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

• October 1--5: workshop Multidisciplinary and multiscale approaches to bridge the gap between molecular and cellular level at the Centro di Ricerca Mathematica (CRM) Ennio De Giorgio in Pisa, Italy.

• September 13--14: Academy meeting, Kristineberg.
• September 11: a new paper published. The paper is S. Engblom, P. Lötstedt, L. Meinecke: Mesoscopic Modeling of Random Walk and Reactions in Crowded Media in Phys. Rev. E 98(3):033304 (2018): (doi).
• August 2: yet another paper published today. The reference is S. Widgren, S. Engblom, U. Emanuelson, and A. Lindberg: "Spatio-temporal modelling of verotoxigenic Escherichia coli O157 in cattle in Sweden: Exploring options for control" in Veterinary Res. 49(78), 2018: (doi). Open access!
• August 1: two new papers published this very day. The first one is P. Bauer, S. Engblom, S. Mikulovic, and A. Senek: "Multiscale modeling via split-step methods in neural firing" in Math. Comput. Model. Dyn. Syst. 24(4):409--425, 2018: (doi). The second one is S. Engblom, D. Wilson, R. Baker: Scalable population-level modeling of biological cells incorporating mechanics and kinetics in continuous time in Roy. Soc. Open Sci. 5(8), 2018: (doi). Both are open access!
• July 5: New paper published (finally)! The reference is J. Liu, S. Engblom, and C. Nettelblad: "Assessing Uncertainties in X-ray Single-particle Three-dimensional reconstructions" in Phys. Rev. E. 98(1):013303 2018: (doi)
• June 20: New paper published! The reference is "Stochastic simulation of pattern formation in growing tissue: a multilevel approach" in Bull. Math. Biol., 2018, (doi). Open access!
• June 11--13: I took part in the eSSENCE-Multiscale Modelling Meeting in Uppsala.
• May 30--June 2: I participated in the Wenner-Gren symposia Antibiotic resistance: Evolutionary concepts versus clinical realities in Stockholm.
• May 29: Served as a member of the PhD grading committe for Kristin Kirchner who successfully defended her thesis Numerical approximation of solutions to stochastic partial differential equations and their moments at Chalmer's University of Technology.
• May 4: Served as a member of the PhD grading committe for Markus Wahlsten who successfully defended his thesis Uncertainty quantification for wave propagation and flow problems with random data at Linköping's university.
• April 18--19: Academy meeting, Stockholm.
• March 23: Served as a member of a PhD grading committe for Stefan Sellman at Linköping's university who defended his thesis Quantifying Risk in Epidemiological and Ecological Contexts.
• March 22: Chairman of the committe for the Unga forskare (Young researcher) competition, in Stockholm. See their description of the event, and the Young Academy's summary.
• February 6--7: Academy meeting, Norrköping.
• February 3: A new preprint entitled Stochastic simulation of pattern formation in growing tissue: a multilevel approach was released on arXiv.
• February 1: Finally published! The work conducted together with Augustin Chevallier has now arrived in final form. The formal journal reference is A. Chevallier and S. Engblom: Pathwise error bounds in multiscale variable splitting methods for spatial stochastic kinetics , SIAM J. Numer. Anal. 56(1):469--498, (2018) (doi).
• January 24: organizing (together with Sanna Koskiniemi) the Young Academy's Interdisciplinary Scientific salon on the theme Antimicrobial Resistance (by invitation only).
• January 16--17: Acting as the external reviewer on the PhD viva by Juan Kuntz Nussio at Imperial College, London. The thesis: Deterministic approximation schemes with computable errors for the distributions of Markov chains.

2017

• December 14: I served as a member of the PhD grading committee of Ranjita Dutta Roy who successfully defended her thesis Allosteric regulation of synaptic processes at Karolinska Institutet.
• December 11: Pavol Bauer successfully defended his thesis Parallelism in Event-Based Computations with Applications in Biology. The opponent was Markos Katsoulakis. Congratulations!
• November 13--17: I was 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. See the talk here.
• 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

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