Auckland Bioengineering Institute


China Scholarship Council (CSC) scholar projects

This page summarises the research projects available to recipients of China Scholarship Council (CSC) scholarships.

Our 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.

 

Please note: This page summarises the research projects available to recipients of China Scholarship Council (CSC) scholarships only. If you are a domestic student please browse the research projects on our 'Doctoral and masters research projects' page.

 

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.


General information about the University of Auckland and China Scholarships Council scholarships:

You can find general information such as the University of Auckland application procedure and frequently asked questions about the CSC scholarships in relation to the University of Auckland on the University of Auckland website.
 

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.

 


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

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 updated:  21 May 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

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
 

Heart model

Modelling congenital heart disease with MRI

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

Co-supervisor: Dr Avan Suinesiaputra – a.suinesiaputra@auckland.ac.nz

We have developed a biventricular finite element model that captures the anatomy of both left and right chambers, myocardium, wall and valves. Our next step in this research is to customize the model to follow the movement of patient’s heart derived from cardiac MR images.

We are seeking a motivated PhD candidate to work on this project who is interested in:

  • mathematical modelling of cardiac function and
  • medical image analysis including registration methods and motion tracking.

The ideal candidate should have a strong background in biomedical engineering or computer science or computer vision, and excellent communication and writing skills. Programming skills, such as Matlab, C/C++ and/or Python, are essential. The successful applicant will need to be able to travel to meet with our collaborators at the University of California San Diego on several occasions during the project.

Project added: 27 November 2014
 

Tumor spheroid modelling

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

Background
The tumour spheroid, which is grown in vitro from human tumour cells, is a very powerful cell culture model in cancer research.  All tumours are initially avascular, and as the cells multiply the tumour core becomes hypoxic.  Bill Wilson’s team at the Auckland Cancer Society Research Centre (ACSRC) develops hypoxia-activated prodrugs (HAPs), compounds that have cytotoxic activity switched on when taken up by a hypoxic cell.  Spheroids provide an important way to test these drugs, and to explore the influence of the factors that determine their effectiveness.

Agent-based spheroid model
In the agent-based approach each cell in the aggregation is simulated as a separate entity that responds to its microenvironment.  A preliminary agent-based model (ABM) for tumour spheroids has been developed, simulating cell growth, division and death taking into account the diffusion and consumption of oxygen and nutrients.

Project aims
The first goal is to calibrate and validate the ABM on the basis of data from tumour spheroid growth experiments with a range of medium conditions.  Once the model has been shown to be capable of reliably predicting the results of these growth experiments, it will be extended to incorporate drug effects, again validating against experiments.  Since radiotherapy is ineffective against hypoxic cancer cells, we are very interested in exploring therapeutic protocols that combine radiation and HAPs, and killing by radiation will also be implemented in the model.  At this point we will be able to design (and test through experiment) optimal combined treatment protocols.

Importance
This project will break new ground in cancer modelling – there are currently no published studies on the 3D agent-based simulation of drug-induced killing of tumours.  Those models of drug therapy that have been published are continuum-based, incapable, we believe, of achieving the level of detail and realism that the agent-based approach provides.  Our opinion seems to be shared by the Marsden reviewers, one of whom wrote: “This proposal is original and has significant merit: Developing a pre-clinical 'in vitro-in silico' drug/RT testing platform would have obvious benefit for integrative oncology research as well as, potentially, for the development of new treatment paradigms; this would be an accomplishment beyond Auckland or NZ, rather it would have an impact on the cancer modeling field itself.”

Requirements
We are looking for a very good student, someone with strong mathematical, computational modelling, and programming skills.  Interest in and willingness to learn basic cell biology is also important – this project is highly interdisciplinary, and will involve working closely with Dr Kevin Hicks, Professor Bill Wilson and the experimental team at the ACSRC.

Project added: 6 October 2014
 

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

Principal supervisor: Dr Jichao Zhao - j.zhao@auckland.ac.nz

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.  

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

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.
 

Smart rubbery robots

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

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.
 

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.

 

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 added: 18 July 2012.

 

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) characterization of structural and mechanical changes in the heart during the progression to heart failure (2) a study of disturbances of heart rhythm in the region surrounding a healed myocardial infarction, and (3) development of flexible computer models of the atrial chambers of the heart that can be used to better understand atrial rhythm disturbances that are commonly observed in heart failure. The individual projects that constitute this research are linked by three common factors. They each utilize novel measurement and imaging techniques to access data that has not previously been available, they seek to integrate experimental information using sophisticated structure-based computer models and they all address explicit clinical problems. We have funded PhD positions in each of these research areas that would suit students with a wide range of interests and skills.

Project updated on 9 April 2013.
 

Skin instrumentation, experiments and modelling

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

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

Tracking the heart: image is everything

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

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

 


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