CBC Annual Report 2015

Center for Biomedical Computing

Annual Report 2015 Last year’s annual report emphasized that CBC is approach- work. In addition to CBC researchers being core member of the ing the end of its funding period, and this fact is of no less impor- FEniCS development community, we continue to fund key tech- tance this year. The focus has remained on reaching milestones nical personnel responsible for software maintenance and less and deliverables laid out in the CBC research plan, and on posi- research-oriented development tasks. As pointed out in several tioning the research team for securing continued funding. Both previous annual reports, this kind of work is essential for bring- focus areas have seen considerable success through 2015. Sev- ing advanced software tools out to a larger community, and it is eral new research projects have been granted from the Research normally very difficult to fund with smaller and more short-term Council of Norway and various international funding agencies, research grants. The substantial long-term funding of a Centerof which serve to reduce the negative impact of the Centre of Ex- Excellence has therefore been essential in providing these ser- cellence grant ending in 2017. However, none of the granted vices to the FEniCS community, and this contribution may end projects have the broad, long-term scope of the CBC, and the up as one of the most important long-term results of the CBC loss of a large and stable funding source will impact the research funding. In May 2016, CBC will host the annual FEniCS work- environment. The group therefore continues to seek new oppor- shop, again manifesting its role as a key partner in the FEniCS tunitiesforcontinuedfundingof thekey activities, and we expect consortium. this situtation to be the normal in years to come. With respect Since the very beginning, CBC has had the aim of both pro- to completing the planned research for CBC milestones, a sub- viding generally applicable computational software tools, and stantial number of the original milestones have been reached at address specific biomedical applications. This split focus has this point, and we are making goodprogresstowardsreaching the continued through 2015, and the continuation and expansion of major software releases and milestones scheduled for the end of our biomedical research is an important part of the Centre’s exit the CBC funding period. strategy. The integration of advanced ICT tools in health care A particularly welcome eventforCBCin 2015wasthe award is a strategic focus area for both National and European author- of the Wilkinson Prize for Numerical Software to Patrick Farrell, ities and funding agencies. Moving towards a stronger focus on Simon Funke, David Ham, and Marie Rognes, for the develop- biomedical applications, and expanding our target areas beyond ment of dolfin-adjoint. The Wilkinson Prize is awarded every the current focus on biofluids and cardiovascular research, are fourth year at the International Congress on Industrial and Ap- important steps for increasing the potentialfor continued funding plied Mathematics, and is one of the most prestigious awards in and for high impact research. Over the last year, computational the fields of numerical mathematics and computationalsoftware. neuroscience has grown from a niche activity on cerebrospinal The dolfin-adjoint software automatically derives and solves ad- fluid flow to become a major application area for CBC research. joint and tangent linear equations from high-level mathematical Many of the tools and techniques developed for cardiovascular specifications of finite element discretizations of partial differen- research can be adapted for use in neuroscience, and the field tial equations. Adjoint mathematical problems have a wide range has a large potentialfor high-impact research. We are pleasedto of applicability in engineering, in particular for optimization and see a number of small-scale research collaborations in this area, sensitivityanalysis,andwhilederivingtheadjointofalinear equa- as well as funding initiatives on various scales. tion is relatively straightforward, performing the same task for a In conclusion, we are pleased with the current state of CBC non-linear or time dependent problem may be extremely difficult. and of computational science in general at our host institution. This task is automated by dolfin-adjoint, and thereby making the The long-term, stable funding combined with the visibility of the powerful analysis based on adjoints available to a much wider Center of Excellence brand has helped us create a vibrant re- group of researchers and engineers. search environment that attracts excellent research talent. At Although dolfin-adjoint has been the most celebrated soft- the time of writing CBC has just entered its last year of funding wareprojectthrough2015,workhascontinuedsteadilyonadding and CoE status, but the future still looks bright for the research featuresand improving other partsof the FEniCS software frame- environment that has been created.

2 WORDS FROM THE DIRECTORS 2 RUNNING THE CENTER 4 Project overview 4 The Scientiﬁc Advisory Board (SAB) 4 People, Recruitment and Gender Diversity 4 Gender diversity 5 SCIENTIFIC ACTIVITIES 6 Computational Middleware 6 Robust Solvers 7 Biomedical Flows and Structures 8 CBC at NTNU 9 Cardiac Computations 10 FEATURED RESEARCH 2015: 11 Generalized geometry handling using Multimesh 11 EDUCATION AND OUTREACH 13 The Simula School of Research and Innovation 13 University Teaching 13 APPENDIX 14 Staff 14 Accounting and Budget 18 Publications 20 Conferences, Workshops and Seminars 28 Other Activities 30 Refereeing Activities 30 Prizes and Recognition 30 Committee Work 30 Organization of Minisymposia and Workshops at Conferences 30 Editorial Boards 31 Invited talks 31 Collaboration partners 33 List of International Guests in 2015 36

3 Project overview The SAB convened at CBC in February 2015, and was presented with research, education and innovation activities within All research activities in CBC are organized in large projects with the scope of the Center’s activity. The generalfeedback from the an appointed project leader and a well-defined project plan. board was that they were pleased with the obtained results and 1) Computational Middleware. This project is devoted to devel- supported the overall choice of research topics and strategy. On oping generic high-performance software componentsforbuilding a more detailed level, the SAB made numerous useful comments the simulation programs needed in the Center. The results also and suggestions, in particular for increased collaboration with serve the global computational science community with a new medical industry. Although most of these collaboration leads are generation of widely applicable computational software. At the of a long-term nature, they may be extremely valuable for in- core of the developmentis the finite elementsoftwaresuite FEn- creasing visibility and relevance of CBC research, and potentially iCS. for securing valuable funding. Several of the SAB’s recommen- dations regarding sustainability and funding opportunities have 2) Robust Solvers. The Robust Solvers project focuses on ef- already been addressed and acted upon, as they will have impact ficient and stable numerical methods with error and uncertainty on our exit strategy. 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). People, Recruitment and

3) Cardiac Computations. This project performs research on med- Gender Diversity ical problems involving models of heart electrophysiology and Recruitmentto the Center. We recruitedseveral newpeopleto mechanics. The current activity is closely aligned with the goals the Center’s activity during 2015, both through the RCN funded ofthe Center for CardiologicalInnovation(CCI), whichisaCenter part of the Center and through research collaboration and exter- for Research Based Innovation funded by the Research Council nallyfundedactivities. All in all we recruited9 new people to the of Norway. Center: 1 postdoctoral fellow, 6 PhDs, and 2 Research trainees. The Cardiac Computations staff was expanded with a Re- 4) Biomedical Flows and Structures. Research in the Biomedi- search Trainee (Kariline Horgmo Jæger), funded by our host in- cal Flows and Structures project centers around biomedical ﬂow stitution. Dr. Benjamin Ragan-Kelley (funded through the Moore and tissue interaction problems of high clinical importance. In Foundation) joined the Computational Middleware project to con- a short to medium time frame, the applications to be targeted tinue hiswork on IPythonand Jupyter. The BiomedicalFlows and are aneurysm formation and rupture in the Circle of Willis, the Structures project has been strengthened with 3 PhD students: relation between Chiari I malformation and cyst formation in the Giulia Pizzichelli (IIT), Karl Erik Holter (SUURPh), Lars Magnus spinal cord, modeling of large cardiovascular networks, and ﬂuid- Valnes (UiO), and one Research Trainee (Aslak Bergersen). In structure interactions in cardiovascular biomechanical systems. addition the PhD student Jacob Sturdy (NTNU) has joined the The research on the lattertwo topics is headedby our partnersat CBC@NTNU node. Finally, the Robust Solvers project strength- the Biomechanics Division at the Department of Structural Engi- ened its work on high performance computing by collaboration neering at the Norwegian University of Science and Technology with Ph.D. student Marcus Noack (Kalkulo), and secured a PhD (NTNU), known as CBC@NTNU in the CBC context. position for Eleonora Piersanti through the SUURPh collaboration.

The Scientific Advisory Board (SAB) Graduated PhD students. Three PhD students graduated from The members of the CBC advisory board provide the Center with CBC during 2015. valuable input, and review the ongoing research activity. Since CBC is a focused Center with a quite narrow research scope, • Ole Løseth Elvetun – in October 2015, Ole Løseth Elve- we benefit from having a small and well informed advisory board tun finished his studies on ”PDE-constrained optimization: that is in tune with our vision and grasp the whole spectre of our Preconditioners and diffuse domain methods”, at the De- activities. The SAB for CBC consists of: partment of Mathematical Sciences and Technology group at the Norwegian University of Life Sciences, with links to the Biomedical Flows and Structure and the Cardiac Com- • Prof. Dr. Carsten Burstedde. Institute for Numerical Sim- putations projects. ulations, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany. The project was mainly concerned with the efficient nu- • Dr.EllenKuhl. AssociateProfessorofMechanicalEngineer- merical solution of optimization problems subject to linear ing, Bioengineering (courtesy), and Cardiothoracic Surgery PDE-constraints, with particular focus on robust precondi- (courtesy), Stanford Mechanics and Computation. tioners and diffuse domain methods. Two studies focused • Dr. Signe Haughton. Director, Global Strategic Alliances, on PDE-constrained optimization problems with inequality Stryker Neurovascular. constraints and problems subject to total variation regu- • Dr. Vanessa Diaz. Department of Mechanical Engineering, larization, one paper concerns the derivation of a robust University College London. preconditioner for a specific PDE-constrained optimization

4 problem motivated by the inverse problem of electrocardio- positions with their new employees. The following PhDs and graphy (ECG), and two papers address the representation postdocs left CBC during 2015 to pursue an academic or indus- of the computational domains. All the theoretical investi- trial career: gations were supported by numerical simulations, and obtained very good agreement between the theoretical and • Dr. Jussi Koivumaki is now a PostdoctoralResearch at the numerical results. University of Eastern Finland

• Jonathan Feinberg – as part of the Robust Flow Solvers • Dr. Kristin Tøndel is now a Research Scientist at Statis- project, Jonathan Feinberg of the High Performance Com- tics Norway, and an Adjunct Associate Professor at the puting group finished his studies on ”Some improvements Norwegian University of Life Sciences and Applications of Non-intrusive Polynomial Chaos Ex- pansions” in August 2015. • Dr. Simone Pezzuto is now a Postdoctoral Research Asso- For scientists to be able to trust their own research results, ciate at USI Universitá della Svizzera italiana (Switzerland) it is imperative to map the uncertainty in the models they use. However, this is often numerically resource intensive. • Dr. Bernardo Lino de Oliveira is now a Research Associate This thesis introducedpolynomialchaos expansions, a com- at King’s College London pletely new research tool to map uncertainty in numerical • Dr. Jonathan Feinberg is now a IT Consultant at Expert models. The thesis makes uncertainty quantification eas- Analytics ier and more accessible to researchers. The research was split into three papers. The first paper demonstrated that • Dr. Ole Løseth Elvetun is now a Production Planner at polynomialschaos expansions are applicable and computa- Norsk Hydro tionally efficient methods for uncertainty quantification in blood flow simulations. The second paper describes a software toolbox developed to give researches easy access to Gender diversity polynomial chaos expansion methods, and finally, the third CBC has continued the close collaboration with our host institu- paper analyses the theoretical framework for polynomial tionSimulatoactivelysearchforandrecruittalentedresearchers, chaos methods. and to strive for a gender diverse research environment without • Mohammed Sourouri – in December 2015, Mohammed compromising on the quality and talent of our researchers. Sourouri finished his studies on ”Scalable Heterogeneous We have adopted the ambition of our host of reaching 25% Supercomputing: Programming Methodologies and Auto- female PhD students, postdocs and full time researchers at Sim- mated Code Generation”, as part of the High Performance ula within 2015, and 30% within 2022. The goal of 25% of Computing group that works on the Computational Mid- total scientific staff has been reached, and our host institution dleware project. Manycore processors such as Graphics has managed to fulfil the ambition of at least 25% female re- Processing Units (GPUs) and Xeon Phis have remarkable searchers on senior level during 2015. Almost 30% of Simulas computational capabilities and energy efficiency, making permanently employed researchscientistsare nowwomen,which these units an attractive alternative to conventional CPUs is well above the average for the ICT sector in Norway. CBC will for general-purposecomputations. The distinct advantages continue to work very actively at every opportunity to achieve a of manycore processors have been quickly adoptedto mod- better gender balance, both by recruiting senior researchers di- ern heterogeneous supercomputers, where each node is rectly from other institutions, and by promoting and supporting equipped with manycore processors in addition to CPUs. internal PhD students and Postdocs to continue their research career. The aim of the project was to develop methodologies for We added 9 new researchers to our projects during 2015, 1 efficient programming of GPU clusters, from a single com- postdocand6PhDstudentsand2ResearchTrainees. Twoofthe putenodeequippedwithmultipleGPUsthatsharethesame six PhDs were women and one of the Research Trainees, which PCIe bus, to large supercomputers involving thousands of makes30%ofthenewemployeesatCBCfemale. Inaddition60% GPUs connectedby a high-speednetwork. The former con- of our summer interns were female. Giving the masterstudents figuration represents a peek into future node architecture an opportunityfor pursuing meaningfulresearch togetherwith our of GPU clusters, where each compute node will be densely researchers will hopefully inspire them to pursue a further career populated with GPUs. For this type of configuration, intra- within research. node communication will play a more dominant role. We presentedprogramming techniques specifically designed to handle intra-node communication between multiple GPUs The importance of female role models. We have taken several more effectively. For supercomputers involving multiple important actions in order to achieve a gender diverse work envi- nodes, we developed an automated code generator that ronment at CBC. As previously mentioned we search actively for delivers good weak-scalability on thousands of GPUs. talented female researchers, and we have female researchers involved in the screening process when we recruit new employees. The work was conducted at Simula Research Laboratory Of equal importance, CBC has active female researchers at and University of California, San Diego. the highest levels of our host organisation and in our SAB. By their undisputed talent and accomplishments they function as CBC alumni. Several of CBC’s former researchers continue to role models and clearly demonstrate that there is an array of op- pursue an academic career outside of our host institution. We are portunities and exciting career possibilities for both genders in happy to report that their academic merits and scientific train- our research field. ing have been recognized and secured them prominent academic

5 Through 2015 the scientiﬁc activities in CBC progressed according to the research plans. Below we give an overview of the main activities and results in 2015. The sections cover the four projects that have been forming CBC through 2015: 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 Solvers and the Biomedical Flows and Structures projects, but the research is described in a separate section, titled CBC@NTNU.

Computational Middleware stencil computations. Last but not least, Simula secured a new IKTPLUSS grant from the Research Council of Norway, inten- As in previous years, the flagship products from Computational sifying the effort in developing source-to-source compilers that Middleware are the FEniCS project and the associated dolfin- target future heterogeneous supercomputers. adjoint, with the new versions FEnics 1.5-1.6 and dolfin-adjoint 1.6 released in 2015. The new software versions provide improvements on many fronts, including scalability for high perfor- Two new subprojects. CBCsecuredfundingfortwonewclosely mance computing to problems with many billions of unknowns, related projects with acronyms OpenDreamKit and Jupyter. new algorithms for adaptive mesh refinement, and more mature OpenDreamKit is a Horizon 2020 European Research Infras- versionsof previouslyreportedwork on mesh generationand mul- tructures that provides substantial funding to the open source timesh finite element assembly. We are particularly proud of the computational mathematics ecosystem. Our main tasks in this prestigious Wilkinson Prize for Numerical Software 2015, which project are related to improving the IPython Notebookinteractive was awarded to dolfin-adjoint, and is an outstanding recognition computing environment with improved support for collaborative oftheresearchdoneintheComputationalMiddlewareandRobust reproducible research and 3D visualization. This project funds a Solvers projects. new two year postdoctoral fellow and a part time position of a CBC researcher beyond the lifetime of the centre. The Jupyter project is funded by the private Sloan foundation, and covers the work of one of the long time main developers of the Jupyter software project for three years at Simula Research Laboratory. Jupyter and the IPython Notebook software allows presenting documents involving text, mathematics, and executable source code. This software has millions of users and was recently used to publish a tutorial on the data analysis process after the recent discovery of gravitational waves at LIGO Caltech.

FEniCS training CBC researchers where invited to lecture FEn- iCS training courses at 3 universities in as many countries during 2015. We continually refine the lecture material to stay up to date with the latest advancements in the software and incor- porate feedback from past lectures. The first lecture in June was part of the Swedish HPC network SNIC; a 2-day FEniCS training course at the University of Lund, Sweden, with 16 participants. Shortly after, a 2-day training course on FEniCS and dolfin-adjoint was held at the NGCM Summer Academy at Uni- versity of Southampton, UK, with 20 participants. And finally in August, the 2015 Summer School on Finite Element Methods was arranged at Beijing University of Technology, with 55 participants. The annual FEniCS workshop was arranged at Imperial Figure 1: Mesh generated from a constructive solid geometry CollegeLondon with a record 53 talksand more than 100 partic- description by mshr ipants, with contributions from CBC both in the form of scientific committee work and several talks and posters. High performance computing research The HPC-oriented research activities continue to center around heterogeneous com- Software components In addition to the flagship middleware puting that simultaneously uses CPUs and hardware accelera- products, CBC researchers write more specialized simulation tors. Related programming methodologies, automated software software for their own research purposes. A new release has tools, and HPC applications have been subjects of intense re- been made of OpenTidalFarm1.5, which is using dolfin-adjointfor search effort, making Simula one of the front-runnersin this niche optimization of tidal energy farms. Journal articles describing the HPC subject. In addition to publications in high-impact HPC jour- previously reported software components OASIS and Chaospy nals such as IEEE Micro, JPDC and IJHPCA, a fully automated were published in 2015. Most of the other notable software source-to-source compiler has taken its initial shape for handling components have not seen new official releases in 2015. Still,

6 continuous improvements were made in 2015 to components for quality software packages for the implementation of cardiac electrophysiology (cbcbeat), cardiac mechanics (pulse), numerical methods. ﬂow problems (cbcﬂow, OASIS), simulation result postprocess- ing (cbcpost, fenicstools), and reproducible building of software Long running software projects will often get citations through stacks (hashdist). one major journal publication, which means new contributions to a successful project will gain less acknowledgment through tra- A journal for numerical software As key players in the in- ditional academic channels. A journal for publishing articles with ternational community for academic numerical software, CBC release notes for open source numerical software provides a way researchers have contributed to establishing the new journal to make the contributions individuals make to larger academic “Archive of Numerical Software”, which aims to software projects more visible and citable. The ideal form and ... provide a venue to promote the design, creation, content of such articles is an ongoing discussion that has not use and re-use of high level applications and high settled yet, and CBC researchers participate in this dialogue.

Robust Solvers The Robust Solvers project continuesits focus on flexible and re- liable numerical methods, with a particular emphasis on a posteriori error control, adaptivity, geometricallyflexible finite element methods, PDE-constrained optimization, and other adjoint-based techniques. In 2015, 13 journal publications resulted from the CBC-fundedresearchactivities. Inadditionanumberofnew studies focusing on bringing the CBC methodology into to the application domains such as clinical cardiac modelling are in progress or have been submitted for publication.

Highlights

• The software package dolfin-adjoint wins the2015 Wilkin- son Prize for NumericalSoftware. dolfin-adjointtargets the Figure 2: Patrick Farrell, Simon Funke, David Ham and Marie E. automatedderivation and solution of tangent linear and ad- Rognes awarded the Wilkinson Prize for Numerical Software at joint models from FEniCS code, The Wilkinson Prize was the InternationalCongress on Industrial and Applied Mathematics established to honour the outstanding contributions of Dr in Beijing, August 2015. James Hardy Wilkinson to the field of numerical software. It is awarded every four years by Argonne National Labora- tory, the National Physical Laboratory, and the Numerical Algorithms Group.

• At the SIAM CSE 2015 conference in Salt Lake City, Utah, US, CBC Adjunct Scientist Anders Logg was awarded Best Minisymposterium prize for organizing a minisymposterium on CSE Software, while CBC ResearcherSimon Funke won Best Poster Award for a poster on dolﬁn-adjoint.

• CBC Adjunct Scientist Patrick Farrell was shortlisted for CutFEM in volumes and on surfaces In 2015, CBC research on the 2015 Leslie Fox Prize in Numerical Analysis for his pa- geometrically flexible numerical methods such as cut finite ele- per "Deflation Techniques for Finding Distinct Solutions of ment methods(CutFEM)hasstartedtogain significantmomentum Nonlinear Partial Differential Equations", published in SIAM with 8 journal publications in high quality scientific computing and Journal on Scientific Computing (2015). applied mechanics and engineering journals. Previous CutFEM results and methods have been extended to new numerical for- • CBC researchersSimon Funke,Valeriya Naumova and Marie mulations of new mathematical problems, including three-field Rognes were each awarded FRINATEK/IKTPLUSS Young formulations of Stokes flow and fluid-structure interaction, to Research Talents research projects (OptCutCell,FunDaHD, higher order methods and notably to new CutFEM formulations Waterscape)in the2015applicationround. Theprojectsall on surfaces. Current research effortsfocus on extendingCutFEM leverage CBC research results and focus on extensions of to an arbitrary number of meshes, a new methodology spear- CBC activities within PDE-constrained optimization, finite headed by CBC researchers August Johansson and Anders Logg, element methods and high-dimensional learning. coined MultiMesh.

7 a posteriori error estimation and adaptive methods. Particular emphasis has been placed on new and challenging physical sce- narios and physiological phenomena such as plate buckling and multiscale PDE-ODE systems such as those encountered in cardiac electrophysiology.

Fluid Mesh + Fluid Structure Interface

Figure 4: Snapshotsof primal (top) and adjoint (bottom)solutions in adaptive multiscale cardiac physiology.

PDE-constrained optimization with applications PDE- constrained optimization problems are typically nonlinear partial Figure 3: Fluid-structure interaction via cut finite element meth- differential equations with multiple solutions. In 2015, CBC Re- ods. Top: Mesh configuration of the computational domain with searchers Patrick Farrell and Simon Funkehave developeda new partially overlapping meshes. Bottom: Velocity and pressure technique for finding multiple solutions of such problems. Simon distributions of stable flow around elastic flap. Funke and co-authors have also continued to drive research into tidal turbine farm efficiency and optimal configurations via PDE- A posteriori error estimation and adaptive methods In 2015, constrained optimization in general and the dolfin-adjoint based we have developed new theoretical and numerical results within software OpenTidalFarm in particular.

Biomedical Flows and Structures could therefore easily result in significant errors. The purposeof the BFS project is to applythe numericalmethods Understanding transition to turbulence, not to mention in and software developed in the Computational Middleware and blood, is a fundamental question that has been addressed for Robust Solvers projects in a few selected important applications, decades but is still poorly understood. This is partially because which have a potential to make an impact on clinical medicine. blood is difficult to see through; hence, standard ways of determining the transition point fail. However, CBC collaborators Bloodflow in the Circle of Willis. The first application concerns have developed a new technique to overcome this difficulty, and the bloodflow in the Circle of Willis, which is an arterial network we have together with them co-designed experiments trying to at the base of the brain. The project is motivatedby the fact that reveal transitionto turbulencein blood,by comparingresultsfrom five percent of the population develop deformed arteries, called numerical simulations to experimental observations. The prelim- aneurysms, and that these aneurysms may rupture and lead to inary results of this work were presented by CBC affiliated PhD a fatal stroke. However, the risk of rupture is low, and surgical student, M. Owais Khan (jointly supervised by Dr Kristian Valen- treatment of the aneurysms is complicated and risky. Assessing Sendstad and Prof. David Steinman) at the Summer Biomechan- the risk of ruptureand deciding on the optimal treatmentfor each ics, Bioengineering & Biotransport Conference, Salt Lake City, aneurysm is therefore both clinically important and extremely Utah, USA, June, 2015. Figure 6 shows a slide from Khan’s talk challenging. where he demonstrated how rheology affects transition to tur- Over thelastdecade, computationalfluid dynamic(CFD) sim- bulence numerically, which showed excellent phenotypic agree- ulations of ’patient-specific’ blood flow has grown to become a ment with experiments. Khan’s talk entitled CFD Simulation of widespread tool in aneurysm research. Compared with a decade Transition to Turbulence for Newtonian vs. Non-Newtonian Flow ago, when aneurysm CFD studies were conducted by fluid me- Through a Stenosis was awarded the Best PhD Student Pa- chanical experts, today the use of CFD in aneurysm research is per prize at the conference. Another welcome recognition from widespread,facilitatedby commercialsolversas wellasthenow- the biomechanics community was received at the Computational routine availability of 3D angiography. The current widespread Fluid Dynamics in Medicine and Biology II conference in August, use of CFD, however, comes at the expense of methodological where Kristian Valen-Sendstad was awarded Outstanding Oral rigour which may be particularly misleading for aneurysms, be- Presentation by Young Scientist for the talk On the Assumption cause, as we have shown earlier, the flow may be transitional, of Laminar Flow in the Cerebrovasculature: Implications for CFD i.e. varying between laminar and turbulent. A novice use of CFD Insights into Aneurysm Initiation and Rupture?.

8 treatment option where some arteries connected to the Circle of Willis are occluded, causing flow reversal. Theoretically the intervention releives the aneurysm of high flow and pressure. In our study, the therapeutic parent artery flow reversal lead to a dramatic increase in aneurysm inflow and wall shear stress (30 to 170Pa)resultingin an increase in intra-aneurysmalcirculation. The enlargement of the circulated area within the aneurysm led to a re-normalization of the wall shear stress and the aneurysm remained stable for more than 8 years thereafter. This study demonstrates that CFD may potentially be used not only for assessing risk of rupture, but also for guiding treatment.

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 associa- tionwiththedevelopmentof syringomelia(cysts withinthe spinal Figure 6: Effects of non-Newtonian rheology on transition to cord). Such cystsare oftenfoundin patientswith theChiari I mal- turbulence. Labels ’N’ and ’NN’ represent Newtonian and non- formation, a state characterized by having abnormal position of Newtonian flow, respectively. the cerebellar tonsils (i.e., the brain is somewhat sunken down Other efforts related to aneurysms include a recently estab- in the neck). The abnormal position of the tonsils obstructs the lished collaboration with renowned Professor Alex Frangi, leader naturalflow ofCSF, andit is hypothesizedthatthe abnormalflow of the now completed EU project @neurist. The collaboration pattern is a cause for syringomelia. has led to an extensive sensitivity study where the effect of res- The enigma of syringomelia has for many years caused de- olution is targeted quantitatively in around 40 aneurysms. This velopment of new and complex models. In 2015, we published quantitativeanalysis is made possible by the research efforts put an extensive computational study involving 300 000 CPU hours FEniCS based flow software, such as OASIS and cbc.flow. of computing on the National HPC resource Abel, where we es- In collaborationwithKartikJainandSabineRoller,University tablished by the brute force of computing which features that of Siegen, Germany, a Direct Numerical Simulation of aneurysms are crucial for spinal cord modeling. It was demonstrated that blood flow (assuming Newtonian rheology and rigid walls) was poro-elastic models are significantly different from elastic mod- performed and published in Computers & Fluids. Using high- els, while other previously proposed features such as the central performance Lattice-Boltzmann Methods (LBM), resolutions of canal or the distinction between white and grey matter had less around 1 billion cells and 9 million time-steps. Indeed, transi- effect. tional flow as predicted by earlier finite element simulations was The computational undertakings that are now possible with found in exactly the same aneurysms with the highly-resolved FEniCS are being recognized. For instance, Kent-Andre Mardal LBM method. was invited plenary speaker at the American Society of Neurora- Together with Angelika Sorteberg, neurosurgeon at Rikshos- diology meeting, the International Hydrocephalus Imaging Work- pitalet, Martin Alnæs have performed our first computational ing Group, and the Cerebrospinal Fluid Dynamics Society Meet- study of "therapeutic parent artery flow reversal" - an invasive ing.

CBC@NTNU at the 28th Nordic Seminar in Computational Mechanics. The BiomechanicsDivision at the Departmentof Structural Engi- In addition to this work, the development of Stochastic Ar- neering at the Norwegian University of Science and Technology terial Flow Simulations (STARFiSh) has continued with Jacob (NTNU), (or CBC@NTNUfor short)has traditionallybeeninvolved Sturdy who was recruited in December 2014 to include carotid in research projects related to cardiovascular biomechanics and and aortic baroreflex regulation,as well as simulatingclosedloop bone mechanics. blood flow with additional models of venous blood flow and car- We have continued to investigate cardiovascular fluid dy- diac function. This work was presented by at two international namicsand regulation,as wellas how uncertaintyin model inputs meetings in 2015. effects model outputs. A paper describing and demonstratingthe Alongside this work, we investigated the role of uncertainty application of uncertainty quantification and sensitivity analysis inarterialwallmodelsonarterialflowandpressurewaves,provid- to cardiovascular models was published in International Journal ing a new perspective on the benefits of state of the art material for Numerical Methods in Biomedical Engineering. One example models when parameters for these models are uncertain. This in this paper evaluated the feasibility of estimating total arterial work was presented at the International Conference on Compu- compliance using typical clinical measurements, also presented tational Bioengineering in 2015.

9 Cardiac Computations

The Cardiac Computations (CC) project in CBC remains focused on modeling heart mechanics and electrophysiology, with the main activity contained in the Computational Cardiac Modeling departmentatSimulaResearchLaboratory. Theactivityisclosely aligned with the Center for Cardiological Innovation (CCI), a cen- terfor research-basedinnovationfundedbythe ResearchCouncil of Norway for 2011-2018. To CBC and Simula, the most important assets of CCI are the partners, in particular Oslo University Hospital, GE Vingmed Ultrasound, and Medtronic. These collaborative partnerships ensure tight links with the Nation’s leading cardiologists and to global industry leaders in medical devices. Figure 7: Illustration of the electrical activity in the atria. Parts As a consequence of these partnerships, the majority of research of the atria are in the resting state (membrane potential -75 mV), in the CCI and the CC project are driven by clinical and industrial while other regions are activated (membrane potential 40 mV). needs. The main focus of the CC project has always been on mod- Research in the CC project made steady progress through eling the ventricles, the main chambers of the heart. However, 2015, maintaining a strong focus on streamlining the workflow there has been a parallel research activity on electrophysiology of buildingpatientspecific computationalmodelsfrom ultrasound and mechanics of the atria, and this activity is currently being images. Important improvements have been made, which greatly upscaled based on two new research grants awarded in 2015. reduces the time from image acquisition to having a running com- Tha AFib-TrainNet(2015-2019)is a Marie Curie InnovativeTrain- putational prototype of the patient’s heart. The next big step in ing Network funded under Horizon 2020, while SysAFib (2016- this research, which we have only started to address, is that of 2018) is funded by the EraNet program. Both focus on improving model validation and uncertainty quantification. Model param- treatment of atrial fibrillation (AF), which is the most common eters describing key quantities such as material properties and cardiac arrhythmia, affecting more than six million Europeans. muscle contractility are believed to vary on an individual basis, The condition is not lethal in itself, but has a number of severe and need to be fitted to each patient. Measurement data avail- implications, including a substantially increased risk of stroke. able for model parameterization are generally sparse and noisy, Treatment of AF is generally challenging, and improved under- and both parameter values and model output will inevitably con- standing of the disease may lead to reduced healthcare costs tain a degree of uncertainty. For clinical use of computational and improvedquality of life for a large group of patients. The new models, quantifying this uncertainty is essential, but has only projects aim to contribute to this understanding through simula- recently been addressed by the research community. Through tions of atrial electrophysiology and mechanics. Because of the 2015 the CC project achieved a number of promising results on lower mass compared to the ventricles, computations involving this topic, including the use of dolfin-adjoint for parameter fitting the atria tend to be less computationally intensive than ventric- and uncertainty analysis. Although still in an early stage, we ular simulations. However, the atria have a complex anatomy, as are enthusiastic about this project since it combines advanced illustrated in Figure 7, and numerous structures and tissue het- mathematics with groundbreaking computational software tools, erogeneities that vary from individual to individual. These factors and applies them in a clinically relevant setting. The first results combine to make accurate, patient-specific atrial simulations a are assumed to be published in 2016. highly non-trivial task.

10 Generalized geometry handling using Multimesh

Many factors need to be considered in a computational model of a physical phenomenon. For example, we must consider which mathematical model is appropriate, which data is suitable for the particular simulation of interest, which computationalmethod we want to use for performing the simulation and which geometry is relevant. The state of the art computational method for mathematical models described by partial differential equations is the ﬁnite element method (FEM). In this method, the geometry – whetherit is a blood vessel or an airfoil – needsto be partitioned into a mesh, made up of elements,see Figure 8.

Figure 9: A sphere represented by ﬂat tetrahedra.

With the Multimesh technology, developed by August Jo- hansson, Benjamin Kehlet and Anders Logg at CBC, we are improving the shortcomings of FEM with respect to geometryrepre- sentation in two ways: allowingfor the use of an exact geometry by theuse ofunﬁttedmeshes, and allowingfor multipleindividual meshes.

Unfitted meshes Using Nietsche’s method1, which was developed in the 70s, in combination with novel use of computational geometry, we can construct finite element methods where the geometry does not have to be approximated by the tetrahedra. Rather, we can design methodsthat make use of whateverrepre- sentation of the geometry used originally. For example, an airfoil is usually designed in a CAD program, and a CAD program often uses spline surfaces as geometry representation. Then we can construct methods that directly obtain the geometrical information from the original spline surfaces. Another example is the geometry of a blood vessel, which is typicallyobtainedfrom medical images and representedin the form of a surface triangulation generated by some preprocessing software such as VMTK2. Figure 8: A mesh of a heart consistingof a partitionof tetrahedra. A key feature of these novel finite element methods is to al- low the original geometrytobe embeddedin amesh,asillustrated in Figure 10 from a recent journal article3. One often says that The elements are typically simple geometric shapes such as the mesh is unfitted, since it does not have to fit the geometry. quadrilaterals, triangles, ortetrahedra. TheFEMdefinesa discrete The natural approach is actually to have the geometry and the mathematical problem on these elements that approximates the solution to be approximated on this background mesh. Since we original partial differential equation, and the accuracy of the so- do not use the mesh as a representation of the geometry, there lution depends on the quality of the elements. For instance, if a will be some extra cost of communicating geometry information mesh contains flat and elongated elements, the accuracy of the to the mesh, where the FEM is defined. However, if the geometry solution given by the FEM may be low. changes through the simulation, then creating a new mesh can Since standard tetrahedra have flat edges, the mesh often be very costly and in many cases almost impossible. In these becomes an approximation of the domain, meaning that if the do- situations an unfitted mesh is advantageous. Examples of ge- main is curved, it is approximatedby a piecewiseflat geometry as ometries that change can be when simulating the dynamics of a illustratedfor a sphere in Figure 9. Such errors, thatis, errors that waterdropletundersurfacetension, or during shapeoptimization, are due to approximation of the geometry, are difficult to analyze where one aims to find the optimal shape of a mechanical part, and often neglected when quantifying the errors of a method. for instance the shape that minimizes internal stresses.

1Über ein Variationsprinzip zur Lösung von Dirichlet-Problemen bei Verwendung von Teilräumen, die keinen Randbedingungen unterworfen sind, J. Nitsche, Abh. Math. Sem. Hamburg 36, 1971 2The Vascular Modeling Toolkit, http://vmtk.org 3High order cut ﬁnite element methods for the Stokes problem, A. Johansson, M. G. Larson and A. Logg, Advanced Modeling and Simulation in Engineering Sciences, 2015 2:24

11 Figure 12: A propeller with a single ﬁtted mesh.

Clearly,thetraditionalmethodof a singlefittedmesh is much simpler, but the design process itself can be significantly simpli- fied if different parts in a simulation can be meshed individually and afterwards merged together as if they were a single mesh. Figure 10: A propeller embedded in a unfitted mesh. In fact, the most difficult and costly part in an engineering design process is creating a geometry that is satisfactory for the Multiple individual meshes The principle of having a mesh that software that generates the mesh. For example, Hughes et. al. in does not have to be aligned with the geometry, as shown in Fig- Isogeometric Analysis (Wiley, 2009) estimates that 80% of the ure 10, can be extended to handle multiple overlapping meshes. effort in a design process is geometrical modeling and meshing, For example, suppose we are designing a propeller. A propeller while the remaining 20% is the actual FEM computation. One can be considered as being composedof four bladesand a center reason for the large efforts spent on meshing is that the creation axle. With the Multimesh technique, the blades and the center of an accurate tetrahedral approximation requires engineers to can havetheirownindividualmeshes,whichare mergedtogether, manuallyedit the geometryand the placementsof the tetrahedra as illustrated in Figure 11. This should be considered in contrast to create a good approximation. to a traditional mesh as in Figure 12. Multimesh is based on three components: Nitsche’s method for setting the data for performing the simulation, computational geometry for computing the intersections of the elements in the mesh, and combinatoricsfor findingthe contributionof each small part to the whole system. A two-mesh Multimesh technique is available in FEniCS version 1.64. The extension to an arbitrary number of meshes will be completed in the summer of 2016, and will be available in Fenics 1.7.

Figure11: A propellerwith individuallymeshedbladesandcenter axle placed on top of each other.

4See The FEniCS Project, http://fenicsproject.org

12 The Simula School of Research and In- school counts as a regular class to be included in their syllabus for the doctoral degree. novation These international collaboration projects together with CBC maintains its tight links with the Simula School of Research Horizon 2020 Marie Sklodowska Curie exchange projects and Innovation(SSRI). All PhD studentsand postdoctoralfellows and individual PhD supervision agreements with University of at CBC are affiliated with SSRI, which provides enhanced sup- Toronto (Canada), University of Siegen (Germany), and IIT (Italy) port in supervision and mentoring, as well as special courses on strengthen the CBC impact on the international research training topics such as entrepreneurship and communication of scientific arena and help to further develop and spread our software. research. For several years, SSRI has worked on expanding the ex- isting research collaboration with University of California, San University Teaching Diego (UCSD) to include a substantial educational component. Althoughofficiallyannouncedin 2016, an eventclearlyworth re- From 2015, this initiative takes the form of a formalised program, porting here is that Prof. Hans Petter Langtangen received Olav the Simula-UiO-UCSD Research and PhD Training Collaboration Thon Foundation’saward for ExcellentEducation. The award was (SUURPh), which is funded directly by the Ministry of Educa- based on many years of pioneering educational work in program- tion and Research. In its current configuration, SUURPh funds ming and a variety of computationalsciences. Langtangen is one eight PhD students in ComputationalPhysiology, as well as sev- of the initiators of the Computers in Science Education (CSE) eral supporting actions. Four of these students are employed initiative at UiO, which has gained considerable momentum and at UiO and four at SSRI. Of these, 3 students are supervised internationalrecognition. Several otherCBC researchers are also by CBC researchers. SSRI coordinates the program, which in- heavily involved in teaching rooted in the CSE philosophy. CBC cludes substantial elementsof transatlantic mobility and student teaching efforts at UiO range from large undergraduate courses supervision. (INF1100 and INF3331) to advanced graduate courses in me- Based on previous pilots, a cornerstone of SUURPh is the chanics, computational physiology, and parallel computing. annual Summer School on Computational Physiology, which in- While the Simula-based CBC staff mostly lecture at the cludes two weeks of intensive instruction at SSRI in June, indi- UiO, while our collaborators and adjunct scientists teach at vidual project work through the summer, and one week of guided numerous institutions, including NTNU (mechanics, biomechan- project preparation and presentation at UCSD in August. Over ics), Chalmers University, UCSD (computer science, bioengineer- the two years 2014 - 2015, 25 participants from institutions in ing), Oxford University (numerical analysis, computing), Univer- 7 different countries have completed the summer school, which sity of Umeå (mathematics), Norwegian University of Life Sci- also includeda numberof invited guest lectureswith much higher ences (mathematics), Telemark University College (mathematics, attendance. For studentsin the PhD program at UiO, the summer physics), and Technical University Munich (statistical learning).

13 In the appendices below, we use several abbreviations:

ADM Administrativesupport Oxford OxfordUniversityCollege BFS BiomedicalFlowsandStructures(CBC project) RCN ResearchCouncilofNorway CBC CenterforBiomedicalComputing RS RobustSolvers(CBCproject) CC CardiacComputations(CBCproject) SRL SimulaResearchLaboratory(CBChostinstitution) CCI CenterforCardiologicalInnovation(CCI) SSRI SimulaSchoolofResearchandInnovation (Center for Research-based Innovation) SUURPh Simula-UiO-UCSD Research and PhD Training Collaboration CM ComputationalMiddleware(CBCproject) UCSD UniversityofCalifornia,SanDiego Ecole EcoledesMinesSt. Etiennes UiO UniversityofOslo F Female UoS UniversityofSiegen HOST SimulaResearchLaboratory(SRL) UoT UniversityofToronto Kalkulo a subsidiary of Simula Research Laboratory UMB NorwegianUniversityofLifeSciences KimS Kim Scholarship CouncilandChongingUniversity UmU UmeåUniversity M Male UW University of Wisconsin NTNU NorwegianUniversity of Science and Technology

Staff

Senior scientists 2015: 21 people, 8.7 man-years

Name Gender Period CBC share Project Funding

Anders Logg M 01.04.2007-30.06.2016 50% RS, CM 60% UMU + 40% CBC Andrew D. McCulloch M 01.07.2009-30.06.2016 20% CC 50% UCSD + 50% SUURPh Aslak Tveito M 01.08.2007-31.03.2017 25% CC HOST Bjørn H. Skallerud M 24.05.2007-31.03.2017 25% BFS NTNU Glenn Terje Lines M 01.08.2007-31.03.2017 100% CC CCI, RCN grant 203489/O30 Hans Petter Langtangen1 M 01.04.2007-31.03.2017 0% CM, RS, BFS HOST Joakim Sundnes M 01.04.2007-31.03.2017 75% CC, RS CBC Kent-Andre Mardal M 01.01.2009-31.03.2017 60% BFS, CM, RS, CC 67% UiO + 33% RCN grant 209951/F20 Leif Rune Hellevik M 24.05.2007-31.03.2017 45% BFS NTNU Marie E. Rognes F 01.06.2012-31.03.2017 61% RS, CM CBC Mats G. Larson M 01.04.2007-30.06.2016 50% CM, RS 50% UmU + 50% CBC Mikael Mortensen M 01.01.2008-30.06.2016 40% RS, CM, BFS 50% UiO + 50% CBC Molly Maleckar F 01.01.2009-31.12.2015 10% CC CCI, HOST Patrick Farell M 15.09.2012-24.02.2017 40% RF, CM 50% Oxford + 50% CBC Samuel Wall M 01.09.2012-31.03.2017 50% CC CCI, RCN grant 203489/O30 Scott Baden M 11.06.2007-30.06.2016 20% CM 25% UCSD + 75% SUURPh Stuart Clark M 01.01.2008-31.12.2015 20% CM, RS Kalkulo Svein Linge M 01.04.2007-30.06.2016 20% BFS CBC Victor Haughton M 15.06.2008-30.06.2016 20% BFS CBC Victorien Prot M 01.09.2008-31.12.2015 50% BFS NTNU Xing Cai M 01.04.2007-31.03.2017 100% CM, RS, CC RCN grant 214113/F20 + FP7grant 621429

1H. P. Langtangen has had a leave of absence during the period 01.01.2015-31.12.2015.

14 Postdoctoral candidates 2015: 11 people, 7.0 man-years

Name Gender Period CBC share Project Funding

August Johansson M 01.01.2014-31.12.2016 79% RS CBC Benjamin Ragan-Kelley M 01.09.2015-31.03.2017 100% CM Moore foundation Johan Elon Hake M 01.01.2012-31.05.2015 50% CC, CM CBC Johannes Langguth M 01.10.2012-31.12.2015 100% CM RCN grant 214113/F20 Kristian Valen-Sendstad M 21.05.2011-01.10.2016 100% BFS CBC Kristin McLeod F 01.10.2013-31.12.2015 100% CC CCI, RCN grant 203489/O30 Kristin Tøndel F 01.01.2014-31.10.2015 100% CC EU FP7 grant VP2HF Martin Alnæs M 01.04.2011-01.04.2015 100% CM, RS, BFS RCN grant 209951/F20 Namit Gaur M 01.07.2012-30.06.2015 100% CM, RS SSRI Simon Funke M 01.11.2013-15.03.2016 83% CM, RS CBC Valeriya Naumova F 01.01.2014-31.12.2015 30% RS HOST

PhD students 2015: 21 people, 16.5 man-years

Name Gender Period CBC share Project Funding

Benjamin Kehlet M 01.09.2010-15.09.2015 64% RS UiO + CBC Eleonora Piersanti F 05.10.2015-04.10.2018 100% RS SUURPh Gabriel Balaban M 01.02.2013-17.04.2016 100% CM, RS CBC Giulia Pizzichelli F 01.01.2015-22.02.2016 100% BFS IIT Henrik Nicolai Finsberg M 01.10.2014-30.09.2017 100% CC RCN grant 205349/F30 Jacob Sturdy M 01.01.2015-17.12.2018 100% BFS CBC@NTNU Jérémie Lagravière M 01.10.2014-30.09.2017 100% CM RCN grant 231746/F20 Jonathan Feinberg M 15.08.2009-01.08.2015 13% CM, RS EU FP7 grant + Kalkulo Karl Erik Holter M 03.11.2015-01.11.2018 100% BFS SUURPh Kartik Jain M 01.06.2013-31.12.2016 100% BFS UoS Lars Magne Valnes M 22.06.2015-22.06.2018 100% BFS UiO Magne Nordaas M 01.07.2013-30.06.2016 100% CM, RS CBC Marcus Noack M 01.01.2015-31.12.2015 100% CM Miroslav Kuchta M 15.09.2012-14.03.2016 100% BFS UiO Mohammed Owais Khan M 01.09.2013-01.09.2016 100% BFS 90% UoT + 10% CBC Mohammed Sourouri M 01.08.2012-30.09.2015 100% CM, RFS RCN grant 214113/F20 Ole L. Elvetun M 01.01.2012-09.10.2015 100% BFS UMB Sareh Bedadfar F 01.01.2013-30.09.2016 100% CCI Ecole Siri Kallhovd F 01.10.2012-31.12.2015 100% CC CCI, RCN grant 203489/O30 Vinzenz Eck M 01.10.2013-01.10.2017 100% BFS NTNU Øyvind Evju M 10.04.2012-10.06.2015 100% BFS RCN grant 209951/F20

Technical and administrative staff 2015: 15 people, 4.3 man-years

Name Gender Period CBC share Project Funding

Ada Ellingsrud, Summer intern F 01.06.2015-30.08.2015 20% CBC@Simula CBC Aslak Bergersen, Research trainee M 01.06.2015-22.11.2016 47% CBC@Simula CBC Christian Brox, Summer intern M 01.06.2015-30.08.2015 37% CBC@Simula CBC Inna Olafsson, Accounting F 01.01.2014-31.12.2015 10% ADM CBC Karoline Horgmo Jæger, Research trainee F 01.11.2015-31.12.2015 100% CBC@Simula CBC Karoline Kalleberg, Summer intern F 01.09.2015-31.12.2015 23% CBC@Simula CBC Johannes Hofaker Ring M 01.01.2008-31.03.2017 100% CBC@Simula CBC Jonathan Feinberg, Research engineer M 01.04.2014-31.12.2014 66% CM, RS EU FP7 grant, RCN 23884/O30 Marie Roald, Summer intern F 01.06.2015-30.08.2015 30% CBC@Simula CBC Martin AlnÃ¦s, Senior Research Engineer M 01.04.2015-31.03.2017 100% CBC@Simula CBC Monica Eriksen, economy and accounting F 01.01.2014-31.12.2015 5% ADM CBC Nina Lillevand, HR ofﬁcer F 01.01.2013-31.12.2015 5% ADM CBC Sjur Urdson Gjerlaug, Research engineer M 01.06.2012-03.06.2015 100% CBC@CCI CCI, RCN grant 203489/O30 Tom David Atkinson, Adm. Manager M 01.05.2007-31.03.2017 50% ADM CBC Øyvind Evju, Research engineer M 10.06.2015-30.06-2016 59% BFS UNN + EUFP7 Fortissimo grant

15 Guest researchers 2014: 8 people, 1.9 man-years

Name Gender Period CBC share Project Funding

Dajilang Lei M 01.03.2014-01.03.2015 100% CM KimS Dmytro Sadovyi M 31.01.2015-27.02.2015 100% CM EUMLS/home institution Giulia Pizzichelli F 01.01.2015-01.07.2015 100% RFS IIT Quiang Lan M 01.09.2014-31.08.2015 100% CM SIU Vitalii Overko M 16.10.2015-13.11.2015 100% CM EUMLS/home institution Yuliya Valchuk F 16.09.2015-15.11.2015 100% CM EUMLS/home institution Yungang Xue M 01.11.2015-30.04.2016 100% CM SIU Yuran Qiao M 01.09.2015-30.09.2015 100% CM SIU

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

Position 2007 2008 2009 2010 2011 2012 2013 2014 2015

Senior scientists 19/7.1 28/13.4 28 /13.8 24/10.5 20/9.0 23/9.2 23/11.4 22/10.3 21/8.7 Post docs 8/4.1 17/8.8 14/10.1 16/9.9 12/7.7 13/9.6 13/10.2 14/11.7 11/7.0 PhD students 7/3.2 16/11.3 18/13.7 19/15.9 20/11.3 16/10.3 17/12.5 18/12.6 21/16.5 Technical and administrative 10/3.5 12/5.8 11/4.1 9/3.3 10/2.8 13/3.6 16/4.9 16/4.7 15/4.3 Guest researchers 0/0 2/0.7 2/1.5 2/0.5 1/0.4 3/0.8 6/2.2 6/1.6 8/1.9 TOTAL 44/17.9 75/40.0 73/43.2 70/40.1 63/31.2 67/33.5 74/41.0 76/40.7 76/38.4

Figure 13: The accumulated man-years of staff associated with the center during 2007-2015

16 Figure 14: The graph show the percentage of man-years associated with the different employee categories during the center period (2007-2015).

17 Accounting and Budget Below, we present the main figures regarding the CBC budgetand 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 annual SFF grant from the Research Council of Norway represented 18% of the total funding available for CBC activities in 2015, 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, other national and international funding opportunities, and collaboration with various research institutions. There is a challenge in bridging the economical gap between how the project was budgeted in 2007, when the cost of a man year was between 600 and 700 kNOK, and the present day cost of running the center. Now (2015) a PhD/postdoc cost 970 kNOK, and a researcher is more than twice that cost. Each senior researcher man-year now cost 3 times as much as originally budgeted. This makes it absolutely essential to secure additional funding, and spend the resources wisely in order achieve our ambitious goals for the center. The accounts does indeed show that we have been successful in regards to secure additional funding, with a combined increase of 60% of Other income and International funding from 2014 (11.431 kNOK) to 2015 (18.535 kNOK). We try to keep this present realityin mind when we recruit new candidates, in order to find the persons that shares our commitment to excellence in research, and can enhance our research endeavors.

Operating Revenues Note Account 2014 Budget 2015 Account 2015 Budget 2016

RCN CBC funding 7,500 5,113 5,113 9,600 Allocation from earlier years 6,698 3,591 3,591 Host - Simula Research Laboratory 5,190 5,512 6,644 4,102 Other income RCN 1 9,547 15,495 International funding 2 1,884 1,865 Other income 3 1,175 Sum operating revenues 30,819 14,216 33,883 13,702

Income in kind: CCI 7,923 University of Oxford 4 188 194 Norwegian University of Life Sciences 5 938 808 NTNU 6 2,345 3,104 SSRI, SI and Simula 7 1,722 3,872 UCSD 8 66 161 University of Oslo 9 1,638 2,667 University of Umeå 10 281 291 University of Toronto 11 855 881 University of Siegen 12 938 970 Chalmers 13 291 IIT 14 970 Sum income in kind 16,894 14,209 Total income 47,713 14,216 48,092 13,702

Operating Expenses Note Account 2014 Budget 2015 Account 2015 Budget 2016

Cost of labour 15,661 10,500 19,177 10,000 Indirect costs 15 9,416 2,616 12,239 2,400 Outsourcing of R&D services 394 250 641 150 Equipment 195 150 185 150 Other operating expenses 16 1,563 700 1,641 1,002 Sum operating expenses 27,228 14,216 33,833 13,702

Operating expenses in kind: Cost of labour 11,826 9,946 Indirect costs 15 3,379 2,842 Outsourcing of R&D services Other operating expenses 16 1,689 1,421 Sum operating expenses in kind 16,894 14,209 Total operating expenses 44,122 14,216 48,092 13,702 Year end allocation 3,591

18 Notes to accouning and budget:

Note 1: Other income RCN (= 15,495):

203489/O30: Center for Cardialogical Innovation (CCI) (= 7,939) 209951/F20: Patient-Speciﬁc Mathematical Modeling with Applications to Clinical Medical: Stroke and Syringomyelia (= 1,719) 214113/F20: User-friendly programming of GPU-enhanced clusters via automated code translation and optimization (= 2,833) 238834/O30: EMC2, Embedded Multi-Core Systems for Mixed Criticality Applications in Dynamic and Changeable Real-Time Environments (= 2,034) 231746/F20: PRoductivity and Energy-efﬁciency through Abstraction-based Parallel (= 970)

Note 2: International funding (= 1 865): Marie Curie IRSES project (EUMLS) (= 73) Scolarship (to Dajilang Lei) from Kim Scholarship Council and Chonging University of Post and Telecommunication; China (= 162) SISC (= 39) Artemis EMC2 Embedded Multi-Core systems for Mixed Criticality Applications in Dynamic and Changeable Real Time Environments (= 407) EU FP7 611823: VP2HF (= 491) H2020 MSCN-INT - AFib-TrainNet (= 27) H2020 EINFRA - OpenDreamKit (= 222) FORTISSIMO - iBrainCloudSAFE (= 137) Nordforsk - AUQ-PDE (= 35) Gordon and Betty Moore Foundation - JUPYTER (= 272)

Note 3: Other income (= 1,175): University Hospital of Northern Norway (UNN) and Kalkulo (= 286) SIU (Senter for internasjonalisering av utdanning) 11 Person Months PhD guest researchers (Qiang Lan (8PM), Yungang Xue (2PM), Yuran Qiao (1PM)) = 970 x 11/12(= 889)

Note 4: Contributions in kind from University of Oxford (= 194): University of Oxford has ﬁnanced in-kind 0.2 man-years researcher (P. Farrell)

Note 5: Contributions in kind from the Norwegian University of Life Sciences (= 808): One PhD student, equaling 0.83 man-years (O. Elvetun).

Note 6: Contributions in kind from the Norwegian University of Science and Technology (NTNU) (= 3,104): NTNU has ﬁnanced in kind a total of 1.20 man-years of senior scientists (V. Prot, Prof. B. Skallerud and Prof. L. R. Hellevik) and the equivalence of 2 man-year of PhD students (V. Eck and J. Sturdy).

Note 7: Contributions in kind from the Simula School of Research and Innovation (SSRI), Simula Innovation (SI) and Simula (= 3,872): Simula Research Laboratory’s subsidiary Simula School of Research and Innovation (SSRI) is responsible for all educational activities in Simula Research Laboratory. Simula Research Laboratory’s subsidiary Simula Innovation (SI) 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 and its subsidiaries has ﬁnanced the work of 3.2 man-years of CBC associated research activity. 1.42 man-years PhDs (K. Jæger, M. Noack, E. Piersanti), 1.0 man-years postdocs (N. Gaur, J. Hake and V. Naumova) and 0.78 researchers (X. Cai, S. Clark, S. Baden, A. McCulloch and A. Tveito).

Note 8: Contributions in kind from University of California, San Diego (UCSD) (= 161): Funding of 0.17 man-year of senior researchers (S. Baden, A. McCulloch).

Note 9: Contributions in kind from the University of Oslo (= 2,667): Four PhD students, equaling 2.16 man-years (B. Kehlet, M. Kuchta, K. E. Holter and L. M. Valnes), and 0.6 man-years research scientist (K.-A. Mardal and M. Mortensen).

Note 10: Contributions in kind from the University of Umeå (= 291): Part time funding of one senior scientist, equivalent to 0.3 man-years (Prof. M. G. Larson)

Note 11: Contributions in kind from the University of Toronto (= 881): Part time funding of a PhD position equaling 0.9 man-years (M. O. Khan).

Note 12: Contributions in kind from the University of Siegen (= 970): Funding of a PhD position equaling 1 man-year (K. Jain).

Note 13: Contributions in kind from the Chalmers (= 291): Part time funding of one senior scientist, equivalent to 0.3 man-years (Prof. A. Logg)

Note 14: Contributions in kind from Istituto Italiano Di Technologica (IIT) (= 970): Funding of a PhD position equaling 1 man-year (G. Pizzichelli).

Note 15: Indirect costs cover the expenses of ofﬁces, administrative support and infrastructure for all employees.

Note 16: Other operating expenses include the cost of scientiﬁc equipment, travelling, workshops, seminars, and visitors.

19 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 2014 2015 TOTAL

Articles in International Journals 22 31 49 35 27 30 29 36 42 301 Refereed Proceedings 8 9 28 19 19 11 15 6 31 146 Proceedings without referee 0 10 10 6 0 1 0 2 1 30 Books 0 1 1 2 1 2 1 1 0 9 Edited Books 0 1 3 0 0 1 2 0 3 10 Chapters in books 2 3 6 4 1 27 1 0 7 51 Technical Reports 1 0 0 0 1 0 1 0 1 4 Manuals 3 0 1 0 0 0 1 0 0 5 Talks 51 76 69 70 51 63 54 55 57 546 PhD theses 0 2 5 1 3 5 1 2 3 22 Posters 0 0 0 0 5 8 3 0 3 19

Annual variations in CBC publication proﬁle 2007–2015.

Articles in International Journals Bressloff, A. G. Brown, B. J. Chung, J. R. Cebral, G. Copelli, W. Fu, A. Qiao, A. J. Geers, S. Hodis, D. Dragomir-Daescu, E. Nordahl, Y. B. Suzen, O. M. Khan, K. Valen-Sendstad, K. Kono, P. G. Menon, P. G. Albal, O. Mierka, R. Munster, H. G. [1] M. S. Alnæs, K.-A. Mardal, S. J. Bakke and A. Sorteberg. Morales,O.Bonnefous,J.Osman,L.Goubergrits,J.Pallares, Computational ﬂuid dynamics evaluation of ﬂow reversal S. Cito, A. Passalacqua, S. Piskin, K. Pekkan, S. Ramalho, treatment of giant basilar tip aneurysm. Interventional Neu- N. Marques, S. Sanchi, K. R. Schumacher, J. Sturgeon, H. roradiology, vol. 21, 2015. Svihlova, J. Hron, G. Usera, M. Mendina, J. Xiang, D. A. [2] M. S. Alnæs, J.Blechta, J.E.Hake, A. Johansson, B. Kehlet, Steinman and G. Janiga. The ComputationalFluid Dynamics A.Logg,C.Richardson, J. Ring, M.E.Rognes andG.N.Wells. Rupture Challenge 2013-Phase II: variability of hemody- The FEniCS Project Version 1.5. Archive of Numerical Soft- namic simulations in two intracranial aneurysms. Journal ware, vol. 3, 2015. of Biomechanical Engineering, vol. 137, pp. 121008/1- 121008/13, 2015. [3] P. Berg, C. Roloff, O. Beuing, S. Voss, S.-I. Sugiyama, N. Aristokleous, A. S. Anayiotos, N. Ashton, A. Revell, N. W. [4] E. Boileau,P. Nithiarasu, P. J.Blanco,L. O. Muller, F.E. Fos-

20 san, L. R. Hellevik, W. P. Donders, W. Huberts, M. Willemet [16] P. Hansbo, M. G. Larson and F. Larsson. Tangential differ- and J. Alastruey. A benchmark study of numerical schemes ential calculus and the ﬁnite element modeling of a large for one-dimensional arterial blood ﬂow modelling. Interna- deformation elastic membrane problem. Computational Me- tional Journal for Numerical Methods in Biomedical Engi- chanics, vol. 56, pp. 87-95, 2015. neering, vol. 31, pp. 1-33, 2015. [17] P.Hansbo and M. G. Larson. A posteriori error estimates for [5] E. Burman, S. Claus and A. Massing. A Stabilized Cut Finite continuous/discontinuous Galerkin approximations of the Element Method for the Three Field Stokes Problem. SIAM Kirchhoff-Love buckling problem. Computational Mechan- J. Sci. Comput., vol. 37, pp. A1705-A1726, 2015. ics, vol. 56, pp. 815-827, 2015.

[6] E. Burman, P. Hansbo, M. G. Larson and S. Zahedi. Cut Fi- [18] P. Hansbo, M. G. Larson and S. Zahedi. Stabilized Finite nite Element Methods on Coupled Bulk-Surface Problems. Element Approximation of the Mean Curvature Vector on Numerische Mathematik, pp. 1-29, 2015. Closed Surfaces. SIAM Journal on Numerical Analysis, vol. 53, pp. 1806-1832, 2015. [7] E. Burman, P. Hansbo and M. G. Larson. A stabilized cut ﬁ- nite element method forpartialdifferential equationsonsur- [19] D. Huang, C. Xun, N. Wu, M. Wen, C. Zhang, X. Cai and Q. faces: The Laplace-Beltrami operator. Computer Methods Yang. Enabling a Uniform OpenCL Device View for Hetero- in Applied Mechanics and Engineering, vol. 285, 188-207, geneous Platforms. IEICE Transactions on Information and pp. 188-207, 2015. Systems, vol. E98-D, pp. 812-823, 2015.

[8] M. Cenanovic, P. Hansbo and M. G. Larson. Minimal surface [20] K. Jain, S. Roller and K.-A. Mardal. Transitional flow in in- computation using a finite element method on an embed- tracranial aneurysms-a space and time refinement study ded surface. International Journal for Numerical Methods below the Kolmogorov scales using Lattice Boltzmann in Engineering, vol. 104, pp. 502-512, 2015. Method. Computers & Fluids, vol. published online, 2015. [21] A. Johansson,J.Chaudhry,V.Carey, D.Estep,V.Ginting, M. [9] J. Chai, J. E. Hake, N. Wu, M. Wen, X. Cai, G. T. Lines, G. Larson and S. Tavener. Adaptive Finite Element Solution J. Yang, H. Su, C. Zhang and X. Liao. Towards Simulation of MultiscalePDE-ODE Systems. ComputerMethodsin Ap- of Subcellular Calcium Dynamics at Nanometre Resolution. plied Mechanics and Engineering, vol. 287, pp. 150-171, International Journal of High Performance Computing Ap- 2015. plications, vol. 29, pp. 51-63, 2015. [22] A. Johansson, M. G. Larson and A. Logg. High order cut [10] X. Dong, M. Wen, J. Chai, X. Cai, M. Zhao and C. finite element methods for the Stokes problem. Advanced Zhang. Communication-Hiding Programming for Clusters Modeling and Simulation in Engineering Sciences, vol. 2, with Multi-Coprocessor Nodes. Concurrency and Compu- 2015. tation: Practice and Experience, vol. 27, pp. 4172-4185, 2015. [23] O.M.Khan, K. Valen-Sendstad and D. A. Steinman.Narrow- ing the Expertise Gap for Predicting Intracranial Aneurysm [11] V. G. Eck, J. Feinberg, H. P. Langtangen and L. R. Hellevik. Hemodynamics: Impact ofSolverNumericsversusMesh and Stochastic sensitivity analysis for timing and amplitude of Time-Step Resolution. American Journalof Neuroradiology, pressure waves in the arterial system. International Journal 2015. for Numerical Methods in Biomedical Engineering, vol. 31, 2015. [24] S. Land, (...), S. Pezzuto, (...), J. Sundnes and S. Niederer. Verification of Cardiac mechanics software: benchmark [12] P. E. Farrell, A. Birkisson and S. W. Funke. Deflation Tech- problems and solutions for testing active and passive ma- niques for Finding Distinct Solutions of Nonlinear Partial terial behaviour. Proceedings of the Royal Society A, vol. Differential Equations. SIAM Journal on Scientific Com- 471, 2015. puting, vol. 37, pp. A2026-A2045, 2015. [25] J. Langguth, N. Wu, J. Chai and X. Cai. Parallel perfor- [13] J. Feinberg and H. P. Langtangen.Chaospy: Anopensource mance modeling of irregular applicationsin cell-centered fi- tool for designing methods of uncertainty quantification. nite volume methodsoverunstructuredtetrahedralmeshes. Journal of Computational Science, vol. 11, pp. 46 - 57, Journal of Parallel and Distributed Computing, vol. 76, pp. 2015. 120-131, 2015.

[14] M. Halappanavar,A.Pothen,A. Azad,F.Manne, J. Langguth [26] J. Langguth, M. Sourouri, G. T. Lines, S. Baden and X. Cai. and A. M. Khan. CodesignLessonsLearnedfrom Implement- Scalable heterogeneous CPU-GPU computations for un- ing Graph Matching on Multithreaded Architectures. IEEE structured tetrahedral meshes. IEEE Micro, vol. 35, pp. 6- Computer, vol. 48, pp. 46–55, 2015. 15, 2015.

[15] P. Hansbo, M. G. Larson and S. Zahedi. Characteristic cut [27] L.C.Lee, J. Sundnes,M.Genet,J.F.Wenkand S.T.Wall.An ﬁnite element methods for convection - diffusion problems integrated electromechanical-growth heart model for simon time dependent surfaces. Computer Methods in Applied ulating cardiac therapies. Biomechanics and modeling in Mechanics and Engineering, vol. 293, pp. 431-461, 2015. mechanobiology, 2015.

21 [28] W. E. Louch, J. Koivumaki and P. Tavi. Calcium Signaling Annals of Biomedical Engineering, vol. February, pp. 1422- in Developing Cardiomyocytes: Implications for Model Sys- 1431, 2015. tems and Disease. The Journal of Physiology,vol. 593, pp. 1047-1063, 2015. [41] R. Venell, S. W. Funke, S. Draper, C. Stevens and T. Divett. Designing Large Arrays of Tidal Turbines: a Synthesis and [29] A. Malthe-Sørenssen, M. Hjorth-Jensen, H. P. Langtangen Review. Renewable& SustainableEnergy Reviews,vol.41, and K. Mørken. Integrasjon av beregninger i fysikkundervis- pp. 454-472, 2015. ningen. Uniped,vol. 4, pp. 303 - 310, 2015. [42] K. P. Vincent, M. J. Gonzales,A. K. Gillette,C. T. Villongco, [30] A. Massing, M. G. Larson, A. Logg and M. E. Rognes. A S. Pezzuto, J. H. Omens, M. J. Holst and A. D. McCulloch. Nitsche-Based Cut Finite Element Method for a Fluid– High-order ﬁnite element methods for cardiac monodomain Structure Interaction Problem. Communications in Applied simulations. Frontiers in Physiology, 2015. Mathematics and Computational Science, vol. 10, pp. 97- 120, 2015.

[31] Y. Morsi, L. R. Hellevik, A. Qiao, M. C. Vayalappil, J. Tu and W. Yang. Cardiovascular hemodynamics: Advancement of numerical and experimental diagnostic tools. Advances in Mechanical Engineering,vol. 7, pp. 1-3, 2015.

[32] M. Mortensen and K. Valen-Sendstad. Oasis: A high- level/high-performance open source Navier-Stokes solver. Computer Physics Communications, vol. 188, pp. 177 - 188, 2015.

[33] J. P. Mynard and K. Valen-Sendstad. A uniﬁed method for estimating pressure losses at vascular junctions. Interna- tional Journal for Numerical Methods in Biomedical Engi- neering, vol. Jul;31(7):e02717, 2015. [34] M. Noack and T. Gillberg. Fast Computation of Eikonal and Edited Books Transport Equations on GPU Computer Architectures. Geo- physics, vol. 80, 2015.

[35] M. Noack. A Two-Scale Method using a List of Active Sub- [1] Encyclopedia of Applied and Computational Mathematics, Domains for a Fully Parallelized Solution of Wave Equa- Edited by B. Engquist, M. Alber, E. Hairer, J. Håstad, A. Iser- tions. Journal of Computational Science, vol. 11, pp. 91- les, H. P. Langtangen,C.LeBris, C.Lubich,A.J.Majda,J.R. 101, 2015. McLaughlin, R. Nieminen, T. Oden and A. Tveito, 1. edition, volume 1, Springer-Verlag, 2015. [36] B. L. de Oliveira, J. Sundnes, S. Wall and A. D. McCulloch. Increased Membrane Capacitance Is the Dominant Mecha- [2] Encyclopedia of Applied and Computational Mathematics, nism of Stretch-DependentConductionSlowing in the Rab- Edited by B. Engquist, M. Alber, E. Hairer, J. Håstad, A. Iser- bit Heart: a Computational Study. Cellular and Molecular les, H. P. Langtangen,C.LeBris, C.Lubich,A.J.Majda,J.R. Bioengineering,vol. 8, pp. 237-246, 2015. McLaughlin, R. Nieminen, T. Oden and A. Tveito, 1. edition, volume 2, Springer-Verlag, 2015. [37] S. Rao, H. Xue, M. Bao and S. W. Funke. Determining tidal turbine farm efficiency in the Western Passage using the [3] ProceedingsoftheMekIT’15EighthNationalConference on disc actuator theory. Ocean Dynamics, pp. 1-17, 2015. ComputationalMechanics., Edited by B. H. Skallerud and H. I. Andersson, International Center for Numerical Methods [38] K.-H. Støverud, M. S. Alnæs, H. P. Langtangen, V. Haughton in Engineering (CIMNE)., 2015. and K.-A. Mardal.Poro-elasticmodelingofSyringomyelia-a systematic study of the effects of pia mater, central canal, median fissure, white and gray matter on pressure wave Chapters in Books propagation and fluid movement within the cervical spinal cord. Computer Methods in Biomechanics and Biomedical Engineering, 2015. [1] X. Cai. Parallel Computing. In Encyclopedia of Applied [39] H. Su, X. Cai, M. Wen and C. Zhang. An Analytical GPU and Computational Mathematics, edited by B. Engquist, Performance Model for 3D Stencil Computations from the Springer Berlin Heidelberg, 2015. Angle of Data Traffic. The Journal of Supercomputing, vol. 71, pp. 2433-2453, 2015. [2] Ø. Evju and K.-A. Mardal. On the Assumption of Laminar Flow in Physiological Flows: Cerebral Aneurysms As an [40] K. Valen-Sendstad, M. Piccinelli, R. Krishnankuttyremaand Illustrative Example. In Modelingthe Heart and the Circula- D. A. Steinman. Estimation of Inlet Flow Rates for Image- tory System, edited by A. Quarteroni, Springer International Based Aneurysm CFD Models: Where and How to Begin?. Publishing, 2015.

22 [3] H. P. Langtangen,U.Rüdeand A. Tveito. Scientiﬁc Comput- Isotropic Active Strain Model of Left Ventricular Mechan- ing. In Encyclopedia of Applied and Computational Mathe- ics. In Statistical Atlases and ComputationalModels of the matics, edited by B. Engquist, Springer-Verlag, 2015. Heart-Imaging and Modelling Challenges, 2015

[4] V. Naumova, K. Hlavackova-Schindler and S. Pereverzyev. [8] A. Ilseng and B. H. Skallerud. Volumetric compression of Granger Causality for Ill-Posed Problems: Ideas, Methods, HNBR and FKM elastomers. In 9. European Conference on and Application in Life Sciences. In Statistics and Causal- ConstitutiveModels for Rubbers IX, Prague, Chech Repub- ity: Methods for Applied Empirical Research, edited by W. lic, 2015, 2015 Wiedermann and A. von Eye, John Wiley & Sons Limited Wiley, 2015. [9] A. Ilseng, B. Skallerud and A. Clausen. Case study of elas- tomer seals using FEM. In MekIT’15 8th National Confer- [5] J. Sundnes. Bidomain Model: Computation.In Encyclopedia ence on Computational Mechanics, Trondheim, Norway, of Applied and Computational Mathematics, edited by B. 2015 Engquist, Springer-Verlag, 2015. [10] K. Jain and K.-A. Mardal. Exploring The Critical Reynolds [6] J. Sundnes. Electro-Mechanical Coupling in Cardiac Tissue. Number For Transition In Intracranial Aneurysms-highly Re- In Encyclopedia of Applied and Computational Mathemat- solved Simulations Below Kolmogorov Scales. In 4th Inter- ics, edited by B. Engquist, Springer-Verlag, 2015. national Conference on Computational and Mathematical Biomedical Engineering - CMBE2015, 2015 [7] A. Tveito, H. P. Langtangen and R. Winther. Computational Partial Differential Equations. In Encyclopedia of Applied [11] S. Kallhovd, S. U. Gjerald, S. Wall, J. Saberniak, K. Haugaa and Computational Mathematics, edited by B. Engquist, and M. Maleckar. Localization and not extent of ﬁbrofatty Springer-Verlag, 2015. inﬁltration is the primary factor determining conduction dis- turbance in a computational model of arrhythmogenic car- diomyopathy. In E-Health and Bioengineering Conference Refereed Proceedings (EHB), 2015

[12] O. M. Khan, K. Valen-Sendstad, D. Biswas, D. Casey, F. Loth and D. A. Steinman. CFD Simulation of Transition to [1] D. Biswas, D. Casey, D. C. Crowder, K. Valen-Sendstad, Turbulence for Newtonian vs. Non-Newtonian Flow Through D. A. Steinman, Y. H. Yun and F. Loth. Characterization of a Stenosis. In The Summer Biomechanics, Bioengineering& Transition to Turbulence for Blood in a S-Shaped Pipe Un- Biotransport Conference, 2015 der Steady Flow Conditions. In The Summer Biomechanics, Bioengineering & Biotransport Conference, 2015 [13] O. M. Khan, K. Valen-Sendstad and D. A. Steinman. Effects of non-Newtonian rheology on transition to turbulence. In [2] J. Bø, A. Bergersen, K. Valen-Sendstad and M. Mortensen. The 2015 AMMCS-CAIMS Congress, 2015 Implementation, verification and validation of large eddy simulation models in Oasis. In MekIT’15 8th National Con- [14] S. C. Kramer, S. W. Funke and M. D. Piggott. A continu- ference on Computational Mechanics, 2015 ous approach for the optimisation of tidal turbine farms. In European Wave and Tidal Energy Conference 2015, 2015 [3] D. M. Culley, S. W. Funke, S. C. Kramer and M. D. Piggott. Tidal stream resource assessment through optimisation of [15] R. Krishnankuttyrema, K. Valen-Sendstad and D. A. Stein- array design with quantification of uncertainty. In European man. Inlet Flow Rate Variation and Onset of Flow Instabil- Wave and Tidal Energy Conference, 2015 ities in the Carotid Siphon. In The Summer Biomechanics, Bioengineering & Biotransport Conference, 2015 [4] D. Darian and M. Mortensen. A pseudo-spectral study of Kelvin-Helmholtzinstability. In MekIT’15 8th NationalCon- [16] M. Kuchta, K.-A. Mardal and M. Mortensen. Characteriza- ference on Computational Mechanics, 2015 tion of the space of rigid motions in arbitrary domains. In MekIT’15 8th National Conference on Computational Me- [5] V. Eck, J. Feinberg, J. Sturdy, H. P. Langtangen and L. chanics, 2015 R. Hellevik. Sensitivity Analysis and Uncertainty Quantifi- cation in a Wave Propagation Model: A Study of Uncer- [17] Q. Lan, N. Gaur, J. Langguth and X. Cai. Towards Detailed tain Arterial Stiffness. In 4th International Conference on Tissue-Scale 3D Simulations of Electrical Activity and Cal- Computational and Mathematical Biomedical Engineering cium Handling in the Human Cardiac Ventricle. In The 15th (CMBE), Paris, June 29-July 3, 2015 International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2015), 2015 [6] V. G. Eck, J. Feinberg, J. Sturdy, H. P. Langtangen and L. R. Hellevik. Uncertainty quantification and sensitivity anal- [18] T. Landet, M. Mortensen and J. Grue. Towards a continuous ysis for wave propagation models of the arterial systemic anddiscontinuousGalerkin methodformulti-phaseflows. In circulation. In ICCB 2015, VI International Conference on MekIT’15 8th National Conference on Computational Me- Computational Bioengineering, Barcelona, 2015, 2015 chanics, 2015

[7] S. Gjerald, J.E.Hake, S. Pezzuto, J. Sundnes and S.T.Wall. [19] K. S. Mcleod, S. Wall and M. Noack. Fast Sweeping vs. Patient-Speciﬁc Parameter Estimation for a Transversely Fast Marching for Eikonal Methods of Electrophysiology -

23 A Potential for Significantly More Efficient Computation?. [31] K. Valen-Sendstad.Are computersimulationsmisleadingus In Cardiac Physiome Workshop, Auckland, New Zealand, about the nature of blood flow in the brain?. In NSCM-28 - 2015 28th Nordic Seminar on Computational Mechanics, 2015

[20] M. Mortensen, M. Kuchta, K.-A. Mardal and J. Verschaeve. BEND|P|Y: Python framework for computing bending of complex plate-beam systems. In MekIT’15 8th National Conference on Computational Mechanics, 2015

[21] M. Naim, F. Manne, M. Halappanavar, A. Tumeo and J. Langguth. Optimizing Approximate Weighted Matching on Nvidia KeplerK40. In IEEE InternationalConferenceon High Performance Computing (HiPC), 2015

[22] T. Roc, S. W. Funke and K. M. Thyng. Standard methodology for tidal array project optimisation: An idealized study of the Minas Passage. In European Wave and Tidal Energy Conference 2015, 2015 Figure 15: Overview of refereed CBC publications 2007–2015. [23] M. Sourouri, J. Langguth, F. Spiga, S. Baden and X. Cai. CPU+GPU Programming of Stencil Computations for Resource-Efficient Use of GPU Clusters. In IEEE 18th In- ternational Conference on Computational Science and En- gineering, 2015 Conference Proceedings [24] D. A. Steinman, M. O. Khan, K. Valen-Sendstad, D. Biswas, D. Casey and F. Loth. Impact of Non-Newtonian Rheology in Transition to Turbulence in Artery Models.. In 4th Inter- national Conference on Computational and Mathematical [1] H. Finsberg, G. Balaban, J. Sundnes, M. E. Rognes and S. Biomedical Engineering, 2015 Wall. Personalization of a Cardiac Compuational Model using Clinical Measurements.In 28th Nordic Seminar on Com- [25] J. Sturdy, V. G. Eck, J. Feinburg, H. P. Langtangen and L. putational Mechanics, 2015 R. Hellevik. Towards robust clinical assessment of arterial compliance. In 28th Nordic Seminar on ComputationalMe- chanics, 2015 Technical Reports [26] J. Sturdy, V. Eck and L. Hellevik. Uncertainty quantification of short term baroreflex regulationof blood pressure. In CMBE15, 4th International Conference on Computational & Mathematical Biomedical Engineering, 2015 [1] J. Lagraviere, P. H. Ha and X. Cai. Is PGAS ready for the challenge of energy efficiency? A study with the NAS [27] J. Sturdy, V. Eck and L.R. Hellevik.A Validationof Coupling benchmark., UiT, 2015 Carotid and Aortic Baroreflex Models to a 1D Blood Flow Model of the Systemic Arterial Tree. In ICCB 2015, VI In- ternational Conference on Computational Bioengineering, Theses 2015

[28] K. Valen-Sendstad. Can Highly Resolved Computational Fluid Dynam- ics Simulations Shed New Light on Aneurysm [1] O. L. Elvetun. PDE-constrained optimization: Precondition- Initiation?. In 4th International Conference on Computa- ers and diffuse domain methods, Ph.D. Thesis, Department tional and Mathematical Biomedical Engineering, 2015 of Mathematical Sciences and Technology Faculty of En- vironmental Science and Technology Norwegian University [29] K. Valen-Sendstad, A. Lauric, D. A. Steinman and A. M. of Life Sciences, 2015. Malek. Flow Instabilities in Volume-Matched Sidewall ICA Aneurysms: A Possible Association with Rupture Status?. [2] J. Feinberg. Some Improvements and Applications of Non- In Congress of Neurological Surgeons, 2015 intrusive Polynomial Chaos Expansions, Ph.D. Thesis, UiO, [30] K. Valen-Sendstad. On the assumption of laminar ﬂow in 2015. the cerebrovasculature: Implications for CFD insights into aneurysm initiation and rupture?. In Computational Fluid [3] M. Sourouri. Scalable Heterogeneous Supercomputing: Dynamics (CFD) in Medicine and Biology II, An Engineering Programming Methodologies and Automated Code Genera- Conferences International (ECI) Conference Series., 2015 tion, Ph.D. Thesis, UiO, 2015.

24 Talks [15] S. W. Funke. Data assimilation in time-dependent blood ﬂow simulations, Ankara, 2015.

[16] S. W. Funke. Mesh-Independent Convergence for PDE- [1] G. Balaban and H. Finsberg.PatientConstrainedVentricular Constrained Optimisation Solvers in Dolﬁn-Adjoint, Salt Stress Mapping, Lugano Switzerland, 2015. Lake City, USA, 2015.

[2] G. Balaban. Dyssynchronous Left Ventricular Stress Es- [17] S. W. Funke. Data assimilation in time-dependent blood timation, Workshop on Advanced Numerical Techniques in flow simulations, London, UK, 2015. Biomedical Computing: Simula Research Laboratory,2015. [18] S.W.Funke. Assimilating 4D-MRI blood flow measurements [3] G. Balaban. Optimal Elasticity and Contraction in the Car- using PDE-constrained optimisation, Oslo, UK, 2015. diac Cycle, Oslo, Simula Research Laboratory, 2015. [19] S. W. Funke and T. Roc. Optimizing tidal turbine farms with [4] D. Bernsteinand M. E. Rognes. Non-Manifold Manifold Sim- high-level tools, Texas A&M, USA, 2015. ulationsUsing FEniCS,FEniCS’15,Imperial College London, UK, 2015. [20] V. Haughton and K.-A. Mardal. Role of CSF flow in the pathogenesis of Syringomyelia, ASNR 53rd Annual Meet- [5] J. Bø, A. Bergersen, K. Valen-Sendstad and M. Mortensen. ing & The Foundation of the ASNR Symposium 2015, April Implementation, verification and validation of large eddy 25 - 30, 2015; Chicago, Illinois, 2015. simulation models in Oasis, MekIT - Conference on Compu- tational Mechanics - NTNU, Trondheim, Norway., 2015. [21] L. R. Hellevik. Plenary Lecture: Computational models for the cardiovascular system and uncertainty quantifica- [6] V. Eck, J. Feinberg, J. Sturdy, H. P. Langtangen and L. R. tion, 28th Nordic Seminar on Computational Mechanics Hellevik. Sensitivity Analysis and Uncertainty Quantifica- (NSCM28), Tallinn, Estonia, 2015, October 22-23, 2015. tion in a Wave Propagation Model: A Study of Uncertain Arterial Stiffness, 4th International Conference on Compu- [22] K. Jain. Direct numerical simulations expose fluctuations tational and Mathematical Biomedical Engineering, France, in the cerebrospinal fluid hydrodynamics of Chiari malfor- 2015. mation, ECI conference on CFD in Medicine and Biology II, [7] P. Farrell.Deflationtechniquesfor distinct solutionsofnon- Albufeira, Portugal, 2015, September, 2015. linear PDEs, 17th IMA Leslie Fox Prize Competition, Glas- [23] K. Jain. On the modeling of transitional physiological flows, gow, UK, 2015, 22 June, 2015. ECCOMAS Young Investigators Conference, Aachen, Ger- [8] P. Farrell.Deflationtechniquesfor distinct solutionsofnon- many, 2015, July, 2015. linearPDEs, IMAConference on NumericalMethodsforSim- [24] K. Jain. Exploring the critical Reynoldsnumberfor transition ulation, Oxford, UK, 2015, 2 September, 2015. in intracranial aneurysms, Computationaland mathematical [9] P.Farrell.Automatedadjointfiniteelementsimulationswith biomedical engineering, Cachan, France, 2015, July, 2015. dolfin-adjoint,AGM ofNAG Ltd (keynote scientificspeaker), Witney, UK, 2015, 18 September, 2015. [25] K. Jain. Assessment and quantification of transitional flow in intracranial aneurysms, Summer biomechanics, bioengi- [10] P. Farrell. Automated adjoint finite element simulations neering and biotransport conference, Utah, USA, 2015, within FEniCS, NASA Langley, Langley, USA, 2015, 5 June, 2015. March, 2015. [26] A. Johansson. High Order Cut Finite Elements Methods, [11] P. Farrell. Deflation techniques for distinct solutions of SIAM CSE 15, Salt Lake City, 2015. nonlinear PDEs, PETSc 20 year anniversary conference, Chicago, USA, 2015, 16 June, 2015. [27] A. Johansson. High Order Cut Finite Element Methods for the Stokes Problem using Fenics Multimesh Features, FEn- [12] J. Feinberg. Polynomial Chaos Expansions part 1: Method iCS ’15, London, 2015. introduction, 2015 eVITA Winter School - Uncertainty Quantification for Physical Phenomena,Geilo,Norway,Jan- [28] A. Johansson. Nitsche Cut Finite Element Methods with uary 18-23, 2015. Higher Order Elements, USNCCM13, San Diego, 2015.

[13] J. Feinberg. Polynomial Chaos Expansions part 2: Practical [29] A. Johansson. Cut composite mesh methods, Enumath implementation, 2015 eVITA Winter School - Uncertainty 2015, Ankara, 2015. Quantification for Physical Phenomena,Geilo,Norway,Jan- uary 18-23, 2015. [30] S. Kallhovd, J. Sundnes and S. T. Wall. Significance of passive material parametersin mechanical models of the heart, [14] J. Feinberg. Polynomial Chaos Expansions part 3: Some Lugano, Switzerland, 2015. advanced topics, 2015 eVITA Winter School - Uncertainty Quantification for Physical Phenomena,Geilo,Norway,Jan- [31] B. Kehlet. Implicitly adaptive time stepping, Oslo, Simula uary 18-23, 2015. Research Laboratory, 2015.

25 [32] N. Kylstad, K.-A. Mardal, V. Haughton and M. E. Rognes. [46] M. E. Rognes, G. Balaban, J. Sundnes and M. Alnæs. Identi- Effect of Spinal Cord Viscoelasticity on Its Response to fying the Parameters of the Heart: Variational Data Assim- CSF Pressure Waves: a Computational Study, ASNR 53rd ilation in Cardiac Mechanics Using Dolfin-Adjoint, FEniCS Annual Meeting & The Foundation of the ASNR Symposium ’15, Imperial College London, UK, 2015. 2015, April 25 - 30, Chicago, Illinois, 2015. [47] M. E. Rognes. New simulation technology driven by medi- [33] A. Logg. Towards an Adaptive Einstein-Vlasov Solver, Oslo, cal challenges: the Biomedical Computing Department @ Simula Research Laboratory, 2015. Simula, Oslo, Simula Research Laboratory, 2015. [48] B. H. Skallerud and V. E. Prot. Contributions of residual [34] M. Maleckar. How many ionic models do we need for mod- strains, hyperelasticity models, and muscle fiber activation elling of the atria?, Atrial Signals 2015, 2015. on mitral valve systolic performance, 9. European Solid Me- [35] M. Maleckar. Putting the pieces together: towards supple- chanics Conference, Madrid, 2015, 2015. menting sparse clinical data with multi physics simulation, [49] J. Sturdy, V. G. Eck, J. Feinburg, H. P. Langtangen and Foundation Teofilo Rossi di Montelera Forum 2015, 2015. L. R. Hellevik. Towards robust clinical assessment of arterial compliance, 28th Nordic Seminar on Computational [36] K.-A. Mardal. Poroelastic modeling of Syringomyelia - the Mechanics, 2015. effects of pia mater, central canal, median fissure, white and grey matter on pressure wave propagation and fluid [50] J. Sundnes, S. Gjerald and S.T.Wall. Computationalmodels movement within the cervical spinal cord, International Hy- of electro-mechanical interactions in the heart, University drocephalus Imaging Working Group, Chicago, 2015. of Uppsala, 2015.

[37] K.-A. Mardal, K. Jain, K. H. Støverud, G. Ringstad and P. [51] K. Valen-Sendstad. On the assumption of laminar ow in K. Eide. On the complexity of the Cerebrospinal fluid flow the cerebrovasculature: Implications for CFD insights into in the upper spinal column - is the assumption of laminar aneurysm initiation and rupture?, Computational Fluid Dy- flow appropriate?, Cerebrospinal Fluid Dynamics Society namics(CFD)inMedicineandBiologyII,AnEngineeringCon- Meeting, Amiens, 2015. ferences International (ECI) Conference series. Albufeira, Portugal, 2015. [38] K.-A. Mardal. Computationalmodelling of the biomechanics in the central nervous system - Chiari and syringomyelia, [52] K. Valen-Sendstad. Are computer simulations misleading Complex materials; Mathematical models and numerical us about the nature of blood flow in the brain?, NSCM-28 - methods, Oslo, 2015. 28th Nordic Seminar on Computational Mechanics, 2015. [53] K. Valen-Sendstad. Lessons learned from simulating blood [39] K.-A. Mardal. Computationalmodelling of the biomechanics flow in the brain: Preaching to the converted?, MPNS in the central nervous system - Chiari and syringomyelia, COST Action MP1404 Simulation and pharmaceutical tech- Simpla meeting, Oslo, 2015. nologies for advanced patient-tailored inhaled medicines, [40] K.-A. Mardal. Flows in complex geometries such as blood Parma, Italy, 2015. vessels and the central nervous system, EarthFlows kick- [54] K. Valen-Sendstad. The 2015 Aneurysm CFD Challenge: off meeting, Oslo, 2015. Are we there yet?, American Society of Mechanical Engi- neers Validation and Verification meeting, New York, USA., [41] K.-A. Mardal. Computationalmodelling of the biomechanics 2015. in the central nervous system - Chiari and syringomyelia, Oslo, Simula Research Laboratory, 2015. [55] K. Valen-Sendstad. The 2015 Aneurysm CFD Challenge: Variability of Segmentations, Hemodynamics, and Hemo- [42] M. E. Rognes. Introduction to dolfin-adjoint and its applica- dynamic Indices: Qualitative and Preliminary Results - In- tions in cardiac electrophysiology, 2015 Summer School in cremental updates, Computational Fluid Dynamics (CFD) in Computational Physiology: Models, Tools, and Techniques Medicine and Biology II, An Engineering Conferences Inter- for Cardiac Applications, 2015. national(ECI) Conferenceseries. Albufeira, Portugal, 2015.

[43] M. E. Rognes. A 2-day training course in FEniCS and dolfin- [56] K. Valen-Sendstad. Can Highly Resolved Computational adjoint, NGCM Summer Academy, University of Southamp- Fluid Dynamics Simulations Shed New Light on Aneurysm ton, 2015. Initiation?, Accounting for complexity in blood flow modelling, Uncertainty Quantification in Predictive Computa- [44] M. E. Rognes. The FEniCS and Dolfin-adjoint Projects, tional Vascular Mechanics, Computational and Mathemati- NGCM Summer Academy, University of Southampton, cal Biomedical Engineering, Paris, France., 2015. 2015. [57] K. Valen-Sendstad. The 2015 Aneurysm CFD Challenge: [45] M. E. Rognes, B. Kehlet, A. Logg and M. Alnæs. Towards Variability of Segmentations, Hemodynamics, and Hemody- a Unified Framework for Automated a Posteriori Error Esti- namicIndices: Qualitativeand PreliminaryResults, Summer mation and Adaptivity in Space-Time, SIAM CSE, Salt Lake Biomechanics, Bioengineering & Biotransport Conference, City, USA, 2015. Utah, USA, 2015.

26 Posters [3] J. Sundnes, S. T. Wall, V. Timmermann and A. Tveito. Mechano-electric feedback as a source of ectopic activity, Gordon Research Conference on Arrhythmia Mechanisms, Lucca, Italy, 2015. [1] S. W. Funke, P. E. Farrell, D. A. Ham and M. E. Rognes. Dolﬁn-adjoint: Automatic adjoint models for FEniCS, The 8th International Congress on Industrial and Applied Math- ematics, 2015. Public Outreach [2] S. W. Funke, P. E. Farrell, D. A. Ham and M. E. Rognes. Dolﬁn-adjoint, automated adjoint models for FEniCS, SIAM Conference on Computational Science and Engineering, [1] B. Kehlet. Små feil, store konsekvenser, Åpen dag, Univer- 2015. sitetet i Oslo, 2015.

27 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 2015 CBC hosted 4 workshops, 1 seminar, and 13 invited talks in 2015, with a total numberof 68 presentations and over 400 participants.

CBC seminar series and journal club 17.09.15: Dask: Parallel Computation with Blocked algorithms and Task The purpose of the seminar series is to present the current status Scheduling by Matthew Rocklin, presented by Min Ragan-Kelley and challangesfor the projects and create a forum for discussion 24.09.15: of scientific topics related to the work in CBC. The seminars are Asurveyoflongestcommonsubsequencealgorithms by Bergroth, open and attendance of and contributions by other interested Hakonen and Raita, presented by Martin Alnæs people are highly welcome. 08.10.15: 08.01.15: The Finite Element Heterogeneous Multiscale Method: a com- A critical review of the aneurysm literature by Kristian Valen- putational strategy for multiscale PDEs by A. Abdulle, presented Sendstad by Simon Funke 20.01.15: 15.10.15: About CSF flow by Giulia Pizzichelli Robust Principal Component Analysis? by Candes et al., pre- 22.01.15: sented by Valeriya Naumova Adaptive Time-Stepping and Computational Stability by Söder- 22.10.15: lind/Wang (J. Comp. and Appl. Math. 185 (2006), 225-243) Basic Principles of Virtual Element Methods by Brezzi et al., presented by Benjamin Kehlet presented by Magne Nordaas 12.02.15: 05.11.15: Pulsatile Fully Developed Flow in Rectangular Channgels by Zero Pressure Ventricular Geometry and Material Parameter Vivian O’Brien presented by Øyvind Evju Estimation by Gabriel Balaban 19.02.15: 12.11.15: Data assimilation concepts and methods by F. Bouttier and P. Algebraic geometry and power sum decomposition by Karl Erik Courtier presented by Simon Funke Holter 12.03.15: 26.11.15: The Mathematics of Marital Conflict: Dynamic Mathematical Single-beat estimation of end-diastolic pressure-volume rela- NonlinearModelingof NewlywedMarital Interaction by Gottman tionship: a novel method with potential for noninvasive applica- et al, presented by Gabriel Balaban tion (Klotz et al) presented by Gabriel Balaban 19.03.15: Frequentism and Bayesianism: A Python-driven Primer by Jake VanderPlas presented by Martin Alnæs Total number of participants: 151 26.03.15: Total number of speakers: 15 Adaptive Stochastic Galerkin FEM by M. Eigel, C. J. Gittelson,C. Total number of talks: 20 Schwab, and E. Zander, presented by Marie Rognes 16.04.15: Damping Noise-Foldingand Enhanced Support Recovery in Com- pressed Sensing by Marco Artina et al., presented by Valeriya Naumova 23.04.15: Devising HDG methods for Stokes flow: An overview by Cock- burn and Shi, presented by August Johansson Workshops 30.04.15: Inverse problems: A Bayesian perspective by A. M. Stuart, presented by Magne Nordaas CBC Workshop on Computational Models in 04.06.15: Biomedicine - February 11, 2015 "Efficient Spectral-Galerkin Method I. Direct solvers for the second and fourth order equations using Legendre Polynomials and Total number of participants: 22 Efficient Spectral-Galerkin Method II. Direct solvers of second Total number of guests outside of CBC: 3 and fourth order equations using Chebyshev polynomials by Jie Total number of speakers: 9 Shen, presented by Mikael Mortensen Total number of talks: 9

28 CBC Seminar on UFLACS, FInAT, PDELab and CBC Workshop on Advanced Numerical Tech- COFFEE to Produce New Capabilities for Fire- niques in Biomedical Computing - December drake, FEniCS and PDELAB - April 21-22, 3, 2015 2015 CBC hosted a workshop on on advanced numerical techniques Total number of participants: 15 in biomedical computing, aiming to bring together national and Total number of guests outside of CBC: 1 international researchers that apply advanced mathematical and Total number of speakers: 2 numerical methods to biomedical problems. Total number of talks: 2 Total number of participants: 25 Total number of guests outside of CBC: 11 CBC Workshop on Less is More: Reduced- Total number of speakers: 10 Total number of talks: 10 order Modelling - June 26, 2015 Our research partners CBC@NTNU arranged a workshop on reduced order modelling at Simula Research laboratory. The workshop was suited for a broad audience within the relevant re- CBC Workshop on Dynamic Adaptivity - De- search ﬁeld and started with an gentle introductionexplaining all cember 9-10, 2015 the basics, deriving equations from ﬁrst principles, and showing Total number of participants: 21 some applications, followed by more technical talks. Total number of guests outside of CBC: 8 Total number of speakers: 9 Total number of participants: 8 Total number of talks: 9 Total number of guests outside of CBC: 1 Total number of speakers: 2 Total number of talks: 4

Figure 17: The number of presentations are stable, while the attendance varies from year to year depending on how many large international arrangements we host. Figure 16: The number of workshops, seminars and talks vary from year to year. For more information on Workshops, Seminars and Talks, please visit our website: cbc.simula.no

29 Other Activities

Refereeing Activities 4. Fellow, International Association of Medical and Biological During 2015, employees at CBC have refereed manuscripts for: Engineering (IAMBE). 5. Fellow, Cardiovascular Section, American Physiological • American Journal og Neuroradiology Society. • Annals of Biomedical Engineering • Archive of Numerical Software M. E. Rognes: • Biomechanics and Modeling in Mechanobiology 1. 2015 Wilkinson prize for Numerical software. • BMJ Open 2. 2015 Simula Research Award. • Computers and Mathematics with Applications 3. BestPosterAwardatSIAMCSE2015,SaltLakeCity,USA. • ComputationalMethodsinAppliedMechanicsandEngineer- ing K. V.-Senddstad: • Computers Physics Communications 1. Outstanding Oral Presentation by Young Scientist award • Energies for the talk On the Assumption of Laminar Flow in the • Geoscientiﬁc Model Development (GMD) Cerebrovasculature: Implications for CFD Insights into • International Journal for Numerical Methods in Biomedical Aneurysm Initiation and Rupture? at Computational Fluid Engineering Dynamics (CFD) in Medicine and Biology II, An Engineer- • Inverse Problems ing Conferences International (ECI) Conference Series, Al- • Journal of Biomechanical Engineering bufeira, Portugal, September, 2015. • Journal of Biomechanics • Journal of Complexity • Journal of Computational Physics • Journal of Fluids and Structures Committee Work • Journal of Mathematical Analysis and Applications M. Alnæs: • Journal of Parallel and Distributed Computing 1. FEniCS 15 Imperial College London 29.06-01.07.2015 • Journal of the Royal Society Interface • International Journal for Numerical Methods in Fluids S. Baden: • OMICS Diabetes & Metabolism 1. PACT2015-The24thInternationalConferenceonParallel • PeerJ Computer Science Architectures and Compilation Techniques. • SIAM Journal of Scientiﬁc Computing 2. IPDPS - 29th IEEE InternationalParallel & Distributed Pro- • SIAM Journal on Matrix Analysis and Applications cessing Symposium, Hyderabad, INDIA, May 25-29, 2015 • SISC Journal of Computational Physics 3. IPDPS - 30th IEEE InternationalParallel & Distributed Pro- • World Journal of Engineering and Physical Sciences cessing Symposium May 23-27, 2016.

X. Cai: Prizes and Recognition 1. ISC 2015 Frankfurt July 12-16, 2015. 2. ICCS 2015 Reykjavik June 1-3, 2015. P. Farrell: 3. ADVCOMP 2015 Nice July 19-24, 2015. 1. 2015 Wilkinson prize for Numerical software. P. Farell: 2. IMA Fox Prize in Numerical Analysis (second place). 1. IMA Conference on Numerical Methods for Simulation, Ox- S. W. Funke: ford, United Kingdom, September 2015 1. 2015 Wilkinson prize for Numerical software. H. P. Langtangen: 2. BestPosterAwardatSIAMCSE2015,SaltLakeCity,USA. 1. High Performanceand ParallelComputingfor MaterialsDe- M. O. Khan: fects and Multiphase Flows, at the Institute for Mathemati- 1. Winner of the Best PhD Student Paper at the Summer cal Sciences (IMS), National University of Singapore, 2015. Biomechanics, Bioengineering & Biotransport Conference, 2. International Conference on ComputationalScience (ICCS) Salt Lake City, Utah, USA, June, 2015. 2014, 2015, 2016.

A. Logg: A. Logg: 1. Winner of the Gyllene Pekpinnen, educational prize at 1. SIAM CSE 2015, Salt Lake City Chalmers.

A. McCulloch: 1. Jacobs School Distinguished Scholar (2009-2015). Organization of Minisymposia and Workshops 2. Co-Director, UCSD Cardiovascular Biomedical Science and at Conferences Engineering Center. 3. Fellow, American Institute of Medical and Biological Engi- X. Cai: neering. 1. IHPCES’15 workshop Reykjavik June 1 2015

30 S. W. Funke: 3. Simula SpringerBriefs on Computing (Editor) 1. Mini-symposium on Efficient Solvers for PDE-constrained Optimization, SIAM CSE15, Salt Lake City, US, March 14- 18, 2015. Invited talks A. Logg: 1. SIAM CSE Software poster session at SIAM CSE 2015 M. Alnæs: 1. The Finite Element Library FEniCS and Simulation of Blood V. Naumova: Flow in Cerebral Aneurysms, Talk at CSB Seminar, Univer- 1. Learning Subspaces, AIP Conference Helsinki, 25-29 May, sity of Stuttgart, 2015 2015. 2. A Domain Specific Languageand Symbolic Library for FEM Formulations of PDEs - the Unified Form Language, FEn- M. E. Rognes: iCS@Imperial Day, Imperial College London, 2015 1. Mini-symposium on Efficient Solvers for PDE-constrained 3. The Unified FormLanguage– Features, implementationand Optimization, SIAM CSE15, Salt Lake City, US, March 14- future, PRISM Workshop, Imperial College London, 2015 18, 2015. P.E. Farrell: 1. Automated adjoint finite element simulations within FEn- Editorial Boards iCS, NASA Langley, Langley, USA, 5 March, 2015 Employees of the center are on the following editorial boards: J. Feinberg: 1. Polynomial ChaosExpansionspart 1: Method introduction, X. Cai: 2015 eVITAWinter School – UncertaintyQuantificationfor 1. Frontiers in Computational Physics Physical Phenomena,Geilo, Norway, January 18-23, 2015 2. International Journal of Web Sciences 2. Polynomial Chaos Expansions part 2: Practical implementation, 2015 eVITA Winter School – Uncertainty Quan- H. P. Langtangen: tification for Physical Phenomena, Geilo, Norway, January 1. Advances in Water Resources 18-23, 2015 2. BIT Numerical Mathematics 3. Polynomial Chaos Expansions part 3: Some advanced top- 3. International Journal of Computational Science and Engi- ics, 2015 eVITA Winter School – Uncertainty Quantifica- neering tion for Physical Phenomena, Geilo, Norway, January 18- 4. Journal of Computational Science 23, 2015 5. Scientific Computing in Springer’s Encyclopedia of Applied and Computational Mathematics (Field Editor) S. Funke: 6. SIAM Journal on Scientific Computing (Editor in Chief) 1. Mesh-Independent Convergence for PDE-Constrained Op- timisation Solvers in Dolfin-Adjoint, Salt Lake City, USA, M. G. Larson: 2015 1. SIAM Journal on Scientific Computing 2. Optimizing tidal turbine farms with high-level tools, Texas A&M, USA, 2015 A. Logg: 1. Archive of Numerical Software V. Haughton: 2. Guest editor for special issue of SISC: Computational Sci- 1. Role of CSF flow in the pathogenesis of Syringomyelia, ence and Engineering ASNR 53rd Annual Meeting & The Foundationof the ASNR Symposium 2015, April 25 - 30, 2015; Chicago, Illinois A. McCulloch: 1. Biophysical Journal, EBM L. R. Hellevik: 2. Cellular and Molecular Bioengineering 1. Plenary Lecture: Computational models for the cardiovas- 3. Drug Discovery Today, Editor in Chief cular system and uncertainty quantification, 28th Nordic 4. Journal of Physiology (Lond), Reviewing Editor Seminar on Computational Mechanics (NSCM28), Tallinn, 5. PLoS Computational Biology, Associate Editor Estonia, October 22-23, 2015 V. Naumova: 1. Frontiers in Applied Mathematics and Statistics A. Johansson: 1. High Order Cut Finite Elements Methods, SIAM CSE 15, J. Sundnes: Salt Lake City, 2015 1. Frontiers in Physics 2. High Order Cut Finite Element Methods for the Stokes 2. Frontiers in Physiology ProblemusingFenicsMultimeshFeatures, FEniCS ’15, Lon- don, 2015 A. Tveito: 3. Nitsche Cut Finite Element Methods with Higher Order El- 1. Computational Differential Equations in the Encyclopedia ements, USNCCM13, San Diego, 2015 of Applied and Computational Mathematics (Field Editor) 4. Cut composite mesh methods, Enumath 2015, Ankara, 2. Computing and Visualization in Science 2015

31 A. Logg: ing, Oslo, 2015 1. AutomatedSolution of DifferentialEquations, Lund Univer- 5. Flows in complex geometriessuch as bloodvessels and the sity, Lund, 2015. central nervous system, EarthFlows kick-off meeting, Oslo, 2. Automated Solution of Differential Equations, Syddansk 2015 universitet, Odense, 2015. 3. Implementingmathematics: domain specific languagesand Marie E. Rognes: automated computing, Keynote talk at FEniCS’16 in Lon- 1. Introductionto dolfin-adjointand its applicationsin cardiac don, 2015. electrophysiology,2015 Summer School in Computational 4. Implementingmathematics: domain specific languagesand Physiology: Models, Tools, and Techniques for Cardiac Ap- automated computing, Chinese Academy of Sciences, Bei- plications, 2015 jing, 2015. 2. A2-daytrainingcourseinFEniCSanddolfin-adjoint,NGCM Summer Academy, University of Southampton, 2015 M. M. Maleckar: 3. The FEniCS and Dolfin-adjoint Projects, NGCM Summer 1. How many ionic models do we need for modelling of the Academy, University of Southampton, 2015 atria?, Atrial Signals, 2015 4. Towards a Unified Framework for Automated a Posteriori 2. Puttingthe piecestogether: towardssupplementingsparse Error Estimation and Adaptivity in Space-Time, SIAM CSE, clinical data with multi physics simulation, Foundation Te- Salt Lake City, USA, 2015 ofilo Rossi di Montelera Forum, 2015 5. The Numerical Waterscape of the Brain, Norway-Russia workshop on Biot’s equations and error estimation, Voss, K.-A. Mardal: Norway, 2015 1. Poroelastic modeling of Syringomyelia – the effects of pia mater, central canal, median fissure, white and grey matter J. Sundnes: on pressure wave propagation and fluid movement within 1. Computational models of electro-mechanical interactions the cervical spinal cord, International Hydrocephalus Imag- in the heart, University of Uppsala, 2015 ing Working Group, Chicago, 2015 2. On the complexity of the Cerebrospinal fluid flow in the K. Valen-Sendstad: upper spinal column – is the assumption of laminar flow 1. Are computer simulations misleading us about the nature appropriate?, Cerebrospinal Fluid Dynamics Society Meet- of bloodflow inthebrain?,NSCM-28 - 28thNordic Seminar ing, Amiens, 2015 on Computational Mechanics 3. Computational modelling ofthe biomechanics in the central 2. The 2015 Aneurysm CFD Challenge: Variability of Seg- nervous system – Chiari and syringomyelia, Complex ma- mentations, Hemodynamics, and Hemodynamic Indices: terials; Mathematical models and numerical methods, Oslo, Qualitative and Preliminary Results - Incremental updates, 2015 Computational Fluid Dynamics (CFD) in Medicine and Biol- 4. Computational modelling ofthe biomechanics in the central ogy II, An Engineering Conferences International (ECI) Con- nervous system – Chiari and syringomyelia, Simpla meet- ference series. Albufeira, Portugal

32 Collaboration partners Presently CBC researchers has more than 100 collaboration partners from 70 different institutions in 18 countries.

Title Name Afﬁliation Country

Dr. Antiga, L. Mario Negri Institute for Pharmacological Research, Ranica Italy Dr. Bakke, S. Rikshospitalet University Hospital Norway Mr. Beentjes, C. H. L. University of Oxford United Kingdom Dr. Birkisson, Á. University of Oxford United Kingdom Dr. Blechta, J. Charles University Czech Republik Prof. Bradley Jr., W. University of California, San Diego USA Prof. Bunge, H.-P. Ludwig-Maximilian University (LMU), Munich Germany Prof. Burman, E. University College London United Kingdom Prof. Dale, A. University of California, San Diego USA Dr. Claus, S. University College London United Kingdom Prof. Clancy, C. University of California at Davis USA Dr. Cotter, C. Imperial College London United Kingdom Mr. Croci, M. University of Oxford United Kingdom Dr. Culley, D. M. Imperial College London United Kingdom Dr. Cui, Y. San Diego Supercomputing Center USA Prof. Dos Santos, R. W. Federal University of Juiz de Fora Brazil Prof. Dössel, O. Karlsruhe Institute for Technology (KIT) Germany Prof. Eide, P. K. Oslo University Hospital Norway Prof. Einevoll, G. T. Norwegian University of Life Sciences (UMB) Norway Prof. Formaggia, L. Politecnico di Milano, Milan Italy Dr. Gallo, D. Politecnico di Torino Italy Prof. Garzon, M. University of Oviedo Spain Prof. Fornasier, M. Technical University of Munich Germany Prof. Frangi, A. University of Shefﬁeld United Kingdom Dr. Giles, W. R. University of Calgary Canada Dr. Gonzales, M. University of California, San Diego USA Dr. Gorman, G. J. Imperial College London United Kingdom Assoc. Prof. Grasmair, M. NTNU Norway Dr. Guccione, J. M. University of California, San Fransisco USA Prof. Haaverstad, R. Haukeland University Hospital Norway Dr. Hale, J. University of Luxembourg Luxembourgh Dr. Ham, D. A. Imperial College London United Kingdom Dr.-Ing. Hasenauer, J. Helmholtz Zentrum München Germany Dr. Helmig, R. University of Stuttgart Germany Prof. Ho, J. Defence Research and Development Canada Canada Prof. Holst, M. University of California, San Diego USA Dr. Hoshijima, M. University of California, San Diego USA Assoc. Prof. Hu, H. P. University of Tromsø Norway Dr. Jensen, A. University of Oslo Norway Dr. Jespersen, T. University of Copenhagen Denmark Dr. Jiang, J. University of Wisconsin, Madison USA Prof. Jimenez, J. University of Massachusetts Amherst USA Dr. Kekenes-Huskey, P. University of California, San Diego USA Assoc. Prof. Ketcheson, D. I. King Abdullah University of Science and Technology (KAUST) Saudi Arabia Prof. Kirby, R. C. Texas Tech University USA Dr. Kiss, G. NTNU and St. Olafs Hospital Norway Dr. Knepley, M. G. University of Chicago USA Dr. Koivumäki, J. University of Eastern Finland Finland Dr. Kramer, S. C. Imperial College London United Kingdom Prof. Loth, F. University of Akron USA Dr. Louch, W. Oslo University Hospital Norway Dr. Maddison, J. M. University of Edinburgh United Kingdom Prof. Dr. Maggioni, M. Duke University USA Prof. Malthe-Sørensen, A. University of Oslo Norway

33 Title Name Afﬁliation Country

Dr. Martin, B. Director of Conquer Chiari Institute USA Dr. Massing, A. Umeå University Sweden Dr. Maurini, C. Uiversité Paris IV France Prof. McCammon, J. A. University of California, San Diego USA Dr. Michailova, A. P. University of California, San Diego USA Prof. Morbiducci, U. Politecnico di Torino Italy Dr. Mynard, J. Murdoch Childrens Research Institute Australia Assoc. Prof. Målqvist, A. Chalmers University of Technology Sweden Prof. Norbotten, J. M. University of Bergen Norway Dr. Omens, J. H. University of California, San Diego USA Prof. Pereira, V. M. University of Toronto Canada Prof. Pereverzyev, S. Austrian Academy of Science Austria Dr. Piccinelli, M. Emory University USA Dr. Piggott, M. D. Imperial College London United Kingdom Prof. Regnier, M. University of Washington USA Dr. Richardson, C. University of Cambridge United Kingdom MD. Ringstad, G. A. Oslo University Hospital Norway Dr. Roch, T. Acadia University and IT Power Consulting Canada Prof. Rocha, B. M. Federal University of Juiz de Flora Brazil Prof. Roller, S. University of Siegen Germany Assoc. Prof. Rosasco, L. Istituto Italiano di Technologia Italy Prof. Rudy, Y. Washington University in St. Louis USA Prof. Ruede, U. University of Erlangen Germany Prof. Sachse, F. B. University of Utah USA Dr. Schnass, K. University of Insbruck Austria Mr. Schott, B. TUM, Munich Germany Dr. Schmidt, S. Universität Würzburg Germany Prof. Scott, R. University of Chicago USA Dr. Seemann, G. Karlsruhe Institute of Technology (KIT) Germany Prof. Sejersted, O. M. Oslo University Hospital Norway Prof. Sethian, J. A. University of California, Berkeley USA Prof. Siltanen, S. University of Helsinki Finland Dr. Sinibaldi, E. Istituto Italiano di Technologia (IIT) Italy Dr. Sommer, G. Graz University of Technology Austria Dr. Sorteberg, A. Rikshospitalet University Hospital Norway Prof. Spiteri, R. J. University of Saskatchewan Canada Prof. Steinmann, D. A. University of Toronto Canada Prof. Stokke, B. T. Department of Physics, NTNU Norway Prof. Strother, C. University of Wisconsin, Madison USA Dr. Sømme, T. O. University of Bergen Norway Dr. Thyng, K. M. Texas A&M University USA Dr. Trayanova, N. Johns Hopkins University, Baltimore USA Dr. Unat, D. Koc University Turkey Prof. Ventios, Y. University College London United Kingdom Prof. Vierendeels, J. Ghent University Belgium Prof. Vito, E. De University of Genova Italy Dr. Wells, G. N. University of Cambridge United Kingdom Dr. Wen, M. National University of Defence Technology (NUDT) China Dr. Wieben, O. University of Wisconsin, Madison USA Prof. Winther, R. University of Oslo Norway Prof. Zhang, C. National University of Defence Technology (NUDT) China Prof. Zunino, P. University of Pittsburgh USA Dr. Ølgaard, K. B. Aalborg University Denmark

34 35 List of International Guests in 2015

In 2015 CBC had 64 international guests from 19 different countries. The Norwegian visitors are not listed. Period Position Name Afﬁliation Nationality June 18 Dr. Chris Villongco University of Calefornia, San Diego American June 15 - 26 PhD student Divya Kernik University of Calefornia, Davis American December 9 - 10 Professor Donna Calhoun Boise State University American June 17 - 18 Dr. Hermenegild Arevalo Johns Hopkins University American June 15 - 26 PhD student Holly Howarth University of Calefornia, San Diego American February 16 - 20 Dr. Joseph Young OptimoJoe American June 18 PhD student Kevin Vincent Uniersity of Calefornia, San Diego American June 15 - 26 PhD student Lauren Dupius Maastricht University American June 15 - 26 PhD student Mitchell Simon University of Calefornia, Davis American June 15 - 26 PhD student Nickolas Forsch University of Calefornia, San Diego American June 16 PhD student Paula Dassbach University of Minnesota American June 17 Dr. Peter Kekenes-Huskey Department of Pharmacology, University of Califor- American nia, San Diego June 23 Dr. Tom Bartol Salk Institute for Biological Studies American June 15 - 26 PhD student Will Valdez University of Calefornia, San Diego American June 15 - 26 Dr. Babken Asatryan Yerevan State Medical University, Clinic of General Armenian and Invasive Cardiology April 20 - 21 Dr. David Ham Imperial College London Australian June 24 - 26 Dr. Jonathan Mynard Murdoch Childrens Research Institute Australian August 31 - PhD student Kat Gilbert Faculty of Medical and Health Sciences, University Australian September 1 of Auckland May 6 - 8; November Dr. Marcus Grasmair NTNU Austrian 16 - 17 December 3 Dr. Wolfgang Wall T. U. München Austrian March 9 - 19 PhD student Andrew McRae Imperial College of London British July 20 - 28 PhD student Dave Culley Imperial College London British April 1 - May 29 PhD student Mohammed Owais Khan University of Toronto Canadian June 19 Dr. William Louch Institute for Experimental Medical Research, Oslo Canadian University Hospital Ullevål June 15 - 26 PhD student Yanyan (Claire) Ji Georgia Institute of Technology Chinese September 1, 2014 PhD student Qiang Lan National University of Defence Technologi (NUDT), Chinese - August 6, 2015 China November 1, 2015 - PhD student Yungang Xue National University of Defense Technology (NUDT), Chinese April 30, 2016 China September 1 - PhD student Yuran Qiao National University of Defense Technology (NUDT), Chinese September 30 China June 18 PhD student Jonas van den Brink University of Oslo Dutch June 15 - 26 PhD student Petrus Rudolphus Elise (Peter) Maastricht University Dutch Huntjens February 5 Dr. Roel Stappers The Norwegian Meterological Institute (DNMI) Dutch June 3 - 4 Professor Samuli Siltanen University of Helsinki Finnish December 3 Professor Christophe Prud’home University of Strasbourg French February 11 Dr. Bettina Knapp Institute of Computational Biology HelmholtzZen- German trum Munich December 9 - 10 Professor Carsten Burstedde Rheinische Friedrich-Wilhelms-UniversitÃ¤t Bonn German April 20 - 21 PhD student Dominic Kempf University of Heidelberg German February 11 Professor Fabian Theis Institute of Computational Biology HelmholtzZen- German trum Munich December 9 - 10 Dr. Johannes Holke Rheinische Friedrich-Wilhelms-Universität Bonn German June 15 - 26 PhD student Laura Pascale Pfeiffer University of Kaiserslautern German December 3 Dr. Lorenz John T. U. München German December 3 Professor Michael Gee T. U. München German December 9 - 10 Professor Rolf Krause USI Lugano German April 20 - 21 Dr. Steffen Müthing Heidelberg University German June 15 - 26 PhD student Andras Horvath University-Medical Center Hamburg-Eppendorf Hungarian June 3 - 4 PhD student Zenith Purisha University of Helsinki Indonesian December 9 - 10 Dr. Gerard Gorman Imperial College London Irish April 20 - 21 PhD student Fabio Luporini Imperial College London Italian December 3 Dr. Federico Negri EPFL, Switzerland Italian December 3 Professor Gianluigi Rozza SISSA Trieste Italian January 1 - July 1 PhD student Giulia Pizzichelli IIT center for micro-biorobotics in Pontedera (PI), Italy Italian

36 Period Position Name Afﬁliation Nationality December 9 - 10 Dr. Martin Kronbichler T. U. München Italian December 9 - 10 PhD student Pietro Benedusi USI Lugano Italian June 18 Dr. Simone Pezzuto Politecnico di Milano, Italy Italian December 3 Professor Adelia Sequeira IST, Lisboa Portugese June 3 - 4 Dr. Axel Målqvist Chalmers University of Technology and University of Swedish Gothenburg December 9 - 10 PhD student Carl Lundholm Chalmers Swedish June 3 - 4 Professor Stig Larsson Chalmers University of Technology Swedish August 3 - 7 Dr. Didem Unat Koc University Turkish August 14 - 30 Professor Andiy Pylypenko Institute of Mathematics of Ukrainian National Ukrainian Academy of Sciences January 31 - Febru- Professor Dmytro Sadovyi Taras Schevchenko National University, Kyiv Ukrainian ary 27 October 16 - PhD student Vitalii Overko Institute of Mathamatics, Kyiv, Ukraine Ukrainian November 13 August 14 - 30 Assoc. Pro- Yevgeniya Sulema National Technical University of Ukraine, Kyiv Poly- Ukrainian fessor technic Institute September 16 - PhD student Yuliya Valchuk National Technical University of Ukraine, Kyiv Poly- Ukrainian November 15 technic Institute April 19 - May 3 Professor Yuluya Mishura Taras Shevchenko National University of Kyiv Ukrainian

37 Visiting address: Martin Linges v. 17, 1364 Fornebu Mailing address: P.O.Box 134, 1325 Lysaker, Norway Phone: +4767828200,fax:+4767828201 Email: [email protected] Org.#: 984648855