Writing self-assembled monolayers with Cs: Optimization of atomic nanolithography imaging using self-assembled monolayers on gold substrates

We report the results of a study into the factors controlling the quality of nanolithographic imaging. Self-assembled monolayer (SAM) coverage, subsequent postetch pattern definition, and minimum feature size all depend on the quality of the Au substrate used in material mask atomic nanolithographic experiments. We find that sputtered Au substrates yield much smoother surfaces and a higher density of {111}-oriented grains than evaporated Au surfaces. Phase imaging with an atomic force microscope shows that the quality and percentage coverage of SAM adsorption are much greater for sputtered Au surfaces. Exposure of the self-assembled monolayer to an optically cooled atomic Cs beam traversing a two-dimensional array of submicron material masks mounted a few microns above the self-assembled monolayer surface allowed determination of the minimum average Cs dose (2 Cs atoms per self-assembled monolayer molecule) to write the monolayer. Suitable wet etching, with etch rates of 2.2 nm min-1, results in optimized pattern definition. Utilizing these optimizations, material mask features as small as 230 nm in diameter with a fractional depth gradient of 0.820 nm were realized.

Development of tumour imaging and therapy strategies utilising unengineered bacteria

The ability of systemically administered bacteria to target and replicate to high numbers within solid tumours is well established. Tumour localising bacteria can be exploited as biological vehicles for the delivery of nucleic acid, protein or therapeutic payloads to tumour sites and present researchers with a highly targeted and safe vehicle for tumour imaging and cancer therapy. This work aimed to utilise bacteria to activate imaging probes or prodrugs specifically within target tissue in order to facilitate the development of novel imaging and therapeutic strategies. The vast majority of existing bacterial-mediated cancer therapy strategies rely on the use of bacteria that have been genetically modified (GM) to express genes of interest. While these approaches have been shown to be effective in a preclinical setting, GM presents extra regulatory hurdles in a clinical context. Also, many strains of bacteria are not genetically tractably and hence cannot currently be engineered to express genes of interest. For this reason, the development of imaging and therapeutic systems that utilise unengineered bacteria for the activation of probes or drugs represents a significant improvement on the current gold standard. Endogenously expressed bacterial enzymes that are not found in mammalian cells can be used for the targeted activation of imaging probes or prodrugs whose activation is only achieved in the presence of these enzymes. Exploitation of the intrinsic enzymatic activity of bacteria allows the use of a wider range of bacteria and presents a more clinically relevant system than those that are currently in use. The nitroreductase (NTR) enzymes, found only in bacteria, represent one such option. Chapter 2 introduces the novel concept of utilising native bacterial NTRs for the targeted activation of the fluorophore CytoCy5S. Bacterial-mediated probe activation allowed for non-invasive fluorescence imaging of in vivo bacteria in models of infection and cancer. Chapter 3 extends the concept of using native bacterial enzymes to activate a novel luminescent, NTR activated probe. The use of luminescence based imaging improved the sensitivity of the system and provides researchers with a more accessible modality for preclinical imaging. It also represents an improvement over existing caged luciferin probe systems described to date. Chapter 4 focuses on the employment of endogenous bacterial enzymes for use in a therapeutic setting. Native bacterial enzymatic activity (including NTR enzymes) was shown to be capable of activating multiple prodrugs, in isolation and in combination, and eliciting therapeutic responses in murine models of cancer. Overall, the data presented in this thesis advance the fields of bacterial therapy and imaging and introduce novel strategies for disease diagnosis and treatment. These preclinical studies demonstrate potential for clinical translation in multiple fields of research and medicine.

Nonlinear optics with cold Rb atoms using tapered optical nanofibres

Optical nanofibres (ONFs) are very thin optical waveguides with sub-wavelength diameters. ONFs have very high evanescent fields and the guided light is confined strongly in the transverse direction. These fibres can be used to achieve strong light-matter interactions. Atoms around the waist of an ONF can be probed by collecting the atomic fluorescence coupling or by measuring the transmission (or the polarisation) of the probe beam sent through it. This thesis presents experiments using ONFs for probing and manipulating laser-cooled 87Rb atoms. As an initial experiment, a single mode ONF was integrated into a magneto-optical trap (MOT) and used for measuring the characteristics of the MOT, such as the loading time and the average temperature of the atom cloud. The effect of a near-resonant probe beam on the local temperature of the cold atoms has been studied. Next, the ONF was used for manipulating the atoms in the evanescent fields region in order to generate nonlinear optical effects. Four-wave mixing, ac Stark effect (Autler-Townes splitting) and electromagnetically induced transparency have been observed at unprecedented ultralow power levels. In another experiment, a few-mode ONF, supporting only the fundamental mode and the first higher order mode group, has been used for studying cold atoms. A higher pumping rate of the atomic fluorescence into the higher order fibreguided modes and more interactions with the surrounding atoms for higher order mode evanescent light, when compared to signals for the fundamental mode, have been identified. The results obtained in the thesis are particularly for a fundamental understanding of light-atom interactions when atoms are near a dielectric surface and also for the development of fibre-based quantum information technologies. Atoms coupled to ONFs could be used for preparing intrinsically fibre-coupled quantum nodes for quantum computing and the studies presented here are significant for a detailed understanding of such a system.

Temperature measurement of cold atoms using transient absorption of a resonant probe through an optical nanofibre

Optical nanofibres are ultrathin optical fibres with a waist diameter typically less than the wavelength of light being guided through them. Cold atoms can couple to the evanescent field of the nanofibre-guided modes and such systems are emerging as promising technologies for the development of atom-photon hybrid quantum devices. Atoms within the evanescent field region of an optical nanofibre can be probed by sending near or on-resonant light through the fibre; however, the probe light can detrimentally affect the properties of the atoms. In this paper, we report on the modification of the local temperature of laser-cooled 87Rb atoms in a magneto-optical trap centred around an optical nanofibre when near-resonant probe light propagates through it. A transient absorption technique has been used to measure the temperature of the affected atoms and temperature variations from 160 μk to 850 μk, for a probe power ranging from 0 to 50 nW, have been observed. This effect could have implications in relation to using optical nanofibres for probing and manipulating cold or ultracold atoms.

Development and characterisation of solution processed vanadium oxide and transparent metal oxide thin films

Metal oxide thin films are important for modern electronic devices ranging from thin film transistors to photovoltaics and functional optical coatings. Solution processed techniques allow for thin films to be rapidly deposited over a range of surfaces without the extensive processing of comparative vapour or physical deposition methods. The production of thin films of vanadium oxide prepared through dip-coating was developed enabling a greater understanding of the thin film formation. Mechanisms of depositing improved large area uniform coverage on a number of technologically relevant substrates were examined. The fundamental mechanism for polymer-assisted deposition in improving thin film surface smoothness and long range order has been delivered. Different methods were employed for adapting the alkoxide based dip-coating technique to produce a variety of amorphous and crystalline vanadium oxide based thin films. Using a wide range of material, spectroscopic and optical measurement techniques the morphology, structure and optoelectronic properties of the thin films were studied. The formation of pinholes on the surface of the thin films, due to dewetting and spinodal effects, was inhibited using the polymer assisted deposition technique. Uniform thin films with sub 50 nm thicknesses were deposited on a variety of substrates controlled through alterations to the solvent-alkoxide dilution ratios and employing polymer assisted deposition techniques. The effects of polymer assisted deposition altered the crystallized VO thin films from a granular surface structure to a polycrystalline structure composed of high density small in-plane grains. The formation of transparent VO based thin film through Si and Na substrate mediated diffusion highlighted new methods for material formation and doping.

Theory and optimisation of 1.3 and 1.55 μm (Al)InGaAs metamorphic quantum well lasers

The use of InGaAs metamorphic buffer layers (MBLs) to facilitate the growth of lattice-mismatched heterostructures constitutes an attractive approach to developing long-wavelength semiconductor lasers on GaAs substrates, since they offer the improved carrier and optical confinement associated with GaAs-based materials. We present a theoretical study of GaAs-based 1.3 and 1.55 μm (Al)InGaAs quantum well (QW) lasers grown on InGaAs MBLs. We demonstrate that optimised 1.3 μm metamorphic devices offer low threshold current densities and high differential gain, which compare favourably with InP-based devices. Overall, our analysis highlights and quantifies the potential of metamorphic QWs for the development of GaAs-based long-wavelength semiconductor lasers, and also provides guidelines for the design of optimised devices.