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Center for Biomedical Computing
Annual Report 2014
CBC is approaching the end of its funding period, and thisreality has had some impact on CBC activities through 2014.Several internal workshops have been organized with the aim ofreviewing the original milestones of the Center, and ensure thatthe collective research efforts are well aligned with these goals.These workshops have left us with the general impression thata considerable number of milestones have already been met, andwe are well on track to complete most of the remaining ones.Although some revisions to the list of goals and milestones havebeen made, these are remarkably small when considering CBC’sten years of operation in a rapidly changing scientific environment.
The term exit strategy has been in focus for many Centers ofExcellence, and has recently received increased attention at CBC.Ten years of considerable funding has been spent on building astrong research community, and the strong desire to maintain thiscommunity after the CBC funding period is shared by the Centermanagement, our host institution, and the Research Council ofNorway. However, the CBC grant represents a substantial fund-ing source for a relatively small host institution, which is chal-lenging to replace from other funding sources. Consequently, theexit strategy adopted by CBC and Simula has been to activelysupport senior researchers in pursuing permanent academic posi-tions at other institutions, and combine this with a strong focuson securing continued funding for the biomedical computing ac-tivity Simula. We believe that maintaining a significant groupat Simula, although most likely smaller than the current size ofCBC, and collaborating closely with former CBC researchers atvarious universities, is a viable way of securing the competenceand long term scientific progress. So far this strategy has workedout well. The most recent appointments of key CBC personnell inpermanent academic positions were Kent-Andre Mardal (2014,University of Oslo) and Anders Logg (2013, Chalmers Univer-sity). Both of these researchers have been central in definingthe scientific profile of the CBC, and they continue to be ac-tive collaborators and contributors to CBC research in their newpositions.
Although we are happy to see key personnel moving to po-sitions at other academic institutions, our aim is to preserve theexisting CBC community at Simula as a natural hub for continuedcollaboration and research on biomedical computing. This goal re-quires maintaining a critical mass of active researchers at Simula,as well as the technical staff that support the software develop-ment and distribution that has been at the core of CBC research.Naturally, the key to fulfilling this goal is to secure continuedfunding, which has received significant attention by CBC andthe other departments and research centers at Simula. Althoughno new large-scale research projects were awarded to the CBCand related activities in 2014, other Simula departments had aremarkable success in securing funding from the Horizon 2020program. This success represents a substantial step forward forSimula, and increases our confidence in the European researcharena as a potential funding source for continued activity.
In the fall of 2014, the Norwegian Ministry of Research andEducation announced that they would fund a new collaborativePhD program involving Simula, the University of Oslo, and the
University of California, San Diego. The announcement markedthe successful conclusion of substantial effort put in by the Sim-ula School of Research and Innovation (SSRI) to establish thiscollaboration. Simula and CBC have had a close research collab-oration with UCSD for more than a decade. The new PhD programbuilds directly on this collaboration, and will be focused on com-putational science and in particular on biomedical applications. Inaddition to being the first educational collaboration of this kindin Norway, and securing tight links with a truly world-class aca-demic institution, the funding of this program is an important steptowards achieving our goal of a lasting research community inbiomedical computing at Simula.
In terms of scientific achievements, 2014 has been anotherexcellent year for the CBC. Publication metrics are maintainedat a high level, with an increase in journal publications from theprevious year. Although it is much to early to evaluate and ranklast year’s publication in terms of their scientific impact, a fewof the papers stand out as particularly central to the research ofthe CBC. As mentioned in last year’s Annual Report, the paper onthe Unified Form Language (UFL) was accepted for publicationin 2013, and published in ACM Transactions on MathematicalSoftware in 2014. In addition to being a core technology in FEn-iCS, and thereby an important building block in much of CBC’sresearch, UFL has received attention outside the FEniCS users’community, and is in use in other software frameworks. Fur-thermore, the software framework for automating the solution ofadjoint problems, as described in this year’s Featured Researcharticle, has been extended to a framework for automated stabilityanalysis, and published in SIAM Journal on Scientific Computing.Finally, Douglas Arnold and Anders Logg published an article ti-tled The Periodic Table of the Finite Elements in the high-profiledSIAM News. Being a welcome attempt to group and organizethe large collection of finite elements developed and used in sci-entific computing, the article has already received substantialattention.
The biomedical applications addressed in CBC publicationsshow a large and increasing variety, covering physical scales fromthe subcellular level to complete organs, and addressing topicsranging from clinically driven problems to fundamental biophys-ical and physiological research. This variety is also illustratedby the two PhD candidates graduating from CBC last year, whoboth focused on biomedical applications. Karen-Helene Støverudinvestigated a neurological abnormality known as the Chiari mal-formation, focusing on flows and deformations in the spinal canaland addressing questions of direct clinical relevance. On the otherhand, Bernardo Lino de Oliveira studied mechano-electric cou-pling in the heart, with his main focus on cellular and sub-cellularmechanisms by which mechanical abnormalities can disturb theelectrophysiology of the heart muscle. Both of these theses alignwell with the long-term development we have planned for andseen in CBC research. We started out with a strong bias towardsmethods and software development, but towards the end of theCBC period we combine this activity with an increasing focuson putting the tools to use for addressing important questions inbiomedical science.
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WORDS FROM THE DIRECTOR 2RUNNING THE CENTER 4Project overview 4The Scientific Advisory Board (SAB) 4People, Recruitment and Gender Diversity 4Gender diversity 5SCIENTIFIC ACTIVITIES 6Computational Middleware 6Robust Solvers 8Biomedical Flows and Structures 9CBC at NTNU 10Cardiac Computations 11FEATURED RESEARCH 2014: 12Adjoint models 12EDUCATION AND OUTREACH 14The Simula School of Research and Innovation 14University Teaching 14APPENDIX 15Staff 15Accounting and Budget 19Publications 22Conferences, Workshops and Seminars 27Other Activities 30
Refereeing Activities 30Committee Work and Recognition 30Editorial Boards 30Conference Committees 31Invited talks 31
Collaboration partners 33List of International Guests in 2014 35
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Project overviewAll research activities in CBC are organized in large projects withan appointed project leader and a well-defined project plan. Afterseeing some adjustments through 2011, the project portfolio hasremained unaltered since, and currently includes the followingfour projects.
1) Computational Middleware. This project is devoted to devel-oping generic high-performance software components for buildingthe simulation programs needed in the center. The results alsoserve the global computational science community with a newgeneration of widely applicable computational software. At thecore of the development is the finite element software suite FEn-iCS.
2) Robust Solvers. The Robust Solvers project focuses on ef-ficient and stable numerical methods with error and uncertaintyestimation, as well as implementation of such methods for prob-lems arising in the two application projects Cardiac Computations(CC) and Biomedical Flows and Structures (BFS).
3) Cardiac Computations. This project performs research on med-ical problems involving models of heart electrophysiology andmechanics. The current activity is strongly influenced by thegoals of the Center for Cardiological Innovation (CCI), which isa Center for Research Based Innovation funded by the ResearchCouncil of Norway. A more elaborate description of the mutualresearch goals of CCI and CBC was provided in the CBC annualreport for 2011.
4) Biomedical Flows and Structures. Research in the Biomedi-cal Flows and Structures project centers around biomedical flowand tissue interaction problems of high clinical importance. Ina short to medium time frame, the applications to be targetedare aneurysm formation and rupture in the Circle of Willis, therelation between Chiari I malformation and cyst formation in thespinal cord, modeling of large cardiovascular networks, and fluid-structure interactions in cardiovascular biomechanical systems.The research on the latter two topics is headed by our partners atthe Biomechanics Division at the Department of Structural Engi-neering at the Norwegian University of Science and Technology(NTNU), known as CBC@NTNU in the CBC context.
The Scientific Advisory Board (SAB)The members of the CBC advisory board provide the center withvaluable input, and review the ongoing research activity. SinceCBC is a focused center with a quite narrow research scope,we benefit from having a small and well informed advisory boardthat is in tune with our vision and grasp the whole spectre of ouractivities. We changed the members of the CBC SAB in 2014in order to gain new perspectives and keep up with the currentand expected future development for the last period of the cen-ter. We would like to thank Professors David Keyes, AndrewMcCulloch and Dr. Debora Wood for their valuable contributionsto CBCs development.
Our new SAB as of June 2014 consists of:
• Prof. Dr. Carsten Burstedde. Institute for Numerical Sim-ulations, Rheinische Friedrich-Wilhelms-Universität Bonn,Germany.
• Dr. Ellen Kuhl. Associate Professor of Mechanical Engineer-ing, Bioengineering (courtesy), and Cardiothoracic Surgery(courtesy), Stanford Mechanics and Computation.
• Dr. Signe Haughton. Director, Global Strategic Alliances,Stryker Neurovascular.
• Dr. Vanessa Diaz. Department of Mechanical Engineering,University College London.
People, Recruitment andGender DiversityRecruitment to the center. We recruited several new people tothe centers activity during 2014, and three of the four projectswere supplied with new personell.
The Cardiac Computations project staff was expanded byDr. Kristin Tøndel (multivariate data analysis, funded by an FP7grant), and Ph.D. student Henrik Finsberg (patient specific car-diac models, funded by the Center for Cardiological Innovation.Dr. Valeria Naumova and Dr. August Johansson joined the RobustSolvers project. Dr. Naumova brings expertise on multi-penaltyregularization and meta learning techniques, while Dr. Johanssonstrengthens the group’s work on multiscale problems, adaptivefinite elements methods and PDE-ODE systems. The Computa-tional Middleware project strengthened its work on high perfor-mance computing by recruiting Ph.D. student Jérémie Lagravière(embedded computing).
Graduated PhD students. Two PhD students graduated fromCBC during 2014.
As part of the Biomedical Flows and Structures project, KarenH. Støverud finished her studies on ”Relation between the Chiari Imalformation and syringomyelia from a mechanical perspective.”in June 2014. The Chiari I malformation is a neurological condi-tion in which parts of the cerebellum is displaced into the spinalcolumn. This causes a partial obstruction of the cerebrospinalfluid (CSF) space surrounding the brain and spinal cord. Chiari Imay cause a wide range of symptoms such as severe headaches,sleep apnea, visual disturbances and muscle weakness. Sec-ondary to a Chiari malformation many patients develop fluid filledcavities, cysts, within the spinal cord tissue, which may causea number of symptoms. The exact relation between Chiari I andcyst formation remains unknown, but the leading hypothesis isthat the development is mechanically driven, caused by abnormalflow fields and pressure gradients in the CSF.
To offer these patients optimal treatment and an increasedquality of life we need a better understanding of the underly-ing causes. The aim of the thesis was first to simulate CSFflow in healthy subjects and Chiari patients under patient spe-cific anatomy and flow conditions, and then to simulate wavepropagation and fluid movement through the spinal cord. Finally,the results from the simulations were related to cyst formationand suggested alternative measures for abnormal CSF flow. Thesimulation results revealed that obstructions of the CSF space,
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as seen in Chiari patients, causes increased pressure gradientsand decreased phase lag between velocity and pressure. Thepressure drop may be estimated from medical images, and a sig-nificant increase in the pressure drop may be used to distinguisha moderate from a severe obstruction.
In November 2014, Bernardo Lino de Oliveira finished hisstudies on ”Computational Models for Cardiac Electromechan-ics.”, as part of the Cardiac Computations project. The aim of thethesis was to contribute to the progress of cardiac modeling bystudying and developing computational models to represent theelectromechanical processes in the heart. Several interestingquestions can be studied using coupled electromechanical mod-els of the heart as many questions are intrinsically related to thecoupling between these problems. These coupled problems giverise to many modeling and numerical challenges, both from theelectrophysiology and mechanics parts and are many times re-lated to the coupling itself. The thesis has made a contribution tothe understanding and development of coupled electromechani-cal models of the heart, and to how these models can be solvedefficiently.
CBC alumni. Several of CBC’s former researchers continue topursue an academic career outside of our host institution. We arehappy to report that their academic merits and scientific train-ing have been recognized and secured them prominent academicpositions with their new employees.
Our principal investigator for the Biomedical Flows and Struc-tures project, Kent-Andre Mardal, accepted a position as asso-ciate professor at the Department of Mathematics, University ofOslo, July 2014. He continues to hold an adjunct position at CBCand is still actively participating in the project and our current re-search.
Dr. Andre Massing completed his postdoc position at CBCDecember 2014, but will continue his research on finite elementmethods together with Professor Mats G. Larson at University ofUmeå on a new project funded by the Swedish Foundation for
Strategic Research.
Gender diversityCBC has continued the close collaboration with our host institu-tion Simula to actively search for and recruit talented researchers,and to strive for a gender diverse research environment withoutcompromising on the quality and talent of our researchers.
We share the ambition of our host of reaching 25% femalePhD students, postdocs and full time researchers at Simula within2015, and 30% within 2022. While the goal of 25% of total sci-entific staff has already been reached, it is more challenging tofulfil the ambition of at least 25% female researchers on se-nior level. Simula is working very actively to achieve this goal,both by recruiting senior researchers directly from other institu-tions, and by promoting and supporting internal PhD students andPostdocs to continue their research career. We added five newresearchers to our projects during 2014, three postdocs and twoPhD students. Two of the three postdocs were women, whichmakes 40% of the new employees at CBC female.
The importance of female role models. We have taken severalimportant actions in order to achieve a gender diverse work envi-ronment at CBC. As previously mentioned we search actively fortalented female researchers, and we have female researchers in-volved in the screening process when we recruit new employees.
Of equal importance, CBC has two active female researchersat the highest levels of our host organisation. By their undis-puted talent and accomplishments they function as role modelsand clearly demonstrate that there is an array of opportunitiesand exciting career possibilities for both genders in our researchfield.
As a closing remark, it is worth noting that although we em-phasize establishing a gender diverse research environment, wewill always regard potential for scientific excellence as the singlemost important criterion for recruiting and promoting staff.
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Through 2014 the scientific activities in CBC progressed according to plan. Below we give an overview of the main activities and resultsin 2014. The sections cover the four projects that have been forming CBC through 2014: Computational Middleware, Robust Solvers,Biomedical Flows and Structures, and Cardiac Computing. The activities at the Norwegian University of Science and Technologycontribute to the Robust Flow Solvers and the Biomedical Flows and Structures projects, but the research is described in a separatesection, titled CBC@NTNU.
Computational MiddlewareIn 2014, improvements in high performance computing was madeboth towards massively parallel computing and exploitation ofnovel hardware. Software for new advanced numerical methodswas published to accompany published journal articles. Auto-mated adjoint methods are now being applied to optimizationproblems in various research areas. Furthermore, the fourth edi-tion of the popular “A Primer on Scientific Programming withPython” by Hans Petter Langtangen was published on SpringerVerlag.
The FEniCS Project. The FEniCS project is an international col-laboration to produce high quality open source scientific software,where CBC is one of the largest partners. To enable research de-manding large scale computations, one of the CBC milestonesis to achieve good compute performance in the FEniCS softwaresuite when employing over 10000 processor cores in parallel ontodays supercomputers. The measure of success is the weakscaling test where the number of processor cores is increasedproportionally to the size of the computation, and the ideal resultis that the computation time stays constant. This is only possibleif the communication between processors is kept low, and to thisend a clever numbering of the equations in large linear systemsis instrumental. In 2014 both researchers at CBC and collabo-
rators at the University of Cambridge carried out weak scalingtests showing FEniCS has already surpassed this milestone for alarge class of computations, although work continues to improveperformance even further.
A number of research visits to leading universities in the UKtook place during 2014 to strengthen ongoing collaborations. Theannual FEniCS workshop titled “FEniCS14 - Expressive and highperformance scientific computing” was held 16th-17th June atThe Center in Paris, a division of the University of Chicago locatedin France, with 22 talks and a keynote lecture held by J. C. Ned-elec. A number of ongoing FEniCS activities at the CBC relatedto improved geometry descriptions were presented at FEniCS14,including the new mesh generation component of FEniCS calledmshr; early prototypes of high-order geometric descriptions inFEniCS; and computational geometry tools and quadrature rulesfor enabling multimesh finite element computations in FEniCS.
Advances in numerical methods for overlapping meshes andfictitious domains represented with level sets were published in2014 in the form of 2 journal articles. The articles are accom-panied by a prototype implementation named libcutfem, whichextends the FEniCS software suite with these advanced meth-ods. Figure 1, taken from one of these articles, shows how astructured background mesh and a smooth level set function iscombined to produce a triangulation of the surface.
Figure 1: A regular background mesh combined with a smooth level set function (left) produces a new triangulation of the surface (right).
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CBC researchers continue to develop open source solversoftware for flow problems, cardiac electrophysiology and car-diac mechanics. Recently a recurring topic is the integrationof automated adjoint methods using dolfin-adjoint to extend thecapabilities of application specific solvers to solve optimizationproblems.
Finally, the journal article about the “Unified Form Language”(UFL), one of the core contributions to FEniCS from CBC, was pub-lished in ACM Transactions on Mathematical Software in 2014and has received 24 citations in the first year – ten times theimpact factor of the journal. UFL is the high level domain specificlanguage in FEniCS that enables symbolic representation and ma-nipulation of equations via their expression trees, an example ofwhich is shown in Figure 2. Simultaneously, the FEniCS bookfrom 2012 has continued to climb steadily to 350 citations.
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Figure 2: Expression tree for L2 discretisation of the Poissonequation, from the UFL article.
Parallel Computing. In preparation for embracing future su-percomputing hardware architectures, which will adopt multi-ple non-CPU accelerators per compute node, research efforts inthe subject of HPC have mainly focused on new programmingmethodologies that suit clusters with multi-accelerator nodes.Asynchronous intra-node data motion, pipelining and a mixtureof data and task parallelism have been found essential to theimplementation of highly scalable numerical kernels for clusterswith compute nodes having multiple Xeon Phi coprocessors orGPUs. Proof-of-concept experiments have been carried out onthe world’s No. 1 supercomputer, the Tianhe-2. Moreover, it isdemonstrated that elaborate hybrid programming can unleash thecomputing capacities of both CPUs and accelerators on heteroge-nous clusters, countering the common wisdom that CPUs shouldonly take care of communication and administration. In total,three journal papers and four conference proceedings papers onHPC were published in 2014. Three additional journal papersthat are based on the research work of 2014 will be published in2015.
Research and code development are also under way to applythe newly developed programming methodologies to computa-tional physiology, with subcellular and cellular calcium dynamicssimulations chosen as the first real-world applications. To en-courage and ease the adoption of the programming methodolo-gies by other researchers, initial work has started to develop anautomated code translator that takes as input annotated serial Ccode and produces as output hybrid MPI+OpenMP+CUDA code.
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Application software. In addition to generally useful computa-tional middleware, researchers at CBC are continually refiningand creating new solver software for specific purposes. Here arethe most central releases from 2014, in addition to FEniCS.
• cbcbeat – cardiac electrophysiology models with consis-tent discrete adjoint models, now extended with improvedRush-Larsen ODE schemes (formerly beatadjoint);
• cbcflow and cbcpost – a flexible framework for solvingthe incompressible Navier-Stokes equations and a postpro-cessing framework for transient FEniCS solvers (formerlyheadflow);
• chaospy 1.0 – numerical tools for performing uncertaintyquantification using polynomial chaos expansions and ad-vanced Monte Carlo methods (formerly PolyChaos andRoseDist joined into one mature project);
• dolfin-adjoint 1.4 – automatically derives adjoint and tan-gent linear models from FEniCS models, and allows to per-form sensitivity analysis, PDE-constrained optimization andstability analysis;
• FEniCS 1.4 – including HPC work in DOLFIN, mesh gener-ation in mshr, and high-order geometry work in the ufl anduflacs subprojects.
• libcutfem – tools for the cut finite element method for multi-physics problems where the boundary or interface is de-scribed by level-set functions;
• OpenTidalFarm 1.4 – software for tidal farm developers tooptimally design turbine farms (this release was a majorrewrite of the previous version);
• Moola 0.1.3 – an optimisation package written in Pythonwith a special focus on PDE-constrained optimisation prob-lems;
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Robust SolversIn 2014, the Robust Solvers project has focused on extendingand refining our research activities in automated development anduse of adjoint models, cut and composite finite element methods,dynamic adaptivity and meshing, and on developing robust newvariational formulations for elastic plates, beams and shells. As aresult, we are now using our simulation methodologies and infras-tructure in completely new application domains and in completelynew ways. With the recruitment of Valeriya Naumova, we havealso strengthened the team with expertise in machine learningand inverse problem regularization.
The Robust Solvers project has also been extraordinarily ac-tive in its scientific outreach activities in 2014: Anders Logg,together with long-term CBC collaborator Douglas Arnold, hasdeveloped the Periodic Table of the Finite Elements, an organi-zation of a wide range of types of finite elements into table form,analogous to the Periodic Table of the (Chemical) Elements. Thetable was described in SIAM News of November 2014, and acopy of the table was widely distributed to all SIAM News sub-scribers together with this issue. The table is also available atfemtable.org.
Figure 4: An example of an element (the Raviart-Thomas elementof polynomial degree 2 on triangles) from the Periodic Table ofthe Finite Elements.
A new project titled Automated uncertainty quantificationfor numerical solution of partial differential equations, hostedat Simula and awarded in 2014 by NordForsk, will build on theFEniCS and Chaospy simulation technologies developed in theCBC to establish a suite of generic tools for forward and inverseuncertainty quantification in the context of partial differentialequations. This new project will leverage and focus existingefforts within the CBC to enable rapid and easy developmentof more reliable numerical solvers across the complete range ofapplication domains.
Automated optimal control and generalized stability analy-sis The dolfin-adjoint methodology and software project (seewww.dolfin-adjoint.org), initiated in 2011, has been substantiallydeveloped and extended in 2014. This project automatically de-rives the discrete adjoint and tangent linear models from a forwardcomputational model written in FEniCS.
Adjoint and tangent linear models are key ingredients inmany algorithms of computational science: in 2014, we havefocused on automating the derivation of generalized stability the-ory. While classical stability theory focuses on the eigenvalues
of an operator linearized about some steady state, generalizedstability theory analyses the generalized eigenvalues associatedwith the propagator of the system, which maps perturbations ininitial conditions to perturbations in the final state. By examin-ing these values, such an analysis can describe and predict theperturbations that will grow maximally over finite time windows.
In addition, we have used dolfin-adjoint in a spectre of newapplication domains, ranging from biomedical applications suchas blood flow and cardiac electrophysiology and mechanics tonext-generation renewable energy applications such as tidal en-ergy. For instance, CBC researchers Simon Funke, Patrick Farrelland their coauthors have used dolfin-adjoint to analyze and op-timize models for the deployment of tidal turbines, leading tosimulated gains in power generation by as much as 50%. More-over, the high-performance electrophysiology software projectcbcbeat (cbcbeat.readthedocs.org), builds on dolfin-adjoint to au-tomatically generate adjoint models for a complete range of celland tissue models allowing for adjoint-based sensitivity analy-sis and optimisation of electrophysiology models. cbcbeat hasdemonstrated excellent weak scaling up to 55 billion degrees offreedom and thousands of cores on ARCHER, the UK National Su-percomputing Service. More details on the dolfin-adjoint projectis found in this year’s featured research article.
Figure 5: The leading perturbation to a double-diffusive salt fin-gering system computed using the generalised stability theoryfeatures of dolfin-adjoint.
Cut and multi-mesh finite element methods This year has seenthe culmination of many years of research on cut and compositefinite element methods. With such methods, the computationaldomain may be described via a set of non-matching meshes orvia fictitious domains described by surfaces or level sets. Suchmethods may offer significant advantages over single, conform-ing mesh methods for instance for handling large deformations orinternal discontinuities in the computational domain. Four jour-nal articles on these techniques applied to fluid flow scenarios,by CBC investigators Mats G. Larson, Andre Massing and An-ders Logg and their coauthors, have been published in prestigiousmathematical journals in 2014.
In addition, a new research direction has been set that ex-tends the methodology and simulation infrastructure from thecase of two overlapping meshes to the challenging and poten-tially game-changing case of an arbitrary finite number of meshes.We have coined the term multimesh finite element methods forthis simulation scenario. This work is spearheaded by AugustJohansson and Anders Logg, and the theoretical foundations areaccompanied by ready-to-use software features in the core FEn-iCS components, allowing for immediate deployment by otherCBC researchers and the extended scientific community.
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Figure 6: The flow around a rotating propeller simulated using amultimesh finite element method and the new FEniCS Multimeshfunctionality.
Error control and dynamic adaptivity The Robust Solvers projectis continuing its research into more reliable numerical methodsthrough a posteriori error estimation and control. In particular,we seek to extend our earlier results on automated error controlfor conforming discretization of stationary variational problems to
the non-conforming and time-dependent case within the remain-der of the CBC project period. A prerequisite for adaptivity anderror control for time-dependent variational formulations is effi-cient and scalable techniques for dynamic mesh refinement andinterpolation between dynamically changing meshes. In 2014,we have improved our algorithms for dynamic mesh adaptivity inthe FEniCS project, including extending serial algorithms to theMPI-parallel case. Moreover, enhanced interpolation schemeshave been studied in the context of the supermeshing method.
Robust finite element methods for elastic plates, beams andshells Elastic plates, beams and shells come with their ownset of simulation challenges. One example is the problem oflocking which is a term that describes the potentially dramaticunderestimation of the displacement and corresponding stressesof elastic structures under traction. In 2014, we have developednew, locking-free finite element methods for the Reissner-Mindlinplate, new formulations for curved beans and new models for lin-ear membrane shell problems. These results demonstrate oursolid and ongoing research activities targeting more robust fun-damental numerical methods.
Biomedical Flows and StructuresThe purpose of the BFS project is to apply the numerical methodsand software developed in the Computational Middleware andRobust Solvers projects in a few selected important applications,which have a potential to make an impact on clinical medicine.
Blood flow in the Circle of Willis. The first application concernsthe blood flow in the Circle of Willis, which is an arterial networkat the base of the brain. The project is motivated by the fact thatfive percent of the population develop diseased arteries, calledaneurysms, and that these aneurysms may rupture and lead toa fatal stroke. However, the risk of rupture is low, and surgicaltreatment of the aneurysms is complicated and risky. Assessingthe risk of rupture and deciding on the optimal treatment for eachaneurysm is therefore both clinically important and extremelychallenging.
Over the last decade, computational fluid dynamic (CFD) sim-ulations of ’patient-specific’ blood flow has grown to become awidespread tool in aneurysm research. Compared with a decadeago, when aneurysm CFD studies were conducted by fluid me-chanical experts, today the use of CFD in aneurysm research iswidespread, facilitated by commercial solvers as well as the now-routine availability of 3D angiography. The current widespreaduse of CFD, however, comes at the expense of methodologicalrigour which may be particularly misleading for aneurysms, be-cause, as we have shown earlier, the flow may be transitional,i.e. varying between laminar and turbulent. A novice use of CFDwould therefore quite easily result in significant errors.
A result of our focus on rigorous methodology and transi-tional flow has received attention even among the clinical re-search community. For instance, Valen-Sendstad and Steinman’sstudy "Mind the Gap: Impact of Computational Fluid DynamicsSolution Strategy on Prediction of Intracranial Aneurysm Hemo-dynamics and Rupture Status Indicators" was shortlisted for the
paper of the year in Americal Journal of Neuroradiology and wasamong this journal’s most read papers in 2014. The paper re-ceived a commentary by Professor Yiannis Ventikos emphasizing"Valen-Sendstad and Steinman, [which] documents in very ro-bust, quantifiable, and indisputable terms "how to do it right" ismost welcome and will certainly become indispensable guidancein the computational hemodynamics for aneurysms community. "The editors of the American Journal of Neuroradiology (AJNR),where the paper was published, seem to have grasped the po-tential impact of the paper and nominated it best research paperof the year. The paper was also featured in the 2014 Decemberedition of the AJNR digest and is on the cover of the special col-lection "Aneurysms and the American Journal of Neuroradiology:The Next 20 Years" by Michele E. Hackley Johnson. In summary,the clinical audience very much seem to have appreciated ourefforts in bringing rigour to the CFD community, not to mentionthe implications for our understanding of the underlying biologicalprocesses.
Figure 7: Image of aneurysms that appear on the front page ofAJNR
Cerebrospinal fluid flow. The second application addressed bythe BFS project concerns the oscillating flow of cerebrospinalfluid (CSF) in the cranio-cervical region, and the flow’s associa-tion with the development of syringomelia (cysts within the spinal
9
cord). Such cysts are often found in patients with the Chiari I mal-formation, a state characterized by having abnormal position ofthe cerebellar tonsils (i.e., the brain is somewhat sunken downin the neck). The abnormal position of the tonsils obstructs thenatural flow of CSF, and it is hypothesized that the abnormal flowpattern is a cause for syringomelia.
In 2014, Linge et. al. published a pilot study cranioverte-bral decompression in idealized geometries in the clinical journal"Journal of Neurosurgery" - our first paper in this clinical jour-nal with (among others) the internationally recognized neurosur-geon and Chiari expert John D. Heiss. Haughton and Mardalpublished an comprehensive review paper "Spinal Fluid Biome-
chanics and Imaging: An Update for Neuroradiologists", a pa-per that has among the 10 most read papers in the journal in2014. Støverud defended her thesis concerning the relation-ship between the Chiari I malformation and syringomyelia with inparticular two important observations based on comprehensivenumerical analysis1 (i) the intracranial cerebrospinal fluid flowplays an significant role for the cervical fluid flow and (ii) thatthe porosity of the spinal cord and the protective pia membraneare crucial for understanding the biomechanics of the spinal cord.It is also remarkable that all the simulations are performed withFEniCS, which is now capable of large-scale simulations of bothfluid and solid mechanics problems.
CBC@NTNUThe Biomechanics Division at the Department of Structural Engi-neering at the Norwegian University of Science and Technology(NTNU), (or CBC@NTNU for short) has traditionally been involvedin research projects related to cardiovascular biomechanics.
For a number of years we have been developing a net-work model for the cardiovascular system. This model cur-rently includes features such as features like lumped mod-els for the heart and terminal vessels, state of the art nu-merical methods, and 1D models for larger veins and arter-ies. The model software is designed to allow flexible networkdefinitions. An important recent development is the incorpo-ration of the network model in a spectral expansions frame-work to allow for stochastic variation in all model parameters.In July 2014 the code was launched as Stochastic ArterialFlow Simulations (STARFiSh) and made available publicly at(http://folk.ntnu.no/vinzenz/STARFiSh-Homepage/).
Several international presentations on the developments re-lated to STARFiSh were given in 2014, and a paper in Interna-tional Journal for Numerical Methods in Biomedical Engineeringwas accepted.
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
Time s
60
80
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120
140
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180
Pre
ssuremmHg
age 19-75
Figure 8: Impact of of age-related changes in the arterial tree onthe pressure in the ascending aorta simulated with STARFiSh.
80°60
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mmHg
4 8 12 16
Time s
200
Internal Carotid Artery
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Pressure
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4 8 12 16
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Femoral Artery
Figure 9: Changes of pressure in the carotid and femoral ar-teries due to gravitational effects during a head-up tilt test inthe absence of neuronal blood pressure control, simulated withSTARFiSh.
ascending aorta
aorticarte
ries
organ arterie
s
right arm
left arm
right leg
left leg
0.0
0.2
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0.8
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age 19
age 75
point ofinflection
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ssuremmHg
0.0 0.8Time s
40
20
Ascending Aorta - backward pressure
timing
amplitude
carotid &
shoulder
Figure 10: Sensitivity analysis of the arterial system to investi-gate the impact of arterial stiffening in different arterial groups onthe backward propagating pressure wave in the ascending aorta,performed with the coupling of STARFiSH and chaospy-toolbox.
1300 000 CPU hours on Abel
10
Cardiac ComputationsThe Cardiac Computations (CC) project in CBC is mainly con-tained in the Computational Cardiac Modeling (CaMo) departmentat Simula, which is also closely connected to the Center for Cardi-ological Innovation (CCI), a center for research-based innovationfunded by the Research Council of Norway. Through 2014, theresearch activity continued to be driven by the clinical and indus-trial needs of the CCI partners, which includes Oslo UniversityHospital, GE Vingmed Ultrasound, and Medtronic. The collabora-tion is an extremely interesting opportunity for Simula’s cardiacmodeling activity, with the potential to bring our computationalmodels into direct clinical use. The activity in the department hasbeen adjusted to fit better with these clinically driven goals , andsubstantial resources are being put into tools for data assimila-tion and construction of computational models from clinical data.Significant progress has been made in this area, computationalmodels are now generated semi-automatically from ultrasoundimages, and are well integrated with the clinical data stream andworkflow.
In addition to the clinically oriented work funded and drivenby the CCI, the CaMo department has activities on fundamentalphysiological phenomena, and also on software and numericalmethods development that are closely related to the other CBCprojects. We have continued to improve and extend the in-houseelectro-mechanics software Pulse, one recent expansion beingthe ability to incorporate growth and remodeling of the heart mus-cle. The heart will grow and change its structure in response to achanging mechanical environment, and such growth and remod-eling is a key determinant of heart failure (HF) development. Theend-goal of therapeutic interventions for HF is often to stop orreverse this process, and to do this successfully it is important tounderstand the fundamental driving mechanisms. Computationalmodels are promising tools to obtain this understanding, but alsoface substantial challenges, for instance the large span of rele-
vant time scales in these problems. Together with collaboratorsat UC Berkeley and Michigan State University, we have extendedour solver tools with a framework suitable for modeling growth,and are currently testing the models on a number of well studiedclinical cases.
In parallel with the development of Pulse, we are workingon replacing it with a new solver based on the Fenics finite el-ement framework. Several prototypes of this solver have beendeveloped and used during the course of the CBC, but only fairlyrecently have they evolved to have a feature list and flexibilitycomparable with our existing solvers. Through 2014, researchersfrom CaMo/CBC developed one such solver for the STACOM LVMechanics Challenge, being organized at the workshop Statis-tical Atlases and Computational Modeling of the Heart, orga-nized in Boston, MA, 18 September 2014. The eight participat-ing groups all built mechanical models based on partial patientdata sets, including essentially geometries and pressures but nostresses or strains. Predicted stress and strain fields were thencompared with the reference data. The Fenics based contribu-tion from CaMo/CBC won the the challenge, the solver has beenmade available as open source software, and now forms the basisfor much of the CCI related patient specific modeling.
Although software tools and clinical workflows have re-ceived most attention through 2014, several studied have beenconducted that address fundamental physiological questions. Infact, the largest volume of published results from the group be-long to this category. This is also the case for the one PhDstudent who graduated from the CC project in 2014. BernardoLino de Oliveira defended his thesis titled Computational modelsof Cardiac Electromechanics in November. The topic of the thesiswas electro-mechanical interactions in the heart, with the mainfocus on mechano-electric feedback effects by which mechani-cal abnormalities can lead to life threatening disturbances of theelectrical activity.
11
Automatic derivation of adjoint andtangent linear modelsToday, computer simulations play a central role in nearly all dis-ciplines of science and engineering. Compared to physical exper-iments they are non-intrusive, cheap, easily repeatable and cansimulate a wide range of scales. In addition, they can provideinformation that goes beyond the capabilities of physical experi-ments, in particular how sensitive the system is with respect toinfinitesimal small changes in its inputs.
Why is this sensitivity information so important? First, itprovides insight on how a physical system responds to changesin its inputs. Answering this question is critical in a number ofbranches in science and engineering. One extremely complex andhigh profiled example is in climate science, where scientists wantto understand how the earth’s climate responds to the increasingcarbon dioxide emissions. Another example, from the biomedicaldomain, is illustrated in Figure 11. Second, sensitivities are akey component for performing model based optimization. Opti-mization is used in a wide range of applications, including optimaldesign, data assimilation, and optimal control. In a biomedicalcontext, model based optimization can be used to design patient-specific therapies that achieve the desired effect with minimalnegative side effects. Finally, sensitivities can be used to deter-mine stability properties of physical systems and for automatederror analysis.
Figure 11: Sensitivity analysis for a computational model of thecerebrospinal fluid in the central canal of a Chiari patient. Left:speed of cerebrospinal fluid on different slices through the spinalcanal; red indicates high speed, blue low speed. Right: sensitivityof the flow energy with respect to changes to the surface; redindicates high sensitivity, blue low sensitivity.
There are two common mathematical techniques for effi-ciently computing sensitivities: the tangent linear approach andthe adjoint approach. Both consider the computational model asa mathematical function with, possibly many, inputs and outputs.The tangent linear model computes sensitivities by propagatinga perturbation from the model inputs to its outputs and is bestsuited for models with few inputs and many outputs. The adjointmodel propagates a perturbation from the output backwards tothe inputs - that is it propagates information backwards in time.This makes the adjoint model very efficient if the model has fewoutputs but many inputs.
Unfortunately, the development of adjoint and tangent mod-els is often prohibitively challenging. For a complex system suchas a weather model it can require decades of development effort.Therefore, tools for automating adjoint and tangent linear mod-els are considered a significant challenge in scientific computing.Indeed, it has been stated in The Art of Differentiating Com-puter Programs: An Introduction to Algorithmic Differentiation,U. Naumann (2012) that:
the automatic generation of optimal (in terms of ro-bustness and efficiency) adjoint versions of large-scale simulation code is one of the great open chal-lenges in the field of High–Performance ScientificComputing.
Over the last two years, researchers at Simula Research Labo-ratory, Oxford University and Imperial College London have de-veloped a new approach for automatically deriving and imple-menting adjoint and tangent linear models2. The resulting soft-ware, dolfin-adjoint, achieves this by automatically analyzing andexploiting the mathematical structure inherent in finite elementmethods, and the high-level approach of the FEniCS project andits symbolic representation of the problem equations3, see fig-ure 12.
Symbolic forward equations
Symbolic adjoint equations
Symbolic derivation (dolfin-adjoint)
Adjoint code
Forward codeCode generation (FEniCS)
Code generation (FEniCS)
Figure 12: dolfin-adjoint automatically derives and implementsadjoint and tangent linear models. It inspects the high-level prob-lem specification provided by the user and symbolically derivesthe associated adjoint or tangent linear versions. It then uses theFEniCS framework to solve both the original and the adjoint ortangent linear problems.
The high degree of automation makes dolfin-adjoint straight-forward and fast to use. In many cases, only a few lines of codeare required to obtain the adjoint or tangent linear model. In ad-dition, we have observed that dolfin-adjoint achieves the optimaltheoretical efficiency and scales from a laptop to thousands ofcores on a supercomputer. The software is now installed andused on two of the world’s fastest supercomputers: Stampedeand ARCHER.
2Automated derivation of the adjoint of high-level transient finite element programs, P. E. Farrell, D. A. Ham, S. W. Funke and M. E. Rognes(2013), SIAM Journal on Scientific Computing 35.4, pp. C369-C393
3Unified Form Language: A domain-specific language for weak formulations of partial differential equations, M. S. Alnæs, A. Logg, K. B.Ølgaard, M. E. Rognes, G. N. Wells (2014), ACM Transactions on Mathematical Software, 40(2), Article 9
12
In this year, we have published an extension of dolfin-adjointfor performing stability analysis4. Stability analysis investigatesthe response of the physical system to input perturbations. Moreprecisely, it computes the perturbations which grow quickest overtime, see Figure 13. This information can then be used to decideif the system is stable or unstable, that is, if small perturbationsare dampened by the system or if they grow over time. Stabil-ity analysis requires solving both the adjoint and tangent linearmodels, which makes their implementation challenging. By usingthe high-level approach of dolfin-adjoint, we were able to entirelyautomated this process. As a result, dolfin-adjoint users can nowperform stability analysis studies by adding only a few extra linesto their simulator codes.
Figure 13: Stability analysis for a reaction-diffusion problem withtwo chemical species. Left: the initial concentration of onespecies. Middle: the concentration after 2000 time units. Right:the perturbation to the initial concentration that grows optimallyin time. The optimal perturbation is localised to the square topromote preferential propagation in certain directions.
Another ongoing effort are improvements to the optimizationframework in dolfin-adjoint. With these improvements, it is nowpossible to solve complex three-dimensional optimisation prob-lems, see figure 14. Here, the aim is to design the optimisationmethods such that the performance of the optimisation does notdegenerate when using high-fidelity models.
Figure 14: Application of dolfin-adjoint to compute the optimaldesign of a heat dissipating device. The image shows a slicethrough the optimized design.
4A framework for the automation of generalised stability theory, P. E. Farrell, C. J. Cotter and S. W. Funke (2014), SIAM Journal on ScientificComputing 36.1, pp. C25–C48
13
The Simula School of Research and In-novationCBC maintains its tight links with the Simula School of Researchand Innovation (SSRI). All PhD students and postdoctoral fellowsat CBC are affiliated with SSRI, which provides enhanced sup-port in supervision and mentoring, as well as special courses ontopics such as entrepreneurship and communication of scientificresearch.
For several years, SSRI has worked on expanding the ex-isting research collaboration with University of California, SanDiego (UCSD) to include a substantial educational component.Through 2014, two particularly important events were the debutof a summer school on Computational Physiology, which includedtwo weeks of intensive instruction at Fornebu in June, individualproject work through the summer, and one week of guided projectpreparation and presentation in La Jolla in August. The summerschool was a collaborative effort between SSRI, UCSD and theUniversity of Oslo (UiO), and is scheduled to continue as an annualevent. In 2014, 14 participants from 11 different nationalitiescompleted the summer school, which also included a number ofinvited guest lectures with much higher attendance. The schoolis scheduled to continue as an annual event, which also countsas a regular class for students registered at the UiO.
An even more exciting event for the SSRI-UCSD collabora-tion took place in the fall of 2014, when it was announced that,from 2015, the Norwegian Ministry of Research and Education hasdecided to fund a substantial trilateral collaborative PhD program.The scientific focus will be on computational medicine with par-ticular applications in cardiac physiology and neuroscience. Thefunding will support 8 new PhD positions on collaborative projectsinvolving Simula, UiO, and UCSD, in addition to travel grants andresearcher exchange visits. The funding provides an excellentopportunity to further strengthen the research and educationalcollaboration between Simula and UCSD. This collaboration, inwhich CBC researchers have played key roles, is already sub-stantial. In total, since 2011, Simula researchers have spentabout five working years at the UCSD campus in La Jolla.
University TeachingCBC researchers contribute substantially to university teach-ing. The Simula-based staff mostly lecture at the University
of Oslo, while our collaborators and adjunct scientists teach atnumerous institutions, including NTNU (mechanics, biomechan-ics), Chalmers University, UCSD (computer science, bioengineer-ing), Oxford University (numerical analysis, computing), Universityof Umeå (mathematics), Norwegian University of Life Sciences(mathematics) and Telemark University College (mathematics,physics).
CBC continues to develop programming courses for largegroups of students at the University of Oslo, in particular the in-troductory programming course for science students (INF1100)and the more advanced course on problem solving with script-ing tools (INF3331). On graduate level, CBC researchers giveadvanced courses on numerical methods, fluid mechanics, andbiomedical modeling.
The FEniCS software has proven to be an excellent platformfor teaching finite element methods and related topics, and isused extensively in the recently revised course on Numerical So-lution of Partial Differential Equations (INF5620) at the Universityof Oslo. This course has been well received at the Departmentof Informatics, and attracts a large number of students for anadvanced numerical course.
As described in previous reports, CBC researchers are cen-tral in the Computers in Science Education ((CSE) program at UiO.The program has received substantial attention nationally and in-ternationally, has received several awards, and is a pioneeringeducational initiative. The aim of the program is to partly replacethe traditional, analytical pen and paper approach with numericalprogramming, and thereby enable students to consider more ad-vanced, interesting, and relevant problems at an earlier stage. Webelieve that the shift towards a more computational approach alsoenables a more in-depth understanding of the underlying physics,since the focus of teaching can shift from advanced algebra andanalytical tools to a more in-depth study of the physical problem.In spite of the very promising results obtained so far, CSE is along-term effort, which requires continued focus on developingtextbooks, teaching infrastructure, and the mindset of Universityprofessors. CBC continues the active involvement in this project.Increasing the awareness of software quality is one particulararea where CBC researchers have unique competence to assistcourse developers at the University.
14
In the appendices below, we use several abbreviations:
ADM Administrative supportBFS Biomedical Flows and Structures (CBC project)CBC Center for Biomedical ComputingCC Cardiac Computations (CBC project)CCI Center for Cardiological Innovation (CCI)
(Center for Research-based Innovation)CM Computational Middleware (CBC project)DoD U. S. Department of DefenceF FemaleHOST Simula Research Laboratory (SRL)KimS Kim Scholarship Council and Chonging UniversityM Male
NTNU Norwegian University of Science and TechnologyOxford Oxford University CollegeRCN Research Council of NorwayRS Robust Solvers (CBC project)SRL Simula Research Laboratory (CBC host institution)SSRI Simula School of Research and InnovationUCSD University of California, San DiegoUiO University of OsloUoS University of SiegenUoT University of TorontoUMB Norwegian University of Life SciencesUmU Umeå UniversityUW University of Wisconsin
Staff
0
2
4
6
8
10
12
14
16
18
Senior
scien!st
Post docs Ph.D.
Students
Tech. and
adm.
Guest
researchers
Development of staff (man-years)
2007
2008
2009
2010
2011
2012
2013
2014
25 %
29 %
31 %
11 %4 %
Staff man-year 2014
Senior scien!st
Post docs
Ph.D. Students
Tech. and adm.
Guest researchers
15
Senior scientists 2014: 23 people, 10.3 man-years
Name Gender Period CBC share Project Funding
Anders Logg M 01.04.2007-31.12.2014 50% RS, CM CBCAndrew D. McCulloch M 01.07.2009-30.06.2015 20% CC 50% UCSD + 50% CBCAslak Tveito M 01.08.2007-31.03.2017 25% CC HOSTBjørn Fredrik Nielsen M 01.08.2007-31.12.2014 20% CC CCI, RCN grant 203489/O30Bjørn H. Skallerud M 24.05.2007-31.03.2017 25% BFS NTNUGlenn Terje Lines M 01.08.2007-31.03.2017 100% CC CCI, RCN grant 203489/O30Hans Petter Langtangen M 01.04.2007-31.03.2017 30% CM, RS, BFS HOSTJoakim Sundnes M 01.04.2007-31.03.2017 100% CC, RS CBC, RCN grant 205349/F30Kent-Andre Mardal M 01.01.2009-31.03.2017 60% BFS, CM, RS, CC RCN grant 209951/F20Leif Rune Hellevik M 24.05.2007-31.03.2017 50% BFS NTNUMarie E. Rognes F 01.06.2012-31.03.2017 100% RS, CM CBCMats G. Larson M 01.04.2007-30.06.2015 50% CM, RS 50% UmU + 50% CBCMikael Mortensen M 01.01.2008-30.06.2015 45% RS, CM, BFS 55% UiO + 45% CBCMolly Maleckar F 01.01.2009-31.12.2014 10% CC CCI, HOSTOle M. Lysaker M 01.01.2012-31.12.2014 20% CC CCI, RCN grant 203489/O30Patrick Farell M 15.09.2012-24.02.2016 35% RF, CM 50% Oxford + 50% CBCSamuel Wall M 01.09.2012-30.06.2016 75% CC CCI, RCN grant 203489/O30Scott Baden M 11.06.2007-30.06.2015 20% CM 50% UCSD + 50% CBCStuart Clark M 01.01.2008-31.12.2014 20% CM, RS KalkuloSvein Linge M 01.04.2007-30.06.2015 20% BFS CBCVictor Haughton M 15.06.2008-30.06.2014 20% BFS 70% UW + 30% CBCVictorien Prot M 01.09.2008-31.12.2014 50% BFS NTNUXing Cai M 01.04.2007-31.03.2017 100% CM, RS, CC 75% CBC + 25% RCN grant 214113/F30
Postdoctoral candidates 2014: 14 people, 11.7 man-years
Name Gender Period CBC share Project Funding
Andre Massing M 20.06.2012-31.12.2014 100% RS, CM CBCAugust Johansson M 01.01.2014-31.12.2016 100% RS CBCJohan Elon Hake M 01.01.2012-31.12.2014 79% CC, CM CCI, RCN grant 205349/F30Johannes Langguth M 01.10.2012-31.12.2014 100% CM RCN grant 214113/F20Jussi Köivumaki M 01.01.2012-31.12.2014 100% CC CCI, RCN grant 203489/O30Kristian Valen-Sendstad M 21.05.2011-01.10.2016 100% BFS CBCKristin McLeod F 01.10.2013-30.09.2015 100% CC CCI, RCN grant 203489/O30Kristin Tøndel F 01.01.2014-31.12.2016 65% CC EU FP7 grantMartin Alnæs M 01.04.2011-01.05.2015 100% CM, RS, BFS RCN grant 209951/F20Namit Gaur M 01.07.2012-30.06.2015 100% CM, RS SSRIOmar al-Khayat M 28.05.2010-31.03.2014 100% CM, RS SSRISimon Funke M 01.11.2013-31.10.2015 79% CM, RS CBCSimone Pezzuto M 01.08.2013-31.07.2015 83% CC RCN grant 205349/F30Valeriya Naumova F 01.01.2014-31.12.2015 33% RS HOST
16
PhD students 2014: 18 people, 12.6 man-years
Name Gender Period CBC share Project Funding
Benjamin Kehlet M 01.09.2010-15.09.2015 58% RS UiO + CBCBernardo Lino de Oliveira M 01.06.2011-31.08.2014 100% CC CBC + RCN grant 205349/F30Fahrsad Goudarzi M 10.01.2010-01.04.2014 100% BFS NTNUGabriel Balaban M 01.02.2013-17.04.2016 100% CM, RS CBCHenrik Nicolai Finsberg M 01.10.2014-30.09.2017 100% CC RCN grant 205349/F30Jérémie Lagravière M 01.10.2014-30.09.2017 100% CM RCN grant 231746/F20Jonathan Feinberg M 15.08.2009-31.12.2014 20% CM, RS EU FP7 grant + CBCKaren-Helene Støverud F 01.01.2010-31.05.2014 100% BFS UiO + CBCKartik Jain M 01.06.2013-31.12.2016 100% BFS UoSMagne Nordaas M 01.07.2013-30.06.2016 100% CM, RS CBCMiroslav Kuchta M 15.09.2012-14.09.2015 100% BFS UiOMohammed Owais Khan M 01.09.2013-01.09.2015 100% BFS 90% UoT + 10% CBCMohammed Sourouri M 01.08.2012-31.07.2015 100% CM, RFS RCN grant 214113/F20Ole L. Elvetun M 01.01.2012-31.12.2015 100% BFS UMBRolv Erlend Bredesen1 M 01.04.2007-13.03.2014 0% CM 90% UiO + 10% CBCSiri Kallhovd F 01.10.2012-30.09.2015 100% CC CCI, RCN grant 203489/O30Vinzenz Eck M 01.10.2013-01.10.2017 100% BFS NTNUØyvind Evju M 10.04.2012-09.04.2015 100% BFS RCN grant 209951/F20
Technical and administrative staff 2013: 16 people, 4.7 man-years
Name Gender Period CBC share Project Funding
Ada Ellingsrud F 01.06.2014-30.08.2014 52% CBC@Simula CBCAslak Bergersen M 01.06.2014-30.08.2014 64% CBC@Simula CBCBenjamin Kehlet M 01.03.2014-01.05.2014 100% CBC@Simula CBCInna Olafsson F 01.01.2014-31.12.2014 10% ADM CBCIben Cathrine Simonsen F 15.02.2013-14.02.2014 100% CBC@Simula CBCJohannes Hofaker Ring M 01.01.2008-31.03.2017 100% CBC@Simula CBCJonas Van Den Brink M 01.06.2014-30.08.2014 52% CBC@Simula RCN-209951/F20Jonathan Feinberg M 01.04.2014-31.12.2014 66% CM, RS EU FP7 grant, RCN 23884/O30Karl Erik Holter M 01.06.2014-30.08.2014 45% CBC@Simula CBCMartine Enger F 01.06.2014-30.08.2014 35% CBC@Simula CBCMonica Eriksen F 01.01.2014-31.12.2014 5% ADM CBCNina Lillevand F 01.01.2013-31.12.2014 5% ADM CBCSjur Urdson Gjerlaug M 01.06.2012-31.12.2014 100% CBC@CCI CCI, RCN grant 203489/O30Tom Andreas Nærland M 01.06.2014-30.08.2014 34% CBC@Simula CBCTom David Atkinson M 01.05.2007-31.03.2017 50% ADM CBCWei Zhang M 01.04.2014-30.09.2014 100% CBC@Simula EU FP7 grant, RCN 23884/O30
Guest researchers 2014: 6 people, 1.6 man-years
Name Gender Period CBC share Project Funding
Alexandra Antoniuk F 18.07.2014-22.08.2014 100% CM EUMLS/home institutionAndrei Pylypenko M 14.11.2014-05.12.2014 100% CM EUMLS/home institutionDajilang Lei M 01.03.2014-01.03.2015 100% CM KimSDmytro Sadovyi M 01.07.2014-31.08.2014 100% CM EUMLS/home institutionTimo Koch M 25.04.2014-25.07.2014 100% CM Home institutionVoldemyr Tesko M 17.07.2014-15.10.2014 40% CM EUMLS/home institution
1R. Bredesen has had a leave of absence during the period 01.01.2013-31.12.2014.
17
Development of staff (no. of individuals/man-years)
Position 2007 2008 2009 2010 2011 2012 2013 2014
Senior scientists 19/7.1 28/13.4 28 /13.8 24/10.5 20/9.0 23/9.2 23/11.4 22/10.3Post docs 8/4.1 17/8.8 14/10.1 16/9.9 12/7.7 13/9.6 13/10.2 14/11.7PhD students 7/3.2 16/11.3 18/13.7 19/15.9 20/11.3 16/10.3 17/12.5 18/12.6Technical and administrative 10/3.5 12/5.8 11/4.1 9/3.3 10/2.8 13/3.6 16/4.9 16/4.7Guest researchers 0/0 2/0.7 2/1.5 2/0.5 1/0.4 3/0.8 6/2.2 6/1.6
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
2007 2008 2009 2010 2011 2012 2013 2014
Guest researchers 0 0,7 1,5 0,5 0,4 0,8 2,2 1,6
Tech. and adm. 3,5 5,8 4,1 3,3 2,8 3,6 4,9 4,7
Ph.D. Students 3,2 11,3 13,7 15,9 11,3 10,3 12,5 12,6
Post docs 4,1 8,8 10,1 9,9 7,7 9,6 10,2 11,7
Senior scien!st 7,1 13,4 13,8 10,5 9 9,2 11,4 10,3
0
5
10
15
20
25
30
35
40
45
50
CBC man-years
Figure 15: The accumulated man-years of staff associated with the center during 2007-2014
2007 2008 2009 2010 2011 2012 2013 2014
Guest researchers 0 0,7 1,5 0,5 0,4 0,8 2,2 1,6
Tech. and adm. 3,5 5,8 4,1 3,3 2,8 3,6 4,9 4,7
Ph.D. Students 3,2 11,3 13,7 15,9 11,3 10,3 12,5 12,6
Post docs 4,1 8,8 10,1 9,9 7,7 9,6 10,2 11,7
Senior scien!st 7,1 13,4 13,8 10,5 9 9,2 11,4 10,3
0 %
10 %
20 %
30 %
40 %
50 %
60 %
70 %
80 %
90 %
100 %
Development of CBC staff
Figure 16: The graph show the percentage of man-years associated with the different employee categories during the center period(2007-2014).
18
Accounting and BudgetBelow, we present the main figures regarding the CBC budget and funding. The operating revenues and expenses represent the fundingand cost that we control our selves. The income in kind and operating expenses in kind presents representative figures from activitiesand 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 16% of the total funding available for CBC activities in2014, instead of the approximately 59% that was originally intended in our proposal. As previously mentioned in these reports, wehave been fortunate to secure a substantial amount of funding to the center through other RCN grants, other national and internationalfunding opportunities, and collaboration with various research institutions.
The 2014 accounts show a surplus of 3 591 kNOK, that we will transfer to the 2015 budget. The 2013 surplus of 6 698 kNOK,have thus been reduced by 3 107 kNOK during 2014. This is mostly an effect of our host institutions policy to calculating and reportingactual costs for their personell. The reported indirect costs for CBC have thus more than doubled from 2013 (3,709) to 2014 (9,416),even though the cost of labour have decreased slightly.
This only accentuates the challenge of bridging the economical gap between how the project was budgeted in 2007, when the costof a man year was between 600 and 700 kNOK, and the present day cost of running the center. Now (2014) a PhD/postdoc cost 938kNOK, 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 forthe center.
We try to keep this in mind when we recruit new candidates, in order to find the persons that shares our commitment to excellencein research, and can enhance our research endeavors.
2007 2008 2009 2010 2011 2012 2013 2014
Other opera!ng expenses 1 864 2 430 1 548 219 930 958 1 427 1 563
Equipment 0 0 0 144 233 209 249 195
Outsourcing R&D 83 866 0 614 1 132 826 455 394
Indirect cost 1 996 3 255 3 938 3 970 4 509 2 733 3 709 9 416
Cost of labour 8 388 16 330 17 287 14 039 12 407 15 510 16 081 15 661
0 %
10 %
20 %
30 %
40 %
50 %
60 %
70 %
80 %
90 %
100 %
Distribu on of cost
Figure 17: The graph shows how the funding have been used during 2007-2014
38 %
22 %
17 %
12 %
7 %4 %
In kind contribu!on; 38%
RCN other funding; 22%
RCN CoE funding; 17%
Simula; 12%
Alloca!on from earlier
years 7%;
47 %
14 %
10 %
10 %
5 %
6 %5 %2 %1 %0 %0 %
CCI; 47%
NTNU; 14%
Simula and subsidiaries
(SSRI, SI) 10%UiO; 10%
UMB; 6%
U of Siegen; 6%
UoT; 5%
UmU; 2%
University of Oxford;
1%
Figure 18: Source of CBC funding (left) and in-kind funding (right) for 2014.
19
Operating Revenues Note Account 2013 Budget 2014 Account 2014 Budget 2015
RCN CBC funding 7,500 7,500 7,500 5,113Allocation from earlier years 4,495 6,698 6,698 3,591Host - Simula Research Laboratory 5,761 5,190 5,190 5,512Other income RCN 1 10,170 9,547International funding 2 694 1,884Other incomeSum operating revenues 28,620 19,388 30,819 14,216
Income in kind:
CCI 3 7,874 7,923Kalkulo AS 640University of Oxford 4 188Norwegian University of Life Sciences 5 906 938NTNU 6 2,129 2,345SSRI, SI and Simula 7 4,606 1,722Imperial College London 227UCSD 8 0 66University of Oslo 9 2,912 1,638University of Umeå 10 181 281University of Toronto 11 859 855University of Wisconsin 24University of Siegen 12 938Simula Innovation 218Sum income in kind 20,575 16,894Total income 49,194 19,338 47,713 14,216
Operating Expenses Note Account 2013 Budget 2014 Account 2014 Budget 2015
Cost of labour 16,081 10,000 15,661 10,500Indirect costs 13 3,709 2,435 9,416 2,616Outsourcing of R&D services 455 729 394 250Equipment 249 100 195 150Other operating expenses 14 1,427 1,166 1,563 700Sum operating expenses 21,921 14,430 27,228 14,216
Operating expenses in kind:
Cost of labour 16,123 11,826Indirect costs 13 4,031 3,379Outsourcing of R&D services 218Other operating expenses 14 203 1,689Sum operating expenses in kind 20,575 16,894Total operating expenses 42,496 14,430 44,122 14,216Year end allocation 6,698 4,958 3,591
Notes to accouning and budget:
Note 1: Other income RCN (= 9,547):
205349/F30: In Silico Heart Failure - Tools for Accelerating Biomedical Research (= 2,843)209951/F20: Patient-Specific Mathematical Modeling with Applications to Clinical Medical: Stroke and Syringomyelia (= 3,066)214113/F20: User-friendly programming of GPU-enhanced clusters via automated code translation and optimization (= 2,712)238834/O30: EMC2, Embedded Multi-Core Systems for Mixed Criticality Applications in Dynamic and Changeable Real-Time Environments (= 691)231746/F20: PRoductivity and Energy-efficiency through Abstraction-based Parallel (= 235)
Note 2: International funding (= 1 884):Travelgrant (to Martin Alnæs) from Imperial College London (= 20)
20
Marie Curie IRSES project (EUMLS) (= 101)Scolarship (to Dajilang Lei) from Kim Scholarship Council and Chonging University of Post and Telecommunication; China (= 782)SISC (= 55)Artemis (= 138)EU FP7 611823: VP2HF (= 788)
Note 3: Contributions in kind from Center for Cardiological Innovation (CCI), RCN 203489/O30 (= 7,923):Funding researchers, postdocs and research engineers (G. Lines, M. Maleckar, O. M. Lysaker, B. F. Nielsen, S. Wall, S. Gjerald, S. Kallhovd, K. McLeod andJ. Koivumäki).
Note 4: Contributions in kind from University of Oxford (= 188):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 (= 938):One PhD student, equaling 1 man-years (O. Elvetun).
Note 6: Contributions in kind from the Norwegian University of Science and Technology (NTNU) (= 2,345):NTNU has financed in kind a total of 1.25 man-years of senior scientists (V. Prot, Prof. B. Skallerud and Prof. L. R. Hellevik) and the equivalence of 1.25man-year of PhD students (V. Eck and F. Goudarzi).
Note 7: Contributions in kind from the Simula School of Research and Innovation (SSRI), Simula Innovation (SI) and Simula (= 1,722):Simula Research Laboratory’s subsidiary Simula School of Research and Innovation (SSRI) is responsible for all educational activities in Simula ResearchLaboratory.Simula Research Laboratory’s subsidiary Simula Innovation (SI) Simula Innovation AS is a commercialisation company owned by Simula Research LaboratoryAS. Their goal is to create national and international demand for ideas and long term research collaboration with Simula Research Laboratory, and todemonstrate that the national commitment to the Simula model is innovative, international and creates value.Simula and its subsidiaries has financed the work of 1.31 man-years of CBC associated research activity. 0.86 man-years postdocs (N. Gaur and V. Naumova)and 0.45 researchers (X. Cai and A. Tveito).
Note 8: Contributions in kind from University of California, San Diego (UCSD) (= 66):Funding of senior researchers (S. Baden, A. McCulloch).
Note 9: Contributions in kind from the University of Oslo (= 1,638):Two PhD students, equaling 1.5 man-years (B. Kehlet and M. Kuchta), and 0.25 man-years research scientist (M. Mortensen).
Note 10: Contributions in kind from the University of Umeå (= 281):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 (= 855):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 (= 938):Funding of a PhD position equaling 1 man-year (K. Jain).
Note 13: Indirect costs cover the expenses of offices, administrative support and infrastructure for all employees.
Note 14: Other operating expenses include the cost of scientific equipment, travelling, workshops, seminars, and visitors.
21
PublicationsCBC only reports publications where a significant part of the research has been funded by CBC. By this we mean that at least one ofthe authors of the reported publications must have his/her main affiliation with CBC, and has contributed to the publication as laid outin 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 fora 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 TOTAL
Articles in International Journals 22 31 49 35 27 30 29 36 259Refereed Proceedings 8 9 28 19 19 11 15 6 115Proceedings without referee 0 10 10 6 0 1 0 2 29Books 0 1 1 2 1 2 1 1 9Edited Books 0 1 3 0 0 1 2 0 7Chapters in books 2 3 6 4 1 27 1 0 44Technical Reports 1 0 0 0 1 0 1 0 3Manuals 3 0 1 0 0 0 1 0 5Talks 51 76 69 70 51 63 54 55 489PhD theses 0 2 5 1 3 5 1 2 19Posters 0 0 0 0 5 8 3 0 16
Ar�cles in Int. Journals
Refereed Proceedings
Proc. without referee
Books
Edited Books
Chapters in books
Technical Reports
Manuals
PhD theses
2014
Annual variations in CBC publication profile 2007–2014.
Articles in International Journals
[1] M. S. Alnæs, A. Logg, K. B. Ølgaard, M. E. Rognes and G.N. Wells. Unified Form Language: a Domain-Specific Lan-guage for Weak Formulations of Partial Differential Equa-tions. ACM Transactions on Mathematical Software, vol.40(2), 2014.
[2] D. Arnold and A. Logg. Periodic table of the Finite Elements.SIAM News, vol. November issue, 2014.
[3] A. G. Buchan, P. E. Farrell, G. J. Gorman, A. J. H. Goddard,M. D. Eaton, E. T. Nygaard, P. L. Angelo, R. P. Smedley-
Stevenson, S. R. Merton and P. N. Smith. The ImmersedBody Supermeshing Method for Modelling Reactor PhysicsProblems With Complex Internal Structures. Annals of Nu-clear Energy, vol. 63, pp. 399-408, 2014.
[4] E. Burman, S. Claus, P. Hansbo, M. G. Larson and A. Mass-ing. CutFEM: Discretizing Geometry and Partial DifferentialEquations. Int. J. Numer. Meth. Eng., pp. 1-36, 2014.
[5] A. G. Edwards, E. Grandi, J. E. Hake, S. Patel, P. Li, S.Miyamoto, J. H. Omens, J. H. Brown, D. M. Bers and A.D. McCulloch. Non-equilibrium reactivation of Na+ currentdrives early afterdepolarizations in mouse ventricle. Circu-lation: Arrhythmia and Electrophysiology, 2014.
22
[6] P. E. Farrell, C. Cotter and S. W. Funke. A Framework for theAutomation of Generalised Stability Theory. SIAM Journalon Scientific Computing, vol. 36, pp. C25–C48, 2014.
[7] S. W. Funke, P. E. Farrell and M. D. Piggott. Tidal TurbineArray Optimisation Using the Adjoint Approach. RenewableEnergy, vol. 63, pp. 658-673, 2014.
[8] J. E. Hake, P. M. Kekenes-Huskey and A. D. McCulloch.Computational modeling of subcellular transport and sig-naling. Curr Opin Struct Biol, vol. 25C, pp. 92–97, 2014.
[9] P. Hansbo, M. G. Larson and K. Larsson. Variational formula-tion of curved beams in global coordinates. ComputationalMechanics, vol. 53, pp. 611-623, 2014.
[10] P. Hansbo and M. G. Larson. Finite element modeling ofa linear membrane shell problem using tangential differen-tial calculus. Computer Methods in Applied Mechanics andEngineering, vol. 270, pp. 1 - 14, 2014.
[11] P. Hansbo, M. G. Larson and S. Zahedi. A cut finite elementmethod for a Stokes interface problem. Applied NumericalMathematics, vol. 85, pp. 90 - 114, 2014.
[12] P. Hansbo and M. G. Larson. Locking Free QuadrilateralContinuous/discontinuous Finite Element Methods for theReissner-Mindlin Plate. Computer Methods in Applied Me-chanics and Engineering, vol. 269(-), pp. 381-393, 2014.
[13] A. Helgeland, K.-A. Mardal, V. Haughton and B. A. P.Reif. Numerical Simulations of the Pulsating Flow of Cere-brospinal Fluid Flow in the Cervical Spinal Canal of a ChiariPatient. Journal of Biomechanics, vol. 47(47(5)), pp. 1082-90, 2014.
[14] H. R. Hiester, M. D. Piggott, P. E. Farrell and P. A. Allison. As-sessment of Spurious Mixing in Adaptive Mesh Simulationsof the Two-Dimensional Lock-Exchange. Ocean Modelling,vol. 73, pp. 30-44, 2014.
[15] J. Koivumäki, R. Clark, D. Belke, C. Kondo, P. Fedak, M.Maleckar and W. R. Giles. Na+ Current Expression in HumanAtrial Myofibroblasts: Its Identity and Functional Conse-quences. Frontiers in Physiology, vol. 5(5), pp. 275, 2014.
[16] J. Koivumäki, G. Seemann, M. Maleckar and P. Tavi. In Sil-ico Screening of the Key Cellular Remodeling Targets inChronic Atrial Fibrillation. PLoS Computational Biology, vol.10(5)(e1003620), 2014.
[17] S. Linge, K.-A. Mardal, A. Helgeland, J. Heiss and V.Haughton. Effect of Cranio-Vertebral Decompression onCSF Dynamics in Chiari I Malformation Studied With Com-putational Fluid Dynamics. Journal of Neurosurgery, vol. 21,pp. 559-564, 2014.
[18] A. Massing, M. G. Larson, A. Logg and M. E. Rognes. AStabilized Nitsche Fictitious Domain Method for the StokesProblem. Journal of Scientific Computing, vol. 61(online),pp. 604-628, 2014.
[19] A. Massing, M. G. Larson, A. Logg and M. E. Rognes. A Sta-bilized Nitsche Overlapping Mesh Method for the StokesProblem. Numerische Mathematik, vol. 128(online), pp. 73-101, 2014.
[20] K. S. Mcleod, R. Guibert, A. Caiazzo, T. Mansi, M. A. Fernàn-dez, M. Sermesant, X. Pennec, I. E. Vignon-Clementel, Y.Boudjemline and J.-F. Gerbeau. Group-Wise Constructionof Reduced Models for Understanding and Characterizationof Pulmonary Blood Flows From Medical Images. MedicalImage Analysis, vol. 18(1), pp. 63-82, 2014.
[21] S. Morotti, A. G. Edwards, A. D. McCulloch, D. M. Bers andE. Grandi. A novel computational model of mouse myocyteelectrophysiology to assess the synergy between Na+ load-ing and CaMKII. The Journal of physiology, vol. 592, pp.1181-1197, 2014.
[22] V. Naumova, M. Fornasier and S. Pereverzyev. ParameterChoice Strategies for Multi-Penalty Regularization. SIAMJournal on Numerical Analysis, vol. 52(4), pp. 1770-1794,2014.
[23] V. Naumova and S. Peter. Minimization of Multi-PenaltyFunctionals by Alternating Iterative Thresholding and Opti-mal Parameter Choices. Inverse Problems, vol. 30(12), pp.1-35, 2014.
[24] O. Nordbø, P. Lamata, S. Land, S. Niederer, J. M. Aronsen, W.E. Louch, I. Sjaastad, H. Martens, A. B. Gjuvsland, K. Tøndel,H. Torp, M. Lohezic, J. E. Schneider, E. W. Remme, N. Smith,S. W. Omholt and J. O. Vik. A computational pipeline forquantification of mouse myocardial stiffness parameters.Comput. Biol. Med., vol. 53, pp. 65–75, 2014.
[25] A. E. Sayed, M. Mortensen and J. Z. Wen. Assessment ofthe presumed mapping function approach for the stationarylaminar flamelet modelling of reacting double scalar mix-ing layers. Combustion Theory and Modelling, vol. 18, pp.552-581, 2014.
[26] D. S. Seljebotn, K.-A. Mardal, J. Jewell, H. K. Eriksen andP. Bull. A Multilevel Solver for Gaussian Constrained CMBRealizations. The Astrophysical Journal Supplement Series,vol. 210(2), 2014.
[27] J. Sundnes, S. Wall, H. Osnes, T. Thorvaldsen and A.D. McCulloch. Improved Discretisation and Linearisationof Active Tension in Strongly Coupled Cardiac Electro-Mechanics Simulations. Computer Methods in Biomechan-ics and Biomedical Engineering, vol. 17(6), pp. 604-15,2014.
[28] V. Tafintseva, K. Tøndel, A. Ponosov and H. Martens. Globalstructure of sloppiness in a nonlinear model. J. Chemomet-rics, vol. 28, pp. 645-655, 2014.
[29] K. Tøndel and H. Martens. Analyzing complex mathemat-ical model behavior by Partial Least Squares Regression-based Multivariate Metamodeling. Wiley InterdisciplinaryReviews: Computational Statistics, vol. 6, pp. 440–475,2014.
[30] K. Tøndel, S. A. Niederer, S. Land and N. P. Smith. Insight intoModel Mechanisms through Automatic Parameter Fitting: Anew Methodological Framework for Model Development.BMC Systems Biology, vol. 8, pp. 59, 2014.
23
[31] K. Valen-Sendstad and D. A. Steinman. Mind the Gap: Im-pact of Computational Fluid Dynamics Solution Strategyon Prediction of Intracranial Aneurysm Hemodynamics andRupture Status Indicators. American Journal of Neuroradi-ology, vol. 35(3), pp. 536-543, 2014.
[32] K. P. Vincent, A. D. McCulloch and A. G. Edwards. Towarda hierarchy of mechanisms in CaMKII-mediated arrhythmia.Frontiers in Pharmacology, vol. 5, 2014.
[33] M. Wen, H. Su, W. Wei, N. Wu, X. Cai and C. Zhang. HighEfficient Sedimentary Basin Simulations on Hybrid CPU-GPU Clusters. Cluster Computing, vol. 17(2), pp. 359-369,2014.
[34] L. Yuan, J. Koivumäki, B. Liang, L. G. Lorentzen, J. H. Svend-sen, J. Tfelt-Hansen, M. Maleckar, N. Schmitt, M. S. Olesenand T. Jespersen. Investigations of the NaVβ1b SodiumChannel Subunit in Human Ventricle; Functional Charac-terization of the H162P Brugada Syndrome Mutant. Heartand Circulatory Physiology, vol. 306(8), pp. H1204-H1212,2014.
[35] W. Zhang, W. Wei and X. Cai. Performance Modeling of Se-rial and Parallel Implementations of the Fractional Adams-Bashforth-Moulton Method. Fractional Calculus and Ap-plied Analysis, vol. 17(3), pp. 617-637, 2014.
[36] W. Zhang, X. Cai and S. Holm. Time-Fractional Heat Equa-tions and Negative Absolute Temperatures. Computers &Mathematics with Applications, vol. 67(1), pp. 164-171,2014.
Interna�onal
78 %
Na�onal and
interna�onal
11 %
Na�onal
0 %
CBC only
11 %
Collabora�on regarding ar�cles in
interna�onal journals in 2014
Books
[1] H. P. Langtangen. A Primer on Scientific Programming withPython, Springer, 2014.
Refereed Proceedings
[1] X. Dong, J. Chai, J. Yang, M. Wen, N. Wu, X. Cai, C. Zhangand Z. Chen. Utilizing Multiple Xeon Phi Coprocessors onOne Compute Node. In Proceedings of ICA3PP 2014, 2014
[2] D. Huang, M. Wen, C. Xun, D. Chen, X. Cai, Y. Qiao,N. Wu and C. Zhang. Automated Transformation of GPU-Specific OpenCL Kernels Targeting Performance Portabil-ity on Multi-Core/Many-Core CPUs. In Proceednigs of Euro-Par 2014, 2014
[3] J. Langguth and X. Cai. Heterogeneous CPU-GPU Com-puting for the Finite Volume Method on 3D UnstructuredMeshes. In 20th International Conference on Parallel andDistributed Systems (ICPADS 2014), 2014
[4] H. Lu, T. Yue, S. Ali, K. Nie and L. Zhang. Automated andIncremental Conformance Checking to Support InteractiveProduct Configuration. In The 25th IEEE International Sym-posium on Software Reliability Engineering (ISSRE), 2014
[5] Y. Shimogonya, K. Valen-Sendstad and D. A. Steinman. ANovel Framework for Classifying Wall Shear Stress Pheno-types in Arterial Disturbed Blood Flow. In World Congressof Biomechanics Proceedings, 2014
[6] M. Sourouri, T. Gillberg, S. Baden and X. Cai. EffectiveMulti-GPU Communication Using Multiple CUDA Streamsand Threads. In 20th International Conference on Paralleland Distributed Systems (ICPADS 2014), 2014
0
10
20
30
40
50
60
70
80
90
2007 2008 2009 2010 2011 2012 2013 2014
Ar cles in Int. Journals
Refereed Proceedings
Chapters in books
Total refereed produc�on
Figure 19: Overview of refereed CBC publications 2007–2014.
Proceedings without referee
[1] G. Balaban, J. Sundnes, M. S. Alnæs and M. E. Rognes. LeastSquares Fitting of a Cardiac Hyperelasticity Model Usingan Automatically Derived Adjoint Equation. In Proceedingsof NSCM-27: the 27th Nordic Seminar on ComputationalMechanics, 2014
[2] P. M. Kekenes-Huskey, A. G. Edwards, J. E. Hake, A. P.Michailova, A. J. McCammon and A. D. McCulloch. A Markov-State Model for the Regulation of the Sarcoplasmic Retic-ulum Ca2+ ATPase by Phospholamban. In Annual meetingin Biophysical society, 2014
24
Theses
[1] B. L. d. Oliveira. Computational models of Cardiac Elec-tromechanics, Ph.D. Thesis, University of Oslo, 2014.
[2] K.-H. Støverud. Relation Between the Chiari I Malformationand Syringomyelia From a Mechanical Perspective, Ph.D.Thesis, University of Oslo, 2014.
Talks
[1] M. S. Alnæs. High level abstractions for finite elementmethods – The Unified Form Language and the FEniCSproject, CBC/Uppsala workshop, Simula Research Labo-ratory, 2014.
[2] M. S. Alnæs. The Unified Form Language – Features, imple-mentation and future, PRISM Workshop, Imperial CollegeLondon, 2014.
[3] S. Baden. Computing at a Million of Mobiles Per Second,Rutgers University, 2014.
[4] S. Baden. Embedded domain specific languages: How ev-eryone can be an expert performance programmer, StonyBrook University, Dept of Biomedical Informatics, 2014.
[5] S. Baden. Engineering for High Performance through Do-main Specific Translations, Royal Institute of Technology,Stockholm, Sweden, 2014.
[6] S. Baden. Engineering for High Performance through Do-main Specific Translations, Computer Science Department,University in Uppsala, 2014.
[7] G. Balaban. Passive Cardiac Mechanics Calibration Us-ing Reduced Order Unscented Kalman Filtering, Uppsala-Simula Scientific Computing Seminar, 2014.
[8] E. Burman, S. Claus, P. Hansbo, M. G. Larson and A. Mass-ing. Cut Finite Element Methods for Multi-Physics Problems(in FEniCS!), 18th European Conference on Mathematics forIndustry, 2014.
[9] X. Cai, J. E. Hake and G. T. Lines. Supercomputing-EnabledStudy of Subcellular Calcium Dynamics, Article in "meta" -a magazine published by the notur project, 2014.
[10] S. W. Funke and M. Nordaas. PDE-Constrained Optimisa-tion in Hilbert Spaces, FEniCS’14 Workshop, University ofChicago center in Paris, France, 2014.
[11] S. W. Funke. Lecture on PDE-constrained optimization withFEniCS, Zhjiang University, Hangzhou, China, 2014.
[12] N. Gaur, L. Qiang, X. Cai and Y. Rudy. ArrhythmogenicMechanisms and Therapeutic Targets for CatecholaminergicPolymorphic Ventricular Tachycardia: A Simulation Study ina Human Ventricular Myocyte, Simula Research Laboratory,2014.
[13] N. Gaur, Q. Lan, X. Cai and Y. Rudy. Mathematical Modelingof Ca Handling and Computational Studies of Ca-relatedArrhythmogenesis in Heart, National University of DefenseTechnology, China, 2014.
[14] S. U. Gjerald, S. Sarvari, H. H. Odland and S. Wall. A genericright ventricle model for simulating patient-specific pacingprocedures from echocardiography data, Workshop on Mod-els for surgical decision support at VPH2014 in Trondheim,2014.
[15] B. Kehlet. Mshr - Mesh Generation in FEniCS, FEniCS’14Workshop, University of Chicago center in Paris, France,2014.
[16] J. Koivumäki, L. Skibsbye, T. Christ, M. Maleckar and T. Jes-persen. Action Potential Repolarisation in Healthy and Fib-rillating Human Atria: Contribution of Small ConductanceCalcium-Activated Potassium Channels, Conference of theScandinavian Physiological Society, 2014.
[17] J. Koivumäki. Computational Models of Cardiac Electro-physiology in Healthy and Fibrillating Human Atria, Seminarat the Institute of Experimental and Clinical Pharmacologyand Toxicology, UKE, Hamburg, 2014.
[18] H. P. Langtangen. How to Easily Implement SophisticatedTailored Algorithms in Computational Turbulence, Depart-ment of Mathematics, University of Oxford, UK, 2014.
[19] H. P. Langtangen. Code Generation for High-Level ProblemSpecification and HPC, London University College, London,UK, 2014.
[20] A. Logg. CCFEM implementation in FEniCS, Simula multi-physics workshop, 2014.
[21] A. Logg. Automated Solution of Differential Equations, Com-puter science and engineering seminar, Chalmers Universityof Technology, Gothenburg, Sweden, 2014.
[22] A. Logg. A Finite Element method for the Einstein-Vlasovsystem, Biocomp lunch seminar, Simula, Oslo, 2014.
[23] A. Logg. Periodic table of the Finite Elements (part I), Com-putational and Applied Mathematics seminar, Chalmers Uni-versity of Technology, Gothenburg, Sweden, 2014.
[24] A. Logg. Automated Solution of Differential Equations, Hy-perfit seminar, University of Copnehagen, Denmark, 2014.
[25] A. Logg. Periodic table of the Finite Elements (part II), Com-putational and Applied Mathematics seminar, Chalmers Uni-versity of Technology, Gothenburg, Sweden, 2014.
[26] A. Logg. Periodic table of the Finite Elements (part III), Com-putational and Applied Mathematics seminar, Chalmers Uni-versity of Technology, Gothenburg, Sweden, 2014.
[27] A. Logg. Multimesh FEM in FEniCS, FEniCS’14 Workshop,University of Chicago center in Paris, France, 2014.
[28] A. Logg. Automated Solution of Differential Equations,Svenska matematikersamfunnets høstmøte, 2014.
[29] A. Logg. Periodic table of the Finite Elements, Biocomplunch seminar, Simula, Oslo, 2014.
25
[30] A. Logg. Vad går at berekna, vad går inte? Om fraktaler -matematiske fantasiskapelser - och kaos, Talk at Senioruni-versitetet in Stockholm, 2014.
[31] K.-A. Mardal, T. Seland, H. P. Langtangen and P. Røtnes. ErZombier En Trussel Mot Menneskeheten?, Upop aften - Detnorske student samfund, 2014.
[32] K.-A. Mardal. On the Assumption of Laminar Flow in theModeling of Physiological Flow, Anvendt og beregningsori-entert matematikk, Bergen, 2014.
[33] K.-A. Mardal, A. Helgeland, V. Haughton, B. A. P. Reifand K.-H. Støverud. On the Assumption of Laminar Flow ofCSF in Chiari Patients, international Chiari Research Group,2014.
[34] K.-A. Mardal, K.-H. Støverud, G. Ringstad and P. K. Eide.CSF Flow at Foramen Magnum, International HydrocephalusImaging Working Group, Montreal, Canada, 2014.
[35] K.-A. Mardal, O. M. Khan, K. Valen-Sendstad and D. A.Steinman. On Numerical Methods for Transitional Flow - Ap-plication to Blood Flow in Aneurysms, Quality and Validationof Computational Cardio-vascular Biomechanics, WCCM-ECCM-ECCOM, 2014.
[36] K.-A. Mardal, K.-H. Støverud, M. Mortensen, K. Jain, B. Mar-tin and S. Pahlavian. Cerebrospinal Fluid Flow in AssociationWith the Central Nervous System - Chiari and Drug Deliv-ery, MS on Computational Biomechanics, WCCM-ECCM-ECCOM, 2014.
[37] A. Massing. Cut Finite Element Methods for Fluid andFluid-Structure Interaction Problems, Advances in Fluid-Structure Interaction, Tokyo, 2014.
[38] A. D. McCulloch. Multi-Scale Modeling of the Failing Heart:From Mouse to Man, Simula-UiO-UCSD Summer School inCardiac Modeling, 2014.
[39] K. S. Mcleod, K. Tøndel, S. Wall and J. Saberniak. Meta-modelling of Structural Abnormalities in the ARVC Heart,VPH conference workshop on Metamodelling methodologyfor easing model construction and validation, 2014.
[40] M. Mortensen. FEniCS - A Free Software Framework for Ef-ficient Solution of Differential Equations, with Applicationsin Mechanics, Prague, 2014.
[41] V. Naumova. Minimization of Multi-Penalty Functionals byAlternating Iterative Thresholding and Optimal ParameterChoices, SIAM Conference on Uncertainty Quantification,2014.
[42] V. Naumova. Meta-Learning Based Blood Glucose Predictorfor Diabetic Smartphone App, SIAM Conference on ImagingScience, 2014.
[43] V. Naumova. Meta-Learning Approach to the Image Denois-ing Problem, SIAM Conference on Imaging Science, 2014.
[44] M. Nordaas. Robust Preconditioners for PDE-ConstrainedOptimization With Limited Observations, European Multi-grid Conference, 2014.
[45] M. E. Rognes. An Adjoint-Enabled Simulation Frameworkfor Cardiac Electrophysiology, FEniCS’14 Workshop, Uni-versity of Chicago center in Paris, France, 2014.
[46] M. E. Rognes. An Adjoint-Enabled Simulation Frameworkfor Cardiac Electrophysiology, CBC and CCI Workshop onCardiac Modelling at Simula Research Laboratory, Fornebu,2014.
[47] M. E. Rognes. Perspectives on the Current State of theArt of Computational Modelling of Fluid Flow in the BrainParenchyma, CBC and CINPLA Workshop on Modelling Liq-uid Transport in the Brain, Simula Research Laboratory,Fornebu, 2014.
[48] M. E. Rognes. In Silico Physiological Flows, Seminar in con-nection with Villani visit at Simula Research Laboratory,Fornebu, 2014.
[49] M. E. Rognes. High-Level Advanced Abstractions and Tech-niques in Finite Element Software, CBC Workshop on Com-putational Modeling with Applications in Biomedicine andGeophysics at Simula Research Laboratory, 2014.
[50] M. E. Rognes. Automated Goal-Oriented Error Control andAdaptivity, RCN site visit to the CBC, Simula ResearchLaboratory, Fornebu, 2014.
[51] M. E. Rognes. Adaptive Finite Elements: Practice and Im-plementation, Centre for Mathematics for Applications, Uni-versity of Oslo, 2014.
[52] J. Sundnes, S. Wall, S. U. Gjerald, J. E. Hake and B. L.d. Oliveira. Patient Specific Models of Cardiac Electro-Mechanics, Seminar at Ecole des Mines, St Etienne, France,2014.
[53] J. Sundnes, S. Wall, S. Pezzuto, J. E. Hake and B. L. d.Oliveira. Computational Models of Electro-Mechanical In-teractions in the Heart, the European Conference for Math-ematics in Industry, Taormina, Italy, 2014.
[54] J. Sundnes. Computational Models of Electro-MechanicalInteractions in the Heart, The Nordic Seminar on Computa-tional Mechanics, Stockholm, 2014.
[55] K. Valen-Sendstad, O. M. Khan, M. Piccinelli and D. A. Stein-man. It’s not the size, but what you do with it: CFD solversettings trump model resolution., Zurich, 2014.
26
Conferences, Workshops and SeminarsWe 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 andposter 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 2014 CBC hosted 6 workshops, 3 seminars, and 21 invited talks in 2014, with a total number of 120 presentations andalmost 600 participants.
CBC seminar series and journal club
The purpose of the seminar series is to present the current statusand challanges for the projects and create a forum for discussionof scientific topics related to the work in CBC. The seminars areopen and attendance of and contributions by other interestedpeople are highly welcome.14.03.14:Numerical Modelling in Oil and Gas industry by Gunnar Staff (fromSchlumberger)21.08.14:Det norske idrettshjertet by Gard Filip Gjerdalen (from Aker Syke-hus)25.09.14:Fractional Step Theta-schemes from Stefan Tureks Incompress-ible Flow Problems by Øyvind Evju09.10.14:Discontinuous Petrov-Galerkin methods (Demkowicz andGopalkrishnan) by August Johansson16.10.14:Higher-Order Finite Element Methods and Pointwise Error Esti-mates for Elliptic Problems on Surfaces (Alan Demlow) by AndreMassing24.10.14:Existence of optimal boundary control for the Navier-Stokesequations with mixed boundary conditions (T. Guerra, A. Sequeiraand J. Tiago) by Simon Funke13.11.14:A decomposition result for biharmonic problems and the Hellan-Herrmann-Johnson method by Magne Nordaas20.11.14:The computation of finite-time Lyapunov exponents on unstruc-tured meshes and for non-Euclidean manifolds (Francois Lekienand Shand D. Ross, 2010) by Martin Alnæs27.11.14:Biomedical applications speed-dating18.12.14:Fundamental Performance limits for ideal decoders in high-dimensional linear inverse problems (Bourrier et. al., 2014) byValeriya Naumova
Total number of participants: 97Total number of speakers: 10Total number of talks: 10
CBC Workshop on the State of FSI and Mul-tiphysics Topics – January 7, 2014The aim of this event was to talk about the state of FSI and othermultiphysics topics in the CBC, and discuss future directions andpossible collaborations.
Total number of participants: 21Total number of guests outside of CBC: 0Total number of speakers: 6Total number of talks: 6
CBC and CINPLA Workshop on Modelling Liq-uid Transport in the Brain – March 14, 2014While neurons appear to be responsible for most of the informa-tion processing in the brain, the role of the more numerous gliacells is less understood. Astrocytes, a subtype of glia cells, havebeen implicated in many supporting roles including provision ofnutrients to brain tissue, maintenance of the right mixture of ionsin the extracellular space between cells, as well as repair of dam-aged neural tissue. Lately, astrocytes have also been suggestedto play a role in brain liquid transport, including the transport ofwaste products out from neural tissue.
Research groups from UiO, CBC and NMBU appear togetherto have the set of methodological tools and skill to address thisproblem. This workshop was hosted at CBC in order for thegroups to present their activities and explore the possibility for ajoint multidisciplinary research project on this topic.Organizers: Centre for Integrative Neuroplasticity (CINPLA) andCentre for Biomedical Computing (CBC)
Total number of participants: 18Total number of guests outside of CBC: 6Total number of speakers: 7Total number of talks: 7
CBC Seminar on Dolfin Adjoint – May 15,2014This 3 hour seminar was targeted towards researchers interestedin computational mathematics to learn to solve PDE-constrainedoptimisation problems with FEniCS. Topics covered included ad-joint and tangent linear models, introduction to dolfin-adjoint,optimisation algorithms, and applications of PDE-constrainedoptimisation. The seminar combined talks, lectures and handson exercises to enable researchers to control the Navier-Stokes
27
equations optimally.
Total number of participants: 15Total number of guests outside of CBC: 1Total number of speakers: 1Total number of talks: 2
2007 2008 2009 2010 2011 2012 2013 2014
# Conferences 0 0 2 0 0 0 1 0
# Workshops 5 12 11 6 8 8 3 6
# Seminars 5 2 6 16 15 17 1 3
# Talks 9 21 12 7 8 7 9 21
0
5
10
15
20
25
CBC events 2007-2014
Figure 20: The number of workshops, seminars and talks varyfrom year to year.
CBC Seminar on Mathematical Modelling ofMedical Systems – May 19, 2014This seminar with Anders Dale was arranged to present anddiscuss research issues of mutual interest. Anders Martin Daleis a prominent neuroscientist and Professor of Radiology andRadiology, Neurosciences, Psychiatry, and Cognitive Science atthe University of California, San Diego (UCSD), and is one ofthe world’s leading developers of sophisticated computationalneuroimaging techniques. He is the founding Co-Director of theMulti-Modal Imaging Laboratory (MMIL) at UCSD.
Total number of participants: 9Total number of guests outside of CBC: 1Total number of speakers: 6Total number of talks: 6
CBC hosted Kickoff workshop for the EMC2
project – May 26-27, 2014EMC2 Embedded Multi-Core systems for Mixed Criticality appli-cations in dynamic and changeable real-time environments is anARTEMIS Joint Undertaking project in the Innovation Pilot Pro-gramme Computing platforms for embedded systems (AIPP5).
Embedded systems are the key innovation driver to improvealmost all mechatronic products with cheaper and even newfunctionalities. They support today’s information society as inter-system communication enabler. A major industrial challengearises from the need to face cost efficient integration of differentapplications with different levels of safety and security on a sin-gle computing platform in an open context. EMC2 finds solutionsfor dynamic adaptability in open systems, provides handling of
mixed criticality applications under real-time conditions, scalabil-ity and utmost flexibility, full scale deployment and managementof integrated tool chains, through the entire lifecycle. The objec-tive of EMC2 is to establish Multi-Core technology in all relevantEmbedded Systems domains. EMC2 is a project of 99 partnersof embedded industry and research from 19 European countrieswith an effort of about 800 person years and a total budget ofabout 100 million Euro.
Total number of participants: 33Total number of guests outside of CBC: 29Total number of speakers: 15Total number of talks: 18
CBC Workshop on Scientific Computing Soft-ware – September 17, 2014This was a joint workshop with Uppsala University on ScientificComputing Software. The young researchers were given an op-portunity to share ongoing projects and investigate the possibilityof joint projects.
Total number of participants: 23Total number of guests outside of CBC: 9Total number of speakers: 15Total number of talks: 15
CBC Workshop with MOX – October 6, 2014The aim of this workshop was to explore possible collaborationson geophysical and biomedical problems where porous mediamodels with (discrete) fractures or channel networks play animportant role. The Laboratory for Modeling and Scientific Com-puting (MOX) started its activity in 2002 with the purpose ofcoordinating and developing the expertise in modeling, numericaland statistical methods present in the Department of Mathemat-ics at Politecnico di Milano. The idea was to establish a commonprocedure for applying these various mathematical techniques toproblems of engineering interest, and to propose to the industrialworld a unique interface to address challenging problems withinnovative tools made available by the most advanced researchin mathematics.
Total number of participants: 21Total number of guests outside of CBC: 3Total number of speakers: 10Total number of talks: 10
CBC Seminar on The Lattice BoltzmannMethod and its Application in Modeling ofPhysiological Flows – October 23, 2014The Lattice Boltzmann Method (LBM) is an alternative techniquefor the numerical simulation of flows, and the LB equation con-verges to the incompressible Navier-Stokes equations under thecontinuum limits of low Mach and Knudsen numbers. The LBmethod is particularly suitable for transient flows, and the na-ture of the scheme allows it to scale to parallel supercomputers
28
thereby allowing for simulation of highly complex ows in realisticgeometries.
The seminar focused on the basics of the method and itslimitations and advantages over classical CFD techniques. Themain focus was the transient nature of the method, and its role insimulating transitional ows at low Reynolds numbers. Jain Kartikalso presented our open source LBM solver Musubi which imple-ments complex features of the LB methods and runs on largescale supercomputers. Finally, he briey presented the resultsof simulations of transitional in physiological applications, witha discussion on the suitability/drawbacks of the LBM in suchapplications
Total number of participants: 13Total number of guests outside of CBC: 9Total number of speakers: 1Total number of talks: 1
CBC and CCI Workshop on Cardiac Modelling- November 5-7, 2014CBC and CCI joined forces to have a workshop on Cardiac Mod-elling. Both local researchers and international experts presentedtheir research across a variety of topics related to mathematicalmodels and modelling of the heart.
Total number of participants: 39Total number of guests outside of CBC: 21Total number of speakers: 24Total number of talks: 24
2007 2008 2009 2010 2011 2012 2013 2014
# Presenta!ons 110 170 69 74 110 120 120
# Par!cipants 270 238 630 378 300 590 500 600
0
100
200
300
400
500
600
700
No. of presenta�ons and par�cipants
Figure 21: The number of presentations are stable, while theattendance is increasing.
For more information on Workshops, Seminars and Talks,please visit our website: cbc.simula.no
29
Other Activities
Refereeing ActivitiesDuring 2014, employees at CBC have refereed manuscripts for:
• ACM Transactions on Architecture and Code Optimization(TACO)
• ACM Transactions on Mathematical Software (TOMS)• Abstract and Applied Analysis• American Journal og Neuroradiology• Annals of Biomedical Engineering• Applied Mathematical Modelling• Biophysical Journal• BioMed Research International• BIT Numerical Mathematics• Cellular and Molecular Biomechanics• Computers and Mathematics with Applications• Drug Discovery Today• GMD (Geoscientific Model Development• IEEE Transactions on Biomedical Engineering• International Journal of Automation and Computing• International Journal of Biomechanics• International Journal of High Performance Computing• Inverse Problems• Journal of Biomechanics• Journal of Complexity• Journal of Mathematical Biology• Journal of Physiology• Journal of Supercomputing• Journal of the Royal Society Interface• Mathematical Biosciences• Mathematical Methods in the Applied Sciences• Numerical Algorithms• Parallel Computing• PLoS ONE, Computational Biology• Radiology• SIAM Journal of Scientific Computing• SIAM Journal on Numerical Analysis
Committee Work and Recognition
S. Baden:1. Euro-Par Advisory Board
H. P. Langtangen:1. Member of the scientific committee for Basic Re-
search Projects in Engineering and Information Technology(“FRITEK”), Research Council of Norway
2. Elected member of the European Academy of Sciences(EAS).
3. Elected member of the Norwegian Academy of Science andLetters (Det norske vitenskapsakademi).
4. Elected member of the IFIP Working Group 2.5
A. McCulloch:1. Jacobs School Distinguished Scholar (2009-2014)2. Co-Director, UCSD Cardiovascular Biomedical Science and
Engineering Center3. Fellow, American Institute of Medical and Biological Engi-
neering
4. Fellow, International Association of Medical and BiologicalEngineering (IAMBE)
5. Fellow, Cardiovascular Section, American PhysiologicalSociety
J. Sundnes:
1. 7th Workshop on Biomedical and Bioinformatics Chal-lenges for Computer Science, at the International Confer-ence on Computational Science, Cairns, Australia, June,2014
A. Tveito:
1. Member of the National Biomedical Computation Resource– Resource Advisory Committee (NBCR RAC) in the UnitedStates, http://www.nbcr.net/
Editorial BoardsEmployees of the center are on the following editorial boards:
X. Cai:
1. International Journal of Web Sciences
H. P. Langtangen:
1. Advances in Water Resources2. BIT Numerical Mathematics3. International Journal of Computational Science and Engi-
neering4. International Journal of Computing Science and Mathemat-
ics5. SIAM Journal on Scientific Computing (Editor in Chief)
M. G. Larson:
1. SIAM Journal on Scientific Computing
A. Logg:
1. Archive of Numerical Software
M. Maleckar:
1. Frontiers in Physics
A. McCulloch:
1. Biophysical Journal, EBM2. Cellular and Molecular Bioengineering3. Drug Discovery Today, Editor in Chief4. Journal of Physiology (Lond), Reviewing Editor5. PLoS Computational Biology, Associate Editor
B. Skallerud:
1. International Journal of Applied Mechanics
J. Sundnes:
1. Frontiers in Physics2. Frontiers in Physiology
A. Tveito:
1. Computational Differential Equations in the Encyclopediaof Applied and Computational Mathematics (Field Editor)
2. Computing and Visualization in Science
30
3. Simula SpringerBriefs on Computing (Editor)
Conference Committees
S. Baden:
1. IPDPS - 29th IEEE International Parallel & Distributed Pro-cessing Symposium, Hyderabad, INDIA, May 25-29, 2015
X. Cai:
1. ISC’14, Leipzig, Germany, June 22-26 20142. VECPAR 2014, Eugene, Oregon, USA, June 30 - July 3,
20143. ADVCOMP 2014, Rome, Italy, August 24 - 28, 2014
P. Farell:
1. IMA Conference on Numerical Methods for Simulation, Ox-ford, United Kingdom, September 2015
H. P. Langtangen:
1. International Conference on Computational Science (ICCS)2014, 2015
2. High Performance and Parallel Computing for Materials De-fects and Multiphase Flows, at the Institute for Mathemati-cal Sciences (IMS), National University of Singapore, 2015
Invited talks
M. Alnæs:
1. The Unified Form Language – Features, Implementation andFuture, PRISM Workshop, Imperial College London, March12, 2014
S. Baden:
1. Computing at a Million Mobiles per Second, Rutgers Uni-versity, October 21, 2014
2. Embedded Domain Specific Languages: How everyone canbe an expert performance programmer, Stony Brook Univer-sity, Department of Biomedical Informatics, 2014
3. Engineering for High Performance through Domain Spe-cific Translations, Royal Institute of Technology, Stock-holm, Sweden, November 27, 2014
4. Engineering for High Performance through Domain SpecificTranslations, Uppsala University, Computer Science De-partment, December 11, 2014
P. Farell:
1. Title not available, 2nd Oxford Workshop on Inference, Iden-tifiability and Model Selection, Oxford, UK, January 2014.
2. Title not available, Warwick-Reading Data AssimilationMeeting, Warwick, UK, May 2014.
3. Title not available, European Conference on Mathematicswith Industry, Taormina, Italy, June 2014.
4. Title not available, Department of Engineering, Universityof Cambridge, June 2014.
5. Adjoint Methods in Computational Science, Engineering,and Finance, Schloss Dagstuhl, Germany, September 2014.
6. Title not available, Research Unit in Engineering Science,University of Luxembourg, September 2014.
7. Title not available, Department of Physics, University ofOxford, October 2014.
S. Funke:
1. Lecture on PDE-constrained optimization with FEniCS,Zhejiang University, Hangzhou, China, March 2014
J. Koivumäki:
1. Computational Models of Cardiac Electrophysiology inHealthy and Fibrillating Human Atria, Institute of Exper-imental and Clinical Pharmacology and Toxicology, UKE,Hamburg, 2014
H. P. Langtangen:
1. How to Easily Implement Sophisticated Tailored Algorithmsin Computational Turbulence, Department of Mathematics,University of Oxford, 2014
2. Code Generation for High-Level Problem Specification andHPC, London University College, 2014
K.-A. Mardal:
1. On the Assumption of Laminar Flow in the Modeling ofPhysiological Flow, University of Bergen, 2014
2. On the Assumption of Laminar Flow of CFS in Chiari Pa-tients, International Chiari Research Group, USA, 2014
3. CSF Flow at Foramen Magnum, International Hydro-cephalus Imaging Working Group, Montreal, Canada, 2014
4. On Numerical Methods for Transitional Flow – Applica-tion to Blood Flow in Aneurysms, in Quality and Validationof Computational Cardio-vascular Biomechanics, WSSM-ECCM-ECCOM, 2014
5. Cerebrospinal Fluid Flow in Association With the CentralNervous System - Chiari and Drug Delivery, in MS on Com-putational Biomechanics, WSSM-ECCM-ECCOM, 2014
6. On the Assumption of Laminar Flow of CFS in Chiari Pa-tients, International Chiari Research Group, USA, 2014
A. Massing:
1. Cut Finite Element Methods for Fluid and Fluid-StructureInteraction Problems, in Advances in Fluid-Structure Inter-action, Tokyo, 2014
M. Mortensen:
1. FEniCS – A Free Software Framework for Efficient Solutionof Differential Equations, with Applications in Mechan-ics, 3rd International Conference on Mechanical Engineer-ing and Mechatronics, Prague, Czech Republic, August 15,2014
V. Naumova:
1. Meta-Learning Approach to the Image Denoising Problem,in SIAM Conference on Imaging Science, 2014
2. Minimization of Multi-Penalty Functionals by AlternatingIterative Thresholding and Optimal Parameter Choices, inSIAM Conference on Uncertainty Quantification, 2014
3. Meta-Learning Based on Blood Glucose Predictor for Di-abetic Smartphone App, in SIAM Conference on ImagingScience, 2014
J. Sundnes:
1. Patient Specific Models of Cardiac Electro-Mechanics, inSeminar at Ecole des Mines, St Etienne, France, 2014
31
2. Computational Models of Electro-Mechanical Interactionsin the Heart in The European Conference for Mathematicsin Industry, Taormina, Italy, 2014
3. Computational Models of Electro-Mechanical Interactionsin the Heart Keynote plenary talk at The Nordic Seminar onComputational Mechanics, Stockholm, November, 2014
32
Collaboration partnersPresently CBC researchers has more than 80 collaboration partners from 55 different institutions in 17 countries.
Title Name Affiliation Country
Dr. L. Antiga Mario Negri Institute for Pharmacological Research, Ranica ItalyDr. S. Bakke Rikshospitalet University Hospital NorwayDr. Á. Birkisson University of Oxford United KingdomProf. H.-P. Bunge Ludwig-Maximilian University (LMU), Munich GermanyProf. E. Burman University College London United KingdomDr. S. Claus University College London United KingdomProf. C. Clancy University of California at Davis USADr. C. Cotter Imperial College London United KingdomDr. D. M. Culley Imperial College London United KingdomDr. Y. Cui San Diego Supercomputing Center USAProf. R. W. Dos Santos Federal University of Juiz de Fora BrazilProf. O. Dössel Karlsruhe Institute for Technology (KIT) GermanyProf. P. K. Eide Oslo University Hospital NorwayProf. L. Formaggia Politecnico di Milano, Milan ItalyProf. M. Fornasier Technical University of Munich GermanyProf. A. Frangi University of Sheffield United KingdomDr. W. R. Giles University of Calgary CanadaDr. M. Gonzales University of California, San Diego USADr. G. J. Gorman Imperial College London United KingdomAssoc. Prof. M. Grasmair NTNU NorwayDr. J. M. Guccione University of California, San Fransisco USAProf. R. Haaverstad Haukeland University Hospital NorwayDr. J. Hale University of Luxembourg LuxembourghDr. D. A. Ham Imperial College London United KingdomDr. R. Helmig University of Stuttgart GermanyProf. J. Ho Defence Research and Development Canada CanadaProf. M. Holst University of California, San Diego USADr. M. Hoshijima University of California, San Diego USADr. H. P. Hu University of Tromsø NorwayDr. A. Jensen University of Oslo NorwayDr. T. Jespersen University of Copenhagen DenmarkDr. J. Jiang University of Wisconsin, Madison USADr. P. Kekenes-Huskey University of California, San Diego USAAssoc. Prof. D. I. Ketcheson King Abdullah University of Science and Technology (KAUST) Saudi ArabiaProf. R. C. Kirby Texas Tech University USADr. G. Kiss NTNU and St. Olafs Hospital NorwayDr. M. G. Knepley University of Chicago USADr. S. C. Kramer Imperial College London United KingdomDr. W. Louch Oslo University Hospital NorwayDr. J. M. Maddison University of Edinburgh United KingdomProf. A. Malthe-Sørensen University of Oslo NorwayDr. B. Martin Director of Conquer Chiari Institute USADr. C. Maurini Uiversité Paris IV FranceProf. J. A. McCammon University of California, San Diego USADr. A. P. Michailova University of California, San Diego USAProf. J. M. Norbotten University of Bergen NorwayDr. J. H. Omens University of California, San Diego USAProf. S. Pereverzyev Austrian Academy of Science AustriaDr. M. D. Piggott Imperial College London United KingdomProf. M. Regnier University of Washington USAMD. G. A. Ringstad Oslo University Hospital NorwayDr. T. Roch Acadia University and IT Power Consulting CanadaProf. B. M. Rocha Federal University of Juiz de Flora BrazilProf. S. Roller University of Siegen GermanyAssoc. Prof. L. Rosasco Istituto Italiano di Technologia ItalyProf. Y. Rudy Washington University in St. Louis USAProf. U. Ruede University of Erlangen Germany
33
Title Name Affiliation Country
Prof. F. B. Sachse University of Utah USAMr. B. Schott TUM, Munich GermanyProf. R. Scott University of Chicago USADr. G. Seemann Karlsruhe Institute of Technology (KIT) GermanyProf. O. M. Sejersted Oslo University Hospital NorwayDr. G. Sommer Graz University of Technology AustriaDr. A. Sorteberg Rikshospitalet University Hospital NorwayProf. R. J. Spiteri University of Saskatchewan CanadaProf. D. A. Steinmann University of Toronto CanadaProf. B. T. Stokke Department of Physics, NTNU NorwayProf. C. Strother University of Wisconsin, Madison USADr. T. O. Sømme University of Bergen NorwayDr. P. Tavi University of Eastern Finland FinlandDr. K. M. Thyng Texas A&M University USADr. N. Trayanova Johns Hopkins University, Baltimore USADr. D. Unat Koc University TurkeyProf. Y. Ventios University College London United KingdomProf. J. Vierendeels Ghent University BelgiumProf. E. De Vito University of Genova ItalyDr. G. N. Wells University of Cambridge United KingdomDr. M. Wen National University of Defence Technology (NUDT) ChinaDr. O. Wieben University of Wisconsin, Madison USAProf. R. Winther University of Oslo NorwayProf. C. Zhang National University of Defence Technology (NUDT) ChinaProf. P. Zunino University of Pittsburgh USADr. K. B. Ølgaard Aalborg University Denmark
2007 2008 2009 2010 2011 2012 2013 2014
# Coll. partners 53 62 67 71 80 80 80
# Coll. ins!tutes 38 41 44 44 50 50 55
# Coll. countries 16 16 14 14 15 15 17
# Interna!onal Guests 45 54 49 26 24 35 112 93
# Visitors in total 85 89 84 71 42 63 162 122
0
20
40
60
80
100
120
140
160
180
Interna�onal collabora�on
34
List of International Guests in 2014
In 2014 CBC had 93 international guests from 24 different countries. The 29 Norwegian visitors are not listed.
Period Position Name Affiliation Nationality
June 18 Mr. Christopher Villangco University of California, San Diego (UCSD) AmericanJuly 6 - 13 Dr. Daniel Roten San Diego Supercomputing Center AmericanJune 24 Dr. David Richards Lawrence Livermore National Laboratory AmericanJune 16 - 27 Mrs. Eilleen Ao-ieong University of California, San Diego (UCSD) AmericanOctober 23 Mr. Joe LaCasa University of Oslo AmericanJuly 7 - 11 Professor Kim Olsen San Diego State University AmericanJune 16 - 27 Mrs. Kimberly McKabe University of California, San Diego (UCSD) AmericanJune 16 - 27 Mr. Steffen Docken University of California, Davis AmericanNovember 5-6 Dr. Tom O’Hara John Hopkins University AmericanJune 24 Professor Wouter-Jan Rappel Department of Physics, University of California, San Diego
(UCSD)American
June 29 - July 11 Dr. Jifeng Cui San Diego Supercomputing Center AmericanSeptember 16 Professor Yoram Rudy CBAC at Washington University in St. Louis AmericanNovember 5-6 Professor Gernot Plank Medical University of Graz AustrianJune 11 Professor Jan Sijbers iMinds-Vision Lab, University of Antwerpen BelgianOctober 23 Dr. Joris Verschaeve University of Oslo BelgianSeptember 16 Dr. Chris Richardson Cambridge University BritishNovember 5-6 Dr. Steven Niederer Kings College London BritishNovember 5-6 Professor Vicente Grau University of Oxford BritishNovember 5-6 Dr. Edward Vigmond University of Bordeaux CanadianNovember 5-6 Dr. William Louch Institute for Experimental Medical Research, Oslo University
Hospital UllevålCanadian
September 16 Dr. William Louch Institute for Experimental Medical Research, Oslo UniversityHospital Ullevål
Canadian
September 17 Mrs. Jing Liu Uppsala University, Sweden ChineseSeptember 16 Dr. Wang Chiangmian University of Oslo ChineseMay 26 - 27 Dr. Pavel Václavek Central European Institute of Technology (CEITEC), Brno Uni-
versity of TechnologyCzech
May 26 - 27 Professor Pavel Zcmcik Faculty of Information Technology, Brno University of Tech-nology
Czech
May 26 - 27 Professor Birger Møller Pedersen Department of Informatics, University of Oslo DanishJune 16 - 27 Mr. Lars Holtse Bonde Technical University of Denmark DanishMay 26 - 27 Mr. Bastijn Vissers Philips Healthcare DutchJune 16 - 27 Mr. Jonas van den Brink University of Oslo DutchMay 26 - 27 Professor Koen Bertels Delft University of Technology DutchMarch 27 Dr. Laura Alisic Bullard Laboratories, Cambridge University DutchNovember 5-6 Dr. Mark Potze Universita della Svizzera Italiana DutchMay 26 - 27 Dr. Mark Van Helvoort Philips Healthcare DutchOctober 23 Mr. Abushet Simanesew University of Oslo EtiopianMay 26 - 27 Dr. Tiberiu Seceleanu Mälardalen University Sweden, ABB Corporate Research FinnishMay 26 - 27 Mr. Jean-Jacques Rodot THALES Communications and Security FrenchNovember 5-6 Dr. Martin Genet ETH Zurich FrenchOctober 22-30 Mr. Benedikt Schott Teschnische Universität München GermanAugust 22 Dr. Christoph Moder Kalkulo AS GermanOctober 6 - 10 Dr. Gunnar Seemann Karlsruhe Institute of Technology GermanMay 26 - 27 Dr. Jürgen Salecker Siemens Corporate Technology GermanMay 26 - 27 Dipl.-Ing. Michael Geissel eVision GermanNovember 5-6 Professor Rolf Krause Universita delle Svizzera Italiana GermanMay 26 - 27 Dipl.-Ing. Rolf Meyer TU-Braunschweig GermanAugust 22 Dr. Sabine Hippchen Kalkulo AS GermanApril 25 - July 25 Mr. Timo Koch Stuttgart University GermanNovember 5-6,June 16 - 27
Mrs. Viviane Timmermann TU Kaiserslauten German
June 5 Professor Yiannis Ventikos Department of Mechanical Engineering, University CollegeLondon
Greek
March 10-21 Dr. Sigriður Sif Gylfadóttir Island Geosurvey (ISOR) IclandicJune 16 - 27 Mr. Abhishek Murthy Stony Brook University, NY IndianJune 16 - 27 Mrs. Tapaswini Das Cardiac Mechanics Research Group, University of California,
San Diego (UCSD)Indian
September 17 Mr. Afshin Zafari Uppsala University, Sweden IranianOctober 5 - 7 Dr. Alessio Fumagalli Laboratory for Modelling and Scientiffic Computing (MOX),
Politechnico de MilanoItalian
June 23 Professor Davide Ambrosi Politecnico Milano ItalianNovember 5-6 Dr. Eleonora Grandi University of California Davis Italian
35
Period Position Name Affiliation Nationality
May 26 - 27 Mr. Francesco Robino School of Information and Communication Technology, KTHRoyal Institute of Technology in Stockholm, Sweden
Italian
May 26 - 27 Mrs. Gaetana Sapienza Mälardalen University Sweden ItalianJune 16 - 27 Mrs. Giulia Pizzichelli Italian Institute of Technology ItalianOctober 5 - 7 Professor Luca Formaggia Laboratory for Modelling and Scientiffic Computing (MOX),
Politechnico de MilanoItalian
March 14 Dr. Maria Franceschini Center for Biological Imaging, Harvard-Massachusetts Insti-tute of Technology (MIT)
Italian
May 26 - 27 Dr. Almudena Diez Visure NAMay 26 - 27 Dr. Andrei Terechko Vector Fabricks NAApril 4 Dr. Andrew McMurry Department of Informatics, University of Oslo NANovember 5-6 Mr. Axel Loewe Karlsruhe Institute of Technology NAMay 26 - 27 Dr. Christoph Scherrer Vienna University of Technology NAMay 26 - 27 Mr. Jan Neskudla Sysgo SRO NAMay 26 - 27 Mr. Jan Rollo Sysgo SRO NANovember 5-6 Dr. Pablo Lamata Kings College London NAMay 26 - 27 Dr. Radouane Oudrhiri Systonomy NAMay 15 Mr. Lukasz Pazkooski Wroclaw University PolishSeptember 17 Mrs. Anastasia Kruchinia Uppsala University, Sweden RussianNovember 5-6 Professor Beatriz Trenor Polytechnical University of Valencia SpanishMay 26 - 27 Dr. Javier Cano Polytechnical University of Valencia SpanishNovember 5-6 Professor Javier Saiz Polytechnical University of Valencia SpanishMay 26 - 27 Dr. Juan-Carlos Péres Polytechnical University of Valencia SpanishMay 26 - 27 Mr. Raúl Santos de la Cámara H.I. Iberia Ingenieria Proyectos SpanishNovember 5-6 Dr. Rodrigo Weber dos Santos Federal University of Juiz de Fora SpanishNovember 5-6 Dr. Sergio Alonso Universitat Politechnica de Catalunya SpanishMay 26 - 27 Mr. Aron Andersson Western Geco SwedishMay 26 - 27 Mr. Daniel Hallmans Mälardalen University Sweden SwedishSeptember 17 Dr. Elisabeht Larsson Uppsala University, Sweden SwedishSeptember 17 Dr. Emanuel Rubensson Uppsala University, Sweden SwedishMay 26 - 27 Dr. Johnny Öberg KTH Royal Institute of Technology in Stockholm, Sweden SwedishSeptember 17 Mr. Karl Ljungkvist Uppsala University, Sweden SwedishJune 16 - 27 Mrs. Karoline Horgmo Jæger University of Oslo SwedishSeptember 17 Mr. Magnus Grandin Uppsala University, Sweden SwedishSeptember 17 Mrs. Malin Källen Uppsala University, Sweden SwedishSeptember 17 Professor Sverker Holmgren Uppsala University, Sweden SwedishJune 6 Dr. Benjamin Stamm Laboratoire Jacques-Louis Lions (LJLL) at the University of
Pierre et Marie Curie (UPMC - Paris VI)Swiss
July 18 - August 22 Dr. Alexandra Antoniouk Institute of Mathematics, Nathional Academy of Sciences(NAS), Ukraine
Ukrainian
November 14 - De-cember 5
Professor Andrei Pylypenko Institute of Mathematics of Ukraineian National Academy ofSciences
Ukrainian
July 1 - August 31 Professor Dmytro Sadovyi Taras Schevchenko National University, Kiev UkrainianJuly 17 - October15
Dr. Voldomyr Tesko Institute of Mathematics, Nathional Academy of Sciences(NAS), Ukraine
Ukrainian
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Visiting address: Martin Linges v. 17, 1364 FornebuMailing address: P.O.Box 134, 1325 Lysaker, NorwayPhone: +47 67 82 82 00, fax: +47 67 82 82 01Email: [email protected].#: 984 648 855