Calendar of 2017
Published:
- Dec 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.
- Dec 11: Pavol Bauer successfully defended his thesis Parallelism in Event-Based Computations with Applications in Biology. The opponent was Markos Katsoulakis. Congratulations!
- Nov 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.
- Oct 10–11: I participated in the international policy arena Uppsala Health Summit.
- Oct 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.
- Sept 26–27: Academy meeting in Uppsala.
- Sept 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.
- Jul 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.
- Apr 26–27: Academy meeting in Stockholm.
- Mar 28: I was one of the jury members in the Young Researcher’s Finale Week. See the post at the Young Academy.
- Mar 16: new release of URDME! Version 1.3 can now be downloaded at www.urdme.org. The new manual can be retrieved via arXiv.
- Mar 9–10: I was involved in organizing Expedition Mundus at SciFest.
- Mar 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.
- Mar 6–7: visit to Lund University, hosted by Alexandros Sopasakis. I gave a talk with the title Data-driven computational Epidemics.
- Feb 8–9: Academy meeting in Gothenburg.
- Jan 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).
- Jan 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.
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