The atom pencil: serial writing in the sub-micrometre domain

The atom pencil we describe here is a versatile tool that writes arbitrary structures by atomic deposition in a serial lithographic process. This device consists of a transversely laser-cooled and collimated cesium atomic beam that passes through a 4-pole atom-flux concentrator and impinges on to micron- and sub-micron-sized apertures. The aperture translates above a fixed substrate and enables the writing of sharp features with sizes down to 280 nm. We have investigated the writing and clogging properties of an atom pencil tip fabricated from silicon oxide pyramids perforated at the tip apex with a sub-micron aperture.

Rapid separation of biologically important low molecular weight compounds by microchip electrophoresis and ultra-fast performance liquid chromatography

The research work in this thesis reports rapid separation of biologically important low molecular weight compounds by microchip electrophoresis and ultrahigh liquid chromatography. Chapter 1 introduces the theory and principles behind capillary electrophoresis separation. An overview of the history, different modes and detection techniques coupled to CE is provided. The advantages of microchip electrophoresis are highlighted. Some aspects of metal complex analysis by capillary electrophoresis are described. Finally, the theory and different modes of the liquid chromatography technology are presented. Chapter 2 outlines the development of a method for the capillary electrophoresis of (R, S) Naproxen. Variable parameters of the separation were optimized (i.e. buffer concentration and pH, concentration of chiral selector additives, applied voltage and injection condition).The method was validated in terms of linearity, precision, and LOD. The optimized method was then transferred to a microchip electrophoresis system. Two different types of injection i.e. gated and pinched, were investigated. This microchip method represents the fastest reported chiral separation of Naproxen to date. Chapter 3 reports ultra-fast separation of aromatic amino acid by capillary electrophoresis using the short-end technique. Variable parameters of the separation were optimized and validated. The optimized method was then transferred to a microchip electrophoresis system where the separation time was further reduced. Chapter 4 outlines the use of microchip electrophoresis as an efficient tool for analysis of aluminium complexes. A 2.5 cm channel with linear imaging UV detection was used to separate and detect aluminium-dopamine complex and free dopamine. For the first time, a baseline, separation of aluminium dopamine was achieved on a 15 seconds timescale. Chapter 5 investigates a rapid, ultra-sensitive and highly efficient method for quantification of histamine in human psoriatic plaques using microdialysis and ultrahigh performance liquid chromatography with fluorescence detection. The method utilized a sub-two-micron packed C18 stationary phase. A fluorescent reagent, 4-(1-pyrene) butyric acid N-hydroxysuccinimide ester was conjugated to the primary and secondary amino moieties of histamine. The dipyrene-labeled histamine in human urine was also investigated by ultrahigh pressure liquid chromatography using a C18 column with 1.8 μm particle diameter. These methods represent one of the fastest reported separations to date of histamine using fluorescence detection.

Integrated genetic analysis systems

The overall objective of this thesis is to integrate a number of micro/nanotechnologies into integrated cartridge type systems to implement such biochemical protocols. Instrumentation and systems were developed to interface such cartridge systems: (i) implementing microfluidic handling, (ii) executing thermal control during biochemical protocols and (iii) detection of biomolecules associated with inherited or infectious disease. This system implements biochemical protocols for DNA extraction, amplification and detection. A digital microfluidic chip (ElectroWetting on Dielectric) manipulated droplets of sample and reagent implementing sample preparation protocols. The cartridge system also integrated a planar magnetic microcoil device to generate local magnetic field gradients, manipulating magnetic beads. For hybridisation detection a fluorescence microarray, screening for mutations associated with CFTR gene is printed on a waveguide surface and integrated within the cartridge. A second cartridge system was developed to implement amplification and detection screening for DNA associated with disease-causing pathogens e.g. Escherichia coli. This system incorporates (i) elastomeric pinch valves isolating liquids during biochemical protocols and (ii) a silver nanoparticle microarray for fluorescent signal enhancement, using localized surface plasmon resonance. The microfluidic structures facilitated the sample and reagent to be loaded and moved between chambers with external heaters implementing thermal steps for nucleic acid amplification and detection. In a technique allowing probe DNA to be immobilised within a microfluidic system using (3D) hydrogel structures a prepolymer solution containing probe DNA was formulated and introduced into the microfluidic channel. Photo-polymerisation was undertaken forming 3D hydrogel structures attached to the microfluidic channel surface. The prepolymer material, poly-ethyleneglycol (PEG), was used to form hydrogel structures containing probe DNA. This hydrogel formulation process was fast compared to conventional biomolecule immobilization techniques and was also biocompatible with the immobilised biomolecules, as verified by on-chip hybridisation assays. This process allowed control over hydrogel height growth at the micron scale.

Optical micro- and nanofibres: Higher mode generation and particle manipulation studies

This thesis is centred on two experimental fields of optical micro- and nanofibre research; higher mode generation/excitation and evanescent field optical manipulation. Standard, commercial, single-mode silica fibre is used throughout most of the experiments; this generally produces high-quality, single-mode, micro- or nanofibres when tapered in a flame-heated, pulling rig in the laboratory. Single mode fibre can also support higher transverse modes, when transmitting wavelengths below that of their defined single-mode regime cut-off. To investigate this, a first-order Laguerre-Gaussian beam, LG01 of 1064 nm wavelength and doughnut-shaped intensity profile is generated free space via spatial light modulation. This technique facilitates coupling to the LP11 fibre mode in two-mode fibre, and convenient, fast switching to the fundamental mode via computer-generated hologram modulation. Following LP11 mode loss when exponentially tapering 125μm diameter fibre, two mode fibre with a cladding diameter of 80μm is selected fir testing since it is more suitable for satisfying the adiabatic criteria for fibre tapering. Proving a fruitful endeavour, experiments show a transmission of 55% of the original LP11 mode set (comprising TE01, TM01, HE21e,o true modes) in submicron fibres. Furthermore, by observing pulling dynamics and progressive mode-lass behaviour, it is possible to produce a nanofibre which supports only the TE01 and TM01 modes, while suppressing the HE21e,o elements of the LP11 group. This result provides a basis for experimental studies of atom trapping via mode-interference, and offers a new set of evanescent field geometries for sensing and particle manipulation applications. The thesis highlights the experimental results of the research unit’s Cold Atom subgroup, who successfully integrated one such higher-mode nanofibre into a cloud of cold Rubidium atoms. This led to the detection of stronger signals of resonance fluorescence coupling into the nanofibre and for light absorption by the atoms due to the presence of higher guided modes within the fibre. Theoretical work on the impact of the curved nanofibre surface on the atomic-surface van der Waals interaction is also presented, showing a clear deviation of the potential from the commonly-used flat-surface approximation. Optical micro- and nanofibres are also useful tools for evanescent-field mediated optical manipulation – this includes propulsion, defect-induced trapping, mass migration and size-sorting of micron-scale particles in dispersion. Similar early trapping experiments are described in this thesis, and resulting motivations for developing a targeted, site-specific particle induction method are given. The integration of optical nanofibres into an optical tweezers is presented, facilitating individual and group isolation of selected particles, and their controlled positioning and conveyance in the evanescent field. The effects of particle size and nanofibre diameter on pronounced scattering is experimentally investigated in this systems, as are optical binding effects between adjacent particles in the evanescent field. Such inter-particle interactions lead to regulated self-positioning and particle-chain speed enhancements.

Polymer and metallodielectric based photonic crystals

The bottom-up colloidal synthesis of photonic crystals has attracted interest over top-down approaches due to their relatively simplicity, the potential to produce large areas, and the low-costs with this approach in fabricating complex 3-dimensional structures. This thesis focuses on the bottom-up approach in the fabrication of polymeric colloidal photonic crystals and their subsequent modification. Poly(methyl methacrylate) sub-micron spheres were used to produce opals, inverse opals and 3D metallodielectric photonic crystal (MDPC) structures. The fabrication of MDPCs with Au nanoparticles attached to the PMMA spheres core–shell particles is described. Various alternative procedures for the fabrication of photonic crystals and MDPCs are described and preliminary results on the use of an Au-based MDPC for surface-enhanced Raman scattering (SERS) are presented. These preliminary results suggest a threefold increase of the Raman signal with the MDPC as compared to PMMA photonic crystals. The fabrication of PMMA-gold and PMMA-nickel MDPC structures via an optimised electrodeposition process is described. This process results in the formation of a continuous dielectric-metal interface throughout a 3D inverted photonic crystal structure, which are shown to possess interesting optical properties. The fabrication of a robust 3D silica inverted structure with embedded Au nanoparticles is described by a novel co-crystallisation method which is capable of creating a SiO2/Au NP composite structure in a single step process. Although this work focuses on the creation of photonic crystals, this co-crystallisation approach has potential for the creation of other functional materials. A method for the fabrication of inverted opals containing silicon nanoparticles using aerosol assisted chemical vapour deposition is described. Silicon is a high dielectric material and nanoparticles of silicon can improve the band gap and absorption properties of the resulting structure, and therefore have the potential to be exploited in photovoltaics.

Enhancing non-refractory aerosol apportionment from an urban industrial site through receptor modelling of complete high time-resolution aerosol mass spectra

Receptor modelling was performed on quadrupole unit mass resolution aerosol mass spectrometer (Q-AMS) sub-micron particulate matter (PM) chemical speciation measurements from Windsor, Ontario, an industrial city situated across the Detroit River from Detroit, Michigan. Aerosol and trace gas measurements were collected on board Environment Canada’s CRUISER mobile laboratory. Positive matrix factorization (PMF) was performed on the AMS full particle-phase mass spectrum (PMFFull MS) encompassing both organic and inorganic components. This approach was compared to the more common method of analysing only the organic mass spectra (PMFOrg MS). PMF of the full mass spectrum revealed that variability in the non-refractory sub-micron aerosol concentration and composition was best explained by six factors: an amine-containing factor (Amine); an ammonium sulphate and oxygenated organic aerosol containing factor (Sulphate-OA); an ammonium nitrate and oxygenated organic aerosol containing factor (Nitrate-OA); an ammonium chloride containing factor (Chloride); a hydrocarbon like organic aerosol (HOA) factor; and a moderately oxygenated organic aerosol factor (OOA). PMF of the organic mass spectrum revealed three factors of similar composition to some of those revealed through PMFFull MS: Amine, HOA and OOA. Including both the inorganic and organic mass proved to be a beneficial approach to analysing the unit mass resolution AMS data for several reasons. First, it provided a method for potentially calculating more accurate sub-micron PM mass concentrations, particularly when unusual factors are present, in this case, an Amine factor. As this method does not rely on a priori knowledge of chemical species, it circumvents the need for any adjustments to the traditional AMS species fragmentation patterns to account for atypical species, and can thus lead to more complete factor profiles. It is expected that this method would be even more useful for HR-ToF-AMS data, due to the ability to better understand the chemical nature of atypical factors from high resolution mass spectra. Second, utilizing PMF to extract factors containing inorganic species allowed for the determination of extent of neutralization, which could have implications for aerosol parameterization. Third, subtler differences in organic aerosol components were resolved through the incorporation of inorganic mass into the PMF matrix. The additional temporal features provided by the inorganic aerosol components allowed for the resolution of more types of oxygenated organic aerosol than could be reliably re-solved from PMF of organics alone. Comparison of findings from the PMFFull MS and PMFOrg MS methods showed that for the Windsor airshed, the PMFFull MS method enabled additional conclusions to be drawn in terms of aerosol sources and chemical processes. While performing PMFOrg MS can provide important distinctions between types of organic aerosol, it is shown that including inorganic species in the PMF analysis can permit further apportionment of organics for unit mass resolution AMS mass spectra.

Aerosol properties associated with air masses arriving into the North East Atlantic during the 2008 Mace Head EUCAARI intensive observing period: an overview

As part of the EUCAARI Intensive Observing Period, a 4-week campaign to measure aerosol physical, chemical and optical properties, atmospheric structure, and cloud microphysics was conducted from mid-May to mid-June, 2008 at the Mace Head Atmospheric Research Station, located at the interface of Western Europe and the N. E. Atlantic and centered on the west Irish coastline. During the campaign, continental air masses comprising both young and aged continental plumes were encountered, along with polar, Arctic and tropical air masses. Polluted-continental aerosol concentrations were of the order of 3000 cm(-3), while background marine air aerosol concentrations were between 400-600 cm(-3). The highest marine air concentrations occurred in polar air masses in which a 15 nm nucleation mode, with concentration of 1100 cm(-3), was observed and attributed to open ocean particle formation. Continental air submicron chemical composition (excluding refractory sea salt) was dominated by organic matter, closely followed by sulphate mass. Although the concentrations and size distribution spectral shape were almost identical for the young and aged continental cases, hygroscopic growth factors (GF) and cloud condensation nuclei (CCN) to total condensation nuclei (CN) concentration ratios were significantly less in the younger pollution plume, indicating a more oxidized organic component to the aged continental plume. The difference in chemical composition and hygroscopic growth factor appear to result in a 40-50% impact on aerosol scattering coefficients and Aerosol Optical Depth, despite almost identical aerosol microphysical properties in both cases, with the higher values been recorded for the more aged case. For the CCN/CN ratio, the highest ratios were seen in the more age plume. In marine air, sulphate mass dominated the sub-micron component, followed by water soluble organic carbon, which, in turn, was dominated by methanesulphonic acid (MSA). Sulphate concentrations were highest in marine tropical air - even higher than in continental air. MSA was present at twice the concentrations of previously-reported concentrations at the same location and the same season. Both continental and marine air exhibited aerosol GFs significantly less than ammonium sulphate aerosol pointing to a significant organic contribution to all air mass aerosol properties.

Study of the kinetics and mechanism of rapid self-assembly in block copolymer thin films during solvo-microwave annealing

Microwave annealing is an emerging technique for achieving ordered patterns of block copolymer films on substrates. Little is understood about the mechanisms of microphase separation during the microwave annealing process and how it promotes the microphase separation of the blocks. Here, we use controlled power microwave irradiation in the presence of tetrahydrofuran (THF) solvent, to achieve lateral microphase separation in high- lamellar-forming poly(styrene-b-lactic acid) PS-b-PLA. A highly ordered line pattern was formed within seconds on silicon, germanium and silicon on insulator (SOI) substrates. In-situ temperature measurement of the silicon substrate coupled to condition changes during "solvo-microwave" annealing allowed understanding of the processes to be attained. Our results suggest that the substrate has little effect on the ordering process and is essentially microwave transparent but rather, it is direct heating of the polar THF molecules that causes microphase separation. It is postulated that the rapid interaction of THF with microwaves and the resultant temperature increase to 55 degrees C within seconds causes an increase of the vapor pressure of the solvent from 19.8 to 70 kPa. This enriched vapor environment increases the plasticity of both PS and PLA chains and leads to the fast self-assembly kinetics. Comparing the patterns formed on silicon, germanium and silicon on insulator (SOI) and also an in situ temperature measurement of silicon in the oven confirms the significance of the solvent over the role of substrate heating during "solvo-microwave" annealing. Besides the short annealing time which has technological importance, the coherence length is on a micron scale and dewetting is not observed after annealing. The etched pattern (PLA was removed by an Ar/O-2 reactive ion etch) was transferred to the underlying silicon substrate fabricating sub-20 nm silicon nanowires over large areas demonstrating that the morphology is consistent both across and through the film.

Development of a dissolvable microneedle influenza vaccine patch

Delivery of large molecular weight biological molecules to the epidermis and dermis is constrained by the tough outer layer of the epidermis, the stratum corneum (sc). Microneedle technologies attempt to overcome this physical barrier using sharp micron-size projections to penetrate the sc. Dissolvable microneedles (DMN), are a particular microneedle design whereby the needle structure is composed of a soluble matrix that upon application to the skin, dissolves releasing the vaccine load into skin. This thesis examines (1) the formulation and processing considerations around DMN fabrication, (2) the immunogenicity of DMN containing trivalent influenza vaccine (TIV) in pre-clinical mouse and pig models and (3) the thermostability of these DMN formulations during storage. The results demonstrate the importance of formulation for microneedle formation and mechanical strength. Trehalose and polyvinylalcohol based formulations produced optimal microneedle structures and were amenable to piezoelectric dispensing; allowing for precise multi-layered DMN to be fabricated. The effect of drying conditions was assessed and found to be critical for DMN mechanical strength and skin penetration. The antibody responses to TIV generated by DMN-mediated vaccination were comparable or greater to those induced by immunization with a commercial TIV via the IM route in mice. DMN mediated immunisation resulted in a significantly broader humoral response to heterotypic influenza viruses compared to IM delivery. Stored at 40°C, a licensed seasonal influenza vaccine incorporated into DMN array was thermostable for at least 6 month as determined by Single Radial Immunodiffusion and immunogenicity in mice. The thesis advances the field of DMN influenza vaccination by elucidating important processing and formulation considerations in the fabrication of highly reproducible DMN. It also demonstrated that DMN can induce broader, larger humoral responses than conventional IM administration while demonstrating enhanced accelerated stability. Crucially, this works advances an automated fabrication system that will allow for clinical translation of DMN.

Photonic packaging: transforming silicon photonic integrated circuits into photonic devices

Dedicated multi-project wafer (MPW) runs for photonic integrated circuits (PICs) from Si foundries mean that researchers and small-to-medium enterprises (SMEs) can now afford to design and fabricate Si photonic chips. While these bare Si-PICs are adequate for testing new device and circuit designs on a probe-station, they cannot be developed into prototype devices, or tested outside of the laboratory, without first packaging them into a durable module. Photonic packaging of PICs is significantly more challenging, and currently orders of magnitude more expensive, than electronic packaging, because it calls for robust micron-level alignment of optical components, precise real-time temperature control, and often a high degree of vertical and horizontal electrical integration. Photonic packaging is perhaps the most significant bottleneck in the development of commercially relevant integrated photonic devices. This article describes how the key optical, electrical, and thermal requirements of Si-PIC packaging can be met, and what further progress is needed before industrial scale-up can be achieved.