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MSc+PhD position Fully Funded -- Massively parallel biomechanics simulation of brain surgery on HECToR
High Performance Computing MSc+Ph.D. position available at the
University of Glasgow on Massively Parallel Brain Surgery Simulation
with the extended finite element method (XFEM and FleXFEM) (University
of Glasgow) -- funding body is EPSRC.
One year MSc in HPC in Edinburgh (all costs covered by funding) + 3 year Ph.D. and access to HecToR,
one of the world's largest super-computer, including training with
experts in massively parallel simulation (10,000+ processors).
Supervisor: Dr Stephane Bordas,Dr Lee Margetts (Manchester)
Collaborators: Prof. Ray Ogden and Prof. Gerhard Holzapfel
Medical experts: two expert surgeons
in Belgium and medical imagery + computer aided/guided surgery
specialists, access to one in 30 interventional MRI scanners.
Eligibility: UK students have full funding. EU students will be discussed on a case-by-case basis.
Non-EU students should apply to ORSAS http://www.orsas.ac.uk/ and must have an outstanding research activity with international publications in leading journals to be considered.
EU Students should have a first class degree and preferably an MSc in numerical methods or/and computaitonal mechanics.
UK students: A Good second class or first class degree (preferred) or MSc in any
field of engineering or science: mathematics, computer science,
physics, biomedical engineering, civil engineering, mechanical
engineering, aerospace engineering, electrical engineering.
Student should be self motivated and hard working with a strong
interest in biomedical engineering and an outstanding background in
Mathematics and Physics.
Standard EPSRC Stipend + all fees covered.
Aims and Objectives
This project aims to devise and
validate a uniquely effective fully parallel surgery simulation tool for use in the
training, rehearsing and objective evaluation of surgeons to eradicate much of the
uncertainty in improving existing and creating new surgical procedures. High
Performance Computing (HPC) is today the only way forward to simulate the
effects of various strategies for cutting and manipulating brain tissue both
accurately and in realtime. Achieving this will provide a stepchange in surgical
Aim The main long term aim of the research in which this studentship is inscribed is to reconcile
realtime and accuracy in brain surgery simulation through cutting edge computational mechanics,
highperformance computing and realistic brain matter mechanical models. Achieving this aim is not
reasonably possible within a Ph.D.level research, the proposed work will provide a detailed proof of
concept required for further research by tackling the following four objectives.
Objectives (1) Optimise accuracy versus computational cost through cuttingedge numerical
methods (2) Develop and test massively parallel algorithms developed by leaders in HPC to achieve
realtime simulations (3) Utilise rigorous experimentallyinformed mathematical models of brain
tissue developed by world leaders in the field (4) Validate and verify the proposed simulation tool.
For the first time in the field of surgical simulation, the increased efficiency (objectives 1 and 2) will
allow realistic nonlinear material models to be used (objective 3) without sacrificing accuracy.
What is there for you in this project?
Benefit to the student: Suitability of the project for training Through the unique HPC training, the
student will acquire cuttingedge skills in highperformance computing. By working closely with Lee
Margetts, and expert in HPC, the proposed project will allow him/her to build upon and hone these
skills beyond the MSc training. What is more, the proposed research is highly multidisciplinary and
will
train the Ph.D. student in computational biomechanics,
which is a leading theme in today's research. More
specifically, two major sets of skills will be acquired:
Numerical methods for evolving discontinuities [OpenXFEM++, FleXFEM, SB] XFEM is one of the
most highly researched fields in computational mechanics 5 articles in 19992000 and 74 in 2006
2007 for a total of 138 journal papers between 1999 and 2008 (source: scirus) and more than 400
citations of the original paper [8]. This method and its sibblings such as the Flexible XFEM
(FleXFEM) is very likely to become an industrial standard in the coming decade. The student will join
SB's group, one of the most active and recognized developers of XFEM today both academically and
industrially, which will be essential in the transfer of his/her skills after the Ph.D.
Element by element massively parallel architectures [ParaFEM, LM] An essential point for this
research is that after his/her Msc, the training of the student in HPC will continue intensively, through
the involvement of Lee Margetts, a recognized expert in massively parallel computing and an
experienced developer of HECToR supported packages. In particular, the student will be gradually
introduced to ParaFEM, developed and maintained by Lee Margetts.
Additionally, the student will benefit from the
ongoing work of the team of Profs. Ogden and Holzapfel
in softtissue modelling and be exposed to some of the leadingedge
research by Prof. Ray
Ogden's group, of the host organisation, a world leading expert in fundamental theory in nonlinear
elasticity. These sets of skills are highly transferable and will provide the individual with a powerful
springboard for a successful career.
Please contact me for more details, this is only a preliminary advert
http://www.civil.gla.ac.uk/~bordas
stephane dot bordas at gmail dot com
See also:
http://www.epsrc.ac.uk/PressReleases/HPCStepsUpAnotherGear.htm
http://www.epcc.ed.ac.uk/training-education/hec/
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Comments
X-FEM tip enrichments
Hi ;
I am modeling quasi-static crack propagation with x-fem .
for calculation of SIFs I used the extrapolation method , but I found that the displacements at the tips are not very smooth and are turbulated. and as the result the SIF calculated are not correct .
Why the displacements are not smooth, and there exist a high gradient in the tip element. is it in X-Fem nature or it is my code problem?!
another thing is that where should the points to be used in SIF calculation be located ?
In FEM they are located at the edges of the crack but in X-FEM there are turbulances near the crack edge and this will affect the results.
thanks
Smoothness of crack tip fields in X-FEM and error estimation
Dear Pooyan,
What you are describing is not a problem with your code (at least not necessarily).
There are many papers on this topic, for instance, I recommend the following:
http://doi.wiley.com/10.1002/nme.1601 by Karihaloo Improving the accuracy of XFEM crack tip fields using higher order quadrature and statically …
Direct evaluation of accurate coefficients of the linear elastic crack tip asymptotic field by Karihaloo again
XFEM for direct evaluation of mixed mode SIFs in homogeneous and bi-materials still by Karihaloo
Derivative recovery and a posteriori error estimate for extended finite elements by Marc Duflot and Stephane Bordas
http://www3.interscience.wiley.com/journal/119054430/abstract by Marc Duflot and Stephane Bordas
A recovery-type error estimator for the extended finite element method based on singular+smooth … by Rodenas, etc.
A Global Explicit Residual Based Error Estimator for the eXtended Finite Element Method in … by Geniaut and Delmas
A simple error estimator for extended finite elements (Marc Duflot and Stephane Bordas and Phong Le)
Numerical Aspects of the extended Finite Element Method by Peters and Hackl
Do let me know if you would like preprints of those articles, which I could provide.Our XFEM matlab code could be of interest to check your code as well. I wonder if you could describe what you mean by extrapolation technique specifically?
Many thanks,
Dr Stephane Bordas
http://people.civil.gla.ac.uk/~bordas