News
Successful midterm evaluation of CBC
The Research Council of Norway has published the results of the midterm evaluation of eight Centres of Excellence after three and half years of activity. The Centre for Biomedical Computing (CBC), hosted by Simula, is assessed as Exceptionally good and is secured funding for the next five years.
The midterm evaluation has been carried out by the Research Council of Norway, and involves the centre's self-evaluation, an assessment of the centre by three international experts, and an overall evaluation made by an interdisciplinary, international evaluation committee set up by the Research Council.
In the report made by the international evaluation committee, it is stated: "CBC is a perfect example of the benefits of the Centres of Excellence, in that the establishment of the Centre has created the opportunity for developing a much broader vision than originally planned (tools developed have wide-spread applications to coupled multiphysics problems) so that the Centre has already exceeded its original ambitions, and, in the process developed unanticipated new national and international collaborations."
The midterm evaluation report is available from the Research Council's website.
PhD defence
12.12.12:On Wednesday December 12, at 13:15, Wenjie Wei successfully defended his PhD Thesis
Effective Use o Multicore-based Parallel Computers for Scientific Computing.
The prevalence of multi-core CPUs during the last decade has provided scientists with the possibility of conducting large-scale computer simulations. However, the multi-core architecture brought not only improved computing capabilities but also more programming challenges due to more complex memory hierarchies. In this thesis, we study how to efficiently utilize the computing power of multi-core CPUs and how to analyze the code performance obtainable on this hardware architecture. A series of interdisciplinary real-world scientific applications have been selected as the cases of study, which arise from computational cardiology and computational geoscience. The PhD investigation has been carried out from different angles: numerical algorithms, parallel programming and performance modeling and prediction. For two applications of cardiology, mixed programming and relevant optimization strategies have produced good performance for multi-core based clusters, when the solution domain is irregular. In three other geoscience applications, we have studied how to use compressed data structures, optimize cache usage and effectively parallelize various numerical schemes for the multi- core architecture. A practical approach to analyzing and predicting code performance is also proposed. It is shown that code implementation and optimization must match both the involved computations and the target parallel platform. Several good practices are summarized for parallel programming and performance analysis on the multi-core architecture, which can be of help to many other scientists.
Prior to the defense, at 11.15, Wenjie Wei presented his trial lecture Tools, models and
techniques for scientific programming on current and future heterogenous systems that combine
multicore hosts with manycore accelerators
.
The adjudication committee:
- Professor Paul H. J. Kelly, Department of Computing, Imperial College London
- Professor Tor Sørvik, Department of Mathematics, University of Bergen
- Professor Carsten Griwodz, Department of Informatics, University of Oslo
Chair of the disputation:
- Lecturer Dag Langmyhr, Department of Informatics, University of Oslo
Supervisors:
- Professor Xing Cai, CBC, Simula Research Laboratory & Department of Informatics, University of Oslo
- Dr. Ola Skavhaug, Simula Research Laboratory
- Professor Dr. Gerhard Zumbusch, Institute for Numerical Simulation, Fredrich-Schiller Universität Jena
On Monday November 5, at 13:15, Paul Roger Leinan successfully defended his PhD Thesis
Biomechanical Modeling of Fetal Veins. The Umbilical Vein and Ductus Venosus Bifurcation
November 5, 2012 MSc Paul Roger Leinan defended his thesis "Biomechanical modeling of fetal veins. The umbilical vein and ductus venous bifurcation". The models developed in the thesis have been used to improve methods for clinical measurement of the amount of blood flow delivered directly towards the fetal heart. An advanced material model for the vein and the surrounding Wharton's jelly within the umbilical chord was also developed. Finally, a generic model for networks of blood vessels was developed. This model may be used for prediction of flow, pressure and wall shear stress in generic networks of both arteries and veins, even though the primary focus in the thesis was the fetal circulatory system. Networks models are also useful as boundary conditions for 3D fluid-structure interaction models of blood flow in compliant vessels.
Prior to the defense, at 10.15, Paul Roger Leinan presented his trial lecture Modeling of Whiplash Injuries from a Biomechanical Point of View
.
The adjudication committee:
- Associate Professor Giancarlo Pennati, Politecnico de Milano, Italia
- Professor Hans Petter Langtangen, Simula Research Laboratory and University of Oslo
- Professor Tore Børvik, Norwegian University of Science and Technology
Chair of the disputation:
- Professor Tore Børvik, Department of Structural Engineering, Norwegian University of Science and Technology
Supervisors:
- Professor Leif Rune Hellevik, Department of Structural Engineering, Norwegian University of Science and Technology
- Professor Bjørn Skallerud, Department of Structural Engineering, Norwegian University of Science and Technology
- Dr.ir. Joris Degroote, Ghent University
On Monday June 18, at 11:15, André Massing successfully defended his PhD Thesis
Analysis and Implementation of Finite Element Methods on Overlapping and Fictitious Domains
In this work, we look at a mathematical method known as Nitsche's method which allows to couple different equations and domains in a flexible way. We investigate how this method can be applied efficiently to challenging 3D problems. Moreover, we strive to extend Nitsche's method to fluid dynamic problems.
Using data structure and algorithms from the field of computational geometry, we were able to implement a flexible and efficient computational framework to solve various problems by the Nitsche method. As an important part of this thesis, we proposed several new Nitsche-based formulation of a fluid dynamic problem (Stokes problem) and proved optimal convergence properties.
The thesis is written within the field of computational mathematics. The work has been conducted at Simula Research Laboratory.
Prior to the defense, at 11.15, André Massing will present his trial lecture Discontinuous Galerkin Methods for Solving Elliptic PDEs
.
The adjudication committee:
- Professor Paul Houston, School of Mathematical Sciences, University of Nottingham
- Professor Mohammad Asadzadeh, Department of Mathematical Sciences, Chalmers University of Technology
- Professor Xing Cai, Simula Research Laboratory / Department of Informatics, University of Oslo
Chair of the disputation:
- Professor Fritz Albregsten, Departments of Informatics, University of ÊOslo
Supervisors:
- Dr. Anders Logg, Simula Research Laboratory / Department of Informatics, University of Oslo
- Professor Mats G. Larson, Department of Mathematics and Statistics, University of Umeå
- Dr. Marie E. Rognes, Simula Research Laboratory / Department of Informatics, University of Oslo
For more information, please read the announcement of the PhD defense at the University of Oslo's web pages (in Norwegian).
27.04.12:
On Friday April 27, at 1315, Sigrid Kaarstad Dahl successfully defend her PhD Thesis
Numerical simulations of blood flow in the left side of the heart
.
Several aspects of hemodynamics have been addressed: fluid-structure interaction between rigid (mechanical) mitral valve during diastolic filling of the left ventricle; influence of pulmonary vein positions in the left atrium on the atrial flow field and velocity profile at the mitral valve plane; 3D mapping of subject specific ultrasound recordings of left ventricle during the heart cycle into a discretised time and space variable boundary condition for CFD simulations of the left ventricle; effect of mitral valve shape on velocity profile in the left ventricle outflow tract during systole.
The committee writes in their assessment that the thesis is an excellent example of cross-disciplinary research at its best, including input from engineering, non-invasive medical imaging, cardiology and surgeons.
Prior to the defence, at 1015, Kaarstad Dahl presented her trial lecture "Pulsatile flow in the arterial system".
The adjudication committee:
- Matts Karlsson, professor, Division for Biomedical Modelling and Simulation, Linkøping University
- Stig Urheim, MD PhD, Department of Cardiovascular and Pulmonary Disease, Oslo University Hospital Rikshospitalet
- Fridtjov Irgens, Professor emeritus, Department of Structrual Engineering, NTNU
Chair of disputation:
- Fridtjov Irgens, Professor emeritus, Department of Structrual Engineering, NTNU
Supervisors:
- Professor Leif Rune Hellevik, Department of Structural Engineering, NTNU
- Professor Bjørn Skallerud, Department of Structural Engineering, NTNU
- Professor Jan Vierendels, Department of Flow and Combustion Mechanics, Ghent University
- Dr Kent Andre Mardal, Simula Research Laboratory
26.03.12
On Monday March 26, Didem Unat successfully defended her PhD thesis "Domain-specific translator and optimizer for massive on-chip parallelism".
It should also be mentioned that Dr. Unat was already granted the prestigious Luis W. Alvarez Postdoctoral Fellowship in Computational Science at Lawrence Berkeley National Lab. The awarded fellowship is a recognition of her scientific contribution to the development of a fully-automated translator and optimizer, which can generate parallel GPU code based on serial source code. This methodology has the potential of greatly increasing the productivity of many computational scientists, because the time spent on painstakingly writing parallel software codes can be considerably saved.
Committee in charge:
- Scott Baden, Professor, Department of Computer Science and Engineering, University of California, San Diego
- Xing Cai, Professor, Center for Biomedical Computing at Simula Research Laboratory, and Department of Informatics at University of Oslo
- Andrew McCulloch, Professor, University of California, San Diego
- Allan Snavely, Professor, San Diego Supercomputer Center (SDSC), University of California, San Diego
- Daniel Tartakovsky, Professor, Department of Mechanical and Aerospace Engineering, University of California, San Diego
- Dean M. Tullsen, Professor, Department of Computer Science and Engineering, University of California, San Diego
Chair of the disputation:
- Scott Baden, Department of Computer Science and Engineering, University of California, San Diego
Supervisors:
- Scott Baden, Department of Computer Science and Engineering, University of California, San Diego
- Xing Cai, Center for Biomedical Computing at Simula Research Laboratory, and Department of Informatics at University of Oslo
16.06.11:
On Thursday June 16, at 13:15, Joachim Berdal Haga successfully defended his PhD thesis "Numerical methods for basin-scale poroelastic modelling.
Poroelastic modelling is a method for computing the interaction between fluids and porous structures, for example in sedimentary rock or biological tissue. Such computations require that large systems of mathematical equations can be solved. In his thesis, Berdal Haga explores and develops methods for solving efficiently such systems arising from modelling sedimentary basins.
The thesis consists of a number of scientific works dealing with various aspects of this problem. Properties of the system is investigated under particular conditions, like large jumps in permeability, and methods that can handle such conditions are developed. The methods are developed in such a way that they can be used for solving the problem by supercomputers with thousands of processors.
Prior to the defence, at 10:15, Berdal Haga presented his trial lecture Iterative solvers for large linear systems.
The adjudication committee:
- Axel Målqvist, Associate professor, Division of Scientific Computing, Uppsala Universitet
- Jan Martin Nordbotten, Professor, Matematisk institutt, Universitetet i Bergen
- Arnold Bertelsen, Professor, Matematisk institutt, Universitetet i Oslo
Chair of the disputation:
- Instituttleder Arne Bang Huseby
Supervisors:
- Harald Osnes, Department of Mathamatics, University of Oslo
- Hans Petter Langtangen, Simula Research Laboratory and Department of Informatics, University of Oslo
20.05.11:
On Friday 20 May, at 13:15, Kristoffer Selim successfully defended his PhD thesis "Adaptive Finite Element Methods for Fluid–Structure Interaction and Incompressible Flow".
On Friday 20 May, at 13:15, Kristoffer Selim will defend his PhD thesis Adaptive Finite Element Methods for Fluid-Structure Interaction and Incompressible Flow. Computer simulation is an important tool in many disciplines of science and engineering. Complex mathematical models are solved in large computer simulations as a complement to experimental techniques and theoretical studies. Selim's thesis focuses on how the quality of such computationally expensive simulations can be ensured, while at the same time making efficient use of the available computer resources.
One such example of a computationally expensive problem is fluid-structure interaction (FSI). This type of problem occurs when a fluid interacts with a solid structure in such a way that the solid structure is deformed and the flow of the fluid itself is altered. The FSI category of problems is of great importance and relevance in many applications. In biomedical research, blood flow in arteries and the human respiratory system are typical examples of problems in this category. In industrial applications, such as the design of airplanes, pipelines and fishing lures, the analysis of the FSI problem is an important part of the engineering process.
In his thesis, Selim investigates and designs adaptive numerical methods for FSI and fluid flow. To ensure that a simulation is of high quality, it is crucial that the accuracy of computed solutions can be determined. Selim's investigation is based on so-called goal-oriented adaptive finite element methods, which provide a general framework for the design of methods that ensure the necessary error control, such that accuracy can be determined. Based on the error estimate one may also design adaptive algorithms for efficient use of the computational resources.
Prior to the defence, at 10:15, Selim presented his trial lecture Multiscale problems and techniques.
The adjudication committee:
- Professor Harald van Brummelen, Eindhoven University of Technology
- Professor Thomas Grätsch, Hochschule für Angewandte Wissenschaften Hamburg
- Joakim Sundnes, Simula Research Laboratory and the University of Oslo
Supervisors:
- Anders Logg, Simula Research Laboratory
- Harish Narayanan, Simula Research Laboratory
- Trond Kvamsdal, NTNU
- Nils Svanstedt, Chalmers
05.05.11:
On Thursday 5 May at 13:15, Kristian Valen-Sendstad successfully defended his PhD thesis "Computational Cerebral Hemodynamics".
Stroke is the third most common reason for death in the Western world. One type of stroke is caused by the rupture of an out-pouch of a blood vessel, called an aneurysm. As much as six per cent of us can develop aneurysms during our life time, and the number of incidences of stroke is on the rise.
Understanding the underlying processes of initiation, growth and rupture of aneurysms is of great importance to both a patient and society in general. Therefore, one has to gain detailed knowledge of blood flow and its effects on the blood vessel wall. Blood flow inside aneurysms has previously been believed to be stable and smooth. However, in Valen-Sendstad's thesis, it is proven through very high-resolution computational fluid dynamics that the flow can be complex and turbulent. This means that the cells inside the blood vessels, or aneurysms, might experience forces much stronger than previously assumed.
The rupture of aneurysms is known to occur more frequently in women than men. Measurements from the blood vessels of 55 patients undergoing angiography, were used to create idealised models of the female and male main blood vessel branches. The shear stress acting on the female blood vessel walls was found to be up to 50 per cent greater than that of the males, and could partially explain why more aneurysms develop and rupture in females.
Prior to the defence, at 10:15, Valen-Sendstad presented his trial lecture Fluid-structure simulations for biological flows.
The adjudication committee
- Professor Francis Loth, Department of Mechanical Engineering, University of Akron, Ohio
- Professor Atle Jensen, Department of Mathematics, University of Oslo
- Professor Carsten Griwodz, Department of Informatics, University of Oslo
Supervisors:
- Professor Hans Petter Langtangen, Simula Research Laboratory
- Senior Research Scientist Kent-Andre Mardal, Simula Research Laboratory
- Senior Research Scientist Anders Logg, Simula Research Laboratory
- Professor Bjørn Anders Pettersson Reif, Norwegian Defence Research Institut
Several new major grants!
At the end of 2010, CBC researchers experienced great success with grant proposals. Kent-Andre Mardal, heading the Biomedical Flows and Structure project in CBC, succeeded with a proposal for the prestigious ERC Starting Grant, but due to budget limitations in the European Research Council, the Research Council of Norway contributed with funding. Joakim Sundnes, deputy manager of CBC, and Sam Wall, Postdoctoral Fellow at CBC, received a substantial grant from the eVita program in the Research Council of Norway. Sam Wall was also successful with a personal postdoc grant in the competitive FRIBIO program in the Research Council of Norway. Finally, Molly Maleckar, heading the Cardiac Computations project in CBC, Sam Wall, and Per Grøttum, Professor of Medicine, together with collaborators at the Oslo University Hospital and the GE company Vingmed Sound, managed to obtain the very prestigious grant Center for Research-Driven Innovation, 2011-2019, from the Research Council of Norway. The topic for this new center takes research from the Cardiac Computations project to clinical practice through new diagnostics, new equipment, and new treatment procedures.
