Postdoctoral researcher high performance multiscale cell based blood flow simulation: The Informatics Institute of the Faculty of Science is one of the large research institutes with the faculty, with a focus on complex information systems divided in two broad themes: ‘Computational Systems’ and ‘Intelligent Systems’.
The institute has a prominent international standing and is active in a dynamic scientific area, with a strong innovative character and an extensive portfolio of externally funded projects.
Faculty of Science – Informatics Institute
- Salary indication: €2,501 to €4,597gross per month
- High Performance Multiscale Computing
Multiscale phenomena are everywhere around us. If we study the origin and evolution of the universe or fracture of materials, if we try to understand health and disease or develop fusion as a potential energy source of the future, in all these cases we find that processes on quite disparate length and time scales interact in strong and non-linear ways. To progress from the current state of the art requires new developments in multiscale computing, as well as at least a factor 100 to 1000 increase in computing capabilities. Advanced multiscale algorithms in combination with petascale resources will help us transition to predictive multiscale science. To make this possible, we have to develop generic multiscale computing algorithms capable of producing high-fidelity scientific results and scalable to petascale and emerging exascale computing systems. We call this High Performance Multiscale Computing (HPMC).
Cell Based Blood Flow Modelling
Blood is a dense suspension of red blood cells, platelets and white blood cells, with many intriguing properties that are far from understood. We have developed a cell based blood flow model, based on a combination of a Lattice Boltzmann Model for the suspending fluid, an Immersed Boundary Method for the fluid structure interaction, and a boundary element method for the mechanical properties of the individual cells. This model was used to probe deeper into the rheological properties of blood (shear thinning at high densities), as well as details of transport of platelets in non-trivial geometries (such as intracranial aneurisms). Moreover, biological models to account for adhesions and aggregation of platelets were added and used to study the initial processes involved in thrombosis in the context of high shear gradients.
Project description
The potential research projects in the spectrum from High Performance Multiscale Computing and its applications in Cell Based Blood Flow Modeling are diverse and numerous. Topics range from research in Computer Science in HPC, via Computational Science research to multiscale computing paradigms and modeling of cell suspensions, to computational biomedicine research to clotting. We seek a Postdoctoral researcher that can operate somewhere in this spectrum, who has a clear vision and drive on where her/his research could be going, and who is capable of collaborating with other scientists on this spectrum.
High Performance Multiscale Computing
One can identify generic multiscale computing patterns arising in multiscale applications that dictate the scope for novel multiscale algorithms at the petascale. You will investigate three such patterns, and their generic mapping to High Performance Computing. In previous projects we developed the Multiscale Modelling and Simulation Framework, which entails a theoretical approach toward multiscale modelling, a simulation framework to develop and run multiscale simulations and a set of tools and middleware to execute and manage multiscale computations on a broad array of computing infrastructure, from the desktop, via clusters and the cloud, to HPC environments.
Embedded in a broader collaboration with a large number of European labs, you will develop multiscale computing patterns for High Performance Multiscale Computing. This will require specifications in the Multiscale Modelling Language (and maybe extensions to this language), implementations in MUSCLE2 (and most probably extensions of this multiscale computing library with HPC capabilities leading to MUSCLE3), development of advanced algorithms for large, dynamic and failure-resistant simulations with automatic load balancing, and finally measuring and predicting the performance of multiscale applications using multiscale computing patterns on HPC systems.
Cell Based Blood Flow Modelling
Based on earlier research, you will extend our cell based blood flow model to much larger geometries (to be able to simulate 1 mm 3 of whole blood), to study in much detail basic transport properties (shear induced diffusion, margination of platelets and white blood cells), to couple this to continuous models of blood flow, thus creating several versions of multiscale models for blood flow and to apply this to transport of platelets and clotting in realistic 3D geometries.
Requirements / Qualifications –
For Postdoctoral position : should have a PhD degree in either Computational Science, High Performance Computing, Computer Science, Computational (bio)Physics, Computational Biomedicine, or related disciplines. The applicant should have relevant experience somewhere on the spectrum of topics as described above.
We seek a researcher with relevant experience in one of the possible research topics, and at the same time being able to collaborate with researchers working on other topics, thus forming a bridge between their own domain and collaborators with the larger European project. Candidates should be able to work in an international multidisciplinary team.
For PhD position: candidate should have a Masters degree in either Computational Science, High Performance Computing, Computer Science, Computational (bio)Physics, Computational Biomedicine, or related disciplines. The applicant should have relevant experience somewhere on the spectrum of topics as described above.
We seek a candidate with relevant experience in one of the possible research topics, and at the same time being able to collaborate with researchers working on other topics, thus forming a bridge between their own domain and collaborators with the larger European project. Candidates should be able to work in an international multidisciplinary team.
Further information
- Prof. Alfons G. Hoekstra
T: +31 (0)20 525 7543
- Computational Science Lab, Faculty of Science
Appointment
The appointment will be full time (38 hours a week) for two years. The gross monthly salary will be in accordance with the University regulations for academic personnel, and will range from €2.501 up to a maximum of €4.597 (scale 10/11) based on a full-time appointment depending on qualifications, expertise and on the number of years of professional experience (valid from 1 January 2016).
The Collective Labour Agreement for Dutch Universities is applicable. There are also secondary benefits, such as 8% holiday allowance per year and the end of year allowance of 8.3%.
English is the working language within the Informatics Institute. Moreover, since Amsterdam is a very international city where almost everybody speaks and understands English, candidates need not be afraid of the language barrier.
Some of the things we have to offer:
- very friendly, interactive and international working environment;
- new building located near the city center (20 minutes by bicycle) of one of Europe’s most beautiful and lively cities;
- access to high-end computing facilities (e.g., cluster with 4,000+ cores).
Job application
In the research statement (see below) you should clearly describe your research vision in relation to the topics that we described, as well as a clear statement which would be your direction of research. Candidates should also include the following information, in separate PDF files (not zipped), using surname, initials and a self-evident word as file names, e.g., Smith J CV:
- a curriculum vitae (including an url allowing download of pdf of M.Sc. thesis — if relevant);
- a letter of motivation (at most 1 page) explaining why you are interested in this position;
- a research statement (at most 2 pages), explaining your research interests and how you think they can be related to the topics mentioned in the Job description above;
- a list of all university courses taken, including a transcript of grades;
- the name and contact details (including email address) of two – three referees who can provide details about your profile (one of whom should be the main supervisor of your Master thesis).
Completed applications should only be submitted via application-science@uva.nl and should state your name, vacancy number 15-443 and the position you are applying for in the subject field. The committee does not guarantee that late or incomplete applications will be considered.
Deadline: 14 December 2015.
Further details and online application –