Potential Student Research Projects
Supervisor: Jonathan P. Mynard, BSc BEng(Hons) MRes PhD
Contact: jonathan.mynard@mcri.edu.au
Website: jpmynard.com
Contents
Is this research for you? ......................................................................................................................... 1
The Heart Research group at MCRI ................................................................................................... 1
1. Modelling cardiovascular transitions at birth ..................................................................... 2
2. Modelling the cardiovascular system throughout childhood........................................ 2
3. Adverse haemodynamics in coarctation of the aorta ....................................................... 3
4. Modelling the pulmonary circulation in paediatric pulmonary hypertension ....... 4
5. Advanced MRI and haemodynamic analyses of congenital heart disease ............... 4
6. Effects of aortic geometry on arterial wave propagation ............................................... 5
Is this research for you?
You are not afraid to solve problems that no one else has tackled. You don’t give up
easily, but you know when to ask for help and how to prioritise. You think
investigating cardiovascular problems in children is worth doing. You have done
some programming and/or medical image analysis and are eager to learn more. You
are self-motivated and have a strong academic record. People have told you that you
are good at writing.
If this describes you, read on …
The Heart Research group at MCRI
The Murdoch Childrens Research Institute (MCRI) is the largest child health
research organisation in Australia and one of the leading paediatric research
institutes internationally. The Heart Research group within Clinical Sciences theme
at MCRI is a truly multi-disciplinary team, with core members possessing strong
international reputations in paediatric cardiology, cardiac surgery, experimental
physiology, immunology, cellular biology and cardiovascular biomechanics. MCRI is
co-located with the Royal Children’s Hospital and our close collaborations with
clinical departments (e.g. Cardiology, Medical Imaging, Neonatology, Cardiac
Surgery) form an ideal setting for both basic and translational research. MCRI is also
co-located with the Department of Paediatrics, University of Melbourne, which
provides extensive support for students.
1. Modelling cardiovascular transitions at birth
Level: PhD
Background: Very soon after birth, massive changes occur in the cardiovascular
system, primarily because the locus of respiration must shift from the placenta to
the lungs. In the fetus, there are several specialised vascular shunts that play a key
role in directing blood flow to the right places (e.g. the ductus arteriosus, which
shunts blood away from the lungs and towards the placenta). Immediately after
birth, rapid and complex changes occur in blood flow patterns across the shunts.
Although the shunts normally close a few days after birth, in sick babies (e.g.
severely preterm babies or those with congenital heart disease), continued shunt
flow may be crucial for survival. However, the dynamics of shunt flow are extremely
difficult to study in human babies due to ethical, practical and technological issues.
Hence, a modelling approach is likely to provide important insights. Our group has
published the most complete models of the fetus and newborn using state-of-the-art
modelling techniques, but little work has been done on modelling blood flow
patterns during the birth transition.
Research aims: Starting with existing models of the fetal and neonatal
cardiovascular system, develop a model of the birth transition. This will incorporate
changes that occur in the heart and in different key regions of the circulation (e.g.
the placenta, lungs and brain). Oxygen transport will be incorporated into the
existing model for the first time. Data from the model will complement and be
validated against data from laboratory-based birth studies in lambs.
Skills/software/key subjects involved:
 One-dimensional blood flow modelling
 Electrical circuit analog models of the heart and microvascular beds
 Matlab
 Perinatal cardiovascular and respiratory physiology
 Potential for components involving 3D computational fluid dynamics
2. Modelling the cardiovascular system throughout childhood
Level: PhD
Background: It is increasingly being recognised that the precursors to adult
cardiovascular disease begin in childhood. However, we currently have limited
information about the normal development of the cardiovascular system during
childhood. Such knowledge is likely to form a crucial foundation for investigating
abnormal cardiovascular development. One-dimensional modelling is a powerful
tool for investigating the cardiovascular system but, surprisingly, no models of the
growing circulation exist.
Research aims: Based on existing models of the adult and newborn cardiovascular
systems, develop methods for incorporating growth and physiological development
based on published data. The resulting model would allow simulation of blood
pressure and flow throughout the circulation of a ‘representative normal’ child at
any time during childhood. By perturbing parameters of the normal development
model, new insights may be gained into the initiation of cardiovascular disease. The
model will be validated against measurements in children. Child-specific models
may also be designed.
Skills/software/key subjects involved:
 Matlab
 One-dimensional blood flow modelling
 Electrical circuit models of the heart and vascular beds
 Cardiovascular and developmental physiology
3. Adverse haemodynamics in coarctation of the aorta
Level: Masters or PhD
Background: Aortic coarctation, a narrowing of the aortic arch, is one of the most
common types of congenital heart disease. Although surgical repair is performed in
early infancy or childhood, patients are considered ‘repaired but not cured’ due to
an alarmingly high rate of early-onset hypertension (60-75%), vascular dysfunction
and thickening of the heart wall. Abnormal shape of the ‘repaired’ aortic arch, which
produces disturbed blood pressure and flow dynamics (haemodynamics), may be an
important risk factor in these patients. However, the current classification of aortic
shape (normal, triangular or rectangular) is controversial, as not all cases can be
clearly classified and many other potentially crucial aspects of aortic geometry are
not accounted for. Exactly which geometric factors cause adverse haemodynamics
(such as turbulence and pressure losses) is unclear, because detailed assessment of
such links is extremely difficult on the basis of limited clinically-available
haemodynamic data.
Research aims: Using state-of-the-art geometric analysis and computational
modelling techniques, investigate specific aspects of aortic geometry that lead to
adverse haemodynamics. ‘Virtual interventions’ will be performed to correct
hypothesized ‘bad aortic geometry’ to assess to what extent this improves
haemodynamics (e.g. reduces turbulence and pressure losses). Findings may
indicate ways in which treatment of aortic coarctation can be improved.
Skills/software/key subjects involved:
 Vascular geometric analysis (vascular modelling toolkit, vmtk)
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Computational Fluid Dynamics
Medical image (MRI) segmentation (e.g. vmtk, Matlab)
Matlab and/or python scripting
Fluid dynamics (e.g. turbulence theory)
4. Modelling the pulmonary circulation in paediatric pulmonary
hypertension
Level: Honours or PhD
Background: High blood pressure in the lungs (pulmonary hypertension)
commonly occurs in children with congenital heart disease and is one of the most
significant and difficult problems faced by paediatric cardiologists. Computer
modelling of the pulmonary circulation has potential to generate new insights into
underlying causes of this problem, and to suggest new diagnostic or treatment
strategies. Limited models of the pulmonary circulation currently exist, however
new techniques are emerging that allow greater focus on this crucial part of the
cardiovascular system.
Research aims: Develop a new model of the pulmonary circulation. By
incorporating this model into an existing model of the entire cardiovascular system,
interactions between pulmonary blood pressure/flow dynamics and the heart will
be assessed. The model will be used to investigate the physiology of pulmonary
hypertension in children with congenital heart disease.
Skills/software/key subjects involved:
 Matlab – one-dimensional modelling
 Electrical circuit (0D) modelling
 Fourier analysis
 Pulmonary physiology
 Congenital heart disease
5. Advanced MRI and haemodynamic analyses of congenital heart
disease
Level: Masters or PhD
Background: In many forms of congenital heart disease, disturbed blood flow
patterns arise from abnormal vascular anatomy or heart function. This causes two
fundamental and interrelated haemodynamic problems, 1) flow turbulence, which
causes dissipation of fluid energy and harms endothelial cells that form the inner
lining of vessel walls and 2) pressure losses, which increase workload on the heart,
increase stress on vessel walls, and/or reduce or adversely redistribute blood flow
to organs and tissues. These factors in turn lead to secondary cardiovascular
diseases or complications. While routine clinical imaging techniques may in some
cases detect turbulence or implicate pressure losses, they cannot accurately map
and quantify them. Two recently described magnetic resonance imaging (MRI)
techniques enable quantitative mapping of turbulence and relative pressure in 2 or
3 dimensions over time, promising unprecedented insights into disturbed flow
patterns. However, their use has not been explored in the context of congenital
heart disease, aside from a few illustrative examples.
Research aims: Develop and validate computational tools for calculating
turbulence and relative pressure maps from 4D (i.e. 3D + time) phase-contrast MRI.
Develop methods for calculating reduced/summary quantities that can be
potentially useful to clinicians. Compare information obtained from 3D versus 2D
spatial information. Explore whether 2D images (which are faster to acquire, but
contain less information) provide sufficient information for diagnostic purposes.
Skills/software/key subjects involved:
 Medical imaging visualisation software (e.g. Paraview)
 Image segmentation (e.g. vascular modelling toolkit, vmtk)
 Matlab and/or python scripting
 Finite element method (FEniCS)
 Fluid dynamics
6. Effects of aortic geometry on arterial wave propagation
Level: Masters or PhD
Background: When the heart starts ejecting blood, it produces a pressure/flow
wave that propagates down the arteries. The speed and transmission efficiency of
this wave are very important in the functioning of the arterial system. For example,
wave reflection causes an increased heart workload. Wave speed is determined by
arterial stiffness, which increases with aging and is a key predictor of cardiovascular
disease. Current knowledge about wave propagation and reflection are almost
entirely based on one-dimensional (1D) models. Although very useful, these models
cannot account for the three-dimensionality of arterial geometry. In particular, the
normal aorta is curved like a candy cane (something that is not represented by 1D
models), while some children with congenital heart disease have unusual aortic
shape due to abnormal development and/or surgery. There is some initial evidence
that aortic shape affects wave reflection, but the mechanisms underlying this are not
known. Such knowledge may have important implications. For example, if it is
demonstrated that certain geometrical features of the aorta produce wave reflection
or wave dissipation, this may lead to refinements of current approaches to surgery
or stent deployment.
Research aims: Perform 3D modelling of pulse propagation in the aorta. Investigate
the effects of aortic curvature, tortuosity and branch positioning on wave reflection
and dissipation. Establish fundamental links between fluid dynamics and wave
reflection.
Skills/software/key subjects involved:
 Vascular geometric analysis (vascular modelling toolkit, vmtk)
 Computational Fluid Dynamics with pulse propagation
 Matlab and/or python scripting
 Vascular physiology and biomechanics
 Haemodynamics