Auckland Bioengineering Institute


Doctoral and masters research projects

About the doctoral projects


The research projects advertised here cover a wide range of bioengineering research, including the mathematical modelling of the physiology and pathophysiology of organ systems, instrumentation and medical device development, systems biology, biomimetics and software development. Some, but not all of these projects will require a strong undergraduate degree in engineering or applied mathematics.

Funded studentships

The funded studentships include tuition fees of $5,000 per annum plus a stipend of $25,000 per annum. Applications are invited from interested students who are eligible to undertake doctoral study at the University of Auckland.

Ask for more information on these projects


If you have any questions about these projects please contact the named supervisor directly.

For general enquiries please contact:

Dr David Long
Associate Director Postgraduate
Email: bioeng-postgrad-advisor@auckland.ac.nz

Funded PhD projects


The roles of oxygen and shear stress in placental vascular development.

Principal supervisor: Dr Alys Clark - alys.clark@auckland.ac.nz

Understanding maternal and fetal interactions in the early stages of pregnancy is key to understanding the fundamental mechanisms that are responsible for pathological pregnancy. Once the relative influence of the mechanisms proposed to be important in normal remodelling are identified, steps can be made toward appropriate management strategies for pathological pregnancies. This project aims to take a combined experimental and computational approach to understand the mechanisms of placental cell migration and proliferation in pregnancy. The project will involve in vitro assessment of cell migration and proliferation and construction of computational models of these processes to relate in vitro data to in vivo conditions.

Project added: 4 July 2014

 

Biological glass: The molecular and cellular determinations of the optical properties of the ocular lens.

Principal supervisor: Dr Ehsan Vaghefi - e.vaghefi@auckland.ac.nz

Although age-related changes to the optical properties of the ocular lens are the leading causes of refractive error (presbyopia) and blindness (cataract), we know little about how the optical properties of the lens are established and maintained at the molecular and cellular levels. Like any glass lens, our biological lens suffers from inherent refractive error, but being a living tissue it compensates for these errors by overexpressing crystalline proteins to create a gradient of refractive index (GRIN).

It is our hypothesis that differences in crystalline subtype expression and processing combined with lens structure and function generate and maintain the GRIN. We have recently shown that inhibition of lens transport increases lens water content and decreases the GRIN, suggesting the GRIN is actively maintained and that changes in lens physiology will affect overall vision quality.

In this application you will investigate how lens structure and function interact to establish and maintain the GRIN, and how alterations in these mechanisms affect our quality of vision. This will increase our understanding of the underlying molecular and cellular origins of common vision disorders, such as development of myopia in children, the transient refractive changes observed in diabetics and the myopic shift that precedes the onset of age related nuclear cataract.

Project added: 31 March 2014

 

Digital design of therapies to combat age related nuclear cataract

Principal supervisor: Dr Ehsan Vaghefi - e.vaghefi@auckland.ac.nz

Age-Related Nuclear (ARN) cataract is associated with oxidative damage to the lens core and is initiated by an age-dependent deterioration of the lens transport system. In the absence of a blood supply, this system maintains lens homeostasis by delivering nutrients and antioxidants to its core.

In this application, you will facilitate efforts to develop anti-cataract therapies by continuing the development of a 3D computer model of lens structure and function that can predict the effects of aging on the individual components of this lens transport system. To complement this modelling approach, you will use MRI to non-invasively measure water diffusion rates in human lenses.

By feeding these values back into my model, we will be able to determine how lens functionality changes with age, an important first step in the development of therapeutic strategies to combat ARN cataract by up regulating the delivery of protective antioxidants to the core of older lenses.

Project added: 31 March 2014

 

New advances in the understanding of gastrointestinal function

Principal supervisor: Associate Professor Leo Cheng - l.cheng@auckland.ac.nz
Secondary supervisor: Dr Peng Du
Funding: funding is available for multiple students through a number of grants.

This project is part of an established research group involving clinicians at Auckland City Hospital, Middlemore Hospital and physicists/clinicians/food scientists at a number of centres in NZ (Riddet Institute). We have strong collaborations with overseas investigators at the Mayo Clinic, Vanderbilt University, University of Lousville and the University of Birmingham at Alabama.

We seek motivated ME and PhD students in a number of different research areas including:

  • mathematical modelling of gastrointestinal electrophysiology and mechanical function;
  • medical imaging and image processing;
  • instrumentation and experimentation.

These projects range from basic research to clinical translation.

PhD students are required to have a Masters' or a 4 year Bachelors' degree (ideally with honours) in the fields of engineering, applied mathematics, physiology or equivalent.

Project updated: 13 November 2013

 

Image-based computer models and mapping studies to investigate mechanisms behind persistent atrial fibrillation

Principal supervisor: Dr Jichao Zhao - j.zhao@auckland.ac.nz
Funding: Health Research Council of New Zealand

We have funding that will cover tuition fees and provide support (an annual tax-free allowance of NZ$25,000, in the form of a fortnightly stipend) for multiple PhD students at the Auckland Bioengineering Institute (ABI), The University of Auckland.

The successful candidates will join a research group in the ABI and the Faculty of Medical Health Sciences, led by Professor Bruce Smaill and Dr Jichao Zhao that is investigating mechanisms of atrial fibrillation. Funding is for three years in the first instance, with possible extension for a further 6 months.

Atrial fibrillation is the most common form of heart rhythm disturbance and the ABI has developed a novel image-based computer model of the atrial chambers that is providing new insight into the factors that contribute to short-lived episodes of atrial fibrillation. This project will extend the model to deal with atrial fibrosis of persistent atrial fibrillation and is part of an international collaboration between the University of Auckland and the Center for Arrhythmia Research, University of Michigan, Ann Arbor.

The research will involve:

  1. image processing;
  2. computer model development and simulation studies;
  3. development of signal processing tools for atrial electrograms acquired in clinical and experimental settings.

We require someone with a Masters' or a Bachelors' degree with Honours (Second Class Honours, Division One or better) in Engineering, Physics or Mathematics. Undergraduate experience in computer modelling, imaging and physiology would be an advantage.

Project added: 30 May 2013.

 

Powering the next generation of implantable devices

Principal supervisor: Associate Professor David Budgett - d.budgett@auckland.ac.nz
Funding: Health Research Council of New Zealand

Smart implantable medical devices consume electrical power, our goal is to keep these devices functioning by wirelessly transmitting power into the body. With a blend of engineering disciplines required, we will develop an implantable pressure monitoring device and create a system that enables long-term chronic monitoring. This work will involve hardware and instrumentation development and miniaturisation, microprocessor software development and experimental validation work. You will be joining an active research team developing smart implantable devices for a range of applications.

 

 

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Unfunded PhD projects


The doctoral projects in this section do not have identified student funding, so student co-operation will be required in applying for scholarships.

 

Smart rubbery robots

Principal supervisor: Associate Professor Iain Anderson - i.anderson@auckland.ac.nz

The Biomimetics lab has secured research funding to support a Master of Engineering student investigating the development of novel types of materials for dielectric elastomer switches (DES). This project has substantial research potential for conversion to a PhD.  

DES are piezo resistive elements that can be combined with artificial muscles to make rubbery robots think: muscles and switches can be arranged to interact and perform simple logical actions. Currently their adoption and use is being held back by poor and unreliable materials that cannot be easily patterned, and that have inconsistent properties.

The lab has secured research funding to work in collaboration with chemical materials experts to develop new switching materials to alleviate these problems. Our collaborator is making the new materials. Our job is to work out how to integrate them into new soft robotic devices.

The candidate should have

  1. A strong BE or BSc.
  2. Good practical skills.
  3. Good communication skills.

Project added: 16 December 2013.

 

Modelling the maternal circulation to understand the causes of pathological pregnancy

Principal supervisor: Dr Alys Clark - alys.clark@auckland.ac.nz

Understanding maternal and fetal interactions in the early stages of pregnancy is key to understanding the fundamental mechanisms that are responsible for pathological pregnancy. Once the relative influence of the mechanisms proposed to be important in normal remodelling are identified, steps can be made toward appropriate management strategies for pathological pregnancies. This project will use biophysically based computational models to provide insight into the role of shear stress in pregnancy. This will establish a new understanding of the relationship between in vitro and in vivo development.

Project added: 14 September 2013.
Updated: 28 May 2014

 

Bioinstrumentation development

Principal supervisor: Associate Professor Andrew Taberner - a.taberner@auckland.ac.nz

Are you interested in developing novel bioinstrumentation for scientific research, medical research and care, or drug delivery? If so, let's talk! The ABI Bioinstrumentation team is always looking for bright, enthusiastic and creative researchers for research at ME and PhD levels. Our areas of research include instrumentation for muscle and soft-tissue characterisation, disease detection, drug delivery, exercise science, and more. We work with leading clinicians, health-care specialists, physiologists, entrepreneurs and other scientists and engineers both in New Zealand and overseas. Possible upcoming projects include:

  • A smart device for monitoring and responding to seated lower-limb movement
  • Development of imaging systems for rapid inexpensive 3D surface deformation
  • Instrumentation for high-throughput muscle cell characterisation.
  • Miniature, portable soft-tissue measuring instruments

 

Biomechanics for breast cancer imaging

Principal supervisors: Professor Martyn Nash - martyn.nash@auckland.ac.nz, Professor Poul Nielsen

A wide range of topics including biomechanics/contact-mechanics, real-time mechanics solutions, stastistical mechanics modelling, bioinstrumentation, stereoscopic imaging, clinical imaging/analysis (x-ray, MRI, ultrasound), image processing/registration, augmented reality applications, development of commercial software applications and many, many more. Join an established team of grad students and post-docs, and interact with clinical collaborators (e.g. at Auckland Hospital), to contribute to the development of clinical application software.

Project updated on 9 April 2013.

 

Cardiac electromechanics modelling

Principal supervisor: Professor Martyn Nash - martyn.nash@auckland.ac.nz

Development of models to investigate whole heart (RV+LV) excitation-contraction coupling and mechano-electrical feedback in the human heart. Applications involve investigating mechanisms of heart failure, arrhythmogenesis and therapies (such as cardiac resynchronisation therapy). This work is in collaboration with Professor Sasha Panfilov (Universiteit Gent).

 

Clinical cardiac electrophysiology and arrhythmias

Principal supervisors: Professor Martyn Nash - martyn.nash@auckland.ac.nz, Dr Chris Bradley

Developing signal processing methods to analyse and interpret dense arrays of electrical signals recorded directly from the surface of human hearts during normal rhythm, ventricular fibrillation, long duration ventricular ischaemia (8-12 mins). Work in collaboration with Dr Peter Taggart and a medical team at the University College London, and Dr Richard Clayton (University of Sheffield).

 

Exchanging models of the Virtual Physiological Human

Principal supervisor: Dr David Nickerson - d.nickerson@auckland.ac.nz
Collaborators: Professor Peter Hunter (ABI), Professor Poul Nielsen (ABI), Dr S Randall Thomas (Paris), Dr Jonathan Cooper (Oxford), Professor Jim Bassingthwaighte (Washington), Dr Bernard de Bono (London/ABI)
Key technologies: Multiscale model and simulation description, model and data exchange standards, semantic web, ontological annotation, repositories.

The ABI has a strong international reputation for the development of standards for encoding mathematical models of physiology using technologies suitable for the exchange of models between software tools. Recent developments in the annotation of such models and the association of models with experimental data have begun to provide the tools needed to encode larger and more complex models than currently possible. The goal of this project is to leverage these emerging technologies to create "computable model descriptions" which enable the exchange of complete simulation experiments of large, multiscale, physiome-style physiological models. This will significantly enhance the model publication and archival technologies available today and greatly improve the scientific methods used in the application of computational modeling to improving our understanding and treatment of human disease.

Project added: 18 July 2012.

 

Modelling the human kidney

Principal supervisor: Dr David Nickerson - d.nickerson@auckland.ac.nz
Collaborators: Dr Kirk Hamilton (Otago), Dr Daniel Beard, Dr Allen Cowley (Medical College of Wisconsin), Assistant Professor Brian Carlson (Milwaukee), Peter Hunter (ABI)
Key technologies: Multiscale modelling, high performance and GPU computation, semantic web, OpenCMISS-Iron, CellML

The Renal Physiome Project at the ABI is focused on developing a biophysically detailed model of the human kidney. We are always on the look-out for talented engineers and scientists to join our motivated team working on this exciting project. Current projects span the modelling spectrum from single proteins through to the whole renal nephron and whole kidney blood flow. Delivery of our research outputs via dynamic and interactive web-based technologies is also an important aspect of our work.

Project updated: 18 July 2012.

 

Laboratory for Animate Technologies

Principal supervisor: Associate Professor Mark Sagar - m.sagar@auckland.ac.nz

Imagine a machine that can not only express what is on its mind, but also allows you to glimpse the mental imagery that it dynamically creates in its mind.

The Laboratory for Animate Technologies is is performing the multidisciplinary research and development of interactive autonomously animated systems which will help define the next generation of human computer interaction and facial animation.

The Lab will simulate the lifelike qualities and observable natural reflexes and dynamic behaviours which we experience when we engage with a person, through realtime computational models of Face and Brain interaction.

By combining multi-scale computational models of emotion, perception, learning and memory are combined to drive highly expressive realistic or abstracted computer generated imagery which is able to engage the user on an emotional level.

State-of-the-art computer vision techniques are being developed to track facial expression and behavior,which is combined with other multimodal input to allow the model to sense the world.

Collaborations with researchers working on different areas of brain function gives them an experimental context in which to test their models in action as they interact with other models in a closed loop system.

To gain insight into the complex interplay of the computational models we will use advanced 3D computer graphics to visualize in new and fantastic ways the simulated activity going on behind the scenes showing the dynamically evolving internal states and mental imagery which is giving rise to the expressive behaviours of the face we are interacting with.

Artistic opportunities abound with the fantastic visual and responsive possibilities as the research will provide a nexus for the Arts and the Sciences.

We conduct both pure and applied research with applications ranging from live digital characters for next generation entertainment media and from interactive architecture to healthcare robotics.

Research projects include:

  • Realtime markerless facial expression recognition and tracking
  • Neural system models of Emotion, Cognition, and reflexive behaviour
  • Unsupervised and reinforcement learning using real time spike timing based neural network models
  • Real time 3D computer graphics for realism and visualization
  • Combining different models of computation
  • Computer vision and speech
  • Biomechanical modelling
  • Robot and artificial muscle control
  • Artistic, design or architectural applications using interactive technology and projective realtime graphics

 

Modelling the complex shape of skeletal muscle

Principal supervisor: Dr Justin Fernandez - j.fernandez@auckland.ac.nz

Skeletal muscles are complex structures in terms of their geometry, material properties, and function. To estimate accurate muscle geometry, we typically segment a series of magnetic resonance images (MRI), which is a time-consuming, manual process. The purpose of this project is to develop statistical shape models of skeletal muscle (using Principal Component Analysis), to assist the rapid segmentation and mesh-generation of subject-specific muscles for clinical application.

Project added: 12 October 2012.

 

Pelvic floor and childbirth research

Principal supervisors: Professor Poul Nielsen - p.nielsen@auckland.ac.nz, Professor Martyn Nash, Dr Jenny Kruger

The ABI has developed a computational model of the pelvic floor muscles and fetal skull in order to simulate the second stage of labour. However the model is constrained at the moment by several factors, one of which is how to model fetal head moulding which commonly occurs during labour. The current childbirth model only includes a fetal skull, which limits the choices of boundary constraints applied to the fetus during the second stage of labour. This project aims to address this by extracting information from ultrasound images of the fetal head and neck, acquired in late pregnancy, using tools such as Matlab, ZINC digitiser and OpenCMISS-Zinc, for segmentation and mesh generation. This would not only enhance the modelling framework but would enable the exploration of different boundary constraints on the fetus, and consequently the ability to simulate the process of fetal head moulding during a vaginal birth. The project will give student the opportunities to collaborate with medical specialists, learn more about medical imaging, and in-depth experience with finite element modelling method. A range of areas including population analysis of fetal skull shape/structure (ultrasound during pregnancy), contact biomechanics, childbirth modelling, fetal head moulding, bioinstrumentation (compliance device) could be explored.

 

Postgraduate work with the Biomimetics Lab

Principal supervisor: Associate Professor Iain Anderson - i.anderson@auckland.ac.nz

Biomimetics is the imitation of natural systems to solve problems and develop new technology. It is extensively used in the pharmaceutical and robotics industries, where it has produced lucrative advances. The Biomimetics Lab is gaining international recognition for our work in the fields of artificial muscle machines, power generation, sensing and control. The lab is skilled at both modelling and rapid prototyping of devices. We believe that ideas should be proven experimentally, and back this philosophy up by producing demonstration devices that we show off around the world.

We research and develop smart and soft machines that can be used for a wide variety of applications. We are on the lookout for smart students. Some of the work on offer includes:

  • Smart materials with integrated soft logic structures
  • Wearable energy harvesters
  • Biomimetic propulsion and air flow control
  • Built-in sensing and health monitoring of artificial muscles
  • Soft electrical machines

We have a very strong team culture. As a new member of the lab you will receive training and help so that your research project can hit the ground running. We need smart brains to get us to our goals. Please drop by and meet the team.

 

Predicting outcome of anterior knee pain surgery

Principal supervisor: Dr Justin Fernandez - j.fernandez@auckland.ac.nz

Anterior knee pain is a common knee disorder, causing pain and discomfort. One potential mechanism of pain is increased mechanical stress in the joint, caused by misalignment of the patella. This misalignment can be due to an ‘over-active’ lateral quadriceps muscle and recent clinical studies have suggested that injection of Botulinum Toxin into the lateral quadriceps can redistribute forces and reduce knee joint stress. The purpose of this project is to use a computational model to test this hypothesis and predict the mechanical stress in the knee joint before and after a Botulinum Toxin injection.

Project added: 12 October 2012.

 

Real-time haptic (touch) feedback for gait retraining

Principal supervisor: Dr Justin Fernandez - j.fernandez@auckland.ac.nz

Movement is fundamental to our existence and movement disorders such as stroke, cerebral palsy and osteoarthritis dramatically impact quality of life. In walking, these disorders can alter muscle and joint forces leading to rapid joint degeneration. The purpose of this project is to estimate muscle and joint forces in real-time and provide skin stretch (haptic) feedback using artificial muscle to alter walking patterns in patients with knee joint osteoarthritis. This novel approach to movement retraining has potential to revolutionise rehabilitation strategies for a wide range of movement disorders.

Project added: 12 October 2012.

 

Redefining the lymphatic anatomy of the armpit in breast cancer

Principal supervisors: Professor Poul Nielsen - p.nielsen@auckland.ac.nz, Professor Martyn Nash

Breast cancer is a fatal disease, which can quickly spread to draining lymph nodes if left untreated. These draining lymph nodes are commonly located in the armpit (i.e. the axilla), however current knowledge of lymphatic anatomy in this region is limited. This project aims to redefine the lymphatic anatomy of the axilla, working in close collaboration with Professor Roger Uren from the Sydney Cancer Center. The student will utilise a large SPECT/CT data from breast cancer patients treated to build a 3D anatomical model of the lymphatic system that will then be used to predict shape changes to the axilla during different clinical procedures. The student will develop skills in image processing, finite element modelling and statistical techniques to make a significant impact to our understanding of breast cancer spread, and clinical practice in breast cancer treatment.

 

Research into structural heart disease

Principal supervisor: Professor Bruce Smaill - b.smaill@auckland.ac.nz

Alterations in the structure of cardiac tissue after a heart attack (myocardial infarction) or as a result of hypertension affect the electrical and mechanical performance of the heart and may lead to life-threatening disturbances of heart rhythm and to pump failure. The Auckland Bioengineering Institute (ABI) leads a major research programme in this area that is funded by the Health Research Council of New Zealand and involves staff and graduate students from the ABI, the School of Medical Sciences and Auckland City Hospital, as well as collaborators in the United Kingdom, Europe and the United States. Projects include: (1) characterization of structural and mechanical changes in the heart during the progression to heart failure (2) a study of disturbances of heart rhythm in the region surrounding a healed myocardial infarction, and (3) development of flexible computer models of the atrial chambers of the heart that can be used to better understand atrial rhythm disturbances that are commonly observed in heart failure. The individual projects that constitute this research are linked by three common factors. They each utilize novel measurement and imaging techniques to access data that has not previously been available, they seek to integrate experimental information using sophisticated structure-based computer models and they all address explicit clinical problems. We have funded PhD positions in each of these research areas that would suit students with a wide range of interests and skills.

Project updated on 9 April 2013.

 

Skin instrumentation, experiments and modelling

Principal supervisors: Professor Poul Nielsen - p.nielsen@auckland.ac.nz, Associate Professor Andrew Taberner, Professor Martyn Nash

Imagine a small trampoline, no larger than a $1 coin. We want you to help us to construct a motorised testing device to stretch the trampoline while monitoring and controlling its tension. This project will involve design and construction, and will require the use and control of some new and interesting "squiggle motors." If you're interested in bioinstrumentation, image acquisition, programming and finitel element modelling, then this could be the project for you! This involves instrumentation, modelling, experimentation.

 

Structure-function relationships in the paediatric lung

Principal supervisor: Dr Alys Clark - alys.clark@auckland.ac.nz

There are currently no biomechanical models of paediatric lung tissue, which differs considerably from the fully developed adult lung. Although large airways and blood vessels change only in calibre from birth, the respiratory regions (which contribute the majority to lung elasticity) continue to develop through childhood. It is essential to capture the impact of these changes on tissue mechanics for longitudinal monitoring of children in via imaging (e.g. CT/MRI). The aim of this project will be to develop age-dependent model of the non-linear elastic properties of respiratory tissue. This will account for changes in the mechanical properties of the lung in development and explain age-related changes in the gas exchange function of the lung.

Project added: 12 October 2012.

 

Tracking the heart: image is everything

Principal supervisor: Professor Alistair Young - a.young@auckland.ac.nz

In collaboration with Siemens Medical Solutions, a major industrial supplier of MRI scanners, we are developing better ways of evaluating heart disease by automatically tracking heart motion using computer modelling. This project will teach you about biomedical image analysis, non-rigid registration, MRI, and diagnosing heart disease.

 

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Masters projects


Smart rubbery robots

Principal supervisor: Associate Professor Iain Anderson - i.anderson@auckland.ac.nz

The Biomimetics lab is investigating the development of novel types of materials for dielectric elastomer switches (DES).

DES are piezo resistive elements that can be combined with artificial muscles to make rubbery robots think: muscles and switches can be arranged to interact and perform simple logical actions. Currently their adoption and use is being held back by poor and unreliable materials that cannot be easily patterned, and that have inconsistent properties.

We are working in collaboration with chemical materials experts to develop new switching materials to alleviate these problems. Our collaborator is making the new materials. Our job is to work out how to integrate them into new soft robotic devices.

The candidate should have

  1. A strong BE or BSc.
  2. Good practical skills.
  3. Good communication skills.

Project updated: 14 August 2014.

 

Design for improving the efficiency of sinus drug delivery

Principal supervisors: Dr Haribalan Kumar hkmu551@aucklanduni.ac.nz, Professor Merryn Tawhai m.tawhai@auckland.ac.nz

Drug delivery to the paranasal sinuses for treating chronic sinusitis is limited. Currently available spray devices have been shown to have poor efficacy and are only capable of distributing drug to a small part of the sinuses. When drug therapy is not successful, surgery is required to enlarge sinus openings and improve airflow. It is hypothesized that the development of devices that optimize drug delivery to the sinus mucosa would lead to significantly better clinical outcomes.

This project would involve computational modeling and testing of design parameters for targeted sinus drug delivery. The parameters affecting drug delivery are nozzle diameter, jet velocity, drug orientation, penetration distance inside the nasal cavity, among others. This could result in hundreds of design points. The optimal design would improve drug residence time and maximize drug transport and deposition. This project will involve use of commercial software such as ANSYS to achieve a goal-driven design optimization. The project might also involve generation of 3D prototypes from Solidworks.

Project added: 5 December 2013.

 

Can you take the pressure? Developing sensors to measure abdominal pressure in real life situations.

Principal supervisor: Jennifer Kruger j.kruger@auckland.ac.nz.

Secondary supervisors: Associate Professor David Budgett, Professor Poul Nielsen

Do you want to create instruments, gather and interpret real-life data? If this is you – read on.

Change in abdominal pressure varies significantly between people. Long term high pressures are known to be a risk factor for women developing pelvic floor disorders (PFD) with 20% of women developing PFD during their lifetime. This is a debilitating and socially isolating problem characterised by pain and incontinence. We have developed an intra-vaginal pressure sensor to measure abdominal pressure during exercise and activities of daily living. We now want to refine the device to enable more accurate long-term measurement of abdominal pressure, and thus improve post operative patient guidelines and recommendations for exercise.

The purpose of this study is to measure abdominal pressure across a range of exercises, BMI and activities of daily living.

Our aim is to use a refined intra-vaginal pressure sensor (developed by you) to measure the range of abdominal pressures during a variety of activities. This data will be used to provide guidance to clinicians treating at-risk or recovering patients.

The existing pressure sensor will be interfaced to a smart phone via Bluetooth and a custom app providing control, diagnostics and data logging. New ideas on the mechanical aspects of the sensor design would be exciting to follow up on too. This project will require skills in instrumentation development and programming.

You will be interacting with participants in the study, sports and exercise practitioners, and urogynaecology surgeons. This instrumentation-based project will make an excellent Masters project but, with data analysis and patient interaction, could develop into a PhD project.

For more information please contact Dr Jennifer Kruger, Associate Professor David Budgett, or Professor Poul Nielsen.

Project updated: 10 June 2014

Project added: 17 November 2013

 

New advances in the understanding of gastrointestinal function

Principal supervisor: Associate Professor Leo Cheng - l.cheng@auckland.ac.nz
Secondary supervisor: Dr Peng Du
Funding: funding is available for multiple students through a number of grants.

This project is part of an established research group involving clinicians at Auckland City Hospital, Middlemore Hospital and physicists/clinicians/food scientists at a number of centres in NZ (Riddet Institute). We have strong collaborations with overseas investigators at the Mayo Clinic, Vanderbilt University, University of Lousville and the University of Birmingham at Alabama.

We seek motivated ME and PhD students in a number of different research areas including:

  • mathematical modelling of gastrointestinal electrophysiology and mechanical function;
  • medical imaging and image processing;
  • instrumentation and experimentation.

These projects range from basic research to clinical translation.

PhD students are required to have a Masters' or a 4 year Bachelors' degree (ideally with honours) in the fields of engineering, applied mathematics, physiology or equivalent.

Project updated: 13 November 2013.

 

Integrating spine biomechanics with NaF imaging to evaluate bone remodelling and pain

Principal supervisor: Dr Justin Fernandez -  j.fernandez@auckland.ac.nz

Funding: This project is funded through a Wishbone Trust Grant for fees and will be matched with a $10k stipend for a student with a suitable GPA.

Lower back pain is a disabling and chronic condition with a high cost to society. Unfortunately, the cause of back pain is multifactorial and difficult to identify. Remodelling of bone, due to mechanical stress, has recently been highlighted as a potential source of pain, although evidence to support this relationship in patients with low back pain is lacking. Positron Emission Tomography (PET) is a functional imaging modality that offers an unprecedented ability to measure bone metabolism using a Sodium Fluoride (18F-NaF) marker.

The purpose of this study is to evaluate whether patients with low back pain have increased uptake of 18F-NaF in regions that correspond to pain and bone remodelling.

Our aim is to use previously collected orthopaedic 18F-NaF PET-CT imaging data sets and develop customised biomechanical models of the lumbar spine to estimate mechanical stress in the bone. Bone stress will be registered with 18F-NaF PET-CT hot spots to evaluate if there is a correlation between regions of hot spots and regions of high mechanical stress and/or pain.

This project will involve interaction with orthopaedic surgeons and a radiologist, and may be converted to a PhD if the student shows interest and potential.

For more information or a chat about the project please contact Dr Justin Fernandez.

Project added: 24 October 2013

 

Exploiting non-exercise activity thermogenesis (NEAT)

Principal supervisors: Associate Professor Andrew Taberner - a.taberner@auckland.ac.nz, Professor Wayne Cutfield, Professor Poul Nielsen

We are in the midst of global obesity pandemic that is largely due to an imbalance between energy intake (food) and energy expenditure (activity) with inactivity as the major cause of this imbalance. Since most members of society have an aversion to exercise, more subtle and indirect measures to enhance energy consumption need to be developed.

The Liggins Institute and the ABI are developing a device that will exploit and increase non-exercise energy expenditure, thereby help to redress the energy imbalance and treat and prevent obesity. Our device is capable of tailoring movement in response to measured lower limb force magnitude and orientation, thus providing a versatile test platform for testing and modifying movement stimuli that encourage energy expenditure.

We now require an engineering student to extend the capabilities of this device to include wireless inertial measurements of limb motion, and to assist with developing methods for measuring and encouraging NEAT. In this project, you will work alongside engineers at the ABI and clinicians and scientists with the Liggins Institute. LabVIEW-Realtime and LabVIEW-FPGA programming will be required, together with conducting measurements in the clinic at the Liggins Institute.

Project added: 2 July 2012.

 

Sensors for flying bats

Principal supervisors: Associate Professor Andrew Taberner - a.taberner@auckland.ac.nz, Professor Poul Nielsen, Associate Professor Stuart Parsons

Bats are the only mammals capable of true flight, during which the vast majority navigate and hunt using echolocation – emission of ultrasonic calls through either the nose or mouth and subsequent reception and processing of returning echoes. Both flight and echolocation are energetically expensive and it is generally accepted that bats link the two to reduce energetic costs. As the pectoralis muscles pull the wing down, they also compress the chest forcing air out of the lungs and a call is made. This theory of energetic savings relies on the fact that bats breath out as the pectoralis contracts (i.e. as the wings move down).

However, evidence to support this assumption is weak: only one study (conducted in 1972) has investigated the breathing patterns of bats in flight and it showed that bats exhale as the wings are moving up. If this result is indeed correct, how bats reduce the energetic cost of flight and echolocation remains a mystery.

This project aims to reproduce, or not, the results of the 1972 study on breathing patterns of bats in flight. To achieve this we need to develop a small wireless sensor and data logger that can be carried by a bat in flight, allowing us to monitor and record the breathing patterns of flying bats. The sensor must have a mass of only a few grams, and not impede the motion of the bat in flight.

Project added: 1 February 2013

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Postgraduate opportunities available elsewhere


Advanced image analysis for prostate cancer using functional imaging and histopathology

Institution: University of Melbourne, Sir Peter MacCallum Department of Oncology, based within the
Peter MacCallum Cancer Centre (Peter Mac).

As Australia’s only public hospital solely dedicated to cancer treatment, research and education, one of Peter Mac’s core visions is to drive the translation of research into innovative clinical treatment approaches. Research at Peter Mac embraces the full spectrum, from fundamental studies on cancer cell growth to major national and international clinical trials of the newest cancer therapies. There is a special focus on identifying the key drivers of cancer growth, the use of advanced imaging techniques to monitor cancer spread, and in developing personalised, molecularly targeted treatments.

Project added: 10 February 2013