Open Access Theses

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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 ,
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, Patrick
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.
Access status: Open Access ,
Di-Amido Xanthene-Stabilised Reactive Main Group Compounds for Small Molecule Activation
(2026) Lim, Li Feng
This thesis describes the use of a xanthene-bridged di-amido ligand, termed "NON", towards the kinetic stabilisation of several types of reactive main group compounds, with the eventual goal of employment in small molecule activation. This extends across a variety of compound types, which has in turn meant that each chapter is written in a somewhat self-contained fashion. Chapter 1 commences with a broad overview of main group chemistry, with particular focus given to its historical development - beginning with the preparation of "Cadet's fuming liquid" in the mid-18th century, and concluding with Robert West's report of the first silicon-silicon double bond, widely credited for sparking a revival of interest in the field. The NON ligand is also introduced, and contrasted against the backdrop of commonly-employed ligands throughout modern main group chemistry. Chapter 2 pertains to low-valent s-block chemistry (with subsumption of the group 12 elements as well), and begins with a relatively detailed introduction to the preparation, electronic structure and reactivity of these compounds - both the more-common homo-bimetallic dimers, as well as the less-understood open-shell monometallic counterparts. The coordination chemistry of the NON ligand to said elements is discussed, following which the preparation of a potential s-block radical is described. Characterisation of its electronic structure and reactivity, including the difficulties encountered therein, constitutes the remaining body of work. Chapter 3 addresses the catalytic efficacy (or lack thereof) of extant group 14 tetrylene complexes in redox-active cross-coupling cycles. Previous reports of oxidative additions and reductive eliminations are discussed, highlighting the potential of tetrylenes in performing redox catalysis. The amenability of NON-ligated tetrylenes towards oxidative additions is investigated, showcasing the flexibility of the xanthene backbone through a "hinging" equilibrium. Subsequent attempts at transmetallation and reductive eliminations are also discussed. Chapter 4 involves both the preparation and reactivity of molecular organocalcium compounds. Following an induction to both of these aspects across archetypal and molecular organocalcium complexes, the nucleophilicity of existing neutral instances is highlighted. The preparation of NON-ligated analogues, now formally anionic in nature, is described alongside numerous demonstrations of their subsequent reactivity. The discovery of an unorthodox preparative route to these compounds is also included. Chapter 5 briefly discusses the aggregation chemistry of alkali metal organometallics, with the small body of work that follows describing a convergent, thermodynamically-governed rearrangement operative for both the group 1 metals as well as thallium. Finally, the chief findings of this thesis are summarised with the supporting information appended thereafter.
Access status: Open Access ,
Framing Native Forests: A Victorian case study
Shelton, Madeline
Australia’s native forests have been a topic of contention between forestry and environmental groups for over half a century. Despite political interventions aimed at reconciling disagreement, conflict between interest groups continue. The news media is a key public forum where these forest topics are debated and characterised. Curious to better understand the nature of Australia’s ongoing forest conflicts, I have used framing analysis to explore the coverage of native forest management issues in the mainstream news media, using Victoria as a case study. I examined how events, issues, actors, and practices are framed in the news coverage, as represented by the Australian Broadcasting Corporation, The Age, The Australian and The Guardian in 2019-2020. A total of 66 news articles about Victorian native forest issues were published during this period; the monthly frequency varied considerably and was related to both natural (e.g. bushfire) and political (e.g. Victorian Government decision to end native forest logging) events. I identified three frames: 1) Save nature, stop logging (SNSL), 2) Forestry, the ultimate renewable (FTUR), and 3) The political balancing act (PBA). The first of these was dominant and proactive; the second largely reactive; and the third relatively minor. I also explored below surface level disagreements to see how each frame perceives ‘nature’, ‘knowledge’, and the ‘other’ groups. The SNSL frame represents nature as ‘pristine’, and of great intrinsic value; in contrast, the FTUR frame represents nature and people in a more interdependent relationship, with both benefiting from sustainable management. The PBA frame holds both of these perspectives. In all frames, ‘science’ is represented as the basis of knowledge, but that science is contradictory, as each frame has its own preferred science. The SNSL strongly frames the ‘other’ in negative, diminishing terms; this is evident to a much lesser extent in the FTUR frame; the PBA frame represents the other in essentially political terms. The visual images used to communicate the SNSL frame, and its consistent coherent advocacy of a simple message, compared to a more reactive and more complex FTUR frame, help explain the impact of the SNSL frame in the media representation and discourse about the future management of Victoria’s native forests
Access status: Open Access ,
A Thirst for Change: Can Irrigation Technologies Reach Nepal Poorest?
(2026) Raut, Manita
In this thesis, I ask a deceptively simple question: Who is able to irrigate, and on what terms, in a landscape shaped by agrarian inequality? Grounded in mixed-methods fieldwork, conducted between April 2023 and January 2024, in two wards of Shambhunath Municipality in Nepal's Madhesh plains, I approach groundwater irrigation not as a neutral technical input but as a socio-material field shaped by land relations, institutional practice, and everyday power. Drawing on political ecology, science and technology studies, I develop the concept of a bundled architecture of access to theorise irrigation as a layered achievement rather than a discrete act of "adoption". Combining a 401-household survey with prolonged ethnographic immersion, in-depth interviews, and visual methods, I show that irrigation unfolds through sequential thresholds. Secure land enables fixed infrastructure. Tubewells condition access to electric pumps as material devices. Electric pumping becomes affordable, stable, and institutionally recognised where enrolment in the electricity system, via a subsidised electric meter, is possible. Each layer presumes the previous . Multivariate analysis reveals that landholding scale is the strongest predictor of access to fixed groundwater infrastructure, particularly tubewells, yet land operates differently across technologies. For tubewells, land serves as both a gateway and a gradient. For electric pumps, infrastructural alignment and social position outweigh land size among landowners. Diesel pumps concentrate where electrification is absent, clustering among socially marginal households as a costly technology of coping rather than a step toward inclusion. Access accumulates rather than diffuses. I find that households cultivating small or insecure plots irrigate through borrowing, renting, and negotiation, assembling water through relations and labour rather than ownership. Women in migrant households increasingly manage electric pumps and fields in practice, while constrained by norms of asset control and institutional recognition. Irrigation support programmes intended to expand access are frequently reinterpreted and captured by locally powerful actors, concentrating infrastructure in areas where land, capital, and institutional visibility already exist. I reframe groundwater irrigation as a lived politics of access. What appears as non-adoption is often structural misalignment rather than individual reluctance. Technology does not travel freely. It settles along lines of property, recognition, and power, reproducing agrarian difference even as it promises transformation. By situating irrigation within everyday relations of land, labour, and recognition, this research points toward a different future for water governance. In an era of climatic uncertainty, the challenge is not only to extend infrastructure but to redesign the socio-technical systems through which groundwater becomes available. Equity will depend on whether irrigation can be organised as a shared livelihood foundation through tenure, electrification, and institutional recognition that accommodate mobility, informality, and collective use, rather than as a privilege secured through position.
Access status: Open Access ,
Governing through Recognition? Riverside Amis Resistance and the Politics of Recognition in Taiwan
(2026) Lin, Yu-Ting
This study examines how the politics of recognition function simultaneously as a mode of governance and a site of resistance in the land rights struggles of three urban Amis riverside communities in New Taipei City, Taiwan. Focusing on the Sanying, Cinemnemay, and Cirakesay communities, it argues that urban space constitutes a crucial site of decolonisation in which Indigenous peoples strive for cultural continuity, sovereign presence, and land justice, rather than the urbs nullius imagined by the settler-colonial state. Through critical analysis, the study reveals how the Taiwanese government, through mechanisms of urban development policy, land commodification, and cultural governance, has continually delimited Indigenous land rights, enabling the state to regulate, monopolize, and define Indigenous claims and subjectivities. The resistance of Amis riverside communities further demonstrates that urban Indigenous housing injustice cannot be reduced to the capitalist notion of individual affordability; instead, it is deeply intertwined with the colonial past, which continues to shape contemporary legal structures and state-produced knowledge of indigeneity, and plays out in market-driven spatial governance. The research draws on Foucault's concept of governmentality to examine how the state produces governable Indigenous subjects through material and discursive forms of governance. It also engages Butler's theory of subject formation to explain how urban Indigenous peoples, once positioned as undertaking 'illegal construction' and as unauthorized occupation, mobilize resistance to challenge dominant governance practices, reassert their subjectivity, and claim legitimacy as urban Indigenous tribes with rights to the city. By analysing land struggles across social movements, discursive challenges, cultural resurgence, and policy negotiations, the study shows how urban Amis communities contest and reconfigure state-led recognition. Their resistance reveals the dynamic and ambivalent nature of recognition politics: recognition operates both as an instrument of state governance and as a means of empowerment through which Indigenous peoples reclaim land rights in Taiwan's settler-state context. The study further argues that the involvement of civic groups enables transformative forms of recognition that challenge the state's unilateral power structures and governance practices, thereby creating conditions for substantive redistribution and social change. Taken together, the findings suggest that recognising Indigenous sovereignty, epistemologies, and relational connections to land is essential to unsettling the structures that sustain colonial domination and to opening possibilities for more just futures.
Access status: Open Access ,
Targeting Heparanase Through Multi-Modal Inhibitor Design and Ancestral Reconstruction
(2026) Kim, Hyunjin
Heparanase (HPSE) is the only known mammalian enzyme that catalyses the degradation of heparan sulfate (HS), a major component of the extracellular matrix and represents a validated therapeutic target in oncology and inflammatory disease. Despite its clinical significance, the development of selective inhibitors has been hindered by three factors. Firstly, glycosidase families have demonstrated a high degree of structural conservation, particularly within their catalytic sites. Secondly, HS mimetics have been shown to possess inherent off-target anticoagulant toxicities. Thirdly, there have been challenges in producing stable, native-like recombinant enzymes for mechanistic characterisation. This thesis addresses these challenges through four distinct but complementary research chapters. Firstly, we introduced a computational-to-experimental pipeline for allosteric peptide inhibitor discovery (see Chapter 2). We identified Peptide 5 as a blueprint for a next-generation inhibitor that functions through a reversible covalent bond at the non-catalytic Cys179 exosite on HPSE, inducing conformational changes that inactivate the enzyme's catalytic activity. In parallel, the characterisation of tyrosine-containing library variants demonstrated that mimicking HS electrostatics through post-synthetic tyrosine sulfation affects potency of binding to HPSE. These findings demonstrate that computational peptide binder design targeting HPSE requires the integration of reactive chemical features, specifically cysteine-targeting moieties or electrostatic mimicry, to achieve biochemical activity. Addressing the well-known limitation of recombinant protein production, the methodology of ancestral sequence reconstruction (ASR) was applied to generate a human-primate-node HPSE ancestor (see Chapter 3). Unlike the previously designed P6 HPSE variant, solubilised through artificial surface change modification, the ASR variant produces robust, chaperone-free solubility while preserving the native electrostatic topology with higher sequence similarity compared to wild-type (WT) HPSE. Biophysical characterisation confirms this structural integrity, revealing a canonical a-helical TIM-barrel fold with a robust melting point (Tm) of 61.49 oC. This establishes a structurally similar, physiologically relevant platform for HPSE structural biology and inhibitor discovery. In Chapter 4, we expanded the design scope to miniprotein scaffolds with the aim of developing novel miniprotein inhibitors of HPSE. To achieve this, we conducted a comparative analysis of two deep learning architectures, namely BindCraft and RFdiffusion, that were targeted towards heparin-binding domains (HBDs), which are critical for substrate recognition. One of the candidates neutralised the electropositive HBD surface potential, excluding extended HS chains through electrostatic remodelling rather than direct active-site obstruction. Finally, we employed fragment-based drug design (Chapter 5) to explore novel chemical space, identifying novel small-molecule scaffolds that inhibit HPSE in the micromolar range. Overall, this thesis advances the knowledge of HPSE inhibition by providing a validated solution to the challenges of recombinant expression and establishing a broad spectrum of inhibitory modalities, ranging from covalent allostery to electrostatic neutralisation, that offers a blueprint for next-generation HPSE therapeutics.
Access status: Open Access ,
Patterns and Limits of Phenotypic Plasticity in Guppies Across Ecological Contexts
(2026) De Moura Campos, Diego
Phenotypic plasticity is an important adaptation for organisms that live under fluctuating environmental conditions. It can create trait variability, broaden the adaptive surface of organisms, and help population persistence. However, investment in phenotypic plasticity may require complex molecular and physiological demands, potentially leading to trade-offs. Under sexual selection, different strategies can lead to the same fitness outcomes, allowing for the diversification of phenotypic plasticity. However, cue reliability and developmental constraints may limit the evolution of specific periods that traits be plastic. Plasticity during early development allow traits to be more flexible, however it can also create mismatches between adult phenotype if environmental conditions change. While plasticity can be exhibited at different life stages, the extent to which animals rely more on plasticity before or after maturity is unknown. For my PhD, I used a series of laboratory experiments to test how different environmental conditions affect phenotypic plasticity in guppies (Poecilia reticulata), a species under strong sexual selection. For chapters 1 and 2, I explore the effects of early-life food restriction on guppy life-history traits under two temperatures. I found that guppies are able to maintain a compensatory growth response after diet restriction even under high temperatures. However, patterns of size and time at maturation were sex specific. My results also showed that the combined effect of high temperature and diet restriction early in life stunted male size, persisting up to eight months after treatment exposure. In chapter 3, I conducted an experiment focusing on the effects of social competition on developmental and sexual traits. I found that developing in a population of higher quality males did not affect either developmental or sexual traits in male guppies. Highlighting that socially cued anticipatory plasticity may not be adaptive for guppies. Finally, in chapter 4 I explored the behavioural plasticity responses of adult guppies to an immune challenge. Specifically, I focused on how an immune challenge affect the expression of behaviours that aid in the avoidance of predation. I found that an immune challenge did not affect anti-predatory responses, however fish showed pronounced sexual differences in behaviour. Taken altogether, my results show that environmental conditions during guppy development affect a limited group of traits, highlighting a possible resilience of guppies to maintain traits at an optimum level. Although the overall phenotypic response appears restricted, the functional significance of the affected traits indicates that developmental conditions can still have meaningful impacts on individual fitness and population dynamics.
Access status: Open Access ,
How ecological features of a virtual environment shape neuronal activity in the mouse visual processing system
(2026) Owensby, Lachlan
Animals must continuously parse rich sensory streams and translate them into behaviour that is adaptive to the current context. This thesis examines how ecologically meaningful visual information and self-initiated behaviour are represented in the mouse brain during interaction with a head-fixed virtual reality (VR) environment. I developed a VR corridor paradigm that preserves experimental control while enabling naturalistic behaviours such as locomotion, exploration, approach to a reward port, and spontaneous licking, so that sensory processing and behavioural dynamics could be quantified alongside neuronal population activity. In Chapter 1, I present an overview of the literature relating to the visual processing system, and how VR can be used to study these processes within a context more ecological than found in traditional lab experiments. Chapter 2 articulates the aims of the project, namely the development of a paradigm utilizing VR which enables investigation of behaviour and visual processes of ecological relevance. Chapter 3 documents iterative optimization of three training protocols. Pilot data obtained during development of the protocols confirmed robust engagement with the reward zone across protocols but revealed limited use of visual trial cues for discrimination, motivating a shift in emphasis from decision performance to sensory processing and neural representation. Chapter 4 details the final experimental design and recording procedures. Mice controlled position on a treadmill while navigating a VR corridor divided into stimulus and reward areas (S+ vs. S- trials defined by wall gratings). Behavioural variables (position, velocity, licking) and extracellular neuronal activity were recorded simultaneously, primarily in V1 with additional subcortical sites. I describe data acquisition, spike sorting, and two complementary activity representations: occupancy-adjusted activity for position-locked analyses and conventional firing-rate metrics for modelling. Chapter 5 shows that mice adopted ecologically interpretable strategies: licking concentrated in the reward zone over sessions, with idiosyncratic differences across animals; locomotion exhibited a robust bimodal velocity distribution reflecting alternation between stationary and running states; and time investment differed across task zones and individuals. Signal Detection Theory analysis indicated decision performance hovered near chance, consistent with weak reliance on the visual trial cue for guiding reward-seeking behaviour. Chapter 6 demonstrates that individual neurons exhibited distinct activation patterns related to spatial position and task area, and that population activity displayed coordinated structure across cortical depth. Occupancy-adjusted maps revealed neurons and populations with preferential firing at specific positions or zones, providing a substrate for spatial encoding during active exploration. Chapter 7 evaluates population representations using dimensionality-reduction and supervised approaches. Unsupervised methods (PCA, t-SNE, UMAP) produced embeddings largely dominated by temporal proximity, with limited structure aligned to task variables. CEBRA-Time captured smooth temporal organization and enabled accurate decoding of time, whereas CEBRA-Behaviour captured dynamics related to locomotion, but otherwise provided limited separation for task labels beyond time. Regularized regression (Lasso, Ridge) predicted task/behavioural variables at near-chance levels when temporal correlations were controlled via trial-wise splits, suggesting weak decodability of these variables from recorded visual populations under the present conditions. Chapter 8 provides a general discussion, arguing that VR provides a powerful compromise between ecological relevance and experimental control for studying sensory processing.
Access status: Open Access ,
Robust Model Predictive Control for Quantum Systems
(2026) Lee, Yun-Yan
The application of Model Predictive Control (MPC) to quantum systems faces fundamental challenges arising from measurement-induced disturbances and the probabilistic nature of quantum dynamics. Unlike classical nonlinear systems, quantum measurements inherently disturb the system state, making feedback control intrinsically model-dependent and stochastic. Within the framework of Positive Operator-Valued Measures (POVMs), this thesis focuses on strong quantum measurements, where each observation induces a complete state collapse on the system. When uncertainty is introduced, the measurement process itself becomes a dominant source of disturbance. To address this, a lower bound on the measurement uncertainty is imposed, quantified as the predicted deviation between the measured quantum state and the nominal MPC trajectory, ensuring that the quantum state can be steered along the designed MPC trajectory while maintaining physical realizability and stability. The thesis further develops a stochastic MPC (SMPC) formulation based on quantum filtering equations, describing the conditional evolution of quantum states under continuous observation. A theoretical equivalence between the proposed SMPC scheme and an optimal control problem is established, providing a tractable computational approach for feedback design in quantum stochastic systems. Finally, to address the limitations imposed by explicit identification of quantum systems in complex quantum systems, a data-driven MPC framework is introduced. Using locally observable dynamics and trajectory data, a data-driven MPC formulation is introduced to realize predictive quantum control without explicit system identification. This framework lays the foundation for measurement-aware and physically consistent quantum MPC.
Access status: Open Access ,
Charge modulation for efficient CO2 capture and reduction reactions: an integrated ab-initio and numerical methods approach
(2026) Mahmoudi, Mohsen
The growing urgency to address environmental challenges, such as air pollution and greenhouse gas (GHG) emissions, has made gas-adsorbent materials (GAMs) a critical focus in materials science. GAMs are essential for advancing carbon capture and storage (CCS) technologies, where their ability to selectively adsorb and sequester carbon dioxide (CO2) prevents its release into the atmosphere. These materials are also used in gas sensors, air filtration, and other monitoring technologies, as well as in various industrial sectors where removing specific gases or impurities can improve safety, process efficiency, and product quality. In this regard, the pursuit of materials with enhanced durability, higher adsorption capacity, controllable gas molecule adsorption, and low energy requirements for regeneration, and also the use of techniques such as charge modulation of host materials to improve performance, are of great importance in research and development. This thesis employs density functional theory (DFT) to conduct a theoretical investigation of charge modulation, exploring both its computational and practical aspects. To this end, a virtual crystal approximation (VCA)-based method is proposed to maintain the plane-averaged electrostatic potential (PAEP) unperturbed in the vacuum region while charging the system. This method, designed to more accurately capture key energy-related parameters, such as shifts in the Fermi level under charge injection, offers improvements over standard techniques. In this model, surface host materials are charged by the atoms arranged at optimum positions around them, creating a quasi-two-dimensional (2D) jellium scenario. On the other hand, through a screening plan adopted in this thesis to identify truly high-performance charge-responsive adsorbents, we present the graphene-like 2D material beryllonitrene (BeN4) with a single-vacancy defect, created by removing one Be atom, as an effective candidate for CO2 capture across different charge states. It is demonstrated how the defected BeN4 responds to the introduced electrons in a highly controllable manner and how strain engineering, acting synergistically, contributes to enhancing the gas separation performance. Nickel diazenide (NiN2), a novel 2D hybrid layer with a pentagonal atomic arrangement, is another material we investigate, focusing on charge modulation through direct charge injection and ion-induced mechanisms. NiN2 undergoes a transition from metallic bulk to a direct band-gap semiconductor, exhibiting high carrier mobility and abundant nitrogen active sites in both monolayer and bilayer forms; however, its CO2 adsorption performance under charge modulation falls short of the threshold required for superior energy efficiency and practical competitiveness. Still, the bilayer, benefiting from zero-gap character and graphite-like mechanical robustness, demonstrates strong potential as a fast, high-capacity anode material for efficient lithium-ion intercalation within the van der Waals (vdW) interlayer space.
Access status: Open Access ,
The experience of middle-class women during and after caesarean deliveries: Bangladesh context
(2026) Khanam, Maksuda
Drawing on twelve months of ethnographic fieldwork in Dhaka, Bangladesh, this thesis examines how biomedical authority shapes childbirth experiences among middle-class women. Caesarean delivery rates among urban, educated women reached 44% by 2022 despite limited medical necessity. Based on interviews with 30 women, 14 medical professionals, 5 pharmacy staff, and 3 government officials, along with participant observation at Square Hospital and Dhaka Medical College Hospital (DMCH), I show how women's seemingly autonomous choices are systematically channelled toward caesarean births. I develop the concept of the 'techno-normal' birth to describe how women redefine natural childbirth to include extensive technological interventions while still considering such deliveries normal. This reflects how middle-class identity is tied to private hospital births as symbols of modernity. Yet the very methods women pursue to secure vaginal birth through routine monitoring, labour induction with Pitocin, and epidurals- paradoxically elevate the likelihood of caesarean delivery. This paradox stems from profound support deficits during pregnancy, where the biomedical system dismisses women's embodied experiences through standardised responses and prioritises technological assessments over lived realities. The erosion of intergenerational knowledge further leaves women unprepared for labour, which they consequently interpret as pathological pain requiring intervention rather than physiological discomfort. Within this context, risk discourse functions as a powerful mechanism of control. Risks are constructed around a wide range of medical and social factors, such as breech presentation, low amniotic fluid, previous miscarriage or even holiday scheduling- all strategically deployed to justify surgical intervention. Many of the women during the interview reported encountering obstetric violence, including denial of information, punitive anaesthesia practices, dissipation of pain and newborns requiring intensive care unit admission despite surgical birth. Some of the women even experience lasting disabilities from anaesthesia complications, acknowledged yet minimised by clinicians as acceptable costs of motherhood. This thesis argues that while middle-class economic privilege grants access to biomedical care, it does not safeguard women from institutional violence or ensure better outcomes. Transforming this landscape requires three interconnected shifts, such as expanding doula services with state support; extending government oversight to monitor non-essential interventions and enforce accountability; and recognising home birth as safe for low-risk pregnancies by integrating midwives and traditional birth attendants into formal health care. Only such systematic change can create birth environments that genuinely respect women's autonomy and well-being beyond the profit-driven medicalisation that currently defines obstetric care in Bangladesh.
Access status: Open Access ,
New Methods to Improve Phylogenomic Inference
(2026) Ivan, Jeremias
A complete set of DNA - known as a genome - provides a powerful resource for inferring evolutionary relationships among species, which are often represented as a bifurcating (phylogenetic) tree. However, it is increasingly appreciated that a single tree is insufficient to capture the full evolutionary history of a study system due to processes such as incomplete lineage sorting (ILS), hybridisation, introgression, and recombination that could create a mosaic of histories along the genomes. Estimation of this variation of local histories - often referred to as gene tree discordance - thus depends on the accuracy of the sequence data and the robustness of the inference methods being used. In Chapter I, I assessed the non-overlapping window method that is commonly-used to address gene tree discordance from a set of aligned genomes, but often with an arbitrary selection of fixed window size. Using simulated chromosomes with different degrees of recombination and ILS, I showed that the Akaike Information Criterion (AIC) provides a less arbitrary approach to select the best window size given the alignment. I then applied this approach to empirical datasets from Heliconius butterflies and great apes, and showed that the best window sizes for these groups range from 125-250bp (for Heliconius butterflies) and 500-1,000bp (for great apes) across chromosomes. In Chapter II, I extended the information-theory-based approach proposed in Chapter I to accommodate variable window sizes, because the size of non-recombining blocks could vary along the chromosomes. To do this, I developed an iterative splitting-and-merging approach that evaluates local improvements in AIC. I showed that using variable window sizes has consistently better accuracy than using fixed window sizes in recovering the 'true' topologies from simulated alignments, with at least 80% accuracy across simulations. I then applied this approach on empirical datasets from Heliconius butterflies and great apes, and further showed that the best window sizes varied substantially across chromosomes. In Chapter III, I leveraged the availability of multiple reference genomes and proposed a phylogenetic method to detect reference bias at individual loci, assuming that in the absence of reference bias, reconstructed sequences of a single locus from the same sample should be identical regardless of the reference being used. Across empirical datasets of nine Eucalyptus species, I found that more than one-quarter of the reconstructed BUSCO loci showed strong evidence of reference bias, which consequently affected the species tree inference. Excluding these putatively biased loci, coupled with using a closely-related reference genome during mapping, resulted in species tree topologies that were more consistent with the published tree. In Chapter IV, I assessed the role of phylogenetic distance as a barrier to introgression in Eucalyptus globulus. To do this, I estimated the proportion of introgression between E. globulus and 56 other Eucalypts using QuIBL (Quantifying Introgression via Branch Lengths). Based on ~1,000 BUSCO loci, I found significant correlations between the proportion of historical introgression, present-day crossability, and pairwise phylogenetic distance, which suggested that the accumulation of genetic changes over evolutionary time has played a central role in shaping hybridisation and introgression patterns of the group. Overall, these chapters highlight two key challenges in phylogenomic analyses: inferring gene trees and assessing reference bias. In response, I proposed two phylogenetic methods and presented one case study that together provide a useful framework for future phylogenomic inference.

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