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Hellander, Andreas
Publications (10 of 42) Show all publications
Ausmees, K., John, A., Toor, S. Z., Hellander, A. & Nettelblad, C. (2018). BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data. BMC Bioinformatics, 19, 240:1-11, Article ID 240.
Open this publication in new window or tab >>BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
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2018 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 19, p. 240:1-11, article id 240Article in journal (Refereed) Published
National Category
Software Engineering Genetics
Identifiers
urn:nbn:se:uu:diva-360033 (URN)10.1186/s12859-018-2241-z (DOI)
Projects
eSSENCE
Available from: 2018-06-26 Created: 2018-09-09 Last updated: 2018-09-13Bibliographically approved
Jallow, A., Hellander, A. & Toor, S. (2017). Cost-aware application development and management using CLOUD-METRIC. In: Proc. 7th International Conference on Cloud Computing and Services Science: . Paper presented at CLOSER 2017 (pp. 515-522). Setúbal, Portugal: SciTePress
Open this publication in new window or tab >>Cost-aware application development and management using CLOUD-METRIC
2017 (English)In: Proc. 7th International Conference on Cloud Computing and Services Science, Setúbal, Portugal: SciTePress, 2017, p. 515-522Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Setúbal, Portugal: SciTePress, 2017
National Category
Software Engineering
Identifiers
urn:nbn:se:uu:diva-326539 (URN)10.5220/0006307505150522 (DOI)978-989-758-243-1 (ISBN)
Conference
CLOSER 2017
Projects
eSSENCE
Available from: 2017-04-29 Created: 2017-07-13 Last updated: 2018-01-13Bibliographically approved
Hellander, S., Hellander, A. & Petzold, L. (2017). Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning. Journal of Chemical Physics, 147(23), Article ID 234101.
Open this publication in new window or tab >>Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning
2017 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 23, article id 234101Article in journal (Refereed) Published
Abstract [en]

The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice hard-sphere simulations with Brownian dynamics or Green's function reaction dynamics, the RDME can be orders of magnitude faster if the lattice spacing can be chosen coarse enough. However, strongly diffusion-controlled reactions mandate a very fine mesh resolution for acceptable accuracy. It is common that reactions in the same model differ in their degree of diffusion control and therefore require different degrees of mesh resolution. This renders mesoscopic simulation inefficient for systems with multiscale properties. Mesoscopic-microscopic hybrid methods address this problem by resolving the most challenging reactions with a microscale, off-lattice simulation. However, all methods to date require manual partitioning of a system, effectively limiting their usefulness as "black-box" simulation codes. In this paper, we propose a hybrid simulation algorithm with automatic system partitioning based on indirect a priori error estimates. We demonstrate the accuracy and efficiency of the method on models of diffusion-controlled networks in 3D.

National Category
Other Chemistry Topics
Identifiers
urn:nbn:se:uu:diva-339766 (URN)10.1063/1.5002773 (DOI)000418648200003 ()29272930 (PubMedID)
Funder
NIH (National Institute of Health), R01-EB014877Swedish Research Council, 2015-03964eSSENCE - An eScience Collaboration
Available from: 2018-02-09 Created: 2018-02-09 Last updated: 2018-02-09Bibliographically approved
Engblom, S., Hellander, A. & Lötstedt, P. (2017). Multiscale simulation of stochastic reaction–diffusion networks. In: Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology: (pp. 55-79). Springer
Open this publication in new window or tab >>Multiscale simulation of stochastic reaction–diffusion networks
2017 (English)In: Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, Springer, 2017, p. 55-79Chapter in book (Refereed)
Place, publisher, year, edition, pages
Springer, 2017
National Category
Computational Mathematics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-331828 (URN)10.1007/978-3-319-62627-7_3 (DOI)978-3-319-62626-0 (ISBN)
Projects
eSSENCE
Available from: 2017-10-05 Created: 2017-10-18 Last updated: 2017-10-18Bibliographically approved
Kaucka, M., Zikmund, T., Tesarova, M., Gyllborg, D., Hellander, A., Jaros, J., . . . Adameyko, I. (2017). Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage. eLIFE, 6, Article ID e25902.
Open this publication in new window or tab >>Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage
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2017 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 6, article id e25902Article in journal (Refereed) Published
National Category
Cell Biology Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-320902 (URN)10.7554/eLife.25902 (DOI)000400576600001 ()
Projects
eSSENCE
Available from: 2017-04-17 Created: 2017-04-26 Last updated: 2018-01-13Bibliographically approved
Hellander, A., Klosa, J., Lötstedt, P. & MacNamara, S. (2017). Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuations. SIAM Journal on Applied Mathematics, 77, 1157-1183
Open this publication in new window or tab >>Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuations
2017 (English)In: SIAM Journal on Applied Mathematics, ISSN 0036-1399, E-ISSN 1095-712X, Vol. 77, p. 1157-1183Article in journal (Refereed) Published
National Category
Computational Mathematics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-326829 (URN)10.1137/15M1052317 (DOI)000408945700004 ()
Projects
eSSENCE
Available from: 2017-07-27 Created: 2017-07-31 Last updated: 2017-12-08Bibliographically approved
Toor, S., Lindberg, M., Fällman, I., Vallin, A., Mohill, O., Freyhult, P., . . . Hellander, A. (2017). SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia. In: Proc. 13th International Conference on e-Science: . Paper presented at e-Science 2017, October 24–27, Auckland, New Zealand (pp. 219-227). Los Alamitos, CA: IEEE Computer Society
Open this publication in new window or tab >>SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia
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2017 (English)In: Proc. 13th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2017, p. 219-227Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Los Alamitos, CA: IEEE Computer Society, 2017
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:uu:diva-334646 (URN)10.1109/eScience.2017.35 (DOI)000426071600024 ()978-1-5386-2686-3 (ISBN)
Conference
e-Science 2017, October 24–27, Auckland, New Zealand
Projects
eSSENCE
Funder
Swedish National Infrastructure for Computing (SNIC)
Available from: 2017-11-16 Created: 2017-11-24 Last updated: 2018-05-25Bibliographically approved
Singh, P. & Hellander, A. (2017). Surrogate assisted model reduction for stochastic biochemical reaction networks. In: Proc. 49th Winter Simulation Conference: . Paper presented at WSC 2017, December 3–6, Las Vegas, NV (pp. 1773-1783). Piscataway, NJ: IEEE
Open this publication in new window or tab >>Surrogate assisted model reduction for stochastic biochemical reaction networks
2017 (English)In: Proc. 49th Winter Simulation Conference, Piscataway, NJ: IEEE, 2017, p. 1773-1783Conference paper, Published paper (Refereed)
Place, publisher, year, edition, pages
Piscataway, NJ: IEEE, 2017
National Category
Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-334364 (URN)10.1109/WSC.2017.8247915 (DOI)000427768601081 ()978-1-5386-3428-8 (ISBN)
Conference
WSC 2017, December 3–6, Las Vegas, NV
Projects
eSSENCE
Available from: 2018-01-08 Created: 2017-11-22 Last updated: 2018-06-16Bibliographically approved
Meinecke, L., Engblom, S., Hellander, A. & Lötstedt, P. (2016). Analysis and design of jump coefficients in discrete stochastic diffusion models. SIAM Journal on Scientific Computing, 38, A55-A83
Open this publication in new window or tab >>Analysis and design of jump coefficients in discrete stochastic diffusion models
2016 (English)In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 38, p. A55-A83Article in journal (Refereed) Published
National Category
Computational Mathematics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-272192 (URN)10.1137/15M101110X (DOI)000371235600003 ()
Projects
UPMARCeSSENCE
Available from: 2016-01-06 Created: 2016-01-12 Last updated: 2017-11-30Bibliographically approved
Kaucka, M., Ivashkin, E., Gyllborg, D., Zikmund, T., Tesarova, M., Kaiser, J., . . . Adameyko, I. (2016). Analysis of neural crest-derived clones reveals novel aspects of facial development. Science Advances, 2(8), e1600060:1-16, Article ID e1600060.
Open this publication in new window or tab >>Analysis of neural crest-derived clones reveals novel aspects of facial development
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2016 (English)In: Science Advances, ISSN 2375-2548, Vol. 2, no 8, p. e1600060:1-16, article id e1600060Article in journal (Refereed) Published
National Category
Cell Biology Bioinformatics (Computational Biology)
Identifiers
urn:nbn:se:uu:diva-300365 (URN)10.1126/sciadv.1600060 (DOI)000383734300009 ()
Projects
eSSENCE
Available from: 2016-08-03 Created: 2016-08-08 Last updated: 2018-01-10Bibliographically approved
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