Projects
Department of Numerical Analysis and Scientific Computing
The Department of Numerical Analysis and Scientific Computing (SCAN) aims to develop mathematical methods and scientific tools to reach a new understanding of complex physical processes. We target fundamental medical and industrial problems where new insights from mathematical modelling can advance today’s knowledge. In support of these applications, we also develop generally useful software tools for facilitating reproducible research practices and the communication of computational ideas.
The SCAN department hosts research projects with multi-disciplinary teams consisting of experts in mathematics, numerical methods, physical modelling and optimization, and scientific software development.
Our research teams focus on publishing novel research results of high relevance and quality. The challenging applications being addressed drive new developments in computational methodologies and scientific software. A key mission of the department is to make these developments accessible to computational scientists and engineers at large through professional, open-source software.
Simula Seminars in Scientific Computing
The Simula Seminars in Scientific Computing is a seminar series where we invite outstanding national and international speakers in scientific computing and application areas such as biology, physiology or geoscience to present their research. On the first Thursday of every month, the Department of Numerical Analysis and Scientific Computing will host a seminar. For more information, click here.
Publications for Department of Numerical Analysis and Scientific Computing
Book Chapter
Finite element software and performance for mixed-dimensional network models
In TBA, TBA. Springer, 2023.Status: Submitted
Finite element software and performance for mixed-dimensional network models
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
Publication Type | Book Chapter |
Year of Publication | 2023 |
Book Title | TBA |
Pagination | TBA |
Publisher | Springer |
Inducing Flow Instabilities in Aneurysm Geometries via the Reynolds-Orr Method
79-89. Vol. 13. Cham: Springer Nature Switzerland, 2023.Status: Published
Inducing Flow Instabilities in Aneurysm Geometries via the Reynolds-Orr Method
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Book Chapter |
Year of Publication | 2023 |
Volume | 13 |
Pagination | 79 - 89 |
Publisher | Springer Nature Switzerland |
Place Published | Cham |
ISBN Number | 978-3-031-25373-7 |
ISBN | 2512-1677 |
URL | https://link.springer.com/10.1007/978-3-031-25374-4https://link.springer... |
DOI | 10.1007/978-3-031-25374-410.1007/978-3-031-25374-4_6 |
Journal Article
Modeling excitable cells with the EMI equations: spectral analysis and iterative solution strategy
TBA (2023).Status: Submitted
Modeling excitable cells with the EMI equations: spectral analysis and iterative solution strategy
Afilliation | Scientific Computing |
Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | TBA |
Publisher | TBA |
URL | https://doi.org/10.48550/arXiv.2308.12145 |
DOI | 10.48550/arXiv.2308.12145 |
SMART: Spatial Modeling Algorithms for Reaction and Transport
Journal of Open Source Software (2023).Status: Submitted
SMART: Spatial Modeling Algorithms for Reaction and Transport
Afilliation | Scientific Computing |
Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Journal of Open Source Software |
Publisher | TBA |
DOI |
Cut finite element discretizations of cell-by-cell EMI electrophysiology models
TBA (2023).Status: Submitted
Cut finite element discretizations of cell-by-cell EMI electrophysiology models
Afilliation | Scientific Computing |
Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | TBA |
Publisher | TBA |
URL | https://doi.org/10.48550/arXiv.2306.03001 |
DOI | 10.48550/arXiv.2306.03001 |
The directional flow generated by peristalsis in perivascular networks - theoretical and numerical reduced-order description
Journal of Applied Physics (2023).Status: Submitted
The directional flow generated by peristalsis in perivascular networks - theoretical and numerical reduced-order description
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Journal of Applied Physics |
Publisher | AIP Publishing |
The modelling error in multi-dimensional time-dependent solute transport models
TBA (2023).Status: Submitted
The modelling error in multi-dimensional time-dependent solute transport models
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Exciting times: Extreme modelling of excitable tissue (EMIx) |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | TBA |
Publisher | TBA |
URL | https://arxiv.org/abs/2303.17999 |
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space – a computational study
PLoS Computational Biology 19, no. 7 (2023): e1010996.Status: Published
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space – a computational study
Afilliation | Scientific Computing |
Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | PLoS Computational Biology |
Volume | 19 |
Issue | 7 |
Pagination | e1010996 |
Date Published | 07/2023 |
Publisher | Public Library of Science |
URL | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1... |
DOI | 10.1371/journal.pcbi.1010996 |
Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation
Fluids and Barriers of the Central Nervous System (2023).Status: Published
Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation
Human brain homeostasis requires carefully regulated transport of nutrients and waste, but its governing mechanisms are hard to quantify. By combining multi-modal gMRI data over 48 hours with high-fidelity inverse computational modelling, we here identify several potential transport mechanisms that best explain the clinical observations. Our findings support the combined roles of local, vascular and glymphatic-type clearance pathways within human brain tissue with tissue flow velocities on the order of $\mu$m/min, local clearance rates at the order of 10**(-3)/min, and enhanced diffusion by a factor 3.5, in sleeping and sleep-deprived subjects. Reduced advection fully explains reduced tracer clearance after sleep-deprivation, supporting the role of sleep and sleep deprivation on human brain clearance.
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Exciting times: Extreme modelling of excitable tissue (EMIx) |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Fluids and Barriers of the Central Nervous System |
Date Published | 08/2023 |
Publisher | Springer Nature |
DOI | 10.1101/2023.01.01.522190 |
simcardems: A FEniCS-based cardiac electro-mechanicssolver
Journal of Open Source Software 88442954520810717, no. 81411347316 (2023): 4753.Status: Published
simcardems: A FEniCS-based cardiac electro-mechanicssolver
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, Department of Numerical Analysis and Scientific Computing, Simulation of Cardiac Devices and Drugs for In-Silico Testing and Certification (SimCardioTest) |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Journal of Open Source Software |
Volume | 88442954520810717 |
Issue | 81411347316 |
Pagination | 4753 |
Date Published | Jan-01-2023 |
Publisher | JOSS |
URL | https://joss.theoj.org/papers/10.21105/joss.04753 |
DOI | 10.21105/joss.04753 |
Publications
Journal Article
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space – a computational study
PLoS Computational Biology 19, no. 7 (2023): e1010996.Status: Published
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space – a computational study
Afilliation | Scientific Computing |
Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | PLoS Computational Biology |
Volume | 19 |
Issue | 7 |
Pagination | e1010996 |
Date Published | 07/2023 |
Publisher | Public Library of Science |
URL | https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1... |
DOI | 10.1371/journal.pcbi.1010996 |
Talks, invited
Computational brainphatics: coupled models of mechanics and electrophysiology in brain tissue
In DigiBrain Symposium, Simula Research Laboratory, Oslo, Norway, 2022.Status: Published
Computational brainphatics: coupled models of mechanics and electrophysiology in brain tissue
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
Publication Type | Talks, invited |
Year of Publication | 2022 |
Location of Talk | DigiBrain Symposium, Simula Research Laboratory, Oslo, Norway |
Finite element simulation of ionic electrodiffusion in cellular geometries
In University of Pennsylvania, Philadelphia, USA, 2022.Status: Published
Finite element simulation of ionic electrodiffusion in cellular geometries
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
Publication Type | Talks, invited |
Year of Publication | 2022 |
Location of Talk | University of Pennsylvania, Philadelphia, USA |
Talks, contributed
Finite element simulation of ionic electrodiffusion in cellular geometries
In CAIMS/SCMAI 2022, Kelowna, Canada, 2022.Status: Published
Finite element simulation of ionic electrodiffusion in cellular geometries
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx), Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Talks, contributed |
Year of Publication | 2022 |
Location of Talk | CAIMS/SCMAI 2022, Kelowna, Canada |
Numerical simulation of electrodiffusion and osmosis in brain tissue
In 9th World Congress of Biomechanics, online, 2022.Status: Published
Numerical simulation of electrodiffusion and osmosis in brain tissue
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2022 |
Location of Talk | 9th World Congress of Biomechanics, online |
Poster
Modeling electrodiffusive, osmotic, and hydrostatic interplay in astrocyte networks
Neuroscience 2022: Society for Neuroscience, 2022.Status: Published
Modeling electrodiffusive, osmotic, and hydrostatic interplay in astrocyte networks
During high neuronal activity, the intra- and extracellular ion concentrations change. These changes affect the osmotic pressure gradients across the membranes of both neurons and astrocytes, leading to water movement and cellular swelling. We asked: Can swelling generate a hydrostatic pressure gradient of sufficient magnitude to drive non-negligible fluid flow within astrocytes or the extracellular space [1]? As it is currently infeasible to measure such intracellular pressure gradients in vivo, computational modeling emerges as a viable alternative to study the interplay between osmotic and hydrostatic forces at the microscale.
In this study, we present a computational model of ionic electrodiffusion, hydrostatic pressures, and transmembrane- and intracompartmental fluid flow in a homogenized astrocytic syncytium surrounded by extracellular space. The model builds on previous models of ionic electrodiffusion [2,3], and potassium buffering [4]. Our findings show that increases in extracellular potassium concentrations in response to neuronal activity induce swelling and hydrostatic pressure gradients within the intra- and extracellular spaces. The fluid flow induced by these hydrostatic pressure gradients alone did not have a significant effect on the transport of potassium within any of the compartments. However, when also accounting for fluid flow induced by osmotic gradients within the astrocytic syncytium, convection played a considerable role in potassium clearance. These findings point at a mechanistic understanding of how astrocytic permeability may impact fluid flow in the brain.
[1] Halnes, G., Pettersen, K. H., Øyehaug, L., Rognes, M. E. & Einevoll, G. T. Astrocytic ion dynamics: Implications for potassium buffering and liquid flow. In Computational Glioscience, 363–391 (Springer, 2019).
[2] Mori, Y. A multidomain model for ionic electrodiffusion and osmosis with an application to cortical spreading depression. Phys. D: Nonlinear Phenom. 308, 94–108 (2015).
[3] Zhu, Y., Xu, S., Eisenberg, R. S. & Huang, H. Optic nerve microcirculation: Fluid flow and electrodiffusion. Phys. Fluids 33, 041906 (2021).
[4] Halnes, G., Østby, I., Pettersen, K. H., Omholt, S. W. & Einevoll, G. T. Electrodiffusive model for astrocytic and neuronal ion concentration dynamics. PLoS computational biology 9, e1003386 (2013).
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Poster |
Year of Publication | 2022 |
Date Published | 11/2022 |
Publisher | Society for Neuroscience |
Place Published | Neuroscience 2022 |
Journal Article
Validating a computational framework for ionic electrodiffusion with cortical spreading depression as a case study
eNeuro 9 (2022).Status: Published
Validating a computational framework for ionic electrodiffusion with cortical spreading depression as a case study
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | eNeuro |
Volume | 9 |
Number | 2 |
Date Published | 04/2022 |
Publisher | Society for Neuroscience |
Book Chapter
A cell-based model for ionic electrodiffusion in excitable tissue
In Modeling Excitable Tissue: The EMI Framework, 14-27. Cham: Springer International Publishing, 2021.Status: Published
A cell-based model for ionic electrodiffusion in excitable tissue
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Book Chapter |
Year of Publication | 2021 |
Book Title | Modeling Excitable Tissue: The EMI Framework |
Series Volume | 7 |
Pagination | 14-27 |
Publisher | Springer International Publishing |
Place Published | Cham |
URL | https://www.springer.com/gp/book/9783030611569 |
Journal Article
Abstractions and automated algorithms for mixed-dimensional finite element methods
ACM Transactions on Mathematical Software 47, no. 4 (2021): 1-36.Status: Published
Abstractions and automated algorithms for mixed-dimensional finite element methods
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | ACM Transactions on Mathematical Software |
Volume | 47 |
Issue | 4 |
Pagination | 1-36 |
Date Published | 09/2021 |
Publisher | ACM |
Accurate numerical simulation of electrodiffusion and water movement in brain tissue
IMA Mathematical Medicine and Biology 38, no. 4 (2021): 516-551.Status: Published
Accurate numerical simulation of electrodiffusion and water movement in brain tissue
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | IMA Mathematical Medicine and Biology |
Volume | 38 |
Issue | 4 |
Pagination | 516–551 |
Date Published | 11/2021 |
Publisher | IMA |
Talks, contributed
Accurate numerical simulation of electrodiffusion and water movement in brain tissue with cortical spreading depression as a case study
In Interpore 13th annual meeting (online). Online, 2021.Status: Published
Accurate numerical simulation of electrodiffusion and water movement in brain tissue with cortical spreading depression as a case study
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Talks, contributed |
Year of Publication | 2021 |
Location of Talk | Interpore 13th annual meeting (online) |
Place Published | Online |
Type of Talk | Conference talk |
PhD Thesis
Computational modelling of electrodiffusion and osmosis in cerebral tissue
In University of Oslo. Vol. PhD, 2021.Status: Published
Computational modelling of electrodiffusion and osmosis in cerebral tissue
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | PhD Thesis |
Year of Publication | 2021 |
Degree awarding institution | University of Oslo |
Degree | PhD |
Journal Article
Finite element simulation of ionic electrodiffusion in cellular geometries
Frontiers in Neuroinformatics 14 (2020): 11.Status: Published
Finite element simulation of ionic electrodiffusion in cellular geometries
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Frontiers in Neuroinformatics |
Volume | 14 |
Pagination | 11 |
Publisher | Frontiers |
DOI | 10.3389/fninf.2020.00011 |
Talks, contributed
Finite element simulation of ionic electrodiffusion in cellular geometries
In Online. Online: 29th annual computational neuroscience meeting, 2020.Status: Published
Finite element simulation of ionic electrodiffusion in cellular geometries
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Talks, contributed |
Year of Publication | 2020 |
Location of Talk | Online |
Publisher | 29th annual computational neuroscience meeting |
Place Published | Online |
Type of Talk | Conference talk |
Proceedings, refereed
Parametric exploration of cellular swelling in a computational model of cortical spreading depression
In 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Montreal, QC, Canada: IEEE, 2020.Status: Published
Parametric exploration of cellular swelling in a computational model of cortical spreading depression
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Proceedings, refereed |
Year of Publication | 2020 |
Conference Name | 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC) |
Pagination | 2491-2495 |
Date Published | 07/2020 |
Publisher | IEEE |
Place Published | Montreal, QC, Canada |
Talks, contributed
A computational model for cerebral electrodiffusion based on explicit geometrical representation
In FEniCS 2019, Washington DC, USA, 2019.Status: Published
A computational model for cerebral electrodiffusion based on explicit geometrical representation
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Talks, contributed |
Year of Publication | 2019 |
Location of Talk | FEniCS 2019, Washington DC, USA |
A mathematical framework for cerebral electrodiffusion based on explicit geometrical representation
In Workshop with UiB, Oslo, Norway, 2019.Status: Published
A mathematical framework for cerebral electrodiffusion based on explicit geometrical representation
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Talks, contributed |
Year of Publication | 2019 |
Location of Talk | Workshop with UiB, Oslo, Norway |
Public outreach
Mathematical modelling of glials - the forgotten brain cell
The "Ada Lovlace day" arranged by EL&IT (Oslo, Norway), 2019.Status: Published
Mathematical modelling of glials - the forgotten brain cell
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Public outreach |
Year of Publication | 2019 |
Publisher | The "Ada Lovlace day" arranged by EL&IT (Oslo, Norway) |
Poster
Modelling of the role of glial cells in cerebral interstitial fluid movement
IMA workshop on Mathematical Modeling of Cortical Spreading Depression and Related Phenomena (Minneapolis, USA), 2018.Status: Published
Modelling of the role of glial cells in cerebral interstitial fluid movement
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Poster |
Year of Publication | 2018 |
Place Published | IMA workshop on Mathematical Modeling of Cortical Spreading Depression and Related Phenomena (Minneapolis, USA) |
Modelling of the role of glial cells in cerebral interstitial fluid movement
FEniCS 2018 (Oxford, UK), 2018.Status: Published
Modelling of the role of glial cells in cerebral interstitial fluid movement
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Poster |
Year of Publication | 2018 |
Place Published | FEniCS 2018 (Oxford, UK) |
Poster
Modelling of the role of glial cells in cerebral interstitial fluid movement
5th HBP School on Future Medicine, Obergurgl, Austria, 2017.Status: Published
Modelling of the role of glial cells in cerebral interstitial fluid movement
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
Publication Type | Poster |
Year of Publication | 2017 |
Place Published | 5th HBP School on Future Medicine, Obergurgl, Austria |