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Prof Miguel Bernabeu
Prof Timm Krueger
No more applications being accepted
Funded PhD Project (Students Worldwide)
About the Project
Blood flow patterns in tumour vasculature are known to be highly irregular, with the distribution of red blood cells (or haematocrit) showing marked deviations from those observed in healthy tissue vasculature. These abnormalities present a challenge for drug delivery and have been linked to tumour hypoxia and enhanced tumour angiogenesis.
To date, many of the available computational models of tumour blood flow describe blood as a homogeneous fluid and employ phenomenological rules to determine haematocrit changes at vessel bifurcations. This is, in part, due to the computational challenges associated with simulating haematocrit changes in a mechanistic way, i.e. by explicitly describing the transport of red blood cells (RBC) in plasma. Unfortunately, such simplified approaches fail to capture the complex haemodynamics encountered in tumours.
Co-supervisors Bernabeu and Krüger have recently developed an extension to the blood flow simulation platform HemeLB that enables the simulation of blood flow as a suspension of RBCs. Close collaborators in Oxford and Barcelona have considerable experience of simulating blood flow and oxygen distributions in tumours and have recently developed a microfluidics assay that recapitulates RBC dynamics in tumour vascular networks. Both computer simulations and microfluidics experiments are informed by novel intravital microscopy data of mouse tumour xenographs generated the Oxford team.
In this project, we aim to integrate data from computer simulations, microfluidic platforms, and intravital microscopy in order to develop a mechanistic understanding of blood flow and oxygen delivery in tumour vasculature. This knowledge will allow us to formulate a theory of transport in the tumour vasculature that is suitable for evaluating therapeutic vascular normalisation strategies.
Supervisors:
• Dr Miguel O. Bernabeu, Centre for Medical Informatics.
• Dr Timm Krüger, School of Engineering.
Requirements
A strong academic track record with a 2:1 or higher in a relevant undergraduate degree, or its equivalent if outside the UK. A strong performance in a relevant postgraduate degree is desirable. Proven experience in one or more of the following is desirable: mathematical modelling, computational fluid dynamics, image processing or competence in one scientific programming language (e.g. C++, Python, Fortran). The successful candidate will work in a highly interdisciplinary environment and should be able to work independently and as part of a distributed international team.
Following interview, the selected candidate will need to apply and be accepted for a place on the Usher Institute Medical Informatics PhD programme. Details about the PhD programme can be found here: https://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=924
Application procedure
Please provide a CV, a personal statement detailing your research interests and reasons for applying, degree certificate(s), marks for your degree(s) and 2 written academic references. All documents should be in electronic format and sent via e-mail to: [Email Address Removed]
For further information about the project contact the primary supervisor: [Email Address Removed]
The closing date for applications is 30 June 2018
Interviews will be held during July 2018.
The studentship will ideally begin in September 2018.
To date, many of the available computational models of tumour blood flow describe blood as a homogeneous fluid and employ phenomenological rules to determine haematocrit changes at vessel bifurcations. This is, in part, due to the computational challenges associated with simulating haematocrit changes in a mechanistic way, i.e. by explicitly describing the transport of red blood cells (RBC) in plasma. Unfortunately, such simplified approaches fail to capture the complex haemodynamics encountered in tumours.
Co-supervisors Bernabeu and Krüger have recently developed an extension to the blood flow simulation platform HemeLB that enables the simulation of blood flow as a suspension of RBCs. Close collaborators in Oxford and Barcelona have considerable experience of simulating blood flow and oxygen distributions in tumours and have recently developed a microfluidics assay that recapitulates RBC dynamics in tumour vascular networks. Both computer simulations and microfluidics experiments are informed by novel intravital microscopy data of mouse tumour xenographs generated the Oxford team.
In this project, we aim to integrate data from computer simulations, microfluidic platforms, and intravital microscopy in order to develop a mechanistic understanding of blood flow and oxygen delivery in tumour vasculature. This knowledge will allow us to formulate a theory of transport in the tumour vasculature that is suitable for evaluating therapeutic vascular normalisation strategies.
Supervisors:
• Dr Miguel O. Bernabeu, Centre for Medical Informatics.
• Dr Timm Krüger, School of Engineering.
Requirements
A strong academic track record with a 2:1 or higher in a relevant undergraduate degree, or its equivalent if outside the UK. A strong performance in a relevant postgraduate degree is desirable. Proven experience in one or more of the following is desirable: mathematical modelling, computational fluid dynamics, image processing or competence in one scientific programming language (e.g. C++, Python, Fortran). The successful candidate will work in a highly interdisciplinary environment and should be able to work independently and as part of a distributed international team.
Following interview, the selected candidate will need to apply and be accepted for a place on the Usher Institute Medical Informatics PhD programme. Details about the PhD programme can be found here: https://www.ed.ac.uk/studying/postgraduate/degrees/index.php?r=site/view&id=924
Application procedure
Please provide a CV, a personal statement detailing your research interests and reasons for applying, degree certificate(s), marks for your degree(s) and 2 written academic references. All documents should be in electronic format and sent via e-mail to: [Email Address Removed]
For further information about the project contact the primary supervisor: [Email Address Removed]
The closing date for applications is 30 June 2018
Interviews will be held during July 2018.
The studentship will ideally begin in September 2018.
Funding Notes
This is a University of Edinburgh funded award and will provide an annual stipend for three years of £14,553 per year (subject to confirmation), plus University fees for UK/EU students.
UK/EU tuition fees only (any eligible non-EU candidates must fund the remainder of the overseas tuition fee).
There will in addition be £1000 funding towards research costs p.a. and up to £300 conference/travel fees p.a.
UK/EU tuition fees only (any eligible non-EU candidates must fund the remainder of the overseas tuition fee).
There will in addition be £1000 funding towards research costs p.a. and up to £300 conference/travel fees p.a.
References
Bernabeu, M.O. et al., 2014. Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis. J R Soc Interface, 11(99), p.20140543-.
Grogan, J.A. et al., 2016. Predicting the influence of microvascular structure on tumour response to radiotherapy. IEEE Transactions on Biomedical Engineering, PP(99).
Krüger, T., Varnik, F. & Raabe, D., 2011. Efficient and accurate simulations of deformable particles immersed in a fluid using a combined immersed boundary lattice Boltzmann finite element method. Computers & Mathematics with Applications, 61(12), pp.3485–3505.
Pries, A.R. et al., 1989. Red cell distribution at microvascular bifurcations. Microvascular Research, 38(1), pp.81–101.
Grogan, J.A. et al., 2016. Predicting the influence of microvascular structure on tumour response to radiotherapy. IEEE Transactions on Biomedical Engineering, PP(99).
Krüger, T., Varnik, F. & Raabe, D., 2011. Efficient and accurate simulations of deformable particles immersed in a fluid using a combined immersed boundary lattice Boltzmann finite element method. Computers & Mathematics with Applications, 61(12), pp.3485–3505.
Pries, A.R. et al., 1989. Red cell distribution at microvascular bifurcations. Microvascular Research, 38(1), pp.81–101.
Project supervisors
Career overview
Miguel O. Bernabeu completed a D.Phil. in Computational Biology at the University of Oxford in 2011, focusing on the development of computational methods for simulating ventricular cardiac electrophysiology. This work laid the foundation for multiple subsequent Ph.D. projects and was crucial to the success of the EU-FP7 grant VPH-preDiCT, which involved collaboration with pharmaceutical companies to integrate mathematical modelling into drug cardiotoxicity research. His research was presented at the Heart Rhythm 2011 conference, a significant event in cardiac science. In 2011, Bernabeu joined the Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX) at University College London, where he investigated the relationship between haemodynamics and vascular remodelling using both computational and experimental methods. His contributions were featured in the New Scientist magazine and published in various journals and conferences. During this period, he recognised the necessity of combining experimental and computational techniques to tackle critical questions regarding blood vessel responses to flow conditions. In 2015, Bernabeu was appointed to The University of Edinburgh as a Chancellor’s Fellow, establishing his first research group at the Centre for Medical Informatics, Usher Institute. He was promoted to Senior Lecturer in 2019. His research group has received funding from several prestigious organisations, including Fondation Leducq, the European Commission, EPSRC, MRC, the British Heart Foundation, The Alan Turing Institute, and Diabetes UK. In May 2021, Bernabeu became the Deputy Director of The Bayes Centre, the university's innovation hub for Data Science and Artificial Intelligence, where he oversees research strategy and delivery as Director of Research.
Research interests
Miguel O. Bernabeu's research focuses on vascular structure and function, particularly the relationship between abnormal vascularisation and various diseases such as myocardial infarction, stroke, and tumourigenesis. Their work aims to advance the understanding of vascular biology and biotransport, translating findings into next-generation vascular normalisation therapies. Specific research interests include the development of automated methods for diagnosing eye and systemic diseases through retinal scans, studying the tumour microvascular environment's impact on treatment, and investigating vascular remodelling during angiogenesis. The approach combines theoretical mathematical modelling and machine learning, in collaboration with vascular and cancer biologists and clinicians.
Computational Medicine
Computational Biology
Cardiac Electrophysiology
Mathematical Modelling
Vascular Biology
Biotransport
Vascularisation
Angiogenesis
Machine Learning
Biomedical Imaging
Retinal Scans
Tumour Microvascular Environment
Vascular Remodelling
Drug Cardiotoxicity
Haemodynamics
Clinical Research
Automated Diagnosis
Research Strategy
Data Science
Artificial Intelligence
Career overview
Professor Timm Krueger is a Professor of Fluid and Suspension Dynamics and the Head of Research Institute at the School of Engineering. They focus on the modelling and simulation of complex fluids on microfluidic scales, particularly in relation to suspensions of deformable particles and red blood cells. Professor Krueger teaches Chemical Engineering to second-year students and serves as the Co-Chair of the University's Research Cultures Forum. They obtained a PhD in Physics from Bochum University, Germany, in 2011, and a Diploma in Physics from Heidelberg University, Germany, in 2007.
Research interests
Professor Krueger's research focuses on the modelling and simulation of complex fluids at microfluidic scales, specifically examining suspensions of deformable particles and red blood cells. They specialise in microfluidics, suspensions and emulsions, blood flow in complex geometries, blood cell separation, inertial microfluidics, the lattice-Boltzmann method, and the immersed-boundary method.
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