This thesis presents several milestones towards the development of an all-fibre photonic waveform synthesiser. The synthesiser design relies on the generation of multiple-octave wide coherent Raman comb in hydrogen confined in hollow-core photonic crystal fibres (HC-PCF), with the ultimate aim to generate the comb of continuous wave (CW) spectral components, thus paving the way to optical wave synthesis with a comparable control as in electronics. The milestones achieved in this thesis entitle the development of new state-of-the-art HC-PCF, the first demonstration of intra-pulse waveform synthesis using transient stimulated Raman scattering (SRS), strong Stokes generation in the CW regime and finally a report on novel dynamics of the hydrogen molecules that enabled the generation of high power Stokes with ultra-narrow linewidth. Within the continuous endeavour in the group of GPPMM, the development of hollow core photonic crystal fibres (HC-PCF) is an essential key element towards the realisation and the development of an optical waveform synthesiser based on the generation and the synthesis of optical frequency combs using stimulated Raman scattering (SRS) process in gas filled HC-PCF. Two types of HC-PCF are developed and fabricated for this objective. The first type is the photonic bandgap (PBG) HC-PCF that is used as a host for selective generation of rotational first-order Stokes in the first stage of the waveform synthesis process due to its low optical loss and narrow transmission bandwidth. The second type is the Kagome lattice HC-PCF, which is used in the second stage of waveform synthesis due to its ultra-broadband transmission. The guidance mechanism of this type of fibre, known as Inhibited Coupling (IC), is examined, through the study of the effect of the newly introduced hypocycloid core shape on confinement loss theoretically and experimentally. A reduction in optical loss figures from a typical value of ~100 dB/km down to ~17 dB/km is achieved by enhancing the negative curvature of the core-contour. In addition, a systematic theoretical and experimental study on the effect of the number of cladding rings upon the confinement and bending loss in Kagome HC-PCF is performed to gain a thorough understanding of the IC guidance mechanism. The two developed fibres have enabled the development of an all-fibre based system, where the generation of intra-pulse periodic train pulse waveform with 17.6 THz repetition rate and ~ 26fs pulse duration are demonstrated. This was achieved by generating a Raman comb using a compact HC-PCF based system and a micro-chip pulsed laser. The experimental parameters were engineered so the Raman process is in a highly transient regime so to amplify from the quantum noise only a single spatio-temporal mode (STM) to the macroscopic level. We experimentally demonstrated the role of this STM amplification in enhancing the phase-locking of the comb spectral components, and subsequently the intra-pulse optical waveform generation. Furthermore, the results show a long lived persistence of the Raman coherence, thus hinting to a possible pulse-to-pulse mode locking. Such findings make this novel Raman excitation an ideal possible alternative to high harmonic generation (HHG) in gases for the field of attoscience. Towards the aim of generating ultra-broad comb in the CW regime, we generated first rotational Stokes in the CW regime with output power higher than 50 W. The Stokes laser power stability and the thermal distribution along the coupled fibre are reported. In addition, the linewidth measurements of the forward and backward Stokes are presented. A novel mechanism of stimulated Raman scattering is reported. The model is based on optically induced nanostructured Raman gain, whereby the population difference is saturated but in 1D periodic sub-wavelength sections over a long interaction length. The results show a multi-watt forward and backward Stokes emission with structured spectrum, and linewidth as narrow as ~ 10 kHz (>5 orders of magnitude shorter than the Raman linewidth as expected from conventional SRS). Observation of rich dynamics that include Rabi splitting, molecular motional sideband and inter-sideband four wave mixing, and finally AC stark induced molecule acceleration is reported.

Evaporitic environments that could provide habitats for life exist on present day Mars, in addition to Recurring Slope Lineae (RSL), which have been observed suggesting a briny liquid in the subsurface with a seasonal occurrence at the surface. Life detection is the focus for future missions, including use of the Raman Laser Spectrometer (RLS) instrument on board the ESA ExoMars rover for this purpose. Martian simulation chambers were used to expose a subset of the α-amino acids (AA) and halophilic (‘salt-loving’) microbes to the surface and near surface environment. Post-exposure, the detectability of biological molecules with Raman spectroscopy (where the Raman spectrum is the biomarker) was examined, with the intention to inform future missions. Results from this work suggest that a statistical method (independent of band intensity) should be used to rigorously define a set of characteristic Raman bands to unambiguously identify AA, a technique applicable to all biomolecules. Following exposure, both AA and halite entombed archaeal halophiles survived a combination of simulated martian conditions, e.g. freeze-thaw cycling resulted in a maximum of 20 % biomarker signal loss for AA. Halophilic microbes survived UV exposure up to 3.5 sols, though with a complete biomarker signal loss. However, cell counts and hence, survival in near surface, freeze-thaw conditions (indicative of RSL conditions) remained similar to the control sample. Furthermore, the Raman biomarker signal remained intact and detectable, regardless of a reduced intensity. Importantly, for AA doped onto crushed basalt the Raman band biomarkers were lost, which has major implications for the ExoMars rover which will crush rock samples before examination with the RLS instrument. Future missions should be designed to examine samples with the Raman spectroscopy instrument prior to any crushing to avoid destroying the biomarker signal that could be used to imply the presence of life.

Possessing high three dimensional optical sectioning capabilities and deriving chemical contrast from the intrinsic molecular vibrations of the sample, coherent anti-Stokes Raman scattering (CARS) microscopy has the ability to deliver high sensitivity non-invasive biological imaging. It is, however, accompanied by a deleterious non-resonant background (NRB) which acts to reduce the contrast and severely complicate analysis. Computational approaches are currently favoured for removing this NRB; however, these result in significant spectrally varying errors. This thesis concerns the development and subsequent implementation of a CARS platform employing a novel, all-optical, non-resonant background removal mechanism: Spectral Interferometric Polarisation Coherent Anti-Stokes Raman Scattering (SIPCARS). Exploiting the phase change that accompanies a Raman resonance and employing an elliptical pump/probe beam and linear Stokes beam, SIPCARS allows the complete removal of the NRB. The resulting SIPCARS spectra encode mode symmetry information into the amplitude response which can be directly related to polarisation resolved spontaneous Raman scattering spectra. Verification of the SIPCARS methodology was achieved using spectra acquired from pure liquid samples which were in complete agreement with the corresponding polarisation resolved spontaneous Raman scattering spectra. The multiplexing limit of the system was assessed using several multi-component polymer bead mixtures and a lower limit of four determined. High signal-to-noise ratio SIPCARS imaging of a HeLa cell in the vibrational fingerprint region was acquired, from which it was possible to identify lipid droplets and subsequently, by producing ratio images, assess their degree of lipid unsaturation and the level of oxidised lipid content. The effect of a naturally derived phytotherapeutic lipid metabolism altering drug on the lipid droplets, contained within wild type N2 Caenorhabditis elegans nematodes, was addressed using SIPCARS. Assessing lipid unsaturation and area fraction, the drug was shown to produce a marked effect: a significant reduction in storage of saturated fatty acids post exposure. Additionally the ability of SIPCARS to differentiate between a variety of different C. elegans mutants was also demonstrated. SIPCARS currently provides perhaps the only viable route to attain truly quantitative NRB-free CARS data; however, expanding on the foundation provided by this thesis, and following further development, it has the potential for profound implications in a wide range of areas including fundamental life sciences research, novel drug characterisation and histopathology.

We present a time-domain impulsive vibrational spectroscopy (IVS) setup capable of recording background- and baseline-free Raman spectra of excited electronic states in condensed-phase molecular systems. The setup records vibrational Raman spectra from 50-3000 cm-1 and is readily extended to follow spectral evolutions with a time resolution of < 20 fs, opening up the possibility for multi-dimensional Raman spectroscopy. Based on the setup, we explore a wide range of photochemical reactions aimed at gaining fundamental insights in the chemistry of excited electronic states. In rhodopsin, we investigate the consequences of vibrational wavepacket motion through a conical intersection. We identify the C11-H hydrogen out-of-plane mode as a coupling mode and devise a general model of how vibrational coherences can be used to obtain otherwise inaccessible structural information. In a second experiment, we determine the photoproduct distribution and dynamics upon isotopic substitution of selected hydrogen atoms along the retinal backbone. The results suggest a re-definition of the traditional Jablonski diagram for ultrafast photoreactions, which proceed faster than vibrational relaxation. In channelrhodopsin-1, we structurally characterise the primary photoproduct in the photocycle to be of 13-cis character. The study highlights the capabilities of IVS to obtain structural information for short-lived intermediate structures which are otherwise challenging to obtain. For the green fluorescent protein and all-trans retinal protonated Schiff base, we identify key excited-state (intermediate) structures and complement the studies with multi-dimensional Raman spectroscopy. The results provide a first picture of the structural origin of energy flow directly after photoexcitation. This thesis emphasises the capabilities of IVS beyond a proof-of-principle experiment and outlines the high potential of time-domain vibrational spectroscopy to reveal detailed structural information on ultrafast processes with high temporal resolution and sensitivity.

Integrated optics is set to revolutionise the translation of laboratory-based, bulky, and expensive spectroscopy instruments to miniaturised, low-cost, automated yet powerful analytical instruments, which will be utilised to tackle challenges faced in a multiplicity of applications from food safety, environmental monitoring, security, personal medicine, pharmacogenetics and rapid point-of-care diagnostics. Waveguides, as the most fundamental integrated optics component, were utilised to replace bulky and alignment-critical free space optics in conventional spectroscopy. Raman spectroscopy, which provides the fingerprint of the analyte, was incorporated into the waveguide platform to be waveguide-enhanced Raman spectroscopy (WERS). The optical confinement provided by waveguide gives rise of the enhancement. The goal of this project is to push the limit of conventional waveguide-enhanced Raman spectroscopy with significantly improved performance while minimising utilisation of costly materials, components and techniques. Electromagnetic models were established to obtain optimised 2D slab waveguide design for maximising Raman excitation. The fabricated waveguide samples made of Ta2O5 on fused silica substrates were in excellent agreement with the design parameters. WERS of bulk toluene liquid and polystyrene film were successfully measured from the conventional configuration of the collection, which was at the waveguide surface. Optimised 110 nm thick Ta2O5 waveguides on fused silica substrates excited at a wavelength of 637 nm were shown experimentally to yield overall system power conversion efficiency of ~5×10-12 from the pump power in the waveguide to the collected Raman power in the 1002 cm-1 Raman line of toluene. For the first time, a power budget analysis of WERS was reported, which aided comparisons of intrinsic WERS performance between different waveguide designs and shed light on the improvements needed for collection efficiency. The spontaneous emission characteristic of an emitted molecule on the presence of a waveguide was analysed. In particular, the spatial radiation distributions were calculated for near-field and far-field radiations. It was found that near-field radiation dominated for the 110 nm thick Ta2O5 waveguide at an excitation wavelength of 633 nm. The emission patterns of both near-field and far-field radiations showed angular characteristic that were different to that from the free-space, which explained the low collection efficiency observed at the waveguide surface, and suggested that collection configuration played a critical role in efficient Raman collection. For the first time, Raman collection from the waveguide front edge showed experimentally 2-3 orders of enhancement in comparison with that from the waveguide surface for bulk liquid toluene and polystyrene film under TM excitation. Theoretical analysis of spatial distributions of an emitted dipole located at the waveguide surface showed features of asymmetric emission for both near-field and far-field radiations. Notably, the waveguide front edge received 71.6% more near-field emission than that at the back edge. By summing up contributions of near-field and far-field radiations, collection from the waveguide front edge compared to that from the waveguide surface had a radiative enhancement factor of 7.2 and area enhancement factor of 7.7, hence a total theoretical collection enhancement factor of 55. For the first time, WERS measurements of monolayers of trichloro(phenyl)silane and p-tolyltrichlorosilane with multiple Raman features were successfully shown by using the simplest all-dielectric slab waveguides. The structural difference of the methyl group between PTCS and TTCS was clearly shown, which validated the measurements. Polarised Raman measurements of TTCS on WERS platform were successfully performed, which resulted in depolarisability ratio being calculated. The tensor nature of Raman polarisability was utilised to calculate the relationship between the depolarisability ratio and the tilt angle of monolayer molecules on waveguide surface. Based on that, tilt angle was predicted to be 300 with the assumptions of randomly oriented molecules in the azimuthal and rotational plane.

This thesis presents the results from a temperature dependant resonance Raman spectroscopy study of HgTe extreme nanowires embedded within SWCNTs. Extreme nanowires are nanowires at the absolute limits of the nanoscale, in this case, just 1-2 atoms in diameter. This work demonstrates that due to the effect of quantum confinement on the electronic wavefunction and the reordering of atoms creating a new allotrope of HgTe never previously measured, new physics of 1D materials is observed. In this body of work we perform resonance Raman spectroscopy experiments with excitation photon energies of 1.65eV to 1.90eV and sample temperatures between 4-300K on an ensemble of HgTe filled single-walled carbon nanotubes. The Raman spectra are analysed and show that 1D HgTe within a SWCNT exhibits new Raman peaks not associated with modification of the bulk material. We couple the Raman results with HRTEM and utilise symmetry arguments to propose two of the fundamental vibrational modes at 47cm⁻¹ and 52cm⁻¹ are associated with vibrations with Bg and Ag symmetry respectively. Most strikingly, our results indicate a decrease in the rate of Raman scattering as a function of increasing temperature, not clearly in-line with the expected behaviour of Raman scattering due to an increase in the thermal phonon population. Through detailed analysis of temperature dependent resonance Raman data we can understand this effect in terms of broadening of the linewidth of the optical transition. We set out the evidence that this result can be understood by a model in which the resonance’s broadening is dominated by the coherence lifetime broadening. This allows us to determine the coherence lifetime of the underlying optical transition: 9fs at 295K and 18fs at 50K. The results are compared with similar results on carbon nanotubes which suggests that the optical transitions responsible for the Raman resonances are excitonic and is likely general to small diameter nanowires. A review of existing and comparable Raman measurements on such nanowires is presented and the implications of the main results in this thesis are discussed in terms of a general interest to the wider physics community.

Low temperature atmospheric pressure plasmas (APPs) create rich environment of reactive particle species and chemical-physical interactions at close-to-room temperature and ambient pressure which calls for a wide range of fundamental and application studies. APPs for biomedical applications is one of the emerging interdisciplinary researches. Its fundamental mechanisms have been studied using different numerical models and various diagnostic techniques. With hundreds of particle species and complex reactions, each species requires unique measurement techniques. In a typical APP, ozone (O3), one of the key species in living-cells inactivation, is produced from the complex reaction chain of short-lived oxygen atoms and excited molecules. Measurement and theoretical predictions of O3 densities can have high uncertainties. The measurements of O3 densities inside the small plasma volume are challenging due to the sensitivity to non-plasma parameters. In this work, two-beam UV-LED absorption spectroscopy has been developed by using a Mach-Zehnder configuration for O3 density measurements on the core of a homogeneous, He-O2 capacitively coupled, 13.56 MHz RF-driven APP. The improved technique allows for high-sensitivity measurement in the order of 10−3 absorption signal with 10−4 of uncertainty. The anticorrelation between O3 density and gas temperature was observed and described based on the plasma chemistry models. For controlling-parameter effect, the duty-cycle in frequency modulations showed a significant influence on the spatial profile of O3 density in the plasma channel. From an application perspective, the developed technique was able to provide 2D O3 density distribution in the effluent region of a co-axial DBD kHz-driven APPJ when applied to biological samples. The correlation between radial O3 density profiles and bacterial inactivation areas was investigated. In the relatively realistic condition with higher H2O vapour admixture, hydroxyl (OH) density, which is one of important radical species, can be measured using the UV absorption technique. Thus, the setup has been adjusted in order to measure both species. Furthermore, O3 density in the CO2-CO conversion 40.68 MHz RF-driven APP, an important process in chemical research, was observed. The O3 density as a function of plasma power and CO2 concentration provided a significant contribution to the main production and destruction channels of the conversion processes.

This study contains the investigation of the formation of carbonate apatite (cAp) from a citrate-stabilized amorphous calcium phosphate (cit-ACP) phase in various ionic solutions. This is primarily realized via in situ Raman spectroscopy by studying the variation of the v1 phosphate stretching mode as a function of maturation time. The transition is complemented by ex situ transmission electron microscopy (TEM) for microstructural characterization. These observations shed light on the possible pathway regulating in vivo formation of cAp in bone. Further, the impact of titanium substitution on the electronic properties of apatite was assessed via structural characterization of titanium substituted hydroxyapatite (Ti/HA) composites performed by ex situ Raman spectroscopy and TEM. Raman studies revealed the formation and evolution of titanium oxide and calcium phosphate related phases, whereas TEM studies showed the morphological evolution of particles. Following cit-ACP transformation, the mechanical and molecular properties of collagen/cAp bio-inspired structures are studied by in situ Raman spectroscopy under mechanical stress. The impact of cAp content on the molecular response of these structures is highlighted by a wavenumber shift of collagen related Raman bands. This interplay between cAp and collagen is associated to the mechanical properties of bone.

Current understanding of complex biological processes and structures relies entirely on available imaging and sensing techniques. As many of these investigation tools suffer from severe limitations, the need for methods which can provide new insight is growing rapidly. Enhanced Raman techniques are becoming increasingly important research tools in biosciences thanks to their unique non-destructive, non-invasive and label-free nature. This work aimed to demonstrate the capabilities of enhanced Raman techniques in life sciences and biomedicine research. The techniques used in this work were surface-enhanced Raman spectroscopy (SERS) and coherent anti-Stokes Raman scattering (CARS). While SERS uses the enhancement of Raman signals by utilising nanoparticles CARS utilises non-linear optical effects to increase signals. Furthermore, SERS is utilised as an analytical technique using spectral information while CARS is used for chemically selective imaging at a vibrational frequency of molecular bond. The studies in this thesis explore the broad scope of applications of both these enhanced Raman techniques. SERS was used for detection of different bacterial strains, where it was shown that using nanopatterned surfaces resulted in improved distinction compared to use of nanoparticles. SERS was also applied to monitor of intracellular metabolic processes. The effect of different treatments to differentiate SHSY-5Y cells was studied and the changes observed were correlated with biochemical analysis. Additionally, novel SERS nanoparticle probes and their potential in life sciences was also investigated. CARS was used to study stem cell differentiation and food deprivation in nematodes. In both the cases the effect of chemical modulators and treatments was also studied. The results showed that label-free imaging using CARS is a viable and superior alternative to conventional staining used to study these processes in biological sciences. Overall, the work in this thesis establishes the use of SERS and CARS as potent tools in the life sciences.

Recent advances have led to the demonstration of trains of attosecond pulses and isolated attosecond pulses in the vacuum ultraviolet (VUV) and extreme ultraviolet (XUV) regions of the electromagnetic spectrum in a number of laboratories. This has raised the possibility of direct time resolved measurements of correlation driven electron dynamics within molecules, with a long term aim of unprecedented control over the dynamics of matter at atomic and molecular length scales. Particular interest has arisen towards the possibility of a charge migration mechanism within molecules, in which purely electron driven processes result in the movement of charge around an excited molecule in the absence of any nuclear dynamics. However, even once these sources have been established, using them in time resolved experiments is challenging. This is due to extremely short time-scales involved, the complexity of the processes under study, and the limitations of currently available attosecond sources. In this thesis I describe the development of novel instrumentation and methods for attosecond pump – probe experiments on electron dynamics in molecules. Strategies for the experimental study of charge migration are reviewed in detail which motivates the design and implementation of a purpose built instrument combining an electron velocity map imaging (VMI) spectrometer and an ion time of flight (iTOF) spectrometer. This instrument is designed in tandem with the development and characterisation of an isolated pulse at the new photon energy of 20eV. This 20eV pulse is intrinsically synchronized with another attosecond pulse at 90eV. Together, the new instrument and light source represent a unique capability for the investigation of electron dynamics in molecules. Finally, the first experimental results are presented and perspectives for future studies using the new developments are discussed.