Doctoral and masters research projects for 2012

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

Funded studentships

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

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

Biomechanics for breast cancer imaging

Principal supervisors: Associate Professor Martyn Nash, martyn.nash@auckland.ac.nz, Associate Professor Poul Nielsen
Funding: for (at least) 1 Doctoral student through NERF funding

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.

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 doctoral research project.

New advances in the understanding of gastrointestinal function

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

Powering the next generation of implantable devices

Principal supervisor: Dr 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.

Research into structural heart disease

Principal supervisor: Associate Professor Bruce Smaill, b.smaill@auckland.ac.nz
Funding: funding is available for two doctoral students through Health Research Council of New Zealand

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.

Satiety: understanding appetite control mechanisms

Principal supervisor: Dr Edmund Crampin, e.crampin@auckland.ac.nz
Funding: funding is available through Foundation for Research, Science and Technology

As part of research program with Plant and Food Research NZ Ltd, recently funded by FRST, we are developing in silica models of nutrient absorption by the gut epithelium. Using data from in vitro models of digestion and cell based assays of nutrient transport and regulation, we will incorporate data on genetic variability in key proteins, from SNP and HapMap datasets, to try to understand differences in nutrient uptake and appetite control between individuals. The PhD project will focus on the development of quantitative systems biology modelling of regulation of gut epithelial macronutrient (glucose) uptake and delivery to the blood stream. The initial focus will be to determine and model phytochemical interactions with this uptake pathway, with subsequent focus on calcium-dependent regulation of uptake via bitter compounds through (bitter) taste receptor TAS2R. The PhD student will use Ingenuity Pathway Analysis software to develop initial hypotheses as to key regulatory pathways.

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

Principal supervisor: Dr Mike Cooling, m.cooling@auckland.ac.nz
Funding: Partial funding from Marsden Grant

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.

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

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Agent-based modelling of bone: clasts versus blasts

Principal supervisor: Dr Gib Bogle, g.bogle@auckland.ac.nz
Funding: Waiting on Marsden fund announcements.

Bone is in a dynamic equilibrium between resorption by cells called osteoclasts, and formation by osteoblasts. The balance between the activities of the two cell types is maintained through a complex set of interlocking processes. Disturbances of the balance lead to bone diseases, the most prevalent being osteoporosis, in which osteoclasts are over-active, and bone density suffers. You will develop a spatio-temporal agent-based model to simulate the motility and interaction of monocytes, osteoclasts and osteoblasts, involving three domains: blood, marrow, and bone. Assistance will be provided by Professor Jill Cornish at the Medical School, and Professor Masuru Ishii in Osaka, Japan.

Agent-based modelling of skin

Principal supervisor: Dr Gib Bogle, g.bogle@auckland.ac.nz
Funding: Waiting on Marsden fund announcements

Skin cells (keratinocytes) are born at the base of the epidermal layer, and over the course of their lives they migrate towards the skin surface. Their progressive differentiation is controlled by chemical signals that ensure that their phenotype is appropriate for their location. Disruption of this order causes many skin diseases, of which psoriasis is a dramatic example. You will develop an agent-based model to simulate the proliferation, migration and differentiation of keratinocytes.

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, cmgui, 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: Dr 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

Cardiac electromechanics modelling

Principal supervisor: Associate 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: Associate 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).

Developing a services architecture for modular biomedical models

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

The biomedical scope and complexity demanded of models is steadily increasing. Current modelling methods typified by one person working on a relatively small biological area developing a bespoke model encoded in some esoteric representation can and should be improved upon. Recent developments in standard mathematical representation and modular model construction should be supported by an online, powerful infrastructure including model component search, composition, visualisation and analysis services.

The goal of this project is to design the first generation of modular model services, demonstrated with a prototype infrastructure. The work will unify a number of existing applications and be developed with the international community in mind, and includes collaborative links with Cambridge (UK), Newcastle-Upon-Type (UK), Minas Gerais (Brazil) and Monash (Australia). It would suit someone with interests in model or knowledge construction and representation, and software development.

An engine out of fuel? mitochondrial and cellular bioenergetics in heart failure

Principal supervisor: Dr Edmund Crampin, e.crampin@auckland.ac.nz

Heart failure can be defined as the inability of the heart to supply enough blood to meet the body's needs. There are many, many changes that occur in during heart failure. One idea that has gained a lot of interest is that in the failing heart there is a deficit in the heart's ability to provide sufficient energy for pumping - that heart failure is, at least in part, a disease of cardiac bioenergetics (put nicely by a cardiologist at Oxford in the title of his paper 'The failing heart - an engine out of fuel'). In collaboration with other Auckland researchers, we have access to data at a number of different levels of cardiac function in normal and failing hearts. This project will use mitochondrial proteomics data, functional data on mitochondrial respiration, and cell function from normal and failing hearts, which together will be used to construct a systems biology model of cardiac bioenergetics during heart failure.

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

Mobilising the T cell army

Principal supervisor: Dr Gib Bogle, g.bogle@auckland.ac.nz
Funding: Waiting on Marsden fund announcements

In an immune response cognate T cells receive and integrate TCR stimulation, and the level of this stimulation determines the course of their activation and proliferation. Working with immunologists at SBS, you will develop a model for TCR signal integration to be incorporated into a cutting-edge agent-based simulator for the lymph node immune response.

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
Funding: Presently unfunded

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

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

Modelling the human kidney

Principal supervisor: Dr David Nickerson, d.nickerson@auckland.ac.nz

The Renal Physiome Project at the ABI is a new project 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 and get in on the ground floor of this exciting project. Current projects underway span the modelling spectrum from single proteins through to the whole renal nephron, as well as dynamic and interactive web-delivered descriptions of these models.

Pelvic floor and childbirth research

Principal supervisors: Associate Professor Poul Nielsen, p.nielsen@auckland.ac.nz, Associate 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 CMGUI, 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: Dr 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.

Redefining the lymphatic anatomy of the armpit in breast cancer

Principal supervisors: Associate Professor Poul Nielsen, Associate 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.

The rumen epithelium

Principal supervisor: Dr Vinod Suresh, v.suresh@auckland.ac.nz
Funding: waiting on the PGP results.

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 instrumentation, experiments and modelling

Principal supervisors: Associate Professor Poul Nielsen, p.nielsen@auckland.ac.nz, Dr Andrew Taberner, Associate 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: 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!

Virtual heart disease: modelling ischaemia in cardiac tissue

Principal supervisor: Dr Edmund Crampin, e.crampin@auckland.ac.nz

Heart attacks happen due to interruption of the blood supply to a region of the heart muscle, as occurs following blockage of a coronary artery. The shape of the affected ('ischaemic') region of heart muscle tissue, and spatial variation of tissue properties such as electrical conductivity, strongly affect electrical propagation through the heart. Disruption of the normal electrical signal can be so severe that the heart no longer effectively pumps blood around the circulation. Particularly important is what happens in the border zone between ischaemic and normal tissue. This project will consider how changed cellular metabolism and transport during ischaemia, combined with knowledge of tissue microstructure, determines the shape and extent of the ischaemic zone. The aim is to improve our understanding of exactly what predisposes the heart to dangerous patterns of electrical activation, including reentry and spontaneous rhythm generation, which lead to heart attack, and to investigate what sorts of interventions (in particular pharmaceutical) may be protective for the heart.

Cybernose: biosensors from insect olfactory receptors

Principal Supervisor: Dr Edmund Crampin, e.crampin@auckland.ac.nz, and Dr Charles Unsworth
Funding: funding is available through Foundation for Research, Science and Technology

In collaboration Plant and Food Research Ltd and with several other groups around New Zealand we are developing technologies required to build a hand-held biosensor using molecular olfaction - i.e. smell. In humans, animals and insects, smell is a key sense. Our team is working on the development of technology for use in biosensors, in particular a small, portable, “electronic nose”. Applications for such an instrument include biosecurity screening of luggage, bomb detection, medical diagnosis through breath analysis, or food industry uses such as identification of undesirable micro-organisms. The project will involve applying neural network classifiers and self organizing maps to learn odourant molecule features that individual receptors respond to, and developing predictive models to find molecular features from receptor activation profile across a panel of receptors.

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.

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.

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.

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

Principal Supervisor: Dr Mike Cooling, m.cooling@auckland.ac.nz
Funding: This project has a grant from the Marsden Fund to support two Masters students for up to $5,200 for fees and $16,000 stipend per student

We aim to help treat and prevent cardiovascular disease, the developed world’s major killer. These projects involve the mathematical modelling of previously identified key intracellular events leading to vascular wall mal-adaptation, which can lead to (for example) aneurysm formation or atherosclerosis. 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.