Open Access Theses

Permanent URI for this collectionhttps://hdl.handle.net/1885/3

To view all theses in this collection, select one of the 'Browse by' options (Issue Date, Author, Title, Subject, Title or Type (of thesis). You can also enter your keyword/s into the text box above and click on Search.

ANU theses are harvested by the National Library of Australia's Trove service and other search engines, making them fully discoverable online.

Find Australian theses.
Full instructions available here

Submit your thesis (Approved ANU research theses only)

Please note: The Abstracts displayed in item metadata are in many cases truncated. For the full Abstracts, see the thesis document files.

Browse

Now showing 1 - 20 of 16433

Access status: Open Access ,
Names, Descriptions And Existence Claims
(1983) Seto, Darryl
Designators are used only in language contexts. The sounds by Wittgenstein’s builders were not designators. There is one consequence of this for philosophy which I wish to point out. A study of any subject cannot be divorced from language and the situations in which the subject appears. Abstractions cannot be studied without looking at sentences where the concept is employed and the context which evokes this sentence. One rule that I would suggest consistent with this is in the philosophy of action. In any context there is a ‘right’ description of the action. Permissible descriptions follow rules in language governing how actions are to be described. A description must be responsive to the context which evokes this comment. Unless there is a story being told or a specific question asked, there is really no ‘right’ description.
Access status: Open Access ,
The Ageing Mind of the Double Brain: Studies in Hemispheric Asymmetry for Global-Local Processing
(2026) Chen, Haiwen
Global-local processing refers to a visual attentional mechanism that involves directing attention either globally (to an overall visual scene) or locally (to the finer elements within the scene). The two hemispheres of the brain demonstrate functional asymmetry for global-local processing, with global processing specialised in the right hemisphere and local processing specialised in the left hemisphere. Healthy ageing has been shown to influence global-local processing, with evidence suggesting that older adults demonstrate a local-processing bias. The right-hemisphere ageing hypothesis has been put forth to explain this bias, proposing that right-hemisphere functions are more vulnerable to ageing. In this thesis, hemispheric asymmetry for global-local processing was investigated using a hierarchical-figures task, in which a large stimulus was made up of several small stimuli. The hierarchical figures were presented briefly to the left or right visual field, such that information was initially processed by the contralateral hemisphere. Study 1 was an investigation of hemispheric asymmetry for global-local processing in neurologically healthy right-handed young (N = 27) and older (N = 34) adults. The question addressed was: Do stimulus categories with different demands on visuospatial-verbal processing (letters, verbalisable objects, and nonverbalisable shapes) influence hemispheric asymmetry for global-local processing in young and older adults? Study 2 was an investigation of the role of the right hemisphere in the non-directional component of attentional orienting in neurologically healthy right-handed young (N = 39) and older (N = 38) adults. The question addressed was: Do older adults demonstrate greater difficulties with disengaging attention from local-level information when correct responding required re-orienting attention to global-level information? Study 3 was an investigation of individual differences in hemispheric asymmetry for global-local processing in neurologically healthy right-handed young (N = 127) and older (N = 58) adults. The questions addressed were: Do individual young and older adults demonstrate right-hemisphere specialisation for global processing and left-hemisphere specialisation for local processing. If so, Do these individual differences in hemispheric asymmetry account for age-related changes in global-local processing? Study 4 was an investigation of age-group differences and individual differences in the perception of the Ebbinghaus illusion in neurologically healthy young (N = 87) and older (N = 58) adults. The question addressed was: Does a local-processing bias reduce susceptibility to the Ebbinghaus illusion? Four key conclusions emerged from this research. First, healthy ageing influences two aspects of global-local processing. Older adults demonstrate greater difficulties: (1) processing global-level information, and (2) disengaging attention from local-level information for the purpose of re-orienting attention to global-level information. Second, hemispheric asymmetry for global-local processing remains intact with age. In young and older adults, the right hemisphere (when compared to the left hemisphere), is more efficient for processing global-level information, and the left hemisphere (when compared to the right hemisphere) is more efficient for processing local-level information. Third, evidence for the right-hemisphere ageing hypothesis was mixed. Although older adults do demonstrate age-related difficulties in global processing, the right hemisphere of older participants was still more efficient compared to the left hemisphere at processing global information. Fourth, there are individual differences in the processing of global-level and local-level information. This thesis provides future research directions for understanding how healthy ageing influences functional hemispheric asymmetry, and the impact this has on visual attention across the life span.
Access status: Open Access ,
On the Spatial Structure and Properties of Cold Neutral Hydrogen Gas In the Milky Way
Lynn, Callum
Despite its long period of study, there still remains no consensus on the dominant processes that control the rate of star formation. Neutral hydrogen (HI), being the most abundant element in the Universe, provides an important tracer, both for large scale galactic morphology and as the fundamental building block of stars. Improving our knowledge of the physical properties of HI and its transition between warm and cold phases is thus key to understanding the cycle of star formation and chemical enrichment in the Milky Way. Despite ongoing efforts, there still remains great uncertainty on the physical properties of cold and warm HI due to observational constraints of previous surveys. Presented here in this thesis are attempts to address questions surrounding the phase distribution and spatial structure of HI through detailed analysis of HI absorption and emission of the Milky Way from the Galactic Australian Square Kilometre Array Pathfinder HI Survey (GASKAP-HI). The first component of my thesis makes use of the Australian Square Kilometre Array Pathfinder (ASKAP) radio telescope, using the ~500 sightlines where HI 21cm absorption was detected in the Milky Way at high Galactic latitudes, and the ~2000 sightlines with no detections. The signal-to-noise is reduced through stacking sightlines to detect warmer gas in absorption. Gas was detected with a temperature of ~1300 K gas ubiquitous throughout the region, along with a lack of temperature variation spatially across the plane-of-sky. The work also provides a test for the efficacy of stacking HI spectra to detect higher temperature gas for future studies, finding that stacking, while producing lower limits on optical depth measurements, still allows for accurate measurements of temperature for components previously hidden under noise. Next, I have analysed the spatial variation of neutral hydrogen cold gas density across the plane-of-sky through computing structure functions of the detected GASKAP-HI absorption sightlines. The warm and cold gas follow different spatial power-law slopes (-2.6 vs -2.3 respectively), with both slopes being shallower than Kolmogorov turbulence (-3.6). The cold gas has a shallower slope due to more power existing on smaller spatial scales, where the cold gas is formed through condensation and shocks. I have also, for the first time, calculated the structure function of temperature of cold HI gas across the plane-of-sky. The structure function slope of the spin temperatures was flat, implying the temperature of cold gas is random across the plane-of-sky, not tied to any specific physical HI structures. Comparing with MHD simulations, the flatness of the structure function may indicate potential uncharacterised errors in the calculation of spin temperatures, and the need for a review of the currently accepted method for estimating temperatures for potential improvements. Finally, I present work focussed on characterising instabilities found in the HI emission data of a Galactic filament. Through Gaussian decomposition tools such as ROHSA, I was able to separate out spatially coherent maps of the individual neutral HI phases from emission data to study their interactions. The cold gas is concentrated within small scale structures undergoing Rayleigh-Taylor instabilities, with the warmer, more diffuse phases of HI gas enveloping the structure. Using the correlation between HI and dust to estimate physical distances to the structure, the wavelength of the Rayleigh-Taylor instabilities is estimated to be approximately 1 parsec in size. The work also investigates the effects of resolution on estimating cold gas mass fractions, since extra-galactic observations lack the spatial resolution of Milky Way surveys. Spatial resolution appears to have no effect on the mean and median cold neutral medium mass fraction, but the maximum value decreases with decreasing resolution.
Access status: Open Access ,
Optical spectroscopy of the red forms of Photosystem II and I
(2026) Morton, Jenn
Research in photosynthesis encompasses a wide array of complex and interconnected processes, requiring the incorporation of concepts from physics, chemistry and biology. This thesis contributes to the understanding of photosynthesis by using low temperature optical spectroscopy to study Photosystem II (PSII) and Photosystem I (PSI). These two catalytic protein complexes are responsible for splitting water to provide electrons for the photosynthetic process, and transferring these electrons across the thylakoid membrane, respectively These enzyme complexes provide a particular challenge for optical spectroscopy as they contain large numbers of chromophores with overlapping absorption bands, which require a combination of optical techniques to separate out. In this work, the techniques of absorption, fluorescence, Circular Dichroism (CD), Magnetic Circular Dichroism and electrochromism have been used to study these enzymes. This thesis has two main themes: the direct observation of the optical spectroscopic properties of the Oxygen Evolving Complex (OEC) in Photosystem II (Publications 1 and 4) and the location of far-red absorbing chlorophylls in PSII and PSI of a red-light adapted cyanobacterium (Publication 2 and 3) The OEC of PSII is the tetramanganese cluster where electrons are extracted in a stepwise fashion from water, resulting in the release of oxygen. In this process, the cluster passes through four metastable S-states. In Publication 1, variable temperature and variable field (VTVH) MCD is used as a tool to identify the spectrum of each S-state in an optically transparent window in the region of 720-800nm. Low temperature MCD spectra of this region shows a series of sharp peaks that are S-state dependent. These features were assigned to a series of Mn(IV) 4A -> 2E "spin flip" transitions. These spectra and their associated assignments provide a new perspective on the electronic and magnetic structure of the OEC. Publication 4 follows on from 1, focusing on the two sub-forms of the S2 state of the OEC. A combination of EPR and MCD enables the identification of these two states as being redox isomers and give insight into the mechanisms of water oxidation. Chroocooccidiopsis thermalis is an extremophile cyanobacteria that can grow in hot and dry conditions. When grown under red-light conditions, this cyanobacteria can produce red absorbing chlorophylls d and f, along with chlorophyll a. In Publication 2, using a range of biophysical techniques, including low temperature optical spectroscopy, we clearly establish that these red absorbing chlorophylls pla a key role in both PSI and PSII and are not just as long wavelength light harvesting pigments as previously reported. Specifically, charge separation in PSI uses chlorophyll f at 745nm and PSII uses chlorophyll d or f at ~727nm. The organism is shown to be able to perform photosynthesis with lower energy light than previously thought possible. Publication 3 is an extension of Publication 2 where the location and function of the red absorbing chlorophyll at ~727nm of PSII in C.thermalis is further investigated. Modelling of low temperature spectroscopic data, CD and electrochromism in particular, yields more information about the location of this pigment within the PSII complex. Previously, ChlD1 was assigned as the most likely candidate for the primary donor. However, the analysis in Publication 3 favours PD2 as the primary donor. This unexpected result requires further experimentation and calculational studies to verify. This thesis shows the strength of applying multiple spectroscopy techniques to complex biological systems and how such data can be used to extract information about both the structure and function of these proteins.
Access status: Open Access ,
Orbital Dynamics of Black Holes in Ultralight Dark Matter Solitons: Eigenmode Excitation and Stone Skipping
(2026) Zhang, Ailun
Gravitational observations from galaxies to the cosmic microwave background point to a dominant non-luminous matter component, yet its microphysical identity remains unknown. Ultralight dark matter (ULDM), consisting of bosons with masses around 10⁻²¹ eV, suppresses small-scale structure through quantum pressure while preserving large-scale successes of cold dark matter. ULDM simulations predict solitonic cores at galactic centres. In the configurations studied here, black holes inside such cores can exhibit "stone skipping": quasi-periodic orbital-radius rebounds suppressed in equal-mass binaries. The mechanism underlying this non-monotonic behaviour has remained unclear. This thesis develops a spectral framework to identify the responsible soliton excitations. The Schrödinger--Poisson system is solved numerically, with black holes evolved in full coupling or as test particles with effective dynamical friction. A finite-domain orthonormal eigenstate basis is constructed in the soliton potential, and the evolving wavefunction is projected onto mode coefficients that encode angular structure. Mode-controlled reconstructions test which seeded modes drive stone skipping, while a semi-analytic model maps the linearised dynamics onto a forced, damped oscillator. Within the tested reconstructions, low-radial-index dipole modes are decisive: retaining them reproduces stone skipping, while removing the dipole sector restores secular decay. Equal-mass binaries weakly excite this sector, and external dipole seeding restores the phenomenon in the tested configurations. Spectral analysis reveals a two-frequency structure, and the reduced model shows how radial excursions can be sustained when a positive orbital-frame driving frequency approaches the epicyclic frequency under sufficiently weak effective damping. The result is a bounded mechanism statement, not a complete resonance-window theorem. The main limitations are friction calibration, finite-domain truncation, and incomplete resonance-window mapping; the direct future tests are moving-frame perturbation theory, friction sweeps, and multi-mode spectral diagnostics
Access status: Open Access ,
Simulating the Amplification, Saturation, and Structure of Turbulent Interstellar Magnetic Fields
(2026) Kriel, Neco
From stars to galaxies, our Universe is observed to be in a magnetised state. In galaxies, for example, magnetic fields shape merger remnants, regulate star formation, and mediate the coupling of plasma motions on small and large scales. However, these fields are not expected to have existed in their current form in the hot, nearly uniform early Universe. Instead, weak seed fields were generated and subsequently amplified as galaxies assembled, where small-scale dynamos (SSDs) provided the most efficient route for field amplification. While SSDs have been explored extensively through analytic theories, laboratory experiments, and direct numerical simulations, the majority of our understanding is built on the assumption of incompressible turbulence. This limits direct application of SSD models to the supersonic, shock-dominated flow regime that characterises most of the interstellar medium. In this thesis I use direct numerical simulations to extend SSD theory to compressible astrophysical regimes, and in the process develop novel statistical methods to extract robust, resolution-independent measurements from stochastic and intermittent flows. I apply these methods to two aspects of SSD evolution that are particularly relevant for galactic magnetism: First, motivated by recent observations of young protogalaxies that reveal magnetic structures coherent on $\sim \mathrm{kpc}$ scales, I test whether compressibility modifies the scale on which magnetic fields become correlated. I show that shock-dominated turbulence shifts magnetic correlation scales from dissipation-regulated $\sim \mathrm{AU}$ scales to as large as $\sim \mathrm{pc}$ in some ISM phases. Compressibility, therefore, provides a pathway to generate substantially larger-scale (seed) fields, which must be further organised by (some yet, unidentified combination of) system-scale processes to reach the observed $\sim \mathrm{kpc}$ coherence. I then turn to the timescale over which SSDs saturate, and to the efficiency of nonlinear amplification once magnetic backreaction becomes important. Across both subsonic and supersonic regimes, I show that the SSD converts a nearly constant fraction of the turbulent kinetic energy flux into magnetic energy, with an efficiency consistent with that measured during the kinematic phase. This provides a direct empirical resolution to a long-standing debate regarding nonlinear SSD growth and suggests a wider universality of magnetic amplification. Finally, as part of a longer-term campaign to enable SSD studies at higher resolution and larger dynamic range, I implement an MHD module in the new open-source, adaptive mesh refinement code \textsc{Quokka}, which was designed from the outset for next-generation GPU-accelerated supercomputers, and will enable the possibility of simulations with a much broader scale separation than is currently practical on CPU-based systems. This implementation couples a Godunov finite-volume scheme to a constrained-transport method that maintains $\nabla\cdot\mVector{b} = 0$ to numerical precision and incorporates stability and error-correction strategies specifically suited to highly compressible flows. This implementation provides a scalable foundation for future extensions that pursue more self-consistent, higher-resolution studies of SSD-driven magnetisation in galactic environments.
Access status: Open Access ,
Shear-Driven Transformations and Plastic Deformation in Diamondoids and C60 under High Pressure
(2026) Heimes, Hendrik
Carbon's flexible bonding produces numerous stable and metastable allotropes. Subjecting carbon materials to high pressure conditions is essential for synthesising technologically relevant sp3-hybridised phases such as nanodiamonds and other ultrahard materials. Conventional sp3 synthesis requires high pressures and temperatures, making it energetically costly. Recently, combining high pressure with high shear stresses has emerged as an alternative, enabling phase transformations at milder pressures, although the effect on carbon reaction pathways remains poorly understood. This thesis examines two classes of molecular crystalline carbon-based materials under pressure: sp3-bonded diamondoid hydrocarbons (adamantane, diamantane, triamantane and tetramantane) and sp2-bonded hollow C60 fullerenes, to assess how precursor structure influences phase evolution and shear-driven transformations. Diamond-anvil cells are used for high-pressure compression, while a rotational diamond anvil cell (rDAC) was used to apply shear. Samples were analysed in situ using X-ray diffraction and Raman spectoscropy. Recovered samples were characterised via transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). Cage-structured diamondoids were found to be mechanically ultra-resilient, withstanding 50 GPa and fully recovering their initial geometry upon decompression. Their main response to compression is plastic flow driven by intermolecular repulsion, while the sp3 framework remains intact. The plastic flow manifests in an anomalous lateral expansion of the sample chamber, pushing out the gasket. The onset of this effect is around 10 GPa and coincides with Raman peak splitting and increasing compressive stiffness. In contrast, C60 molecules irreversibly transform under pressure. Initial cross-linking stiffens the structure, followed by cage collapse into sp3-rich phases. Non-hydrostatic conditions reduce the collapse threshold from 45 GPa to 30 GPa. Upon collapse, amorphous carbon with 85% sp3 bonding, interlaced by nanodiamond (ND) bands and residual C60 fragments forms. Inducing shear through twisting the sample under pressure in the rDAC enables the molecular collapse at pressures as low as 12 GPa, when the molecular system is sufficiently cross-linked. Shearing at 15-17 GPa produces dense sp3-rich amorphous carbon with up to 3.4 g/cm3 and 95% sp3 bonding, interlaced with ND bands and a continuous ND surface layer. Shearing at higher pressures forms homogeneous high-density amorphous carbon without ND. Lastly, a henomenological model to estimate shear strain in the rDAC is introduced, demonstrating that the setup is influenced by grain size, boundary slip, elasticity and rigidity. This model shows that even modest twist can cause shear strains over 10%, coinciding with the yield point of most materials. This indicates that the rDAC experimental setup introduces plastic deformation which considerably reduces phase transformation thresholds. The results of this thesis demonstrate a moderate-pressure, ambient-temperature route to bulk sp3-bonded carbon phases and highlight shear as a potent driver of carbon phase transformation. These findings open various future research avenues in applying shear-driven synthesis approaches in other carbon precursor materials, utilising functionalised fullerene precursors for targeted amorphous carbon synthesis with desirable atom terminations, and tackling the challenge of quantifying shear stresses in high pressure experiments.
Access status: Open Access ,
Encouraging residents’ stewardship of street trees in Canberra: Perspectives in the context of the ACT Government's Street Forestry Program
(2021) Choy, Ming Hui
Urban forests are increasingly important as a ‘nature-based solution’ to climate change, and for the many other benefits they deliver to urban residents. Therefore, many cities globally are focusing on enhancing the extent and quality of their urban forests. Canberra, Australia’s capital city, introduced an Urban Forest Strategy in recognition of these issues. One of its goals is to engage residents in stewardship of street trees in their neighbourhoods, which requires a better understanding of residents' perceptions and attitudes to these trees. Whilst there is some knowledge of these amongst Canberra residents, there are also gaps, particularly about residents’ willingness to play a stewardship role for urban trees. Furthermore, most literature situates urban tree stewardship in the context of organised neighbourhood groups, with less focus on individual stewardship. This thesis therefore explores Canberra residents’ attitudes and behaviours to stewardship of street trees in their neighbourhoods, in the context of an ACT Government pilot initiative, the Street Forestry Program, and considers the implications for such initiatives. In April and May 2021, the Street Forestry Program conducted a survey of residents and pop-up consultations in six suburbs, and a webinar. I was able to draw on the survey results, undertake participant observations at consultations and the webinar, and conduct interviews with residents in two suburbs. Results suggest a widespread view that street trees are important, for a range of reasons: the top five were aesthetic, shading, biodiversity, carbon sequestration and erosion control. Around 70% of survey respondents reported that they engaged in stewardship behaviour, primarily watering trees and picking up branches and leaves; this proportion was greatest in the 45-65 age group. Interview responses suggest the main factors influencing stewardship behaviour are individual motivations, perceptions and attitudes; personal circumstances; and government policies and programs. These factors were incorporated into a model of stewardship behaviour for trees on public land in Canberra, adapted from that of Moskell and Allred. Interviewees appreciated the Street Forestry Program for its inclusiveness and efforts to green the suburbs, but had greater expectations for the Program and the ACT Government in the broader context of urban greening issues in Canberra. These results suggest that, to encourage stewardship by residents, the ACT Government should engage in a suite of best practices: these include an adaptive approach to community engagement, guided by models of public participation; strengthening of coordination of operations; and collaboration with neighbourhood groups. Further research should expand upon the foundations established by this study, addressing the knowledge gaps identified here, including wider themes of equity in urban development and socio-demographic factors. Like the Street Forestry Program, this study was limited in scope. A larger sample population across a wider range of Canberra suburbs would help inform future work to foster urban tree stewardship. Nevertheless, the findings of this study inform and support the ACT Government’s efforts to foster urban tree stewardship behaviour in the community, which will in turn facilitate the success of Canberra’s Urban Forest Strategy.
Access status: Open Access ,
Navigating Quiet and Pressure Politics: Leadership Perspectives from Australian Peak Bodies
(2026) Essery, Aiden
Interest groups are central actors in Australian federal policymaking. Much of the literature examines variations in how they operate within technocratic arenas or the public sphere, often predicting systematic divergence between business and cause groups. This thesis explores that assumption through the distinction between quiet and pressure politics, shifting attention from observable strategy to leader sense-making. Drawing on semi-structured interviews with chief executives from national business (n = 15) and cause peak bodies (n = 15), and using inductive reflexive thematic analysis, this study identifies nine shared themes demonstrating substantial convergence in how leaders conceptualise advocacy modes. Rather than treating quiet and pressure politics as structurally determined by constituency type, the analysis foregrounds leadership discretion and professional field norms within Australia's pluralist Westminster system. The argument develops in three parts. First, convergence emerges from how leaders conceptualise policymakers, the public and interest groups. Policymakers are understood as operating under cognitive and organisational constraints, the public is seen as episodically engaged and largely delegatory between elections, and peak bodies are positioned as professional intermediaries translating complexity into usable evidence. These shared interpretations stabilise quiet politics as the professional norm. Low-visibility, evidence-based engagement is framed as consistent with delegated representation and institutional incentives in a bounded policymaking environment. Second, pressure politics is conceptualised as a deviation from this norm and governed by a discernible escalation process. Leaders describe thresholds that must be crossed before public conflict becomes legitimate, typically when issues are reframed as materially threatening to core member interests. Escalation is preceded by attempts to resolve concerns within quiet channels and is constrained by reputational risk, relational costs and operational complexity. Insider status is treated as scarce and fragile, and pressure campaigns are often coordinated through coalitions to distribute costs and strengthen messaging. The exceptional character of pressure politics is central to its credibility. Third, leaders conceptualise the two modes as jointly regulating the level of conflict in policymaking. Quiet politics sustains trust, access and the ongoing provision of expert evidence. The credible possibility of escalation underpins responsiveness: policymakers are perceived to remain attentive in private channels partly because organised backlash remains available. At the same time, a frequent use of pressure politics would erode deterrent value and long-term group access. Effective advocacy, therefore, depends on calibrating movement between modes to maintain sufficient conflict to secure responsiveness without destabilising long-term relationships. Across nine shared themes, business and cause peak bodies converge around a professionalised logic in which quiet politics operates as the default mode, pressure politics emerges through a structured escalation process and both modes are strategically calibrated to shape policymaker responsiveness to expert evidence. By centring leader sense-making, the thesis extends neopluralist scholarship at the micro and meso levels, demonstrating how shared professional norms compress structural differences between group types within Australian federal policymaking.
Access status: Open Access ,
SimTeller: Improving the Realism of Simulated DNA Alignments and Machine-Learning Detection for Simulated Alignments
(2026) Zeng, Manyuan
Phylogenetics infers evolutionary relationships from DNA or protein sequence alignments. Simulated alignments are widely used in phylogenetics because they provide known ground truth and large-scale reproducible data. However, original simulation workflows often simplify the evolutionary process, reducing the realism of simulated datasets and limiting the performance of downstream machine-learning methods. This thesis addresses two interconnected research questions: how to improve the realism of simulated DNA alignments, and whether more realistic simulated datasets can improve machine-learning–based alignment classifiers. The first part developed an improved simulation workflow by incorporating ancestral sequence reconstruction (ASR) and mixture-model approach into the original simula- tion pipeline. To support large-scale mixture-model simulation, this project constructed the first large-scale database of mixture-model parameters and root sequences for 30,773 empirical DNA alignments. The existing Seqsharp classifiers generally failed to effectively classify alignments generated under the improved workflow, suggesting a smaller gap between the improved simulated data and empirical alignments. The second part investigated whether the improved simulated datasets could produce better alignment classifiers. I trained SimTeller, a set of new alignment classifiers us- ing convolutional neural network (CNN) and gradient boosting tree (GBT) approaches. Compared with Seqsharp, SimTeller demonstrated stronger robustness, practical ap- plicability, and generalisation ability across independent and cross-condition testing datasets. These results further confirmed that the improved simulation workflow from the first part may also benefit a broader range of phylogenetic machine-learning applications. Overall, this thesis developed an improved simulation workflow for DNA alignments and proposed SimTeller, a set of machine-learning–based classifiers that may serve as useful tools for evaluating the realism of simulated alignments
Access status: Open Access ,
Doing Good or Looking Good? The Impact of Geopolitical Competition on Australia's Aid Performance in the Pacific
(2024) Vacaflores, Isabella
In the shadow of a “new Cold War” between China and the West, heightened geopolitical competition is being observed worldwide. This thesis investigates how such tension has manifested itself through the mechanism of aid, focusing on the case of Australia and China in the world’s most aid-dependent region, the Pacific. Using multiple regression analysis, this study examines whether geopolitical competition helps explain a phenomenon whereby aid in the region seemingly and inexplicably underperforms. Surprisingly, results suggest that projects delivered to Pacific Island countries that are more geopolitically important to Australia reportedly perform better. However, further analysis indicates that this is possibly due to biased performance assessments rather than actual improvements. Additionally, evidence of a “political turn” in the thinking and motives of the Australian aid program underscores concerns about the extent to which aid in the Pacific is genuinely “doing good” versus merely “looking good”. The study offers new insights into the factors influencing aid performance and raises concerns about the reliability of such assessments, especially when they concern recipients that are geopolitically important to a donor.
Access status: Open Access ,
Enhanced Second Harmonic Generation in Dual-Resonance 3R-MoS2 Metasurfaces, Roles of the Q Factor and Absorptance
(2026) Yang, Wenkai
Resonant dielectric metasurfaces supporting quasi-bound states in the continuum (q-BICs) provide a powerful platform for enhancing light-matter interactions and nonlinear optical processes such as second-harmonic generation (SHG). In this thesis, SHG in dual-resonance 3R-MoS2 metasurfaces is investigated through a combined theoretical, numerical, and experimental study. Traditionally, SHG intensity has been assumed to scale with the square of the resonance quality factor (Q^2). However, experiments show that samples with similar Q values can exhibit very different SHG outputs, indicating that, for the sample-to-sample variations studied here, pump absorptance also plays an important role in determining the nonlinear response. Based on temporal coupled-mode theory (TCMT), a compact expression is used to describe the dependence of SHG intensity on both the resonance quality factor (Q) and the pump absorptance (A), highlighting the balance between field confinement and pump coupling in the present structure. To verify this, dual-resonance 3R-MoS2 metasurfaces were designed and fabricated, combining reflective and q-BIC resonances. Numerical simulations and optical measurements show overall consistency with the TCMT-based description. The best-performing sample exhibits a conversion efficiency of about 0.002% and an SHG enhancement of approximately 40 times compared with an unpatterned flake of the same thickness. These results clarify the role of pump absorptance together with the resonance Q factor in the dual-resonance metasurfaces studied in this thesis and provide guidance for the analysis and design of nonlinear metasurfaces based on similar resonant platforms.
Access status: Open Access ,
The feeding ecology of Cat Ba Langurs (Trachypithecus poliocephalus) on Cat Ba Island, Vietnam.
(2026) Ruskin, Kayla
The Cat Ba langur (Trachypithecus poliocephalus) is a Critically Endangered colobine species, endemic to Cat Ba Island, Vietnam. Intense hunting pressure saw the population decline to just 50 individuals in 2000 and - although strict protection measures have helped control poaching on the island - the long-term survival of the species is still threatened due to the small size of the population, isolation of subgroups and ongoing threats to their habitat. Data on the diet and nutritional ecology were collected between May 2016 and April 2017 on two reproductive groups (Group A and Group B) living in the Cua Dong subpopulation to determine the quality of their habitat and whether food availability is limiting the growth of the population. Knowledge on the feeding ecology of a species is important because it provides information about their ability to survive in lower-quality habitats and the key resources required in their habitat to ensure their ongoing survival and the growth of the population. The two groups of langurs spent most of their time eating leaves (63.36% and 66.57%) and fruit (12.49% and 13.65%), consuming young leaves more often than mature leaves and unripe fruit more often than ripe fruit. Flowers, stems, seeds, bark and petioles made up the rest of their diet. The langurs fed on a total of 103 food items from 56 different plant species. Group A consumed 18 species for more than 1% of the time, while Group B consumed 14 species for more than 1% of the time, accounting for 73.96% and 72.19% of their diets, respectively. Only three species consumed by the langurs were found among the top 20 species in their habitat and only two of the three were consumed for more than 1% of the time. This all suggests the langurs were being selective about their food choices and not just eating foods based on the frequency they were found within their habitat. The average concentrations of nutrients in the langur's food items were roughly similar to those found in the foods of other Asian colobines, except for copper and manganese, which were slightly lower. In addition to this, the average levels of crude protein, copper, zinc, sodium and iron in all plant parts tested were lower than the adequate nutrient concentrations put forward by the National Research Council for non-human primates. Despite this, however, there was no indication the langurs were suffering from any kind of nutrient deficiency, suggesting the current nutrient levels in the diet are sufficient for the species. The strong negative correlation between the concentration of ADF and NDF in young leaves eaten by the langurs and the selectivity index of the food items, suggests the monkeys were selecting young leaves with low fibre concentrations and may indicate a high overall fibre content in the plants at the site. Feeding-related agonistic incidents, along with avoidance behaviours, indicates that contest competition is occurring in this subpopulation. Group A had a higher number of feeding-related agonistic incidents, fewer individuals nearby when feeding and a higher rate of agonism overall, compared to Group B. This may be due to the large area of home range overlap Group A has with a bachelor group, which could lead to faster depletion of food resources. Additionally, the intergroup encounters observed in this study were more aggressive when they involved the adult male from a reproducing group and the bachelor group compared to when they involved the adult males from the two reproducing groups, suggesting that group take-over attempts could be a problem in this subpopulation. These problems will continue to get worse if the size of the subpopulation increases without the ability to expand the area they currently inhabit or move to another subpopulation. Thus, the small area currently inhabited by the Cua Dong subpopulation and the lack of connection between subpopulations could be limiting the growth of the population.
Access status: Open Access ,
MicroR159 is a genetic switch between growth and pathogen defense in Plants
(2026) Evivie, Ejiro
MicroR159 (miR159) is an evolutionarily conserved microRNA family present across all terrestrial plants. It targets a subset of genes encoding R2R3 MYB-domain transcription factors known as GAMYB through highly conserved binding sites, ensuring their strong post transcriptional repression. Although GAMYB genes are constitutively transcribed, their expression is completely silenced by miR159, a process reinforced by conserved RNA secondary structures flanking the binding site. Disruption of this silencing, either through inhibition of miR159 function or by expressing miR159-resistant GAMYB transgenes, results in severe growth inhibition, emphasizing the importance of GAMYB silencing for normal development. To investigate the transcriptional consequences of miR159 loss of function, RNA-seq datasets from mir159 loss-of-function plants were analysed. These included the 35S- MIM159 Nicotiana benthamiana lines constitutively expressing the miR159 MIMIC (a miR159 inhibitor) and the mir159ab Arabidopsis T-DNA mutant. In Arabidopsis, miR159 disruption caused strong suppression of stress and defense related biological processes, with 18 of the 20 downregulated gene ontology categories associated with response pathways, including defense response and plant-pathogen interaction. Also, defense genes such as PR1 were among the most downregulated differentially expressed genes. This transcriptional profile closely mirrored that of the 35S-MIM159 N. benthamiana, indicating conserved defense gene repression upon miR159 inhibition in these two species. However, this pattern contrasted sharply with previous findings from the 35S-MIM159 N. tabacum, where defense genes and pathways, were strongly induced. These contrasting transcriptomic outcomes, despite all three species exhibiting similar growth inhibition upon loss of miR159 function, suggest species-specific regulatory processes operating downstream of GAMYB. To further dissect GAMYB associated transcriptional responses, a transgenic miR159-resistant and estradiol inducible GAMYB construct was generated and introduced into Arabidopsis and N. tabacum. Induced GAMYB expression in both species led to transcriptomic enrichment for genes associated with abiotic and biotic stress responses. This association suggests that GAMYB expression activates pathways involved in defense against microbial and insect attack, positioning miR159 as a molecular switch between growth and broad-spectrum defense. The persistent yet silenced GAMYB transcript may function as a latent regulator, rapidly activating defense-associated transcriptional programs upon derepression, indicating a potential role in stress-responsive priming.
Access status: Open Access ,
Fire and vegetation history at Jervis Bay through the Holocene
(2026) Pecenko, Alexander
Bushfires are a defining feature of the Australian landscape, which is shaped by fire-dependent and fire-tolerant vegetation. The scale and severity of the 2019-2020 Black Summer fires in coastal New South Wales starkly illustrated the need for detailed vegetation and fire histories to improve fire management. Understanding Australia's fire regimes is therefore increasingly critical amid escalating environmental degradation driven by climate change, pollution, urban expansion, and the post-British invasion disruption of Aboriginal Australians' cultural burning practices. To add to this understanding, this thesis presents the first palaeoecological reconstruction of Holocene vegetation history and fire regimes at Cararma Inlet on the Beecroft Peninsula near Jervis Bay in southeast Australia. Vegetation, fire and hydrological history was reconstructed through a detailed pollen, mollusc and charcoal analysis of sediment cores from the Carama Inlet - a low lying infilled estuarine setting on the northern shores of Jervis bay National Park. This work showed that throughout the Holocene, terrestrial vegetation was dominated by Casuarinaceae and Myrtaceae, reflecting their fire tolerance and ecological adaptability. Herbs such as Amaranthaceae/Chenopodiaceae and Poaceae were consistently abundant, indicating resilience to saline conditions. Ferns were most prevalent during the early Holocene, but declined as the climate became warmer and drier. Mangroves (Avicennia) expanded from the mid Holocene onward, driven by stable estuarine substrates, reduced freshwater inflow and lower sedimentation rates. The central aim of the fire regime reconstruction was to develop and apply predictive models to determine palaeo-fire temperatures and combusted plant taxa. Fourier-transform infrared spectroscopy (FTIR) was applied to reference charcoal produced from five representative tree taxa (Avicennia marina, Casuarina, Eucalyptus botryoides, E. tereticornis, and Melaleuca), with the results interpreted in relation to vegetation dynamics, climate variability and anthropogenic impacts. Charcoal was produced using both controlled muffle furnace heating and a novel open-flame combustion method, and analysed in attenuated total reflection and reflection modes. The predictive models demonstrated that combustion temperature is the primary driver of spectral variation in muffle furnace-derived charcoal, whereas plant taxa are not statistically distinguishable. Models trained on charcoal from the open-flame method did not yield statistically significant predictions for either temperature or taxa. The FTIR analysis of palaeo-charcoal showed that fire frequency, severity, and charcoal accumulation rates at Jervis Bay were lowest in the early Holocene, highest during the mid Holocene, and variable in the late Holocene. Most Holocene fires were relatively cool (300 C), reflecting the dominance of less flammable estuarine vegetation, moist environmental conditions, and likely Aboriginal cultural burning. The mid Holocene's higher proportion of hotter fires (700 C) was associated with increased abundance of combustible Eucalyptus and Casuarina and a warming climate. Since British invasion (110 cal. yr. BP), fire activity has peaked, intensified by environmental degradation, increased anthropogenic ignitions, reduced cultural burning, and the expansion of highly flammable vegetation. By integrating climate, sea level change (hydrology), vegetation dynamics, fire regimes and human impacts, this thesis reveals a strong link between vegetation abundance and composition and fire behaviour, and provides a comprehensive reconstruction of the Holocene palaeo-environment at Jervis Bay.
Access status: Open Access ,
Dynamic light manipulation with tunable metasurfaces
(2026) Yang, Ziwei
Over the past few decades, applied physics has grown rapidly through advances in nanofabrication, material engineering, and computational modeling. These developments have transformed the study of light-matter interactions at the micro- and nanoscale from theoretical prediction to experimental realization, accelerating nanoscience and enabling major discoveries. Metasurfaces, planar optical systems composed of subwavelength resonators, arise from the understanding of light scattering by nanoscale particles. By confining and resonantly enhancing light, they enable subwavelength modulation of amplitude, phase, and polarization. Through this control, metasurfaces achieve functionalities beyond bulk optics, including multifunctional metalenses and beam deflectors, and enable applications in quantum photonics, optical neural networks, and spatiotemporal energy control. However, in conventional static metasurfaces, both geometry and materials are fixed upon fabrication, restricting operation to a specific regime and preventing adaptation to changing conditions. Overcoming this limitation requires tunability without compromising optical quality, speed, or efficiency, an enduring challenge in the field. This thesis addresses this problem by developing a unified strategy for tunable metasurfaces that combine low-loss materials, controllable external stimuli, and predictive theoretical models. It achieves dynamic performance and strong modulation within the intrinsic trade-off between depth and speed through three complementary directions: (i) designing high-quality static building blocks that define the performance ceiling; (ii) developing large-response materials and mechanisms for electrical, magnetic, and optical control; and (iii) formulating analytical and numerical models that link static and dynamic operation. Together, these directions realize a scalable, high-performance platform for active and reconfigurable photonics. The first part builds the foundation for tunable meta-optics. Monolithic silicon-carbide (SiC) metalenses with parabolic and cubic phase profiles in the near infrared are designed, fabricated, and experimentally verified. Their high focusing efficiency and compatibility with SiC quantum emitters highlight dielectric metasurfaces as robust, low-loss platforms for efficient light manipulation. The second part demonstrates tunability through low-loss, large-response media. Electrical and thermal modulation of liquid-crystal-integrated metasurfaces provides full-range phase control, while magnetic-field-driven and optical-torque-induced reorientation enable contactless, reversible tuning of linear and nonlinear responses. Ultrafast modulation in III-V semiconductor metasurfaces is also achieved via femtosecond excitation, enhancing the resonant Q-factor and inducing temporal-interface frequency conversion. The final part develops analytical and numerical models to predict tunable-metasurface behavior. Frameworks based on anisotropic field interactions, temporal coupled-mode theory, and carrier dynamics are validated through full-wave simulations. These models unify static and dynamic design principles, offering quantitative insight into optical control and forming a general toolset for time-dependent photonic analysis. Altogether, this thesis establishes an experimentally verified and theoretically grounded foundation for tunable metasurfaces, advancing the field toward adaptive, multifunctional, and ultrafast photonic technologies.
Access status: Open Access ,
It’s All About Space: How Middle-Class Asian Australian Travellers’ Expectations of Airline Travel are Centred Around Space Inside the Airplane Cabin
(2026) Kim, Nicholas
This research project will analyze passengers’ expectations for commercial aviation - focussing in particular on the airplane cabin. In-depth interviews were conducted with nine participants from middle-class Asian Australian backgrounds. Participants were asked questions about airplane behaviours and preferences, airline consumerism and class, airport security, and politics. A key theme of this research was that many passengers’ expectations of commercial aviation were connected to the concept of space inside the airplane cabin. Participants associated the confined space of the airplane cabin, with the deprivation of certain freedoms. They also associated having more space with being more comfortable. Participants also held expectations for purchasing space in their airline consumerism decisions. Whilst within the airplane cabin, participants indicated that they held expectations for having personal space. Participants also identified the airplane cabin as a shared public space which is associated with expected rules and behaviours. Finally, participants acknowledged differential access to space through the imposition of airport security, and discrimination based on social class-based identities, in restricting access to the business and first class cabins. A second key finding was that participants were guarded against people who they perceived as different. The implications of the key finding that space was central to participants’ expectations of air travel are political, in terms of who has access to space, and how much space they have access to. The implications of the second key finding are that the negative perceptions of human differences identified in the airplane can be applied to addressing social cohesion in Australian society
Access status: Open Access ,
Communicable Disease Applied Epidemiology in South Australia
(2026) Montgomery, Joshua
The South Australian Health (SA Health) Communicable Disease Control Branch (CDCB) aims to reduce the incidences of communicable and infectious diseases in South Australia (SA). This thesis details the projects undertaken as part of my field placement at CDCB. The projects comprise an epidemiological study of syphilis positivity rates and sociodemographic predictors of geographical variation in testing rates in the public pathology system in SA, an analysis of the descriptive epidemiology of varicella in SA, an outbreak of COVID-19 Delta variant at a SA winery, and an evaluation of the SA COVID-19 rapid antigen testing (RAT) surveillance system. This thesis also describes other experiences related to public health, fieldwork, presenting, and teaching undertaken during this program. Combined, these projects and experiences fulfil the major and minor requirements of the Master of Philosophy in Applied Epidemiology program at The Australian National University.
Access status: Open Access ,
Bayesian well-made surprises: theory, modelling and insight
(2026) Chieppe, Cynthia
Good narrative surprise is highly sought after for its entertainment value and insight-like characteristics, and plot twists are the underpinning of entire genres, from long-form detective fiction to short jokes and humorous narratives. Although we understand many writing techniques behind successful surprises and the psychological mechanisms they leverage in the audience, a large part of the enjoyability of narrative surprise is highly subjective and seems to evade analysis. This itself is unsurprising, but furthermore it's unclear what aspects of surprise are formally modellable, and to what extent a formal approach can be applied to the analysis of narrative surprises. Existing formal models of narrative surprise, mainly from computational narrative, are primarily concerned with generating novel surprising narratives, rather than analysing existing ones, and have rarely been used outside of computational narrative research. In this work, we first outline formal requirements for a model of narrative surprise that is suitable for both analytical and generative purposes, and for use by a cross-disciplinary audience. We then propose a formal model of narrative surprises, based on operationalisations of narrative theory into computer science formalisms. Our proposed model is based on Markov Logic Networks (MLNs), which encode audience knowledge and inferences throughout the narrative into first-order logic. By operationalising the qualities of ``well-madeness'' of a surprise into functions of the MLNs' outputs, our model produces estimates of those qualities. We evaluated the performance of our model by quantitatively comparing its outputs to ratings of the same qualities collected from participants in two studies. We found that when comparing two variants of the same narrative that differ in a given quality, our model's outputs change between the two variants in a way that is consistent to the ratings of the human participants, in particular for the qualities of consistency and divergence (a kind of surprisingness). We also qualitatively evaluated the model's adherence to the requirements we previously outlined, and found that it satisfies several, being versatile and expressive. Our work lays foundations for future research into formally modelling narrative surprises by contributing on multiple levels: a set of requirements that other formal models of surprise can be designed around and evaluated with, a prototype model of narrative surprise, a small curated corpus of short narratives with surprises, and an experimental scale for measuring key qualities of ``well-madeness'' of a surprise. Our results suggest that while the well-madeness of a narrative surprise is heavily subjective, it is nonetheless related to patterns in the audience's knowledge and inferences about the narrative, and that some of those patterns can be formally modelled and computationally analysed to further our understanding of the narrative, and of narrative surprises as a whole.
Access status: Open Access ,
Identification of signal transduction and accessory protein requirements for resistance responses mediated by the tomato I-3 gene for Fusarium wilt resistance.
Rima, Sharmin
Fusarium wilt of tomato is a vascular disease caused by the fungus Fusarium oxysporum f. sp. lycopersici (Fol). Fol secretes a number of effector proteins that facilitate host infection, including the SIX1 (Secreted In the Xylem 1) protein. Besides its role in pathogenicity, SIX1 can also trigger defence activation in tomato plants expressing the I-3 resistance protein, and so SIX1 is also designated Avr3. In this study, I explored the virulence function of the Avr3/SIX1 protein and the activation of defence signalling following its recognition by I-3. I also explored the possibility that SIX1 homologues from F. oxysporum f. sp. cubense (Foc) tropical race 4 (TR4) could restore FolSIX1 virulence on Fol-susceptible tomato plants and its avirulence on I-3 tomato plants in a SIX1 deletion mutant. Unlike other R/Avr gene combinations, co-agroinfiltration of I-3 and Avr3/SIX1 does not induce necrosis in Nicotiana tabacum or N. benthamiana. Therefore, I started my experiments by attempting to develop a rapid assay system based on a plant defence response other than necrosis/necrosis to assay I-3-mediated defence activation in N. benthamiana (Chapter 2). I made a chitinase promoter:gusA reporter construct based on an N. benthamiana orthologue of a chitinase gene that showed a 30-fold increase in expression 2 days post-inoculation of I-3 tomato plants with an isolate of Fol carrying Avr3 gene. I also checked whether this gene was suitable as a good reporter by using RT-PCR. I confirmed it was not constitutively expressed in leaves of N. benthamiana. However, it was induced by Agrobacterium, making an agroinfiltration approach impractical. I therefore generated a transgenic N. benthamiana line expressing both I-3 and the reporter, using purified Avr3/SIX1 infiltration to activate I-3-mediated signalling. In collaboration with Daniel Yu and Megan Outram from the Williams Laboratory, Research School of Biology, I expressed and purified Avr3 protein for experimental use (Chapter 3). I infiltrated purified Avr3 protein into N. benthamiana leaves to investigate potential virulence functions (Chapter 4). Surprisingly, Avr3 induced callose deposition in N. benthamiana despite suppressing flg22-induced ROS accumulation. In tomato plants, infiltration of Avr3 protein induced an I-3-dependent cell-death or necrotic response indicative of defence activation. We also attempted to express and purify the N- and C-terminal domains of Avr3 to identify which domain was responsible for these responses. Although we were able to express and purify only the N-terminal domain, this domain was sufficient to induce callose deposition, suppress ROS production in N. benthamiana, and induce I-3-dependent necrosis in tomato. I then leveraged the ability of purified Avr3 protein to induce I-3-specific necrosis to develop an assay system based on virus-induced silencing (VIGS) to investigate downstream signalling (Chapter 5) as an alternative to the chitinase promoter:gusA reporter (Chapter 2). Silencing of downstream signalling components BAK1, SOBIR1, EDS1, SAG101 and NRG1 showed major roles, and NPR1, NPR3, and NRC1 demonstrated partial roles in I-3 mediated defence in tomato plants. Purified Avr1 protein supplied by Daniel Yu was also used as a positive control for VIGS of signalling components known to be required by the I resistance protein. I was also interested in whether the tomato I-3 resistance protein could recognise any of the SIX1 proteins encoded by three homologues of SIX1 present in Foc TR4 (Chapter 6). If so, there would be the potential to use I-3 in banana as a gene for resistance to Foc TR4. The three gene sequences were synthesised to make restoration constructs transferred into a SIX1 deletion mutant of Fol. Expression of the Foc TR4 SIX1 genes during tomato infection by the resulting Fol transformants was confirmed by RT-PCR, but none was found to restore the loss of SIX1 function in Fol.

Cultural advice

Browse

Recent Submissions