Uppsala universitet UPMARC 
Stefan Engblom
Short CV: (pdf)
Publications: (pdf)

Stefan Engblom

Stefan Engblom
Associate professor, 
Docent in Scientific Computing and Numerical Analysis
Office Phone
+46 18 471 27 54 
+46 18 51 19 25 
Mailing Address
Scientific Computing
Information Technology
Box 337
SE-751 05 Uppsala
Visiting Address
Polacksbacken Building 2
Room 2414a
         Find me at the Mathematics Genealogy Project...
...at the Research Gate...
...at Google Scholar...
...at ORCID....
...at arXiv.

I am...
...a member of the board of the Department of Information Technology...
...the current faculty advisor of UPPSALA SIAM Chapter...
...and I currently act as the Convener of the Teacher's Team in Advanced Scientific Computing...
...finally, I am associated with the Linnaeus center of excellence UPMARC, Uppsala Programming for Multicore Architectures Research Center, where I currently serve as a deputy member of the board.

On the national side I am an elected member of the Young Academy of Sweden for the period 2016--2021. See my presentation web-page there.

Swedish Young Academy

Latest news and upcoming activities

  • October 10--11: I participated in the international policy arena Uppsala Health Summit.
  • October 5: I just published two chapters related to ongoing research in URDME. The first one is S. Engblom: Stability and Strong Convergence for Spatial Stochastic Kinetics (Chapter 3.3, (doi)). The second is S. Engblom, A. Hellander, P. Lötstedt: Multiscale Simulation of Stochastic Reaction-Diffusion Networks, (Chapter 2.4, (doi)), both in Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, by Springer.
  • September 26--27: Academy meeting in Uppsala.
  • September 4: we just published a chapter on SimInf. The reference is S. Engblom and S. Widgren: Data-driven computational disease spread modeling: from measurement to parametrisation and control, Chapter 11 (doi) in Disease Modelling and Public Health, Part A, Volume 36 of Handbook of Statistics by Elsevier.
  • July 20: a preprint with Per Lötstedt and Lina Meinecke was posted on arXiv. The title of the paper is Mesoscopic Modeling of Random Walk and Reactions in Crowded Media and here we develop a multiscale modeling method wherby the diffusion in a crowded environment may be simulated via a highly efficient mesoscopic model. An implementation of this method, including the numerical experiments performed in the paper, is scheduled for release with URDME version 1.4.
  • June 26: Major version 5.0.0 of SimInf released on CRAN. As before the manual is available at arXiv. For a quick example, see the animation Modeling and simulation of the spread of VTEC.
  • June 13: a paper with Dan Wilson and Ruth Baker was posted on arXiv. The title of the paper is Scalable population-level modeling of biological cells incorporating mechanics and kinetics in continuous time. Selected examples of the method are presented in the paper. An implementation of the method is scheduled for release with URDME version 1.4.
  • June 12: Robin Eriksson joined as a PhD student. The title of his project is Computational Modeling, Parameterization, and Evaluation of the spread of Diseases. Welcome!
  • May 12: a paper with Anders Goude was posted on arXiv. The paper concerns a high order panel method with applications in airfoil design. The actual method has been implemented in our GPU-branch of the FMM2D-code and the experiments of the paper may be reproduced using the scripts distributed. Download here: freeware page.
  • May 9: I hosted a visit to Uppsala by Andreas Milias-Argeitis from the University of Groningen.
  • April 26--27: Academy meeting in Stockholm.
  • March 28: I was one of the jury members in the Young Researcher's Finale Week. See the post at the Young Academy.
  • March 16: new release of URDME! Version 1.3 can now be downloaded at www.urdme.org. The new manual can be retrieved via arXiv.
  • March 9--10: I was involved in organizing Expedition Mundus at SciFest.
  • March 8: Jing Liu gave her 1/2-time seminar entitled Flash X-ray single particle imaging in 3D: computational scalability and resolution assessment 10--12 in B/A7:111. The external reviewer was Silvelyn Zwanzig.
  • March 6--7: visit to Lund University, hosted by Alexandros Sopasakis. I gave a talk with the title Data-driven computational Epidemics.
  • February 8--9: Academy meeting in Gothenburg.
  • January 13: a paper with Vikram Sunkara was published. The paper is "Preconditioned Metropolis sampling as a strategy to improve efficiency in posterior exploration" and discusses a kind of two-level strategy to obtain full posterior exploration in stochastic models of chemical kinetics. See IFAC-PapersOnLine 49(26):89--94 (2016): (doi).
  • January 2: a paper we have worked on during some time (with Carl Nettelblad and Jing Liu) was submitted and posted on arXiv. The title is "Assessing Uncertainties in X-ray Single-particle Three-dimensional reconstructions" and here we design a method by which the accuracy of reconstructions using X-ray lasers can be determined. See the arXiv-post.

Open project proposals:
Computational cell population models: multiscale and multiphysics modeling

There are several openings for interesting and challenging projects within the software framework URDME. Suggestions include high-performance software development, advanced new modeling, and improving simulation efficiency and flexibility, as well as machine learning and data mining techniques. Precise suggestions for projects suitable to MSc/BSc-theses can be formulated upon request.
More details can be found here.


Fall 2017:Advanced Numerical Methods 1TD050 (10.hp)

Spring 2017: Scientific Computing II 1TD395 (5.0hp).
Fall 2016: Advanced Numerical Methods 1TD050 (10.hp)
Spring 2016: Numerical methods in stochastic modeling and simulations (7.5hp, graduate course).
Spring 2016: Scientific Computing II 1TD395 (5.0hp).
Spring 2015: Scientific Computing II 1TD395 (5.0hp).
Fall 2014: Numerical Functional Analysis (5.0hp, graduate course).
Spring 2014: Finite element methods II 1TD254 (5.0hp).
Fall 2012: Finite element methods 1TD253 (5.0hp).
Spring 2012: Classic Articles in Numerical Analysis (7.5hp, graduate course).
Fall 2010: Finite element methods 1TD253 (5.0hp).


I am interested in Scientific Computing, in Numerical Analysis and -Modeling, and in High-Performance Computing. My main focus of applications has so far been in the Biosciences at broad, but I've also taken an interest in Engineering applications, and in Data-driven research. Current active research projects include fast event-based models for spatial chemical kinetics and epidemics, modeling of living cells, parallelism and efficiency in imaging with X-ray lasers, and auto-tuning in CPU/GPU implementations of adaptive fast multipole methods.

In case you are interested in doing a project work or a MSc-thesis, please feel invited to contact me for further discussions.

Read more (including publications and talks).


Please feel free to and use my software (Matlab/C/Mex) under a very liberal license. The software provided here includes a fairly wide range of subroutines useful in research, computations and for fun.

Please mail comments, suggestions, references, criticism. Please do not send support questions.

Download here.


If a picture tells more than a thousand words then a GIF-animation should tell at least a million...

SimInf and Data-driven epidemiological simulations:

URDME simulating stochastic spatial kinetics:
Surfactant in two-phase fluid flow (simulations by Minh Do-Quang):
Fibers in Stokes flow:
The master equation:
Autotuning (simulation by Marcus Holm):
Flow around airfoils (simulations by Paul Deglaire):


I am involved in teaching Tango at Tangogruppen Cambalache.


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