2,752 research outputs found

    Undergraduate Catalog of Studies, 2023-2024

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    Undergraduate Catalog of Studies, 2023-2024

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    Quantification of blood flow index in diffuse correlation spectroscopy using a robust deep learning method

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    Significance: Diffuse correlation spectroscopy (DCS) is a powerful, non-invasive optical technique for measuring blood flow. Traditionally the blood flow index (BFi) is derived through nonlinear least-square fitting the measured intensity autocorrelation function (ACF). However, the fitting process is computationally intensive, susceptible to measurement noise, and easily influenced by optical properties (absorption coefficient μ_a and reduced scattering coefficient μ_s^') and scalp and skull thicknesses. Aim: We aim to develop a data-driven method that enables rapid and robust analysis of multiple-scattered light’s temporal ACFs. Moreover, the proposed method can be applied to a range of source-detector distances instead of being limited to a specific source-detector distance. Approach: We present a deep learning architecture with one-dimensional convolution neural networks, called DCS neural networks (DCS-NET), for BFi and coherent factor (β) estimation. This DCS-NET was performed using simulated DCS data based on a three-layer brain model. We quantified the impact from physiologically relevant optical property variations, layer thicknesses, realistic noise levels, and multiple source-detector distances (5, 10, 15, 20, 25, and 30 mm) on BFi and β estimations among DCS-NET, semi-infinite, and three-layer fitting models. Results: DCS-NET shows a much faster analysis speed, around 17,000-fold and 32-fold faster than the traditional three-layer and semi-infinite models, respectively. It offers higher intrinsic sensitivity to deep tissues compared with fitting methods. DCS-NET shows excellent anti-noise features and is less sensitive to variations of μ_a and μ_s^' at a source-detector separation of 30 mm. Also, we have demonstrated that relative BFi (rBFi) can be extracted by DCS-NET with a much lower error of 8.35%. By contrast, the semi-infinite and three-layer fitting models result in significant errors in rBFi of 43.76% and 19.66%, respectively. Conclusions: DCS-NET can robustly quantify blood flow measurements at considerable source-detector distances, corresponding to much deeper biological tissues. It has excellent potential for hardware implementation, promising continuous real-time blood flow measurements

    The development of liquid crystal lasers for application in fluorescence microscopy

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    Lasers can be found in many areas of optical medical imaging and their properties have enabled the rapid advancement of many imaging techniques and modalities. Their narrow linewidth, relative brightness and coherence are advantageous in obtaining high quality images of biological samples. This is particularly beneficial in fluorescence microscopy. However, commercial imaging systems depend on the combination of multiple independent laser sources or use tuneable sources, both of which are expensive and have large footprints. This thesis demonstrates the use of liquid crystal (LC) laser technology, a compact and portable alternative, as an exciting candidate to provide a tailorable light source for fluorescence microscopy. Firstly, to improve the laser performance parameters such that high power and high specification lasers could be realised; device fabrication improvements were presented. Studies exploring the effect of alignment layer rubbing depth and the device cell gap spacing on laser performance were conducted. The results were the first of their kind and produced advances in fabrication that were critical to repeatedly realising stable, single-mode LC laser outputs with sufficient power to conduct microscopy. These investigations also aided with the realisation of laser diode pumping of LC lasers. Secondly, the identification of optimum dye concentrations for single and multi-dye systems were used to optimise the LC laser mixtures for optimal performance. These investigations resulted in novel results relating to the gain media in LC laser systems. Collectively, these advancements yielded lasers of extremely low threshold, comparable to the lowest reported thresholds in the literature. A portable LC laser system was integrated into a microscope and used to perform fluorescence microscopy. Successful two-colour imaging and multi-wavelength switching ability of LC lasers were exhibited for the first time. The wavelength selectivity of LC lasers was shown to allow lower incident average powers to be used for comparable image quality. Lastly, wavelength selectivity enabled the LC laser fluorescence microscope to achieve high enough sensitivity to conduct quantitative fluorescence measurements. The development of LC lasers and their suitability to fluorescence microscopy demonstrated in this thesis is hoped to push towards the realisation of commercialisation and application for the technology

    Exploring topological phonons in different length scales: microtubules and acoustic metamaterials

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    The topological concepts of electronic states have been extended to phononic systems, leading to the prediction of topological phonons in a variety of materials. These phonons play a crucial role in determining material properties such as thermal conductivity, thermoelectricity, superconductivity, and specific heat. The objective of this dissertation is to investigate the role of topological phonons at different length scales. Firstly, the acoustic resonator properties of tubulin proteins, which form microtubules, will be explored The microtubule has been proposed as an analog of a topological phononic insulator due to its unique properties. One key characteristic of topological materials is the existence of edge modes within the energy gap. These edge modes allow energy to be transferred at specific frequencies along the edges of the material, while the bulk remains unaffected. In the case of microtubules, its ability to store vibrational energy at its edges and the sensitivity to changes in local bulk structure align with the properties of topological insulators. Furthermore, the appearance of edge modes in topological phononic insulators is determined by the local interactions of the bulk material. Even small changes in the local structure can shift the resonant frequency of the edge mode or completely extinguish it. Similarly, the ability of microtubules to shorten or overcome energy barriers is greatly affected by changes in their local bulk structure. This suggests a parallel between the impact of local bulk structure on both topological insulators and microtubules. This similarity has led to the proposal that microtubules could serve as an analog of topological phononic insulators, providing insights into their dynamics and potential applications in fields such as chemotherapy drug development and nanoscale materials. Secondly, the application of topological phonons in the realm of acoustic metamaterials will be examined. Acoustic waves have recently become a versatile platform for exploring and studying various topological phases, showcasing their universality and diverse manifestations. The unique properties of topological insulators and their surface states heavily rely on the dimension and symmetries of the material, making it possible to classify them using a periodic table of topological insulators. However, certain combinations of dimensions and symmetries can impede the achievement of topological insulation. It is of utmost importance to preserve symmetries in order to maintain the desired topological properties, which necessitates careful consideration of coupling methods. In the context of discrete acoustic resonant models, efficiently coupling resonators while simultaneously preserving symmetry poses a challenging question. In this part, a clever experimental approach is proposed and discussed to couple acoustic crystals. This modular platform not only supports the existence of topologically protected edge and interface states but also offers a convenient setup that can be easily assembled and disassembled. Furthermore, inspired by recent theoretical advancements that draw on techniques from the field of C*-algebras for identifying topological metals, the present study provides direct observations of topological phenomena in gapless acoustic crystals. Through these observations, a general experimental technique is realized and developed to demonstrate the topology of such systems. By employing the method of coupling acoustic crystals, the investigation unveils robust boundary-localized states in a topological acoustic metal and presents a reinterpretation of a composite operator as a new Hamiltonian. This reinterpretation enables the direct observation of a topological spectral flow and facilitates the measurement of topological invariants. Through these investigations, the aim of this dissertation is to deepen our understanding of the significance and potential applications of topological phonons in diverse systems

    Undergraduate Catalog of Studies, 2022-2023

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    Spatial frequency domain imaging towards improved detection of gastrointestinal cancers

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    Early detection and treatment of gastrointestinal cancers has been shown to drastically improve patients survival rates. However, wide population based screening for gastrointestinal cancers is not feasible due to its high cost, risk of potential complications, and time consuming nature. This thesis forms the proposal for the development of a cost-effective, minimally invasive device to return quantitative tissue information for gastrointestinal cancer detection in-vivo using spatial frequency domain imaging (SFDI). SFDI is a non-invasive imaging technique which can return close to real time maps of absorption and reduced scattering coefficients by projecting a 2D sinusoidal pattern onto a sample of interest. First a low-cost, conventional bench top system was constructed to characterise tissue mimicking phantoms. Phantoms were fabricated with specific absorption and reduced scattering coefficients, mimicking the variation in optical properties typically seen in healthy, cancerous, and pre-cancerous oesophageal tissue. The system shows accurate retrieval of absorption and reduced scattering coefficients of 19% and 11% error respectively. However, this bench top system consists of a bulky projector and is therefore not feasible for in-vivo imaging. For SFDI systems to be feasible for in-vivo imaging, they are required to be miniaturised. Many conditions must be considered when doing this such as various illumination conditions, lighting conditions and system geometries. Therefore to aid in the miniaturisation of the bench top system, an SFDI system was simulated in the open-source ray tracing software Blender, where the capability to simulate these conditions is possible. A material of tunable absorption and scattering properties was characterised such that the specific absorption and reduced scattering coefficients of the material were known. The simulated system shows capability in detecting optical properties of typical gastrointestinal conditions in an up-close, planar geometry, as well in a non-planar geometry of a tube simulating a lumen. Optical property imaging in the non-planar, tubular geometry was done with the use of a novel illumination pattern, developed for this work. Finally, using the knowledge gained from the simulation model, the bench top system was miniaturised to a 3 mm diameter prototype. The novel use of a fiber array producing the necessary interfering fringe patterns replaced the bulky projector. The system showed capability to image phantoms simulating typical gastrointestinal conditions at two wavelengths (515 and 660 nm), measuring absorption and reduced scattering coefficients with 15% and 6% accuracy in comparison to the bench top system for the fabricated phantoms. It is proposed that this system may be used for cost-effective, minimally invasive, quantitative imaging of the gastrointestinal tract in-vivo, providing enhanced contrast for difficult to detect cancers

    Lanthanide-doped upconversion nanoparticles (UCNPs) for biomedical applications

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    This thesis examines the need for new antibacterial materials to treat small colony variants (SCVs) of Staphylococcus (S.) aureus bacteria and their parental strains. While ZnO-based nanoparticles (NPs) activated by ultraviolet (UV) and short wavelength visible light have been researched for their antibacterial properties, the potential benefits of incorporating UCNPs to allow activation by near-infrared (NIR) light have been overlooked. This study aims to fill this research gap by comprehensively investigating the synthesis and performance of ZnO-coated lanthanide-doped upconversion nanoparticle (UCNP) composites activated by NIR light against S. aureus SCVs and parental strains. Furthermore, this research addresses the limited understanding of the potential risks associated with UV emission from UCNPs used as fluorescent probes in super-resolution microscopy (SRM). Despite extensive research on the usage of UCNPs as fluorescent probes for SRMs, the potential cytotoxic effects of UV emission from UCNPs have not been thoroughly studied. To advance cellular imaging techniques and ensure cellular viability, a comprehensive investigation of UV emission from UCNPs is necessary. This thesis aims to identify and quantify UV emission by UCNPs used in SRM and develop strategies to minimise UV emission and mitigate potential cytotoxic effects. These two main aims are addressed in three results chapters. The first aim, the focus of chapters 2 and 3, focuses on the synthesis UCNP@ZnO composites that can be activated by NIR light for antimicrobial photodynamic therapy (aPDT) applications against S. aureus SCVs and parental strains. Chapter 2 reports the synthesis and performance of these composites, showing these materials to be effective antibacterial therapies against S. aureus SCVs, while chapter 3 improves upon the performance of these composites by careful tuning of the UCNP core and provides enhancements to the ZnO shell composition to improve reactive oxygen species generation and add a second mode of action in the form of silver nanoparticles. The second aim of this research is covered in chapter 4, which reports an investigation into the UV emission from UCNPs used as fluorescent probes in SRM. The work posits the need to understand the UV emission properties of these UCNPs as knowledge of these and the potential for cytotoxic effects are crucial for optimizing cellular imaging experiments and ensuring accurate and reliable results. Chapter 4 identifies design features and compositions that can limit UV emission, thereby minimizing the risk of phototoxicity and advancing the field of cellular imaging. Overall, the findings from this research have the potential to contribute to the development of safer and more effective targeted antibacterial therapies and enhance the understanding of UV emissions in cellular imaging techniques.Thesis (Ph.D.) -- University of Adelaide, School of Chemical Engineering, 202
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