Auckland Bioengineering Institute


Doctoral and masters projects for China Council scholars

This page summarises the research projects available to recipients of the China Scholarship Council.

About the research projects


This page summarises the research projects available to recipients of the China Scholarship Council only. If you are a domestic student please browse the research projects on our 'Doctoral and masters research projects for 2013' page.

The project topics cover a wide range of bioengineering research, including mathematical modelling, instrumentation, software development, physiology and medical device development, which have been specifically designed for the research of tomorrow in China.

We welcome applicants with a strong background in engineering, applied mathematics, computer science, or physiology.

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

Doctoral projects


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

Principal supervisor: Dr Gib Bogle, g.bogle@auckland.ac.nz

Background
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 20,000 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, 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.

The project will use literature parameters and experimental parameters derived from ongoing studies on spheroids. In particular a unique aspect of this project will be the use of nutrient and drug transport parameters obtained from experiments on multicellular layers, a planar version of spheroids which allow diffusion.

This project is a first step in developing models of tumour growth and response to therapy, including angiogenesis and remodeling, which will integrate aspects of tumour physiology.

Project added: 8 October 2012.

Automated hybrid analytic and numerical analysis of declaratively represented mathematical models

Principal supervisor: Dr Andrew Miller, ak.miller@auckland.ac.nz

Declarative mathematical modelling languages like CellML, which can be used to represent mathematical models of biological systems, represent equations in a symbolic form, allowing them to be analytically transformed. These transformations have the potential to greatly accelerate numerical computations (such as integrating a system of differential-algebraic equations over time to find a time course) and make larger problems feasible, when compared to pure numerical analysis. This project will explore what can be done by combining automated symbolic computation with numerical computation, and help push the boundaries of the scale of analysis that can be automatically performed on declaratively represented mathematical models.

Bioengineering software

Principal supervisor: Randall Britten, r.britten@auckland.ac.nz

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, 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 Prof Sasha Panfilov (University of Utrecht).

Clinical cardiac electrophysiology and arrhythmias

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

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 Richard Clayton (University of Sheffield).

Exchanging models of the Virtual Physiological Human

Principal supervisor: Dr David Nickerson, d.nickerson@auckland.ac.nz
Collaborators: Peter Hunter, Poul Nielsen (ABI), S Randall Thomas (Paris), Jonathan Cooper (Oxford), Jim Bassingthwaighte (Washington), 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.

Inertial sensing for rehabilitation and sport performance

Principal supervisor: Dr Thor Besier, t.besier@auckland.ac.nz

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: Dr 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 cellular communication in the lungs

Principal supervisor: Dr Vinod Suresh, v.suresh@auckland.ac.nz

The alveolar epithelium consists of two cell types with different structures and functions. Communication between the cell types occurs by diffusion of chemical species in the extracellular medium and direct exchange through channels that connect the cells. Use mathematical modelling and imaging techniques to explore cellular communication under normal and pathological conditions.

Modelling heat transfer in the hands

Principal supervisor: Dr Vinod Suresh, v.suresh@auckland.ac.nz

Blood vessels in the skin are sensitive to changes in ambient temperature. Cold temperatures cause arteries to constrict in order to limit the loss of heat from warm blood. When this normal thermoregulatory mechanism goes awry, a condition called Raynaud’s phenomenon may be the result. People suffering from this condition have hands that are unusually sensitive to cold. Arteries supplying the hands over constrict and cause the fingers to turn blue or white. The recovery from cold is also slower than normal. It is estimated that 3 – 5% of the population suffer from this condition and it could indicate an increased chance of developing more serious connective tissue disorders later in life. A common diagnostic test for Raynaud’s phenomenon measures the temperature response of the fingers after a cold challenge, but the test does not measure the degree to which blood flow is impaired. The aim of this project is to determine if thermal imaging and mathematical modelling can be used to quantitatively estimate blood flow.

Modelling the cerebral circulation to understand high blood pressure

Principal supervisors: Professor Peter Hunter: p.hunter@auckland.ac.nz, Dr Harvey Ho, Professor. Julian Paton

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 Fernande, 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.

Modelling the human kidney

Principal supervisor: Dr David Nickerson, d.nickerson@auckland.ac.nz
Collaborators: Kirk Hamilton (Otago); Dan Beard, Allen Cowley, 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.

New advances in the understanding of gastrointestinal function

Principal supervisor: Dr Leo Cheng, l.cheng@auckland.ac.nz

This project is part of an established research group involving clinicians at Auckland City Hospital and physicists/clinicians/food scientists at a number of centres in NZ (Riddet Institute) and overseas (Mayo Clinic, Vanderbilt University, University of Mississppi). Funding is available for motivated ME and PhD students in a number of different research and 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.

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 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.

Powering the next generation of implantable devices

Principal supervisor: Dr David Budgett, d.budgett@auckland.ac.nz

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.

Predicting outcome of anterior knee pain surgery

Principal supervisor: Dr Justin Fernande, 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 Fernande, 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, 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.

The rumen epithelium

Principal supervisor: Dr Vinod Suresh, v.suresh@auckland.ac.nz

The rumen of the cow is a 100 litre fermentation chamber that converts plant matter into energy-rich substrates which are absorbed through the epithelium lining the rumen. Use imaging and mathematical modelling to explore the structure of the rumen epithelium and understand its role in transporting nutrients.

Skin cancer therapy

Principal supervisor: Dr Mike Cooling, m.cooling@auckland.ac.nz

Skin cancer is a serious health problem in New Zealand. Pharmacological skin cancer treatments are designed to reverse the effect of mutations in the cancer cells and make such cells behave normally again. But, some of the most promising drugs cause abnormal behaviour in non-cancerous cells. The attempted cure can often lead to new, different cancers in the surrounding normal tissue.

In the case of one commonly-used drug, the main cellular signalling pathway concerned, details of several common mutations and the mechanical basis for the drug itself are all believed to be known, some of these having come to light during 2012.

We aim to use engineering principles to make sense of the collected observations from from real human skin, and a realistic skin culture developed at the University of Auckland, and use this knowledge to suggest better drug combinations and drug targets.

Project added: 1 March 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.

Teach a computer to build a model

Principal supervisor: Dr Mike Cooling, m.cooling@auckland.ac.nz

Mathematical models can be constructed from smaller, component models - perhaps each individually representing one player or relationship in a model- that are used as building blocks to construct the larger whole. We have recently produced a set of principles that make model components easy to connect to one another, and a collection of model components following those principles. Computers can use these components if they understand what the elements of the components mean, and how to connect those elements together. This can be partially achieved by tagging elements with agreed labels.Recently, such labels have been developed across many areas of bioengineering, and we have developed ways of tagging our component models with these labels.

This project is about bringing these techniques together and exploring how they can be used to get the computer to assist (or even automate?) model construction, conversion and interoperability.

Project added: 1 March 2013.

Tracking the heart: image is everything

Principal supervisor: Associate 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.

The virtual eye project

Principal supervisor: Dr Jason Turuwhenua, j.turuwhenua@auckland.ac.nz

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!

Understanding the intracellular events which lead to vascular wall mal-adaptation

Principal supervisor: Dr Mike Cooling, m.cooling@auckland.ac.nz

We aim to help treat and prevent cardiovascular disease, the developed world’s major killer. The project involves mathematical modelling, laboratory experimentation and computational analysis of key intracellular events leading to vascular wall mal-adaptation, which can lead to (for example) aneurysm formation or atherosclerosis. There is a significant international component, via existing collaborations with MIT (USA), BioSym (Singapore), Monash (Australia) and Newcastle-Upon-Tyne (UK). The mathematical models will also form foundational entries in a repository of cell-signalling models for use by researchers worldwide. Previous experience in the specific methods is not necessary. This project represents an exciting platform for a self-motivated candidate who will make the most of the multiple opportunities presented.

Top

Masters projects


An in-vivo tool for grading severity of diabetes

Principal Supervisor: Dr Jason Turuwhenua, j.turuwhenua@auckland.ac.nz

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, 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.

Heart-lung interaction in lung pathology

Principal supervisors: Associate Professor Merryn Tawhai, m.tawhai@auckland.ac.nz, Dr Alys Clark
Funding: this project is for a fully funded Masters, but has the potential to be converted to a PhD.

Lung diseases that affect the pulmonary blood vessels can cause elevation of right ventricular pressure. In acute pulmonary embolism (occlusion of lung arteries by blood clots) the drastic increase in right heart pressure can cause sudden heart failure; in chronic disease both the heart and pulmonary arteries remodel to accommodate escalating blood pressures. This project will validate a computational approach to predict right heart pressure during acute and chronic pulmonary embolism. Patient-specific models of the lung will be derived from medical imaging and patient data, and function will be validated against clinical measurements of pulmonary artery pressure.

Project added: 11 July 2012.

Modelling cranial injury and back spatter using smooth particle hydrodynamics

Principal supervisors: Dr Raj Das r.das@auckland.ac.nz (Mechanical Engineering); Dr Justin Fernandez j.fernandez@auckland.ac.nz (Auckland Bioengineering Institute); Dr Michael Taylor (Forensic Science Lab ESR)
Funding: Environmental Science and Research (Crown Research Institute)

In the context of the investigation of serious crime and its resolution in court, some of the most difficult issues to resolve include distinguishing between accidental, intentional and suicidal causes of death, the specific role of individuals in the causing of injury or death, especially their intent and degree of force used, determining the nature of the injuring cause (eg type of weapon used) and assessing the viable biomechanical scenarios for injury causing events.

Essential to solving some of these problems is a thorough understanding of the mechanism of wounding and blood spatter and the development of valid methods to be able to distinguish one mechanism from another. Relatively little is known about the specific physics and fluid dynamics of blood spatter, but this has not stopped 'experts', with little or no appreciation of the science involved, giving sometimes controversial opinion evidence in courts around the world.

In cranial gunshot wounding it is thought that the initial contact between the bullet and the skin tissue produces spattered material with some sort of splashing mechanism. This spattered material can transfer to the firearm or the shooter which is sometimes used as evidence of proximity and therefore guilt. It would be valuable to be able to make predictions about the extent and range of this spatter.

The objectives of this project are to determine if the mechanism of splashing associated with bullet impact on human tissue can be numerically modelled and whether such models can be used to make realistic predictions about backspatter. The project has two parts: the use of physical models to test various wounding mechanism hypotheses, and the use of mathematical modelling techniques to simulate wounding and bloodshed. This project proposes aims to refine the current available physical models and to complement this by adding mathematical modelling techniques to simulate wounding and bloodshed.

This project is for a fully funded Masters but has the potential to be extended to a PhD.

Predicting function in the ageing lung

Principal supervisors: Associate Professor Merryn Tawhai, m.tawhai@auckland.ac.nz, Dr Alys Clark
Funding: this project is for a fully funded Masters, but has the potential to be converted to a PhD.

Lung diseases that affect the pulmonary blood vessels can cause elevation of right ventricular pressure. In acute pulmonary embolism (occlusion of lung arteries by blood clots) the drastic increase in right heart pressure can cause sudden heart failure; in chronic disease both the heart and pulmonary arteries remodel to accommodate escalating blood pressures. This project will validate a computational approach to predict right heart pressure during acute and chronic pulmonary embolism. Patient-specific models of the lung will be derived from medical imaging and patient data, and function will be validated against clinical measurements of pulmonary artery pressure.

Project added: 11 July 2012.

Representing mathematical models of spatially varying systems through functional abstraction

Principal supervisor: Dr Andrew Miller, ak.miller@auckland.ac.nz

As the complexity of mathematical models increases, the need for specialist representation languages that allow such complex models to be assembled increases. One promising approach is to represent mathematical models as a series of transformations from abstract forms (for example, a list of reacting species and their reaction and diffusion rates) into more concrete forms (for example, a collection of equations). If new transformations can be defined by modellers, creating new domain specific languages, modellers will have a great deal of flexibility to describe biological systems succinctly, while still enabling interoperability between different tools that need to use the model. This project will involve defining a language for modelling spatially varying systems using functional abstraction, and investigating what types of domain specific language and models can be represented succinctly in that language.

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

Transcranial direct current stimulation

Principal Supervisor: Dr Ehsan Vaghefi e.vaghefi@auckland.ac.nz, Dr Ben Thompson

Transcranial direct current stimulation (tDCS) is a widely used noninvasive stimulation technique that can alter the balance of excitation and inhibition within the human neocortex. As abnormal patterns of excitation and inhibition are a key factor in the aetiology of a variety of neurological disorders, tDCS has become a potentially powerful therapeutic tool. While tDCS has been shown to be effective in influencing cortical excitability, there are large individual differences in response. A key factor contributing to this variation is likely to be individual differences in anatomy such as skull thickness, cerebro-spinal fluid distribution, patterns of sulci and gyri etc. each of which will influence the distribution of electrical current within the brain and therefore the therapeutic outcome of tDCS. The aim of this study is to evaluate how anatomical variations influence the flow of electric current and how this affects the outcome of tDCS.

The study will have two phases. First, we will develop a 3D model of electrical current distribution within the brain based on anatomical T1 and DTI MRI scans. In the second phase, we will assess the extent to which current distribution correlates with the tDCS-induced changes in neural excitability. The study will be conducted using datasets from six individual patients with a visual disorder known as amblyopia. The datasets consist of detailed clinical measurements, measurements of the behavioural effects of tDCS, T1 anatomical MRI images, DTI images, detailed functional mapping of the visual cortex, and fMRI measurements of visual cortex activation after real and sham (control) tDCS. These datasets have already been acquired.

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