mode profile not shown). The irradiance profile at

700 nm clearly demonstrates coupling of the core mode to the surface states of the core

surround, as indicated by the loss peak at 700 nm in the measured loss spectrum based

on a cut-back from 2 m to 0.85 m. The single central lobe of the guided mode interacts

strongly with the sample, and the rigid core boundaries restrict diffusion of chemicals

away from (or into) the illuminated volume. Quantitative spectroscopic studies of very

small sample volumes, selectively introduced into the core, become possible.

The transmission property of the same kagome HC-PCF when filled with the sol-

vent toluene was also investigated and the measured normalized transmission spectrum

is shown in Figure 3.4 to exhibit broadband guidance in the visible up to 860 nm. The

transverse irradiance profile measured using the CW excitation source at 488 nm dis-

played an asymmetric mode profile indicating coupling into multiple higher order modes

and consequently the loss of the fundamental mode could not be measured. The reason

for the multimode behavior of the fiber when filled with toluene can be easily understood

3.3. PHOTOLYSIS OF METAL COMPLEXES 49

as the refractive index of toluene is higher than that of fused silica [140], the fiber becomes

index-guided with a V parameter given by VPCF(λ) = 2πΛ/λ√n2

core − n2eff, where λ is the

wavelength of operation, Λ is the pitch of the cladding structure and ncore and neff are

the effective refractive indices of the core and the cladding [141, 142]. The number of

guided modes can therefore be approximated by V 2PCF/2 ≈ 90 modes. With careful opti-

cal alignment, keeping the bend radius of the fiber large (≥ 15 cm) and avoiding twisting

of the fiber, it was possible to minimize the number of guided modes and maximize the

irradiance concentrated in the core region.

3.3 Photolysis of Metal Complexes

Platinum-based anticancer dugs such as cisplatin (cis-[PtIICl2(NH3)2]) are well-established

therapeutic compounds. However, as they do not discriminate between cancerous and

healthy tissues, their use is constrained by severe dose-limiting side effects [143], as well

as acquired resistance to the drug. In order to overcome these problems, research in the

field is moving towards the use of inert, nontoxic platinum complexes that can be locally

activated by light at the tumor site [127, 144]. Photoactivated drugs are routinely used

in photodynamic therapy for the effective treatment of a number of cancers, including

those of the skin, brain, lung and esophagus [145-147]. The ongoing research and de-

velopment of new metal-based complexes aim to provide more potent anticancer drugs

which are less oxygen dependent (due to the hypoxic nature of most tumor cells [145,

148]) and less biologically reactive in order to minimize the potential for cytotoxicity of

the inactive drug precursors. We demonstrate here a highly-controlled photochemical

reactor based on PCF with the prospect of simultaneously activating and monitoring

the reaction dynamics of such anitcancer drugs, combined with the advantages offered

by PCF-based sensors. The photoaquation of the readily available and nontoxic metal

complex vitamin B12 (cyanocobalamin, CNCbl) was studied as a proof of principle for the

PCF photochemical reactor.


N N

NN

Co

CH3 CH3

H3C

H3C

CH3

CONH2

H2NOC

H

CONH2

CONH2

CH3

CONH2

CH3

H2NOC

CH3

O

NH

H3C HOPOO

O

O

OHN

N CH3

CH3

HO

C

N

N N

NN

Co

CH3 CH3

H3C

H3C

CH3

CONH2

H2NOC

H

CONH2

CONH2

CH3

CONH2

CH3

H2NOC

CH3

O

NH

H3C HOPOO

O

O

OHN

N CH3

CH3

HO

OH2

hv

− CN−, + H2O

IIIIII

CNCbl [H2OCbl]+

Figure 3.5: The photochemical conversion of CNCbl to [H2OCbl]+.

3.3.1 Photoaquation of Cyanocobalamin

Irradiation of CNCbl in aqueous solution causes exchange of CN− for H2O, forming

[H2OCbl]+ (aquacobalamin or B12b) (Figure 3.5), a photoreaction with a very low quan-

tum yield (Φ ∼ 10−4 at pH 6) [149, 150]. Cobalamins such as CNCbl possess a low-spin

Co3+ configuration with near-octahedral geometry at the center of the corrin ring. The

Co3+ is ligated equatorially by four nitrogen atoms of the ring and axially by a nitrogen

of the tethered base 5,6-dimethylbenzimidazole (DBI). A number of ligands can occupy

the upper axial position [151, 152].

The absorption spectra of many cobalamins are highly similar, since the corrin ring

is responsible for the dominant spectral features, namely the α and β bands (ε ≈ 8000−

10000 M−1cm−1) in the visible spectral region and the Soret (γ) band (ε ≈ 25000

M−1cm−1) in the UV region [151, 152]. The α and β bands (Figure 3.6) both arise

from the same π → π∗ transition, the more intense α band being the electronic origin,

and the β band the first member of a progression in a vibrational mode, primarily in-

volving C=C stretches of the corrin ring [153]. Within the cobalamins, the wavelength


400 450 500 550 600 6500

3000

6000

9000

Wavelength [nm]

ε[L

mol-1

cm

-1]

hν

αβ

γ

CNCbl

[H2OCbl]

+

Figure 3.6: Changes in the absorption spectrum measured in a 1 cm cuvette as a resultof the photochemical conversion of CNCbl to [H2OCbl]+ in pH 2.5 buffer.

at which the α band is seen approximately parallels the nephelauxetic effect [154]; in the

case of photoaquation, exchange of CN− for OH2 decreases the electron density at Co3+

and the α absorption band moves to shorter wavelengths.

Although it has been suggested that the DBI group which coordinates CoIII from

beneath the ring is readily replaced by H2O in acidic solution [155], spectral analysis of

the Soret (γ) band of CNCbl and [H2OCbl]+ in extremes of both acid and base has led

to the conclusion that DBI remains attached [156]. Dissociation of DBI (and replacement

with H2O) is only considered significant below pH ≈ 0 for the cobalamins in general [154],

and furthermore it is estimated that DBI is bound particularly tightly in CNCbl, three

orders of magnitude more than in CH3Cbl, for example [157]. The pK a corresponding

to protonation and displacement of the imidazole base of CNCbl has been determined as

0.11 (H2O/H2SO4) [158]. It is reasonable to assume, therefore, that under the conditions

of the experiment, DBI does not dissociate from cobalt in either the CN− or H2O adduct.

3.3.2 Experimental Results

Photochemical experiments were performed on solutions of cyanocobalamin in citric acid

/ phosphate buffer (pH 2.5 to 7.5) using the optical setup described in Section 2.3. The

absorption spectra of cobalamins are dominated by the α and β bands (ε ≈ 8000− 10000

M−1cm−1) in the visible spectral region and the Soret (γ) band (ε ≈ 25000 M−1cm−1) in

the UV region [151, 152], as shown in Figure 3.6. Quantitative absorption spectra were

obtained by referencing the spectra to that of the buffer solution. The molar absorptivity


spectrum ε(λ) integrated over the fiber length 0 < z < L follows from the Beer-Lambert

law, A = εcL, taking the form given by

ε(λ) =

∫ L0ε1(λ)c1(z) + ε2(λ)c2(z)dz

c0L, (3.1)

where ε1,2(λ) are the molar absorptivitity spectra and c1,2(z) the spatial concentration

profiles of CNCbl and [H2OCbl]+. The initial concentration of the sample is c0. The

photochemical reaction was accurately monitored by the spectral changes to the α and

β bands. The typical temporal behavior of the absorption spectrum during photolysis is

shown in Figure 3.7(c). Figure 3.7(b) shows the absorption spectrum before irradiation

(i.e., of pure CNCbl) and 100 s after full conversion to [H2OCbl]+. Upon excitation, both

α and β bands are shifted to shorter wavelengths, resulting in a decrease in absorption

for λ = 530 to 600 nm and an increase in absorption for λ = 450 to 530 nm. Figure 3.7(a)

shows the decrease in absorption for the peak of the α band at λ = 550 nm, indicated

by the black dashed line on the colormap in Figure 3.7(c). The observed changes are in

good agreement with previous work [149, 150].

The rate of photoconversion of CNCbl to [H2OCbl]+ has previously been shown to

depend on the pH of the solution. Cyanocobalamin is most stable to photoaquation

between pH 7 to 8 and converts more rapidly at both the higher and lower extremes of pH

[150]. To investigate this effect, the temporal evolution of absorption at 500 and 550 nm

during the photolysis of CNCbl at pH 2.5 and 7.5 was measured in both the cuvette

and in the kagome HC-PCF and is shown in Figure 3.8. The cuvette measurements

were carried out on 1 mL of 125 µM buffered aqueous CNCbl solution at an excitation

power of 9.5 mW. The fiber measurements were performed using a sample volume of

approximately 100 nL (4 µM) and only 10 µW of power at pH 2.5 and 20 µW at pH 7.5.

The photochemical conversion occurred roughly 1000 times faster in the fiber than in the

cuvette, even though the excitation power remained below 20 µW. Previous studies of the

photoaquation of CNCbl required much higher lamp powers (> 100 W) [149, 150] and/or

acidic conditons (pH 4.75) [159].


4000

5000

6000

7000

ε[L

mo

l-1cm

-1]

550 nm

ε[L

mo

l-1cm

-1]

0 10 20 30 40 50

1000

2000

3000

4000

5000

6000

Time of exposure at 488 nm [s]

450

500

550

600

0250050007500

Wa

ve

len

gth

[n

m]

ε [Lmol-1

cm-1

]

hν

α

β

CNCbl

[H2OCbl]

+

(a)

(b) (c)

Figure 3.7: Photolysis of CNCbl at pH 2.5 in 39 cm of kagome HC-PCF. (a) Measuredtemporal evolution of molar absorptivity at 550 nm taken at 500 ms intervals over aperiod of 50 s. (b) Molar absorptivity spectra of CNCbl before irradiation (thick curve)and after 100 s of irradiation at 488 nm (fine curve). (c) Colormap showing the measuredevolution of molar absorptivity spectrum with time of exposure at 488 nm using 10 µWof optical power.

3.3.3 Reaction Kinetics

The photochemical evolution of the absorption spectra upon excitation can be modeled

using the configuration diagram in Figure 3.9. The photophysical transitions and nature

of the excited electronic states of CNCbl have been investigated using TD-DFT [160,

161]. Irradiation of CNCbl results in excitation from the ground state (S0) to an initially

excited π-π∗ state, which is followed by (sub-picosecond) internal conversion to a lower

energy excited singlet state (S1) − a state best characterized as being of π3d character.


0 20 40 60Exposure time at 488 nm [s]

2

4

6

8

ε[�

10

3Lm

ol-1

cm

-1]

Kagome HC-PCF

500 nm

550 nm

pH 2.5

0 5 10 154

6

8

10

Exposure time at 488 nm [hours]

Cuvette

500 nm

550 nm

pH 2.5

10

0 200 400 600Exposure time at 488 nm [s]

2

4

6

8

ε[�

10

3Lm

ol-1

cm

-1]

500 nm

550 nm

pH 7.5

0 5 10 154

6

8

Exposure time at 488 nm [hours]

500 nm

550 nmpH 7.5

Figure 3.8: Temporal evolution of measured and theoretically-fitted (solid curves) molarabsorptivity at 500 (circles) and 550 nm (squares) for photolysis of CNCbl in a cuvette(right column) and a kagome HC-PCF (left column) at pH 2.5 (top row) and 7.5 (bottomrow). The quantum yields obtained from the theoretical fits were 6.88 × 10−4 at pH 2.5and 9.95 × 10−5 at pH 7.5 in the kagome HC-PCF, and 5.46 × 10−4 at pH 2.5 in thecuvette.

The relative photostability of CNCbl compared to alkylcobalamines is attributed to the

fast subsequent radiationless decay to the ground state from the S1 excited state (τ ∼ 7

ps in H2O) [161]. If the molecule does not decay from S1 to the ground state, it undergoes

intersystem crossing (ISC) to a low-lying ligand-field (LF) state, populating − either

directly or indirectly − a LF triplet state, in which the Co-CN bond is weakened and

from which photoaquation can occur [149].

The quantum yield of the reaction was calculated by modeling the number densities

in the three states in Figure 3.9 using the following coupled rate equations,

∂n0(t)

∂t= − Ip

hνpσ0n0(t) + Γ10n1(t), (3.2)

∂n2(t)

∂t= ΓISCn1(t), (3.3)

n0(t) + n1(t) + n2(t) = const., (3.4)


ground state[Co-CN]

S0 ground state

photochemistry[Co-OH2]+non-radiative

decay (τ ~ 7 psin H2O)

intersystem crossing

T1 Φ ~ 10-4 (~ pH 6)

photoexcitation

ground stateground state

radiativeradiativedecay (τ ~ 7 ps

O)

T1

internal conversion (< 1 ps)

π-π*

S1 (π3d)

ΓISC

Γ10

LF state

Figure 3.9: Configuration diagram depicting the photoaquation of CNCbl ([CoIII-CN] to[CoIII-OH2]). Transitions are represented by the dashed (non-radiative) and solid (ra-diative) lines. The quantum yield for the photochemistry is thought to be low due tocompeting rapid internal conversion from S1 to S0. Non-radiative decay from T1 to S0 isassumed negligible in the model. Lifetimes are from ref. [161].

where n0,1,2(t) are the number densities at S0, S1 and T1, Ip and hνp the power density and

photon energy of the pump light, σ0 the absorption cross-section at the pump wavelength

for excitation from the S0 to the π-π∗ state, Γ10 is the non-radiative decay rate from S1

back to S0 and ΓISC is the rate for intersystem crossing. The third equation follows from

the conservation law. The quantum yield, which describes the fraction of CNCbl excited

to S1 converted to [H2OCbl]+ upon irradiation, has the form given by

Φ =ΓISC

Γ10 + ΓISC

. (3.5)

The differential equations (Equations 3.2 to 3.4) were numerically solved and fitted

to the experimental data, taking into account the exponential decay of the 488 nm pump

irradiance (caused by fiber loss and absorption) by integrating along the length of the

fiber,

Ip(z) = I010−∫ z0 α(ξ)dξ (3.6)

where I0 is the initial pump irradiance and α(ξ) is the combined position-dependent


pH Quantum yield (×10−4)[a]

2.5 6.73± 0.33

3.5 6.56± 0.15

4.5 5.30± 0.27

5.5 3.87± 0.23

6.5 1.59± 0.33

7.5 0.99± 0.01

Table 3.1: Quantum yields from theoretical fits of data for the photolysis of CNCbl at

pH 2.5 to 7.5 in a kagome HC-PCF. [a] Mean ± SE.

2.5 3.5 4.5 5.5 6.5 7.50

2

4

6

8

pH

Qu

an

tum

yie

ld [

�1

0-4

]

Figure 3.10: Theoretically fitted quantum yields obtained from measurements of photol-ysis in kagome HC-PCF (squares). The bars indicate the standard error and the dashedcurve is intended as guide for the eye only.

attenuation due to fiber loss and absorption. It is important to note that only one

free parameter, namely the quantum yield, was used to fit the experimental data to the

theoretical model. We find excellent agreement between our model and the data (Figure

3.8). The quantum yields for aqueous vitamin B12 determined at pH 2.5 to 7.5 are listed

in Table 3.1.

The measurements were repeated for six pH values at different fiber lengths, sample

concentrations and excitation power, and the results are summarized in Figure 3.10. The

small standard deviation demonstrates the reproducibility of the method. The results

showed that the quantum yield increases with decreasing pH, as expected [150].

3.4. PHOTOSWITCHING OF AZOBENZENE MOLECULES 57

3.3.4 Discussion

In summary, the use of HC-PCF for the simultaneous quantitative assay of cyanocobal-

amin and aquacobalamin in aqueous solution has been demonstrated on a nanoliter scale.

Laser-driven changes in the absorption spectrum are monitored within the fiber. This

new method requires not only 104 times less sample volume compared to conventional

techniques, but also greatly reduced excitation power, allowing system minimization us-

ing cheap on-chip diode lasers. Furthermore, the reaction is 1000 times faster as a result

of the strong confinement of both sample and light in the hollow core. The procedure

should therefore find wide application, enabling rapid investigation of photochemical reac-

tions with modest quantum yields. Implementation of PCFs as flow reactors would allow

continuous optimization of exposure conditions and reagent parameters, and integration

of the reactor into an optical tweezer/particle guidance setup [162] would open up new

opportunities for in vitro investigation of photoactive anticancer complexes [126]. The ex-

ploitation of PCFs as optofluidic devices offers significant advantages including minimal

consumption of reagents and flexibility for integration into other microfluidic circuitry for

improved performance.

3.4 Photoswitching of Azobenzene Molecules

Azobenzene chromophores are widely recognized as one of the most important and ver-

satile classes of synthetic organic compounds, and have received much attention in both

fundamental and applied research. With two phenyl rings separated by an azo (−N=N−)

bond, azobenzene serves as the parent molecule for a host of aromatic azo compounds.

The strong electronic absorption maximum can be tuned via the combination of the prop-

erties of the azo group and the substitution of the aromatic ligands, resulting in intense

colors of dye over the whole visible range. Furthermore, the thermal and chemical robust-

ness of these azo compounds, combined with non-complex synthetic methodologies and

low production costs, has prompted extensive study of azobenzene-based structures as

dyes and colorants [163, 164]. The mesogenic shape of the molecule also finds holographic

applications in which azobenzene chromophores embedded in polymers (azo polymers) are

used in gratings and liquid crystalline media [165-167]. When azobenzene is push-pull sub-


NN

N Nhν

hν', Δ

Figure 3.11: Reversible isomerization between the trans (left) and the cis (right) geometricisomers of azobenzene.

stituted (i.e. when it has strong electron-donating and electron-attracting substituents),

a very large permanent electrical dipole moment is formed which can yield high optical

nonlinearity with extensive nonlinear optical applications [168-170]. One of the most in-

teresting properties of the azobenzene chromophores, and the focus of this section, is the

switching between two geometric isomers upon UV-vis irradiation. This readily induced

photoisomerization is rapid, reversible and of high quantum yield, allowing large host

systems incorporating azobenzenes to be used as photoswitches [171, 172].

The photoreaction studied in Section 3.3, namely the photolysis of cyanocobalamin,

is a relatively slow and irreversible process under the experimental conditions imposed on

the sample. This section demonstrates that the PCF reactor can also be used to study

fast, reversible photoswitching processes in real-time, exemplified here by the photoiso-

merization of two azobenzene derivatives.

3.4.1 Isomerization of Azo Dyes

The reversible isomerization between the trans and cis geometric isomers of azobenzene

is depicted in Figure 3.11. Azo aromatic chromophores can be classified based on the en-

ergetic ordering of their n-π∗ and π-π∗ electronic states as azobenzene, aminoazobenzene

or pseudo-stilbene. The azobenzene-type molecules, which are similar to the unsubsti-

tuted azobenzene, exhibit a low irradiance n-π∗ absorption band in the visible, and a high

irradiance π-π∗ band in the UV. The n-π∗ and π-π∗ bands of the aminoazobenzenes are

closely-space in the violet or near-visible UV. In the pseudo-stilbene class, the substitu-

tion of electron donor and acceptor substituents (push-pull configuration) shifts the π-π∗

and the n-π∗ bands such that they effectively overlap. The three classes therefore display

the colors of yellow, orange and red, respectively. The readily induced and reversible

isomerization about the azo bond between the trans- and cis-isomers can occur via pho-


400 500 6000

0.5

1

1.5

Wavelength [nm]

A(λ

)Absorption spectrum

Trans

PSS

0 1200 2400 36001.25

1.4

1.55

1.7

Time [s]

PSS → trans (back)

kfit

= 0.0011 � 0.0001 s-1

λmax

= 450 nm

λpump

= 450 nm

400 500 6000

0.5

1

1.5

Wavelength [nm]

A(λ

)

Trans

PSS

0 600 1200 18001.55

1.6

1.65

1.7

Time [s]

kfit

= 0.0015 � 0.0007 s-1

λmax

= 450 nm

λpump

= 532 nm

(a) (b)

(c) (d)

Figure 3.12: Changes measured in the absorption spectra and the temporal evolution ofthe absorbance for the thermal back reaction of DO1 in toluene in a 1 cm cuvette, excitedat λ = 450 nm ((a) and (b)) and 532 nm ((c) and (d)), as indicated by the dashed lines onthe absorption spectra. The dashed curves on the temporal evolution of the absorbanceare theoretical fits to the experimental data, yielding thermal rate constants of 0.0011 ±0.0001 and 0.0015 ± 0.0007 s−1 for excitation at λ = 450 and 532 nm, respectively. Themeasurements were taken at the University of Edinburgh, United Kingdom.

tochemical and thermal processes. In this section, the ’forward’ reaction is used to refer

to the trans → cis isomerization, while the ’back’ or ’reverse’ reaction refers to the cis →

trans isomerization. The trans-isomer has a planar elongated form, while the cis-isomer

assumes a bent geometry with the phenyl rings twisted at right angles to the C−N=N−C

plane [173]. Upon irradiation with light, the thermally stable trans molecules are con-

verted to the cis form, while the cis molecules can be converted back to the trans form

either photochemically or thermally. The isomerization process is completely reversible

and free from secondary reactions. After a certain irradiation time, the equilibrium state

of the three competing conversion processes, known as the photostationary state (PSS),

is reached. The rates and extent (determined by the concentration of cis-isomer in the

PSS) of isomerization depend on several factors including the irradiance, wavelength of

irradiation, temperature, substituents and the solvent.


In order to demonstrate the effect of some of these factors, a series of forward and

thermal back reactions were undertaken for 4-(4-Nitrophenylazo)diphenylamine (disperse

orange 1, DO1) and N-Ethyl-N-(2-hydroxyethyl)-4-(4-nitrophenylazo)aniline (disperse red

1, DR1) in the solvents cyclohexane and toluene, irradiated with λ = 450, 488 and 532 nm

radiation. Figure 3.12 shows the changes in the absorption spectra and the temporal evo-

lution of the absorbance for the thermal back reaction of DO1 in toluene, measured in a

1 cm cuvette. The sample was excited at λ = 450 nm and 532 nm to demonstrate the

dependence of the concentration of the cis-isomer in the PSS on excitation wavelength.

The advantage of pumping near the absorption maximum of the trans-isomer was im-

mediately evident: the absorbance decreased by 20% for the PSS induced by 450 nm

radiation, indicating that at least 20% of the molecules had been converted to the cis

form; on the other hand, for PSS induced by 532 nm radiation, the absorbance has only

decreased by 5%.

As the thermal isomerization was the sole process taking place, it can be described by

a simple first-order kinetic equation written as

−dccis(t)

dt=dctrans(t)

dt= kccis(t) (3.7)

where ccis(t) and ctrans(t) are the concentrations of the cis- and trans-isomers after time t

of thermal back reaction, and k is the thermal rate constant. The temporal evolution of

the absorption spectrum for the thermal back reaction can therefore be derived by using

the Beer-Lambert law in Equation 3.7 as

A(t) = [A(0)− A(∞)] exp(−kT ) + A(∞), (3.8)

whereA(0) andA(∞) are the absorbance at the start and end of the thermal back reaction,

respectively. The dashed curves on the temporal evolution of the absorbance (Figure

3.12(b) and (d)) are the theoretical fits to the experimental data using Equation 3.7 with

fitted thermal rate constants of 0.0011 ± 0.0001 and 0.0015 ± 0.0007 s−1 for the excitation

at λ = 450 and 532 nm. The agreement in the fitted thermal rate constants within the

error margin is expected as the thermal back reaction rate should be independent of the

wavelength at which the sample had been excited to reach the PSS.

Figure 3.13 shows the measured temporal evolution of molar absorptivity for the for-

ward and thermal back reactions of 15 µM of DR1 in cyclohexane and toluene in a 1 cm


0 2 4 6 82

2.4

2.8

Time of exposure at 488 nm [min.]

ε[×

10

4Lm

ol-1

cm

-1]

trans → PSS (forward)

DR1 in cyclohexane

λ = 488 nm

0 3 6 9 122

2.4

2.8

Time [min.]

PSS → trans (back)

DR1 in cyclohexane

λ = 488 nmk

fit= 0.0082 � 0.0007 s

-1

0 0.5 1 1.5 2

2

2.5

3

Time of exposure at 488 nm [min.]

ε[×

10

4Lm

ol-1

cm

-1]

DR1 in toluene

λ = 473 nm

(a) (b)

(c)

0 0.6 1.2 1.8 2.4

2

2.5

3

Time [min.]

= 473 nm

= 0.020 � 0.003 s

DR1 in toluene

λ

kfit

-1

(d)

Figure 3.13: Temporal evolution of molar absorptivity for the forward and thermal backreaction of 15 µM of DR1 in cyclohexane ((a) and (b)) and toluene ((c) and (d)) in a1 cm cuvette, excited with 200 µW at λ = 488 nm. The dashed curves on the temporalevolution of the molar absorptivity for the thermal back reactions are theoretical fits tothe experimental data, yielding the thermal rate constants 0.0082 ± 0.0007 and 0.020 ±0.003 s−1 for DR1 in cyclohexane and toluene, respectively.

cuvette, excited with 200 µW of optical power at 488 nm. Disperse red 1, with the

azobenzene unit substituted with an electron-donating group on one benzene ring and an

electron-withdrawing group on the other, belongs to the group of push-pull azobenzenes

(which places the molecule in the pseudo-stilbene spectra class) [174]. Push-pull azoben-

zene derivatives have a permanent dipole moment and the thermal cis-trans isomerization

is much faster than that for the nonpolar azobenzenes. The isomerization is strongly sol-

vent dependent as shown in Figure 3.13, whereby DR1 in the polar solvent (toluene) has

a much higher thermal rate constant compared to that in the nonpolar solvent (cyclo-

hexane). This effect can be understood by considering the planar structural geometry

of the trans-isomer, which provides a greater de-localization of the π electrons. A polar

solvent aids in this de-localization of the π electrons to reduce the energy further (in

comparison to the less polar cis form), thereby increasing the cis → trans isomerization


1.5

2.5

3.5

= 450 nm

PSS (forward)trans →

(a)

400

425

450

475

500

024

Wa

ve

len

gth

[n

m]

TransPSS

ε [ 10 Lmol cm ]�4 -1 -1

(b)0 8 16 24

Time of exposure at 488 nm [s]

(c)

trans (back)PSS →

0 280 560 840

1

2

3

2.5

1.5

Time [s]

ε[

10

L

mo

l

cm

]

�4

-1

-1

(e)

ε[

10

L

mo

l

cm

]

�4

-1

-1

(d)

kfit

= 0.012 � 0.001 s-1

λmax

= 450 nm

λpump

= 488 nm

λmax

Figure 3.14: Photoisomerization of DO1 (0.75 µM) in toluene in 39 cm of kagome HC-PCF. (a) Measured temporal evolution of molar absorptivity at 455 nm taken at 1 sintervals over a period of 15 s. (b) Molar absorptivity spectra of DO1 before irradiation(thick curve, trans-isomer) and after 65 s of irradiation at 488 nm (fine curve, PSS). (c)Colormap showing the measured evolution of molar absorptivity spectrum with time ofexposure at 488 nm using 3 µW of optical power. (d) Measured temporal evolution ofmolar absorptivity at 455 nm over a period of 14 minutes of cis-trans thermal isomeriza-tion. (e) Color map showing the measured evolution of molar absorptivity spectrum withtime of thermal back reaction at 450 nm.

rate. The effect is most pronounced for push-pull azobenzenes due to their intrinsically

higher polarity.

3.4.2 Reversible Isomerization in PCF

The photoisomerization of DO1 in toluene was performed in the kagome HC-PCF shown

in Figure 3.1 at ambient temperature in dark room conditions using the optical setup

described in Section 2.3. Quantitative absorption spectra were obtained by referencing the

spectra to that of the solvent and the molar absorptivity spectrum obtained at the output

of the fiber was given by Equation 3.1, where the subscripts 1 and 2 now represent the

trans- and cis-isomers. The forward photoisomerization of DO1 in toluene was accurately

monitored by the decrease in the absorption maximum in the visible, corresponding to


the n-π∗ (S1 state) transition. The spectral changes were monitored for a period at least

four times longer than that necessary to reach the PSS. The temporal behavior of the

absorption spectrum during photoisomerization is shown in Figure 3.14(c). Figure 3.14(b)

shows the absorption spectrum before irradiation (thick curve), assumed to be that of

pure trans molecules as the trans-isomer is the energetically favored configuration in the

ground electronic state due to greater π electron de-localization and steric interaction. The

spectrum at the end of the experiment (fine curve) after 65 s of irradiation at λ = 488 nm

corresponds to the absorption spectrum of the PSS. Upon excitation, the decrease in

the absorption maximum of the n-π∗ chromophore for the trans-isomer is coupled to the

increase in the absorption maximum of the π-π∗ chromophore for the cis-isomer located

further into the UV, which was beyond the available wavelength range of the probe beam

used in the setup; however, the onset of the isosbestic point, that is, the wavelength

at which both the trans- and cis-isomers have the same molar absorptivity (visible in

Figure 3.12 at around 388 nm) can be observed near 400 nm. The temporal evolution of

the absorption peak of the trans-isomer at 450 nm (indicated by the dashed line on the

colormap in Figure 3.14(c)) is shown in Figure 3.14(a). The results show that despite the

very low excitation power of 3 µW used, the PSS was readily reached within 10 s. In the

PSS, the absorptivity has decreased by 40%, indicating that at least 40% of the molecules

are in the cis form. In comparison, 1 W of excitation power (five orders of magnitude

higher than that used in the fiber) would be required to achieve the same irradiance level

and hence reaction dynamics in a 1 cm cuvette.

The excitation source was switched off after 65 s of irradiating the sample to allow

the sample to thermally relax back to the trans form. The temporal evolution of the

molar absorptivity was monitored over 14 minutes as shown in Figure 3.14(e). The mea-

sured evolution of the trans absorption maximum at 450 nm is shown in Figure 3.14(d),

demonstrating that the reaction was completely reversible, and the absorbance measured

at the end of the experiment coincided with that measured initially, indicating that no

irreversible secondary reactions took place. The thermal rate constant for the cis-trans

thermal isomerization of DO1 in toluene measured in the HC-PCF was obtained by fitting

the experimental data use the rate equation in Equation 3.7 to be k = 0.012± 0.001 s−1.

The much higher apparent thermal rate constant measured in the fiber compared to that


obtained from measurements in the cuvette shown in Figure 3.12 was unexpected as the

thermal back reaction is a first order process, independent of the concentration and volume

of sample used in the experiments. A possible factor which could induce the difference

in the thermal rate constant measured is the change in temperature. From the Arrhe-

nius equation, k(T ) = A exp(−EA/RT ), where R is the Boltzmann constant, and using

an activation energy EA of 72 kJ/mol and ln(A) of 22 [175], the temperature difference

between the two different laboratories in which the cuvette and fiber measurements were

performed would have to be ∼ 25 K to induce the difference in the measured thermal

rate constants. This seems unrealistically high. This discrepancy stimulated further in-

vestigations to establish plausible causes for the marked differences in the experimental

results.

Another possible source of discrepancy could come from the probe light. Without

making changes to the configuration of the experimental setup and dark room condi-

tions, the absorption spectrum of the azo molecule in its thermally stable trans form was

monitored using the broadband light source, namely the xenon lamp, at various average

lamp powers. Figure 3.15(a) shows the measured temporal evolution of the absorbance

at the n-π∗ absorption peak of the trans-isomer, for average lamp powers of 0.02, 0.55

and 1.15 µW between λ = 400 and 500 nm. It was observed that despite the very low

average lamp power used, the resulting irradiance in the 19 µm hollow fiber core was still

high enough to induce photoisomerization, ranging from I = 70.5 W/m2 (for P = 0.02

µW) to 4050 W/m2 (for P = 1.15 µW). The n-π∗ absorption of the cis-isomer, which

is non-zero in the wavelength range of 400 to 500 nm, would similarly cause the reverse

cis-trans photoisomerization. For the thermal isomerization measurement performed, the

xenon lamp was required to be on for the duration of the spectrometer integration time,

which was 500 ms in this case, during which sufficient (and undesirable) effect occurred

and could have led to the discrepancies in the rate constants measured in the cuvette

and the fiber. Another noticeable effect observed was the dependence of the extent of

photoisomerization on the irradiance. As shown in Figure 3.15(b), the relative change

in the absorbance at the PSS, given by [A(0)−A(PSS)]/A(0), increased with irradiance,

indicating increased fraction of cis-isomer in the PSS.

Due to the broadband nature of the pump source, which was originally intended as


0 0.4 0.8 1.20.43

0.46

0.49

Average power of xenon lamp [µW]

[A(0

)-A

(PS

S)]

/A(0

)

0 40 80 120

0.55

0.7

0.85

1

Exposure time [s]

Absorb

ance

0 4 8 120.5

0.65

0.8

0.95

Exposure time [s]

Absorb

ance

1.15 µW

0.55 µW

0.02 µW

(a)

(b)

Figure 3.15: (a) Measured temporal evolution of absorbance at the absorption peak oftrans-DO1 in toluene irradiated with a broadband xenon lamp with average powers of 1.15,0.55 and 0.02 µW. Inset: zoomed-in figure for the first 12 s. (b) Measured dependence ofthe relative change in the absorbance at the PSS on irradiance, extracted from the datain (a). The dashed curves are intended as guide for the eye only.

the probe beam, further analysis of the data would require knowledge of the cis-isomer

absorption spectrum and the spectral density of the xenon lamp in this wavelength range.

An accurate cis absorption spectrum could be extrapolated by the Fischer method [176],

which requires the measurements for temporal absorption dynamics at two different exci-

tation wavelengths. Due to the influence of the probe beam on the rate of photoisomer-

ization in both the forward and reverse directions, in addition to the stepwise pump-probe

cycle implemented for the measurements, solution to the coupled rate equations describing

the reaction kinetics becomes complicated and requires tedious numerical computation,


S0

S0

ground statetrans

S1

S1

FC

TS

photoexcitation

photoexcitation

thermal reverse isomerization (ms – s)

ground statecisk

ΓCT

ΓTC

(~ps)S1

SS1

photoexcitation ΓCT

Figure 3.16: Configuration diagram depicting the isomerization paths of trans ⇀↽ cis.The trans- and cis-isomers can theoretically excite to different transition states (TS)simultaneously but are indistinguishable in the experiments. A simplified model assum-ing excitation to the same Franck-Condon (FC) excited state from the ground states isemployed.

and is the subject of on-going progress.

3.4.3 Reaction Kinetics

The photoisomerization of the cis- and trans-isomers can be modeled using the configura-

tion diagram in Figure 3.16. For the experiments described here, photoisomerization was

induced via direct excitation to the S1 (n-π∗ transition) state in the visible. The trans- and

cis-isomers can theoretically excite to different transition states (TS), however, as both

processes occur simultaneously and are indistinguishable in the experiments, the model

has been simplified to assume a configuration in which both isomers are photo-excited

to the same Franck Condon (FC) excited state before relaxing into the metastable TS.

From the TS a fraction of the excited molecules revert back to the initial trans form,

while the rest undergo photoisomerization to the cis-isomer. In addition, the thermal

reverse isomerization takes place from the cis ground state to the trans ground state.

In the experiments, the sum of the decays from the excited state, and hence the overall

quantum yield for trans-cis isomerization, was measured in the photo-excitation experi-


ments, while the additional back reaction measurements allow the thermal rate constant

to be determined (see Equation 3.7). The reaction kinetics can be described by modeling

the number densities in the three states in Figure 3.16 using the following coupled rate

equations,

∂nT(t)

∂t= − Ip

hνpσTnT(t) + ΓCTnTS(t) + knC(t), (3.9)

∂nC(t)

∂t= − Ip

hνpσCnC(t) + ΓTCnTS(t)− knC(t), (3.10)

nT(t) + nTS(t) + nC(t) = 1, (3.11)

where nT,C,TS(t) are the normalized number densities in the trans, cis and transition

states, Ip and hνp the power density and photon energy of the pump light, σTC and σCT

the absorption cross-section at the pump wavelength for excitation from the trans and

cis states to the TS, ΓCT is the decay rate from TS to trans and ΓTC is the rate for

photoisomerization. The third equation follows from the conservation law. The quantum

yield, which describes the fraction of trans excited to TS which are converted to cis upon

irradiation, has the form given by

Φ =ΓTC

ΓTC + ΓCT

. (3.12)

Under the assumption that the molecules do not spend any time in TS, Equation 3.10

can be re-written as:

∂nC(t)

∂t= − Ip

hνpσCnC(t) + Φ

Iphνp

nT(t)− knC(t). (3.13)

In the photostationary state, ∂nC(t)/∂t = 0 and the fraction of molecules in the cis form

is given by

nC =ΦIp/hνp

(σT + σC)Ip/hνp + k. (3.14)

It can be seen from Equation 3.14 that in the limit of high irradiance Ip and excitation

at the isosbestic point, so that σT = σC, the quantum yield for the forward reaction can

be obtained from the fraction of cis-isomer in the photostationary state.

3.4.4 Discussion

The results have demonstrated real-time monitoring of fast, reversible photoswitching pro-

cesses induced in PCF photoreactors. The strong enhancement of light-matter interaction


in the tiny hollow fiber core has led to undesirable effects in which the broadband probe

beam also induces photoisomerization in both direction, therefore interfering with the ac-

tual pump-probe measurement and hindering the quantitative determination of reaction

rate constants. Implementation of the Fischer method to extrapolate the full absorption

spectrum of the cis-isomer and integration of the spectrum into the numerical computa-

tion of the solution to the coupled rate equations is in progress and should lead to further

insight into the reaction kinetics. Furthermore, by incorporating the experiment in a

femtosecond spectroscopy setup, the enhanced temporal resolution and the possibility for

two-photon photoisomerization could help clarify the on-going debate on the mechanism

of isomerization [177, 178]. In addition, the stepwise measurement approach has proven

to complicate the analyses of reaction dynamics in which thermally reversible back re-

actions retard the efficiency and rate of the photo-induced forward reaction. The huge

computational time required for modeling the stepwise reaction kinetics can be resolved

by implementing the experimental setup in a counter-propagating pump-probe configura-

tion to allow for continuous sample irradiation and spectra collection, and is detailed in

Appendix A.

Chapter 4

Spectroscopy in PCF

4.1 Introduction

As already addressed in Section 1.5, the advances in PCF design have generated much

interest in exploring its use as vehicles for optical sensors, in particular as the post-

processing step is no longer required thanks to the fiber microstructure. Additionally, PCF

sensors can strongly reduce the sample volume required for measurements and provide

the robustness and flexibility needed for fiber sensors. In the context of absorption-

based PCF sensor designs, hollow-core PBG-PCF offers an ideal environment for optical

spectroscopy by virtue of its ability to maximize light-matter interaction at path lengths

that are much longer than achievable in conventional sample cells. However, practical

application is limited to narrow-band spectroscopic gas sensing measurements [138, 179],

as the transmission bandwidth of the hollow-core PBG-PCF is typically narrower than

100 nm, impeding its competitiveness as liquid-based chemical sensors requiring detection

of broad spectral features.

In this chapter, a quantitative broadband fiber sensor based on evanescent-wave sens-

ing in the cladding holes of an air-suspended SC-PCF is demonstrated in Section 4.2.

As the evanescent-wave sensors preferentially probe surface effects, significant differences

between bulk and in-fiber measurements can result. Results from the investigation of sur-

face interactions between the fiber surfaces and the sample are presented and discussed

in Section 4.3, concluded with suggestions for further investigative ventures.

69

70 CHAPTER 4. SPECTROSCOPY IN PCF

4.2 Evanescent-Wave Sensing

In order to overcome the limited bandwidth of hollow-core PBG-PCF, sensors based on

SC-PCFs have been proposed and demonstrated in the literature [87, 89]. The most

common design of an index-guiding PCF consists of a solid silica core surrounded by a

periodic array of silica webs and air holes that make up the cladding. The propagating

light in the solid core of the index-guiding PCF probes the sample in the cladding holes

via an evanescent field. By manipulating the core size and the pitch of the cladding air

holes, the amount of evanescent field available can be varied. However, the maximum

achievable fraction of power overlap in the cladding holes in these fibers is usually too low

(typically 5% or less) to allow ultra-high sensitivity sensing [85, 86].

An index-guiding PCF design that strongly enhances the power overlap in the cladding

holes consists of a solid silica rod held in air by three silica nanowebs. This allows direct

access to the fiber core for sensing applications [83, 180]. By varying a single structural

parameter, the fraction of evanescent field available for sensing can be controlled while

maintaining the broad transmission window of silica. Experiments have been reported in

which the narrow spectral lines of acetylene were resolved using the evanescent field of

light propagating in such fibers [88, 136]; however, sensing experiments in these fibers have

only been non-quantitative and limited to a narrow frequency range, failing to exploit the

full potential of these fibers. In this section, quantitative detection of an environmen-

tally hazardous industrial chemical is demonstrated in these fibers, with the capability of

accurately resolving the sub-peaks of the broad absorption spectrum.

4.2.1 Fiber Characteristics

The air-suspended SC-PCFs used in the experiments were fabricated using the conven-

tional stack-and-draw process described in Section 1.4. The preform of the fiber contains

only three capillaries. This simple preform illustrates another advantage of this fiber over

hollow-core PBG-PCF, the preform of which typically contains over 300 capillaries and

rods. During the fiber drawing process, the core size of the fiber, which determines the

amount of evanescent field available for sensing, can be controlled via the scale-down ratio

of the preform. Using this technique, kilometers of fibers with ten different core diameters

4.2. EVANESCENT-WAVE SENSING 71

Fiber 1 Fiber 2 Fiber 3 Fiber 4

Figure 4.1: High resolution SEM of the core region of four different air-suspended solid-core fibers. The effective core diameter of the fiber is defined as the diameter of the largestcircle that can be drawn in the core region. The effective core diameter for the fibers are0.87 µm, 1.03 µm, 2.32 µm and 2.98 µm for fibers 1 to 4, respectively. The inset showsthe hollow cladding region of fiber 2 with a diameter of 64 µm. The thicknesses of thenanowebs that hold the fiber cores in place vary between 160 and 500 nm.

in the range of 0.8 to 3.0 µm were fabricated.

Figure 4.1 shows typical SEM images of the fibers drawn. Three nanowebs with

thicknesses between 160 and 550 nm hold the central silica core in place. The effective

core diameter, deff, of the air-suspended SC-PCF is defined as the diameter of the largest

circle which can be inscribed in the core region. For fibers 1 to 4 shown in Figure 4.1, the

core diameters are 0.873, 1.03, 2.32 and 2.98 µm, respectively. The hollow cladding region

(see the inset of fiber 2) acts as an easily accessible sample chamber and has a typical

diameter of 30 to 70 µm. The uniformity of the structural parameters along the fiber

was verified from high resolution SEM images. For most samples, variations of less than

3.5% over tens to 100 m were detected. The largest variation in deff observed was less

than 7%. For the fibers used in the experiments, the observed variations were below 2%.

This analysis demonstrates that the stack-and-draw process allows highly reproducible

and flexible fabrication of air-suspended SC-PCFs.

4.2.1.1 Transmission and Losses

The transmission and loss spectra are important because they provide guidelines to the

wavelength range and maximum fiber length that can be used in the sensing experiments,

as discussed in Section 2.2. Figure 4.2 (a) shows the broadband transmission windows

for 2.9 m of fiber 2 (solid curve) with air cladding from λ = 500 to 1350 nm and from

λ = 1450 to beyond 1750 nm. The absorption line near λ = 1400 nm is attributed to


-60

-40

-20

0

No

rma

lize

d t

ran

sm

issio

n [

dB

]

Air cladding

D2O cladding

(a)

600 800 1000 1200 1400 16000

6

12

18

Wavelength [nm]

Lo

ss [

dB

/m]

(b)

Figure 4.2: (a) Transmission (normalized to the supercontinuum source) and (b) lossspectra for 2.9 m of fiber 2 with air cladding (solid curves) and 1.0 m of fiber 4 infiltratedwith heavy water (D2O, dashed curves). The transmission spectra show that the fibersguide light over a broad wavelength range, allowing sensing measurements between 500and 1750 nm. The loss spectra for both the air- and D2O-filled fibers are flat over a broadwavelength range, implying that the length of a fiber can be adjusted without changingthe shape of the transmission spectrum.

OH− contamination during the fiber drawing process. This absorption can be reduced

by drying the silica preform or by pre-treatment with chlorine gas. The dashed curve in

Figure 4.2(a) shows the transmission window for 1 m of fiber 4 infiltrated with heavy water

(D2O). The refractive index of D2O is similar to that of H2O. However, all absorption

bands are shifted to longer wavelengths due to the almost doubled moment of inertia of

D2O compared to H2O, which reduces the vibrational frequencies by a factor of about√

2. The measured transmission of the D2O-filled fiber indeed displayed an absorption

band at 1600 nm, which accords with the H2O absorption band at 1190 nm, shifted by

∼√

2 [181]. The transmission spectra showed that the fibers guide light over a broad

wavelength range, allowing sensing measurements between 500 and 1750 nm.


ca

lcu

late

dm

ea

su

red

� = 500 nm � = 700 nm � = 800 nm � = 975 nm � = 1000 nm1

0

0.5

Figure 4.3: Normalized mode profiles (time-averaged z-component of the Poynting vector,Sz) of fiber 2 with H2O-filled cladding. All images are 2.5 × 2.5 µm2. The white curvesoverlaying the images indicate the contours of the fiber structure obtained from SEM. Theimages show the measured (top row) and calculated (bottom row) Sz profiles at wave-lengths 500, 700, 800, 975 and 1000 nm. The contour lines are 0.1 apart (in normalizedunits).

A typical loss spectrum for fiber 2 with air cladding is shown in Figure 4.2 (b). The

spectrum reveals a low-loss region with losses below 0.2 dB/m between λ = 500 and

900 nm. The maximum observed loss within the transmission windows of this fiber was

4 dB/m. The loss spectrum was also measured in fiber 4 filled with D2O. The losses are

slightly higher than in the unfilled fiber 2 but remain below 3 dB/m over the wavelength

range between 500 and 1220 nm. For typical sensing measurements, fiber lengths of less

than 20 m suffice. It can therefore be concluded that losses do not limit the performance

of these fiber sensors. The loss spectra for both the air- and D2O-filled fibers are flat over

a broad wavelength range, which leads to the conclusion that the length of a fiber can be

adjusted without changing the shape of the transmission spectrum.

4.2.1.2 Mode Field Distribution

The sensing mechanism in air-suspended SC-PCFs is based on the overlap between the

evanescent field of the guided mode and the sample. In quantitative sensing experiments

it is essential to know the fraction of power, φ, in the cladding holes that is available for

interaction with the sample. Measurements of the mode profiles of the fibers at various

wavelengths were taken with a CCD beam profiler (WinCamD-UHR-1310) by imaging


the output facet of the fiber onto the CCD with a 60×0.85NA microscope objective.

The CCD camera was placed at a distance of about 2 m from the imaging objective to

ensure that only the core region was imaged by the beam camera. The scale of the images

obtained was calibrated by translating the fiber coupling stage over known distances. The

resulting normalized beam profiles for H2O-filled fiber 2 at λ = 500, 700, 800, 975 and

1000 nm are shown in the top row of Figure 4.3. The measured profiles show that the

mode is confined to the core region at shorter wavelengths, and extends further into the

cladding holes as the wavelength increases, implying that a larger power fraction in the

cladding holes is available for sensing.

The mode profiles were also calculated using the finite element method (FEM). The

calculations were based on contours extracted from SEM images of the measured fibers

and consequently do not contain any freely adjustable parameters. The fiber structure is

discretized using triangular elements of 0.05 µm in the core region and larger elements in

the cladding region to achieve a realistic discretization of the fiber structure. The bottom

row of Figure 4.3 shows the calculated time-averaged z-component of the Poynting vector,

Sz, of fiber 2 with H2O-filled cladding at the same wavelengths as the measured beam

profiles. The measured and calculated mode profiles are in good agreement, and both

display an increase in the amount of evanescent field in the cladding region with increasing

wavelength.

Some irradiance profiles calculated using the FEM revealed discontinuities on a sub-

100 nm scale across the glass-air (core-cladding) boundary. These discontinuities are

attributed to field enhancement effects caused by the discontinuity in the normal com-

ponent of the electric field given by the ratio between the dielectric constants of the two

media [182]. These near-field features do not appear in the measured beam profiles in

Figure 4.3 since they have dimensions that are well below the free space diffraction limit

of the light. Scanning near-field optical microscopy can be used to resolve such features

[182].

The dependence of the calculated power fraction in the cladding holes on the core

diameter is shown in Figure 4.4(a) for a H2O-filled fiber at λ = 700 (solid curve) and 1000

nm (dashed curve). The value of φ increases with decreasing deff as more light becomes

available in the cladding holes for sensing. Figure 4.4(b) shows the dependence of φ on the


0.6 1.2 1.8 2.40

20

40

Effective core diameter [µm]

% p

ow

er

in c

lad

din

g

H2O cladding

700 nm

1000 nm

(a)

450 650 850 10500

20

40

Wavelength [nm]

Core diameter = 1.045 µm

H2O cladding

Air cladding

(b)

Figure 4.4: (a) Dependence of calculated cladding power fraction in a H2O-filled fiberon effective core diameter at λ = 700 (solid curve) and 1000 nm (dashed curve). Thepower fraction is shown to increase with decreasing core diameter. The square symbolsare power fractions for fiber 2 obtained from the measured mode profiles. (b) Calculatedwavelength dependence of cladding power fraction for fiber 2 with both H2O- (solid curve)and air-filled (dashed curve) cladding. Both curves show that φ increases with wavelength.The data points are experimental values obtained from measured mode profiles and arein quantitative agreement with theory (within 3%).

cladding medium and wavelength of the light propagating in the core. It is shown that by

inserting an aqueous sample into the holes, the field extends further into the cladding due

to the decreased index contrast. The power fraction also increases with wavelength, as

light with longer wavelengths is less tightly confined to the solid core. The experimental

power fractions in the cladding were extracted from the measured mode profiles shown in

Figure 4.3. The beam profiles were multiplied with masks generated from the SEM images.

The optimum position and orientation of the masks were determined by an automated

cross-correlation routine, in which the amount of light in the glass core was optimized.

The data points (square symbols) in Figures 4.4(a) and (b) show the resulting measured

power fractions for a range of wavelengths and demonstrate quantitative agreement with

the calculated power fractions to within 3% over the entire wavelength range.

4.2.1.3 Dispersion

Another important characteristic of the fiber is the fiber dispersion, as shown in Figure

4.5(a). The dispersion for fibers 3 (circles) and 4 (squares) was measured with white

light interferometry [183] using the PCF SC source. Results from the measurements were

compared to FEM calculations taking into account the dispersion of silica. The calculated


600 800 1000 1200-200

-100

0

100

Wavelength [nm]

Dis

pe

rsio

n [

ps⋅km

-1n

m-1

]

(a)

Fiber 3 (measured)

Fiber 3 (calculated)

Fiber 4 (measured)

Fiber 4 (calculated)

0.5 1 1.5 2 2.5 3

600

700

800

900

Effective core diameter [µm]

Ca

lcu

late

d Z

DW

[n

m]

(b)

Figure 4.5: (a) Measured and calculated dispersion of fiber 3 and 4 in the wavelengthrange between 600 and 1200 nm. The measured data for fiber 3 (circles) and fiber 4(squares) show a ZDW at 846 and 887 nm, respectively. The solid and dashed curvesrepresent dispersion curves obtained from FEM calculations without free parameters, andagree very well within 2 ps·km−1nm−1 with a polynomial fit (not shown) of the measureddata points over the entire wavelength range. The inset shows the dependence of thecalculated ZDW on the effective core diameter (diamonds). The dotted line is a linear fitthrough the calculated data points.

dispersion of fibers 3 and 4 between λ = 600 and 1200 nm is shown as the solid and dashed

curves in Figure 4.5(a), respectively. The calculated dispersion of both fibers agrees within

2 ps·km−1nm−1 with a polynomial fit (not shown) through the measured data points over

the entire wavelength range. The excellent agreement between the measurements and

the theory is remarkable since no parameters were freely adjustable, exemplifying the

accuracy of the FEM calculations.

The region near the zero dispersion wavelength (ZDW) is particularly interesting for

nonlinear optical experiments. Fibers 3 and 4 have ZDWs at 846 and 887 nm, respectively.

The ZDW can be tailored for nonlinear experiments in either the solid core of the fiber

or in the cladding holes. The ZDWs of the fibers are controlled by deff. Figure 4.5(b)

shows the dependence of the first calculated ZDW (diamonds) on deff. The first ZDW

shifts toward the blue as the core size decreases, in agreement with the silica strand model

[184].

Supercontinuum generation has been demonstrated by launching regeneratively am-

plified Ti:sapphire pulses into a 10 cm long air-suspended solid-core fiber [87]. While

the generated SC was 730 nm broad, the pulse irradiance in their experiment exceeded

1 TWcm−2 (assuming a conservatively estimated coupling efficiency of 1%). The high

peak irradiance and short fiber length suggest that the ZDW did not play a dominant


role in the experiment. Clearly, by carefully tuning the ZDW to lie close to the pump

wavelength, the required pulse irradiance for SC generation can be dramatically reduced,

allowing the use of standard Ti:sapphire or microchip lasers as pump sources. We propose

that such efficient SC generation could be used in single-fiber sensors in which both the

SC source and sample chamber are combined. In such systems, the dispersion of the

sample should also be taken into account. As an example: from FEM modeling of the

dispersion of fiber 3, we have obtained that the ZDW changes from 846 to 1090 nm upon

infiltration with water. This redshifted ZDW is close to the wavelength of the Nd:YAG

microchip laser (1064 nm), typically used for SC generation in ESM-PCF.

4.2.2 Results

An aqueous NiCl2 solution (in which nickel is present largely as [Ni(H2O)6]2+) was chosen

as the analyte to demonstrate broadband chemical sensing in the air-suspended SC-PCF.

NiCl2 is a compound that is commonly used for electroplating and also in batteries.

It is hazardous for the environment and particularly toxic to aquatic organisms. The

LC50/96 h1 for water organisms is about 100 mg/L, corresponding to c = 4.2 × 10−4 M.

Unfortunately, efficient monitoring of NiCl2 concentrations is hampered by the low molar

absorptivity of [Ni(H2O)6]2+. Thus, NiCl2 is a compount highly suitable for testing the

performance of the proposed PCF sensor.

In order to compare the measurement to standard spectroscopic techniques, a NiCl2

concentration of 2.1× 10−2 M was chosen, which is just detectable in a L = 1 cm cuvette

measurement. To obtain the reference molar absorptivity spectrum, the transmission of a

collimated halogen light source through the cuvette with the sample was measured using

a USB spectrometer. The fine curve in Figure 4.6(a) shows the absorbance in the λ =

550 to 875 nm range, obtained by normalizing to the transmission through a H2O-filled

cuvette. The absorbance reaches a maximum value of 0.4 dB at λ = 720 nm. The fine

curve in Figure 4.6(b) shows the resulting molar absorptivity spectrum.

The absorption spectrum of [Ni(H2O)6]2+ is known to exhibit three broad absorption

bands between 350 and 1400 nm, arising from spin-allowed d -d electronic transitions.

1Lethal Concentration 50: concentration in water having 50% chance of causing death to aquatic life

after 96 h exposure.


550 650 750 8500

2

4

Wavelength [nm]

Absorb

ance [dB

] (a) PCF

cuvette

550 650 750 8500

1

2

Wavelength [nm]

ε[L

mol-1

cm

-1]

(b) PCF

cuvette

Figure 4.6: (a) Absorbance spectra of an aqueous 2.1×10−2 M NiCl2 solution, normalizedto H2O reference, measured in a 1.1 m long piece of fiber 2 (thick curve) and in a 1 cmstandard cuvette (fine curve). Two subpeaks at 660 and 720 nm could be resolved inboth spectra. The absorbance signal measured has strongly increased from 0.4 dB in thecuvette to 4.7 dB in the fiber. (b) Molar absorptivity spectra obtained from the modifiedBeer-Lambert law, taking into account the power fraction in the fiber cladding. Theexcellent agreement is striking since no parameters were freely adjusted.

The central absorbance band splits into two maxima at 660 and 720 nm (in accordance

with the literature values of 656 and 720 nm [185, 186]), exhibited molar absorptivities

of 1.5 and 2.1 Lmol−1cm−1, respectively. This central absorbance corresponds to the

3A2g →3 T1g(3F) electronic transition. In the absence of coupling, this would be expected

to give a single maximum. However, due to the presence of strongly coupled electronic

states (in this case 3T1g and 1Eg), a superposition of several transitions is detected, giving

rise to the two maxima observed [187].

For the fiber-based measurement, fiber 2 with deff = 1.05 µm and φ = 10.4% at

700 nm, the center of the absoprtion band for NiCl2, was chosen. According to the ideal

sensing parameter diagram (see Figure 2.2), the optimum fiber length required for a 5 dB

absorbance signal is 1.1 m (displayed as a square in Figure 2.2). The fiber was connected

to liquid cells and initially filled with de-ionized H2O to obtain a reference spectrum. The

sample volume in the fiber (1 µL) is reduced by three orders of magnitude compared to

the cuvette measurement (1 mL). The transmission through the fiber was recorded and

subsequently, the H2O in the fiber was replaced by an aqueous NiCl2 solution (21 mM).

The thick curve in Figure 4.6(a) shows the resulting absorbance spectrum, obtained by

normalizing the NiCl2 data to the transmission through the same fiber filled with H2O.

The same broad absorption band as that measured in the cuvette was observed between

4.3. MICROSCALE SURFACE CHEMISTRY 79

λ = 600 and 800 nm. Importantly, the fiber spectrum also resolves the two peaks at

660 and 720 nm, illustrating that the fiber does not introduce spectral artifacts. The

maximum measured absorbance of 4.7 dB is in good agreement with the prediction. A

direct quantitative comparison between the fiber data and the reference sample is made in

Figure 4.6(b). Here, the ε(λ) spectrum of NiCl2 was extracted by applying the modified

Beer-Lambert law on the absorbance data, with φ = 10.4% at 700 nm also taken into

account. The striking agreement between the in-fiber measurement (thick curve) and

the reference spectrum measured in the the standard cuvette (fine curve) demonstrates

that the air-suspended SC-PCF can be used in quantitative broadband chemical-sensing

measurements.

4.2.3 Discussion

A quantitative broadband fiber sensor based on evanescent-wave sensing in the cladding

holes of an air-suspended SC-PCF has been demonstrated. The measured mode profiles

were in good agreement with numerical calculations based on the finite element method

made without free parameters. The fraction of light in the hollow cladding can be tuned

via the core diameter of the fiber. Dispersion measurements were in excellent agreement

with the theory and demonstrated tuning of the zero dispersion wavelength via the core di-

ameter. The applicability of the proposed evanescent-wave PCF sensor was demonstrated

by measuring the broad absorption peak of an aqueous NiCl2 solution and showing excel-

lent agreement with the reference spectrum measured in a standard cuvette despite three

orders of magnitude lower sample volume used.

4.3 Microscale Surface Chemistry

4.3.1 Self-Aggregation and Photobleaching of Methylene Blue

Methylene blue, MB, is a cationic thiazine dye with a broad spectrum of applications

ranging from antidote for cyanide poisoning [188], antiseptic in veterinary medicine, to in

vitro diagnostic in biology, cytology, hematology and histology [189, 190]. Furthermore,

its photochemical activity is well-established, given its common role as a sensitizer in


various areas of photochemistry including photogalvanic cells [191, 192], singlet oxygen

production [193] and reductive electron transfer [194], as a result of the relatively long-

lived triplet state (450 µs in the triplet state, compared to 30 to 390 ps of the singlet

state) and high quantum yield (φT = 0.52) [194, 195].

Like many thiazine dyes, MB readily undergo self-aggregation to form dimers (and

higher aggregates) [196] in aqueous solution in spite of like-charge repulsion. The reaction

for dimerization takes the following form

2MBKD⇀↽ (MB)2, (4.1)

where KD is the equilibrium constant of the dimerization process given by

KD =[(MB)2]

[MB]2. (4.2)

[MB] and [(MB)2] are the concentrations of the MB monomer and dimer, and KD is

reported in literature to vary between 2000 and 6000 Lmol−1 [197-200], the variation in

the values obtained was mainly due to the differences between the actual experimental

conditions under which the experiments were performed, such as the temperature and the

pH of the buffer. The main forces responsible for the aggregation of the dye molecules are

hydrogen bonding, van der Waals forces and the predominant force due to hydrophobic

interactions (i.e. water acts as a catalyst in inducing aggregation) [201]. We assumed that

dimerization is the only self-aggregation process MB can undergo under the experimental

conditions here. Therefore [MB]total = [MB] + 2[(MB)2], and from Equation 4.2 it follows

that the concentration of the monomer, [MB], can be obtained by solving the following

quadratic equation,

2KD[MB]2 + [MB]− [MB]total = 0. (4.3)

Solutions of methylene blue in de-ionized water were prepared with concentrations

ranging from 0.415 to 20.8 µM by serial dilutions from a stock solution. From Equation 4.2

and taking the median of KD = 3000 Lmol−1 reported in various literature sources [197-

200], approximately 87% of the 20.8 µM sample is in its monomer form. Figure 4.7(a)

shows the molar absorptivity spectrum of a 20.8 µM MB sample in water, measured in a

standard 1 cm cuvette. The absorption peaks at λ = 612 and 665 nm have the coefficients

ε = 2.46 × 104 and 4.48 × 104 Lmol−1cm−1, respectively. The peak near λ = 660 nm is

attributed to the monomer, while the peak near λ = 610 nm is due to the dimer.


480 560 640 720 8000

1.6

3.2

4.8

Wavelength [nm]

ε[×

10

4L

mo

l-1cm

-1] (a)

20.8 μM

480 560 640 720 8000

8

16

24

Wavelength [nm]

(b) t = 0

3 min.

5 min.

6 min.

2.08 μM

480 560 640 720 8000

14

28

42

Wavelength [nm]

(c)t = 0

10 min.

13 min.

16 min.

ε[×

10

4L

mo

l-1cm

-1]

1.04 μM

480 560 640 720 8000

40

80

120

Wavelength [nm]

(d)

t = 0

4 min.

8 min.

12 min.

0.415 μM

Figure 4.7: (a) Molar absorptivity spectra of methylene blue in water, measured in astandard 1 cm cuvette. For a 20.8 µM sample (solid curve), the absorption peak near660 nm is attributed to the monomer, while the peak near 610 nm is due to the dimer. (b)Photobleaching of MB (2.08 µM) in suspended solid-core fiber (fiber 2, 107 cm) inducedby irradiation using the broadband PCF SC source. Absorption of the sample in thewavelength range of 480 to 800 nm completely vanished after 10 minutes of irradiationwith an average irradiance ∼ 100 kWcm−2. Subsequent measurements using (c) 1.04 and(d) 0.415 µM of MB in 117 and 100 cm of fiber 2 demonstrated similar photobleachingeffects. All measurements were performed until absorption in the wavelength range of 480to 800 nm has completely vanished.

The dye can undergo photoreduction process by visible light [201], resulting in the

doubly reduced form of MB, leuco-MB (LMB), which is colorless. This photobleaching

phenomenon of MB from its bright blue color is due to the covalent modification of the

molecule upon excitation from an excited singlet state to the excited triplet state. Exper-

iments with the aim of monitoring the photoreduction process in the PCF photochemical

reactor were performed using fiber 2 of the air-suspended SC-PCF shown in Figure 4.1.

Figure 4.7(b) shows the changes in the molar absorptivity spectrum of a 2.08 µM MB

sample in 107 cm of fiber 2, as a result of photobleaching induced by irradiation using

the broadband PCF SC source. It was observed that the absorption band in the wave-

length range of 480 to 800 nm completely vanished after 10 minutes of irradiation with an


average optical power of several mW, corresponding to an irradiance of ∼ 100 kW/cm2.

Subsequent measurements, shown in Figures 4.7(c) and (d), using 1.04 and 0.415 µM of

MB in 117 and 100 cm of fiber 2, demonstrated similar photobleaching effects. All mea-

surements were performed until the absorption band in the wavelength range of 480 to

800 nm has completely vanished. A much lower power was used initially for optimization

of fiber alignment for all three measurements to avoid photobleaching effects. Guidance

of the fundamental mode in the solid fiber core was confirmed for the wavelength range of

interest before each measurement. The higher-than-expected molar extinction coefficients

obtained in all three in-fiber measurements (compared to that obtained in the bulk mea-

surement in cuvette as shown in Figure 4.7(a)) suggest aggregation of the dye molecules

on the silica surface, leading to the higher apparent concentration of the sample. Note

that while no quantitative comparison between the initial ε spectra can be made for the

different sample concentrations due to the different initial infiltration conditions (namely

the duration of infiltration before the first “t = 0” spectrum was taken), further exami-

nation of the spectra revealed that the absorption peak near 610 nm increases (relative

to the amplitude of the sub-peak near 640 nm) with increasing sample concentration,

indicating the increase in the formation of dimer aggregates on the silica surfaces. Such

surface-induced aggregation of the dye molecules have also been observed and reported

in a microstructured-core fiber for evanescent-wave sensing [87].

Further insight into the extent of adsorption of MB on the fused silica nanowebs can

be obtained by deducing the surface density of the sample. The absorption coefficient,

α(λ), is defined by the fraction of total optical power absorbed per unit length, and can

be written in the form of

α(λ) =

∮CρSσ(λ)I(r) · dr∫

SI(r)ds

, (4.4)

where ρS is the surface number density of adsorbed molecules, σ(λ) is the absorption

cross-section of one molecule and I(r) is the the irradiance of the light propagating in

the core of the fiber at the position vector r on the contour C. The concept of the

calculation is as depicted in the inset of Figure 4.8. In the numerator of Equation 4.4, the

absorbed optical power is obtained by performing closed line integral along the contours

of all the cladding holes immediately adjacent to the core of the fiber. The total power is

evaluated in the denominator by integrating I(r) across the entire cross-section of the fiber,


0 3 6 9 12 15 180

0.3

0.6

0.9

1.2S

urf

ace d

ensity [×10

-12

mol/cm

2]

Exposure time [minutes]

dr

C

1

0

0.5

Figure 4.8: The variation in the calculated total surface density of MB along the innersurface for the photoreduction of 0.415 µM of MB in 100 cm of fiber 2 with irradiationtime. Approximately 6% of the molescules that passed through the fiber are estimatedto have remained in the fiber due to adsorption. The dotted curve is a fitted Gaussiancurve with a decay constant of 0.27 ± 0.0019 min−1. The concept of the closed contourline integral performed in the calculations can be visualized in the inset; the contour linesfor Sz are 0.1 apart in normalized units.

including the cladding region. I(r) was obtained from the irradiance profile calculated

using FEM for the entire cross-section of the fiber, while the absorption cross-sections

σ(λ) and attenuation coefficients α(λ) were obtained from the experimentally measured

data shown in Figures 4.7(a) and (d), respectively.

The calculated surface density of MB along the inner surface of the fiber cladding

holes is shown in Figure 4.8 for the photoreduction of 0.415 M of MB in 100 cm of fiber 2

with irradiation time (see Figure 4.7(d)). As shown, the calculated surface density for

the initial measurement at t = 0 is 10−12 mol/cm2. The fiber used was 1 m of fiber

2 with a cladding diameter of 64 µm, which corresponds to a total inner fiber surface

area of approximately 4 cm2. Therefore approximately 4 ×10−12 mol of MB molecules

were adsorbed onto the inner fiber surface, with each molecule occupying approximately

13 nm2 of the inner fiber surface. For comparison, the three-dimensional molecular size

of MB is 1.43 nm × 0.61 nm × 0.4 nm [202]. In addition, the fiber was infiltrated at

a rate of approximately 1 mLh−1 for at least 10 minutes before the first spectrum (the

t = 0 spectrum) was taken. One can therefore assume that at least 0.17 mL of the


sample has passed through the fiber. This corresponds to approximately 7 ×10−11 mol

of total MB molecues that have “seen” the surface of the fiber. From the 4 ×10−12 mol

of MB molecules which were adsorbed onto the inner fiber surface, one can estimate that

approximately 6% of the molecules that passed through the fiber have remained in the

fiber. It is therefore possible to quantify the decrease in the surface density of MB due

to photoreduction as a function of exposure time. The MB was determined to reduce to

the colorless LMB form (undetectable via absorption spectroscopy within the operating

wavelength range) at a rate of 0.27 ± 0.0019 min−1. Further quantitative analysis of

the adsorption dynamics would require controlled infiltration conditions. However, the

preliminary result has clearly demonstrated the affinity of the MB molecules to adsorb

onto the fiber surfaces.

In order to further investigate the affinity of the MB molecules to adsorb on the silica

surfaces, the photobleaching experiments were performed in a hollow-core kagome PCF.

Figure 4.9(a) shows the photobleaching of a 20.8 µM MB sample in ∼ 30 cm of the

kagome fiber induced by irradiation using the broadband PCF SC source. The measured

spectral shape agrees with that of the same sample measured in the cuvette (solid curve

in Figure 4.7(a)). Initial inspection of the result reveals that the molar absorptivity of

the dye molecule measured in the HC-PCF is lower than that measured in bulk. This

suggests that some molecules may have moved out of the active sensing region of the fiber

core and adsorbed onto the surface surrounding the core where they are only very weakly

detectable by light.

Figure 4.9(b) shows the variation in the molar absorptivity spectrum demonstrating

effect of adsorption in 36 cm of the kagome fiber. The spectrum taken after the initial

infiltration of 0.415 µM of MB sample (at t = 0, curve 1) shows approximately 78%

lower absorption at the absorption peak than expected from bulk measurement in the

cuvette. This indicates that at least 78% of the dye molecules were adsorbed on the silica

surface surrounding the hollow fiber core, where the irradiance of the core mode is low

and could not detect the sample efficiently. The high concentration of adsorbed molecules

is a result of the large surface-to-volume ratio (which is inversely proportional to the

core diameter and in this case ∼ 105 m−1, three orders of magnitude higher than the

conventional 1 cm cuvette) provided by the microstructured fiber. Continuous infiltration


550 600 650 7000

30

60

90

Wavelength [nm]

ε[×

10

3L

mo

l-1cm

-1] (c)First infiltration

Second infiltration

550 600 650 7000

3

6

9

Wavelength [nm]

(a)6 min.

24 min.

ε[×

10

3L

mo

l-1cm

-1]

550 600 650 7000

11

22

33

Wavelength [nm]

(d)1: First infiltration

2: 4 min. irrad.

3: Second infiltration 1

2

3

550 600 650 7000

14

28

42

Wavelength [nm]

(b)1: t = 0

2: 29 min.

3: 33 min.

4: 88 min. irrad.

2

3

4

1

Figure 4.9: (a) Photobleaching of MB (20.8 µM) in kagome HC-PCF (∼ 107 cm) inducedby irradiation using the broadband PCF SC source. (b) Increase in the molar absorptivityspectrum as a result of continuous infiltration of MB (0.415 µM) in 36 cm of the kagomePCF (curves 1 to 3). Irradiation of the sample without the infiltration of new sampleinto the fiber displayed photobleaching effect similar to that observed in the previous ex-periments (curve 4). (c) Multiple discontinuous infiltration of MB (0.415 µM) in 34.5 cmof the kagome PCF showed an increase in the measured molar absorptivity beyond thatmeasured in the bulk. (d) Multiple infiltration and photobleaching experiments performedin 50 cm of silanized kagome PCF. The measurements showed a molar absorptivity spec-trum (initially lower than the bulk values) that increased with infiltration attempts, anddecreased upon irradiation without infiltration of new sample into the fiber, displayingsimilar dynamics of the results compared to that of the non-silanized fibers.

of the sample through the fiber revealed an increase in the measured absorption, and

the expected value (bulk value measured in the cuvette) was obtained after 33 minutes

of continuous infiltration, the spectral shape of which agreed with that measured in the

cuvette. It is postulated that the continuous infiltration of the sample had eventually

saturated the inner silica surface of the hollow fiber core with the dye molecules. A

coating was effectively formed on the inner surface of the fiber core and forced the newly-

infiltrated molecules to the active sensing region defined by the mode propagating in the

fiber core. The PCF SC source remained on during the 33 minutes of infiltration at a

low average power level of 17 µW, corresponding to an irradiance level of 2.4 W/cm2


(four orders of magnitude lower than that used in the suspended SC-PCF), to prevent

possible/significant counter-effect of photobleaching on the absorption spectra measured.

The infiltration of the sample was subsequently stopped while the SC source was left on to

irradiated the sample in the fiber for 88 minutes. The spectrum obtained after 88 minutes

of irradiation showed that photobleaching took place at a much reduced rate compared

to those performed in the air-suspended SC-PCF shown in Figures 4.7(b) to (d). As the

rate of photoreduction is independent of the concentration of the solution, the reduced

photobleaching rate observed in the HC-PCF can be attributed to the much lower power

level used to induce the reduction.

A separate experiment in which infiltration of the 0.415 µM MB sample through

34.5 cm of the kagome fiber was performed in a stop-and-go configuration (i.e. the sam-

ple infiltration was stopped for an undefined period of time during which the absorption

spectrum was recorded, after which the infiltration was restarted). The results shown

in Figure 4.9(c) showed that the measured molar absorptivity increased with increasing

infiltration attempts. This increase in absorption, and hence the apparent sample concen-

tration within the fiber core, was possibly due to the physisorbed dye molecules coming

off the surfaces in the subsequent infiltration, which allowed them to become free and

detectable in the core volume again. Fringe-like features were also observable in both

spectra in Figure 4.9(c). The spectral position of these features coincide on both spectra,

and were at a spacing of 3.66 nm. The irradiance profile of the beam exiting the fiber

revealed a double-lobe structure, indicating the propagation of higher order modes in the

fiber core. Using the following equation for the propagation constants of straight dielectric

guides [103]:

βnm =2π

λ

{1− 1

2

(unmλ

2πa

)2}

(4.5)

where unm is the mth root of the equation Jn−1(unm) = 0, λ is the wavelength and a

is the radius of the guide. The propagation constants, and therefore the beat length,

for the EH11 and TE01 modes can be calculated to be 3.47 nm, which is close to the

experimentally observed value. Consequently, intermodal dispersion can give rise to the

fringes observed.

In order to combat the undesirable effects of dye molecule adsorption on the silica sur-


face surrounding the hollow fiber core, surface-treated fiber samples were prepared by infil-

trating the fiber with a 2% v/v solution of dimethyldichlorosilane in 1,1,1-trichloroethane

and left to stand for several hours to achieve hydrophobic surfaces. The fiber was rinsed

with isopropyl alcohol and then dried by purging with air before use. The photobleaching

and multiple sample infiltration experiments were repeated in 50 cm of the silanized fiber.

Figure 4.9(d) shows that irradiation of the sample (without infiltration of new sample

into the fiber) decreased the absorption signal (curve 1→2), while multiple infiltration of

the 0.415 µM MB sample increased the molar absorptivity towards the expected value

measured in bulk, as indicated by the progression from curve 2 to 3. The results displayed

similar dynamics to that of the unsilanized fiber, indicating that the initial attempt in

surface treament of the fiber was unsuccessful. Several ideas have been recently proposed

to reduce or completely eliminate the effect of adsorption on the silica surface: as the

polarity of the aqueous sample and the surface is the key factor, it has been suggested

that the interaction potential between the molecules and the silica surface can be tuned

by replacing water with an inorganic salt as the buffer solution.

4.3.2 Discussion

Efficient adsorption of methylene blue dye molecules on the inner silica surfaces was ob-

served. Opposite effects on the magnitude of the measured molar absorptivity spectra were

demonstrated in the solid and hollow-core of two types of PCF. In particular, an index-

guiding PCF design with moderate evanescent field extending into the cladding region can

provide novel platforms for interrogating surface-bound molecules on the nanoscale. De-

velopment of such devices necessitates further quantitative analyses of the adsorption and

desorption processes, including well-controlled sample infiltration and residence time. It is

instructive to perform bulk measurements using planar fused silica substrate as reference

for comparison with the in-fiber measurements.

It has been demonstrated that several phenothiazines such as methylene blue were able

to form oligomeric tau species upon binding to inhibit neurodegeneration in vitro [203,

204]. The development of methylene blue as an Alzheimer drug to prevent the aggregation

of tau and amyloid proteins can be efficiently studied in PCF. Furthermore, the possibility

to use methylene blue to generate singlet oxygen which then photochemically changes the


vitamin B12 [205] can aid towards optimization of photoactivated anticancer drugs.

Chapter 5

Conclusions and Outlook

The enhanced light-matter interaction made possible by the photonic crystal fiber offers

a multitude of applications in various branches of chemistry. In particular, the novel

demonstration of utilizing the photonic crystal fiber as a highly efficient photochemical

reactor opens up new regimes of “doing chemistry”, many of which may one day find their

permanent place in common measurement equipments or as routine laboratory techniques.

Here we discuss possible applications of the work presented in this thesis.

5.1 Optical Tweezers and Photodynamic Therapy

The work on the photoaquation of vitamin B12 presented in Chapter 3 was intended

to study the feasibility of efficiently inducing and monitoring photochemical processes

in the photonic crystal fiber chemical reactor. These reactions are similar to that of the

photoactivated anticancer drugs currently under intensive research and development. The

success in this initial case study suggests that the photonic crystal fiber is a well-suited

candidate for testing the effectiveness of these drugs. The next stage would involve testing

these drugs on cancer cells in a well-controlled environment. Recently, precise control over

a particle against fluidic counterflow was demonstrated in a liquid-filled photonic bandgap

fiber [162]. By combining a photonic crystal fiber chemical reactor with an in-fiber cell

guidance setup, the optical and mechanical response of a cancer cell to the synthetic drugs

under test can immediately be obtained via a range of sensing modalities available for

photonic crystal fiber sensors.

89

90 CHAPTER 5. CONCLUSIONS AND OUTLOOK

5.2 Microfluidic Flow Reactor

The small dimensions of the microfluidic channels in the fiber’s microstructure provide

unique opportunities for the implementation of photonic crystal fibers as miniature flow

reactors. Such flow reactors would allow continuous on-line optimization of the expo-

sure conditions and reagent parameters in a reaction. In addition, most biochemical

experiments are performed in fluidic environments. The exploitation of photonic crystal

fibers as optofluidic devices offers significant advantages including minimal consumption

of reagents and mechanical flexibility. Furthermore, recent experiments have shown that

photonic crystal fibers can be integrated into existing planar microfluidic circuitry [206].

5.3 Mass Spectrometry

Mass spectrometry is a common analytical technique used in the laboratories to deter-

mine the elemental composition of a sample, and is an integral routine used in chemical

synthesis, including the development of therapeutical anticancer complexes. It is there-

fore of great interest to incorporate microfluidic photonic crystal fiber circuitry in a mass

spectrometer setup to accommodate direct measurements of the products of photochem-

ical reactions. Such a setup could also allow for the quantitative spectroscopic assay of

reaction products and monitoring of the reaction kinetics. Preliminary results from a

separate project have already confirmed the feasibility of such a setup configuration.

5.4 Surface Chemistry Using Higher-Order Modes

The experiments on the self-aggregation and photobleaching of methylene blue in Chap-

ter 4 have demonstrated that the reaction kinetics of molecules with high affinity to ad-

sorb onto the fiber surfaces can be efficiently studied by taking the advantage of the high

surface-to-volume ratio offered by the microstructure of the photonic crystal fibers. A well-

defined optical mode propagating in the fiber is capable of detecting minute changes in the

composition of the sample via, for example, absorption spectroscopy. It has been demon-

strated that higher-order modes propagating in hollow-core photonic crystal fibers can be

selectively excited by using holograms electronically generated by a spatial light modu-

5.5. FINAL REMARKS 91

lator [64]. By careful excitation of both the fundamental mode and a surface-sensitive

higher order mode in a hollow-core photonic crystal fiber, it is possible to measure the

local concentration gradients across the core volume of the fiber.

5.5 Final Remarks

The examples outlined above give a clear indication to the breadth of research possibilities

in photonic crystal fibers, utilizing the unprecedented interplay between light and matter

within the fiber’s microstructure. The novelty in the development of photonic crystal fiber

lies in its cross-disciplinary applications, bridging different fields in science and technology.

With no foreseeable limitation to the future prospects in sight, the continual development

in the novel applications of photonic crystal fiber devices is to be anticipated.

Appendix A

Counter-Propagating Pump-Probe

Setup

In Section 3.4 the HC-PCF photochemical reactor was demonstrated to track the fast and

reversible photoswitching process of an azobenzene derivative. While the experiments

were able to show the complete reversibility of the photochemical reaction, quantitative

analyses of the reaction dynamics has proven to be a computation intensive task. There

are two interconnecting factors contributing to the need for tedious numerical computa-

tion. First, the wavelengths of the excitation sources used to induce the photochemical

reactions were chosen to coincide with the main absorption feature of interest, so that

efficient photochemical conversion can be achieved. However, as the pump beam is at a

much higher irradiance than the broadband probe beam used to measure the absorption

spectra, the excitation signal would completely saturate the USB spectrometer (which is

a grating spectrometer based on CCD arrays). The use of a narrow band-pass filter at

the entrance of the spectrometer could help solve the issue of the limited dynamic range

provided by the spectrometer, however, the filter would also completely block out signals

within the wavelength range of interest.

It was therefore proposed that a modified pump-probe setup with counter-propagating

beams be implemented for the PCF-based photochemical reactors. A schematic diagram

is shown in Figure A.1 depicting the main configuration of the setup. In this configura-

tion, the broadband probe beam is the only beam propagating along the path towards

the spectrometer. The excitation light still propagates through the entire length of the

93

94 APPENDIX A. COUNTER-PROPAGATING PUMP-PROBE SETUP

4x4x

10x 20x

Broad-band

Spectro-meter

Computer

Excitation

CCD

Sample fiber

ESM PCF

MMF

BS1

BS2

10x 20xESM PCF

BS1

10x

BS2

CCD

Figure A.1: Schematic diagram of the modified pump-probe setup with counter-propagating beams for PCF photochemical reactors.

sample fiber, however, only along the opposite direction to the propagating probe beam.

Both the pump and probe beams are spatially filtered by a separate ESM-PCF to ensure

optimum coupling efficiency into the sample fiber, with the aid from CCD beam cameras

on both sides of the setup. The beam splitters BS1 have a splitting ratio of 50:50, while

the beam splitters BS2 which are placed in front of the CCD cameras have splitting ratios

of 92:8, as only a small fraction of the light is required for imaging. Preliminary imple-

mentation of this setup configuration revealed that upon incidence of the pump beam on

the uncoated liquid cell window, strong reflection results which propagate in the reverse

direction (i.e., towards the spectrometer), and “aligns” itself efficiently into the multimode

fiber connected to the spectrometer. A further improvement has thus been made to the

setup, by introducing a 10◦ wedge in the liquid cells to divert any reflection off the liquid

cell window, as shown in the setup schematic.

As the incoming beam is no longer at normal incidence to the liquid cell window,

it is instructive to determine whether refraction of the broadband source at different

wavelengths would hamper the coupling efficiency into the fiber. Consider the schematic

diagram in Figure A.2 showing the glass window at 10◦ tilt, with n1, n2 and n3 denoting the

regions of air, window and liquid, respectively. By applying Snell’s law for an incoming

beam at 10◦ incidence, and using the dispersion relation for fused silica to obtain the

refractive indices of fused silica at λ = 380 and 750 nm (i.e. the visible wavelength

95

�380

�750

10°

nwindow

nair

d

d·tan�750d·tan�

380

Figure A.2: Schematic diagram showing the effect of refraction due to the tilted liquidcell window. Diagram exaggerated and not to scale.

range), nfused silica(380 nm) = 1.4725 and nfused silica(750 nm) = 1.4542. The refracted

angles are calculated to be at 2.1611◦ and 2.1883◦. For window thicknesses ranging from

0.08 to 1 mm used in the experiments, the separation of the longer and shorter wavelength

components varies between 38 to 475 nm and should pose no problem in the coupling of

the broadband source into the hollow fiber core.

List of Publications

1. J. S. Y. Chen, T. G. Euser, N. J. Farrer, P. J. Sadler, M. Scharrer, and P. St.J.

Russell, “Photochemistry in Photonic Crystal Fiber Nanoreactors,” Chemistry - A

European Journal, 16(19), 5607-5612 (2010).

2. T. G. Euser, M. K. Garbos, J. S. Y. Chen, and P. St.J. Russell, “Precise balancing of

viscous and radiation forces on a particle in a liquid-filled photonic bandgap fiber,”

Optics Letters, 34(23), 3674-3676 (2009).

3. T. G. Euser, G. Whyte, M. Scharrer, J. S. Y. Chen, A. Abdolvand, J. Nold, C. F.

Kaminski, and P. St.J. Russell, “Dynamic control of higher-order modes in hollow-

core photonic crystal fibers,” Optics Express 16(22), 17972-17981 (2008).

4. T. G. Euser, J. S. Y. Chen, M. Scharrer, P. St.J. Russell, N. J. Farrer, and P.

J. Sadler, “Quantitative broadband chemical sensing in air-suspended solid-core

fibers,” Journal of Applied Physics 103, 103108 (2008).

5. J. S. Y. Chen, T. G. Euser, G. O. S. Williams, A. C. Jones, and P. St.J. Russell,

“Photoswitching in Photonic Crystal Fiber,” in Advanced Photonics: OSA Optics &

Photonics Congress (EurOPC), SThB3. Karlsruhe, Germany. 21 - 24 June 2010.

6. J. Chen, A. Hangauer, R. Strzoda, T. G. Euser, J. S. Y. Chen, M. Scharrer, P. St.J.

Russell, and M. Amann, “Sensitivity Limits for Near- Infrared Gas Sensing with

Suspended-core PCFs directly coupled with VCSELs,” in Conference on Lasers and

Electro-Optics (CLEO), JThB7. San Jose, USA. 16 - 21 May 2010.

7. J. Chen, A. Hangauer, R. Strzoda, M. Amann, T. Euser, J. S. Y. Chen, M. Schar-

rer, P. Russell, “Near-infrared gas sensing using hollow waveguides and PCFs di-

97

98 LIST OF PUBLICATIONS

rectly coupled to VCSELs,” in Field Laser Applications in Industry and Research

(FLAIR). Grainau, Germany. 6 - 11 September 2009.

8. J. S. Y. Chen, T. G. Euser, N. J. Farrer, P. J. Sadler, and P. St.J. Russell, “Photo-

chemistry in photonic crystal fibers,” in European Conference on Lasers and Electro-

Optics (CLEO-Europe), CH1.3. Munich, Germany. 14 - 19 June 2009.

9. M. K. Garbos, T. G. Euser, J. S. Y. Chen, and P. St.J. Russell, “Controlled particle

guidance in a liquid-filled single-mode hollow-core photonic crystal fiber,” in Optical

Trapping Applications (OTA), OMA6. Vancouver, Canada. 26 - 30 April 2009.

10. T. G. Euser, J. S. Y. Chen, M. Scharrer, and P. St.J. Russell, “Quantitative broad-

band chemical sensing in air-suspended solid-core fibers,” in Conference on Lasers

and Electro-Optics (CLEO), CMZ6. San Jose, USA. 4 - 9 May 2008.

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Curriculum Vitae

Personal Information

Name: Jocelyn Ssu-Yin Chen

Date of Birth: 8 July 1983

Place of Birth: Taichung City, Taiwan

Gender: Female

Nationality: New Zealander

Education

Max-Planck Institute for the Science of Light, Erlangen, Germany

University of Erlangen-Nuremberg, Erlangen, Germany

Ph.D., Physics September 2006 – August 2010

Thesis: Nanochemistry and Sensing in Photonic Crystal Fibers

Advisors: Professor Philip St.J. Russell and Dr. Tijmen G. Euser

University of Auckland, Auckland, New Zealand

M.Sc. (Hons.), Physics March 2005 – February 2006

Thesis: Optical Parametric Amplification in Photonic Crystal Fibers

Advisors: Professor John D. Harvey and Dr. Stuart G. Murdoch

University of Auckland, Auckland, New Zealand

B.Tech. (Hons.), Optoelectronics March 2001 – December 2004

Thesis: High-Speed Infrared Laser Hygrometer

Advisors: Professor Rainer Leonhardt and Dr. Igor Shvarchuck

121

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