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

Funded PhD projects

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

Principal supervisor: Dr Ehsan Vaghefi -

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 -

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


Body language for wearable electronics

Principal supervisor: Associate Professor Iain Anderson

Update, 17 April 2014. Thankyou to all of those who have expressed interest in this project. The place has now been filled.


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

Supervisors: Dr Alys Clark -, Dr Joanna James (Obstetrics and Gynaecology)

The placenta is responsible for providing all the nutrients required to allow a healthy baby to develop. It’s vasculature develops via vessel branching and elongation (angiogenesis and vasculogenesis).  Two factors that appear to have a major influence on this development are biomechanical stress and oxygenation. Both have been implicated in pathological pregnancies as contributors to poor placental and fetal growth, but how perturbations to the normal placental environment in terms of these factors influence growth are largely unknown. Maternal and fetal blood flow in and around the placenta determine the stress felt by placental tissue, which influences its ability to grow. This blood flow also influences the level of oxygenation in the placental tissue, which is physiologically hypoxic in early pregnancy.

This project is part of a collaborative effort between the Auckland Bioengineering Institute and Obstetrics & Gynaecology which aims to develop a ‘virtual placenta’ using a combination of experimental and computational techniques. We aim to quantify the effects of oxygen and shear stress on placental cell proliferation and migration and to translate this into in vivo function using computer models. This project would suit a student with a background in biology and an interest in learning mathematical/computational techniques or a student whose background is in a quantitative discipline with an interest in pursuing biological experimentation.  

Project added: 20 November 2013


New advances in the understanding of gastrointestinal function

Principal supervisor: Associate Professor Leo Cheng -
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


Modeling ductus venosus blood flow: A window to fetal health

Principal supervisor: Dr David
Secondary supervisors:
Professor Frank Bloomfield (Liggins Institute), Professor Peter Stone (FMHS)
ABI Emerging Researcher Fund

Overarching aims
This project has two main aims:

  1. to better understand blood flow through the ductus venosus (DV); and
  2. to develop improved prenatal assessment techniques.

These aims will be achieved through mathematical modeling, technology development, standardization of ultrasound protocols, and risk stratification.

The fetal liver is the first to receive from the placenta oxygenated and nutrient-rich blood. This blood perfuses the hepatic circulation, and variable amounts bypass the liver through the vascular shunt, the DV: variable amounts of blood from the umbilical vein flows directly to the inferior vena cava. The degree of shunting is related to fetal health. For example, a response to intrauterine distress is an adaptive mechanism known as “brain sparing”: Highly oxygenated, nutrient-rich blood is redistributed to primarily the heart and brain. The regulatory mechanisms of DV shunting are not fully understood.  A “gold standard" to assess fetal health is measuring DV blood flow by Doppler ultrasound. Even though DV blood flow assessed by ultradound is recognized as a clinically important measure of fetal health, interpreting blood flow measures and how they relate to fetal health is not fully understood.

We are developing anatomically based computational fluid dynamics models of the DV blood flow based on clinical ultrasound measurements.

Project added: 11 November 2013


Agent-based PK-PD modelling of the killing of tumour spheroids

Principal supervisor: Dr Gib Bogle -
Secondary supervisors:
Dr Kevin Hicks (FMHS), Professor Bill Wilson (FMHS)
Funding: Marsden Fund. Funding will cover tuition fees and an annual stipend of $25,000.

A tumour develops from a single cancer cell that proliferates in an uncontrolled manner.  This is true both for the initial cancer occurrence and for the metastatic tumours that are seeded from the initial tumour.  When a tumour is diagnosed and removed, it often leaves behind many tiny “seed” tumours that are currently impossible to detect and require chemotherapy.  A very useful weapon in the arsenal of cancer researchers is the ability to grow avascular tumours in vitro, up to about 50,000 cells.  Some cell types can be cultured in suspension, in which case the tumour takes a roughly spheroidal shape.  These tumour spheroids provide an experimental vehicle for testing cancer-killing drugs, and the world-leading Auckland Cancer Society Research Centre (ACSRC) at the Medical School has extensive experience both in the development of anti-cancer drugs and in the testing of these drugs on cultured cells and in these tumour spheroids.

Model development
The project is to develop a model to simulate the growth of a tumour spheroid, and the effect of drugs on this growth.  The nutrients and oxygen diffuse from the boundary into the interior of the tumour while being consumed by tumour cells, leading to decreasing concentrations of these vital constituents in the core as the tumour expands.  Cell behaviour in the absence of pharmaceutical intervention is determined by the levels of O2 and nutrient in the cell’s immediate vicinity; a cell may divide rapidly, slowly, or not at all, and if severely deprived it will die.  Consequently a spheroid is a diffusion limited structure which ultimately develops a necrotic core as observed in tumour nodules. The first project stage is to simulate these processes.

In the second stage of the project the model will be extended to include pharmacokinetic and pharmacodynamic (PK-PD) processes and radiation, enabling it to simulate the effects of drug therapy.  The ACSRC team is in the forefront globally in the effort to develop drugs that exploit tumour hypoxia – these are chemical compounds that are non-toxic when the ambient oxygen level exceeds some threshold, but are transformed into cytotoxic compounds when the oxygen level falls below that threshold.  The project will be a close collaboration with the ACSRC team, and its primary goal will be to assist them in their drug development and in the design of optimal combined drug/radiation treatment protocols.

Project description updated to include funding: 11 November 2013
Project added: 8 October 2012.


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

Principal supervisor: Dr Jichao Zhao -
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 -
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.




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 -

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 -
Funding: funding available

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.


Bioengineering software

Principal supervisor: Randall Britten -

Bioengineering software is a new and emerging field, with a wide range of exciting research areas. The goal is to invent and build the software and databases of the virtual Physiome, which will allow for analysis, simulation and visualisation of physiological systems at all relevant spatiotemporal scales. This is an ambitious project, and is being undertaken as a global collaboration. The ABI is a recognised world leader in this area, and has strong partnerships in the USA and Europe. Examples are the following projects: CellML, FieldML, OpenCMISS-Iron, OpenCMISS-Zinc, Physiome model repository, Cardiac Atlas project. Masters or PhD level research opportunities include the following topics:

  • Advanced multi-scale visualisation (and use of technologies such as OpenGL, WebGL and distributed visualisation software architecture)
  • Symbolic computer representation of mathematical models
  • Approaches to Physiome scale model databases and image databases
  • Application of new techniques in multi-scale multi-physics bioengineering simulation such as the use of GPGPUs, HPC systems and parallelisation of numerical algorithms
  • Other related bioengineering software research areas


Bioinstrumentation development

Principal supervisor: Associate Professor Andrew Taberner -

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 -, 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 -

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 -, 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 -
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 -
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.


Inertial sensing for rehabilitation and sport performance

Principal supervisor: Associate Professor Thor Besier -

Inertial sensors using accelerometers, magnetometers, and gyroscopes are becoming smaller and cheaper and offer an exciting alternative to traditional optical methods to record human motion. The purpose of this project is to integrate inertial sensing data with a rigid body model (OpenSim) to obtain accurate estimates of joint motion and forces. This project will involve collaboration with researchers at Stanford University and result in novel products for rehabilitation and sports.

Project added: 17 April 2013.


Laboratory for Animate Technologies

Principal supervisor: Associate Professor Mark Sagar -

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 cerebral circulation to understand high blood pressure

Principal supervisors: Dr Harvey Ho -, Professor Peter Hunter, Professor Julian Paton (University of Bristol)
Funding: Presently unfunded

Despite the armory of anti-hypertensive medication, high blood pressure remains a global clinical problem with 0.9 billion people affected worldwide; this equates to 1 in 3 people (male or female). This causes heart failure, cardiac arrest, atherosclerosis, kidney failure and stroke. Remarkably, 23% of patients taking anti-hypertensive medication are drug resistant and remain with dangerously high blood pressure indicating that we do not fully understand the causes of this pathology.

We aim to determine why in the hypertensive brain there is an inability to increase blood flow adequately when neuronal activity/metabolism increases or blood pressure falls as occurs during sleep.


Modelling the complex shape of skeletal muscle

Principal supervisor: Dr Justin Fernandez -

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 -, 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 -

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 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 -

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 -

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 -, 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 -

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 -, 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 -

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 -

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.


The virtual eye project

Principal supervisor: Dr Jason Turuwhenua -

The virtual eye project is about developing an optically and mechanically 3D model of the eye, i.e., that can "see" what a person sees. It is intended that the eye be used for investigating issues of interest to health care professionals in eye related research. You would be working with clincians, vision scientists and engineers on a problem involving one or more of the following: mechanics, optics, vision and visualization!


Masters projects

Smart rubbery robots

Principal supervisor: Associate Professor Iain Anderson -

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.


Design for improving the efficiency of sinus drug delivery

Principal supervisors: Dr Haribalan Kumar, Professor Merryn Tawhai

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.


What is your intra-abdominal pressure doing?

Principal supervisor: Jennifer Kruger

Secondary supervisors: Associate Professor David Budgett, Professor Poul Nielsen

Change in intra-abdominal pressure (IAP) occurs continuously in response to activities of daily living and during exercise.  These fluctuations vary enormously between people but long term ‘high’ pressures are known to be a risk factor for women developing pelvic organ prolapse.  1 in 5 women will develop prolapse during their lifetime, which is a debilitating and socially isolating problem: characterised by pain and incontinence.

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

Our aim is to use an intra-vaginal pressure sensor (developed at the ABI) to estimate the range of IAP during a variety of activities. This data will be used to provide guidance information to clinicians treating at risk, or recovering patients.

The existing sensor will be further developed to facilitate data logging to a smart phone over Bluetooth and incorporate an accelerometer. This project will require skills in instrumentation development and programming.

You will also be interacting with participants in the study, sports and exercise practitioners, and urogynaecology surgeons.  This project 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 Jennifer Kruger, Associate Professor David Budgett or Professor Poul Nielsen.

Project added: 17 November 2013


New advances in the understanding of gastrointestinal function

Principal supervisor: Associate Professor Leo Cheng -
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.


Micromachining a Blood Vessel

Principal supervisor: Dr David Long -

Overarching Aim
To construct 3D tissue scaffolds into physiologically representative blood vessels, whose 3D geometry has been determined using non-invasive in vivo imaging

Since human vascular endothelial cells were first cultured in the early 1970s, cell culture systems have been integral for studying and understanding the structure and function of these cells. Although in vitro studies have been valuable, a key to continued utility is the design and fabrication of cell culture systems that more accurately reflect in vivo conditions. Traditional planar cell culture fail to capture the in vivo environment. A 3D cell culture system whose geometry and flow conditions better capture the in vivo physiology is needed.

The aims of this project are:

  1. to use non-invasive imaging, image processing, micromachining to construct milli- and micro-fluidic devices of physiologically representative 3D blood vessels from tissue scaffolds;
  2. to perform in vitro perfusion experiments using the engineered tissue scaffolds with an endothelialized lumen.

Project added: 12 November 2013


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

Principal supervisor: Dr Justin Fernandez -

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


An in-vivo tool for grading severity of diabetes

Principal Supervisor: Dr Jason Turuwhenua -

It may be possible to detect/assess the severity of diabetes by looking at the tortuosity of corneal nerves imaged using in-vivo laser scanning confocal microscopy (IVCM). In this project you will investigate image processing and classification techniques for this purpose. We’re interested in developing a system that can do this task automatically.


Exploiting non-exercise activity thermogenesis (NEAT)

Principal supervisors: Associate Professor Andrew Taberner -, 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 -, 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


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