Stefan Engblom, TDB, Uppsala universitet

Stefan Engblom

Publications: (pdf)

	Information Technology : Scientific Computing 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
	Find me at the Mathematics Genealogy Project... ...at the Research Gate... ...at Google Scholar... ...at ORCID.... ...at ResearcherID .... ...at arXiv... ...at GitHub. I am... ...the Head of the Division of Systems and Control... ...the program coordinator for the Master's programme in Computational Science... ...the current faculty advisor of UPPSALA SIAM Chapter... 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. Latest news and upcoming activities June 17: Open PhD position! I am looking for a PhD student in the project Computational modeling of populations of cells. Feel invited to contact me directly by mail for a discussion about the project. Apply here. Deadline to apply: July 31st. 2020 Summer! June15: Opinion piece with Tove Fall, Paul Franks, Maria Gomez, and Alexander Medvedev. June 4: I gave an invited guest-lecture in the Cancer Biology course organized by Femke Heindryckx. June 2: an opinion piece on the Swedish Covid-19 strategy published with Lars Calmfors, Tove Fall and others. April 22--23: (Online) Academy meeting. April 3: (Online) Chairman of the Jury in the Unga forskare (Young researcher) competition, in Stockholm. April 1: another opinion piece published with Tove Fall and others. March 31: Jing Liu successfully defended her PhD thesis Towards Fast and Robust Algorithms in Flash X-ray single-particle Imaging. The opponent was Helmut Grubmueller. Congratulations! March 20: an opinion piece published with Tove Fall and others. Feburary 13: preprint with Jonathan Bull released: Distributed and Adaptive Fast Multipole Method In Three Dimensions. Download the daFMM3D-software at stenglib. February 5--6: Academy meeting in Stockholm. January 27: release of URDME 1.4.0 at www.urdme.org. January 16: start of graduate course Numerical methods in stochastic modeling and simulations (7.5hp). Welcome! January 13--14: TDB Internal conference 2020. 2019 December 12: I gave a short talk concerning in silico alternatives to animal experiments entitled Scientific computing and the single cell... the cell population. Host: SciLife Lab. December 10: meeting with The Young Korean Academy of Science and Technology (Y-KAST) in Stockholm hosted at KVA. December 4--5: Academy meeting, London, UK. December 2: Half-time seminar by Robin Eriksson entitled Bayesian epidemiological modeling over network data. External reviewer Umberto Picchini. November 27: Opinion piece published in Curie: Forskare hinner inte meritera sig på fem år (in Swedish). November 26: Guest lecture Results of computations: communication and responsibility in the project course in Computational Science. November 7--8: I visited the University of Stuttgart and gave a seminar entitled Stochastic modeling for the single cell and the cell population: considerations for data-driven methodologies in the Systems Biology Seminar series. Thanks Nicole Radde for hosting! October 30: a new preprint submitted. The item is Flash X-ray diffraction imaging in 3D: a proposed analysis pipeline by J. Liu, S. Engblom, and C. Nettelblad, and it can be found on arXiv. October 25: a new preprint submitted. This manuscript is the result of quite extensive work and a productive collaboration. Doing something with real data is hard! The item is Bayesian epidemiological modeling over high-resolution network data by S. Engblom, R. Eriksson, and S. Widgren, and it can be found on arXiv. October 23: together with Carolina Wählby I hosted one of the IT-department's 20 year anniversary seminar. See the Facebook-post here. October 15--16: Swedish e-Science Academy, Lund. September 30--October 4: I participated in the conference ENUMATH in Egmond aan Zee, The Netherlands. I gave a talk entitled Bridging the single cell with the cell population: opening up for data-driven methodologies./li> September 11--12: Academy meeting, Stockholm. August 28: conference proceedings paper on our (early) results of modeling African swine fever published. S. Widgren, T. Rosendal, S. Engblom, and K. Ståhl: SimInf for spatio-temporal data-driven modeling of African swine fever in Swedish wildboar, in GeoVet 2019. Novel spatio-temporal approaches in the era of Big Data (url). August 12--14: I participated in the organization of the Young Academy's Research Summer School. June 3--5: I participated in the conference Multiscale Modelling of Materials and Molecules in Uppsala where I gave a short talk entitled Bayesian epidemiologial modeling: with little and without data. May 27: Member of the grading commiittee for M. Ghahremanpour who successfully defended his PhD thesis Alexandria: A General Drude Polarizable Force Field with Spherical Charge Density. Congratulations!. May 25th: Academy meeting, Uppsala. May 3rd: Start of the PhD-level course in Numerical Functional Analysis (5--7.5hp)! Welcome! Please visit the course web-page. May 2nd: I arranged (with Tove Fall and Aryo Makko) the meeting Stand up for the scientific perspective, in Stockholm, Gamla Stan. April 24--25: Academy meeting, Luleå. March 28: I acted as chairman of the committe for the Unga forskare (Young researcher) competition, in Stockholm. Read their own summary of the event. Congratulations! March 20--21: Meeting with the Baltic and Nordic Young Academies, in Stockholm. February 6--7: Academy meeting, Stockholm. February 2: New paper published. The reference is J. Liu, G. Schot, and S. Engblom: Supervised classification methods for flash X-ray single particle diffraction imaging in Opt. Express, 27(4):3884--3899 (2019) (doi). Open access! 2018 December 13: Guest lecturer on the course Project in computational science on the topic Results of computations: communication and responsibility December 7: I served as a member of the grading committee at the PhD defense of Gabriela Malenova entitled Uncertainty quantification for high frequency waves. Congratulations!. November 28--29: Academy meeting November 13: UPMARC day. October 26: a new preprint submitted. The item is Supervised Classification Methods for Flash X-ray single particle diffraction Imaging by J. Liu. G. van der Schot and S. Engblom, and it can be found on arXiv. October 16--17: eSSENCE Academy, Uppsala. 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. I gave a talk entitled From the bottom and up: bridging the single cell with the cell population. 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. Research I am interested in most aspects of Scientific Computing, in Numerical Modeling and -Analys in particular, and in High-Performance Computing. My main focus of applications are 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 multiscale modeling and parameterization of living cells in a population, machine learning methods in imaging with X-ray lasers, auto-tuning in CPU/GPU implementations of adaptive fast multipole methods, and Bayesian approaches for compute intensive spatial stochastic data-driven models in epidemics. 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). 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. Teaching Spring 2020: Scientific Computing I 1TD393 (5.0hp). Spring 2020: Numerical methods in stochastic modeling and simulations (7.5hp, graduate course). Fall 2019: Scientific Computing II 1TD395 (5.0hp). Previously also given 2018, 2017, 2016, 2015. Spring 2019: Numerical Functional Analysis (7.5hp, graduate course) Fall 2017:Advanced Numerical Methods 1TD050 (10.hp) Fall 2016: Advanced Numerical Methods 1TD050 (10.hp) Spring 2016: Numerical methods in stochastic modeling and simulations (7.5hp, graduate course). 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). 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 I am involved in teaching Tango at Tangogruppen Cambalache.