Pawsey Internship Alumni: Celebrating Achievement!

Since 2005, more than 250 students have spent more than 2500 weeks researching and contributing to computational algorithms, data science, cloud computing, and more – through the Pawsey Summer Internship Programmes.

The story does not stop at the 2500 hours…

… These Alumni keep on giving through:

  • Activities “close to home”, e.g., participating as Pawsey Intern Mentors and Intern poster judges, and
  • Activities in the wider community, through their contributions to science, industry, government, education and more.

Pawsey Intern Alumni are recognised and celebrated here. Click on a profile below to view short summaries, or search using the filters.

If you’re a Pawsey Alumni and you would like to have your profile included, contact training@pawsey.org.au. Let’s celebrate you!

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Blake Armstrong
(2020/2021)
Alumn Year:   2020/2021
GPU-accelerated molecular dynamics simulations of complex biomolecular phenomena

The project investigated the use of GPU-acceleration in molecular dynamics (MD) simulations of complex biomolecular systems. This was done using the AMBER suite of molecular simulation programs, in which a fast GPU MD simulation engine, pmend.cuda, has been developed such that the entirety of the MD calculation is performed on the GPU while the CPU core only drives the simulation.

Vocation:       Student
Institution:     Curtin University
https://www.youtube.com/watch?v=jciHno7TVp0&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=1
Check out Blake’s video on his internship.
Supervisor:    Ricardo Mancera
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Daniel Lim
(2020/2021)
Alumn Year:   2020/2021
A global phylogenetic search for bioplastic degrading genes

Polyhydroxyalkanoates (PHAs) are a family of microbially-made polyesters that are meant to quickly degrade in the environment, but this degradation is reliant on microbially-secreted PHA depolymerases, whose taxonomic and environmental distribution have not been well-defined. As a result, the impact of increased PHA production and disposal on global environments is unknown. This Intern Project searched the global databases for metagenomes to analyze the distribution of PHA depolymerase genes in microbial communities from diverse aquatic, terrestrial and waste management systems.

Vocation:       Student
Institution:     The University of Western Australia
https://www.youtube.com/watch?v=JsIYApQGc74&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=2
Check out Daniel’s video on his internship.
Supervisor:    Daniel Murphy
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David Adams
(2020/2021)
Alumn Year:   2020/2021
Latent Space Phenotyping in a High Performance Computing Environment

In 2020, a paper entitled ‘Latent Space Phenotyping: Automatic Image-Based Phenotyping for Treatment Studies’ was published in Plant Phenomics (https://spj.sciencemag.org/journals/plantphenomics/2020/5801869/). The paper outlines a novel alternative to traditional image analysis methods for phenotyping without the need for complex and bespoke image analysis pipelines. The source code has been made available (https://github.com/p2irc/lsplab). The project was developed in Python, using Tensorflow and leverages nVidia GPUs (CUDA/cuDNN). This Intern Project looked at modernising that project on supporting infrastructure (a supercomputing environment or a cloud environment).

Vocation:       Student
Institution:     The University of Western Australia
Supervisor:    George Sainsbury
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Jack Downes
(2020/2021)
Alumn Year:   2020/2021
Semantic Change Detection - Evaluation and Analysis

Semantic change detection (SCD) is an important problem for many industries. For example, rail network operators need to identify early warning signs of deteriorating conditions of supporting structure to avoid derail accidents. Where existing detection problems aim to recognise and locate known objects, SCD aims to recognise and locate characteristics of objects that deviate from what is expected. SCD is a challenging machine learning task. This Intern Project set up baselines for advanced research in SCD, by performing and analysis and then comparing several deep learning-based change detection approaches recently proposed in the literature, such as those based on Generative Adversarial Networks (GANs), Deep Convolutional Autoencoders (CAEs), and Long Short Term Memory (LSTM) models.

Vocation:       Student
Institution:     Curtin University
https://www.youtube.com/watch?v=pcXeDmgsuDA&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=3
Check out Jack’s video on his internship.
Supervisor:    Sonny Pham
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Jackson Crowley
(2020/2021)
Alumn Year:   2020/2021
Using Molecular Dynamics Simulations to understand the Membrane Interaction of Small Molecules Capable of Improving Batten’s Disease

Batten disease is a group of genetically inherited, neuro-degenerate diseases, most of which start in early childhood. Batten is always fatal, usually in the late teens or twenties and there is no treatment to reverse or halt disease progression. The overall aim of this Intern Project was to use molecular dynamics (MD) simulations, that combined with wet-lab experiments, to improve understanding of recently discovered lead molecules to treat Batten. In addition, the simulations will assist to develop technology to screen for more lead molecules.

Vocation:       Student
Institution:     University of Technology Sydney
https://www.youtube.com/watch?v=CizVLJzMBZs&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=4
Check out Jackson’s video on his internship.
Supervisor:    Evelyne Deplazes
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Jordan Makins
(2020/2021)
Alumn Year:   2020/2021
Feature extraction and Prediction models for context-aware and adaptive Analytics in Sports

Soccer is a popular sport around the world. Effective soccer analytics could improve team performance regardless of resources by maximizing the potential of existing players, analysing opponents’ game strategies, and highlighting players’ features, which are usually undervalued in predicting winning. In this Intern Project, we explored machine learning (ML) approaches to design feature extraction and prediction models for context-aware and adaptive Soccer Analytics. We explored three types of context-aware machine learning approaches: Bayesian network, Decision Tree, and Deep Neural Networks; and one advanced adaptive machine learning approach: Forest Deep Neural Network (fDNN)

Vocation:       Student
Institution:     The University of Western Australia
https://www.youtube.com/watch?v=CG1Fpq-vmHQ&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=5
Check out Jordan’s video on his internship.
Supervisor:    Sajib Mistry
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Kate Bain
(2020/2021)
Alumn Year:   2020/2021
Angular-differential electron transfer in fast proton-helium collisions

Understanding electron transfer in ion-atom collisions is essential for a variety of applications, ranging from astrophysical processes, such as solar wind and nuclear fusion, to modern cancer treatment techniques like hadron therapy. The goal of this Intern Project was to perform accurate calculations of differential cross sections for electron capture in high-energy (MeV regime) proton-helium collisions using a semiclassical wave-packet convergent close-coupling (WP-CCC) method recently developed in our group [Alladustov et al 2019 Phys. Rev. A 99 052706].

Vocation:       Student
Institution:     Curtin University
Supervisor:    Alisher Kadyrov
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Keaton Wright
(2020/2021)
Alumn Year:   2020/2021
Deep generative models for geosciences

The Intern Project explored applications of deep generative models in geoscientific model development. Applying deep learning algorithms to parameter estimation problems has received active interest from both academia and industry in recent years. Modern deep neural networks allow for fast reconstruction of various subsurface properties with a sufficient degree of accuracy. At the same time, realistic models require large datasets for training, which are not always possible to obtain from real data. Using deep generative models can significantly improve the performance. The project used the latest development in deep learning algorithms and worked with real data.

Vocation:       Student
Institution:     The University of Western Australia
https://www.youtube.com/watch?v=z6BniVBCqdk&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=6
Check out Keaton’s video on his internship.
Supervisor:    Vladimir Puzyrev
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Mitchell Gill
(2020/2021)
Alumn Year:   2020/2021
Optimising machine learning pipelines for genomic prediction

Genomic prediction has been a staple of plant and animal breeding, but ‘classic’ approaches cannot suitably model large datasets or complex additional datasets, such as time-series weather data. ‘Modern’ approaches such as the construction of Artificial Neural Networks can be highly effective for prediction of complex data. The Intern Project built ensembled Artifical Neural Networks that took already existing genomic and weather data in two streams to calculate phenotypic predictions. The input data was divided into training, testing and hold-out sets, where the neural network was built upon training and testing data and ideally could accurately predict phenotypes from the hold out set. Once built the Neural Networks were further optimised, taking advantage of the GPU backend for optimal hyper-parameter selection, to improve the phenotypic predictions in crop breeding.

Vocation:       Student
Institution:     The University of Western Australia, Australia
https://www.youtube.com/watch?v=Yy_gvQ7hEHI&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=7
Check out Mitchell’s video on his internship
Supervisor:    David Edwards
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Rebecca Green
(2020/2021)
Alumn Year:   2020/2021
Large scale simulations of electrified liquid-liquid interfaces

The transfer of ions across liquid-liquid interfaces is key to many technological applications, such has heavy metal extractions and sensing. Although, there is a phenomenological understanding of how this process occurs, there is no detailed molecular picture of the ion transfer process in the presence of electric fields. The group has recently developed a method to correctly simulate the effect of an external electric field in heterogenous systems, which was tested on the interfaces between two immiscible liquids, water and 1,2-Dichloroethane (DCE) (the most commonly used system for sensing applications). This Intern Project continued this work by studying the properties of the water/DCE interface in the presence of electrolytes on both sides of the interfaces, focusing on determining how the structure of the interface changes with the concentration of the electrolytes and on computing the transfer potential of various ions from one liquid phase to the other.

Vocation:       Student
Institution:     The Australian National University
https://www.youtube.com/watch?v=D835Z3ZtiW8&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=8
Check out Rebecca's video on her internship.
Supervisor:    Paolo Raiteri
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Reese Horton
(2020/2021)
Alumn Year:   2020/2021
Particle transport simulations using Monte Carlo method

This Intern Project focused on computational and theoretical physics based on high-performance computing, specifically implementing a new parallelization framework for the Monte Carlo simulation computer code and performing relevant modeling calculations. In the Project, Reese studied charged particle transport in a hydrogen-helium plasma, which is particularly relevant to fusion research. The present version of the code was implemented on one node with no parallelization. Monte Carlo simulation code is very computationally intensive and appropriate parallelization needed to be implemented. In addition, approaches to visualization of the obtained results were investigated and implemented.

Vocation:       Student
Institution:     Curtin University
https://www.youtube.com/watch?v=h0Y9ORjEEnk&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=9
Check out Reese's video on his internship.
Supervisor:    Dimitry Fursa
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Tavis Bennett
(2020/2021)
Alumn Year:   2020/2021
Quantum Combinatorial Optimisation

We now know a quantum computer can solve an enormously large set of linear equations, can simulate a wide range of Hamiltonians representing chemical and biological systems, can perform various linear transformations including Fourier transforms, and can efficiently evaluate inner products and distances in super high dimensional vector space, the last of which is particularly useful in machine learning. In this Intern Project, we explored potential applications in combinatorial optimization, which are known to be notoriously difficult to solve, even approximately in general. The group recently developed a promising quantum algorithm, taking advantage of intrinsic quantum correlations and quantum parallelism, to deal with combinatorial optimization problems that scale up exponentially. The Intern Project helped to validate this algorithm through large-scale high-performance simulation of an actual quantum computer.

Vocation:       Student
Institution:     The University of Western Australia
https://www.youtube.com/watch?v=4myfyya7D3s&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=10
Check out Blake's video on his internship.
Supervisor:    Jingbo Wang
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Thai Nguyen
(2020/2021)
Alumn Year:   2020/2021
Teenage Sleep Study Visualisation

Thai took the sleep dataset that is being collected globally by students and, with the support of the Pawsey Visualisation Team, developed interactive web-based visualisations to enable high school students to explore and understand the dataset. The Intern Project is being undertaken with the goal of further growing the dataset and expanding the initial portal to include STEM educational materials and “voices” of scientists and experts.

Vocation:       Student
Institution:     The University of Western Australia
https://www.youtube.com/watch?v=CRWtcDEHFxI&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=11https://www.youtube.com/watch?v=CRWtcDEHFxI&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=11
Check out Thai's video on his internship.
Supervisor:    Linda McIver
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Tushar Nagar
(2020/2021)
Alumn Year:   2020/2021
Automatic detection of Mercurian impact craters - preparation of the Bepi Columbo mission

Impact craters across the surface of planetary bodies are of great importance to understand the formation and the evolution of celestial bodies. Secondary craters result from the debris ejection from a primary impact and lead to the formation of long chains of smaller craters on the surrounding ground. The team developed a Crater Detection Algorithm trained on Mars, detecting 94 million impact craters > 25m in diameter. The team is retraining the algorithm on the Moon, and will then turn its attention to Mercury. Mercury exhibits the most unusual secondary crater population in the Solar System. The analysis of secondary craters smaller than 1 km in diameter has never been performed because they are too numerous to be counted by hand. The goal of this Intern Project is to perform analysis on Mercury using the Messenger/MDIS-NAC (1.1m/px) by creating a training dataset using this set of imagery, to retrain the current model. The resulting automatic impact crater catalog will be used by the Bepi-Columbo mission to help target areas of interest.

Vocation:       Student
Institution:     Monash University
Supervisor:    Konstantinos Servis
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Xavier Barton
(2020/2021)
Alumn Year:   2020/2021
Binning ticks: Developing pipelines for analysing tick metagenomics

In recent years, public and government concern in Australia about the potential for tick-borne diseases in people has increased considerably. Uncertainty about Australian Lyme disease-like illness requires evidence-based science to identify the microorganisms responsible and provide conclusive data about the speed of infection after tick attachment. This Intern Project identified appropriate bioinformatic pipelines to assign taxonomy to multiple sourced samples (tick, vertebrate host, microbe), which contributed to ultimately improve diagnostic tests, treatment protocols, and the control of tick-borne diseases

Vocation:       Student
Institution:     Murdoch University
https://www.youtube.com/watch?v=bVr78tV2I8Q&list=PLmu61dgAX-aa1DW3RZ2abc_MNiicfT28x&index=12
Check out Xavier’s video on his internship
Supervisor:    Charlotte Oskam
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Adam Singor
(2019/2020)
Alumn Year:   2019/2020
Photon collisions with atoms and molecules: Rayleigh and Raman scattering

Rayleigh and Raman scattering: This research project in computational and theoretical physics used Pawsey’s high-performance computing, implementing a new parallelization framework for the photon collision computer code and performed relevant modeling calculations. The problem of photon-atom scattering was addressed using a fully quantum approach based on the evaluation of the Kramers-Heisenberg-Waller (KHW) matrix elements. Appropriate parallelization was implemented to improve computational performance

Institution:     Curtin University
Supervisor:    Dimitry Fursa
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Ashling Charles
(2019/2020)
Alumn Year:   2019/2020
Mapping conservation in the human genome with single-base-pair resolution

The goal of the Intern Project was to develop a containerised workflow solution for DNA Zoo genome alignments to human genome using the LASTZ sequence alignment program. The project planned to take advantage of the HPC and Nimbus Research Cloud architecture at Pawsey’s to test the primary alignment processing stages, using the DNA Zoo genome assemblies of diverse mammal species to human. This work is foundational to doing any comparative work, and to a key desideratum: mapping conservation in the human genome with single-base-pair resolution

Vocation:       Computer Science Intern
Institution:     Water Corporation, Australia
Supervisor:    Parwinder Kaur
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Callan Wood
(2019/2020)
Alumn Year:   2019/2020
GPU Acceleration of Carbon Molecular Dynamics Simulations

The goal of the Intern Project was to port the EDIP interatomic potential developed by the Curtin Carbon Group to GPU-enabled systems. This project continued the development of HPC capability in the Curtin Carbon Group. A number of years ago the group ported the EDIP interatomic potential to LAMMPS as part of a Pawsey Internship Project. The routines proved extremely valuable, underpinning a successful ARC Discovery Project and establishing the group as international leaders in this field. By expanding our capability into GPUs, the group planned to continue to push the boundaries of what is possible with molecular dynamics simulation.

Supervisor:    Nigel Marks
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Charlie Rees
(2019/2020)
Alumn Year:   2019/2020
Optimised automatic 3D geophysical inversion for HPC infrastructure

3D geophysical inversion is a core method for resolution of the subsurface, for a wide range of applications, but in particular is used for minerals and petroleum exploration. The goal of this Intern Project was to derive new workflows to build a “one step” process to generate 3D geophysical inversion models from native-format data, as is collected in airborne surveys. This data is inherently anisotropic as it is collected along long lines, densely sampled (e.g. 10m), but with a much greater separation between lines (e.g. 400 m). Most inversion procedures require a number of pre-processing steps, which are sub-optimal (e.g., time consuming, extensive manual input, numerous assumptions).
Modern approaches are taking advantage of HPC infrastructures that permit much more comprehensive and precise models to be implemented. The ability to rapidly and rigorously build 3D models is burgeoning as “live-data” environments and on demand services become more common

Supervisor:    Alan Aitken
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Edric Matwiejew
(2019/2020)
Alumn Year:   2019/2020
Simulation of Quantum Statistical Algorithms

Edric worked on the simulation of quantum statistical algorithms. The key to this project was the calculation of extremely large matrix exponentials using algorithms parallelised by MPI. These codes simulated the quantum statistical algorithms that were proposed by the quantum research group at UWA.

Vocation:       PhD Student
Institution:     The University of Western Australia, Australia
https://youtu.be/dEpPbwKL13g
Watch Edric's video from their internship at Pawsey
Supervisor:    Prof Jingbo Wang
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Jack Mutrie
(2019/2020)
Alumn Year:   2019/2020
Exploring structure, dynamics and aggregation propensity of Apolipoprotein A-I (ApoA-I)

The ability of proteins to fold spontaneously in their native structure or functional state is essential for biological function. Failure to fold in the native shape may lead to misfolding and aggregation of proteins into insoluble aggregates, known as amyloid fibrils. These fibrous deposits have been linked to debilitating and age-related diseases, such as Alzheimer’s, Parkinson’s, type-II diabetes and others. The Intern Project studied the role of mutations on the structure, dynamics and aggregation propensity on the lipid-oriented protein: apolipoprotein A-I (apoA-I). The accumulation of this protein as amyloid fibril has been associated with atherosclerotic plaques. The work was done in collaboration with the experimental research group led by Dr Michael Griffin from the Bio21 Institute and University of Melbourne.

Supervisor:    Nevena Todorova
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Jarrod Greene
(2019/2020)
Alumn Year:   2019/2020
A deep learning approach to evaluating mechanical properties

The Intern Project aimed at calibrating a multiphysics geomechanical simulator against experimental data using a Deep Learning (DL) approach. A specificity of the simulator used was its novel constitutive model controlling the mechanical behaviour from state variables like temperature and pore pressure. Since those properties were not directly measured, the calibration could only be obtained through an inversion process. Traditional approaches to inverse problems are largely based on deterministic gradient-based methods, which are limited by non-linearity and non-uniqueness of large-scale problems in high-dimensional parameter spaces. The non-linear physical couplings involved in multiphysics problems make this process extremely challenging, even for expert users, and therefore are particularly suitable for Artificial Intelligence (AI) methods.

Supervisor:    Vladimir Puzyrev
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Joel Dunstan
(2019/2020)
Alumn Year:   2019/2020
Critical Infrastructure Monitoring with Deep Learning

This Intern Project evaluated and compared state-of-the-art semantic segmentation methods (DeconvNet, UNet, SegNet, PSPNet, FastSCNN, DeepLabV3) for critical infrastructure monitoring. Semantic segmentation is usually the first task in any scene analysis application, providing useful information about the different foreground and background objects in the scene. The project compared the methods on benchmark segmentation datasets, and then applied them to specific applications where scenes containing critical infrastructure needed to be analysed. The project recommended the most suitable methods based on the overall speed and accuracy.

Vocation:       Sales Assistance
Institution:     Jaycar Electronics
Supervisor:    Sonny Pham
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Joseph Sigar
(2019/2020)
Alumn Year:   2019/2020
Building HPC workflows to detect novel repeat expansions in next-generation sequencing data

Repeat expansions of short tandem repeats (STRs) are responsible for over twenty-five human neurological disorders, including Huntington disease, spinocerebellar ataxias and intellectual disabilities (e.g. Fragile-X). Many disorders showing anticipation go undiagnosed as we do not know all the possible repeat expansions. Next-generation sequencing (NGS) may be used to detecting novel repeat expansions but requires computationally intensive algorithms. The goal of this Intern Project was to scan for novel repeat expansions genome-wide in hundreds of NGS samples by creating analysis pipelines using a workflow manager to help analyse NGS samples for evidence of repeat expansions and by incorporating the running of several packages for repeat detection, including HipSTR, STRetch, ExpansionHunter and exSTRa.

Vocation:       Biometrician
Institution:     Statistics for the Australian Grains Industry
Supervisor:    Nicola Armstrong
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Mitchell Cavanagh
(2019/2020)
Alumn Year:   2019/2020
ew Martian impact craters detection

The aim of this Intern Project was to automate the detection of new impact craters on the surface of Mars by using a Crater Detection Algorithm. The pipeline of data treatment involved training on images containing already known new impact craters, which were then applied on all high-resolution imagery dataset currently available, with preferential focus on dust-free regions.

Vocation:       PhD Student
Institution:     International Centre for Radio Astronomy Research (ICRAR)
Supervisor:    Anthony Lagain
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Tarun Bonu
(2019/2020)
Alumn Year:   2019/2020
Characterisation and comparative analyses of immune genes in marsupials

Tarun worked on the characterisation and comparative analyses of immune genes in marsupials. The goal of the project was to develop a containerised workflow solution to map the already characterised 800 genes vital to the immune response in the human genome for the 18 marsupial genomes available now. Among these genes are the highly divergent immune genes, such as cytokines, natural killer cell receptors, and antimicrobials. The work revealed the level of complexity of the marsupial immunome as compared to the human.

Vocation:       Data Scientist
Institution:     Monash University
Supervisor:    Sonika Tyagi
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Ailin Guan
(2014/2015)
Alumn Year:   2014/2015
Image Deblurring for improved 3D reconstructions

Images deblurring is a newly arising research area, especially for improving 3D reconstructions which are commonly used in many disciplines. Images are not always captured under ideal circumstances, which will result in lower quality images. The degraded quality images can affect the quality of some 3D reconstruction features; this will eventually lead to difficulty of 3D reconstruction, missing parts and holes in the 3D models. This project is to find an effective deblurring algorithm for images that are taken underwater for 3D reconstruction process. We focus on deblurring blurred images caused by defocus and motion, as either type of these blurred images will destroy details we need in 3D reconstruction process.

https://vimeo.com/showcase/3323011/video/123269445
Click here to view Ailin's presentation
Supervisors:   Dr Andrew Woods (Curtin University) & Dr Petra Helmholz and Joshua Hollick
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Alex Bennet
(2014/2015)
Alumn Year:   2014/2015
Meshing and Visualisation of large CFD datasets

Alex participated in the Pawsey Summer Internship Program in 2014/2015. Alex participated through Curtin University, School of Public Health.

Accurate understanding and simulation of airflow through lungs could lead to advances in aerosol medicine delivery, knowledge of lung function and other benefits to public health. Computational fluid dynamics (CFD) simulations of this kind have been carried out previously using the open source software OpenFOAM, however the sensitivity to certain input variables on lung models is yet to be tested and doing so will be important for their validation. This work looks at the sensitivity of lung airflow simulations to the expansion ratio of the lung model itself, i.e. the ratio between the lung before a breath is taken and the lung at full inflation.

Vocation:       UWA
https://vimeo.com/showcase/3323011/video/123269446
Click here to view Alex's presentation
Supervisors:   Ben Mullins & Andrew King and Ryan Mead-Hunter
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Alexander Bray
(2014/2015)
Alumn Year:   2014/2015
An alternate approach to solving quantum collision equations: Solving the CCC equation without a singularity

Alexander participated in the Pawsey Summer Internship in 2014/2015. He participated through Curtin University, Theoretical Physics.

The probabilities involved in atomic collisions can be calculated through a method known as convergent close coupling (CCC). The existing technique of solving the CCC equation involves integration over a singularity. Here, we present an alternate method using an analytical solution to the Green’s function, which yields the same results as the original formulation and yet is free from singularities.

Institution:     Curtin University
https://vimeo.com/showcase/3323011/video/123269447
Click here to view Alex's presentation
Supervisors:   Igor Bray & Prof Dmitry Fursa and Associate Prof Alisher Kadyrov
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Benjamin Courtney-Barrer
(2014/2015)
Alumn Year:   2014/2015
A Clock for the Square Kilometre Array

The Square Kilometre Array (SKA) is a global next-generation radio telescope project aiming to answer fundamental questions about our universe. A key technical challenge in building the SKA is providing a stable clock reference to each antenna. We have designed and tested a system which can stably disseminate a clock signal (10MHz) over a fibre network while actively compensating fluctuations in the fibre. The system has a stability of ~10-4 at 1s for up to 5km lengths, and has recently been verified on the Australian Square Kilometre Array Pathfinder (ASKAP) telescopes.

https://vimeo.com/showcase/3323011/video/123272963
Click here to view Benjamin's presentation
Supervisors:   Dr. Sascha Schediwy (UWA) & Dr. Sascha Schediwy (UWA)
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Hannah Klinac
(2014/2015)
Alumn Year:   2014/2015
Data interaction using human-computer interaction devices on 3D displays

Hannah participated in the Pawsey Summer Internship Program in 2014/2015. She participated through the Pawsey Supercomputing Centre.

Supervisors:   Dr Andrew Squelch & Yathunanthan Sivarajah and Paul Bourke
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Jonathan Teo
(2014/2015)
Alumn Year:   2014/2015
Exploring the Plausibility of Extracting Dimensional Measurements of Fish from Single-Camera Footage

This project aims to explore the plausibility of extracting dimensional measurements of fish from single-camera underwater footage. The extracted data could lead to estimates of body mass/biomass which can be used as indicators of fish health and stress. At present this is generally done by capturing live fish or using expensive stereo-camera setups.

The ability for researchers to monitor a marine habitat less invasively using cameras would reduce the impact they have on the habitat. The ability to analyse single-camera footage could add value to the existing abundance of underwater footage. Large volumes of video could be analysed, producing new data from old resources. Various methods were explored over the course of eothis project: photogrammetry/3D reconstruction from still frames; object recognition using cascading classifiers; and image segmentation using background subtraction.

Institution:     Curtin University
https://vimeo.com/showcase/3323011/video/123272965
Click here to view Jonathan's presentation
Supervisor:    Dirk Slawinski (CSIRO Life & Environmental Sciences)
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Kirsty Butler
(2014/2015)
Alumn Year:   2014/2015
The galactic structures of radio galaxies - a first look at what GAMA can tell us about MWACs sources

This project is a first step in investigating the galactic structures of radio galaxies in the Murchison Widefield Array Commissioning Survey (MWACS) and Galaxy And Mass Assembly (GAMA) catalogues. I look at the 69 deg^2 G23 region, yielding 40 matches and a smaller catalogue of 15 sources with redshifts. A full cross-match between all the GAMA regions and the new GLEAM survey is thus predicted to have ~200 matches for which a more comprehensive study of radio host galaxies can be made.

https://vimeo.com/showcase/3323011/video/123272967
Click here to view Kirsty's presentation
Supervisors:   Professor Carole Jackson & Professor Simon Driver
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Lewis Howard
(2014/2015)
Alumn Year:   2014/2015
Convergence of Ionization Cross Sections in the CCC Method for Electron - Atom Scattering

This project explored how large a Laguerre basis is needed in the Convergent Close-Coupling (CCC) method before convergence in the estimate of the SDCS is reached for electron scattering on atomic Hydrogen in the S-Wave model. The study found that a Laguerre basis size of 16 resulted in an estimate that was converging for incident electrons of 44.4 eV, a basis size of 17 was required for 54.4 eV electrons and a basis size of 19 for 64.4 eV electrons.

https://vimeo.com/showcase/3323011/video/123272966
Click here to view Lewis's presentation
Supervisors:   A/Prof. Alisher Kadyrov & A/Prof. Alisher Kadyrov
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Liu Yi
(2014/2015)
Alumn Year:   2014/2015
High performance 3D Reconstruction

3D reconstruction using images has become more important in different disciplines such as heritage mapping and marine science. Some of these image datasets are very large and require numerous days of processing. The goal of this project is to implement a parallel solution on the iVEC supercomputers to reduce computing time allowing a time realistic processing of large image datasets.

https://vimeo.com/showcase/3323011/video/123279688
Click here to view Liu's presentation
Supervisors:   Dr. Petra Helmholz & Joshua Hollick, Dr. Andrew Woods (Curtin University)
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Mitchell Chiew
(2014/2015)
Alumn Year:   2014/2015
We’re getting closure: New solutions for pulsar searching in the SKA era

In this project we look at the performance of the bispectrum method for detecting transient sources in interferometric data. We test a relation predicted to exist between the signal to noise ratio (SNR) of an interferometric detection of a pulsar versus the channel width of visibility data in the correlator. We used data gathered from the Giant Metrewave Radio Telescope (GMRT), and formed the closure triangles from those antennas to synthesise a time-domain signal from the combined array. We test a newly derived analytical relationship between SNR and number of channels and demonstrate that it is possible to use the bispectrum method to achieve better transient detection than ever before.

https://vimeo.com/showcase/3323011/video/123279689
Click here to view Mitchell's presentation
Supervisors:    Dr Richard Dodson & Dr Ramesh Bhat (ICRAR)
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Peter Kroeger
(2014/2015)
Alumn Year:   2014/2015
How to use a basic OpenFOAM case for wave analysis

This project was undertaken to assist Dr Andrew King in the process of developing a Computational Fluid Dynamics (CFD) simulation that analyses and estimates the potential power generation from two wave energy harvesting device designs. Due to the time constraints of the internship, this project focussed on the preliminary aspects of this analysis – calculating the forces on the wave energy harvesting devices by a wave scheme that replicates the conditions found off the coast of Perth, Western Australia.

https://vimeo.com/showcase/3323011/video/123279690
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Supervisor:    Dr Andrew King (Curtin University)
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Reece Harvey
(2014/2015)
Alumn Year:   2014/2015
Radio galaxies as revealed by the GLEAM and AT20G surveys

In order to aid the process of interpreting data across a very broad frequency range, we have developed a new technique for comparing the spectral forms of various types of radio galaxy, and defined a set of classifications based on these forms, successfully linking them back to the current understanding of radio galaxy behaviour.

https://vimeo.com/showcase/3323011/video/123062447
Click here to view Reece's presentation
Supervisor:    Dr Tom Franzen and Dr John Morgan
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Sam McSweeney
(2014/2015)
Alumn Year:   2014/2015
Massively Parallel Simulations for Carbon

The environment-dependent interaction potential for carbon (CEDIP) is implemented in LAMMPS, and its parallel efficiency is benchmarked using the Pawsey Centre’s Magnus supercomputer. CEDIP performs significantly better than the original (non-LAMMPS) version for large numbers of CPUs, and the same as (or, for larger systems, slightly poorer than) other carbon potentials.

https://vimeo.com/showcase/3323011/video/123279694
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Supervisors:   Dr. Nigel Marks & Dr. Paolo Raiteri (Curtin University)
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Samuel Warnoch
(2014/2015)
Alumn Year:   2014/2015
Connect the Kinect With Dome and Cylinder 3D Game-based Environments

Developing camera-tracking applications and other interface devices using cheaply available commercial software and hardware that allow participants to have their gestures, movements, and group behaviour be fed into the virtual environment either directly or indirectly in order for presenters to present 3D virtual worlds to remotely located audiences while appearing to be inside those virtual worlds has immediate practical uses.

https://vimeo.com/showcase/3323011/video/123279691
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Supervisor:    Erik Champion (Curtin University)
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Thuy Pham
(2014/2015)
Alumn Year:   2014/2015
Interfacial Properties of Methanol – Water and Ethanol –Water Mixtures

The interfacial properties of methanol-water and ethanol – water mixtures were studied by using molecular dynamics simulation. The surface tension, density distributions of water, methanol, ethanol and their hydrophobic and hydrophilic groups were analysed. The results show good agreements to the previous literatures. It is followed by studying the angle between the water dipole and the positive z-axis of the simulation box in terms of cosine. The presents of positive peaks at different concentrations of the alcohol confirm the existence of the second water layer. The water density from the vapour phase to the positive peak of the water dipole order was analysed in both systems. This new adoption of the second water layer has helped to quantify the amount of the water molecules, which have specific orientations at different alcohol compositions and confirm a relation to the surface tension.

https://vimeo.com/showcase/3323011/video/123279759
Click here to view Thuy's presentation
Supervisors:   Dr Chi M.Phan & Mr Cuong V. Nguyen (Department of Chemical Engineering, Curtin University)
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Dylan McCarthy
(2012/2013)
Alumn Year:   2012/2013
SkuareView Client
https://vimeo.com/showcase/3323012/video/123389909
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Jack Moore
(2012/2013)
Alumn Year:   2012/2013
Why must we live in a world without Giant Ants?
https://vimeo.com/showcase/3323012/video/123391594
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Jackson Bailey
(2012/2013)
Alumn Year:   2012/2013
Positronium Formation in Positron-Hydrogen Scattering
https://vimeo.com/showcase/3323012/video/123389911
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Supervisors:   Dr Alisher Kadyrov & Prof Igor Bray, Institute of Theoretical Physics - Curtin University
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John Snadden
(2012/2013)
Alumn Year:   2012/2013
SCIENCE! Geothermal Energy
https://vimeo.com/showcase/3323012/video/123388903
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Josh Izaac
(2012/2013)
Alumn Year:   2012/2013
Micromagnetism and GPUs
https://vimeo.com/showcase/3323012/video/123388899
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Supervisors:   Dr Peter Metaxas & Dr Vincent Baltz
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Joshua Hollick
(2012/2013)
Alumn Year:   2012/2013
3D Reconstruction of the HMAS Sydney II & HSK Kormoran
https://vimeo.com/showcase/3323012/video/123388900
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Ken Di Vincenzo
(2012/2013)
Alumn Year:   2012/2013
Visualising the Role of Topology in the Transformation of Carbon Onions to Nanodiamonds
https://vimeo.com/showcase/3323012/video/123389905
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Ken Hing Yeong
(2012/2013)
Alumn Year:   2012/2013
Whale Pattern Matching Upgrade
https://vimeo.com/showcase/3323012/video/123391595
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Supervisor:    Mark Case
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Matt Drage
(2012/2013)
Alumn Year:   2012/2013
Improvement of the Execution Time of a Cellular Automata Model for Subsidence Prediction
https://vimeo.com/showcase/3323012/video/123391596
Click here to view Matt's presentation
Supervisor:    Dr Jose Saavedra Department of Mineral and Energy Economics
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Rebecca Tung
(2012/2013)
Alumn Year:   2012/2013
3D Hydrothermal Simulations of the Perth Basin
https://vimeo.com/showcase/3323012/video/123391869
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Supervisors:   Heather Sheldon & Thomas Poulet and Peter Schaubs CSIRO
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Scott Thomas
(2012/2013)
Alumn Year:   2012/2013
Galaxies and the Electromagnetic Spectrum
https://vimeo.com/showcase/3323012/video/123388902
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Thomas Loke
(2012/2013)
Alumn Year:   2012/2013
Quantum Compilers and Jigsaw Puzzles
https://vimeo.com/showcase/3323012/video/123389908
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Andrew Cannon
(2011/2012)
Alumn Year:   2011/2012
Compression and Multi-resolution for Radio-astronomy Images
https://vimeo.com/showcase/3323013/video/123394676
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Chris Malajczuk
(2011/2012)
Alumn Year:   2011/2012
Cryoprotecting Agents
https://vimeo.com/showcase/3323013/video/123583489
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Supervisors:   Prof Ricardo Mancera & Dr Zak Hughes
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Chris Murphy
(2011/2012)
Alumn Year:   2011/2012
Quantum Discord
https://vimeo.com/showcase/3323013/video/123393861
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Grace Beven
(2011/2012)
Alumn Year:   2011/2012
Extracting 3D Models from Images of the HMAS Sydney Wreck
https://vimeo.com/showcase/3323013/video/123393860
Click here to view Grace's presentation
Supervisors:   Dr Andrew Hutchinson, Curtin University & Andrew Woods and Paul Burke
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Harrison Black
(2011/2012)
Alumn Year:   2011/2012
Input Output Server
https://vimeo.com/showcase/3323013/video/123394672
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Jianxiong Dai
(2011/2012)
Alumn Year:   2011/2012
CO2 Storage in Geological Formations
https://vimeo.com/showcase/3323013/video/123394675
Click here to view Jianxiong's presentation
Supervisors:   Dr Stefan Iglauer & Dr Andrew King
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Jonathan Goodwin
(2011/2012)
Alumn Year:   2011/2012
Visualisation Software for 2-particle Discrete Quantum Walks
https://vimeo.com/showcase/3323013/video/123394673
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Maryam Masoum
(2011/2012)
Alumn Year:   2011/2012
Understanding the Interactions of Complex Carbohydrates with Proteins using Molecular Docking
https://vimeo.com/showcase/3323013/video/123393859
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Ran Li
(2011/2012)
Alumn Year:   2011/2012
Do machines have emotions? Just like…
https://vimeo.com/showcase/3323013/video/123591489
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Steven Murray
(2011/2012)
Alumn Year:   2011/2012
A Tomography for Radio Astronomical Data Cubes
https://vimeo.com/showcase/3323013/video/123393858
Click here to view Steven's presentation