Faculty of Science 2

Outstanding Doctoral Thesis Award

ZEBARDASTAN, Negar

Thesis Title

Van der Waals Epitaxy of Transition Metal Dichalcogenides on Graphene

Supervisors

• Professor Jennifer May MacLeod  (Associate Supervisor)
• Professor Nunzio Motta  (Principal Supervisor)
• Professor Kostyantyn Ostrikov  (Associate Supervisor)

Citation

This research is a fundamental study of the direct epitaxial growth of MoS2 on diverse types of graphene substrates, including self-standing and graphene/SiC, using chemical vapour deposition (CVD). The size, quality, and growth rate of epitaxial graphene on SiC, subsequently used as a substrate for the formation of MoS2, is controlled with high precision using a novel face-to-face technique in ultra-high vacuum. The effect of growth parameters and substrate characteristics on the CVD growth of MoS2 are investigated to design an optimised viable approach for the growth of high-quality MoS2/Graphene heterostructures.

Doctor of Philosophy

ACEVEDO ZAMORA, Marco Andres

Thesis Title

Petrographic Microscopy of Geologic Textural Patterns and Element-Mineral Associations with Novel Image Analysis Methods

Supervisors

• Professor Balz Samuel Kamber  (Principal Supervisor)
• Associate Professor Christoph Schrank  (Associate Supervisor)

Citation

Polarised light microscopy of rock slices (thin sections) – petrography – remains a foundational tool in geoscience research. Surprisingly, the study of rock thin sections has largely remained an analogue task. This project aimed at translating modern image analysis from digital pathology and geographic information systems to petrography. The abundance of minerals and their optic-axis orientation was automated with newly developed software ‘pipelines’ and mineralogy algorithms. This included the recognition of minerals as objects within complex microscope images that were also combined with chemical maps of the thin sections. The proposed dimensionality reduction techniques revealed previously unrecognised features.

ALHAIDAR, Abdulrahman Haidar A

Thesis Title

Computational Exploration of Two-Dimensional Materials for Photocatalytic Water Splitting

Supervisors

• Professor Aijun Du  (Principal Supervisor)
• Associate Professor Liangzhi Kou  (Associate Supervisor)
• Professor Ting Liao  (Associate Supervisor)

Citation

Two-dimensional (2D) materials have outstanding electronic and physical properties, both in theory and practice, which make them suitable for hydrogen production using water splitting. The exploration of new 2D materials that have excellent visible-light absorption and suitable band alignment is essential for efficient photostatic water splitting. In this work, we computationally studied structural properties, edge positions of the conduction band minimum (CBM) and the valence band maximum (VBM), and electronic, and optical properties for unexplored 2D materials using density functional theory (DFT).

BARBHUIYA, Tabassum Khair

Thesis Title

Development of Novel Strategies to Modulate the Activity of Integrator Complex Subunit 3 (INTS3) and Polo-Like Kinase 1 (PLK1)

Supervisors

• Dr Mark Nathaniel Adams  (Associate Supervisor)
• Adjunct Professor Neha Gandhi  (Principal Supervisor)
• Professor Derek John Richard  (Associate Supervisor)

Citation

The mammalian DNA damage occurs via several exogenous and endogenous agents. These damages, if not repaired, contribute to genomic instability, which is a hallmark of cancer. In response to such damaging events cells are facilitated with damage response mechanisms involving DNA repair events, and cell cycle progression, working in highly coordinated fashion. This research focuses on structural investigation of three protein-protein interaction complexes participating in DNA damage repair and cell cycle pathway: INTS3-hSSB1, PLK1-CDCA3 and CDCA3-Cdh1. It further involves disruption of interaction between these protein partners using small molecule and peptides with strategic focus on anticancer therapeutics discovery.

BOTHA, Imke

Thesis Title

Adaptive Bayesian Algorithms for Complex State Space and Mathematical Models

Supervisors

• Professor Christopher Colin Drovandi  (Principal Supervisor)
• Dr Robert Kohn  (External Supervisor)
• Dr Leah Frances South  (Associate Supervisor)

Citation

Calibrating statistical models to data can be a challenging task, particularly when the model is difficult or time consuming to evaluate. Methods that infer the parameters of these models often require significant practitioner effort and/or computational resources to run, or make simplifying assumptions about the model. This thesis develops novel parameter inference methods that address each of these issues. The new methods require minimal practitioner input, are faster to run, and can be applied in more general settings.

BUCHHORN, Katie Louise

Thesis Title

Bayesian Design for Sampling Anomalous Data on River Networks

Supervisors

• Professor James Matthew McGree  (Principal Supervisor)
• Distinguished Professor Kerrie Lee Mengersen  (Associate Supervisor)
• Dr Edgar Santos Fernandez  (Associate Supervisor)
• Associate Professor Paul Pao‑Yen Wu  (Associate Supervisor)

Citation

Data is fundamental to good decision making, but data collection is often costly and difficult. Efficient designs for collecting high-quality, relevant data are therefore essential. This research advances Bayesian methods for experimental design and machine learning methods for anomaly detection, applying these advancements to the monitoring of river networks. This helps in understanding ecosystems and promoting sustainable management. The methods handle complex dependencies and high-dimensional data and are widely applicable to other challenges in environment, health, business, and society.

DAVIES, Laurence

Thesis Title

Contributions to Bayesian Transdimensional Algorithms

Supervisors

• Professor Christopher Colin Drovandi  (Principal Supervisor)
• Dr Alan Ley-Cooper  (External Supervisor)
• Dr Matthew Sutton  (Associate Supervisor)
• Dr Gentry White  (Associate Supervisor)

Citation

When conducting statistical data analyses, often multiple competing mathematical models are proposed. Assigning a weight to each model depending on how well they fit the data is a computationally challenging problem, especially when the mathematical models being considered are complex. This thesis develops novel statistical algorithms for addressing this model selection problem that are more computationally efficient and automated compared to previous approaches. A motivating example in the geosciences is presented, and subsequently, the novel algorithms demonstrated on challenging new examples and canonical examples from existing literature.

DONALD, Rickey John

Thesis Title

The Synergies of Integrating Renewable Electrolytic Hydrogen Production and Wastewater Treatment

Supervisors

• Dr Fanny Anne Boulaire  (External Supervisor)
• Dr Robert Laurence Burdett  (Associate Supervisor)
• Associate Professor Jonathan Gerald Love  (Principal Supervisor)
• Professor Graeme John Millar  (Mentoring Supervisor)

Citation

Renewable hydrogen can reduce carbon emissions in hard-to-electrify industries, but its production is currently expensive and restricted by present-day infrastructure. This research project demonstrates how existing wastewater treatment plants can be leveraged to build a new industry that integrates renewable hydrogen production with wastewater treatment for net zero emissions. Co-locating renewable hydrogen production at existing wastewater treatment plants derives synergies from sharing oxygen and water streams. In this project, a new mass and energy simulation model of the integrated plant was developed. Outcomes from the model demonstrated the environmental and economic benefits and analysed control strategies and their sensitivities.

DOOHAN, Brendan Thomas

Thesis Title

Acoustic Signalling and Subspecies Divergence in Two Australasian Treecreepers (Climacteridae)

Supervisors

• Professor Susan Jayne Fuller  (Principal Supervisor)
• Associate Professor David Alan Hurwood  (Associate Supervisor)
• Professor Paul Roe  (Associate Supervisor)

Citation

Australasian treecreepers have diversified into most woodland habitats throughout Australia, yet little is known about the mechanisms behind this diversification at the intra-species level. This thesis explored the morphometrics, systematics, acoustics, and behaviour of two treecreeper species (Climacteris picumnus and Cormobates leucophaea) to identify the potential mechanisms leading to subspecies divergence. The results of the project identified that geographic isolation, not bird song, is responsible for subspecies divergence in both species. These results have provided a better understanding of the biology of C. picumnus and Co. leucophaea and provide valuable insight into the evolution of Australia’s woodland bird species.

DRAIDI, Wala Mohammad Amin

Thesis Title

Integrating Machine Learning and Bayesian Statistics in Spatial Small Area Analysis: Methods and Application

Supervisors

• Mr Reid Malseed  (External Supervisor)
• Distinguished Professor Kerrie Lee Mengersen  (Principal Supervisor)
• Dr Aiden Kristopher Price  (Associate Supervisor)
• Associate Professor Mery Helena Thompson  (Associate Supervisor)

Citation

Machine learning and Bayesian statistical analysis are effective tools for extracting insights from data. In this thesis, these methods are applied and extended to identify geographic and socio-demographic patterns in spatial data. A case study focuses on the analysis of developmental vulnerabilities in children in Australia, with particular attention on the impact of preschool attendance. The findings are communicated through an interactive digital dashboard. This research contributes to enhancing spatial data analysis for children’s health data, informs educators, facilitates more targeted interventions, and supports public health decision-making.

FORBES, Owen Paul

Thesis Title

Statistical Machine Learning Methods for Neuroscientific Data: Analysing Brain Activity, Psychopathology and Cognitive Function in Adolescents

Supervisors

• Distinguished Professor Kerrie Lee Mengersen  (Principal Supervisor)
• Dr Edgar Santos Fernandez  (Associate Supervisor)
• Associate Professor Paul Pao‑Yen Wu  (Associate Supervisor)

Citation

This thesis aims to advance the use of neuroscience data to improve understanding of youth mental health. The research focused on development of advanced statistical machine learning methods to analyse neuroscience data, with a particular emphasis on electroencephalography (EEG). Innovations include a unique EEG phenotyping method, a Bayesian model averaging framework for clustering, and a nested functional analysis framework for EEG activity. These advancements deepen our understanding of the relationships between brain activity, cognition and mental health in young people, and lay the groundwork for more personalised approaches in mental health care and early risk detection.

GAUCI, Steven Charles

Thesis Title

Printing Dynamic Materials via 3D Laser Lithography

Supervisors

• Distinguished Professor Christopher Winfried Barner‑Kowollik  (Principal Supervisor)
• Associate Professor James Peter Blinco  (Associate Supervisor)
• Dr Bryan Tuten  (Associate Supervisor)

Citation

Light-driven 3D printing merges precision-controlled chemical reactions with intricate fabrication. Central to 3D printing are photoresists, which are light-sensitive materials that can undergo a distinct transforming under specific wavelengths. The advancement of light-driven 3D printing involves imparting adaptable behaviour to printed structures, critical for erasing them post-printing. This erasing capability, achieved through judiciously designed photoresists with labile linkages, facilitates the removal of support materials, and for the degradation of cellular scaffolds. The presented work focuses on developing photoresists for 3D light-driven applications – utilising light-stabilised dynamic materials – to fabricate degradable structures, showcasing a significant stride in this evolving technology.

HUET, Olivier Dominique Y

Thesis Title

Development of Improved Mathematical Models for Droplet Impaction on Plant Leaf Surfaces

Supervisors

• Professor Scott William McCue  (Principal Supervisor)
• Professor Timothy John Moroney  (Associate Supervisor)
• Dr Ravindra Pethiyagoda  (Associate Supervisor)

Citation

While agrichemical spraying aims to protect crops and help produce more food, the chemicals can harm the environment. This doctorate studies how tiny spray droplets behave when they hit the plant surfaces.  In particular, this research aims to investigate how adding surfactants to the spray formulation can enhance the retention of sprayed products on the plants themselves. The methodology includes a combination of careful experimental work and detailed computational modelling and high-performance computing. Better retention not only mitigates the environmental impact but also reduces costs for farmers and saves water.

HUETTNER, Nick

Thesis Title

Investigations into the Macrocyclization of Poly(2-oxazoline)s and Poly(2-oxazine)s

Supervisors

• Professor Timothy Dargaville  (Principal Supervisor)
• Associate Professor Hendrik Clemens Wolfgang Frisch  (Associate Supervisor)
• Dr Anja Sabrina Goldmann  (External Supervisor)
• Dr Kristian Kempe  (External Supervisor)

Citation

This thesis takes a step towards the efficient synthesis of cyclic polymers, which have recently gained significant attention as potent materials in biomedical applications. Using biomedically-relevant poly(2-oxazoline)s and poly(2-oxazine)s, a combination of synthetic and computational approaches identified the importance of the so far overlooked polymer structure on the cyclisation reaction. Additionally, it was shown that control over oligomer formation during cyclisation can be a valuable tool to adjust material properties of biomedically-relevant hydrogel systems, highlighting the applicability of not only pure cyclic polymers but also cyclic/oligomer mixtures.

IZUAGBE, Aidan Essie

Thesis Title

Development of Photoresponsive Metal Based Single-Chain Nanoparticles

Supervisors

• Distinguished Professor Christopher Winfried Barner‑Kowollik  (Principal Supervisor)
• Dr Bryan Tuten  (Associate Supervisor)

Citation

A precise interplay exists between the macromolecular scaffold and catalytically active metal centres within enzymes, resulting in nature's ultimate catalysts. Although replicating the precision of enzymes in the laboratory is challenging, the quest for enzyme-like catalysis has led to catalytic —often metal-based — single-chain nanoparticles (SCNPs). SCNPs can be enhanced with functionalities not found within enzymes, critically, photoresponsivity. The current thesis focuses on incorporating photoswitches into the scaffold of metal-containing SCNPs. Here, photo-induced isomerisation leads to distinct morphological changes, affecting access to the metal centres that act as either catalytic or structure-forming elements within SCNPs.

JAMES, Tess Alexandra

Thesis Title

Factors Affecting Transgene Expression in Arabidopsis thaliana

Supervisors

• Distinguished Professor James Langham Dale  (Associate Supervisor)
• Dr Benjamin Dugdale  (Principal Supervisor)
• Professor Robert Maxwell Harding  (Mentoring Supervisor)

Citation

This thesis investigated the optimisation of plant transgene sequences as an approach to maximise accumulation of the gene product and reduce the occurrence of sequence-specific gene silencing. An ‘endogene-like’ construct design was evaluated in model plant Arabidopsis thaliana with the goal of maintaining stable, high-level gene expression over multiple generations. Many agricultural and research applications of plant genetic modification require transgene expression to be consistently high and stable over multiple generations, but endogenous RNA silencing in plants can counteract this by suppressing expression of the transgene. Recommendations were made for improving plant transgene expression levels and stability through construct design.

KOOHI, Maedeh

Thesis Title

Development of Nanoformulations for the Enhanced Delivery of Target Drugs

Supervisors

• Associate Professor Peter John Cabot  (External Supervisor)
• Associate Professor Mohd Nazrul Islam  (Associate Supervisor)
• Associate Professor Emad Kiriakous  (Principal Supervisor)

Citation

This work provides nanoformulations of some potential anticancer drugs that could improve drug delivery into prostate cancer cells. For this purpose, two types of nanoparticles (mesoporous silica nanoparticles) were produced, and the potential anticancer drugs were encapsulated into the nanoparticles. After investigating and examining the prepared nanoformulations in the laboratory, the best potential anticancer formulation was found.

LEWIS, Brett Maxwell

Thesis Title

Substrate Attachment in Colonial Scleractinia

Supervisors

• Dr Luke David Nothdurft  (Principal Supervisor)
• Professor Peter James Prentis  (Associate Supervisor)
• David John Suggett  (External Supervisor)

Citation

This thesis investigates the complexities of asexual reproduction and substrate attachment in modern reef-building coral (Scleractinia). Chapter 1 employs innovative imaging techniques, including 3D volume microscopy (PFIB), to explore coral cell ultrastructure, immune response, and tissue behaviours crucial for attachment. In Chapter 2, the study defines when attachment achieves mechanical self-sustainability against external forces. It unveils species-specific attachment resistance thresholds, providing timelines for self-attachment and enhancing fragmentation-based reef restoration methods. Chapter 3 employs cutting-edge microscopy to enhance the understanding of the newly discovered lappet-like appendage, emphasizing its evolutionary importance in the emergence of asexual reproduction and modern reef-building coral.

LI, Fang

Thesis Title

An Investigation into the Diagnosis and Pathogenesis of Equine Pituitary Pars Intermedia Dysfunction

Supervisors

• Dr Patricia Anne Harris  (External Supervisor)
• Professor Martin Nicholas Sillence  (Principal Supervisor)
• Associate Professor Melody Anne de Laat  (Associate Supervisor)

Citation

The thesis investigates a degenerative disease called PPID that affects older horses. Currently, the diagnosis of PPID relies on measuring a hormone known as ACTH, but this method may not be reliable. The study aimed to better understand PPID, and to identify other blood markers that could be used to develop a better diagnostic test. The research has uncovered new information about ACTH, dopamine and insulin in horses, and the commercialisation of a new test is now being explored.

NDUKWE, Audrey Raluchukwu Nwanneka

Thesis Title

Design, Synthesis and Testing of Oxazolidinone Antimicrobials That Target Biofilms

Supervisors

• Dr Nathan Boase  (Associate Supervisor)
• Professor Kathryn Fairfull‑Smith  (Principal Supervisor)
• Neha Gandhi  (External Supervisor)
• Associate Professor Makrina Totsika  (Associate Supervisor)

Citation

Antibiotics are the treatment of choice for bacterial infections, but their loss of effectiveness presents a global public health issue. The threat from antimicrobial resistance not only lies in single-celled bacteria but in communities of bacteria that aggregate and form biofilms. Antibiotic development has primarily focused on single-celled bacteria with limited consideration of the role of biofilms on disease progression. Bacteria in biofilms are up to 1000 times more resistant to antibiotics than their single-celled counterparts causing relapsing infections that are challenging to treat. This thesis investigates strategies to develop the oxazolidinone antibiotic class as biofilm eradication agents using nitroxides.

SCHUURS, Zachariah Pieter

Thesis Title

Molecular Recognition of Anion Binding Proteins: Characterization and Inhibition

Supervisors

• Dr Laura Vanda Croft  (Associate Supervisor)
• Adjunct Professor Neha Gandhi  (Principal Supervisor)
• Professor Derek John Richard  (Associate Supervisor)

Citation

Anionic molecules play essential roles in our biology, controlled by a complex system of proteins that when something goes wrong, critical health problems can arise. This thesis combined computational tools and laboratory-based assays to investigate how some of these proteins recognise molecules and attempt to find small molecules that could help address these health problems. The three publications each study a different protein – LexA, which helps bacteria develop antibiotic resistance; human single-stranded binding protein 1, implicated in cancer; and the SARS-CoV-2 spike protein, studying how it infects cells.

SISLEY, Harry Michael

Thesis Title

Large-Scale Multi-Product Multi-Region Supply Chain Optimisation for Fresh Seasonal Crops under Crop Rotation

Supervisors

• Associate Professor Paul Gerard Corry  (Principal Supervisor)
• Dr Guvenc Dik  (Associate Supervisor)
• Professor James Matthew McGree  (Associate Supervisor)

Citation

This project applied operations research techniques to the production planning of an agricultural supply chain in Australia. The supply chain dealt with fresh seasonal crops with strict crop rotation requirements. This necessitated shifting production up and down the country to ensure demand could be satisfied year-round. The models could produce optimal production plans at the daily level for up to fifteen months into the future.

SOBENKO HATUM, Paula

Thesis Title

Dynamic Bayesian Networks for Predicting Marine Ecosystem Resilience to Extreme Climate Events - a Seagrass Study

Supervisors

• Kathryn Mcmahon  (External Supervisor)
• Distinguished Professor Kerrie Lee Mengersen  (Associate Supervisor)
• Associate Professor Paul Pao‑Yen Wu  (Principal Supervisor)

Citation

This research underscores the critical role of seagrass as a primary producer, essential for biodiversity and vulnerable to climate change, particularly due to increased marine heatwaves. Utilising a Dynamic Bayesian Network (DBN) approach, this study models the dynamic processes affecting seagrass meadows and provides a framework for adapting DBNs to diverse ecological settings, enhancing model reuse. Key contributions include a Monte Carlo method for integrating climate projections with DBNs to predict long-term seagrass health. The studies culminate in a toolset that facilitates effective visualisation, analysis, and management of seagrass ecosystem resilience under varying climate scenarios, advancing ecological modelling and management.

UTAMI, Ni Wayan Febriana

Thesis Title

Optimal Tree Species to Stabilise Slopes at Baroon Pocket Dam Catchment, Maleny, South East Queensland

Supervisors

• Professor Jennifer Firn  (Principal Supervisor)
• Associate Professor Jessica Trofimovs  (Associate Supervisor)

Citation

Baroon Pocket Dam Catchment in Queensland, Australia, is a high-risk area for landslides because of its steep slopes and history of forest clearing for agriculture. This research aimed to understand the growth of different tree species above and below ground in three identified landslide active zones: ranging from high to low. Araucaria spp. after 8 years of growth successfully stabilised a previously high-risk unstable slope. Seedlings of Eucalyptus and Araucaria spp. were also able to survive high movement plots even in very high rainfall years. Future research should investigate the cost-effectiveness of more diverse tree plantations and different tree spacing regimes.

WHEBELL, Riley Mark

Thesis Title

Mathematical Modelling of Droplets on Plant Leaf Surfaces

Supervisors

• Professor Scott William McCue  (Associate Supervisor)
• Professor Timothy John Moroney  (Principal Supervisor)
• Dr Ravindra Pethiyagoda  (External Supervisor)
• Professor Ian William Turner  (Associate Supervisor)

Citation

This project saw the development of new techniques for mathematical modelling of sprayed droplet retention on plant crops, using virtual reconstructions of real plants and a novel particle-based droplet model. By synthesising leaf data scanned at multiple length scales, the surface reconstruction approach builds realistic leaf surfaces upon which the droplet model is applied to simulate realistic wetting phenomena. The flexible scattered data interpolation methods for surface reconstruction handle large, noisy datasets robustly. The droplet model employs pairwise forces between particles to mimic cohesion and adhesion, which is found to quantitatively reproduce surface tension and wetting physics.

YIN, Hanqing

Thesis Title

Computational Exploration of Alloy- and Defect Engineering in Rational Design of Electrocatalysts

Supervisors

• Dr Stuart Bell  (Associate Supervisor)
• Professor Aijun Du  (Principal Supervisor)
• Distinguished Professor Dmitri Golberg  (Associate Supervisor)

Citation

This PhD program is a comprehensive exploration of utilising alloy- and defect engineering in rational catalyst design. Based on density functional theory (DFT) simulations, this study proposed several practical and economical electrocatalysts with excellent theoretical performance for dinitrogen reduction (N2RR), nitrate reduction (NO3RR) and hydrogen evolution (HER), etc. The outputs in this project can serve as novel strategies towards highly efficient electrocatalysis process and provide conceptual insights for engineering practice.