2019/20 summer research scholarship program · faculty of science, summer research scholarship,...

Faculty of Science, Summer Research Scholarship, Project List 2019/2020 Last updated 27 August 2019

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2019/20 Summer Research Scholarship Program Research Projects offered by Faculty of Science Schools

School of Agriculture and Food Sciences ...................................................................................... 2

School of Biological Sciences ......................................................................................................... 9

School of Chemistry and Molecular Biosciences ......................................................................... 20

School of Earth and Environmental Sciences .............................................................................. 47

School of Mathematics and Physics ............................................................................................ 49

School of Veterinary Science ....................................................................................................... 80

How to apply

The UQ Summer Research Scholarship Program is offered by a number of schools in the Faculty of Science during the summer vacation period (mid‐November to mid‐February). This document provides you with a list of available projects.

1) Browse the projects. You may select a school from the table of contents above to be taken directly to their listed research projects.

2) Contact a potential supervisor in the area of your interest, or the contact person listed, to discuss your interest to undertake their research project. Gain the research project supervisor’s tentative approval, and include this with your full UQ Summer Research Scholarship application.

3) Submit your application via StudentHub.


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School of Agriculture and Food Sciences

Supervisor Prof Melissa Fitzgerald Duration: 6 weeks

Contact Details:

Email ‐ [email protected]

Optimising a cooking method for a new variety of rice.

The Australian rice industry is about to release a new variety of soft‐cooking long grain rice. We have found that this rice needs to be tested with different ratios of water to find the best ratio of rice and water. The project will involve developing the cooking method, and validating this with sensory profiling and texture testing.

Number of student places available: 1

Expected outcomes:

Sensory profiling, rice quality testing, interaction with industry, and the importance of cooking methods on a food label.

Suitable for:.

Anyone with an interest in working with industry and a love of rice.

Other important details: Interested students must contact the supervisor/s, prior to submitting an application. Evidence of supervisor support is required to be uploaded as part of the application process.

Preferred if the student knows something about rice, but we are happy to provide rice knowledge.


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Supervisor A/Prof Brett Ferguson Duration: 8 weeks

Contact Details:

Email: [email protected] Phone: (07) 3346 9951 Office: John Hines Building (62), Room 212 St Lucia Campus

Functional characterisation of novel components involved in the development and control of legume nodules

Nitrogen fertiliser use in agriculture is inefficient, costly and can be environmentally damaging. Legume crops represent an economically and environmentally sound alternative, as their symbiotic relationship with nitrogen‐fixing soil bacteria enables them to thrive in the absence of nitrogen fertiliser. The bacteria (commonly referred to as rhizobia) are housed in specialised root organs, called nodules. Identifying critical components of legume nodulation is now needed to optimise the process and improve agriculture sustainability. This project aims to discover and functionally characterise novel molecular factors that act in the development and control of legume nodules. Findings will considerably enhance the current nodulation model and could help underpin strategies to reduce the reliance on nitrogen fertiliser use in agriculture.


Expected outcomes:

Findings are anticipated to advance our understanding of how various genes and signals function in the development and regulation of legume nodules. Successful outcomes could also help to generate future publications

Techniques will include growing and maintaining soybean plants and compatible Bradyrhizobium bacteria, and will incorporate additional methods that may include generating transgenic soybean ‘hairy roots’ using Agrobacterium rhizogenes, fixing and treating roots to detect GUS activity, bioinformatic analyses, primer design and quantitative RT‐PCR to confirm the regulation of candidate genes, etc.

Suitable for:.

Students interested in any of biotechnology, molecular biology, genetics and/or plant science.



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Supervisor Dr Nana Satake Duration: 6‐8 weeks

Contact Details:

Email – [email protected]

Building 83‐N103, St Lucia campus

Surface Free Fatty Acid analysis of microencapsulated oils

In the development of microencapsulated PUFA oils, some encapsulants are not as effective in encapsulating oils as expected. Residual oil on the microcapsule surface quickly oxidises and gives of rancid fishy smells and detrimental to the final product.

To determine the efficiency of the encapsulation processes, the residual surface free fat can therefore be assessed. Although this can be conducted by traditional lipid extraction methods, this can be laborious with variable in reproducibility of results.

The aim of the project is to develop and validate an analytical method, from sample preparation to analysis, to consistently determine and quantitate surface oil residues that enables assessment of the efficacy of the oil encapsulation processes.


Expected outcomes:

GCMS analytical assay method development, validation and sample analysis

Suitable for:. Basic background knowledge in analytical chemistry and an interest in gas chromatography analysis.


Evidence of completing a course in analytical chemistry will be favourable.


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Supervisor Prof Melissa Fitzgerald

Dr Dara Daygon

Duration: 8 weeks

Contact Details:


Quality evaluation of rice samples grown in Northern Australia

At present, Australian rice industry is only focused in the southern areas of New South Wales. As rice the demand for rice continuously increase, the industry plans on expanding on new areas in the tropical regions of Queensland and Northern Territories. It is our aim to aid these endeavours by testing out the quality of rice produced in the new growing sites.

This 8‐week project aims to analyse the physical, chemical and sensory properties of rice harvested in the dry season of 2019.


Expected outcomes:

The scholars will learn the international standards in rice quality analysis. They will gain knowledge and exposure to the specific types of rice favoured by different market niche. Finally, the results of this project would contribute to the development of the Australian Rice industry.

Students will be trained in the use of the following equipment: Rapid Visco Analyser (RVA), Differential Scanning Calorimetry (DSC), Spectrophotometer, Qualysense Grain sorter, High power liquid chromatography (HPLC), and grain processing machineries such as rice dehusker and polisher.

Suitable for:. Students with particular interest in cereal chemistry and for those who would like to gain skills and experience in food quality analysis and sensory evaluation.

Students with experience in basic laboratory skills (eg. pipetting, preparation of chemical solutions, etc.)



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Supervisor Prof Melissa Fitzgerald

Dr Dara Daygon

Duration: 8 weeks

Contact Details:


Optimisation of molecular markers for detecting adulteration and authenticity in commercial rice products.

Premium value of rice could vary significantly depending quality and origin. In recent events, there has been a growing instance of mislabelling misleading information in rice packaging by dishonest traders. There were also instances of adulteration, which is defined as a process by adding inferior rice to premium rice. It has been difficult to differentiate rice varieties based on visual observation only and thus, a more objective ways of accurately distinguishing between the varieties is essential. This project aims to develop single‐grain detection system using molecular biology tools to enable the detection of mixtures in commercial rices.


Expected outcomes:

Students will be trained on the use of molecular biology apparatus such as polymerase chain reaction (PCR), acrylamide gel electrophoresis, etc. Students will also learn about primer design and basic bioinformatics analysis tools and genome browsers. The results of this project would contribute to the development of the Australian Rice industry.

Suitable for:. Students with particular interest in molecular biology techniques.

Students with experience in basic molecular biology laboratory skills (eg. polymerase chain reaction gel electrophoresis, etc.)



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Supervisor Prof Susanne Schmidt Duration: 6 weeks

Contact Details:


Telephone – 07 3365 1050, 0408 707 984

Location – 62‐329, St Lucia Campus

Towards the circular economy: recycled phosphorus and how it is used by plants

Nutrient recycling will reduce environmental footprints and increase the efficiency of farming. International collaborations give us access to recycled phosphorus formulations with different chemical properties, including solubility. This project will test how plants can access these phosphorus sources, which will assist the design of next‐generation fertilisers.


Expected outcomes:

The scholar will

(i) design a multifactorial experiment, (ii) empirically test the growth of two crops (ancient land race, elite cultivar) with

different recycled phosphorus formulations in four week glasshouse experiment,

(iii) harvest the biomass and analyse the data statistically, (iv) interpret the findings and write a ‘short communication’ style manuscript.

Suitable for:. Plant science students with interest in nutrient stewardship


Commences at the end of Semester 2 to complete the glasshouse experiment before UQ closes for the Christmas break.


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Supervisor Dr Cristina Martinez Duration: 8 weeks

Contact Details:


Telephone – +61 7 336 52051

Release dynamics and crop recovery of Enhanced Efficiency Nitrogen Fertilisers (EEFs)

At present, fertilizer nitrogen use efficiency (NUE) in crop industries is typically low (only 20 – 40% of applied N is taken up by the crop), with the balance either retained in the soil or lost to the environment (e.g. to the atmosphere via denitrification, or to waterways via runoff and leaching). Improving NUE therefore represents a win‐win‐win for society (improved yields, food security), the economy (farmer profitability) and the environment (climate change mitigation, better water quality). Enhanced Efficiency Fertilizers (EEFs) aim to improve NUE, by synchronizing fertilizer N supply with crop N demands. Technologies include controlling N release from fertilizer into the soil (CR), or attempting to manipulate the rate of fertilizer N transformation to forms most vulnerable to environmental loss (e.g. NO3‐N) via microbial inhibitors (urease, UI, or nitrification, NI, inhibitors). A lack of process‐level knowledge of how these technologies behave under field conditions is limiting their effective use. Factors contributing to this uncertainty include: (a) different N demand and uptake dynamics in different crops; (b) variable soil types and characteristics; (c) different fertilizer application strategies; and (d) variable rainfall environments. This research focuses on fertilizer application strategies (i.e. fertilizer application rates, timing of application, and placement), to evaluate their agronomic performance and release dynamics.


Expected outcomes:

This research will provide a detailed evaluation of EEF products, which will help to inform the fertilizer industry (product development, improved grower recommendations), improve returns on fertilizer N investments for end users, and improve environmental performance. Students will gain experience in designing and setting up large‐scale field trials/experiments, field sampling and lab processing of soil/plant samples, within a project that is industry funded.

Suitable for:. Students interested in soil and/or plant sciences. Fieldwork will take place at Gatton where field trials are located, so students must be willing/capable of travelling to/from Gatton.



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School of Biological Sciences

Supervisor A/Prof Cynthia Riginos Duration: 8 weeks

Contact Details:


Monitoring plankton on the Great Barrier Reef for Crown‐of‐Thorns seastars

Crown‐of‐Thorns Seastars (CoTS) are among the greatest threats to the corals of the Great Barrier Reef. These coral predators follow a boom‐bust cycle where adults consume live corals and greatly diminish coral cover on affected reefs. It is unclear, however, how regularly COTS larvae appear in plankton samples and whether pulses of COTS larvae predict future adult densities. This student project will combine new DNA‐based tools for detecting COTS larvae and microscopy to map the presence and larval‐development stage of COTS larvae in plankton samples from the GBR. The student will work with researchers at both UQ (Riginos) and AIMS (Uthicke).


Expected outcomes:

The scholar will gain experience with quantitative PCR and sample sorting techniques. There are many possible side projects that a student could develop and lead depending on interest and enthusiasm.

Suitable for:. Suitable for a student with some previous laboratory experience and demonstrated organizational and record‐keeping skills. The project is especially relevant for a student with interests in marine science and genetics.


The scholar would be expected to spend 1‐2 weeks at the project start in Townsville visiting collaborating researchers at AIMS. Transport and accommodation costs will be covered.


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Supervisor Dr Karen Cheney Duration: 8 weeks

Contact Details:


Office – Goddard Building, Room 112, St Lucia campus

Understanding colour perception in coral reef fish

Colour vision is essential for many animals to find food and mates, and avoid predation. However, the visual systems of most animals differ from that of humans. We therefore use visual modelling and behavioural experiments to understand how animals perceive objects in their environment. You will be trained in running behavioural experiments with coral reef fish to understand how fish perceive colour patterns.


Expected outcomes:

Running animal behavioural experiments, experimental design, visual modelling, spectrophotometry and animal husbandry

Suitable for:. All training will be provided. However, the students must be interested in neurobiology, marine science, visual ecology, animal behaviour and/or fish biology.



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Supervisor Dr Milos Tanurdzic Duration: 8 weeks

Contact Details:


Functional genomics of noncoding RNA in the wheat genome

The student will explore gene expression patterns of long non‐coding RNA in wheat during various developmental stages


Expected outcomes:

Lab research experience. Exciting discoveries. Zest for life!

Suitable for:. Students in genetics, molecular biology, plabt biology, biotech



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Supervisor A/Prof Diana Fisher Duration: 8 weeks

Contact Details:


Marsupial neuronal morphology

We are investigating neuronal morphology in several different developmental stages in the Tammar wallaby and the Fat‐tailed dunnart in two distinct brain areas – motor and visual cortex. We are digitalising neurons using Neurolucida, utilising several different cutting edge techniques – starting from conventional Golgi‐Cox staining (in collaboration with QBI), scanning through high‐resolution bright field Nikon microscope (in collaboration with SBMS) and finishing with digitalisation via a supercomputer and Neurolucida 360.We are aiming at describing the development of neuronal morphology and detecting differences in shape and complexity between species with different life histories and ecologies.


Expected outcomes:

We are aiming at high‐profile journal publications both on our descriptive and hypotheses driven papers. We will be the first to provide developmental series of neuronal morphology in marsupials, and also the first to provide with comprehensive cross species comparison of several distinct neuronal types between species.

Suitable for:. Students interested in neuroscience and comparative methods



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Supervisor Dr Gurion Ang

Prof Meron Zalucki

Duration: 8 weeks

Contact Details:


Behavioural ecology of the cycad blue butterfly Theclinestes onycha

The cycad blue butterfly Theclinestes onycha is an endemic butterfly distributed across most parts of QLD. Their larvae are specialist feeders of both native and introduced cycad plants. This project explores the behavioural ecology (focussed on oviposition and/or feeding behaviour) of these butterflies to determine their success on introduced cycad plants in urban landscapes.


Expected outcomes:

A comparative understanding of adult butterfly oviposition (egg‐laying) behaviour and larval feeding behaviour of the cycad blue butterfly across native and introduced cycad species

Suitable for:. A second or third year student that has completed BIOL2010 Ecology. Students who have taken courses on entomology, field ecology, and/or animal behaviour are encouraged to apply.


The project involves on campus ‘field’ work outside of laboratories, through the summer.


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Supervisor Dr Abigail Pastore Duration: 8 weeks

Contact Details:


Facilitation in Widflowers

Our lab has seen evidence of facilitation between species of wildflowers in their natural habitat in WA, but we don’t know how or why these plants are facilitating each other when we expect them to be competing. This project tests the hypothesis that having more neighbours increases the water available for plants and thus would increase plant growth. Experiments were run in WA last winter to test this hypothesis. Data was taken, but needs to be processed and analysed.


Expected outcomes:

Project involves Image Analysis, Data Entry and Data Analysis

Suitable for:. Undergrads interested in ecology and statistics


Applicants will need to be available before and after Christmas break.


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Supervisor Mrs Carolina Montenegro‐Chong

Prof John Pandolfi

Duration: 8 weeks

Contact Details:


Historical fisheries of our coastal seas

Fisheries have had a great impact in changing marine fish populations. Depletion of commercially important fish stocks and overexploitation of fish species are major concerns for managers and inhibit conservation efforts.

Using historical data (e.g: archaeological and palaeoecological records, historical fishing records, naturalist species lists, etc.) to reconstruct past fish population sizes has informed and improved current conservation targets and key stock assessments parameters by providing quantitative estimates of past abundances levels and community dynamics.

The aim of this project is to document changes in the coral trout and red emperor fisheries dynamics in Australia through time using historical data.


Expected outcomes:

To document past changes in catch rates, abundances, and effort (CPUE) of the coral trout and red emperor through time.

Inform predictions of future stock trajectories and improve knowledge for management and conservation purposes.

The data collected form this project will also form part of a PhD research in historical fisheries.

Suitable for:. Students interested in marine ecology, historical ecology and fisheries biology.



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Supervisor Dr Gal Eyal

Prof John Pandolfi

Duration: 6‐8 weeks

Contact Details:


Revealing multiscale spatial trends in coral reefs with advanced image‐based modelling

We are developing a computer vision platform for automatic identification and segmentation of the coral reef benthos. The successful outcome of this project requires plenty of training and testing data; manually labelled images. The students will learn how to identify coral reef organisms by learning how to classify and label benthic images from various regions, including coral reefs of Australia, the Red Sea, and the Caribbean region.


Expected outcomes:

The students will gain knowledge in marine invertebrate identification and image analysis tools.

Suitable for:. Highly motivated students with basic knowledge of marine invertebrate, preferably in tropical marine environments. Ability to work in collaboration with other students and professional colleagues in a virtual environment (online).


This project is an international collaboration with researchers from Israel (Marine Imaging Lab http://csms.haifa.ac.il/profiles/tTreibitz/index.html)and Spain.


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Supervisor Dr Jan Engelstaedter Duration: 8 weeks

Contact Details:


Quantifying fitness landscapes of antibiotic resistance

Antibiotic resistance is a major global problem in medicine and public health. The fate of resistance mutations is determined by its fitness effects on the bacteria carrying them, both in presence and absence of drugs. In this project the student will quantify these fitness effects for a range of drug resistance mutations and also investigate how fitness effects change when several resistance mutations are present in the same bacterium (i.e., estimate epistasis). The ultimate goal of characterising these ‘fitness landscapes’ is to improve our ability of predicting which drug resistance mutations will spread in a given scenario of drug use.


Expected outcomes:

Improved microbiology lab skills and understanding of the genetics of antibiotic resistance, insights into the research process in the field of evolutionary genetics

Suitable for:. Students with a major in genetics, microbiology or related fields. Basic lab skills and a keen interest in evolutionary questions are essential.



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Supervisor Dr Jan Engelstaedter Duration: 8 weeks

Contact Details:


Simulating the evolutionary dynamics of parasite host‐shifts

Host shifts refer to the process where a parasites switches from one host species to another one. Over long periods of time, this gives rise to complex dynamics producing entangled evolutionary trees of both hosts and parasites. We have recently developed an R package containing functions to simulate this process. The aim of this project is to improve this code with respect to modularity, extendibility and speed, with the ultimate goal of implementing inference methods based on the simulations. Specific project aims can be adjusted depending on the students interests and skills.


Expected outcomes:

Learn how to work with scientific software, insights into research process in the field of computational evolutionary biology

Suitable for:. Students with a strong quantitative background, e.g. with a major in computer science, physics or applied mathematics. Coding skills in R and/or C required but background in biology is not essential.



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Supervisor A/Prof Paul Ebert Duration: 8 weeks

Contact Details:


Telephone ‐ +61 7 336 52973

Genetic screen for new quiescence mutants

Quiescence, a metabolically suppressed state, can be triggered by stresses in the environment. It is used in various ways in all organisms as a means of increasing the chance of survival until conditions improve. One example is that cancer cells can evade chemotherapy by entering a quiescent state from which they can emerge later, resulting in progression of the disease. Another example is the suspension of reproduction under conditions of starvation or other stress.

In this project, you will screen C. elegans for mutant lines that are defective in their ability to enter oncogene‐associated quiescence and/or reproductive quiescence. The mutated genes will be identified by next generation DNA sequencing. These genes will assist in understanding both shared and unique features of distinct quiescence mechanisms.

Number of student places available: 1 (possibly 2)

Expected outcomes:

Discovery of new genes that control quiescence

Suitable for:.



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School of Chemistry and Molecular Biosciences

Supervisor Prof Alan E Mark Duration: 8 weeks

Contact Details:


Telephone – 07 3365 4180

Office – Room 331, Building 76, St Lucia Campus

The development and validation of the Automated Topology Builder (ATB).

The ATB is a web based molecular topology builder and repository used by 1000's of researchers worldwide involved in materials research and computational drug design. The site currently contains parameters for over 270,000 compounds (see: https://atb.uq.edu.au). You will be part of a team focused on further improving the reliability of the parameters generated.


Expected outcomes:

You will assist by either a) testing the predictive power of the parameters for a range of compounds by calculating properties such as their free energy of solvation in different environments or b) by helping to further develop the algorithms and code underlying the ATB web site.

Suitable for:. The project is suitable for students with a background in physical chemistry, medicinal chemistry, programming or (bio)informatics. Knowledge of python is an advantage.



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Contact Details:


Telephone – 07 3365 4180


Modelling membrane‐peptide interactions

The interactions of peptides with membranes is a key step in many cellular processes. Changes in the assembly of transmembrane helices is a key step in signalling by cytokine receptors (e.g. growth hormone receptor). Anti‐microbial peptides, which bind to and destroy membranes, are a first line of defence against bacterial infection. The project will involve using molecular dynamics simulation techniques to model the interaction of different peptides and proteins with model membranes. It will shed light on how particular peptides assemble into functional complexes within cell membranes.


Expected outcomes:

You will learn how molecular dynamics simulation techniques to model cellular systems at an atomic level. You will also examine how different membrane environments modulate the interactions between peptides.

Suitable for:. Students should have an interest in applying computational approaches to understanding how cell work at an atomic level. Students should have a background in chemistry, biochemistry or biophysics. Experience with Linux based systems is an advantage but not essential.



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Contact Details:


Telephone – 07 3365 4180


Understanding the morphology of organic semiconductors at an atomic level.

Multicomponent organic thin films are at the heart of modern display technologies, organic photovoltaics, and advances in flexible electronics. The mechanical and opto‐electronic properties of these films critically depend on their structure and morphology at an atomic level. The aim of this project is to use computer simulation techniques to determine how different deposition procedures (vapour or solution processing) affect the packing and spatial arrangement of emitter and host molecules used in the production of organic light emitting diodes (OLEDs) and other nanoscale devices.


Expected outcomes:

You will assist by running simulations of different mixtures of components and analysing aspects such the spatial arrangement of the components.

Suitable for:. The project is suitable for students with a background in physics, physical chemistry, computational sciences.



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Supervisor Prof Avril Robertson

A/Prof Fraser

Duration: 8 weeks

Contact Details:


Antifungals targeting Cryptococcus Neoformans

Depending on the candidate, this project will investigate one of the following:

Synthesis of novel antifungal agents, building on our previous research in this area

investigate our novel molecules to examine development of resistance and/or mode of action

Cryptococcus neoformans is a leading cause of death in HIV/AIDS patients. Infection occurs in immunocompromised patients after airborne basidiospores or desiccated yeast cells are inhaled, ultimately entering the alveoli. The C. neoformans fungus can cause pneumonia or, more frequently, disseminate to the central nervous system to manifest as meningoencephalitis. Without treatment this disease is uniformly fatal.

Current treatment is focussed on multidrug therapy comprising only three available drugs amphotericin B, flucytosine and fluconazole. Alarmingly resistance to all three drugs has been observed and novel antifungal agents are urgently needed.


Expected outcomes:

If the applicant is from a chemistry background, they will learn solution and solid phase synthesis techniques, purification and characterisation methods. If synthesis is successfully completed the molecule may be tested for antifungal activity.

If the student is more interested in the biology, fungal techniques will be learned and applied to the established antifungal compound series.

Suitable for:. This project is open to applications from UQ enrolled students only with a background and interest in drug discovery.

To pursue synthetic chemistry the applicant must have completed CHEM2054 as a minimum.

To pursue the resistance development microbiology would be highly desirable.

Previous research experience, e.g., SCIE3260, is considered an advantage.



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Supervisor Prof Avril Robertson Duration: 8 weeks

Contact Details:


Novel Anti‐inflammatory compounds targeting the innate immune system

Inflammasomes are part of the innate immune system responsible for processing and subsequent release of the potent pyrogenic cytokines, interleukin 1β and interleukin 18. Inhibiting inflammasomes (such as NLRP3, AIM2, NLRC4) using small molecules is an exciting strategy for future treatment of inflammatory diseases including asthma, type 2 diabetes and also disorders of the brain such as Parkinson’s and Alzheimer’s diseases. In the Robertson group, there is more than one compound series and innate immune target under investigation in this area.


Expected outcomes:

The student will learn and develop synthetic, purification and analytical skills contributing to our series for future patent and/or publication.

Suitable for:. This project is open to applications from UQ enrolled students only with a background and interest in drug discovery/organic chemistry. Must have completed CHEM2054 as a minimum. Previous research experience, e.g., SCIE3260, an advantage.



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Supervisor Prof Avril Robertson Duration: 8 weeks

Contact Details:


Diazirine Photoaffinity Probes in Drug Discovery

This project will explore the chemistry of diazirine photoaffinity probes.

When these probes are activated (using light of a particular wavelength, heat or ultrasonication) they covalently bind to nearby molecules or proteins. These exciting tools have been employed in drug discovery to identify compound binding site(s), map ligand interactome within the cellular milleau and diazirine containing amino acids have even been incorporated into proteins by native cellular machinery.

To fully exploit this technology in an efficient manner, it is highly desirable to expand the synthetic methodology and shorten synthetic routes through new innovative approaches. The project can focus on either of these areas.


Expected outcomes:

Students will be trained to synthesise diazirine photoaffinity probes, purify and characterise their molecules.

Suitable for:. This project is open to applications from UQ enrolled students only with a background and interest in drug discovery/organic chemistry. Must have completed CHEM2054 as a minimum. Previous research experience, e.g., SCIE3260, an advantage.



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Supervisor Prof Bernie Carrol Duration: 6‐8 weeks

Contact Details:


Office – Room 76‐359, St Lucia campus

Systemic RNA interference (RNAi) in plants

Gene silencing is a highly conserved process in plants and animals. It is of fundamental importance to gene regulation, virus defence, genome response to environment, and genome evolution. Remarkably, when silencing is triggered against a virus or an abundantly expressed gene in plants, it can spread throughout the organism. This systemic signally pathway is a particularly important defense mechanism against viruses. The aim of this project is to identify plant genes required for systemic movement of gene silencing in plants. Expected outcomes include increased understanding of the role of RNAi in defence against viruses. The findings may also be relevant to mechanisms of gene silencing in animals.


Expected outcomes:

Applicants can expect to gain experience and knowledge in PCR‐based genotyping of plants for mutations in genes involved in RNAi, grafting Arabidopsis plants, genetic mapping, screening for a reporter gene, and collection and analysis of data. Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for:. This project is open to applications from students with a strong interest in molecular genetics, genetic and epigenetic mechanisms, year 2 or 3 undergraduate students.



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Supervisor Prof Bostjan Kobe Duration: 6‐10 weeks

Contact Details:


Structural studies of proteins involved in infection and immunity

The aim of this project is to use structural biology to understand the molecular basis of processes involved in infection and immunity. The work has implications for treating a range of infectious and inflammatory diseases and cancer, or for minimizing plant disease. We are focusing in particular on the proteins involved in cytoplasmic signalling by Toll‐like receptors, bacterial pathogenesis, and effector‐triggered immunity by plants. The main techniques will involve protein expression, purification, crystallization and structure determination, molecular interaction analyses and characterization of functional effects of site‐directed mutants.

Number of student places available: Up to 3

Expected outcomes:

Scholars will gain skills in various lab techniques mentioned above and have an opportunity to contribute to publications based on their research. Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for:. A background in biochemistry, biophysics and other relevant areas is an advantage. We are looking for motivated students with interest in research in the areas the lab works in.



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Supervisor Prof Craig Williams Duration: 6‐10 weeks

Contact Details:


Natural Product Isolation – Desert Plants

The student will perform plant metabolite extraction, purification, isolation and structure elucidation.


Expected outcomes:

Scholars will gain skills in chromatography and new molecule elucidation and characterisation, which may provide an opportunity to generate publications from their research. Students will be asked to produce a report at the end of their project.

Suitable for:. Those students that have successfully completed CHEM3004 and/or CHEM3001.



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Supervisor Prof Craig Williams Duration: 6‐10 weeks

Contact Details:


Advanced Organic Synthesis

The student will perform a range of advanced synthetic organic chemistry techniques to gain experience in constructing bioactive molecules.


Expected outcomes:

Scholars will gain skills in synthetic organic chemistry and molecule characterisation, which may provide an opportunity to generate publications from their research. Students will be asked to produce a report at the end of their project.

Suitable for:. Those students that have successfully completed CHEM3001.



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Supervisor Prof Debra Bernhardt Duration: 8 weeks

Contact Details:


Telephone ‐ +61 7 3346 3939

Alloy catalyst design for synthesis of graphene and boron nitride sheets for application in new technologies

Graphene has attracted great attention due to its distinct properties and promising applications in optoelectronics, catalysts, spintronics, sensors, super capacitors, solar cells, and lithium ion batteries etc. To fully utilize the superior properties of graphene, developing techniques for the scalable synthesis of high quality and large‐area graphene is essential. Chemical vapour deposition (CVD) growth of graphene on transition metal substrates is the most promising method for production of high quality, large area films at a reasonably low cost. Alloy catalysts such as CuNi has been found to be an efficient catalyst for the fast growth of high quality. However, if there is any other efficient alloy catalyst for the CVD growth of graphene remains unclear due to the lacking of understandings on the growth mechanism of graphene on alloy catalyst. This project aims to study the graphene growth mechanism on PtAu alloy catalysts and the decomposition of methane on the PtAu surface will be explored firstly. By doing first principles theoretical calculations, the first step of graphene growth (e.g. methane decomposition) will be understood and the growth rate of graphene on PtAu surface will be estimated.


Expected outcomes:

The students may gain knowledge about catalysis and crystal growth, skills in data collection and analysis, co‐authorship publication is quite possible. Students may also be asked to produce a report or oral presentation at the end of their project.

Suitable for:. Students with a background in chemistry, physics or material science at year 3‐4.



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Supervisor A/Prof Elizabeth Krenske Duration: 8 weeks

Contact Details:


Computer simulations of bioactive molecules

This project will use sophisticated computer simulations to study how drug candidates interact with biological molecules. The aim of the project is to understand what controls how a drug molecule binds to its intended target in the body, and how to tailor the properties of bioactive molecules. These insights will help in the design of new anti‐cancer drug leads.


Expected outcomes:

Scholars will gain skills in computer‐based molecular modelling. They will use software to perform simulations and will learn how these types of simulations can be applied to drug design as well as many other areas of chemistry. Students may be asked to produce a short written report at the end of their project.

Suitable for:. This project is open to applications from UQ enrolled students majoring in Chemistry who have studied organic chemistry at 2nd and/or 3rd year level and have an interest in biological, organic, and/or theoretical chemistry.



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Supervisor Dr Ben Woodcroft Mr Rhys Newell Dr Rob Hoelzle

Duration: 8 weeks

Contact Details:


Exploring differential methylation and SNP variation in climate‐critical environmental communities with long‐read sequencing

State‐of‐the‐art high throughput long read sequencing technologies allow for a myriad of new insights into microbial communities to be made, but many of these techniques have not previously been applied to environmental samples. This project will analyse Nanopore long read sequencing data applied to samples from Stordalen Mire in northern Sweden. Permafrost at the mire is thawing causing drastic changes in the microbial communities that live there, encouraging the growth of organisms which further exacerbate climate change by releasing the potent greenhouse gas methane. The project will investigate the ways complex polysaccharides are degraded into carbon dioxide and methane by comparing the responses of the microbial community to the addition of carbohydrates. The project will aim to implicate genes in the metabolism of these carbohydrates by observing their regulation (through methylation analysis of Nanopore long read datasets) and the different growth patterns of individual strains (using the shorter but more accurate Illumina NextSeq read datasets). Such information would allow for deeper understanding about the roles played by these organisms in nutrient cycling processes in an environment heavily affected by anthropogenic climate change.


Expected outcomes:

The student will gain expertise in the bioinformatic analysis of metagenomic data

Suitable for:. Suitable for students with a basic knowledge of microbial biology and some familiarity with the Linux command line interface. Additional skills using programming languages (e.g. R or Python) for data analysis would be desired.



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Supervisor A/Prof Jack Clegg Duration: 8 weeks

Contact Details:


New components for the synthesis of metal‐organic frameworks

Metal‐Organic Frameworks are a class of polymeric material formed from organic and metallic components. This project will explore new ways to form these materials following an innovative hierarchical self‐assembly methodology.


Expected outcomes:

A new organic component will be designed and prepared before its interactions with a variety of metal ions will be investigated. This project will require some synthetic laboratory work.

Suitable for:. UQ enrolled students only who have completed CHEM2054 as a minimum.



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Supervisor A/Prof Jack Clegg Duration: 8 weeks

Contact Details:


Trapping Guest Molecules in Metal‐Organic Frameworks

Metal‐Organic Frameworks are a class of polymeric hybrid material formed from organic and metallic components. These materials have large surface areas and high porosity and are finding application in gas sequestration and separation technologies. Accordingly it is possible to trap a large variety of guest molecules inside them. In this project you will investigate the binding of different solvent molecules inside one of these frameworks to explore selectivity and potential separation applications.


Expected outcomes:

Techniques you learn in our group may include: Organic Synthesis, Inorganic Synthesis, Crystal Engineering, Xray diffraction, NMR, IR, UV‐Vis, Mass Spectrometry, and just about anything else you can imagine!

Suitable for:. UQ enrolled students only who have completed CHEM2054 as a minimum.



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Supervisor Dr Jack Wang Duration: 8 weeks

Contact Details:


Telephone ‐ +61 7 3365 4611

Office – Room 76‐426, St Lucia Campus

Developing Blended Learning Resources in Microbiology

Continually increasing class sizes in Higher Education (E.g. >1000 in many first year UQ courses) have highlighted the necessity of innovative delivery of learning experiences. Blending the Face‐to‐Face on‐campus learning at UQ with interactive online resources can improve flexibility in learning modes available to students and provide instructors with additional teaching tools to maximise student engagement. This project will involve creating screencasts, videos, animations, and podcasts to enrich the blended learning experience at UQ, and evaluating their effectiveness through a rigorous mixed‐methods strategy. This includes surveying and interviewing students and instructors across a number of Higher Education courses to map out the effective features of online and face‐to‐face learning activities, which will contribute to Teaching and Learning policy in Higher Education.


Expected outcomes:

Survey design and analysis, focus group interviews, generating and analysing video and multimedia content, coding and thematic analyses of qualitative and quantitative data, communicating with a variety of audiences.

Suitable for:. Students in Biological Sciences majors (E.g. Biochemistry & Molecular Biology, Genetics, Microbiology) would be appropriate for this project. Experience in video production would be beneficial for the project.



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Supervisor A/Prof Joseph Rothnagel Duration: 6‐8 weeks

Contact Details:


Characterisation of peptides encoded by short open reading frames

Short peptides (sPEPs) that are encoded by short Open Reading Frames (sORFs) are surprisingly common in eukaryote genomes. Significantly, a mutation in a sPEP has been associated with a human genetic disorder. Recent bioinformatic and ribosomal footprinting studies have helped identify several thousand sORFs with coding potential and several sPEPs have also been identified by mass spectrometry. However, their role in cellular functions remains to be determined. You will identify and characterize sPEPs using bioinformatic tools, proteomics (mass spec) and cell biology. You will help to determine the contribution of sPEPs to the human proteome, and provide insights into their roles. This project will involve analysing raw proteomic (mass spec) data


Expected outcomes:

You will gain skills in proteomics; specifically in sample preparation for mass spec, mass spec data analysis, and bioinformatics.

Suitable for:. Knowledge of molecular and cell biology methods. Bioinformatics and computational skills would be an advantage.


Relevant background information can be seen here: https://www.nature.com/articles/nrg3520


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Supervisor A/Prof Shi‐Chun Lo (Lawrence) Duration: 8 weeks

Contact Details:


Telephone ‐ +61 7 334 67657

Office – Centre for Organic Photonics & Electronics (COPE), Levels 7/9 Chem Building (68), St Lucia Campus

Synthesis of highly luminescent organic materials

The project aims to develop highly luminescent organic chromophores that will be used for organic optoelectronic devices such as organic light‐emitting diodes (OLEDs for displays and lightings), organic photodetectors and organic lasers. Compared to inorganic counterparts, organic semiconductors offer many key advantages such as more light‐weight, highly tunable, relatively cheaper and easier in materials synthesis and fabrication. The interests and demands on highly luminescent organic chromophores have been increasing in particular for bio‐applications (such as bio‐imaging, sensing) or organic electronics. It is challenging to generate organic chromophores with strongly luminescent in both solution and solid state, and simultaneously exhibit appropriate energy levels for charges injection in devices. The project will develop new organic semiconductor chromophores and study their properties for the potential in next‐generation organic light‐emitting lighting and/or lasers.


Expected outcomes:

Students are expected to learn how to design, synthesis, purify and characterise organic chromophores (semiconductors), as well as the working principles and usage in organic electronic devices. Students will work closely with physics collaborators at QU’s School of Mathematics and Physics.

Suitable for:. Students have strong interest in organic materials development and synthesis as well as learning how organic electronics will work and play roles in our next generation lighting and laser technologies.

Solid organic synthetic knowledge and skills from CHEM2054 and CHEM3016 (CHEM2060 & CHEM3001 will be beneficial).



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Supervisor Dr Marloes Dekker Nitert Duration: 8 weeks

Contact Details:


Telephone ‐ +61 7 3365 4633

Dietary intake and gut microbiota composition in pregnancy

Dietary intake is an important determinant of the composition of the gut microbiota. In pregnancy, the composition of the gut microbiota changes and this is associated with changes in gut wall barrier function and inflammation. It is unclear how dietary intake in late pregnancy alters the composition of the gut microbiota. In this project, you will investigate the role of macro‐ and micronutrient intake on the composition of the gut microbiota in women at 28 weeks gestation.


Expected outcomes:

This project introduces you to bioinformatic analysis of 16S rRNA data, and teaches you the development and testing of PCR and QPCR assays.

Suitable for:. This project is suitable for students with an interest in metabolism and dietary intake. A basic understanding of biochemistry is important. While this project does not involve coding, an interest in large dataset analysis is critical.



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Supervisor A/Prof Mikael Boden Duration: 8 weeks

Contact Details:


Inferring the properties of ancient enzymes

The Boden group is developing methods for computationally inferring the sequence of ancestral variants of proteins. This project will map information assigned to known family members onto ancestors, guided by phylogenetic relationships. This will assist efforts to identify what enzymes to reconstruct in the lab, and how to optimise their function or activity.


Expected outcomes:

Experience with research, problem solving, software development for web services, e.g. querying of biological databases and visualisation

Suitable for:. Successful completion of bioinformatics courses; strong programming and problem solving skills



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Supervisor A/Prof Mikael Boden Duration: 8 weeks

Contact Details:


Tool for finding biology in time and space

Transcriptome data is increasingly available over developmental time, from different but spatially related cell types (e.g. via single‐cell RNA‐seq). These data sets are unwieldy and contain many patterns that are best explained by chance. This project will develop tools for a larger study which aims to determine statistical enrichment of spatial or temporal patterns, informing developmental biology‐collaborators of what changes in gene outputs that drive spatial and temporal phenotypes.


Expected outcomes:

Experience with research, problem solving, software development for statistical analysis

Suitable for:. Successful completion of bioinformatics courses; strong programming and problem solving skills



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Supervisor Prof Stephen Barker Duration: 6‐9 weeks

Contact Details:


The ticks of the rats and birds of New Guinea: aspects of their host‐associations and relationships to altitude.

Aims: To discover aspects of the host‐associations and relationships to altitude of some ticks.

Methods: microscopy and computer work (Microsoft Excel)


Expected outcomes:

Scholars will gain skills in microscopy and data collection, handling and analysis, critical‐thinking, through one‐on‐one interaction with Professor Barker.

Suitable for:. This project suits someone with sound computer skills and an interest in arthropod‐vectors of disease, climate and maps.



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Supervisor Prof Stephen Barker Duration: 6‐9 weeks

Contact Details:


Tick‐paralysis in dogs and cats

Aims: To discover why there are more cases of tick‐paralysis in dogs and cats in some years and at some places, than in other years and other places.

Methods: computer work (Microsoft Excel) and simple Geographic Information Systems (GIS) approaches.


Expected outcomes:

Scholars will gain skills in data handling and analysis, critical‐thinking, through one‐on‐one interaction with Professor Barker.

Suitable for:. This project suits someone with sound computer skills and an interest the epidemiology of arthropod‐vectors of disease, climate and maps.



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Supervisor Prof Stephen Barker Duration: 8 weeks

Contact Details:


A scholarly assessment of the development of the discipline of tick‐biology from Homer (about 322 B.C.) to 1988

Aims: To consider in a scholarly way the development of the discipline of tick‐biology from Homer (about 322 B.C.) to 1988

Methods: analyses of eight‐volume “Bibliography of ticks and tick borne disease” by the late Harry Hoogstraal. Computer work (Microsoft Excel). Thinking.


Expected outcomes:

Scholars will gain skills in data handling and analysis, critical‐thinking, through one‐on‐one interaction with Professor Barker.

Suitable for:. This project suits someone and an interest the history of science and of the development of scientific thinking on infectious agents like ticks and the diseases ticks are associated with.

Sound computer skills required.



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Supervisor A/Prof Vito Ferro Duration: 8 weeks

Contact Details:


Adventures in carbohydrate chemistry

The project involves the synthesis and characterization of novel glycoconjugates for biological evaluation.


Expected outcomes:

Students will learn how to synthesise, purify and characterise compounds of biological interest.

Suitable for:. This project is open to applications from UQ enrolled students only with a background in organic chemistry. Must have completed CHEM2054/3016 as a minimum.



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Supervisor Prof Mark Schembri Duration: 8 weeks

Contact Details:


Understanding phase variation of the type 1 fimbriae virulence factor in multidrug resistant uropathogenic E. coli

Uropathogenic Escherichia coli (UPEC) of sequence type 131 (ST131) are a pandemic multidrug resistant clone associated with urinary tract and bloodstream infections. Type 1 fimbriae, a major UPEC virulence factor, are essential for ST131 bladder colonization. The globally dominant sub‐lineage of fluoroquinolone‐resistant ST131 strains possess an ISEc55 insertion in the fimB gene that controls phase‐variable type 1 fimbriae expression via the invertible fimS switch promoter. We have shown that this fimB mutation reduces inversion of the fimS switch from the ‘off’ to the ‘on’ orientation in the ST131 reference strain EC958, thus affecting the expression of type 1 fimbriae. We have also assessed the orientation of the fimS switch promoter using a specific PCR and restriction digest assay.

This project will

(i) use bioinformatic analysis of large genome datasets to determine the prevalence of the fimB::ISEc55 insertion in E. coli, and

(ii) develop amplicon sequencing as a new method to assess fimS switching in EC958 and compare this to fimS switching in other UPEC reference strains.


Expected outcomes:

Students will

(i) gain knowledge in UPEC biology and fimbrial adhesins, (ii) develop skills in bioinformatics and the analysis of large datsets, (iii) develop skills in PCR, and (iv) apply Illumina‐based amplicon sequencing to investigate phase variable gene

expression.

This knowledge will provide a platform for future molecular biology investigation in this area. Students will have the opportunity to give an oral presentation to the research group at the end of the project.

Suitable for:. This project is open to applications from 3rd year students with an interest in microbiology.



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Supervisor Dr Kirsty Short Duration: 8 weeks

Contact Details:


Room 433, MBS Building, St Lucia Campus

Glycaemic oscillations and severe influenza

Type 1 and Type 2 diabetes mellitus significantly increases the risk of developing a severe influenza virus infection. Historically, it has been suggested that this increased susceptibility is the result of elevated blood glucose levels. However, using novel in vitro and in vivo models, our preliminary data provide the first evidence that blood glucose variability, rather than average blood glucose levels, increases the severity of a primary influenza virus infection. This project will build upon these data and assess the role of diabetic glycaemic oscillations in severe influenza


Expected outcomes:

Cell culture, virology, molecular biology

Suitable for:. Those interested in virology/immunology


All students will need to be vaccinated against influenza virus before working in the laboratory.


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School of Earth and Environmental Sciences

Supervisor Dr Renjie Zhou Duration: 8 weeks

Contact Details:

School of Earth and Environmental Sciences Email: [email protected] Office: Steele Building (Building 3), Room 255B

Advanced methods in determining the age of Earth materials

Geochronology, the science of determining the age of minerals and rocks, is at the core of geoscience. Students will work with the state‐of‐the‐art facilities at the Faculty of Science and produce and interpret data from samples collected in Australia and elsewhere. Project topics may involve environmental, tectonic, or mineralizing processes, depending on students’ background and interest. Students will gain hands‐on experience in laser ablation ICP MS, microprobe, and scanning electron microscope.

Number of student places available: 1‐3

Expected outcomes:

A presentation within the research group.

Suitable for:.

Students who have completed ERTH1501 or ERTH1000 and have some chemistry background are encouraged to apply. Students who have completed ERTH2005 (Mineralogy) or ERTH2006 (Igneous & Metamorphic Petrology) will be given priority.



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Supervisor Dr Scott Lieske Duration: 8 weeks

Contact Details:


Office: Building 35, Room 537, St Lucia campus

Untangling high dimensional socio‐ecological and spatial data using visual analytics

The importance of adopting a coupled human and natural systems approach to research related to resource management, sustainability, conservation and community planning has been established in the literature for decades. Yet, the challenges of synthesizing complex, multi‐dimensional data across disparate ecological, socio‐economic, and cultural dimensions persist as a major impediment to cross‐sectoral research in human‐ecological systems. Here, we visualize inter‐dependencies amongst environmental, ecological and human use factors in the Mekong River Basin with both geographic information systems and a visual analytics toolkit that together identify functional relationships among factors and spatial patterns. The visual approach provides a tractable method to analyse complex human‐natural systems that translates complex patterns into accessible language.


Expected outcomes:

Literature review, data analytics, synthesis, academic writing

Suitable for:. Upper level honours track undergraduate students with strong GIS‐based spatial analysis skills and strong tabular data analysis skills.


Project will focus on the use of ESRI GIS and macrofocus High‐D software: https://www.high‐d.com/


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School of Mathematics and Physics

Supervisor Prof Warwick Bowen Duration: 10 weeks

Contact Details:


Photography at millions of frames per second for bioimaging

Coherent ultrafast photography is a new technique recently developed to allow imaging at millions of frames per second. The key concept is to encode time information onto spatial position, so that a single shot of an image gives both spatial structure and temporal dynamics. However, current implementations of the technique use a complicated convolution‐and‐then‐deconvolution process that both degrades resolution and requires high levels of data processing. This project will develop a new approach to coherent ultrafast photography to overcome these challenges.


Expected outcomes:

The project will involve designing an optical imaging apparatus that allows time information to be encoded unambiguously, without convolution, onto the observed image. The applicant will learn about optical imaging and signal processing. The outcomes of the project are expected to have high relevance, increasing the spatial resolution of ultrafast microscopy, and allowing it to operate in real‐time without sophisticated data processing techniques. This could, for example, provide new insights into biological dynamics, allowing them to be spatially resolved at microsecond rates.

Suitable for:.

The ideal applicant should already have experience in design of optical imaging systems, and in modelling them, particularly including modelling diffraction and Fourier techniques.



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Supervisor Prof Matthew Davis Duration: 6‐8 weeks

Contact Details:


Quantum engines with Bose‐Einstein condensates

Trying to understand how to make heat engines more efficient provided the impetus behind the development of the laws of thermodynamics, one of the most powerful frameworks of physics today. The question of how thermodynamics and applies at the microscopic scale motivates the study of quantum engines, in which quantum features such as superposition and entanglement are incorporated into the engine cycle.

This project will design and study engine protocols for superfluid Bose‐Einstein condensates, with a view to demonstrating such a protocol in the laboratory at UQ that is part of the ARC Centre of Excellence for Engineered Quantum Systems.


Expected outcomes:

The student will learn how to perform simulations of the dynamics of many‐body quantum systems. If the project goes well it could lead to further research projects and has the potential for publication in a research journal.

Suitable for:.

Self‐motivated third year physics students who are interested in pursuing research in theoretical and computational quantum physics.



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Contact Details:


Nonequilibrium superfluid flows

The aim of this project is to make a connection between classical mechanics and quantum mechanics ‐ looking for the signatures of classical trajectories in the quantum wave functions. This is potentially interesting for superfluids, as to some extent they behave as classical fluids. This would require adding the effects of particle interactions ‐ an additional nonlinear term in the Schrodinger equation.


Expected outcomes:

Students will learn how to solve the linear and nonlinear Schrodinger equation computationally with sources and sinks. The results may influence the UQ experimental program on Bose‐Einstein condensates.

Suitable for:.




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Contact Details:


Pairing phase of the attractive Bose gas

In the 1970s there was speculation that the cause of superfluidity in helium‐4 was not due to Bose‐Einstein condensation, but a form of Cooper pairing between attractive bosons, similar to that which occurs for electrons in superconductors. More recent calculations for the homogeneous system suggest that the temperature for the pairing transition is higher than for BEC ‐ but that both are preceded by the mechanical collapse of the gas. This collapse is however prevented in finite systems. This project will use the classical field method to determine whether a pairing phase is possible for degenerate Bose gas with attractive interactions, and compare the results to the predictions of the Hartree‐Fock‐Bogoliubov method.


Expected outcomes:

The student will learn how to apply analytical and computational quantum‐many body methods to Bose‐Einstein condensates. The hope is to uncover a new possible phase of matter, and to describe how to observe it in the laboratory.

Suitable for:.




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Contact Details:


Superfluidity under a quench of interaction strength in a persistent current.

One of the key insights of Landau was to derive a phenomenological formula for the critical velocity in a superfluid. In a Bose gas this is related to the speed of sound, which is directly related to the strength of repulsive interaction between particles. By making use of something known as a “Feshbach resonance” in the scattering properties of two atoms, it is experimentally possible to tune the strength of interactions in a Bose gas. This project will look at a ring system in which there exists a persistent current that if left undisturbed will never decay. However, if the interaction strength is sufficiently reduced, the speed of sound will decrease below the speed of the current and the superflow will break down. This project will characterize the non‐equilibrium dynamics as the flow breaks down and thermalizes. It should be able to be related to the well‐known “Kibble‐Zurek” mechanism for phase transitions.


Expected outcomes:

The student will learn how to apply computational methods to solve the nonlinear Schrodinger equation. A complete set of results with appropriate interpretation could be turned into a publication.

Suitable for:.




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Supervisor Prof Matthew Davis

Professor Margaret Mayfield


Contact Details:


Statistical physics model of abundances and interactions in plant communities

This project aims to use the methods of statistical physics to help understand the equilibrium and dynamics and of interacting plant communities with Prof Margie Mayfield in the School of Biological Sciences. Prof Mayfield’s group has collected a significant amount of data on plant abundances, and shown that the data suggests that nonlinear interactions between the plants affect their seed production. We hope to gain a new understanding of this data using equilibrium models of statistical mechanics. See:

Higher‐order interactions capture unexplained complexity in diverse communities

Margaret M. Mayfield & Daniel B. Stouffer

Nature Ecology & Evolution 1, Article number: 0062 (2017)

doi:10.1038/s41559‐016‐0062


Expected outcomes:

Hopefully we will show that physics methods can be used to help understand the interactions between plants in a community.

Suitable for:.

Self‐motivated science students with strong quantitative skills who are interested in pursuing an interdisciplinary project covering theoretical physics and biology. Knowledge of statistical mechanics is desirable.



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Supervisor Dr Duy‐Minh Dang Duration: 8 weeks

Contact Details:


Applications of Neural Networks in quantitive finance.

The project aims at studying the applications Neural Networks (NNs) to solve high‐dimensional (semi‐) linear Partial Differential Equations (PDEs) arising in computational finance. Another focus is on investigating the suitability of NNs in solving financial stochastic control problems formulated as multi‐dimensional controlled PDEs.


Expected outcomes:

An understanding of how to design, build and train suitable Neural Networks for PDE formulations of problems arising in finance. Students will be asked to produce a technical report, and/or to deliver an oral presentation.

Suitable for:.

This project is open to applications from 3‐4 year or Honour/Master students with a sufficiently strong background in stochastic processes (Ito calculus, stochastic differential equations) and partial differential equations.

Some prior knowledge in machine learning techniques, such as neural networks, are desirable, but not strictly required.

Strong programming skills (in Matlab or Python) and familiarities with basic financial concepts/products are preferred.



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Supervisor Prof Geoffrey Goodhill Duration: 8‐10 weeks

Contact Details:


Computational neuroscience: decoding neural activity and behaviour

We aim to understand the computational principles by which stimuli in the world are represented by patterns of neural activity, and how these representations emerge during development. To do this we are recording the activity of hundreds to thousands of neurons simultaneously, at single‐cell resolution, in the brain of the larval zebrafish, and also recording zebrafish behaviour. These data require the development of sophisticated mathematical/computational tools. You will join an interdisciplinary team working on these problems.


Expected outcomes:

You will be exposed to an interdisciplinary environment ranging from experimental neuroscience to mathematical analysis. The main deliverables will be Matlab code implementing particular algorithms for analysing our data.

Suitable for:.

A strong background in mathematics and computer programming is required. Previous knowledge of biology is optional.


Further background can be obtained from the following article: http://cns.qbi.uq.edu.au/pub/avitan18.pdf


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Supervisor Professor Ross McKenzie Duration: 8 weeks

Contact Details:


Theoretical condensed matter physics

What is the simplest effective Hamiltonian that can describe the essential magnetic, structural, and chemical properties of a broad class of spin‐crossover materials?

More information is available at

https://condensedconcepts.blogspot.com/search/label/spin‐crossover


Expected outcomes:

Student will gain experience at doing research in condensed matter theory.

Some of the skills to aim for are here ‐ https://condensedconcepts.blogspot.com/2017/06/the‐educational‐value‐of‐undergraduate.html

Student must produce a report and give an oral presentation at the end of their project.

More information about my expectations is available at https://condensedconcepts.blogspot.com/2013/10/what‐does‐my‐supervisor‐expect‐of‐me.html

Suitable for:. A highly motivated student with a strong background in physics and mathematics and a strong interest in complex materials



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Supervisor Dr Matias Benedetto Duration: 6 weeks

Contact Details:


Analyses of experimental data in fractured specimens

Fracture initiation and propagation is an important aspect of material failure. In some cases, i.e. brittle materials, structures fail with loads much below the one given by their strength due to the presence of notches and cracks that initiate fracture. Several theories and numerical models are currently proposed in the literature to obtain estimates of failure loads in structures where fracture is present.


Expected outcomes:

The students will be asked to get acquainted with the latest scientific trends in the study of fracture initiation and modelling of fracture processes. They are expected to confront recent experimental data with the current leading theories and modelling techniques, and then critically evaluate how the current state of knowledge can provide accurate justification of the data.

Suitable for:. Students with an interest in applying their mathematical skills to a real world problem. Students with an interest in the mathematical modelling of physical phenomena and engineering applications.



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Supervisor Dr Zoltan Neufeld

Dr Hamid Khataee

Duration: 8 weeks

Contact Details:

Email – [email protected]; [email protected]

Mechanics of collective cell migration.

In multicellular organisms, most cells are able to move, e.g. during tissue formation, maintenance, and defence. Moving cells also contribute to diseases, e.g., cancer. Yet, the mechanics underlying collective motion of cells remains elusive. This project aims to advance our preliminary developed mathematical and computational models for cell migration, and also analyse experimental images and movies.


Expected outcomes:

Students will gain skills in data analysis, computational simulations, and mathematical modelling. Students may also be asked to give oral presentation which will improve their presentation skills. There might be an opportunity to generate publications from their research.

Suitable for:. This project is open to applications from UQ students with a background in computer programming and differential equations. Students from engineering, computer science, mathematics, physics, biology or related fields are welcome to apply.



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Supervisor Mr Isaac Lenton

Dr Timo Nieminen


Contact Details:


Using machine learning to estimate particle size/refractive index from optical trap stiffness

Optical tweezers can be used to trap and manipulate microscopic particles. The strength of the optical trap depends on the size and refractive index of the particle. If the particle size, shape and refractive index are known, the trap stiffness can be easily calculated using computer models. However, the inverse problem: calculating the particle size, shape and refractive index from the trap stiffness is significantly more complex.


Expected outcomes:

In this project, you will explore using an artificial neural network to solve the inverse problem. You will learn how to train an artificial neural network using Keras/TensorFlow; explore different network architectures; and evaluate the accuracy of this approach. At the end of the project you should produce a report summarising your results and the viability of this method for determining the particle properties.

If the applicant is interested, there is also an opportunity to experimentally verify the results. This will involve learning how to operate an optical tweezers experiment, experimentally calculate trap stiffness and use the artificial neural network to predict particle size/refractive index.

Suitable for:. Experience programming in Python or Matlab is desirable. Suitable for 2‐4 year students (including honours students).



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Dr Timo Nieminen


Contact Details:


Fast estimation of optical forces and torques using an artificial neural network

Forces and torques on particles in optical tweezers can be calculated semi‐analytically using a variety of methods. However, most of these methods are slow, taking minutes, hours or even days depending on the properties we are interested in exploring. We have recently demonstrated that machine learning, specifically artificial neural networks, can be used for fast and accurate calculation of optical forces on spherical particles.

In this project, you will extend this method to particles without rotational symmetry: i.e. you will explore particles which can rotate in the trap and which require calculation of both forces and torques. This project will involve using the physics computer cluster to generate training data for the neural network, train the neural network, and evaluate different network architectures including methods of describing the orientation of particles.


Expected outcomes:

You will learn how to use the physics computer cluster including how to submit jobs using SLURM. You will learn how to train an artificial neural network using Keras/TensorFlow; explore different network architectures; and evaluate the accuracy of this approach. At the end of the project you should produce a report summarising your project outcomes.

Suitable for:. Experience programming in Python or Matlab is desirable. Suitable for 2‐4 year students (including honours students).



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Dr Timo Nieminen


Contact Details:


Testing multiple particle scattering methods and the Rayleigh hypothesis

The scattering of light by a particle can be described by a matrix, often called the T‐matrix or transition matrix, which describes how each of the incoming beam modes scatters into outgoing beam modes. There are multiple ways to calculate the T‐matrix, for spheres there is a semi‐analytical expression for the coefficients in the T‐matrix. A T‐matrix can also be used to describe scattering by multiple particles. Multiple methods exist for combining individual particle T‐matrices to generate a combined T‐matrix, however it is unclear if these methods will work when circumscribing spheres around the separate particles overlap.

The aim of this project is to explore the validity of multiple particle T‐matrix methods for non‐spherical particles when the circumscribing spheres overlap and thus probe the Rayleigh hypothesis.


Expected outcomes:

You will learn how to simulate light scattering by particles using the T‐matrix method and the discrete dipole approximation. You will learn about multiple particle T‐matrix methods, their validity and the Rayleigh hypothesis. At the end of the project you should produce a report summarising your project outcomes.

Suitable for:. Experience programming in Matlab is desirable. Suitable for students with a background in mathematics or physics, 3‐4 year students (including honours students). The project could also be extended to an honours project.



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Dr Timo Nieminen


Contact Details:


Calculating optical forces on bacterial flagella and other tiny structures

Optical tweezers can be used to trap small cells and bacteria such as sperm or E coli. These particles have small structures they use to move or attach to surfaces. To understand the optical forces acting on these structures and if trapping these particles using optical tweezers affects their normal function, we would like to quantify the forces and stresses acting on flagellar and other small structures.

This project will involve modelling the light scattering by the flagella using the discrete dipole approximation and calculation of the force along the structure.


Expected outcomes:

You will learn how to simulate scattering and calculate forces using the discrete dipole approximation. At the end of the project you should produce a report summarising your project outcomes.

Suitable for:. Experience programming in Matlab is desirable. Suitable for students with a background in mathematics or physics, 2‐4 year students (including honours students).



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Supervisor Dr Alexander Stilgoe Duration: 6‐8 weeks

Contact Details:


Feasibility of polarised light based nano‐particle imaging based on beam shaping

Imaging is a cornerstone of most modern science. Visible light based imaging can normally resolve objects as small as about 200nm (about half a wavelength). Phase resolution can be much smaller, on the order of 20nm.

This project aims to determine how such an excellent phase resolution can be used to image nano‐particles and other objects such as bacterial flagella.

The project will involve experimental investigation of dynamic computer control of laser radiation and possibly some theoretical modelling of the detection of light scattering off of nano‐particles. The current outline for the project starts with estimations of the amount of light needed to perform phase detection of nano‐particles, followed by experimental work to detect the particles.


Expected outcomes:

This project is arranged so that a student can focus on a particular topic and provide experiences that can be tailored to the needs of the student.

Students can learn about a range of topics, including: Beam shaping, experimental design/control and data capture, laser physics, nano‐particle scattering, microscopy, dynamic phase contrast imaging.

The expected deliverables are the data from the investigation, and a short summary of the findings from the study.

Suitable for:. 2—4 year students with backgrounds in either: Physics, Biophysics, or Mathematics.


Please contact me to know more about the project. If you are interested in this project but unsure about your requisite background knowledge I welcome any questions.


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Contact Details:


Modelling electromagnetic fields near objects

Computational modelling is of radiation in the near‐field reveals how light is distorted by an object, which is of critical importance for apparatus such as microscopes and optical tweezers. There are a number of different representations and approximations of electromagnetic fields. Approximate methods are inaccurate but can be stable. Exact representations of fields using boundary conditions are exact (in the mathematical sense) but fail due to numerical instability.

This project is aimed to investigate how various representations of electromagnetic field modelling fails near objects can be modified to perhaps sacrifice some accuracy in the exact representation to gain some numerical stability.

This project will involve computer simulation of lasers and their linear interactions with matter. The current outline is to start the project with modelling near‐fields with the already derived exact model and re‐represent it using a different basis (wavefunction) to accurately model the near‐field of light scattering off an object.


Expected outcomes:


Students can learn about a range of topics, including: wavefunction representations, scattering modelling, computational simulation of wavefunctions and electromagnetism.


Suitable for:. 2—4 year students with backgrounds in either: Physics or Mathematics.




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Contact Details:


Total control of light

What’s the link between a sugar cube and an optical lens? Both can be used to focus light! Sugar is known as a random scattering medium, through precise characterisation of the sugar and control of the incoming wavefunction of light, the random scattering can be undone and the light focused.

This project aims to better understand how the polarisation of light impacts this system.

This project will involve some theoretical or experimental work depending on which aspect of the project most appeals to the student. The current outline is to first become familiar with scattering transformations and then consider what occurs to the scattering at different polarisations. This can be performed either in the lab or with computer simulation.


Expected outcomes:


Students can learn about a range of topics, including: light scattering modelling, experimental design/control involving lasers and optics, computational simulation of wavefunctions and polarisation interactions.






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Supervisor Dr Alexander Stilgoe Duration: 6 weeks

Contact Details:


Non‐conservative optical forces and the fundamental light—mater interaction

A generalised vector field can be split up into a component described by the gradient of a scalar potential and a component described by a vector potential. In a conservative closed path net zero energy is exchanged between the particle and field. If the force is non‐conservative, then there is an energy flow between the field and the particle.

This project aims to better understand how the torque induced by scattered circularly polarised light can cause a distortion in the transmitted light which can change the apparent position of the scatterer.

This project will involve some theoretical or experimental work depending on which aspect of the project most appeals to the student. The current outline is to first become familiar with multi‐polar wavefunction representations of scattered light can be investigated in an experimental system for analysis to give some insight into the interaction of light with matter and how energy is exchanged.


Expected outcomes:


Students can learn about a range of topics, including: wavefunctions and scattering modelling, experimental design/control involving lasers and optics, conservation of energy and momentum.






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Contact Details:


Simultaneous measurement of force, torque, position and orientation of dielectric particles

The force acting upon a particle can be measured with a position‐sensitive‐detector (PSD) which measures the centroid of scattered light—an intensity measurement. To determine the torque the field of light needs to be determined as well. Holographic techniques can be used to determine the phase as well as amplitude of light and thus the field can be found.

This project aims to better understand how to measure both the linear and angular momentum transferred to matter by combining scattering measurements with holography to optically characterise a particle manipulated with light.

This project will involve some theoretical or experimental work depending on which aspect of the project most appeals to the student. The current outline is to first become familiar with experimental laser physics and light measurement using camera and silicon detectors.


Expected outcomes:


Students can learn about a range of topics, including: laser scattering measurements, experimental design/control, theoretical modelling of laser scattering.






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Contact Details:


Accurate ray tracing

Ray tracing is one of the most successful descriptions of scattering of fast moving particles (such as light). Ray optics, paraxial wave optics and electromagnetic theory have different propagation characteristics and different computational complexity and at some level describe different kinds of interactions.

This project aims to determine practical regimes of applicability to create full and realistic models of optical systems including polarisation, spatial mode shaping and high‐numerical aperture optics for more accurate modelling of optical tweezers and other kinds of microscopy.

This project will involve some theoretical or experimental work depending on which aspect of the project most appeals to the student. The current outline is to first become familiar with when ray optics, paraxial optics, and electromagnetic modelling best preserve information about transmission through an optical system, then would be a theoretical and/or experimental investigation to verify the bounds of applicability.


Expected outcomes:


Students can learn about a range of topics, including: optics, experimental design/control, Fourier optics, computer simulation.






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Supervisor Mr Joshua Calcino Duration: 6‐8 weeks

Contact Details:


Understanding substructures in Protoplanetary Disks

Planets are formed in the disk of material that exists around young stars, and for this reason we call them protoplanetary disks. New instruments and telescopes are capable of resolving protoplanetary disks in extraordinary detail, and these observations are challenging our ideas of planet formation.

One way of inferring what is occurring in protoplanetary disks is by performing numerical simulations and then comparing these simulations with observations. Planets and stellar companions leave signatures in protoplanetary disks, such as spiral arms, gaps, or cavities, which are usually much easier to detect than the perturbing body. By matching these observable morphological features, we can learn about the perturbing bodies in the system.

An interested student will undertake a project to match the observed morphology of a protoplanetary disk, or make predictions about what disk morphologies we should observe if we assume a planet or stellar population exists in protoplanetary disks.


Expected outcomes:

The student will gain skills in numerical simulations and learn about the exciting field of protoplanetary disks. The student will present their research to the astronomy group towards the end of the project.

Suitable for:. A suitable student should have experience using a Linux/Bash terminal. No experience with High Performance Computers is necessary.



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Supervisor Dr Austin Lund Duration: 6 weeks

Contact Details:


Optimising classical simulations of quantum sampling algorithms

There are particular algorithm that operate on quantum enabled hardware are expected to substantially outperform their classical counterparts. Experiments on quantum computing platforms to date are yet to demonstrate a conclusive speed up over classical platforms performing the same tasks. Quantum sampling algorithms are the current leading prospect for demonstrating a quantum speed‐up on near term quantum hardware. However, the boundary of where this speed‐up occurs depends greatly on what the best possible classical algorithms are. This project will concentrate on optimising classical algorithms to help clarify where the boundary for demonstrating the supremacy of quantum algorithms is.


Expected outcomes:

In this project scholars will learn about the latest in quantum sampling algorithms and in particular the applications to optical quantum computing. Actual simulations of quantum optical systems on computational hardware will be performed and contributions to the latest knowledge about the best classical algorithms for sampling with realistic noise models.

Suitable for:. This project is open to applicants who have completed third year quantum mechanics and have a background in computer programming.


This project is part of the research of the ARC Centre of Excellence for Quantum Computation and Communications Technology, http://cqc2t.org and UQ’s Quantum Optics and Quantum Information group http://qoqi.org/.


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Supervisor Prof Warwick Bowen Duration: 8 weeks

Contact Details:


Quantum‐enabled super‐resolution imaging

Super‐resolution imaging is a critical tool for understanding living biology, since most of the molecules involved are far smaller than the wavelength of light and therefore cannot be resolved with conventional microscopes. This project will analyse a new type of super‐resolution imaging, that breaks the usually Rayleigh limit to resolving the separation of two emitters. It will first analyse the limits to the performance of this technique due to the quantisation of light, and then make explore how quantum correlations between photons can be used to improve performance.


Expected outcomes:

The project will involve designing an optical imaging apparatus that allows quantum super‐resolution imaging. The applicant will learn about optical imaging and signal processing. The outcomes of the project are expected to have high relevance, increasing the performance of super‐resolution microscopy. This could, for example, provide new insights into the biological dynamics of protein conformational changes.

Suitable for:. The ideal applicant should already have experience in design of optical imaging systems, and in modelling them, particularly including modelling diffraction and Fourier techniques.



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Supervisor Dr Joel Corney Duration: 8 weeks

Contact Details:


Coupled modes in whispering‐gallery resonators

Optical resonators formed from microspheres or microdisks support high‐quality "whispering gallery modes", in which the incoupled light circulates many times in a highly confined space. This provides a way of enhancing nonlinear optical effects, leading for example to novel quantum states of light.

In this theoretical project, you will calculate the nonlinear dynamics than ensues when the resonator can support multiple simultaneous modes. In particular you will explore the impact of various competing or enhancing effects on the threshold response of the device.


Expected outcomes:

You will develop skills in analytic and computational approaches in theoretical physics. You will be required to produce a short report and to give an informal talk at the end of the project.

Suitable for:. Some knowledge of quantum physics is essential (equivalent to a second‐year course on the topic). Familiarity with ordinary differential equations would be an advantage.



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Supervisor A/Prof Tim McIntyre Duration: 8 weeks

Contact Details:


Spectroscopic investigation of radiating hypersonic flow

The X2 expansion tube is a flow facility capable of replicating the conditions experienced by a spacecraft as it enters a planetary atmosphere. A test gas is heated and accelerated into the test section of the facility reaching speeds of around 10 km/s and temperatures up to 10,000 K. This project will develop and apply spectrally resolved measurement techniques to investigate various species present in the test gas.


Expected outcomes:

The scholar will gain experience in working in an experimental laboratory developing an optical technique of general interest to the research group. The scholar can also expect to spend time assisting other researchers with their experimental measurements.

Suitable for:. Students with a physics or engineering background. Some understanding of geometric optics and/or spectroscopy would be of benefit.


A maximum of two students will be taken on to work on this project.


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Supervisor A/Prof Tim McIntyre

Dr Margaret Wegener

Duration: 8 weeks

Contact Details:


Development of e‐learning modules for teaching undergraduate physics

Online interactive simulations are used across a number of undergraduate physics courses at UQ. They are designed to allow students to visually investigate the underlying physics – students can vary relevant parameters and observe their influence on the system. This project will require students to develop a computational model of a physical phenomena and convert it into a format that can be used in a web‐based environment.


Expected outcomes:

The scholar will gain experience in developing teaching material including the use of newer on‐line interactive approaches.

Suitable for:. Students with a physics or engineering background with an interest in the scholarship of teaching and/or pursuing teaching as a career. Some programming experience would also be useful.


A maximum of two students will be taken on to work on this project.


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Supervisor Fred Roosta‐Khorasani Duration: 8 weeks

Contact Details:


Telephone ‐ +61 7 336 53259

Hartley Teakle Building (83), Room S518, St Lucia Campus

Acceleration of the classical Newton’s method for optimization

In this project, we aim to investigate ways to accelerate the convergence of the classical Newton’s method for optimization. As it stands, there is no such accelerated scheme available and any positive result in this direction can make a significant difference in the optimization of many scientific and machine learning models.


Expected outcomes:

The students will study new optimization algorithms and the underlying mathematical concepts and in the process, the students will develop valuable programming skills

Suitable for:. Students with good knowledge of calculus, linear algebra, and potentially optimization



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Supervisor Dr Dietmar Oelz Duration: 8 weeks

Contact Details:


Modelling and simulation in cell biology

Typically projects are available in the mathematical/computational modelling and simulation of cell biology. Areas of particular interest are cellular morphogenesis, intra‐cellular transport, (collective) cell migration and mechanical aspects of Neurobiology.


Suitable for:. Students with interest in and intuition for applications, programming skills, curiosity and self‐motivation.

Starting from year 3



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Supervisor Dr Dietmar Oelz Duration: 8 weeks

Contact Details:


Applied PDEs

Typically projects are available in the context of mathematical models of phenomena related to cellular morphogenesis, intra‐cellular transport, (collective) cell migration and mechanical aspects of Neurobiology.


Suitable for:. Talent and interest in Applied Mathematics and PDEs, curiosity and self‐motivation.

Starting from year 3



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Supervisor Dr Magdalena Zych Duration: 8 weeks

Contact Details:


Office – Parnell Building 7‐307, St Lucia Campus

Effects of mass superpositions in neutrinos on their propagation

Neutrinos are elementary particles, being part of the Standard Model of Particle Physics. According too our current understanding of neutrino physics, in typical physical scenarios a neutrino is produced in a quantum superposition state of different masses. It is currently believed there are three possible mass states of neutrinos, and different superpositions of these states are referred to as neutrino flavours.

The values of the neutrino masses are estimated to be small, and neutrinos are very difficult to detect. A few experiments have reported data that may not fit the current picture of neutrino physics, and it is believed these results may signal some new physics.

In this project we will take a different approach. We will only consider standard physics to analyse how the difference in the masses will affect propagation of neutrinos depending on the initial state in which they are born.

Subsequently, we will investigate how the difference in propagation will affect the type of mass superposition, i.e. the neutrino flavour, that would be detected after some time of neutrino free propagation.


Expected Outcomes:

You will gain research skills and expand your knowledge in theoretical physics. This project will allow you to learn the following techniques and concepts

physics of neutrino oscillations;

path integral formulation of quantum mechanics;

relativistic quantum theory;

quantum correlations

There will be an opportunity to co‐author a publication from this research.

Suitable for:. Project open to 2nd – 4th year students familiar with basic quantum mechanics and relativity; familiarity with general relativity will be an asset.



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School of Veterinary Science

Supervisor Dr Erika Meler Duration: 8‐10 weeks

Contact Details:


Use of activity trackers to measure owner compliance with weight loss program in dogs.

The use of activity trackers in humans is widespread and nowadays common use. These are mostly used to objectively record people activity and to ensure that adequate number of calorie‐burning activities are achieved in a day. Some companies have developed similar devices for dogs. The new generations of pet trackers allow monitoring of heart rate, respiratory rate as well as activity level. We have already investigated the reliability and accuracy of one of these devices and would like to start looking into practical applications. Obesity is a common issue in animals as it is in humans nowadays. Weight loss programs rely on a restricted calorie diet and exercising plans. We would like to study the benefits of using an activity tracker collar to motivate clients but also monitor compliance to the exercise program for overweight and obese dogs.


Expected outcomes:

The student will be expected to:

‐ Familiarize with the activity monitoring device ‐ Run pilot testing on different dogs ‐ Participate to the design of the study ‐ Collect data for the study ‐ Participate in the analysis of the data ‐ Present the preliminary results of the study in a school, university and/or

professional meeting ‐ Participate in the writing of the manuscript for publication

Suitable for:. Suitable for any student interested in animals as well as new technologies related to health. Therefore veterinary students or IT students are encouraged to apply but all students enrolled at UQ should feel free to put an application in. The study will be mainly based at Gatton campus around summer break. Students usually located at St Lucia can use the free intercampus bus running daily between both campuses.

Mainly, this project requires an individual who is enthusiastic and proactive as well as reliable and hardworking. Having advanced knowledge and interest in technologies in relation with the medical field as well as data collection and statistical analysis would be particularly valued but is not mandatory. Although beneficial, specific veterinary skills are not required for this project. However, the student is expected to be able to handle a dog with confidence and without apprehension.



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Contact Details:


Exploring the information required by referring veterinarians in specialist referral summaries

The Small Animal Veterinary Teaching Hospital of the University of Queensland (UQ‐SAVTH) provides high level specialist care for animals. Specialists share their daily duties in the hospital between student teaching, patient care, client communication, medical record and referral summary writing. Writing thorough referral summaries for a patient visit takes time away from the patient and students. No study has yet looked into what referring veterinarians expect to find in a referral summary and what is the best way for specialists to present useful and comprehensive information in a concise and time efficient manner. The main purposes of this prospective qualitative study are:

to explore what are the critical pieces of information that referring veterinarians expect to find in a referral summary through an online survey

to identify how much variations in expectations there is between referring veterinarians

to draft a standardised referral summary template that would save the most time to specialist working at the UQ‐SAVTH and comply with the needs of referring veterinarians

This project has been designed with the following practical ideas in mind:

1) to ensure quality and satisfaction of service to referring veterinarians,

2) to understand better the similarities and differences between referring veterinarians with regards to specialist referral summaries,

3) to save time to specialists clinical teachers to allow them to concentrate on their primary audience, the students.


Expected outcomes:

Suitable for any student interested in animals as well as practice management. Therefore veterinary students, medical school or business school students are encouraged to apply but all students enrolled at UQ should feel free to apply. The study will involve some meetings at Gatton but could be done in part remotely. Students usually located at St Lucia can use the free intercampus bus running daily between both campuses.

Mainly, this project requires an individual who is enthusiastic and proactive as well as reliable and hardworking. Having advanced knowledge and interest in business management in relation with the medical field as well as data collection and statistical analysis would be particularly valued but is not mandatory. Some specific knowledge about the veterinary industry would be an asset for this project but is not required to apply.

Suitable for:. The student can expect to:

‐ learn about the organisation of the veterinary industry ‐ be involved and learn about study design ‐ be involved and learn about creating an online survey


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‐ be involved and learn about data analysis ‐ present the preliminary results of the study in a school, university and/or

professional meeting ‐ participate in the writing of the manuscript for publication



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Contact Details:


Observation of workflow within the UQ small animal teaching hospital, identification of inefficiencies and bottlenecks, and suggestions for improvement.

The Small Animal Veterinary Teaching Hospital of the University of Queensland (UQ‐SAVTH) has a double mission of serving the community and providing outstanding animal care as well as teaching final year veterinary students. Clinical teaching occurs all throughout the process of patient management within the hospital and can slow down the workflow and make operations less streamlined. The main purposes of this observational study are:

to analyse the timing and duration of clinical and teaching activities performed by clinical teachers throughout the day

to identify causes of bottlenecks and inefficiencies

to formulate a plan for a strategic improvement of the workflow


1) to incorporate clinical teaching activities within hospital operation as best as possible to reduce bottlenecks,

2) to ensure efficient patient flow within the UQ‐SAVTH, offer outstanding client service and also allow students and clinical teachers to finish their day on time,

3) to increase the number of cases per day that can be processed through the hospital for an increased case exposure for students and also an increase of revenue for the teaching hospital.


Expected outcomes:

The student can expect to:

‐ learn about workflow in a veterinary hospital ‐ be involved and learn about study design ‐ perform data collection ‐ be involved and learn about data analysis ‐ present the preliminary results of the study in a school, university and/or


Suitable for:. Suitable for any student interested in animals as well as practice management. Therefore veterinary students, medical or business school students are encouraged to apply but all students enrolled at UQ should feel free to apply. The study will be mainly based at Gatton campus around summer break. Students usually located at St Lucia can use the free intercampus bus running daily between both campuses.

Mainly, this project requires an individual who is enthusiastic and proactive as well as reliable and hardworking. Having advanced knowledge and interest in business management in relation with the medical field as well as data collection and statistical analysis would be particularly valued but is not mandatory. Some specific knowledge about the veterinary industry would be an asset for this project but is not required to apply.


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Contact Details:


A comparison of the diversity of cases, financial outcomes and professional collaboration between a small animal hospital located in an urban and a rural location.

The Small Animal Veterinary Teaching Hospital of the University of Queensland (UQ‐SAVTH) was once located in the middle of the city in St Lucia campus. The UQ SAVTH was moved to the rural campus of Gatton in 2012. The location of a practice determines to some degree the type of cases seen, the amount of money spent per cases and the number of general practitioners referring cases. The main purposes of this descriptive retrospective study are:

to compare the variety of the cases presented to the UQ SAVTH at Gatton campus between 2014 and 2016 and at St Lucia campus between 2010 and 2012,

to compare the average amount spent per consultation in the two UQ hospitals,

to compare the number of referring veterinarians collaborating with the University development in both settings


1) to ensure appropriate variety of cases and exposure of students, interns and residents graduating from UQ Gatton campus,

2) to understand better the socio‐economics parameters of the area and be able to implement financial help and solutions for owners to afford care for their animals,

3) to know better the pool of referring veterinarians participating to the growth of the University and develop with them strategies to increase the referral pool of cases and future collaborations.


Expected outcomes:

The student can expect to:

‐ learn about clinic software from which the data will be extracted ‐ learn about the veterinary industry ‐ be involved and learn about study design ‐ be involved and learn about data analysis ‐ present the preliminary results of the study in a school, university and/or


Suitable for:. Suitable for any student interested in animals as well as practice management. Therefore veterinary students or business school students are encouraged to apply but all students enrolled at UQ should feel free to apply. The study will be mainly based at Gatton campus around summer break. Students usually located at St Lucia can use the free intercampus bus running daily between both campuses.

Mainly, this project requires an individual who is enthusiastic and proactive as well as reliable and hardworking. Having advanced knowledge and interest in business management in relation with the medical field as well as data collection and statistical


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analysis would be particularly valued but is not mandatory. Some specific knowledge about the veterinary industry would be an asset for this project but is not required to apply.



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Supervisor Dr Joerg Henning Duration: 6 weeks

Contact Details:


Descriptive analysis and mapping of snake injuries in Southeast Queensland

Data collected on snakes submitted to a wildlife hospital will be analysed in this project to describe causes of injuries, diagnoses and outcomes of hospitalisation. The locations of snake injuries will be mapped. The applicant for this research project is expected to conduct data management and data analysis under supervision.


Expected outcomes:

The applicant will gain skills in data analysis. It is expected that a report will be produced by the applicant, which should lead to a scientific application.

Suitable for:. This project would suit a Bachelor of Veterinary Science student with a strong interest in data analysis. As this project will require the analysis of data, basic skills in spreadsheets, database software and statistical analysis are required.


The start date is flexible and will be discussed between the supervisor and the successful applicant.


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Supervisor Dr Mark Haworth Duration: 8 weeks

Contact Details:


Telephone – 0410 689 978

Clinicopathological characteristics, treatment and outcomes of elapid snake envenomation in dogs and cats in Australia

Using a Vetcompass data set we seek to define regional differences in snake envenomations in cats and dogs in Australia. Risks posed to companion animals by elapid snakes will be illustrated by an evaluation of historical, clinical, diagnostic, treatment, and outcome data. Maps of the spatiotemporal distribution of envenomations will be produced. This research will help update and improve upon previous smaller scale reports that may have been influenced by reporting bias. It will allow to better understand differences that are clinically reported in small animals.


Expected outcomes:

Development of summary statistics compiled in a report with potential contribution to manuscript drafting and editing.

Suitable for:. This project would suit a student with a strong interest in epidemiology, and emergency medicine. An aptitude with data handling and statistical analysis would be an advantage.


The starting date is flexible and can be discussed the project supervisor.


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Supervisor Dr Karen Jackson Duration: 8 weeks

Contact Details:


Office – Rm 138, Building 8114, Gatton campus

Evaluation of 4 methods of leucocyte counting in avian species

Avian leucocyte measurement is plagued with inaccurate results due to the presence of nucleated thrombocytes which are similar in size and appearance to lymphocytes. There are multiple stains and methods used to measure avian leucocyte numbers and we wish to compare 5 methods (Phloxine B, Nate‐Herricks conventional, Nate‐Herricks unconventional, toluidine blue, and manual WCC estimate) to determine the most accurate method of leucocyte counting for our laboratory in the future


Expected outcomes:

Research skills – time management, daily study planning, accurate result documentation and collation

Laboratory skills – pipetting, accurate dilutions

Clinical pathology skills – haemocytometer use, evaluation of avian blood smears

Suitable for:. Veterinary Science and Veterinary Technology students

Students with an interest in clinical pathology and laboratory work as the vast majority of this project involves bench time



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Supervisor Dr Karen Jackson

Dr Mark Haworth

Duration: 8 weeks

Contact Details:



Coombs’ testing of canine RBCs exposed in vitro to red bellied black snake venom

Canine EDTA blood samples will be mixed with varying dilutions of red bellied black snake venom and evaluated at different time points for Coombs’ positivity to investigate the potential for an immune‐mediated component to the anaemias in this clinical patients.


Expected outcomes:


Blood collection skills


Clinical pathology skills – Coombs’ testing via 96‐well plate

Suitable for:. Veterinary Science students




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Supervisor Dr Karen Jackson

Dr Mark Haworth

Duration: 8 weeks

Contact Details:



Morphologic effects of red bellied black snake venom on canine erythrocytes

Canine EDTA blood samples will be mixed with varying dilutions of red bellied black snake venom and evaluated over time for morphologic changes (i.e. ecchinocytosis, spherocytosis, unexpected morphologies)


Expected outcomes:


Blood collection skills


Clinical pathology skills – RBC morphology evaluations

Suitable for:. Veterinary science students




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Supervisor Dr Allison Stewart Duration: 8‐10 weeks

Contact Details:

Email –[email protected]

Antibody response to Hendra vaccination in foals

Hendra virus (HeV) is a uniquely Australian zoonotic virus of horses, posing significant economic, animal welfare, and public health concerns. The virus is transmitted from bats to horses.

An equine vaccine Equivac® HeV is available and antibody titres greater than 1:32 are considered protective. All horses at UQ are vaccinated, with foals vaccinated at 4‐6 months of age.

The ideal time to vaccinate foals is unknown. The project will involve bleeding foals (and mares) at birth and then every month until vaccination, then weekly for 3 weeks after vaccination.

The students will also be able to assist with a variety of other research projects being performed by the faculty supervisors or other members of the equine Veterinary team. We are also collecting samples from Hendra vaccinated adult horses to help validate a new ELISA test for measuring antibody titres and the student will assist on this project.


Expected outcomes:

Handling and blood collection from mares and foals. Sample processing. Hendra vaccination website data collection. Data entry. Research methods, preparation of a poster, literature review and/or manuscript

Suitable for:. Veterinary Science, Veterinary Technology, Equine Science, Agricultural Science or Science degrees. Previous horse handling experience is desirable but not essential.


Much of the work will be performed outside in the mornings with the horses. Meticulous record keeping and basic excel spreadsheet skills essential.


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Supervisor Dr Natalie Fraser Duration: 8‐10 weeks

Contact Details:


Maternal antibody transfer of antibodies against Hendra virus vaccine in foals and mares

Hendra virus (HeV) is a uniquely Australian zoonotic virus of horses, posing significant economic, animal welfare, and public health concerns. The virus is transmitted from bats to horses.

An equine vaccine Equivac® HeV is available and antibody titres greater than 1:32 are considered protective. All horses at UQ are vaccinated, with foals vaccinated at 4‐6 months of age.

Immunity in the equine neonate is conferred via transfer of passive immunoglobulins through ingestion of colostrum. Maternal antibody titres in foals may offer a short period of protection against HeV. The ideal time to vaccinate foals is unknown. The project will involve bleeding foals (and mares) at birth and then every month until vaccination.

The students will also be able to assist with a variety of other research projects being performed by the faculty supervisors or other members of the equine Veterinary team


Expected outcomes:

Handling and blood collection from mares and foals. Sample processing. Hendra vaccination website data collection. Data entry. Research methods, preparation of a poster, literature review and/or manuscript

Suitable for:. Veterinary Science, Veterinary Technology, Equine Science, Agricultural Science or Science degrees. Previous horse handling experience is desirable but not essential.


Much of the work will be performed outside in the mornings with the horses. Meticulous record keeping and basic excel spreadsheet skills essential.

2019/20 summer research scholarship program · faculty of science, summer research scholarship,...

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