Auckland Bioengineering Institute


Doctoral and masters research 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. They are separated into funded and unfunded, PhD and masters projects. Some, but not all of these projects will require a strong undergraduate degree in engineering or applied mathematics.
 

Funded PhD studentships

The funded PhD studentships include tuition and other compulsory fees, plus a stipend of $27,000 per annum. Applications are invited from interested students who are eligible to undertake doctoral study at the University of Auckland.
 

On this page

Opportunities last updated on 18 May 2016.

To find out more


About postgraduate study at the Auckland Bioengineering Institute:

Please contact our Associate Director Postgraduate, Dr David Long at bioeng-postgrad-advisor@auckland.ac.nz.


About a specific project:

If you do want more information about a specific project after you have read the information below, please contact the projects's principal supervisor directly.

 

Project lists


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Funded PhD projects


Targeted ablation therapy for treatment of gastrointestinal dysrhythmias

Principal supervisor:

Portrait of

Leo Cheng
Associate Professor
Email: l.cheng@auckland.ac.nz

Co-supervisors:

Portrait of

Tim Angeli
Research Fellow
Email: t.angeli@auckland.ac.nz

Portrait of

Greg O'Grady
Senior Research Fellow
Email: greg.ogrady@auckland.ac.nz

Funding:

Funding is available for a PhD student through the University of Auckland Doctoral Scholarship program, dependent on meeting the undergraduate GPA requirement.

Funding is available for an ME student as part of a Health Research Council project grant and / or Medical Technologies Centre of Research Excellence studentship. Graduates of the Department of Engineering Science (UoA) may be eligible for Masters funding via the Andrew Pullan Bioengineering Scholarship.

Project Description:

Contractions of the gastrointestinal (GI) tract are controlled by rhythmic, propagating electrical events, termed ‘slow waves’. Recent development and translation of high-resolution GI mapping, where slow wave activity is recorded simultaneously across a dense array of hundreds of electrodes, has uncovered a range of disorganised patterns of gastric slow wave conduction (‘dysrhythmias’) associated with GI disorders. The recent discovery and classification of these gastric dysrhythmias has now provided a pathophysiological basis through which novel therapies can be investigated.

In cardiac electrophysiology, a range of therapeutic tools are routinely used in clinical practice for correcting dysrhythmias, including radio-frequency (RF) ablation. Comparatively, therapeutic approaches for correcting gastric dysrhythmias remain undeveloped. The opportunity now exists to utilise the validated GI mapping foundation that we have established to investigate gastric ablation as a novel therapeutic approach for treating gastric dysrhythmias.

The aims of this project are to:

  1. Quantify the effects of ablation temperature, power, time, and catheter design on lesion formation in the gastric muscle via anatomical and histological analysis.
  2. Utilise gastric ablation to block slow wave conduction, validated via high-resolution gastric mapping, and quantify the electrophysiological effects.
  3. Utilise targeted gastric ablation at sites of gastric dysrhythmia, identified by high-resolution gastric mapping, to abolish dysrhythmic conduction mechanisms.

The student will have the opportunity to work closely with leading bioengineers and clinicians at the Auckland Bioengineering Institute, as well as international clinical collaborators (e.g., Mayo Clinic, USA). You will devise, develop, and implement novel techniques for modulating slow wave activation, in vivo. These results will be used to provide new therapeutic options for complex gastrointestinal disorders.

Candidate Requirements:

An ideal candidate should have interests in:

  1. Translating engineering toward clinical medicine
  2. Experimental electrophysiology
  3. In vivo experimentation
  4. Biomedical device design and implementation
  5. Computational analysis

Project added 13 November 2015

Linear synchronous motors for medical devices

Principal supervisors: Associate Professor Andrew Tabernera.taberner@auckland.ac.nz

Co-supervisors: Dr Bryan Ruddy

Funding: This project is funded by the MedTech CoRE, will include enrolment in a doctoral training program and is due to begin in early 2016.

Description:

Linear synchronous motors are flexible, powerful, and efficient actuators that have seen little use to date in biomedical applications. We are looking for a student to work on the application of these actuators to drug delivery and rehabilitation robotics, developing motor designs optimized to each task along with their compact, self-contained motor controllers.

The goal of this project will be to use the optimization methods previously developed by the investigators to create plug-and-play actuator systems for these new applications, and to examine the performance of these systems, as well as the overall medical device performance enabled by the new motors.

Project added:  29 September 2015

 

Optimal linear synchronous motor design

Principal supervisors: Dr Bryan Ruddyb.ruddy@auckland.ac.nz

Co-supervisors:  Associate Professor Andrew Taberner

Funding: This project is funded by the MedTech CoRE, will include enrolment in a doctoral training program and is due to begin in early 2016.

Description:

Existing models of electromagnetic motors have a limited ability to describe the magnetic behavior of iron components, yet the simplest and most compact linear synchronous motors use iron extensively in their magnetic circuits. The goal of this PhD project is to develop a mathematical model of a linear synchronous motor that can accurately describe its performance if it contains highly-saturated iron components and/or discontinuous iron structures, and to validate the model by building and testing iron-containing motors.

Project added:  29 September 2015

 

Novel techniques for the analysis of the repolarisation phase of gastric slow wave activity

Principal supervisors: Associate Professor Leo Chengl.cheng@auckland.ac.nz

Co-supervisors:  Dr Niranchan Paskaranandavadivel, Dr Peng Du

Funding:

Funding is available for PhD or ME students as part of a Health Research Council project grant. Graduates of the Department of Engineering Science at the University of Auckland may be eligible for Masters and PhD funding via an Andrew Pullan Bioengineering Scholarship.

Description:

Stomach contractions are governed by an underlying bio-electrical event known as slow wave activity. Slow wave dysrhythmias have been linked to a number of major digestive disorders. The recent development and application of high-resolution electrical mapping techniques has enabled critical advances in understanding normal and dysrhythmic patterns of gastric slow wave activity.

A key hypothesis developed from these studies was that the refractory phase of gastric slow wave activity could be a significant factor in the initiation and maintenance of dysrhythmic patterns. This project will aim to develop a new generation of high-resolution mapping techniques for studying the refractory phase of slow wave activity in the stomach. It will focus on the following two novel techniques:

  1. A high-resolution multi-electrode mapping device that makes contact with the stomach and records monophasic electrical potentials. Our novel high-resolution mapping analysis techniques will be applied to reconstruct the sequence of the underlying gastric electrical activation.
  2. Through our collaboration with Professor Jack Rogers at the University of Alabama at Birmingham (UAB), we will apply optical mapping techniques to the stomach. Optical mapping involves the use of voltage sensitive dyes and optical sensors to map electrical patterns, enabling analysis of repolarisation of gastric electrical activity with outstanding spatial and temporal resolution.

The candidate will have the opportunity to work with leading bioengineers and clinicians in extracellular mapping at the Auckland Bioengineering Institute and the University of Alabama at Birmingham (UAB). You will devise, develop and implement novel electrode platforms, and apply novel signal processing techniques to analyse and interpret findings. The findings will used to improve our understanding of the initiation, maintenance and termination of complex slow wave dysthymias recorded clinically.

Candidate requirements:

An ideal candidate should have interests in

  1. device prototyping/development and electrode construction
  2. experimental electrophysiology
  3. signal processing, quantitative analysis and data presentation
  4. engineering, physics and applied maths

Project added:  11 February 2015

 

An experimental and theoretical analysis of electrogastrography (EGG)

Principal supervisor: Dr Peng Du - peng.du@auckland.ac.nz

Co-supervisors: Associate Professor Leo Cheng, Dr Greg O'Grady

Funding:

Funding is available for PhD or ME students as part of a Health Research Council project grant. Graduates of the Department of Engineering Science at the University of Auckland) may be eligible for Masters and PhD funding via an Andrew Pullan Bioengineering Scholarship.

Description:

One of the major regulators of stomach contractions are electrical events known as slow waves. The accurate analysis of stomach slow wave activity is presently limited to invasive recording techniques. Electrogastrography (EGG) is a non-invasive method of recording the electrical activity on the skin surface that reflects the activity originating in the walls of the stomach (essentially the stomach’s equivalent to the ECG). EGG holds major potential as a routinely deployable tool to aid in the diagnosis of gastric slow wave dysrhythmias and digestive diseases.

However, there are several technical and physiological limitations that have prevented EGG from becoming a routine diagnostic tool.

One approach to improve our understanding of EGG is to isolate the electrical source of the organ and infer the resultant body surface potential by conducting torso tank experiments. The signal of an electrically active organ is typically simulated using an artificial source. This particular experimental preparation provides extensive access to, and control of, relevant parameters as well as the option of both qualitative and quantitative evaluations of the associated changes in the EGG.

The central aim of the proposal is to use a torso phantom setup for electrophysiological recordingand the mathematical modelling validation of both forward and inverse applications. An existing torso-tank setup will be used to help interpret the EGG signals associated with the major classes of gastric dysrhythmias. The project is will have significant impact on the theory and practice of EGG.

The candidate will have the opportunity to work closely with bioengineers and clinicians at the Auckland Bioengineering Institute and international collaborators. You will devise, develop and implement novel experimental techniques, and apply signal processing and computational simulations to validate these experiments. The ultimate aim will be to work closely with clinicians and to apply the techniques and findings in a clinical setting.

Candidate requirements:

An ideal candidate should have interests in

1.       signal processing;

2.       engineering, physics and applied maths;

3.       experimental electrophysiology (e.g., ECG, EEG, EMG etc);

4.       mathematical modelling.

Project added:  11 February 2015

 

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 updated: 21 May 2015.

 

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, therefore student co-operation will be required in applying for scholarships.
 

Endothelial Mechanobiology - Intracellular force transmission and cellular function

Principal Supervisor: Dr David Longd.long@auckland.ac.nz

Endothelial cells are continually exposed to mechanical stimuli. In response to mechanical stimuli, these cells respond by translating them into biochemical signals. The interaction between mechanical stimuli and biochemical signals play an important role in the both health and disease. 

A combination of confocal microscopy, mathematical/computational cell mechanics, statistical modelling, traction force microscopy, and many more are being used to study a wide range of topics - including intracellular force transmission within endothelial cells, the primary cilia, cytoskeleton organization, statistical models of endothelial cells, and many more. 

If you would like to discuss potential opportunities, please contact the principal supervisor.

Project added 16 October 2015.

 

The Endothelial Glycocalyx 

Principal Supervisor: Dr David Longd.long@auckland.ac.nz

Strategically located at the interface between circulating blood and the endothelium is the endothelial glycocalyx layer (EGL). The EGL is a hydrated gel-like layer of membrane-bound macromolecules that is expressed on the luminal surface of, and regulated by, vascular endothelial cells. It protects the vascular wall from stresses produced by the direct exposure to blood flow. The susceptibility of the vessel wall to disease is attributable to the adaptive capacity of the vascular wall to the local microenvironment.

A combination of confocal microscopy, novel chemical reporters, cell culture models, live-cell imaging, traction-force microscopy, mathematical modelling, and more are being used to study the endothelial glycocalyx. 

If you would like to discuss potential opportunities, please contact the principal supervisor.

Project added 16 October 2015.

 

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.

 

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.

 

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 Mike Cooling (ABI), Dr S Randall Thomas (Paris), Dr Jonathan Cooper (Oxford), Professor Jim Bassingthwaighte (Washington), Dr Bernard de Bono (London/ABI), Associate Professor John Gennari (Washington), Professor Dan Cook (Washington).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 updated: 21 May 2015.

 

Modelling the human kidney

Principal supervisor: Dr David Nickerson - d.nickerson@auckland.ac.nz
Collaborators: Dr Kirk Hamilton (Otago), Professor Daniel Beard, Assistant Professor Brian Carlson (Michigan), Distinguished Professor 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: 21 May 2015

 

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

 

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.

 

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. characterisation 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.

 

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.

 

Top

Masters projects


Targeted ablation therapy for treatment of gastrointestinal dysrhythmias

Principal supervisor

Portrait of

Leo Cheng
Associate Professor
Email: l.cheng@auckland.ac.nz

Co-supervisors

Portrait of

Tim Angeli
Research Fellow
Email: t.angeli@auckland.ac.nz

Portrait of

Greg O'Grady
Senior Research Fellow
Email: greg.ogrady@auckland.ac.nz

Funding:

Funding is available for an ME student as part of a Health Research Council project grant and / or Medical Technologies Centre of Research Excellence studentship. Graduates of the Department of Engineering Science (UoA) may be eligible for Masters funding via the Andrew Pullan Bioengineering Scholarship.

Project Description:

Contractions of the gastrointestinal (GI) tract are controlled by rhythmic, propagating electrical events, termed ‘slow waves’. Recent development and translation of high-resolution GI mapping, where slow wave activity is recorded simultaneously across a dense array of hundreds of electrodes, has uncovered a range of disorganised patterns of gastric slow wave conduction (‘dysrhythmias’) associated with GI disorders. The recent discovery and classification of these gastric dysrhythmias has now provided a pathophysiological basis through which novel therapies can be investigated.

In cardiac electrophysiology, a range of therapeutic tools are routinely used in clinical practice for correcting dysrhythmias, including radio-frequency (RF) ablation. Comparatively, therapeutic approaches for correcting gastric dysrhythmias remain undeveloped. The opportunity now exists to utilise the validated GI mapping foundation that we have established to investigate gastric ablation as a novel therapeutic approach for treating gastric dysrhythmias.

The aims of this project are to:

  1. Quantify the effects of ablation temperature, power, time, and catheter design on lesion formation in the gastric muscle via anatomical and histological analysis.
  2. Utilise gastric ablation to block slow wave conduction, validated via high-resolution gastric mapping, and quantify the electrophysiological effects.
  3. Utilise targeted gastric ablation at sites of gastric dysrhythmia, identified by high-resolution gastric mapping, to abolish dysrhythmic conduction mechanisms.

The student will have the opportunity to work closely with leading bioengineers and clinicians at the Auckland Bioengineering Institute, as well as international clinical collaborators (e.g., Mayo Clinic, USA). You will devise, develop, and implement novel techniques for modulating slow wave activation, in vivo. These results will be used to provide new therapeutic options for complex gastrointestinal disorders.

Candidate Requirements:

An ideal candidate should have interests in:

  1. Translating engineering toward clinical medicine
  2. Experimental electrophysiology
  3. In vivo experimentation
  4. Biomedical device design and implementation
  5. Computational analysis

Project added 13 November 2015

Automatic segmentation and motion tracking of papillary and trabecular structures from Cardiac MRI

Supervisors: Professor Alistair Young a.young@auckland.ac.nz, Dr Avan Suinesiaputra a.suinesiaputra@auckland.ac.nz

In some cardiac patient groups, such as hypertrophic cardiomyopathy and congenital heart defects, the assessment of ventricular mass and volumes is significantly affected by the presence of papillary muscles and trabeculae. However, in the current clinical analysis of cardiac MRI, papillary muscles and trabeculae are usually excluded from the ventricle. The reason is the difficulty to delineating these irregular structures, which creates a low reproducibility of the analysis. This has been a challenge by the medical image analysis community to develop a fast, accurate and highly reproducible automated segmentation algorithm.

What we are looking for in a successful application

We want a student with a strong interest in developing a computer algorithm for image segmentation and motion tracking. Ideally, this would be a computer science or bioengineering student.

Objectives

  • Develop an algorithm to segment papillary muscles and trabeculae from cardiac MRI using either Matlab or C/C++.
  • Extend the algorithm to track motion of papillary muscles and trabeculae throughout the cardiac cycle with the constraint of a constant mass.


Project added 16 October 2015.

Scar quantification from Cardiac MRI

Supervisors: Professor Alistair Young a.young@auckland.ac.nz, Dr Avan Suinesiaputra a.suinesiaputra@auckland.ac.nz

The heart attack is a common cause of death. In this disease, parts of the heart become scarred, and this hinders activation of the heartbeat. This project seeks to identify and quantify regions of scar in MRI images of the heart. Although scar tissues appear bright in the images, variations in the contrast due tissue composition and imaging artefacts are still causing the difficulty to quantify scar tissue accurately. Scar quantification from MRI plays an important role in the diagnosis of cardiac disease, which includes assessment of myocardial viability, predicting improvement in cardiac resynchronisation therapy, and management of patients with tachycardia.
 

What we are looking for in a successful application

We want a student with a strong interest in developing a computer-assisted diagnostic tool, which can accurately segment and quantify scar tissue from MRI examinations.  Ideally, this would be a computer science, electrical engineering or bioengineering student.
 

Objectives

  • Develop an algorithm to delineate scar tissues either semi or fully automatically.
  • Develop an algorithm to quantify the degree of scar tissue
  • Test and validate the algorithm.
  • Optionally, to do benchmarking with an open-access challenge data available from (R. Karim et al., JCMR 2013).
  • Prepare a report.

Project added 16 October 2015

Modelling odorant transport and nasal airflow to better understand subject-specific smell decrement in spaceflight

Principal supervisors: Dr Bryan Caldwell - bjc263@cornell.edu, Dr Haribalan Kumar (h.kumar@auckland.ac.nz)

Collaborator: Associate Professor Jean Hunter, Cornell University, NY

Funding: Stipend is available for the period of Master’s degree completion

Perception of smell and its change for astronauts in space can be understood using tilted bed rest studies. Fluid shift to the upper body induced by tilted bed rest alters the nasal airway, resulting airflow, and may affect breathing and sense of smell. This nasal smell-structure relationship may be subject-specific.

We can estimate airflow and resulting odorant transport using computational fluid dynamics simulations. The predicted transport can then be compared with individual scores for smell from different substances and altered airflow measurements obtained from subjects tested during 70-days of tilted bed rest at the NASA Flight Analog Research Unit, in Galveston, Texas.

In this project, the student will segment magnetic resonance images, build 3D nasal airway geometry, and simulate airflow and odorant transport. Understanding the distribution of drugs by intranasal delivery are additional goals. The candidate should be interested in computer modeling and simulation using commercial software packages.

Nasal MR images and odorant identification data are supplied for this project by Associate Professor Jean Hunter, Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY.

If you wish to learn more details about this project, contact:  Dr Bryan Caldwell (bjc263@cornell.edu), or Dr Haribalan Kumar (h.kumar@auckland.ac.nz).
 

Project added: 31 August 2015
 

Simulating drug and radiation interactions using agent-based and Green’s function models

Principal supervisor: Dr Gib Bogle - g.bogle@auckland.ac.nz DDI: 09 923 7030

Co-supervisor: Kevin Hicks, Auckland Cancer Society Research Centre (ACSRC) - k.hicks@auckland.ac.nz, DDI: 09 923 6090

Advisors: Professor Bill Wilson, Professor Timothy Secomb (University of Arizona, Tucson, USA)

Funding: Assistance with enrolment fees and a stipend are available to suitably qualified applicants

Project Aims:

This project is linked to a recently-awarded Marsden grant to develop agent-based models for growth and therapeutic interactions in multicellular tumour spheroids. Spheroids are an experimental model for avascular tumour nodules and the extravascular space between capillaries in tumours.  We use spheroids to build on our model guided strategies for developing prodrugs to target tumour hypoxia. Hypoxic cells in tumours are a major limitation to anticancer therapy; radiation is inefficient at killing hypoxic cells and many anticancer drugs cannot diffuse to hypoxic cells in tumours.

This project builds on our pharmacokinetic/pharmacodynamic model-guided approach to developing drugs to target tumour hypoxia, thereby complementing the action of radiotherapy and chemotherapy. We have developed an agent-based model of spheroid growth and therapy and this model is being calibrated against experiments on growth and treatment of spheroids in in vitro experiments. The project will involve using the agent-based model to simulate cell killing and growth delay in spheroids after radiation, hypoxia activated drugs and combinations, under a range of treatment regimes, together with further development of the computer program. This will involve comparing the model simulations to published data/simulations in the first instance1-4. Predictions from the simulations will be compared to data generated in spheroid experiments and will guide the design of experiments to test the agent-based model. Simulations of cell killing will also be performed in microvascular networks using our published Green’s function model2,5.

The student will work with Dr Gib Bogle and his PhD student on this project, together with Dr Hicks and Professor Wilson and their students at the ACSRC.

Requirements: We are looking for students with a background in mathematical/physical sciences with good computational, data analysis and writing skills. Some understanding of biological processes would be an advantage.

Skills taught:

  • Mathematical modelling in cancer
  • Pharmacokinetic/ pharmacodynamic modelling and simulation
  • Programming (Fortran90/C++)
  • Using the NeSI supercomputer system

References:

  1. Wouters BG, Brown JM. Cells at intermediate oxygen levels can be more important than the "hypoxic fraction" in determining tumor response to fractionated radiotherapy. Radiat Res 1997;147:541-50.
  2. Hicks KO, Pruijn FB, Secomb TW, Hay MP, Hsu R, Brown JM, Denny WA, Dewhirst MW, Wilson WR. Use of three-dimensional tissue cultures to model extravascular transport and predict in vivo activity of hypoxia-targeted anticancer drugs. J Natl Cancer Inst 2006;98:1118-28.
  3. Cardenas-Navia LI, Secomb TW, Dewhirst MW. Effects of fluctuating oxygenation on tirapazamine efficacy: Theoretical predictions. Int J Radiat Oncol Biol Phys 2007;67:581-6.
  4. Carlson DJ, Keall PJ, Loo BW, Jr., Chen ZJ, Brown JM. Hypofractionation results in reduced tumor cell kill compared to conventional fractionation for tumors with regions of hypoxia. Int J Radiat Onc Biol Phys 2011;79:1188-95.
  5. Hicks KO, Siim BG, Jaiswal JK, Pruijn FB, Fraser AM, Patel R, Hogg A, Liyanage HDS, Dorie MJ, Brown JM, Denny WA, Hay MP, Wilson WR. Pharmacokinetic/pharmacodynamic modeling identifies SN30000 and SN29751 as tirapazamine analogues with improved tissue penetration and hypoxic cell killing in tumors. Clin Cancer Res 2010;16:4946-57.

Project added: 11 March 2015

 

Image-based analysis and modelling of the pacemaker cells in the stomach and small intestine

Principal supervisor: Associate Professor Leo Cheng - l.cheng@auckland.ac.nz

Co-supervisors: Dr Peng Du, Dr Greg O'Grady

Funding:

Funding is available for an ME student as part of a Health Research Council project grant.  Graduates of the Department of Engineering Science (UOA) may be eligible for Masters funding via an Andrew Pullan Bioengineering Scholarship.

Description:

The contractions of the stomach and intestines (also known as the gastrointestinal tract) are governed by underlying electrical events, generated by a network of pacemaker cells called the interstitial cells of Cajal (ICC) and the enteric nervous system (ENS). The degradation of the ICC and ENS networks are associated with a number of significant gastrointestinal disorders. For example, in gastroparesis (a condition commonly associated with diabetes) the loss of ICC correlates with disease severity. Analyses of the structure and function of the ICC and ENS networks are an active area of intense research.

The main aim of this project is to quantify structural changes in ICC and ENS networks by developing and applying structural-based numerical metrics to experimentally-obtained images. A secondary aim of this project is to develop an image-based mathematical modelling framework to simulate and study the effects of ICC and ENS changes on gastric electrical activity and the resultant muscular contractions. The outcomes of this project will be a key step towards accurate diagnosis of a number of currently non-specific digestive diseases.

The candidate will have the opportunity to work closely with leading bioengineers and clinicians at Auckland Bioengineering Institute and the neurophysiologists based at the Université Libre de Bruxelles in Belgium. You will devise, develop and implement novel techniques to solve large scale image processing and computation problems. These results will be used to provide novel insights into current clinical challenges.

Candidate requirements:

An ideal candidate should have interests in:

  1. physiology, engineering, physics, applied mathematics
  2. numerical analysis and quantification techniques;
  3. 2d and 3d image processing techniques;
  4. mathematical modelling and finite element/difference methods.

Project added:  11 February 2015

 

Novel techniques for the analysis of the repolarisation phase of gastric slow wave activity

Principal supervisors: Associate Professor Leo Chengl.cheng@auckland.ac.nz

Co-supervisors:  Dr Niranchan Paskaranandavadivel, Dr Peng Du

Funding:

Funding is available for ME students as part of a Health Research Council project grant. Graduates of the Department of Engineering Science at the University of Auckland may be eligible for Masters funding via an Andrew Pullan Bioengineering Scholarship.

Description:

Stomach contractions are governed by an underlying bio-electrical event known as slow wave activity. Slow wave dysrhythmias have been linked to a number of major digestive disorders. The recent development and application of high-resolution electrical mapping techniques has enabled critical advances in understanding normal and dysrhythmic patterns of gastric slow wave activity.

A key hypothesis developed from these studies was that the refractory phase of gastric slow wave activity could be a significant factor in the initiation and maintenance of dysrhythmic patterns. This project will aim to develop a new generation of high-resolution mapping techniques for studying the refractory phase of slow wave activity in the stomach. It will focus on the following two novel techniques:

  1. A high-resolution multi-electrode mapping device that makes contact with the stomach and records monophasic electrical potentials. Our novel high-resolution mapping analysis techniques will be applied to reconstruct the sequence of the underlying gastric electrical activation.
  2. Through our collaboration with Professor Jack Rogers at the University of Alabama at Birmingham (UAB), we will apply optical mapping techniques to the stomach. Optical mapping involves the use of voltage sensitive dyes and optical sensors to map electrical patterns, enabling analysis of repolarisation of gastric electrical activity with outstanding spatial and temporal resolution.

The candidate will have the opportunity to work with leading bioengineers and clinicians in extracellular mapping at the Auckland Bioengineering Institute and the University of Alabama at Birmingham (UAB). You will devise, develop and implement novel electrode platforms, and apply novel signal processing techniques to analyse and interpret findings. The findings will used to improve our understanding of the initiation, maintenance and termination of complex slow wave dysthymias recorded clinically.

Candidate requirements:

An ideal candidate should have interests in

  1. device prototyping/development and electrode construction
  2. experimental electrophysiology
  3. signal processing, quantitative analysis and data presentation
  4. engineering, physics and applied maths

Project added:  11 February 2015

  

An experimental and theoretical analysis of electrogastrography (EGG)

Principal supervisor: Dr Peng Du - peng.du@auckland.ac.nz

Co-supervisors: Associate Professor Leo Cheng, Dr Greg O'Grady

Funding:

Funding is available for ME students as part of a Health Research Council project grant. Graduates of the Department of Engineering Science at the University of Auckland) may be eligible for Masters funding via an Andrew Pullan Bioengineering Scholarship.

Description:

One of the major regulators of stomach contractions are electrical events known as slow waves. The accurate analysis of stomach slow wave activity is presently limited to invasive recording techniques. Electrogastrography (EGG) is a non-invasive method of recording the electrical activity on the skin surface that reflects the activity originating in the walls of the stomach (essentially the stomach’s equivalent to the ECG). EGG holds major potential as a routinely deployable tool to aid in the diagnosis of gastric slow wave dysrhythmias and digestive diseases.

However, there are several technical and physiological limitations that have prevented EGG from becoming a routine diagnostic tool.

One approach to improve our understanding of EGG is to isolate the electrical source of the organ and infer the resultant body surface potential by conducting torso tank experiments. The signal of an electrically active organ is typically simulated using an artificial source. This particular experimental preparation provides extensive access to, and control of, relevant parameters as well as the option of both qualitative and quantitative evaluations of the associated changes in the EGG.

The central aim of the proposal is to use a torso phantom setup for electrophysiological recordingand the mathematical modelling validation of both forward and inverse applications. An existing torso-tank setup will be used to help interpret the EGG signals associated with the major classes of gastric dysrhythmias. The project is will have significant impact on the theory and practice of EGG.

The candidate will have the opportunity to work closely with bioengineers and clinicians at the Auckland Bioengineering Institute and international collaborators. You will devise, develop and implement novel experimental techniques, and apply signal processing and computational simulations to validate these experiments. The ultimate aim will be to work closely with clinicians and to apply the techniques and findings in a clinical setting.

Candidate requirements:

An ideal candidate should have interests in

1.       signal processing;

2.       engineering, physics and applied maths;

3.       experimental electrophysiology (e.g., ECG, EEG, EMG etc);

4.       mathematical modelling.

Project added:  11 February 2015

 

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.

 

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

Principal supervisor: Dr 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

 

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 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: 21 May 2015

 

Sensors for flying bats

Principal supervisors: Associate Professor Andrew Taberner - a.taberner@auckland.ac.nz, Professor Poul Nielsen, Dr Anthony Hickey

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 updated: 29 September 2015

 


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