Center for Biomedical Computing

Annual Report 2013

the user’s problem specification into fast C++ code, but UFL is not limited to FEniCS - others are using UFL as a user-friendly front-end to their more low-level finite element codes. The UFL paper received exceptionally positive reviews, and we expect it to be a highly cited paper. The FEniCS book and the DOLFIN paper from 2010 are both already climbing towards 200 citations!

CBC has at the time of this writing only three more years to go, yet this is typically the duration of most research projects in today’s funding regime. Many of the milestones of the revised research plan from 2011 have been accomplished, and the remaining ones are already within reach. This gives room for positioning knowledge and human resources to meet the challenges that lie ahead of CBC in 2017. The long-term research undertaken in CBC definitely takes time, and we now realize (like many other Centers of Excellence) that it takes a ten-year period to build a sufficiently strong scientific foundation to attack the fundamental and important research questions in the field. Continued success with research funding will depend critically on the scientific stature of the senior researchers, the capabilities of FEniCS and other software packages, and on strategic collaborations. These factors will be governing much of the freedom that is left in the remaining three years of CBC. Various leads are already being followed. An interesting opportunity for CBC scientists is the newly awarded center in computational neuroscience at the University of Oslo, named CINPLA. People from CBC played a key role in the proposal for this center. The University will fund six or more PhD positions and expects the center to create a vibrant environment that can produce a strong application for a Center of Excellence in 2017. Additional resources and funding from the Research Council have already been attracted to the project. We are now in a phase of the Center of Excellence project where most scientists work with the more long-term and difficult problem settings in the research plan. For example, we have for quite some time been searching for a physics-based theory that can explain the pathological condition known as syringomelia a cyst in the spinal cord that causes serious neurological symptoms. In 2013, PhD candidate Karen-Helene Støverud did extensive model studies of how abnormal Cerebrospinal fluid in the spinal canal can induce flow and deformation in the spinal cord that may explain the formation of cysts. This is not a complete theory yet, but a promising demonstration of how mathematical modeling and computer simulations can help establish fundamental medical understanding. The success of CBC relies heavily on such demonstrations. A couple of years back, PhD student Kristian Valen-Sendstad and co-workers discovered that blood flow in the vicinity of aneurysms in the brain is much more complex than previously established. Kristian continued as a postdoc in David Steinman’s world-famous group in Toronto. This group has now changed its focus to work on complex (turbulent) blood flow in other contexts to arrive at a physical explanation why aneurysms are common in the brain but not outside. This is an encouraging example how CBC research makes impact and contribute to significant advances also outside the center. One of the major highlights in 2013 was the acceptance of Martin Alnæs’ UFL paper. UFL is the high-level language used in the FEniCS software to specify partial differential equation problems. Much of the success of and interest in FEniCS come from the very attractive syntax of UFL. In FEniCS, UFL is used to turn

The biggest computer in the world, i.e., the number one machine on the Top 500 list of supercomputers, is currently at the National University of Defense Technology in China. We are proud that CBC scientist Xing Cai and his team were selected as primary testers of this supercomputer three months prior to the official opening. The test period allowed heavy experimentation with the most powerful computing resources of our time, and offered a very attractive testbed for the parallel computing technologies being developed in CBC. In addition, CBC scientists managed to run several simulations of subcellular calcium dynamics with unprecedented resolution. It is expected that Norwegian Centers of Excellence take on the organization of scientific conferences. CBC did so in 2013 when we hosted the 26th Nordic Seminar on Compuational Mechanics. This is a popular annual event that takes place in the Nordic and Baltic countries. About one hundred participants were present at our premises. This year the conference had a natural focus on computational biomechanics. CBC is very greatful to the organizers, with Anders Logg in the lead, who put in huge efforts to get all details right and make this conference a deemed success. A nice observation is that the upcoming young senior scientists in CBC are regularly being invited as keynote speakers at international conferences. Kent-Andre Mardal gave keynote talks at the International Symposium on Modelling of Physiological Flow in Chia Laguna, Sardinia, Italy and at the Preconditioning Conference 2013 in Oxford, UK (and we can add that Anders Logg was a keynote speaker EuroSciPy 2011 and PDESoft 2012). Anders Logg has been a key scientist in CBC, working with development of new numerical methods and with the FEniCS package in particular. Anders left CBC in August 2013 for a full professorship in Computational Mathematics at Chalmers University of Technology in Gothenburg. Anders continues to collaborate intensively with CBC, and his move has opened up collaboration and recruitment opportunities at Chalmers. CBC continues to serve academia with excellent candidates for the top positions. At the time of this writing, it is a fact that another key scientist, Kent-Andre Mardal, will strengthen the University of Oslo in a full professorship at the Department of Mathematics. Kent-Andre has been instrumental for the bioflows activity in CBC, as well as in the development of numerical methods and FEniCS. He will continue to collaborate closely with CBC and take an adjunct position. We are very proud that CBCans do so well in the strong competition for professorships at the universities. Such permanent positions strengthen the long-term funding of our projects and ensure that these leading scientists can continue continue their research after the lifetime of CBC.

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WORDS FROM THE DIRECTOR RUNNING THE CENTER Organizational Changes The Scientific Advisory Board (SAB) People, Recruitment and Gender Diversity Gender diversity SCIENTIFIC ACTIVITIES Computational Middleware Robust Solvers Biomedical Flows and Structures CBC at NTNU Cardiac Computations FEATURED RESEARCH 2013: Ciari I malformation and syringomyelia EDUCATION AND OUTREACH The Simula School of Research and Innovation University Teaching APPENDIX Staff Accounting and Budget Publications Conferences, Workshops and Seminars Other Activities

2 4 4 4 4 4 6 6 8 10 11 12 13 13 16 16 16 17 17 19 22 28 30

Media Appearances Refereeing Activities Committee Work and Recognition Editorial Boards Conference Committees Organization of Minisymposia and Workshops at Conferences Invited talks

30 30 30 31 31 32 32

Collaboration partners List of International Guests in 2013

33 35

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Organizational Changes

• Dr. Debora Wood. Head of Department, Pipelines and Materials, Det Norske Veritas (DNV).

PhDAll research activities in CBC are organized in large projects with an appointed project leader and a precise project plan. After seeing some adjustments through 2011, the project portfolio has remained unaltered since, and currently includes the following four projects.

People, Recruitment and Gender Diversity

1) Computational Middleware. This project is devoted to developing generic high-performance software components for building the simulation programs needed in the center. The results also serve the global computational science community with a new generation of widely applicable computational software. At the core of the development is the finite element software suite FEniCS.

Recruitment to the center. During the last half of 2013, we recruited a PhD and a Postdoc to strengthen our focus on the Biomedical Flows and structures, Computational Middleware and Robust Solvers projects. The Biomedical Flows and Structures project has been additionally strengthened through collaboration and joint supervision of a PhD student at University of Toronto and another PhD student at the University of Siegen. The CBC@NTNU group have also recruited a new PhD to continue their work on developing a cardiovascular network model. Thus have all four research topics received strengthening during 2013.

2) Robust Solvers. The Robust Solvers project focuses on efficient and stable numerical methods with error and uncertainty estimation, as well as implementation of such methods for problems arising in the two application projects Cardiac Computations (CC) and Biomedical Flows and Structures (BFS).

Graduated PhD students. One PhD student graduated during 2013: Tor Gillberg’s finished his studies on ”Fast and accurate front propagation for simulation of geological folds.” in November 2013. Simulations of geological folds are a key ingredient in the Compound Earth Simulator (CES), an industrial software tool used in the exploration of oil and gas. In this thesis, local approximation techniques were investigated with respect to accuracy and efficiency. Several novel algorithms were also introduced, of which some are accelerated by parallel implementations on both multicore CPUs and Graphic Processing Units. These algorithms are able to simulate folds at a fraction of the time needed by the CES industry code, while retaining the same level of accuracy. Complicated tasks that previously needed several minutes to be computed can now be performed in just a matter of a few seconds, thus significantly improving the CES user experience. The thesis was written within the field of Scientific Computing. The work has been conducted at Simula Research Laboratory and Kalkulo AS supported by a “Nærings PhD” grant from the Research Council of Norway.

3) Cardiac Computations. This project performs research on medical problems involving models of heart electrophysiology and mechanics. The current activity is strongly influenced by the goals of the Center for Cardiological Innovation (CCI), which is a Center for Research Based Innovation funded by the Research Council of Norway. A more elaborate description of the mutual research goals of CCI and CBC was provided in the CBC annual report for 2011. 4) Biomedical Flows and Structures. Research in the Biomedical Flows and Structures project centers around biomedical flow and tissue interaction problems of high clinical importance. In a short to medium time frame, the applications to be targeted are aneurysm formation and rupture in the Circle of Willis, the relation between Chiari I malformation and cyst formation in the spinal cord, modeling of the mitral valve in the heart, modeling of large cardiovascular networks, and fluid-structure interactions in cardiovascular biomechanical systems. The research on the latter three topics is headed by our partners at the Biomechanics Division at the Department of Structural Engineering at the Norwegian University of Science and Technology (NTNU), known as CBC@NTNU in the CBC context.

CBC alumni. Several of CBC’s former researchers continue to pursue an academic career outside of our host institution. We are happy to report that their academic merits and scientific training have been recognized and secured them prominent academic positions with their new employees. Our principal investigator Anders Logg accepted a position as full professor at Chalmers University of Technology August 2013, but continues to hold an adjunct position at CBC and is still actively participating in our current research.

The Scientific Advisory Board (SAB) The members of the CBC advisory board provide the center with valuable input, and review the ongoing research activity. Since CBC is a focused center with a quite narrow research scope, we benefit from having a small and well informed advisory board that is in tune with our vision and grasp the whole specter of our activities. Presently our SAB consists of:

Gender diversity

• Prof. David Keyes. Dean of Mathematical and Computer Sciences and Engineering, King Abdullah University of Science and Technology (KAUST). • Prof. Andrew McCulloch. Department of Bioengineering, University of California, San Diego (UCSD).

CBC has continued the close collaboration with our host institution Simula to actively search for and recruit talented researchers, and to strive for a gender diverse research environment without compromising on the quality and talent of our researchers.

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We share the ambition of our host of reaching 25% female PhD students, postdocs and full time researchers at Simula within 2015, and 30% within 2022. This sets a challenging goal for the years to come. In our experience, the most challenging part of this ambition is to obtain the desired gender diversity on the senior level, because of the so-called ”leaky pipeline”1 . CBC has two active female researchers at the highest levels of our host organisation. By their undisputed talent and accomplishments they clearly demonstrate that there is an array of opportunities and exciting career possibilities for both genders in our research field.

The award was a grant of 2 million NOK, which is a subsidy to the resources that are already being used at Simula in the work towards gender balance. Minister of Education Torbjørn Røe Isaksen handed out the award, and praised Simula for ”providing evidence that diversity can contribute to international success and outstanding research results”, after commenting that we cannot afford to neglect scientific talent. The Ministry of Education and Research stated that it was the first time that the Gender Equality Award was given to a research center with world–leading research groups2 . Aslak Tveito, Managing Director for Simula, commented that ”We are very happy to have received the Gender Equality Award. This award will strengthen our work towards an even better balance, and even better scientific evaluation.”

Simula wins Gender Equality Award. Given by the Norwegian Ministry of Education and Research, the Gender Equality Award (Likestillingsprisen) promotes gender equality in research institutes, Universities and University Colleges. The award is given to the institution that has the foremost regimen for improving its gender balance, and our host institution was the winner for 2013.

As a closing remark, it is worth noting that although we emphasize establishing a gender diverse research environment, we will always regard potential for scientific excellence as the single most important criterion for recruiting and promoting staff.

1 See:

http://blog.sciencewomen.com/2007/03/leaky-pipeline.html http://www.regjeringen.no/en/dep/kd/news-and-latest-publications/News/2024/likestillingsprisen-til-simula-research.html?id=749255 2 See:

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Through 2013 the scientific activities in CBC progressed according to plan. Below we give an overview of the main activities and results in 2013. The sections cover the four projects that have been forming CBC through 2013: Computational Middleware, Robust Solvers, Biomedical Flows and Structures, and Cardiac Computing. The activities at the Norwegian University of Science and Technology contribute to the Robust Flow Solvers and the Biomedical Flows and Structures projects, but the size of this activity is so substantial that the research is described in a separate section (CBC@NTNU).

Computational Middleware

Parallel Computing. The HPC research encompassed several activities during 2013, with the most important ones arising from the newly established strategic collaboration with National University of Defense Technology (NUDT), China, who developed the world’s No.1 supercomputer: Tianhe-2. A joint effort by researchers from both sides resulted in huge-scale simulations of subcellular calcium dynamics with nanometer resolution, using up to 25% of Tianhe-2’s total capacity, (see Figure 1). These successful simulations, which will pave way for a more thorough scientific investigation of this topic in cardiac modeling, were among Tianhe’s very first scientific applications. The NUDT collaboration also prompted an investigation of performance programming of Intel’s MIC architecture, the latest hardware addition to the HPC landscape. In addition, the topic of GPU programming, using both CUDA and OpenCL, was strengthened during 2013. In total, the HPC-related activities produced five published/accepted journal papers and four peer-reviewed proceedings papers.

The FEniCS Project. In 2013, the FEniCS finite element software project saw a surge of new activity with the release of three new versions labeled 1.1–1.3. This more rapid release schedule is planned to continue such that continual improvements are quickly available to users. A seminar was arranged with four researchers from CBC visiting Jesus College, Cambridge in January 2013 to plan for development of more advanced multiphysics features in FEniCS. Following this seminar, the main focus of the development this year has been on computational geometry, improved performance and parallel scalability, preparations for solving large problems, and general improvements to usability, stability, maintainability and performance. It is now possible to solve PDEs on manifolds, generate meshes from constructive solid geometry descriptions, as well as solving a large number of ODEs coupled with vertices of a mesh as needed for cardiac computing applications. FEniCS is regularly used in university courses, as well as in master and PhD student projects. The annual FEniCS Workshop was held 18-19 March 2013 at Jesus College, Cambridge, with 23 talks and more than 60 participants, highlighting the strong position FEniCS has gained in the UK, in particular at Imperial College London where spin off projects based on the FEniCS components UFL and FFC have been launched. The FEniCS book has now been cited more than 150 times in the two years since its release, and the open source project has attracted additional academic developers contributing to the continual improvement of the software and supporting the user community.

In the aspect of additional research funding, two successes can be attributed to HPC in 2013. Specifically, CBC became partner of a large-scale EU Artemis project named EMC2. The CBC share of this EU grant amounts to 36 man-months, with a research focus on development of a domain-specific language and automated code translator targeting real-time processing of seismic data. Another grant, provided by RCN, arose from a joint proposal with University of Tromsø, on the subject of new programming models that facilitate future energy-efficient HPC. The CBC share of this grant is a 3-year PhD student position, which will start in October 2014.

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Figure 1: Snapshots from a nanometer–resolution simulation of a subcellular calcium wave. The simulation was done on Tianhe-2: the world’s currently most powerful supercomputer. • CamFIN – a framework for the simulation and optimization of the mechanical activity of the heart;

Application software. In addition to the FEniCS project, a number of smaller software packages have been produced from CBC supported activities. Some focus on a particular method and others are application specific.

• Tanganyika – an implementation of mono- and multiadaptive Galerkin methods of arbitrary polynomial order for ODEs;

• Gotran – a General ODE TRanslator for easy definition of ODE systems;

• RoseDist – a library for uncertainty quantification using an iso-probabilistic Rosenblatt transformation;

• GOSS – a General ODE System Solver fro solving ODEs;

• chaospy – a library for uncertainty quantification using polynomial chaos expansion;

• SubCell – a problem solving environment for subcellular problems;

• dolfin-adjoint – automatic derivation of the discrete adjoint and tangent linear models, by recording the sequence of forward model equations solved in a DOLFIN program and

• GillStep – a tool to define and solve discrete and stochastic Markov models using a modified Gillespie solver;

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using this to symbolically derive the corresponding adjoint model equations to be solved;

scribed by level-set functions; • uflacs – algorithms for effective translation of symbolic equations with complicated tensor algebra expressions to high performance low level code;

• Mint – a source-to-source (C-to-CUDA) code translator and optimizer targeting stencil methods; • beatadjoint – a problem and solver collection for cardiac electrophysiology models with consistent discrete adjoint models;

• oasis – a fractional step Navier-Stokes solver with performance exceeding OpenFOAM and CDP; • fenicstools – tools for postprocessing in FEniCS based solvers;

• headflow – a set of Navier-Stokes solvers in a framework with boundary conditions and postprocessing features motivated by blood flow applications;

• vmtk – the vascular modeling toolkit has received CBC contributions for setting boundary conditions on cerebrospinal fluid flow geometries;

• dolfin-olm – a library for solving PDEs on non-aligned overlapping meshes, using Nietsche’s method and unfitted discontinuous Galerkin to realize the interface coupling;

• hashdist – a tool for building and managing custom software distributions based on a functional approach. The project and open source software development was funded by the American Department of Defence;

• cutfem – tools for the cut finite element method for multiphysics problems where the boundary or interface is de-

Figure 2: From a simple formulation the Chaospy toolbox can create random variables with non-standard dependency structures. It will also automatically numerically estimate properties like (a) the probability density function and (b) random number generator.

Robust Solvers

tive project between researchers at the CBC, University of Oxford and Imperial College London. The dolfin-adjoint project (dolfinadjoint.org) automatically derives the discrete adjoint and tangent linear models from a forward FEniCS computational model. Adjoint models are key ingredients in many algorithms of computational science, such as in sensitivity analysis; parameter identification and data assimilation; optimal control, shape and topology optimization; goal-oriented error estimation and adaptivity; and predictability analysis. While deriving the adjoint model associated with a linear stationary forward model is straightforward, the development and implementation of adjoint models for nonlinear or time-dependent forward models is notoriously difficult because of the challenges in derivation and implementation

In 2013, the Robust Solvers project has garnered the academic fruits of the investigations of previous years including the publication of our ground-breaking work on automated, goal-oriented error control. Our current efforts have continued to be centered around the development of more robust and efficient methods and solvers for the solution of problems encountered in the biomedical flow, cardiac and geoscientific application domains. Automated derivation of adjoint models. This year, the Robust Solvers project made a great leap forward with the development and release of the software project “dolfin–adjoint”, a collabora-

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of control flow. dolfin–adjoint relies on an entirely new, high-level abstraction for developing discrete adjoint models, namely to treat the computational model as a sequence of equation solves. This is in contrast to traditional, low-level, algorithmic differentiation (AD) tools which consider the model as a sequence of elementary instructions. The higher–level abstraction enables a number of advantages including unsurpassed performance: dolfin–adjoint

yields models with optimal theoretical efficiency, which can automatically employ optimal checkpointing schemes and inherits parallel support from the forward model. The underlying methodology is documented in a series of journal articles either published this year or scheduled for 2014. Moreover, we are, with much anticipation, looking forward to the exciting potential of this software across the CBC including in the biomedical flows, cardiac and geoscientific application domains.

Figure 3: Optimised location of 256 tidal turbines in the Pentland Firth, Scotland via dolfin–adjoint. Preconditioning for optimal control. PDE-constrained optimization problems; that is, problems in which one seeks the optimal state of some objective functional constrained by a set of partial differential equations, are ubiquitous and of immense importance across computational science. Such problems may be attacked numerically via iterative optimization techniques or using so-called one-shot methods: the latter involving the solution of very large and typically ill-posed, linear systems of equations. The numerical solution of these linear systems in turn require appropriate preconditioning.

Figure 4: In uncertainty quantification, polynomial expansions can be used as part of model approximation. By carefully selecting the expansion tailored to the probability space, very high accuracy can be achieved. For example, the Hermite expansion is optimal for the Gaussian probability distribution. In 2013, CBC authors have presented a new framework for constructing efficient preconditioners for inverse problems based on Riesz mappings. The construction is remarkably general and significantly extends the current state of the art. Moreover, our work and expertise on preconditioning has impact above and beyond the Center itself. For instance, in 2013 we have created efficient preconditioners for statistical analysis of cosmic background radiation arising from the Big Bang.

Fluid–structure interaction on overlapping meshes. The CBC spearheads the technological development and use of finite element methods on cut and composite meshes. With cut and composite mesh methods, the computational domain may be described via a set of overlapping and non-matching meshes or via fictitious domains described by surfaces or level sets. Such methods may offer significant advantages over single, conforming mesh methods for instance for handling large deformations in

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in layered media for porous media applications. The second application develop pertained to the modelling of geological folds. These folds deform layers that are initially horizontal but various folding regimes exist depending on the forces involved and the rock rheology. Modelling these folds using a front-propagation technique allows constructs distance fields from the fold horizon. These fields can be used to map geological properties to the deformed domain. In addition, new algorithms were applied in domain decomposition that allowed for more accurate solutions to the problem as well as for massive parrallelism to be used, such as required in GPU computing.

fluid-structure interactions or internal discontinuities in the computational domain. In 2013, our work in this area has focused both on tackling computational problems of increasing complexity and the widespread dissemination of our methodology and technologies. Our previous work has been extended from being centered around Newtonian fluid flow problems to considering both fluidstructure interaction and viscoelastic fluids. Moreover, the researcher team have organised a number of mini-symposia at international conferences, given a number of conference presentations, and further enhanced its software technologies. A number of contributions describing the developments over the last years are now accepted for publication in major international journals. Computational geoscience applications. Two applications in computational geoscience were particularly visible for CBC in 2013. First, a stochastic toolkit has been developed, and although specifically applied for geoscience applications, the toolkit is useful for uncertainty quantification in any scientific application of numerical modelings. The toolkit enables deployment of a series of stochastic methods and sampling techniques, and handles multivariate stochastic variables. Furthermore, the toolkit allows for variance reduction techniques in order to facilitate faster convergence of the method for complex numerical problems. Also in 2013, the toolkit was tested on diffusion-based

Figure 5: Optimised topology of heat conducting device via dolfinadjoint

Biomedical Flows and Structures l = 1cm

The purpose of the BFS project is to apply the numerical methods and software developed in the Computational Middleware and Robust Solvers projects in a few selected important applications, which have a potential to make an impact on clinical medicine.

Upper extension

Originally segmented geometry (region of interest)

Blood flow in the Circle of Willis. The first application concerns the blood flow in the Circle of Willis, which is an arterial network located at the base of the brain. The project is motivated by the fact that aneurysms frequently develop in this area, and these aneurysms may rupture and lead to a fatal stroke. However, the risk of rupture is low, and surgical treatment of the aneurysms is complicated and risky. Assessing the risk of rupture and deciding on the optimal treatment for each aneurysm is therefore both clinically important and extremely challenging.

Lower extension l = 3cm

Figure 6: The model of the spinal canal plus the extensions in a patient with the Ciari I malformation.

Earlier, we brought up the issue of whether turbulence might be present in cerebral aneurysms. Following up on this issue, Dr. Kristian Valen-Sendstad and Prof. David Steinman of the University of Toronto, have published a paper in Americal Journal or Neuroradiology demonstrating that space and time resolutions widely used for cerebral aneurysms studies are not sufficient for flow investigations in aneurysms.

Cerebrospinal fluid flow. The second application addressed by the BFS project concerns the oscillating flow of cerebrospinal fluid (CSF) in the cranio-cervical region, and the flow’s association with the development of syringomelia (cysts within the spinal cord). Such cysts are often found in patients with the Chiari I malformation, a state characterized by having abnormal position of

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Figure 7: Contours of the General Reynolds number for a vertical plane (a) at x=0.101, and a horizontal plane (b) at z=0.097, both at t=T0 .

the cerebellar tonsils (i.e., the brain is somewhat sunken down in the neck). The abnormal position of the tonsils obstructs the natural flow of CSF, and it is hypothesized that the abnormal flow pattern is a cause for syringomelia. The research on CSF fluid flow is highlighted in this years Featured Research article, but some additional results are mentioned here. Together with researchers at FFI, we performed an extensive CFD study of CSF in a patient with a Chiari I malformation at resolutions previously used. The study, involving about 60 million cells, revealed that the flow condition in that particular patient was close to transition to turbulence. That is, as we have already establised for blood flow in cerebral aneurysms, the abnormal anatomy appears to induce transition from smooth

and predictable laminar flow in healthy subjects to chaotic flow with regions of turbulent flow causing the developement of these serious pathologies. Figure 6 shows the computational geometry, while Figure 7 shows the local Reynolds number of the flow. Clearly the local Reynolds number is around 2000 in several places, which is known to be a critical threshold in stationary pipe flow. Furthermore, we have investigated the effect of rest and exercise on CSF velocities and pressure in idealized models. The conclusion of this study is that exercise increases CSF velocities and pressure gradients - proposing an explaination for the fact that patients with the Chiari I malformation often experience pain during exercise.

CBC@NTNU

in 2012. Essential in the development will be the incorporation of the network model in a polynomial chaos expansion framework to allow for stochastic variation in the model parameters to mimic individual variation of relevance to personalized medicine, and to develop/implement physiological models for the boundary conditions (e.g. heart models, kidney models and models for peripheral vessels). In particular the polynomial chaos expansion effort will be done in close collaboration with CBC researchers at Simula. The model work will be strongly coupled to international efforts on developing multiscale and multiphysics modeling frame-

The Biomechanics Division at the Department of Structural Engineering at the Norwegian University of Science and Technology (NTNU), (or CBC@NTNU for short) has traditionally been involved in research projects related to cardiovascular biomechanics and bone mechanics. Vinzenz Eck was recruited for a PhD-project in 2013 to further develop an existing network model for the cardiovascular system, developed by Paul Roger Leinan who defended his thesis 3 See: 4 See:

http://vph-institute.org/ http://virtualrat.org

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works for the cardiovascular system “Virtual Physiological Human”3 and “Virtual Physiological Rat”4 . A specific goal of the modelling work will be to extend the prediction scope of a recently developed model of how hypertension develops in ageing individuals5 , and through this contribute to the development of a

The first results for this project was presented at 3rd International Conference on Computational and Mathematical Biomedical Engineering CMBE2013 16-18 December 2013, Hong-Kong.

Cardiac Computations

validating patient specific heart models.

The Cardiac Computations (CC) project in CBC is mainly contained in the Computational Cardiac Modeling (CaMo) department at Simula Resarch Laboratory. The main focus of research in the CaMo department is the clinical goals defined by the Center for Cardiological Innovation (CCI), which is a center for researchbased innovation funded by the Research Council of Norway. The CCI has been in operation since 2011, and involves close collaboration with industrial partner GE Vingmed Ultrasound and the cardiologists at Oslo University Hospital. However, the CaMo department is also home to research focusing on numerical methods and computational tools, with close connections to the other activities in CBC. In recent years, the field of computational cardiac modeling and simulation has matured in both scope and methodology such that it can contribute significantly to the present understanding of heart physiology and disease. The CaMo department at Simula stays at the forefront of this development through a focus on both development of state-of-the-art heart simulation tools, and the targeted application of these tools to gain mechanistic insight into diverse biophysical cardiac phenomena. In the area of tools development, the focus through 2013 has been on developing an efficient pipeline for building patient specific heart models from images, and on improving the efficiency and flexibility of the in-house Pulse electro-mechanics solver. Both of these tools are important building blocks for the scientific investigations and clinical work that is planned in the CCI. Substantial progress has been made through 2013. Detailed, image based heart electro-mechanics models are now built in less than an hour, and the numerical efficiency and robustness of the solver is continuously improved. The work continues in 2014, mainly focusing on further improving computational efficiency and

As also described in the Computational Middleware section, CBC reserachers have been among the first to run scientific applications on the world’s largest supercomputer, the Tianhe-2. The application was a sub-cellular simulator of calcium diffusion, with spatial resolution and geometrical detail far beyond any existing computer models of this phenomena. The simulations give insight into the complex dynamics of calcium signaling in heart muscle cells, which is essential for understanding the function of the heart in health and disease. In addition to the biological insight, running scientific simulations on the worlds largest computer has brought up a number of questions related to parallel computing and numerical solution of differential equations with extreme spatial and temporal resolution.

5 See:

new drug targeting paradigm based on computational physiology.

In addition to image based modeling and sub-cellular simulations, scientific applications in CC include all relevant physical scales, and a wide range of electrical, chemical, and mechanical phenomena. Electrical and mechanical phenomena in the mammalian heart are tightly coupled; electrical activation precedes and triggers mechanical activation, and mechanical deformation of the tissue influences the electrical properties (mechanoelectric feedback or MEF). A large volume of research has been devoted to studying either electrical or mechanical phenomena, but a number of questions cannot be answered without considering the tight coupling of these processes. Mathematically, the problem is formulated as a system of partial and ordinary differential equations, and the challenge lies in development of methods and software to solve the problem efficiently. Possible applications of the simulator include the heart’s performance (cardiac output) under normal and pathological conditions, analysis of predisposing factors for arrhythmias and prospective drug treatments, as well as further insight into defibrillation mechanisms.

http://arxiv.org/abs/1305.0727

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Ciari I malformation and syringomyelia

expands such that some CSF is squeezed out of the brain and down in the spinal canal, causing an oscillatory motion with the heartbeats in the spinal canal. The Chiari I malformation obstructs the flow and causes abnormal velocity and pressure. CBC scientists have for several years worked closely with medical professor Victor Haughton at the University of Wisconsin in Madison to uncover the details of the altered fluid mechanics caused by the Chiari I malformation. A long-term goal has been to test and develop theories why the altered fluid mechanics may induce cyst formation within the spinal cord.

Some people have a too small skull such that the lower part of the brain is squeezed down in the neck. This is known as the Chiari I malformation. (A medic would explain this condition by saying that the cerebellar tonsils are displaced into the upper cervical spinal canal). Secondary to a Chiari I malformation, patients develop fluid-filled cavities (cysts) within the spinal cord tissue. This condition is referred to as syringomyelia, and typical symptoms include headache, double vision, and motor dysfunction. It is believed that there is a causal relationship between the Chiari I malformation and syringomyelia, but the details of this relationship remain unknown. Many theories have been proposed, and the common belief is that altered fluid mechanics in the spinal canal and the cord is the main cause of syringomyelia. An effective treatment is to perform surgery and remove a part of the skull such that normal fluid mechanics conditions are restored. Why is fluid mechanics important in this problem setting? Within the brain, we have a water-like fluid called the cerebrospinal fluid or CSF for short. At each heartbeat, the brain

A Chiari I malformation is diagnosed from MR images. The degree of abnormal displacement of the brain does not correlate with the risk of developing syringomyelia. Moreover, there is presently no simple, objective criterion to distinguish Chiari patients who need surgical management for syringomyelia from others who do not. Indicators that predict the need for and extent of surgical treatment are needed. We search for such indicators using mathematical models of the CSF flow and the fluid-structure interaction between the flow and the tissue in the spinal cord.

Figure 8: Left: Normal anatomy of the brain with CSF space and the spinal cord. Right: Anatomy of a Chiari patient, characterized by downwardly displaced brain and a cyst in the spinal cord (syringomyelia).

some regions has features of flow transitioning to turbulent flow6 . Such Direct Numerical Simulations (DNS) of transitional flow are very time consuming as the spatial and temporal resolution has

Studies on CSF flow. In this year, we have published studies on several aspects of CSF flow. Our simulations in a patient+specific model of a Chiari patient demonstrate laminar CSF flow that in

6 Numerical simulations of the pulsating flow of cerebrospinal fluid flow in the cervical spinal canal of a Chiari patient. Helgeland A, Mardal K. A., Haughton V, Reif B. A. J Biomech. 2014

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to be very high to follow the growth or damping of small flow perturbations. However, the findings are fundamental since the current knowledge states that the flow is laminar. We observed that the central canal within the spinal cord, which is an inconstant structure in the adult human, changes pressure gradients within the spinal cord, leading to radial movement of the interstitial fluid that is present inside the cord7 . Simulations in a simplified model showed that obstruction of the fluid space, caused by the Chiari I malformation, increases fluid pressures and velocities and changes the phase between pressure and velocity waves8 , an observation relevant to the work of Stoodley and other that suggest the phase difference has an important role in the development of cysts. Our analysis of pressure and velocity in both Chiari patients and normal subjects show that the flow resistance is diminished in the Chiari patients compared with normal healthy adults9 . We reported that simulations in idealized anatomic models, where the geometry of the malformation can be varied in a controlled manner, show that an increase in heart rate increases the CSF pressure during a hearbeat10 . Computational fluid dynamics (CFD) using our solvers built with the FEniCS software provides both pressure and velocity estimates with high temporal and spatial resolution. A firm con-

clusion by now is that CFD models have advanced our understanding of CSF fluid mechanics. However, one criticism of CFD-based methods is that the results may fail to agree with in vivo measurement methods such as Phase Contrast MR (PC MR). A study of flow using three-dimensional flow measurements (4D MR Flow Imaging) found discrepancies between the computational and the direct measurement approaches. The reason might be the quality of the PCMR data or flaws in the CFD model. To investigate this issue, we simulated pulsatile CSF flow in several anatomic models. Unlike existing anatomic models, our models were extended to include additional parts of the brain and the geometrically complicated CSF space further above the malformation. The results compared well with the 4D MR flow measurements. Velocities in the anatomic model of a specific Chiari patient were more than four times those in the model with normal anatomy. In narrow portions of the CSF space, flow jets formed (Figure 9). The simulations were also capable of producing vortices similar to those demonstrated in 4D MR imaging in Chiari patients (Figure 9). The improved agreement between simulations and physical measurements may result from the use of a more complete anatomic model, where there are less assumptions on the entry flow patterns (i.e., the velocity boundary conditions).

Figure 9: Flow results at peak inflow in a patient with normal anatomy. Left: Streamlines show uniform and unidirectional flow. Right: A zoomed image shows a vortex forming in the 4th ventricle in the brain because of flow in opposing directions. 7 Effect of the central canal in the spinal cord on fluid movement within the cord. Drøsdal I. N., Mardal K.A., Støverud K. H., Haughton V. Neuroradiol J. 2013 Oct;26(5):585-90. Epub 2013 Nov 7. 8 CSF pressure and velocity in obstructions of the subarachnoid spaces. Støverud K. H., Langtangen H. P., Haughton V, Mardal K.A. Neuroradiol J. 2013 Apr;26(2):218-26. Epub 2013 May 10. 9 Estimation of CSF flow resistance in the upper cervical spine. Mardal K.A., Rutkowska G, Linge S, Haughton V. Neuroradiol J. 2013 Feb;26(1):106-10. Epub 2013 Jan 19. 10 Simulating CSF flow dynamics in the normal and the Chiari I subarachnoid space during rest and exertion. Linge S. O., Mardal K.A., Haughton V, Helgeland A. AJNR Am J Neuroradiol. 2013 Jan;34(1):41-5.

14

Figure 10: Flow results at peak inflow in a Chiari patient. (a) Velocities are more than four times those in the normal model. (b) Streamlines show flow jets and increased formation of vortices.

the simulations. The following specific anatomic features were tested: anisotropic elasticity (or more precisely, anisotropic white matter), a stiff and/or permable membrane surrounding the cord, and an open central canal in the cord. The results showed that an open canal in the center of the cord and a stiff and thick membrance clearly affected the movement of fluid within the cord. In particular, these physical features facilitated radial pressure gradients that promoted radial fluid flow. This is a first indication of the mechanisms of cyst formation, but a more complete theory is yet to be uncovered. The most important conclusion is that we now know of essential anatomic features that must be included in future models and what features that have minor effect and can be ignored.

Another focus in the previous year was to investigate the effect of CSF pressure waves on the spinal cord tissue. We used physical measurements of the waves and imposed these as boundary conditions on an anatomic model of the cord tissue. The properties of the cord were based on MR images of a cadaver spinal cord. The tissue was considered poro-elastic, i.e., an elastic material with pores filled with water-like fluid. The pressure waves in the CSF flow would then induce elastic deformations and flow within the cord tissue. The overall goal was to find conditions where the fluid-structure interaction in the tissue is of a type that can explain the formation of fluid-filled cavities (syringomyelia). In the present study, the key question was to find what features of a physical model that are important to include in

15

The Simula School of Research and Innovation

CBC scientists teach at various institutions: UCSD (computer science, bioengineering), University of Oslo (mechanics), University of Umeå (mathematics), Norwegian University of Life Sciences (mathematics) and Telemark University College (mathematics, physics). CBC continues to develop programming courses for large groups of students at the University of Oslo, in particular the introductory programming course for science students (INF1100) and the more advanced course on problem solving with scripting tools (INF3331). On graduate level, CBC researchers give advanced courses on numerical methods, fluid mechanics, and biomedical modeling. The FEniCS software has proven to be an excellent platform for teaching finite element methods and related topics. A course in Computational Continuum Mechanics was developed for the eVITA winter school in 201211 , and reused in a short course at the Federal University of Juiz de Fora, Brazil, in October 2013. FEniCS is also used extensively in the recently revised course on Numerical Solution of Partial Differential Equations (INF5620) at the University of Oslo. This course has been well received at the Department of Informatics, and attracts a large number of students for an advanced numerical course.

CBC has access to well-developed infrastructure for career development of new researchers through the Simula School of Research and Innovation (SSRI). All PhD students and postdoctoral fellows at CBC are affiliated with SSRI, which provides enhanced support in supervision and mentoring, as well as special courses on topics such as entrepreneurship and communication of scientific research. During 2013, SSRI has continued to strengthen the ongoing research and educational collaboration with University of California, San Diego (UCSD). An important part of building the relation between SSRI and UCSD is to support collaborative visits to UCSD by Simula both students and more advanced researchers. Through 2013, travel grants from SSRI have enabled 18 researchers from seven Simula departments and centers to visit UCSD. The list includes several CBC researchers, and the duration of the visits have been from one week to five months. Since 2011, Simula researchers have spent about four working years at the UCSD campus in La Jolla. All these visits have paved the way for strong scientific collaboration across several research fields. The personal connections built between collaborators at the two institutions have led to new scientific insight, strong publications, and new funding opportunities. For instance, collaboration between the Computational Geosciences Department at Simula and the Department of Computer Science and Engineering at UCSD has led to the ongoing RCN-funded CBC project on GPU computing. There are multiple on-going discussions concerning other project proposals involving Simula and UCSD, and both institutions are dedicating PhD and postdoctoral positions to collaborative projects. CBC researcher Dr. Molly Maleckar continued in her role as Director of SSRI in 2013. She has continued to develop SSRI as a valuable resource within Simula, and in particular to strenghten the education and research collaboration with UCSD. Notably, a new, joint summer school on computational physiology is set to debut in summer 2014. The summer school is a collaborative effort between SSRI, UCSD and the University of Oslo, and CBC researchers are central in organizing and teaching. The participants will be given a thorough introduction to the fundamental principles of mathematical modeling in physiology, with particular focus on cardiac electrophysiology and mechanics. These general introductory lectures will be followed by targeted research lectures and a mandatory research project. The school will be open to graduate students from both Norway and UCSD.

Computers in Science Education (CSE). As described in previous reports, CBC teachers are closely involved in the CSE project, which aims to change the way science is taught at universities. By partly replacing the traditional, analytical pen and paper approach with numerical programming, our goal is to enable students to consider more advanced and relevant problems at an earlier stage. Furthermore, the traditional way of teaching normally requires a high focus on advanced algebra and local tricks needed to solve problems analytically. Numerical solution methods are often more general, and allow the students to focus more on the problem formulation and the interpretation of the results. We believe that this shifted focus results in a more in-depth understanding of the underlying physics. CSE is a very long-term effort, and a number of challenges lie ahead. For example, there is an urgent need for new textbooks and other teaching material where hands-on programming and simulation are integrated with classical theory, and there are still many professors who need to adopt and develop the computational approach to science teaching. However, the CSE project has attracted a lot of attention both nationally and abroad. The introduction to CSE for engineering students is a part of the new national plan for the engineering education at colleges and universities; the CSE project won the award for an excellent learning environment at the University of Oslo and also at the national level (NOKUT’s prize); and all the new bachelor programs in science at the University of Oslo are expected to excel in computer models, programming, and simulation by adopting best practices from the CSE project. CBC continues the active involvement in this project. Increasing the awareness of software quality is one particular area where CBC researchers have unique competence to assist course developers at the University.

University Teaching A large number of senior CBC researchers are involved with university teaching. The Simula-based staff mostly lecture at the Department of Informatics, University of Oslo, while our collaborators at the Biomechanics Division at NTNU offer courses at the Department of Structural Engineering at NTNU. Several adjunct

11 See

http://www.sintef.no/Projectweb/eVITA/Winter-Schools/2012/

16

In the appendices below, we use several abbreviations:

ADM BFS CBC CC CCI CM DoD F HOST M

Administrative support Biomedical Flows and Structures (CBC project) Center for Biomedical Computing Cardiac Computations (CBC project) Center for Cardiological Innovation (CCI) (Center for Research-based Innovation) Computational Middleware (CBC project) U. S. Department of Defence Female Simula Research Laboratory (SRL) Male

NTNU RCN RS SRL SSRI UCSD UiO UoT UMB UmU UW

Norwegian University of Science and Technology Research Council of Norway Robust Solvers (CBC project) Simula Research Laboratory (CBC host institution) Simula School of Research and Innovation University of California, San Diego University of Oslo University of Toronto Norwegian University of Life Sciences Umeå University University of Wisconsin

Staff Senior scientists 2013: 23 people, 11.4 man-years Name Anders Logg Andrew D. McCulloch Aslak Tveito Bjørn Fredrik Nielsen Bjørn H. Skallerud Glenn Terje Lines Hans Petter Langtangen Joakim Sundnes Kent-Andre Mardal Leif Rune Hellevik Marie E. Rognes Mats G. Larson Mikael Mortensen Molly Maleckar Ole M. Lysaker Patrick Farell Samuel Wall Scott Baden Stuart Clark Svein Linge Victor Haughton Victorien Prot Xing Cai

Gender

Period

M M M M M M M M M M F M M F M M M M M M M M M

01.04.2007-31.12.2013 01.07.2009-30.06.2014 01.08.2007-31.03.2017 01.08.2007-31.12.2013 24.05.2007-31.03.2017 01.08.2007-31.03.2017 01.04.2007-31.03.2017 01.04.2007-31.03.2017 01.01.2009-31.03.2017 24.05.2007-31.03.2017 01.06.2012-31.03.2017 01.04.2007-30.06.2014 01.01.2008-31.12.2013 01.01.2009-31.12.2013 01.01.2012-30.06.2013 15.09.2012-14.09.2013 01.09.2012-30.06.2016 11.06.2007-30.06.2013 01.01.2008-31.12.2013 01.04.2007-30.06.2014 15.06.2008-30.06.2014 01.09.2008-31.12.2013 01.04.2007-31.03.2017

CBC share 67% 10% 25% 20% 45% 100% 30% 100% 100% 45% 100% 40% 50% 50% 20% 70% 100% 20% 50% 20% 20% 45% 100%

17

Project

Funding

RS, CM CC CC CC BFS CC CM, RS, BFS CC, RS BFS, CM, RS, CC BFS RS, CM CM, RS RS, CM, BFS CC CC RF, CM CC CM CM, RS BFS BFS BFS CM, RS, CC

HOST HOST HOST CCI, RCN grant 203489/O30 NTNU CCI, RCN grant 203489/O30 HOST HOST, RCN grant 205349/F30 HOST, RCN grant 209951/F20 NTNU CBC 50% UmU + 50% CBC 60% UiO + 40% CBC CCI, HOST CCI, RCN grant 203489/O30 70% Imp. College + 30% CBC CCI, RCN grant 203489/O30 50% UCSD + 50% CBC SSRI CBC 70% UW + 30% CBC NTNU HOST, RCN grant 214113/F30

Postdoctoral candidates 2013: 13 people, 10.2 man-years Name

Gender

Andre Massing Christoph Moderer Johan Elon Hake Johannes Langguth Jussi Köivumaki Kristian Valen-Sendstad Kristin McLeod Lyudmyla Vynnytska Martin Alnæs Namit Gaur Omar al-Khayat Simon Funke Simone Pezzuto

M M M M M M F F M M M M M

Period

CBC share

20.06.2012-31.12.2014 01.01.2013-31.10.2014 01.01.2012-31.12.2014 01.10.2012-30.09.2014 01.01.2012-31.12.2013 21.05.2011-31.12.2014 01.10.2013-30.09.2015 01.05.2010-31.12.2013 01.04.2011-01.05.2015 01.07.2012-30.06.2015 28.05.2010-31.03.2014 01.11.2013-31.10.2015 01.08.2013-01.08.2015

100% 50% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100%

Project

Funding

RS, CM CM CC, CM CM CC BFS CC CM CM, RS, BFS CM, RS CM, RS CM, RS CC

60% RCN grant 180450/V30 + 40% CBC SSRI RCN grant 205349/F30 RCN grant 214113/F20 CCI, RCN grant 203489/O30 67% UoT + 33% CBC CCI, RCN grant 203489/O30 SSRI RCN grant 209951/F20 SSRI SSRI CBC RCN grant 205349/F30

PhD students 2013: 17 people, 12.5 man-years Name

Gender

Alessio Lavecchia Benjamin Kehlet Bernardo Lino de Oliveira Fahrsad Goudarzi Gabriel Balaban Jonathan Feinberg Karen-Helene Støverud Magne Nordaas Miroslav Kuchta Mohammes Sourouri Muhammed Owais Khan Ole L. Elvetun Rolv Erlend Bredesen1 Siri Kallhovd Tor Gillberg Vinzenz Eck Øyvind Evju

M M M M M M F M M M M M M F M M M

Period

CBC share

01.10.2012-30.09.2015 01.09.2010-31.08.2014 01.06.2011-31.05.2014 10.01.2010-09.01.2014 01.02.2013-31.01.2016 15.08.2009-01.04.2014 01.01.2010-31.05.2014 01.07.2013-30.06.2016 15.09.2012-14.09.2015 01.08.2012-31.07.2015 01.09.2013-01.09.2014 01.01.2012-31.12.2014 01.04.2007-13.03.2013 01.10.2012-30.09.2015 01.03.2010-04.11.2013 01.10.2013-01.10.2017 10.04.2012-09.04.2015

50% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100%

Project

Funding

RS, CM RS CC BFS CM, RS CM, RS BFS CM, RS BFS CM, RFS BFS BFS CM CC CM BFS BFS

RCN grant 180450/V30 UiO + CBC RCN grant 205349/F30 NTNU SSRI SSRI + CBC UiO + CBC CBC UiO RCN grant 214113/F20 90% UoT + 10% CBC UMB 90% UiO + 10% CBC CCI, RCN grant 203489/O30 Kalkulo AS and RCN grant 202101/I40 NTNU RCN grant 209951/F20

Technical and administrative staff 2013: 16 people, 4.9 man-years Name

Gender

Adrian Roaldssønn Hope Anders Elstad Johnsen Bjørn Mikkel Lepperød Dag Sverre Seljebotn Nina Lillevand Iben Cathrine Simonsen Ingeborg Sauge Torpe Jarle Sogn Johannes Hofaker Ring Mikkel Brudvik Sanderud Nina Kristine Kylstad Sareh Bedadfahr Sjur Urdson Gjerlaug Solveig Masvie Steve Cole Tom David Atkinson

M M M M F F F M M M F F M F M M

1 R.

Period

CBC share

01.06.2013-30.08.2013 01.01.2013-31.12.2013 01.06.2013-30.08.2013 01.11.2012-01.10.2013 01.01.2013-31.12.2013 15.02.2013-14.02.2014 01.06.2013-30.08.2013 01.06.2013-30.08.2013 01.01.2008-31.03.2017 01.06.2013-30.08.2013 01.06.2013-30.08.2013 01.04.2013-15.08.2013 01.06.2012-31.05.2013 01.06.2013-30.08.2013 01.01.2010-01.03.2014 01.05.2007-31.03.2017

100% 22% 33% 22% 10% 100% 67% 60% 100% 17% 60% 100% 100% 54% 10% 50%

Project

Funding

CBC@Simula CBC@Simula CBC@Simula CBC@Simula ADM CBC@Simula CBC@Simula CBC@Simula CBC@Simula CBC@Simula CBC@Simula CBC@Simula CBC@CCI CBC@Simula ADM ADM

RCN-209951/F20 CBC SI DoD HOST HOST CBC CBC CBC RCN-209951/F20 CBC HOST CCI, RCN grant 203489/O30 SI HOST CBC

Bredesen has had a leave of absence during the period 01.01.2013-31.12.2013.

18

Guest researchers 2013: 6 people, 2.2 man-years Name

Gender

Huayou Su Nan Wu Nataliia Vasylieva Jun Cai Benedict Schott Susanne Claus

M M F M M F

Period

CBC share

01.09.2012-30.08.2013 01.09.2012-30.08.2013 08.11.2013-31.12.2013 06.09.2013-04.02.2014 05.08.2013-26.10.2013 11.04.2013-26.10.2013

100% 100% 100% 100% 100% 40%

Project

Funding

CM CM CM CM CM CM

HOST/NUDT RCN grant 214113/F20 HOST/home institution RCN grant 214113/F20 HOST/home institution HOST/home institution

Development of staff (no. of individuals/man-years) Position

2007

2008

2009

2010

2011

2012

2013

Senior scientists Post docs PhD students Technical and administrative Guest researchers

19/7.1 8/4.1 7/3.2 10/3.5 0/0

28/13.4 17/8.8 16/11.3 12/5.8 2/0.7

28 /13.8 14/10.1 18/13.7 11/4.1 2/1.5

24/10.5 16/9.9 19/15.9 9/3.3 2/0.5

20/9.0 12/7.7 20/11.3 10/2.8 1/0.4

23/9.2 13/9.6 16/10.3 13/3.6 3/0.8

23/11.4 13/10.2 17/12.5 16/4.9 6/2.2

TOTAL

44/17.9

75/40.0

73/43.2

70/40.1

63/31.2

67/33.5

74/41.0

Accounting and Budget Below, we present the main figures regarding the CBC budget and funding. The operating revenues and expenses represent the funding and cost that we control our selves. The income in kind and operating expenses in kind presents representative figures from activities and people within the CBC project, but with the funding and costs outside of CBC’s books. The SFF grant from the Research Council of Norway represented 15% of the total funding available for CBC activities in 2013, instead of the approximately 60% that was originally intended in our proposal. As previously mentioned in these reports, we have been fortunate to secure a substantial amount of funding to the center through other RCN grants and national and international collaboration. While securing funding is necessary, the resources must also be spent wisely. The 2013 accounts show a surplus of 6 698 kNOK, that we will transfer to the 2014 to 2017 budget. The main reason for this surplus have been our careful selection process when we hunt for new and promising candidates. A 3-year PhD requires an investment of almost 3 million NOK, or almost 35% of our annual Center of Excellence funding from RCN. We try to keep this in mind when we recruit new candidates, in order find the person that shares our commitment to excellence in research, and that can enhance our research endeavors.

19

Operating Revenues RCN CBC funding Allocation from earlier years Host - Simula Research Laboratory Other income RCN International funding Other income Sum operating revenues Income in kind: CCI Kalkulo AS Norwegian University of Life Sciences NTNU SSRI Imperial College London UCSD University of Oslo University of Umeå University of Toronto University of Wisconsin Simula Innovation Sum income in kind Total income Operating Expenses

Note

Account 2012

Budget 2013

Account 2013

Budget 2014

7,500 4,495 4,679

7,500 4,495 5,761 10,170 694

7,500 6,698 5,190

1 2

7,500 2,481 4,639 10,011 100 24,731

16,674

28,620

19,388

3,530 440 877 3,493 2,280

2,000

19,388

3 4 5 6 7 8 9 10 11 12 13

Note

Cost of labour Indirect costs Outsourcing of R&D services Equipment Other operating expenses Sum operating expenses Operating expenses in kind: Cost of labour Indirect costs Outsourcing of R&D services Other operating expenses Sum operating expenses in kind Total operating expenses Year end allocation

14

15

14 15

232 1,950 175 526 22

100 2,000 150

13,525 38,256

8,150 24,824

7,874 640 906 2,129 4,606 227 0 2,912 181 859 24 218 20,575 49,194

Account 2012

Budget 2013

Account 2013

Budget 2014

15,510 2,733 826 209 958 20,236

10,500 2,000 500 200 300 13,500

16,081 3,709 455 249 1,427 21,921

10,000 2,435 729 100 1,166 14,430

9,740 2,435

5,705 1,630

1,350 13,525 33,761 4,495

815 8,150 21,650 3,174

16,123 4,031 218 203 20,575 42,496 6,698

14,430 4,958

900 1,000 2,000

Source of CBC funding (left) and in-kind funding (right) for 2013.

20

Notes to accouning and budget: Note 1: Other income RCN (= 10,170): 180450: YFF - Automation of Error Control with Application to Fluid-Structure Interaction in Biomedicine (= 505) 205349/F30: In Silico Heart Failure - Tools for Accelerating Biomedical Research (= 3,615) 209951/F20: Patient-Specific Mathematical Modeling with Applications to Clinical Medical: Stroke and Syringomyelia (= 3,235) 202101/I40: Fast Matching and Level Set Methods in Geological Modeling (= 75) 214113/F20: User-friendly programming of GPU-enhanced clusters via automated code translation and optimization (= 2,635) 225340/F11: Clinically driven Electromechanical Models of the Heart (= 104) Note 2: International funding (= 694): Column of Hope, Chiari and Syringomyelia Research Foundation (= 61) SISC (= 53) NSCM26 (= 240) Department of Defense (= 341) Note 3: Contributions in kind from Center for Cardiological Innovation (CCI) (= 7,874): Funding researchers, postdocs and research engineers (G. Lines, M. Maleckar, M. Lysaker, B. F. Nielsen, S. Wall, S. Gjerald, S. Kallhovd, K. McLeod and J. Koivumäki). Note 4: Contributions in kind from Kalkulo (= 640): Part time funding and supervision of one PhD student (T. Gillberg). Note 5: Contributions in kind from the Norwegian University of Life Sciences (= 906): One PhD student, equaling 1 man-years (O. Elvetun). Note 6: Contributions in kind from the Norwegian University of Science and Technology (NTNU) (= 2,129): NTNU has financed in kind a total of 1.35 man-years of senior scientists (V. Prot, Prof. B. Skallerud and Prof. L. R. Hellevik) and the equivalence of 1.2 man-year of PhD students (V. Eck and F. Goudarzi). Note 7: Contributions in kind from the Simula School of Research and Innovation (SSRI) (= 4,606): Simula Research Laboratory’s subsidiary Simula School of Research and Innovation (SSRI) is responsible for all educational activities in Simula Research Laboratory. The Simula School has financed the work of 0.3 man-years of technical personel (S. Behdadfar), 0.5 man-years PhDs (A. Lavecchia), 3.5 man-years postdocs (O. al-Khayat, N. Gaur, L. Vynnytska and C. Moderer) and 0.75 researchers (S. Clark and A. Tveito). Note 8: Contributions in kind from Imperial College London (= 227): Imperial College has financed in-kind 0.25 man-years researcher (P. Farrell) Note 9: Contributions in kind from the University of Oslo (= 2,912): Three PhD students, equaling 3 man-years (B. Kehlet, M. Kuchta and K. Støverud), and 0.3 man-years research scientist (M. Mortensen). Note 10: Contributions in kind from the University of Umeå (= 181): Part time funding of one senior scientist, equivalent to 0.2 man-years (Prof. M. G. Larson) Note 11: Contributions in kind from the University of Toronto (= 859): Part time funding of a PhD position equaling 0.3 man-years (M. O. Khan) and a postdoctoral position equaling 0,66 man-years (K. Valen–Sendstad). Note 12: Contributions in kind from the University of Wisconsin (= 24): Part time funding of adjunct researcher (V. Haughton). Note 13: Contributions in kind from Simula Innovation (= 218): Simula Innovation AS is a commercialisation company owned by Simula Research Laboratory AS. Their goal is to create national and international demand for ideas and long term research collaboration with Simula Research Laboratory, and to demonstrate that the national commitment to the Simula model is innovative, international and creates value. Simula Innovation funded three students that worked as technical support for our research teams from June to August 2013. (S. Masvie, N. K. Kylstad, and B. M. Lepper/od) Note 14: Indirect costs cover the expenses of offices and infrastructure for all employees. Note 15: Other operating expenses include the cost of scientific equipment, travelling, workshops, seminars, and visitors.

21

Publications CBC only reports publications where a significant part of the research has been funded by CBC. By this we mean that at least one of the authors of the reported publications must have his/her main affiliation with CBC, and has contributed to the publication as laid out in Simula’s publication guidelines: http://simula.no/research/publication-guidelines. Publications from people with part time positions at CBC are generally not counted, unless the research is particularly relevant for a CBC project. Such exceptions from the main rule are few, and must in all cases be approved by the director of the center.

Publication

2007

2008

2009

2010

2011

2012

2013

TOTAL

Articles in International Journals Refereed Proceedings Proceedings without referee Books Edited Books Chapters in books Technical Reports Manuals Talks PhD theses Posters

22 8 0 0 0 2 1 3 51 0 0

31 9 10 1 1 3 0 0 76 2 0

49 28 10 1 3 6 0 1 69 5 0

35 19 6 2 0 4 0 0 70 1 0

27 19 0 1 0 1 1 0 51 3 5

30 11 1 2 1 27 0 0 63 5 8

29 15 0 1 2 1 1 1 54 1 3

223 109 27 8 7 44 3 5 434 17 16

Articles in International Journals

[5] P. Farrell, D. Ham, S. Funke and M. E. Rognes. Automated Derivation of the Adjoint of High-Level Transient Finite Element Programs. SIAM Journal on Scientific Computing, vol. 35(4), pp. 369–393, 2013.

[1] J. Chai, M. Wen, N. Wu, D. Huang, J. Yang, X. Cai, C. Zhang and Q. Yang. Simulating Cardiac Electrophysiology in the Era of GPU-Cluster Computing. IEICE Transactions on Information and Systems, vol. E96-D(12), pp. 2587-2595, 2013.

[6] A. Johansson and M. Larson. A High Order Discontinuous Galerkin Nitsche Method With Fictitous Boundary. Numerische Mathematik, vol. 123(4), pp. 607-628, 2013. [7] P. M. Kekenes-Huskey, T. Liao, A. K. Gillette, J. E. Hake, Y. Zhang, A. P. Michailova, A. McCulloch and A. McCammon. Molecular and Subcellular-Scale Modeling of Nucleotide Diffusion in the Cardiac Myofilament Lattice. Biophysical Journal, vol. 105(9), pp. 2130, 2013.

[2] J. Chai, H. Su, M. Wen, X. Cai, N. Wu and C. Zhang. ResourceEfficient Utilization of CPU/GPU-Based Heterogeneous Supercomputers for Bayesian Phylogenetic Inference. The Journal of Supercomputing, vol. 66(1), pp. 364-380, 2013. [3] I. N. Drøsdal, K.-A. Mardal, K.-H. Støverud and V. Haughton. Effect of the Central Canal in the Spinal Cord on Fluid Movement Within the Cord. The Neuroradiology Journal, vol. 26(5), pp. 585-590, 2013.

[8] A. Krishnamurthy, C. T. Villongco, J. Chuang, L. R. Frank, V. Nigam, E. Belezzuoli, P. Stark, D. E. Krummen, S. Narayan, J. H. Omens and A. McCulloch. Patient-Specific Models of Cardiac Biomechanics. Journal of Computational Physics, vol. 244(0), pp. 4-21, 2013.

[4] Ø. Evju, K. Valen-Sendstad and K.-A. Mardal. A Study of Wall Shear Stress in 12 Aneurysms With Respect to Different Viscosity Models and Flow Conditions. Journal of Biomechanics, vol. 46(16), pp. 2802-2808, 2013.

[9] L. C. Lee, S. Wall, D. Klepach, L. Ge, Z. Zhang, R. Lee, A. Hinson, J. H. Gorman, R. Gorman and J. Guccione. AlgisylLVR With Coronary Artery Bypass Grafting Reduces Left

22

Ventricular Wall Stress and Improves Function in the Failing Human Heart. International Journal of Cardiology, vol. 168(3), pp. 2022-2028, 2013.

[23] M. E. Rognes and A. Logg. Automated Goal-Oriented Error Control I: Stationary Variational Problems. SIAM Journal on Scientific Computing, vol. 35(3), pp. 173–193, 2013.

[10] P. R. Leinan, J. Degroote, T. Kiserud, B. H. Skallerud, J. Vierendeels and L. R. Hellevik. Velocity Profiles in the Human Ductus Venosus: a Numerical Fluid Structure Interaction Study. Biomechanics and Modeling in Mechanobiology, vol. 12(5), pp. 1019-1035, 2013.

[24] D. A. Steinman, Y. Hoi, P. Fahy, L. Morris, M. Walsh, N. Aristokleous, A. Anayiotos, Y. Papaharilaou, A. Arzani, S. Shadden, P. Berg, G. Janiga, J. Bols, P. Segers, N. Bressloff, M. Cibis, F. Gijsen, S. Cito, J. Pallareacutes, L. Browne, J. Costelloe, A. Lynch, J. Degroote, J. Vierendeels, W. Fu, A. Qiao, S. Hodis, D. Kallmes, H. Kalsi, Q. Long, V. Kheyfets, E. Fino, K. Kono, A. Malek, A. Lauric, P. Menon, K. Pekkan, M. E. Moghadam, A. Marsden, M. Oshima, K. Katagiri, V. Peiffer, Y. Mohamied, S. Sherwin, J. Schaller, L. Goubergrits, G. Usera, M. Mendina, D. Habets, K. Valen-Sendstad, J. Xiang, H. Meng, Y. Yu, G. Karniadakis, N. Shaffer and F. Loth. Variability of Computational Fluid Dynamics Solutions for Pressure and Flow in a Giant Aneurysm: the ASME 2012 Summer Bioengineering Conference CFD Challenge.. Journal of Biomedical Engineering, vol. 135(2), 2013.

[11] P. R. Leinan, T. Kiserud and L. R. Hellevik. Human Ductus Venosus Velocity Profiles in the First Trimester. Cardiovascular Engineering and Technology, vol. 4(3), pp. 257-266, 2013. [12] P. Li, G. T. Lines, M. Maleckar and A. Tveito. Mathematical Models of Cardiac Pacemaking Function. Frontiers in Physics, vol. 1(20), 2013. [13] S. Linge, K.-A. Mardal, V. Haughton and A. Helgeland. Simulating CSF Flow Dynamics in the Normal and the Chiari I Subarachnoid Space During Rest and Exertion. American Journal of Neuroradiology, vol. 34(1), pp. 41-15, 2013.

[25] J. Sundnes, S. Wall, H. Osnes, T. Thorvaldsen and A. McCulloch. Improved Discretisation and Linearisation of Active Tension in Strongly Coupled Cardiac Electro-Mechanics Simulations. Computer Methods in Biomechanics and Biomedical Engineering, vol. 0(0), pp. 1-12, 2013.

[14] K.-A. Mardal, G. Rutkowska, S. Linge and V. Haughton. Estimation of CSF Flow Resistance in the Upper Cervical Spine. The Neuroradiology Journal, vol. 3(2), pp. 49-53, 2013. [15] K.-A. Mardal, J. Schoberl and R. Winther. A Uniformly Stable Fortin Operator for the Taylor–Hood Element. Numerische Mathematik, vol. 123(3), pp. 537-551, 2013.

[26] K. Valen-Sendstad, K.-A. Mardal and D. A. Steinman. HighResolution Computational Fluid Dynamics Detects HighFrequency Velocity Fluctuations in Bifurcation, But Not Sidewall, Aneurysms of the Middle Cerebral Artery. Journal of Biomechanics, vol. 18;(46(2)), pp. 402-7, 2013.

[16] A. Massing, M. Larson and A. Logg. Efficient Implementation of Finite Element Methods on Nonmatching and Overlapping Meshes in Three Dimensions. SIAM Journal on Scientific Computing, vol. 35(1), pp. C23-C47, 2013.

[27] L. Vynnytska, M. E. Rognes and S. R. Clark. Benchmarking FEniCS for Mantle Convection Simulations. Computers & Geosciences, vol. 50(1), pp. 95–105, 2013.

[17] M. R. Meswani, L. Carrington, D. Unat, A. Snavely, S. Baden and S. Poole. Modeling and Predicting Performance of High Performance Computing Applications on Hardware Accelerators. International Journal of High Performance Computing Applications, vol. 27(2), pp. 89-108, 2013.

[28] W. Wei, S. R. Clark, H. Su, M. Wen and X. Cai. Balancing Efficiency and Accuracy for Sediment Transport Simulations. Computational Science & Discovery, vol. 6(1), pp. 015011, 2013.

[18] C. T. Miller, C. N. Dawson, M. W. Farthing, T. Y. Hou, J. Huang, C. E. Kees, C. T. Kelley and H. P. Langtangen. Numerical Simulation of Water Resources Problems: Models, Methods, and Trends. Advances in Water Resources, 2013.

[29] M. Wilhelms, H. Hettmann, M. Maleckar, J. Koivumäki, O. Dössel and G. Seemann. Benchmarking Electrophysiological Models of Human Atrial Myocytes. Frontiers in Computational Physiology and Medicine, vol. 3(487), 2013.

[19] B. F. Nielsen and K.-A. Mardal. Analysis of the Minimal Residual Method Applied to Ill-Posed Optimality Systems. SIAM Journal on Scientific Computing, vol. 35(2), pp. A785-A814, 2013.

Books

[20] B. F. Nielsen, O. M. Lysaker and P. Grøttum. Computing Ischemic Regions in the Heart With the Bidomain Model; First Steps Towards Validation. IEEE Transactions on Medical Imaging, vol. 32(6), pp. 1085-1096, 2013.

[1] M. Larson and F. Bengzon. The Finite Element Method: Theory, Implementation, and Applications, Springer, 2013.

Edited Books

[21] C. Pradal, G. Varoquaux and H. P. Langtangen. Publishing Scientific Software Matters. Journal of Compuational Science, vol. 4(5), pp. 311-312, 2013.

[1] A. M. Bruaset and A. Tveito. Conversations About Challenges in Computing, Springer, 2013.

[22] M. E. Rognes, D. Ham, C. Cotter and A. McRae. Automating the Solution of PDEs on the Sphere and Other Manifolds in FEniCS 1.2. Geoscientific Model Development, pp. 20992119, 2013.

[2] A. Logg, K.-A. Mardal and A. Massing. Proceedings of the 26th Nordic Seminar on Computational Machanics, Published Electronically, 2013.

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Chapters in Books

[12] H. Su, N. Wu, M. Wen, C. Zhang and X. Cai. Performance of Sediment Transport Simulations on NVIDIA’s Kepler Architecture. In Proceedings of the International Conference on Computational Science, ICCS 2013, 2013

[1] A. P. Michailova, A. G. Edwards, J. E. Hake, M. Hoshijima and A. McCulloch. Calcium Signaling in Cardiomyocyte Models With Realistic Geometries. In Cardiac Electrophysiology: From Cell to Bedside, edited by D. Zipes and J. Jalife, Elsevier, 2013.

[13] H. Su, N. Wu, M. Wen, C. Zhang and X. Cai. On the GPU Performance of 3D Stencil Computations Implemented in OpenCL. In Proceedings of International Supercomputing Conference, ISC 2013, 2013

Refereed Proceedings [1] R. S. Campos, R. M. Amorim, B. L. d. Oliveira, B. M. Rocha, J. Sundnes, L. P. S. Barra, M. Lobosco and R. W. d. Santos. 3D Heart Modeling With Cellular Automata, Mass-Spring System and CUDA. In Lecture Notes in Computer Science, 2013

[14] K. Valen-Sendstad and J. P. Mynard. A Quasi-Analytical Method for Calculating Junction Pressure Losses in 1D Vascular Network Models: Validation With High-Resolution CFD. In 3rd International Conference on Computational and Mathematical Biomedical Engineering - CMBE2013, 2013

[2] S. Claus, A. Massing and E. Burman. A Stabilized Nitsche Fictitious Domain Formulation for the Three-Field Stokes Problem. In Proceedings of the 26th Nordic Seminar on Computational Mechanics, 2013

[15] K. Valen-Sendstad and D. A. Steinman. Impact of CFD Solution Strategy on Predicted Aneurysm Hemodynamics: Good News and Bad News. In Proceedings of 8th international symposium on Biomechanics in Vascular Biology and Cardiovascular Disease, 2013

[3] J. Feinberg and H. P. Langtangen. Uncertainty Quantification of Diffusion in Layered Media by a New Method Based on Polynomial Chaos Expansion. In Seventh National Conference on Computational Mechanics MekIT’13, 2013 [4] J. Feinberg and S. R. Clark. RoseDist: Generalized Tool for Simulating With Non-Standard Probability Distributions. In MODSIM2013, 20th International Congress on Modelling and Simulation, 2013 [5] B. Kehlet and A. Logg. Quantifying the Computability of the Lorenz System. In Proceedings of the VI International Conference on Adaptive Modeling and Simulation (ADMOS 2013), 2013 [6] M. Kuchta and M. Mortensen. A Second Order Fast Sweeping Method for the Eikonal Equation Based on Minimization. In The Nordic Seminar on Computational Mechanics, 2013

Overview of refereed CBC publications 2007-2013.

[7] J. Langguth, N. Wu, J. Chai and X. Cai. On the GPU Performance of Cell-Centered Finite Volume Method Over Unstructured Tetrahedral Meshes. In Proceedings of the 3rd Workshop on Irregular Applications: Architectures and Algorithms, 2013

Technical Reports [1] T. Gillberg, A. M. Bruaset, M. Sourouri and Ø. Hjelle. Parallel Solvers for Static Hamilton-Jacobi Equations in Three Dimensions, Simula Research Laboratory, 2013

[8] M. Larson and F. Bengzon. Component Mode Synthesis for Laminar Viscous Incompressible Fluid Flow. In Recent Advances in Scientific Computing and Applications, 2013

Manuals

[9] O. M. Lysaker, B. F. Nielsen and S. Wall. Computing Ischemic Regions in the Heart: on the Use of Internal Electrodes. In Computing in Cardiology Conference (CinC), 2013

[1] K.-A. Mardal and H. P. Langtangen. Combining FEniCS With Your Favorite Software in C, C++, Fortran, Or MATLAB, 2013

[10] M. Mortensen, K.-A. Mardal, B. Martin and S. Pahlavian. Preliminary Study of the Impact of Spinal Cord Nerve Roots and Denticulate Ligaments on Drug Movement in the Cervical Spinal Subarachnoid Space. In The Nordic Seminar on Computational Mechanics, 2013

Theses

[11] K.-H. Støverud, K.-A. Mardal and H. P. Langtangen. Effect of Oscillatory Cerebrospinal Fluid Pressure on Fluid Movement in the Spinal Cord. In Seven’th National Conference on Computational Mechanics (MekIT’13), 2013

[1] T. Gillberg. Fast and Accurate Front Propagation for Simulation of Geological Folds, PhD Thesis, Faculty of Mathematics and Natural Sciences, University of Oslo, 2013.

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Talks

[17] Ø. Evju, K.-A. Mardal, S. J. Bakke and A. G. Sorteberg. Patient-Specific Simulations of Vasospasm in 3 Different Cases, Modelling Physiological Flows, 2013.

[1] M. S. Alnæs. Status of Effective Translation of Complicated Forms in FEniCS - the UFLACS Project, Jesus College, Cambrigde, 2013.

[18] P. Farrell. Using Adjoints to Answer Scientific Questions, CBC and CCI Workshop on Advancing Numerical Technologies in the Cardiac Domain, May 15, 2013.

[2] M. S. Alnæs. Towards Navier-Stokes Data Assimilation for Hemodynamics Using Automated Adjoint Methods, V International Symposium on Modelling of Physiological Flows (MPF2013), 2013.

[19] T. Gillberg. Developing and Implementing Parallel Algorithms for Fold Simulations in 3D, N/A, 2013. [20] J. E. Hake. A General ODE Translator (Gotran): Towards a Versatile Tool for General ODEs, CBC and CCI Workshop on Advancing Numerical Technologies in the Cardiac Domain, May 15, 2013.

[3] M. S. Alnæs. Computational Investigation of Parent Artery Flow Reversal for Basilar Top Aneurysm, 5th Asia Pacific Congress on Computational Mechanics & 4th International Symposium on Computational Mechanics, 2013.

[21] A. R. Hope. Analysis of a System of Elliptic Partial Differential Equations and Its Possible Boundary Conditions When Discretized With Hermite and Lagrange Elements, CBC seminar series, 2013.

[4] M. S. Alnæs. Data Assimilation With Navier-Stokes Splitting Schemes and Dolfin-Adjoint, CBC and CCI Workshop on Advancing Numerical Technologies in the Cardiac Domain, May 15, 2013.

[22] B. Kehlet. Quantifying the Computability of the Lorenz System, International Conference on Adaptive Modeling and Simulation (ADMOS2013), 2013.

[5] M. S. Alnæs. Status of Effective Translation of Complicated Forms in FEniCS, CBC seminar series, 2013.

[23] J. Koivumäki. Re-Parametrisation of Atrial INa: INa,late and DV/dtmax Dependence on RMP As Test Cases, NECCEVISEE Workshop, 2013.

[6] S. Baden. Computing at a Million Mobiles Per Second, National University of Defense Technology, Changsha, China, 2013.

[24] J. Koivumäki. Human Atrial Myocyte Studies in Silico, NECCEVISEE Workshop, 2013.

[7] S. Baden. Computing at a Million Laptops Per Second, 21st High Performance Computing Symposia, San Diego, 2013.

[25] H. P. Langtangen. Bringing Flow Simulations to the Clinic, Invited lecture at the Scientific Computing and Imaging Institute (SCI Institute), University of Utah, USA, 2013.

[8] G. Balaban. Automatic Differentiation of a Fluid-Structure Interaction Problem, FEniCS’13, Cambridge, 2013.

[26] H. P. Langtangen. Building Simulation Software for the Next Decade: Tools and Trends, Keynote talk at the 13th International Workshop on Mantle and Litosphere Dynamics, Klækken hotel, Norway, 2013.

[9] G. Balaban. Patient Specific Passive Cardiac Material Parameter Estimation Using Nonlinear Least Squares, Laboratory meeting, 2013. [10] G. Balaban. Automatic Differentiation of a Fluid-Structure Interaction, Visit to Univercity of Toronto, 2013.

[27] G. T. Lines, O. M. Lysaker and B. F. Nielsen. Observability of Ischemia and the Need for Patient Specific Geometrical Models in Inverse ECG, Computing in Cardiology, Zaragoza, Spain, 2013.

[11] X. Cai. Scientific Computing on Accelerator-Based Supercomputers, Guest lecture at FFI, September 20, 2013.

[28] A. Logg. The FEniCS Project - Organization, Practices, Maintenance and Distribution, CBC seminar series, 2013.

[12] X. Cai. Adopting Heterogeneous Hardware Platforms for Scientific Computing, Guest lecture at Technical Unviersity of Denmark, December 5, 2013.

[29] O. M. Lysaker, B. F. Nielsen and S. Wall. Computing Ischemic Regions in the Heart: on the Use of Internal Electrodes, Computing in Cardiology, 2013.

[13] X. Cai. Introduction to Scientific Writing, Intensive course given at National University of Defence Technology, China, October 17-19, 2013.

[30] K.-A. Mardal. On the Assumption of Laminar Flow in the Modeling of Physiological Flow, Modelling of physiological flows (MPF 2013), 2013.

[14] X. Cai. User-Friendly Parallel Programming: Methodologies and Tools, Minisymposium at SIAM CSE’13, February 25, 2013.

[31] K.-A. Mardal. Operator Preconditioning for Well-Posed and Ill-Posed Problems, Preconditioning 2013, 2013.

[15] X. Cai, D. Unat and S. Baden. Mint: a User-Friendly C-toCUDA Code Translator, Talk given at SIAM CSE’13, February 25, 2013.

[32] K.-A. Mardal and B. F. Nielsen. Efficient Preconditioning of Optimality Systems With Non-Self-Adjoint State Operators, IFIP 2013, minisymposia Preconditioning for PDEConstrained Optimization, Linz, Austria, 2013.

[16] O. L. Elvetun and B. F. Nielsen. PDE-Constrained Optimization Problems With Box Constraints, International Conference on Preconditioning Techniques for Scientific and Industrial Applications, Oxford, 2013.

[33] A. Massing. A Robust Nitsche-Based Fixed-Grid Method for Fluid Problems With Applications to Domain-Bridging and FSI Problems, FEF2013, San Diego, 2013.

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[49] M. Sourouri. When One GPU Is Not Enough, HPC workshop, Simula Research Laboratory, Oslo, Norway, 2013.

[34] A. Massing. Analysis and Implementation of Nitsche-Based Domain-Bridging Method for Fluid Problems, SIAM CSE’13, Boston, 2013. [35] A. Massing. Finite Element Methods for Cut and Composite Meshes Using FEniCS, FEniCS’13, Cambridge, 2013.

[50] K.-H. Støverud. Effect of Oscillatory CSF Pressure on Fluid Movement in the Spinal Cord, V International Symposium on Modelling Physiological Flow (MPF2013), 2013.

[36] A. Massing. Cut and Composite Mesh Methods for FluidStructure Interaction Problems With Large Deformation, Coupled Problems 2013, Ibiza, 2013.

[51] K.-H. Støverud. Effect of Oscillatory Cerebrospinal Fluid Pressure on the Spinal Cord Tissue, CBC seminar series, 2013.

[37] A. Massing. Nitsche-Based Finite Element Methods on Cut and Composite Meshes, AMCG Seminar, Imperial College, London, 2013.

[52] J. Sundnes. Patient-Specific Models of Cardiac ElectroMechanics, Federal University of Juiz de Fora, 2013. [53] K. Valen-Sendstad and D. A. Steinman. Impact of CFD Solution Strategy on Predicted Aneurysm Hemodynamics: Good News and Bad News, 8th International Symposium on Biomechanics in Vascular Biology and Cardiovascular Disease, Rotterdam, 2013.

[38] A. Massing. Nitsche-Based Finite Element Methods on Cut and Composite Meshes, USNCCM12, Raleigh, 2013. [39] A. Massing. Nitsche-Based Cut and Composite Mesh Methods for Fluid and Fluid-Structure Interaction Problems, XFEM 2013, Lyon, 2013.

[54] K. Valen-Sendstad. Impact of CFD Solution Strategy on Predicted Aneurysm Hemodynamics: Good News and Bad News, CBC seminar series, 2013.

[40] A. Massing. Computing Physiological Flows: From Cutting Meshes and Automated Code Generation to Optimization of Flow, Mox Seminar, Politecnico di Milano, Milan, 2013.

Posters

[41] M. Mortensen. FEniCS: a Free Software for the Automated and Efficient Solution of Differential Equations, University of Waterloo, Department of Mechanical and Mechatronics Engineering, Seminar Series, 2013.

[1] O. L. Elvetun and B. F. Nielsen. PDE-Constrained Optimization Problems With Box Constraints; Effective Solution and Real World Applications, Applied Inverse Problems, Daejeon, South Korea, 2013.

[42] M. Mortensen. FEniCS and Its Application in Biomedical Computing, Charles University in Prague, Czech Republic, 2013.

[2] J. Koivumäki, M. Maleckar and P. Tavi. Mechanisms Promoting Chronic Atrial Fibrillation: Role of Remodelled Intracellular Calcium Handling and Cellular Hypertrophy, Gordon Research Conference on Cardiac Arrhythmia Mechanisms, 2013.

[43] M. Mortensen. Preliminary Study of the Impact of Spinal Cord Nerve Roots and Denticulate Ligaments on Drug Movement in the Cervical Spinal Subarachnoid Space, Nordic Semiar on Computational Mechanics, 2013.

[3] J. Koivumäki, T. Christ, U. Ravens and M. Maleckar. The Controversial Late INa in Human Atrial Myocytes: a Computational Analysis of Ranolazine’s Effects, 37th Annual Meeting of the ESC Working Group on Cardiac Cellular Electrophysiology, 2013.

[44] M. E. Rognes. FEniCS on a Moebius Strip, CBC seminar series, 2013. [45] M. E. Rognes. Solving PDEs Over Manifolds With FEniCS, FEniCS’13, Cambridge, 2013.

Preprints

[46] M. E. Rognes. An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology, CBC/CCI workshop "Advancing numerical technologies in the cardiac domain", 2013.

[1] D. S. Seljebotn, K.-A. Mardal, J. Jewell, H. K. Eriksen and P. Bull. A Multilevel Solver for Gaussian Constrained CMB Realizations, 2013

[47] J. Sogn. Nitsche Based Methods for Unfitted Meshes for the Brinkman Problem, CBC seminar series, 2013.

Public outreach

[48] M. Sourouri. Automated Code Generation for Coupling Heterogeneous Computing Devices, Extreme Scaling Workshop 2013, Boulder, CO, USA, 2013.

[1] J. Sundnes. Why do some hearts stop, and what does an ischemia do to the heart?, Teknisk Ukeblad, April 28, 2013.

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Overview of CBC publications 2007-2013.

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Conferences, Workshops and Seminars We have used the following rule of thumb to make a distinction between conferences, workshops, and seminars: Conference: A formal event over several days, with at least 50 participants. It may include one or more workshops, seminars and poster sessions. Workshop: A formal event, containing several talks organized in sessions. Seminar: A less formal meeting between researchers which includes one or more talks with discussions. During 2013 CBC hosted 1 conference, 3 workshops, 1 seminar, and 9 invited talks in 2013, with a total number of 120 presentations and more than 500 participants.

CBC seminar series

Total number of talks: 13

The purpose of the seminar series is to present the current status and challanges for the projects and create a forum for discussion of scientific topics related to the work in CBC. The seminars are open and attendance of and contributions by other interested people are highly welcome. 24.01.13: Hashdist – an attempt to solve the problem of scientific software distribution by Dag Sverre Seljebotn 07.02.13: FEniCS on a Moebius strip by Marie Rognes 07.03.13: The FEniCS Project – Organization, Practices, Maintenance and Distribution by Anders Logg 14.03.13: Status of effective translation of complicated forms in FEniCS by Martin Sandve Alnæs 11.04.13: A Method for Fluid Structure Interaction by Jan Helmig 11.04.13: Impact of CFD Solution Strategy on Predicted Aneurysm Hemodynamics: Good News and Bad News by Kristian Valen-Sendstad 16.04.13: Source of Error in image-based CFD of Common Carotid Arteries by Owais Khan 18.04.13: Spectral/hp-Element Methods for High–Order Solutions of Viscoelastic Free Surface Flows by Susanne Claus 30.04.13: Effect of Oscillatory Cerebrospinal Fluid Pressure on the Spinal Cord Tissue by Karen-Helene Støverud 16.05.13: The Neanderthal Talk by Håvard Hegdal 30.05.13: Status of my PhD project by Øyvind Evju 22.08.13: A robust method for handling embedded interfaces in complex fluid and fluid–structure (–contact) interaction problems by Benedikt Schott 03.10.13: Nitsche based methods for unfitted meshes for the Brinkman problem by Jarle Sogn

CBC Workshop on CBC 2007–2017 and beyond – January 17, 2013 The aim of this event was to consolidate what we have done the first half and set out pointers for the last part and not least how we should prepare ourself for when CBC is no more. Total number of participants: 44 Total number of guests outside of CBC: 6 Total number of speakers: 12 Total number of talks: 12

CBC Workshop on Using the GPU for Scientific Computing: Coding Concepts and a Look at Applications in Structural Geology – February 13, 2013 The Graphics processor or GPU is opens up new possibilities for fast computing and on-the-fly manipulation of data and models. This workshop introduced key concepts in GPU-computing with advice on how to write code and use translators that make GPU coding accessible. Examples included the modelling of geological folds using algorithms that facilitate on-the-fly manipulation of large geological fold and fault models and transforming seismic data-sets. Total number of participants: 13 Total number of guests outside of CBC: 0 Total number of speakers: 4 Total number of talks: 4

CBC and CCI Workshop on Advancing Numerical Technologies in the Cardiac Domain – May 15, 2013 The topics included serendipity finite elements, multi-scale diffusion phenomena, code generation for ODEs, and adjoint techniques and applications in the cardiac domain. Total number of participants: 15 Total number of guests outside of CBC: 3

Total number of participants: 155 Total number of speakers: 13

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countries in the International Association for Computational Mechanics (IACM). NSCM aims to be a meeting place for researchers developing computational methods and scientists and engineers focusing on challenging applications in broad aspects of mechanics. In particular, presentations by graduate students are welcome. Plenary speakers: - Erik Burman, Chair of Computational Mathematics at University College London - Elena Celledoni, Professor at the Department of Mathematical Sciences, at NTNU - Jakob Søndergaard Jensen, Associate Professor at the Department of Mechanical Engineering, Technical University of Denmark - Juho Könnö, Team Leader for the Structural Analysis team at Wärtsilä - Garth N. Wells, Hibbitt Reader in Solid Mechanics at University of Cambridge and Fellow of Jesus College

Total number of speakers: 6 Total number of talks: 6

CBC Seminar on Computer Architecture – September 10-11, 2013 The featured speaker was Prof. Chunyuan Zhang, who is a key member of the researcher team that built Tianhe-2 at National University of Defense Technology (NUDT), China. Tianhe-2 is the most powerful supercomputer in the world today. Total number of participants: 26 Total number of guests outside of CBC: 16 Total number of speakers: 2 Total number of talks: 4

For more information about the event, please visit: http://nscm26.org/

CBC hosted conference: The 26th Nordic Seminar on Computational Mechanics – October 23-25, 2013

Total number of participants: 94 Total number of guests outside of CBC: 79 Total number of speakers: 70 Total number of talks: 71

CBC hosted the 26th Nordic Seminar on Computational Mechanics, October 23-25, 2013. The Nordic Seminar on Computational Mechanics (NSCM) is organized annually by the Nordic Association for Computational Mechanics (NoACM), which represents the Nordic and the Baltic

For more information on Workshops, Seminars and Talks, please visit our website: cbc.simula.no

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Other Activities Media Appearances

• • • • • • • •

1. Teknisk Ukeblad; April 28 - 2013: “Hvorfor stanser hjertet hos noen, og hva gjør et infarkt med hjertet?” The article titled “Why do some hearts stop, and what does an ischemia do to the heart?” focus on our studies on heart failure, and in particular on our efforts on improving the computational models of the heart. These models are very mathematical challenging and time consuming to calculate. We work on improving the models with regard to efficiency and accuracy, which in turn will promote a better understanding of our heart. Our combined focus on the electrical and mechanical behavior of the heart not only helps us to understand how the heart work, but may also provide solutions to why and how hearts fail and how we can prevent and treat heart diseases. http://www.tu.no/it/2013/04/28/hvorfor-stanserhjertet-hos-noen-og-hva-gjor-et-infarkt-med-hjertet.

• • • • • • • • • • • • • • • • • • •

This article was also publishet on the webpages of the Research Council of Norway: http://tinyurl.com/nnau39q 2. A3 Magazine – Scientific and Cultural Journalism of the Federal University of Juiz de Fora; Issue: 4 - 2013; Page 25-26: “Modelos computacionais cardiacos vao aprimorar tratamentos e salvar vidas” The article focus on the CBC effort to develope mathematical models of the heart, and how cardiac computer models will improve treatments and save lives.

Committee Work and Recognition

Refereeing Activities During 2013, employees at CBC have refereed manuscripts for: • • • • • • • • • • • • • • • • • • • • • • •

Journal of Biomechanics Journal of Cellular and Molecular Cardiology Journal of Neurosurgery Journal of Parallel and Distributed Computing Journal of Physiology Journal of Royal Society Journal of Visualization International Journal for Numerical Methods in Biomedical Engineering International Journal of Water Resources and Environmental Engineering Magnetic Resonance in Medicine Mathematical Biosciences Medical Research Council, New Zealand Medical Research Council, United Kingdom National Institutes of Health, USA National Science Foundation Neurology Numerical Linear Algebra and Applications PLoS ONE, Computational Biology Science: Translational Medicine SIAM Journal of Scientific Computing SIAM Journal on Matrix Analysis and Applications SISC Journal of Computational Physics Simulation Modeling Practice and Theory Springer (book review) Transactions in Biomedical Engineering Transactions of MathematicalSoftware (TOMS) Water Resources Research

S. Baden: 1. Euro-Par Advisory Board

American Journal of Physiology American Journal of Radiology American Journal og Neuroradiology ASME Journal of Biomechanical Enginering Biophysical Journal Cellular and Molecular Biomechanics Cellular and Molecular Bioengineering Circulation Circulation Research Computer Methods in Biomechanics and Biomedical Engineering Computers Computational Methods in Medicine Computers Physics Communications Drug Discovery Today EMBS Europace Frontiers in Physiology Frontiers in Pharmacology Howard Hughes Medical Institute IEEE Transactions on Biomedical Engineering IEEE Transactions on Medical Imaging Journal of Applied Physiology Journal of Biomechanical Engineering

O. L. Elvetun: 1. Received the DAAD - Research grant for doctoral candidates and young academics and scientists H. P. Langtangen: 1. Member of the scientific committee for Basic Research Projects in Engineering and Information Technology (“FRITEK”), Research Council of Norway A. McCulloch: 1. Jacobs School Distinguished Scholar (2009-2014) 2. Cardiac Biomedical Science and Engineering Center 3. Scientific Advisory Biard of Ventrix, Salgomed and Insilicomed 4. Fellow, American Institute of Medical and Biological Engineering (IAMBE) 5. Fellow, Cardiovascular Section, American Physiological Society A. Tveito: 1. Member of the National Biomedical Computation Resource – Resource Advisory Committee (NBCR RAC) in the United States, http://www.nbcr.net/

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1. Computational Differential Equations in the Encyclopedia of Applied and Computational Mathematics (Field Editor) 2. Computing and Visualization in Science 3. SIAM Journal on Scientific Computing

K. Valen-Sendstad: 1. Recieved a Government of Canada Post-Doctoral Research Fellowship for his studies of turbulence in cerebral aneurysm hemodynamics http://tinyurl.com/abzbl3t

Conference Committees

Editorial Boards Employees of the center are on the following editorial boards:

T. D. Atkinson: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013

S. Baden: 1. Europar conference series

S. Baden: 1. External review Committee for PPoPP14, Orlando, Florida, February 2014

X. Cai: 1. Frontiers in Computational Physics 2. International Journal of Web Sciences

X. Cai: 1. Co-chair of program committee: IHPCES-2013 Workshop, Barcelona, June 5, 2013 2. Member of technical committee: SC´13, Denver, November 17-22, 2013 3. Member of program committee: ISC´13, Leipzig, June 1620, 2013 4. Member of program committee: PDSEC-13, Boston, May 24, 2013

H. P. Langtangen: 1. Advances in Water Resources 2. BIT Numerical Mathematics 3. International Journal of Computational Science and Engineering 4. International Journal of Computing Science and Mathematics 5. International Journal of Oceans and Oceanography 6. Journal of Computational Science 7. Mathematical Modelling and Applied Computing 8. Scientific Computing in the Encyclopedia of Applied and Computational Mathematics (Field Editor) 9. SIAM Journal on Scientific Computing (Editor in Chief)

H. P. Langtangen: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013 2. SIAM Conference on Computational Science and Engineering 2013 3. Co-Chair SIAM Conference on Computational Science and Engineering 2013

M. G. Larson: 1. SIAM Journal on Scientific Computing

A. Logg: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013

A. McCulloch: 1. American Journal of Physiology: Heart & Circulatory Physiology 2. Biophysical Journal 3. Cellular and Molecular Bioengineering 4. Cellular and Molecular Bioemechanics 5. Computer Methods in Biomechanics and Biomedical Engineering 6. Drug Discovery Today: Disease Models 7. Frontiers in Systems Physiology 8. International Journal of Cardiovascular Medicine and Science 9. Journal of Physiology (Lond) 10. PLoS Computational Biology 11. Synthetic and Systems Biology

K.-A. Mardal: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013 A. McCulloch: 1. International Scientific Program Committee member, International Congress of Physiological Sciences, Birmingham, 2013 2. 2013 International Society for Heart Research, San Diego, California, USA, July 2013 A. Massing: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013

M. Maleckar: 1. Frontiers in Physics B. Skallerud: 1. International Journal of Applied Mechanics

M. Mortensen: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013

J. Sundnes: 1. Frontiers in Physics 2. Frontiers in Physiology

M. Rognes: 1. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013

A. Tveito:

J. Sundnes:

31

Invited talks

1. International Conference on Computational Science, Barcelona, Spain, June 5-7, 2013 2. Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Osaka, Japan, July 3-7, 2013 3. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, USA, October 4-7, 2013 4. Nordic Seminar on Computational Mechanics (NSCM26), Oslo, Norway, October 23-25, 2013

S. Baden: 1. Computing at a million mobiles per second, National University of Defense Technology, Changsha China, October 2013 2. Computing at a million laptops per second, 21st High Performance Computing Symposia, San Diego, April 2013 X. Cai: 1. Scientific computing on accelerator-based supercomputers, Guest lecture at FFI, September 20, 2013 2. Adopting heterogeneous hardware platforms for scientific computing, Guest lecture at Technical University of Denmark, December 5, 2013

Organization of Minisymposia and Workshops at Conferences

H. P. Langtangen: 1. Bringing Flow Simulations to the Clinic, Scientific Computing and Imaging Institute (SCI Institute), University of Utah, USA, March, 2013 2. Building Simulation Software for the Next Decade: Tools and Trends, Keynote talk at the 13th International Workshop on Mantle and Litosphere Dynamics, Klækken hotel, Norway, 2013

X. Cai: 1. 3rd International Workshop on Advances in HighPerformance Computational Earth Sciences (IHPCES– 2013), at ICCS´13, Barcelona, June 5, 2013 2. Minisymposium on User-friendly Parallel Programming: Methodologies and Tools, at SIAM-CSE´13, Boston, February 25, 2013 J. Feinberg: 1. Uncertainty Quantification Used in Geo-Modelling, SIAM Conference on Computational Science and Engineering, Boston, USA, February 25-March 1, 2013

J. Koivumäki: 1. In silico screening of the key cellular remodeling targets in chronic atrial fibrillation, , CMRG Lab meeting, San Diego, 2013 2. Re-parametrisation of atrial INa: INa,late and dV/dtmax dependence on RMP as test cases, NECCEVISEE Workshop, Copenhagen, 2013 3. Human atrial myocyte studies in silico, NECCEVISEE Workshop, Copenhagen, 2013

A. Massing: 1. Fixed–grid Methods and Applications to Multi-Physics and Domain Bridging Problems, SIAM Conference on Computational Science and Engineering, Boston, USA, February 25-March 1, 2013 2. Methods for Cut and Composite Meshes: Theory, Algorithms and Applications, USNCCM12, Raleight, USA, July 22-25, 2013

K.-A. Mardal: 1. On the assumption of laminar flow in the modeling of physiological flow, International Symposium on Modelling of Physiological Flow in Chia Laguna, Sardinia Island, Italy, 2013 2. Operator preconditioning for well-posed and ill-posed problems, Preconditioning Conference 2013, Oxford, UK

M. Rognes: 1. Adjoint Models: Development and Applications, SIAM Conference on Computational Science and Engineering, Boston, USA, February 25-March 1, 2013

A. McCulloch: 1. Multi-Scale Modeling of the Failing Heart: From Mouse to Man, Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, April 18, 2013 2. Multi-Scale Modeling for Heart Physiology and DiseaseScientific Sessions of the American Heart Association, Dallas, TX, November 19, 2013 3. New Concepts and Developments in Multi-Scale Modeling with Continuity, 7th International CellML Workshop, Waiheke Island, Auckland, New Zealand, March 26, 2013

J. Sundnes: 1. Computational Modeling of Heart Electrophysiology and Mechanics, SIAM Conference on Computational Science and Engineering, Boston, USA, February 25-March 1, 2013 L. Vynnytska: 1. Adjoint method in the Earth Science, SIAM Conference on Computational Science and Engineering, Boston, USA, February 25-March 1, 2013

32

Collaboration partners Presently CBC has more than 80 collaboration partners from 50 different institutions in 15 countries.

Title

Name

Affiliation

Country

Project

Prof. Prof. Mr. Dr. Dr. Dr. Prof. Prof. Prof. Prof. M.Sc. Prof. Dr. Dr. Dr. Dr. Mr. Prof. Prof. Prof. Dr. Prof. Dr. Prof. Prof. Dr. Dr. Dr. Dr. Prof. Dr. Dr. Prof. Prof. Dr. Dr. Dr. Dr. Dr. Prof. Dr. Dr. Dr. Dr. Dr. Dr. Prof. Mr. Prof. Dr. Dr. Dr. Mr. Prof. Dr. Dr.

D. Abramson D. Ambrosi S. Annerel L. Antiga L. Autin S. Bakke D. Beard D. M. Bers H.-P. Bunge E. Burman L. Cattaneo W. Chen T. Christ S. Claus C. Cotter Y. Cui J. Degroote O. Dössel R. W. Dos Santos H. K. K. Eriksen A. Edwards P. K. Eide L. R. Frank L. Formaggia A. Frangi W. R. Giles S. Glimsdal M. Gonzales J. M. Guccione R. Haaverstad D. A. Ham R. Helmig J. Ho M. Holst M. Hoshijima T. Jespersen J. Jiang P. Kekenes-Huskey R. C. P. Kerckhoffs R. C. Kirby G. Kiss M. G. Knepley A. Krishnamurthy W. Louch T. Løseth J. M. M. Guccione A. Malthe-Sørensen K. Mathiassen J. A. McCammon A. P. Michailova P. Moireau H. Narayanan J. Nilsen J. M. Norbotten J. H. Omens M. D. Piggott

Monash University, Melbourn Politecnico di Milano Ghent University Mario Negri Institute for Pharmacological Research, Ranica Scripps Research Institute Rikshospitalet University Hospital Medical College of Wisconsin University of California, Davis Ludwig-Maximilian University (LMU), Munich University College London Politecnico di Milano, Milan Hohai University Universitätsklinikum Hamburg-Eppendorf University College London Imperial College London San Diego Supercomputing Center Ghent University Karlsruhe Institute for Technology (KIT) Federal University of Juiz de Fora University of Oslo University of California, San Diego Oslo University Hospital University of California, San Diego Politecnico di Milano, Milan University of Sheffield University of Calgary Norwegian Geotechnical Institute University of California, San Diego University of California, San Fransisco Haukeland University Hospital Imperial College London University of Stuttgart Defence Research and Development Canada University of California, San Diego University of California, San Diego University of Copenhagen University of Wisconsin, Madison University of California, San Diego University of California, San Diego Texas Tech University NTNU and St. Olafs Hospital University of Chicago University of California, San Diego Oslo University Hospital Statoil University of California, Berkeley (and San Francisco) PGP, University of Oslo University of Oslo University of California, San Diego University of California, San Diego Institut national de recherche en informatique et en automatique, INRIA University of Oslo University of Oslo University of Bergen University of California, San Diego Imperial College London

Australia Italy Belgium Italy USA Norway USA USA Germany United Kingdom Italy China Germany United Kingdom United Kingdom USA Belgium Germany Brazil Norway USA Norway USA Italy United Kingdom Canada Norway USA USA Norway United Kingdom Germany Canada USA USA Denmark USA USA USA USA Norway USA USA Norway Norway USA Norway Norway USA USA France Norway Norway Norway USA United Kingdom

BFS CC CBC@NTNU BFS CC BFS BFS BFS CG, CM CM, RS CM, RS CM CC CM, RS CM, RS CM CBC@NTNU CC CC BFS CC BFS BFS CM, RS BFS CC CM CC BFS CBC@NTNU CM, RS BFS CBC@NTNU BFS BFS CC BFS CC BFS, CC CM RS CM BFS CC CG, CM CC CM BFS BFS BFS CBC@NTNU CC CM BFS BFS BFS

33

Title

Name

Affiliation

Country

Project

Prof. Prof. Prof. Prof. Mr. Prof. Prof. Dr. Dr. Prof. Dr. Prof. Dr. Dr. Prof. Prof. Prof. Dr. Dr. Dr. Dr. Dr. Prof. Prof. Prof. Prof. Dr. Dr. Dr. Dr. Prof. Prof. Prof. Prof. Dr.

B. M. Rocha S. Roller U. Ruede F. B. Sachse B. Schott R. Scott B. M. Rocha A. Scotti G. Seemann O. M. Sejersted J. Skogseid N. P. Smith G. Sommer A. Sorteberg R. J. Spiteri D. A. Steinmann C. Strother T. O. Sømme P. Tavi A. Terrel A. Thurmond N. Trayanova F. N. van de Vosse B. M. Rocha J. Vierendeels W. A. Wall M. Wen G. N. Wells O. Wieben M. Wilhelms R. Winther C. Zhang J. Zhang P. Zunino K. B. Ølgaard

Federal University of Juiz de Flora University of Siegen University of Erlangen University of Utah TUM, Munich University of Chicago Federal University of Juiz de Flora Politecnico di Milano, Milan Karlsruhe Institute of Technology (KIT) Oslo University Hospital Statoil Kings College London Graz University of Technology Rikshospitalet University Hospital University of Saskatchewan University of Toronto University of Wisconsin, Madison University of Bergen University of Eastern Finland University of Texas at Austin Statoil Johns Hopkins University, Baltimore Eidhoven University of Technology Federal University of Juiz de Flora Ghent University TUM, Munich National University of Defence Technology (NUDT) University of Cambridge University of Wisconsin, Madison Karlsruhe Institute for Technology (KIT) CMA, University of Oslo National University of Defence Technology (NUDT) Carnegie Mellon University University of Pittsburgh Aalborg University

Brazil Germany Germany USA Germany USA Brazil Italy Germany Norway Norway United Kingdom Austria Norway Canada Canada USA Norway Finland USA Norway USA The Netherlands Brazil Belgium Germany China United Kingdom USA Germany Norway China USA USA Denmark

CC BFS CG, CM BFS CM, RS RS CC CM, RS CC CC CG, CM BFS CBC@NTNU BFS CC RS BFS CG, CM CC RS CG, CM CC CBC@NTNU CC CBC@NTNU CM, RS CM CM, RS BFS CC BFS, RS CM BFS CM, RS RS

34

List of International Guests in 2013

In 2013 CBC had 112 international guests from 27 different countries. The 50 Norwegian visitors are not listed. Period

Position

Name

Affiliation

Nationality

May 14-21 August 29-30 January 31

Dr. Professor Research Scientist Dr. Professor Mr. Dr.

Andrew Gillette Dave Stegman Fernando Perez

University of Arizona, and University of California, San Diego University of California, San Diego University of Calefornia, Berkeley

American American American

Jeff Jewell K. C. Park Nathaniel Trask Peter Kekenes-Huskey

American American American American

Robert Petersen Mark Lindsay

NASA Jet propulsion Laboratory University of Colorado Brown University Department of Pharmacology, University of California, San Diego University of California, San Diego University of Western Australia

Bernhard Semlitsch Stephan Reiter Joris Verschaeve Garth Wells Robert Smallshire Philippe Couturier Chunyuan Zhang Hong Wang Huayou Su

KTH Oslo Python Norwegian Geotechnical Institute, NGU University of Cambridge Oslo Python Technical University of Denmark National University of Defense Technology, China Norwegian University of Science and Technology, NTNU National University of Defense Technology, Changsha, China

Austrian Austrian Belgian Brittish Brittish Canadian Chinese Chinese Chinese

Jianjing He

Norwegian University of Science and Technology, NTNU

Chinese

Ju Ren Jun Chai

National University of Defense Technology, China National University of Defence Technologi (NUDT), China

Chinese Chinese

Nan Wu

National University of Defense Technology, Changsha, China

Chinese

Wei Zhang Fernando Perez

DNV, Det Norske Veritas University of California, Berkeley

Chinese Columbian

Mario Lena Demetriou Jan Blechta Jaroslav Hron

Zwipe AS Charles University in Prague Charles University in Prague, Mathematical Institute

Cypriot Czech Czech

Jaroslav Zapomel Casper Schytte Hemmingsen Erik Lund

Czech Danish Danish

Esben Toke Christensen Henrik R. Nagel Jakob Søndergaard Jensen

VSB - Technical University of Ostrava Technical University of Denmark Aalborg University, Dep. of Mechanical and Manifacturing Engineering Aalborg University Norwegian University of Science and Technology, NTNU Technical University of Denmark

Jan Høgsberg

Technical University of Denmark

Danish

Jens Glud Mads Hejleesen Mark Laier Brodersen Michael Rygaard Hansen Michael Sandholm Jepsen Niels Dollerup Niels Leergaard Pedersen

Aalborg University Technical University of Denmark Technical University of Denmark Dep. of Engineering, University of Agder Aalborg University Aalborg University Technical University of Denmark

Danish Danish Danish Danish Danish Danish Danish

René Sørensen Søren Heide Lambertsen Steen Krenk

Aalborg University Aalborg University Technical University of Denmark

Danish Danish Danish

January 31 October 23-25 June 23 May 15-22 August 29-30 February 2-5 October 23-25 February 13 October 23-25 October 23-25 February 13 October 23-25 September 10-11 October 23-25 September 1, 2012 - August 31, 2013 October 23-25 September 10-11 September 6, 2013 - February 4, 2014 September 1, 2012 - August 31, 2013 September 10-11 January 28 - February 1 September 10-11 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 September 10-11 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25

Mr. Research Assistant Professor Mr. Mr. Dr. Dr. Mr. Mr. Professor Dr. PhD Associate Professor Dr. Mr. Visiting Scolar Mr. Research Scientist Mrs. Mr. Assistant Professor Professor Mr. Professor Mr. Dr. Associate Professor Associate Professor Mr. Mr. Mr. Professor Mr. Mr. Associate Professor Mr. Mr. Professor

35

American Australian

Danish Danish Danish

Period

Position

Name

Affiliation

Nationality

January 31

Research fellow Mr. Dr. Mr. Dr. Dr. Professor Mr. Dr. Dr. Professor Dr. Professor Dipl.-Math.

Lex Nederbragt

Dutch

Ljubov Feklistova Antti Niemi Atle Kivelä Harri Hakula Juha Kuortti Juhani Pitkäranta Juho Könnö Mika Juntunen Mika Malinend> Reijo Kouhia Badr Ghorbal Chapelle Dominique Benedikt Schott

Center for Ecological and Evolutionary Synthesis (CEES) at University of Oslo University of Tartu, Estonia Aalto University Aalto University, School of Science Aalto University, School of Science Aalto University, School of Science Aalto University, School of Science Wärtsilä Finland Oy Aalto University, School of Science CSC - IT Center for Science Tampere University of Technology Simula Research Laboratory INRIA Saclay Ile De France Technische Universitet Munich (TUM)

Estonian Finnish Finnish Finnish Finnish Finnish Finnish Finnish Finnish Finnish French French German

Benedikt Schott Carsten Burstedde Ewald Quak Hans-Peter Bunge Julia Wiebe Marcus Noack

Teschnische Universität München University of Bonn, Germany Centre for Nonlinear Sciences, Tallin Technical University Munich University Simula Research Laboratory Friedrich Schiller University Jena, Germany

German German German German German German

Sabine Hippchen Susanne Claus

Simula Research Laboratory University College London

German German

Susanne Claus Denes Matetelki Jain Kartik Pranav Singh Vamsidhar Reddy Razieh Behjati Domenico Solazzo Elena Celledoni Serena Rasconi Simone Ferlin-Oliveira Carlo Lovadinia Alexandr Oltu Austin Bingham Cyrille Verrier Felix Nairz Igor Rafienko Lee Jeonhung Natalya Ramzina Piotr Minakowski Rolf Stenberg Yapi Donatien Achou Marcin Wojewodzic

German Hungarian Indian Indian Indian Iranian Italian Italian Italian Italian Italian Moldova NA NA NA NA NA NA NA NA NA Polish

José Pedro Blasques Andrei Ermakov Eugene Benilov Kseniia Ignateva Kuchta Miroslav

University College London Roxar University of Siegen Oslo Python Simula and Department of Informatics, University of Oslo Oslo Python, Simula Research Laboratory Oslo Python Norwegian University of Science and Technology, NTNU University of Oslo Oslo Python, Simula Research Laboratory University of Pavia Uni Research, Uni Computing Oslo Python Oslo Python Oslo Python, Roxar Software Solutions Oslo Python Aalto University, School of Science NTNU Charles University in Prague Aalto University, School of Science Simula Research Laboratory Center for Ecological and Evolutionary Synthesis (CEES) at University of Oslo Technical university of Denmark St. Petersburg State University Department of Mathematics, University of Limerick, Ireland Saint-Petersburg State University University of Oslo

Alic Vedad Anders Eriksson Claes Johnson Dan Johan Jonsson Daniel Åkesson Erik Burman Fredrik Larsson Göran Sandberg Jim Brouzoulis Jonas Lindemann Kenneth Runesson

Lund University KTH Mechanics KTH HPC group UiT Lund University University College London Chalmers University of Technology Lund University Chalmers University of Technologi Lund University Chalmers University of Technology

Swedish Swedish Swedish Swedish Swedish Swedish Swedish Swedish Swedish Swedish Swedish

October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 September 18 October 23-25 August 5 - October 26 October 23-25 September 06 April 17 November 13 June 23 February 10-14; September 18 September 18 April 11-19; August 15 - October 26 October 23-25 February 13 October 23-25 February 13 September 10-11 February 13 February 13 October 23-25 January 31 February 13 October 23-25 September 10-11 February 13 February 13 February 13 February 13 October 23-25 October 23-25 October 23-25 October 23-25 June 23 January 31 October 23-25 October 23-25 January 17 October 23-25 Jannuary 31, October 23-25 October 23-25 October 23-25 October 23-25 September 10-11 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25 October 23-25

Mr. Professor Dr. Professor Mss. Diploma Geophysicist Dr. Dr. Dr. Mr. Mr. Mr. Mr. Mrs. Mr. Professor Dr. Mrs. Professor Dr. Mr. Mr. Mr. Mr. Dr. Dr. Mr. Professor Mr. Research fellow Dr. Dr. Professor Mss. Research fellow Dr. Professor Professor Dr. PhD Professor Professor Professor Dr. Mr. Professor

36

Portugese Russian Russian Russian Slovenian

Period

Position

Name

Affiliation

Nationality

October 23-25

Associate Professor Mr. Professor Professor Dr. Dr.

Kent Persson

Lund University

Swedish

Ola Flodén Peter Hansbo Ragnar Larsson Aymen Said Nataliia Vasylieva

Swedish Swedish Swedish Tunisian Ukrainan

Alexandra Antoniouk

Lund University Jönköping University Chalmers University of Technology Simula Research Laboratory Institute of Applied Mathematics and Mechanics NASU, Ukraine Kiev University of Technology

Anna Kyrelova

Kiev University of Technology

Ukrainian

October 23-25 October 23-25 October 23-25 September 18 November 8 - December 31 January 28 January 28

Research Scientist Research Scientist

37

Ukrainian

Visiting address: Mailing address: Phone: Email: Org.#:

Martin Linges v. 17, 1364 Fornebu P.O.Box 134, 1325 Lysaker, Norway +47 67 82 82 00, fax: +47 67 82 82 01 [email protected] 984 648 855