Stefan Engblom

Position

Associate professor, 

Docent in Scientific Computing and Numerical Analysis
 

Office Phone

+46 18 471 27 54 

Fax

+46 18 51 19 25 

Email

stefan.engblom@it.uu.se
 

Mailing Address

Scientific Computing
Information Technology
Box 337
SE-751 05 Uppsala
Sweden
 

Visiting Address

Polacksbacken Building 2
Room 2414a

Latest news and upcoming activities

• November 13--17: I am one of the speaker at the Workshop IV: Uncertainty Quantification for Stochastic Systems and Applications, part of the Program Complex High-Dimensional Energy Landscapes at IPAM, UCLA, CA, USA.
• October 10--11: I will participate in the international policy arena Uppsala Health Summit.

• 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:
"Stochastic simulations and Inverse problems"

Teaching

Research

Freeware

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.

Animations

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:

• Modeling and simulation of the spread of VTEC

URDME simulating stochastic spatial kinetics:

• Min oscillations in E. coli
• Stochastic Morphogenesis

Surfactant in two-phase fluid flow (simulations by Minh Do-Quang):

• Bubbles

Fibers in Stokes flow:

• 200 periodic fibers
• Stable solutions
• Smoke rings (simulations by Jennifer Grünig)

The master equation:

• A simple example.
• A bistable system.
• Rare event in a bistable system.
• Weak inhibition.
• A population model.

Autotuning (simulation by Marcus Holm):

• Autotuning of cylinder flow simulation on multicore CPU/manycore GPU system.

Flow around airfoils (simulations by Paul Deglaire):

• Cylinder flow at low Reynolds and at medium Reynolds.
• Flow around a flat plate at low Reynolds.
• Flow around static wings: FX79w151a at low Reynolds,
  NACA0015 at medium Reynolds.
• Wing pitchup: NACA0012 at medium high Reynolds,
  NACA8818 at medium high Reynolds.

Miscellaneous:

• Colliding galaxies!

Miscellaneous