Contact

	Stefan Engblom

Position: PostDoc
Office phone: +46-8-790 63 33
Fax: +46-8-790 09 30
E-mail: steng@csc.kth.se
Mailing address: CSC/NA KTH, S-100 44 Stockholm, Sweden
Visiting address: Lindstedtsvägen 3, room 1526

Short CV: (pdf)
List of publications: Until 2010 (pdf) (bbl)

KTH / CSC / NA / Stefan Engblom
At the Mathematics Genealogy Project

Research

I started my work at CSC/KTH in January 2009 and have so far been a bit involved in Anna-Karin Tornberg's effort at simulating fibers suspended in fluids. As of September I am joining the Linné FLOW Centre to work also on multiphase flow.

Previous research

Efficient methods for computing numerical solutions to stochastic descriptions of chemical reactions. The underlying mathematical description is a continuous-time Markov chain and the equation governing the probability density is called the Master Equation. Unfortunately, the master equation cannot be solved numerically for more than, say, five molecular species due to the exponential growth of work and memory requirements ('curse of dimensionality'). Stochastic descriptions of chemical reactions are needed to describe the chemical processes taking place inside living cells with few copy numbers of each molecular species. Usual models for cell simulation are based on the reaction rate equations which form a system of nonlinear ordinary differential equations. Such models ignore the stochastic fluctuations in the cells and are therefore less accurate.

Computational systems biology group at the Department of Information technology, Uppsala University

I have also been involved in a project at the Division for Electricity and Lightning Research, Uppsala University called "Electric power generation from winds". The ultimate goal of the project is to provide more efficient wind turbines. I have been working together with Paul Deglaire and, lately, Anders Goude. The work has resulted in a two-dimensional random vortex method simulating fluid flows around general airfoils at a quite high Reynolds number. My contribution has been focused around a user-friendly and very efficient implementation of the fast multipole method.

Freeware

Please feel free to download 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.

Update 100202 New release with several minor improvements, better support for different platforms and better make-files.

Update 100104 I am planning a completely new release of the fast multipole code based on adaptive meshes. I am interested in getting in touch with persons that can aid in testing the beta version on various platforms in order to maximize stability and reliability. Please mail me if you can help me in this regard; state your Matlab-version and your mex-extension. I'll immortalize all helpers in an 'Acknowledgment'-file!

Animations

If a picture tells more than a thousand words then a GIF-animation should tell at least a million... The master equation: A simple example. A bistable system. Rare event in a bistable system. Weak inhibition. A population model. 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. Colliding galaxies! (will take a while to download)

Publications

Parallel in Time Simulation of Multiscale Stochastic Chemical Kinetics

In Multiscale Model. Simul. 8(1):46--68, 2009: (doi)
Reached #2 and #3 at the top 20 list of most downloaded papers in Multiscale Model. Simul. for the months October and September 2009, respectively.

Technical report: (abstract), (pdf)

Also available via arXiv.

S. Engblom, J. Cullhed, A. Hellander: The URDME Manual version 1.0 Technical report: (abstract), (pdf) Also available via arXiv. Download the URDME-package through the download-link.

Numerical Solution Methods in Stochastic Chemical Kinetics PhD thesis

Spectral Approximation of Solutions to the Chemical Master Equation In J. Comput. Appl. Math. 229(1):208--221, 2009: (doi)

S. Engblom, L. Ferm, A. Hellander, P. Lötstedt: Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes In SIAM J. Sci. Comput. 31(3):1774--1797, 2009: (doi) Technical report: (abstract), (pdf) Also available via arXiv.

Galerkin Spectral Method applied to the Chemical Master Equation In Commun. Comput. Phys. 5(5):871--896, 2009: (abstract), (pdf)

P. Deglaire, S. Engblom, O. Ågren, H. Bernhoff: Analytical solutions for a single blade in vertical axis turbine motion in two-dimensions

Gaussian quadratures with respect to discrete measures Technical report: (abstract), (pdf)

Computing the Moments of High Dimensional Solutions of the Master Equation In Appl. Math. Comput. 180(2):498--515, 2006: (doi) Technical report: (abstract), (pdf)

Talks

Mesoscopic Stochastic Modeling of Reaction-Diffusion Processes In the KCSE Seminar series at the KTH Computational Science and Engineering Centre in Stockholm, Sweden, February, 2010: (pdf).

Simulation of stochastic reaction-diffusion processes on unstructured meshes At the First Swedish meeting on Theory and Mathematics in Biology and Medicine, held at the Centre for Interdisciplinary Mathematics in Uppsala, Sweden, December, 2009: (pdf).

Numerical Solution Methods in Stochastic Chemical Kinetics PhD dissertation defense (pdf) succesfully presented the 28th of November, 2008. Opponent: Wilhelm Huisinga. Grading committe: Jesper Oppelstrup, Stig Larsson and Lina von Sydow.

Simulation of stochastic reaction-diffusion processes on unstructured meshes Invited talk given at the Fraunhofer-Chalmers Centre in Gothenburg, Sweden, October, 2008: (pdf).

Parallel Solution of Multiscale Stochastic Chemical Kinetics At the Dahlquist Fellowship Workshop at KTH, Stockholm, Sweden, October, 2008: (pdf). The same talk was given at the ICNAAM conference at Kos, Greece, September, 2008.

Numeriska metoder för den kemiska masterekvationen Licentitate seminar (pdf in swedish) succesfully presented the 27th of September, 2006. External reviewer: Anders Szepessy, KTH.

Numerical solution methods for the master equation At the IHP-EU Network Workshop/Winter school 2005: "Breaking complexity" in Bad Honnef, Germany, December, 2005: (pdf)

Miscellaneous

I have been involved in teaching Tango at Tangogruppen Cambalache.

Tango

Sidansvarig: Stefan Engblom, CSC/NA [KTH]
steng@csc.kth.se
Uppdaterad: 20010-02-02