Projects
Waterscape: The Numerical Waterscape of the Brain
Your brain has its own waterscape: Whether you are reading or sleeping, fluid flows through your brain tissue and clears out waste. New medical research has shown that this waterscape is more essential than what was previously believed and that this flow is indeed crucial for the brain's well-being. In particular, the waste accumulation is linked to neurological diseases such as dementia (Alzheimer's disease) and to brain swelling caused by stroke.
Today, our understanding of the brain's cleansing process is dominated by experimental studies on mice during which pieces of brain tissue close to the skull are removed and studied via microscope. However, such methods have their weaknesses: It is hard or even impossible to look deep enough into the brain and it is not feasible to study the human brain with the same techniques.
This project, "The Numerical Waterscape of the Brain", aims to develop a new computational technology platform that instead allows for studying the brain's waterscape through numerical computations and simulations. The project will develop new, reliable numerical methods for computing the flow of tissue fluid through the brain, will evaluate and compare different models and scenarios, and will validate the simulation results using data from physical experiments. The project will also push forward and use computer simulations as virtual experiments to see how sleep can affect the fluid flow through brain tissue and how to ensure best possible clearance of waste through the waterscape.
The project will yield new mathematical models and numerical methods together with freely available open source simulation software for further use and new studies. As such, the project will provide an entirely new avenue for understanding the brain's waterscape.
Final goal:
The primary objective of this project is to develop a new numerical and technological foundation for computational studies of tissue fluid circulation and metabolic solute transport through the brain under both normal and pathological conditions.
Funding source:
Research Council of Norway, FRINATEK
Publications for Waterscape: The Numerical Waterscape of the Brain
Journal Article
Accurate discretization of poroelasticity without Darcy stability – Stokes-Biot revisited
BIT Numerical Mathematics 61 (2021): 941-976.Status: Published
Accurate discretization of poroelasticity without Darcy stability – Stokes-Biot revisited
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2021 |
| Journal | BIT Numerical Mathematics |
| Volume | 61 |
| Pagination | 941-976 |
| Publisher | Springer |
| DOI | 10.1007/s10543-021-00849-0 |
Parameter robust preconditioning by congruence for multiple-network poroelasticity
SIAM Journal of Scientific Computing 43, no. 4 (2021): B984-B1007.Status: Published
Parameter robust preconditioning by congruence for multiple-network poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2021 |
| Journal | SIAM Journal of Scientific Computing |
| Volume | 43 |
| Issue | 4 |
| Pagination | B984–B1007 |
| Publisher | SIAM |
| DOI | 10.1137/20M1326751 |
Proceedings, refereed
A mixed framework for topological model reduction of coupled PDEs
In 9th edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering. CIMNE, 2021.Status: Published
A mixed framework for topological model reduction of coupled PDEs
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2021 |
| Conference Name | 9th edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering |
| Publisher | CIMNE |
| URL | https://www.scipedia.com/public/Gjerde_Rognes_2021a |
| DOI | 10.23967/coupled.2021.005 |
Parameter robust preconditioning for multi-compartmental Darcy equations
In Numerical Mathematics and Advanced Applications ENUMATH 2019. Vol. 139. Springer International Publishing, 2021.Status: Published
Parameter robust preconditioning for multi-compartmental Darcy equations
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2021 |
| Conference Name | Numerical Mathematics and Advanced Applications ENUMATH 2019 |
| Volume | 139 |
| Edition | 1 |
| Pagination | 794–797 |
| Publisher | Springer International Publishing |
| DOI | 10.1007/978-3-030-55874-1 |
Journal Article
Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo
International Journal for Numerical Methods in Biomedical Engineering 37, no. 1 (2020): e3412.Status: Published
Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Waterscape: The Numerical Waterscape of the Brain, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Journal Article |
| Year of Publication | 2020 |
| Journal | International Journal for Numerical Methods in Biomedical Engineering |
| Volume | 37 |
| Issue | 1 |
| Pagination | e3412 |
| Date Published | 11/2020 |
| Publisher | Wiley |
| URL | https://onlinelibrary.wiley.com/doi/full/10.1002/cnm.3412 |
Intracranial pressure elevation alters CSF clearance pathways
Fluids and Barriers of the CNS 17 (2020).Status: Published
Intracranial pressure elevation alters CSF clearance pathways
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, 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 | Fluids and Barriers of the CNS |
| Volume | 17 |
| Number | 29 |
| Date Published | 04/2020 |
| Publisher | Springer Nature BMC |
| Keywords | brain mechanics, Cerebrospinal Fluid, Intracranial pressure |
| DOI | 10.1186/s12987-020-00189-1 |
PhD Thesis
Multilevel Monte Carlo methods for uncertainty quantification in brain simulations
In The University of Oxford, 2020.Status: Published
Multilevel Monte Carlo methods for uncertainty quantification in brain simulations
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | PhD Thesis |
| Year of Publication | 2020 |
| Degree awarding institution | The University of Oxford |
Journal Article
Magnitude and direction of aqueductal cerebrospinal fluid flow: large variations in patients with intracranial aneurysms with or without a previous subarachnoid hemorrhage
Acta neurochirurgica 161 (2019): 247-256.Status: Published
Magnitude and direction of aqueductal cerebrospinal fluid flow: large variations in patients with intracranial aneurysms with or without a previous subarachnoid hemorrhage
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | Acta neurochirurgica |
| Volume | 161 |
| Number | 2 |
| Pagination | 247–256 |
| Publisher | Springer |
| Place Published | Acta neurochirurgica |
Delayed clearance of cerebrospinal fluid tracer from choroid plexus in idiopathic normal pressure hydrocephalus
Journal of Cerebral Blood Flow & Metabolism 2530 (2019): 0271678X1987479.Status: Published
Delayed clearance of cerebrospinal fluid tracer from choroid plexus in idiopathic normal pressure hydrocephalus
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | Journal of Cerebral Blood Flow & Metabolism |
| Volume | 2530 |
| Pagination | 0271678X1987479 |
| Date Published | Jul-09-2019 |
| Publisher | SAGE journals |
| Place Published | Journal of Cerebral Blood Flow and Metabolism |
| ISSN | 0271-678X |
| URL | http://journals.sagepub.com/doi/10.1177/0271678X19874790http://journals.... |
| DOI | 10.1177/0271678X19874790 |
Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields
Fluids and Barriers of the Central Nervous System 16 (2019): 32.Status: Published
Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | Fluids and Barriers of the Central Nervous System |
| Volume | 16 |
| Number | 1 |
| Pagination | 32 |
| Date Published | 09/2019 |
| Publisher | BMC |
| URL | https://europepmc.org/articles/pmc6767654 |
| DOI | 10.1186/s12987-019-0152-7 |
Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow
Your brain has its own waterscape: whether you are reading or sleeping, fluid flows through the brain tissue and clears waste in the process. These physiological processes are crucial for the well-being of the brain. In spite of their importance we understand them but little. Mathematics and numerics could play a crucial role in gaining new
insight. Indeed, medical doctors express an urgent need for multiscale modeling of water transport through the brain, to overcome limitations in traditional techniques. Surprisingly little attention has been paid to the numerics of the brain’s waterscape however, and fundamental knowledge is missing.
In response, the Waterscales ambition is to establish the mathematical and computational foundations for predictively modeling fluid flow and solute transport through the brain across scales – from the cellular to the organ level. The project aims to bridge multiscale fluid mechanics and cellular electrophysiology to pioneer new families of mathematical models that couple macroscale, mesoscale and microscale flow with glial cell dynamics. For these models, we will design numerical discretizations that preserve key properties and that allow for whole organ simulations. To evaluate predictability, we will develop a new computational platform for model adaptivity and calibration. The project is multidisciplinary combining mathematics, mechanics, scientific computing, and physiology.
If successful, this project enables the first in silico studies of the brain’s waterscape across scales. The new models would open up a new research field within computational neuroscience with ample opportunities for further mathematical and more applied study. The processes at hand are associated with neurodegenerative diseases e.g. dementia and with brain swelling caused by e.g. stroke. The Waterscales project will provide the field with a sorely needed, new avenue of investigation to understand these conditions, with tremendous long-term impact.
Final goal
The Waterscales ambition is to establish the mathematical and computational foundations for predictively modeling fluid flow and solute transport through the brain across scales – from the cellular to the organ level.
Funding source
This project has received funding from the European Union’s Horizon 2020 ERC grant agreement no. 714892. (ERC-2016-STG - ERC Starting Grant)
Partners
Simula Research Laboratory
Media presence
Publications for Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow
Journal Article
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 |
Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study
PLOS ONE (2023).Status: Accepted
Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
| Publication Type | Journal Article |
| Year of Publication | 2023 |
| Journal | PLOS ONE |
| Publisher | PLOS |
| URL | https://www.biorxiv.org/content/10.1101/2022.09.07.506967v1 |
| DOI | 10.1101/2022.09.07.506967 |
The role of clearance in neurodegenerative disease
SIAM Journal on Applied Mathematics (2023).Status: Published
The role of clearance in neurodegenerative disease
| Afilliation | Scientific Computing |
| Project(s) | 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 | SIAM Journal on Applied Mathematics |
| Date Published | 07/2023 |
| Publisher | SIAM |
| URL | https://doi.org/10.1101/2022.03.31.486533 |
Optimal control of Hopf bifurcation points
SIAM Journal on Scientific Computing 45, no. 3 (2023).Status: Published
Optimal control of Hopf bifurcation points
| Afilliation | Scientific Computing |
| Project(s) | 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 | SIAM Journal on Scientific Computing |
| Volume | 45 |
| Issue | 3 |
| Publisher | SIAM |
| URL | https://epubs.siam.org/doi/abs/10.1137/22M1474448 |
| DOI | 10.1137/22M14744 |
A-posteriori error estimation and adaptivity for multiple-network poroelasticity
ESIAM: Mathematical Modelling and Numerical Analysis 57 (2023): 1921-1952.Status: Published
A-posteriori error estimation and adaptivity for multiple-network poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | 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 | ESIAM: Mathematical Modelling and Numerical Analysis |
| Volume | 57 |
| Number | 4 |
| Pagination | 1921 - 1952 |
| Date Published | 07/2023 |
| Publisher | ESAIM |
| URL | https://doi.org/10.1051/m2an/2023033 |
| DOI | 10.1051/m2an/2023033 |
Public outreach
Paneldeltager i Abels tårn
In Vil vi kunne gjøre opptak av våre drømmer i fremtiden? NRK P2, 2023.Status: Published
Paneldeltager i Abels tårn
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Public outreach |
| Year of Publication | 2023 |
| Secondary Title | Vil vi kunne gjøre opptak av våre drømmer i fremtiden? |
| Date Published | 05/2023 |
| Publisher | NRK P2 |
| Type of Work | Radio / Podcast |
| URL | https://radio.nrk.no/podkast/abels_taarn/sesong/202305/l_e3cb7694-7667-4... |
Hjerneprat med Marte Julie Sætra og Gaute Einevoll - Del 3
YouTube: Simula, 2023.Status: Published
Hjerneprat med Marte Julie Sætra og Gaute Einevoll - Del 3
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Public outreach |
| Year of Publication | 2023 |
| Date Published | 01/2023 |
| Publisher | Simula |
| Place Published | YouTube |
| Type of Work | Videocast |
| URL | https://youtu.be/pTq-GZVZjh0 |
Hjerneprat med Marte Julie Sætra og Gaute Einevoll - Del 2
YouTube: Simula, 2023.Status: Published
Hjerneprat med Marte Julie Sætra og Gaute Einevoll - Del 2
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Public outreach |
| Year of Publication | 2023 |
| Date Published | 01/2023 |
| Publisher | Simula |
| Place Published | YouTube |
| Type of Work | Videocast |
| URL | https://youtu.be/BP9tY6AUMQU |
Exciting times: Extreme modelling of excitable tissue (EMIx)
Our brains are composed of excitable intertangled tissue consisting of neurons, glial cells, interstitial space and blood vessels, featuring an intricate and unique interplay between ion and water movement, electrical activity, and cellular swelling. Mathematical modelling and simulation could unravel elusive mechanisms underlying these processes, but key theory and technology are lacking. In response, the EMIx ambition is to establish mathematical and technological foundations for detailed modelling and simulation of electrical, chemical and mechanical interplay between brain cells, allowing for pioneering in-silico studies of brain signalling, volume balance and clearance. We will pursue an interdisciplinary approach targeting research questions in applied mathematics, scientific computing, and glio- and neuroscience via mathematical and computational techniques leveraging experimental findings.
If successful, EMIx will introduce new mathematical frameworks for modelling electrical, chemical and mechanical interactions in detailed representations of excitable tissue via coupled mixed-dimensional partial differential equations. We will design and openly distribute numerical methods that allow for extreme high-resolution--high realism simulations of such models. We will create innovative in-silico platforms for studying neuronal-glialextracellular interactions at unprecedented detail and create new insight into the mechanisms underlying the role of the brain's star cells (astrocytes) in brain ion and volume balance. Ultimately, EMIx will provide a new avenue of investigation for understanding physiological processes in the brain underlying oedema and neurodegenerative diseases.
Publications for Exciting times: Extreme modelling of excitable tissue (EMIx)
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 |
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 |
I currently work on the IdentiPhy project where I am hired as a senior research engineer to develop tools and software to analyse and model heart-on-chip systems.
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 |
Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study
PLOS ONE (2023).Status: Accepted
Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
| Publication Type | Journal Article |
| Year of Publication | 2023 |
| Journal | PLOS ONE |
| Publisher | PLOS |
| URL | https://www.biorxiv.org/content/10.1101/2022.09.07.506967v1 |
| DOI | 10.1101/2022.09.07.506967 |
Talks, contributed
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space
In 32nd Annual Computational Neuroscience Meeting. Organization for Computational Neuroscience, 2023.Status: Published
Neural activity induces strongly coupled electro-chemo-mechanical interactions and fluid flow in astrocyte networks and extracellular space
| 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 | 2023 |
| Location of Talk | 32nd Annual Computational Neuroscience Meeting |
| Publisher | Organization for Computational Neuroscience |
Publications
Journal Article
A-posteriori error estimation and adaptivity for multiple-network poroelasticity
ESIAM: Mathematical Modelling and Numerical Analysis 57 (2023): 1921-1952.Status: Published
A-posteriori error estimation and adaptivity for multiple-network poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | 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 | ESIAM: Mathematical Modelling and Numerical Analysis |
| Volume | 57 |
| Number | 4 |
| Pagination | 1921 - 1952 |
| Date Published | 07/2023 |
| Publisher | ESAIM |
| URL | https://doi.org/10.1051/m2an/2023033 |
| DOI | 10.1051/m2an/2023033 |
Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study
PLOS ONE (2023).Status: Accepted
Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing, Exciting times: Extreme modelling of excitable tissue (EMIx) |
| Publication Type | Journal Article |
| Year of Publication | 2023 |
| Journal | PLOS ONE |
| Publisher | PLOS |
| URL | https://www.biorxiv.org/content/10.1101/2022.09.07.506967v1 |
| DOI | 10.1101/2022.09.07.506967 |
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 |
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 |
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 |
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 |
Optimal control of Hopf bifurcation points
SIAM Journal on Scientific Computing 45, no. 3 (2023).Status: Published
Optimal control of Hopf bifurcation points
| Afilliation | Scientific Computing |
| Project(s) | 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 | SIAM Journal on Scientific Computing |
| Volume | 45 |
| Issue | 3 |
| Publisher | SIAM |
| URL | https://epubs.siam.org/doi/abs/10.1137/22M1474448 |
| DOI | 10.1137/22M14744 |
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 |
I currently work on the IdentiPhy project where I am hired as a senior research engineer to develop tools and software to analyse and model heart-on-chip systems.
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 |
The role of clearance in neurodegenerative disease
SIAM Journal on Applied Mathematics (2023).Status: Published
The role of clearance in neurodegenerative disease
| Afilliation | Scientific Computing |
| Project(s) | 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 | SIAM Journal on Applied Mathematics |
| Date Published | 07/2023 |
| Publisher | SIAM |
| URL | https://doi.org/10.1101/2022.03.31.486533 |
Talks, invited
Brains in motion - computational modelling of the brain's waterscape
In Fluid Mechanics, Combustion, & Engineering Physics Seminar, University of California San Diego, San Diego, US, 2023.Status: Published
Brains in motion - computational modelling of the brain's waterscape
| 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, invited |
| Year of Publication | 2023 |
| Location of Talk | Fluid Mechanics, Combustion, & Engineering Physics Seminar, University of California San Diego, San Diego, US |
Brains in motion - computational modelling of the brain's waterscape
In Oden Institute Seminar, University of Texas at Austin, TX, US, 2023.Status: Published
Brains in motion - computational modelling of the brain's waterscape
| Afilliation | Scientific Computing |
| Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2023 |
| Location of Talk | Oden Institute Seminar, University of Texas at Austin, TX, US |
Perivascular pathways and the dimension-2 gap
In Numerical Analysis and Scientific Computing Seminar, Courant Institute, NY, US, 2023.Status: Published
Perivascular pathways and the dimension-2 gap
| Afilliation | Scientific Computing |
| Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2023 |
| Location of Talk | Numerical Analysis and Scientific Computing Seminar, Courant Institute, NY, US |
Perivascular pathways and the dimension-2 gap
In Scientific Computing Seminar, Brown University, Providence, Rhode Island, US, 2023.Status: Published
Perivascular pathways and the dimension-2 gap
| Afilliation | Scientific Computing |
| Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2023 |
| Location of Talk | Scientific Computing Seminar, Brown University, Providence, Rhode Island, US |
Perivascular pathways and the dimension-2 gap
In CMOR Colloqium Series, Rice University, Houston, TX, US, 2023.Status: Published
Perivascular pathways and the dimension-2 gap
| 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 | 2023 |
| Location of Talk | CMOR Colloqium Series, Rice University, Houston, TX, US |
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 |
Journal Article
A scalable solver for a stochastic, hybrid cellular automaton model of personalized breast cancer therapy
International Journal for Numerical Methods in Biomedical Engineering 38, no. 1 (2022): e3542.Status: Published
A scalable solver for a stochastic, hybrid cellular automaton model of personalized breast cancer therapy
| 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 | International Journal for Numerical Methods in Biomedical Engineering |
| Volume | 38 |
| Issue | 1 |
| Pagination | e3542 |
| Date Published | 10/2021 |
| Publisher | Wiley |
| URL | https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/cnm.3542 |
| DOI | 10.1002/cnm.3542 |
CSF circulation and dispersion yield rapid clearance from intracranial compartments
Frontiers in Bioengineering and Biotechnology 12 (2022).Status: Published
CSF circulation and dispersion yield rapid clearance from intracranial compartments
| 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 | Frontiers in Bioengineering and Biotechnology |
| Volume | 12 |
| Date Published | 09/2022 |
| Publisher | Frontiers |
| URL | https://www.frontiersin.org/articles/10.3389/fbioe.2022.932469/full |
| DOI | 10.3389/fbioe.2022.932469 |
Geometrically reduced modelling of pulsatile flow in perivascular networks
Frontiers in Physics 10 (2022).Status: Published
Geometrically reduced modelling of pulsatile flow in perivascular networks
Flow of cerebrospinal fluid in perivascular spaces is a key mechanism underlying brain transport and clearance. In this paper, we present a mathematical and numerical formalism for reduced models of pulsatile viscous fluid flow in networks of generalized annular cylinders. We apply this framework to study cerebrospinal fluid flow in perivascular spaces induced by pressure differences, cardiac pulse wave-induced vascular wall motion and vasomotion. The reduced models provide approximations of the cross-section average pressure and cross-section flux, both defined over the topologically one-dimensional centerlines of the network geometry. Comparing the full and reduced model predictions, we find that the reduced models capture pulsatile flow characteristics and provide accurate pressure and flux predictions across the range of idealized and image-based scenarios investigated—at a fraction of the computational cost of the corresponding full models. The framework presented thus provides a robust and effective computational approach for large scale in-silico studies of pulsatile perivascular fluid flow and transport.
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2022 |
| Journal | Frontiers in Physics |
| Volume | 10 |
| Publisher | Frontiers |
| URL | https://www.frontiersin.org/article/10.3389/fphy.2022.882260 |
| DOI | 10.3389/fphy.2022.882260 |
Human intracranial pulsatility during the cardiac cycle: a computational modelling framework
Fluids and Barriers of the Central Nervous System 19 (2022): 1-17.Status: Published
Human intracranial pulsatility during the cardiac cycle: a computational modelling framework
| 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 | 2022 |
| Journal | Fluids and Barriers of the Central Nervous System |
| Volume | 19 |
| Number | 1 |
| Pagination | 1-17 |
| Publisher | Springer |
| URL | https://doi.org/10.1101/2022.05.19.492650 |
Robust approximation of generalized Biot-Brinkman problems
Journal on Scientific Computing 93, no. 3 (2022): 77.Status: Published
Robust approximation of generalized Biot-Brinkman problems
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2022 |
| Journal | Journal on Scientific Computing |
| Volume | 93 |
| Issue | 3 |
| Pagination | 77 |
| Date Published | 11/2022 |
| Publisher | Springer |
| URL | https://arxiv.org/abs/2112.13618 |
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 |
Talks, invited
Cell-based modelling and simulation of excitable tissue
In Simula Research Laboratory, Oslo, Norway, 2022.Status: Published
Cell-based modelling and simulation of excitable tissue
| Afilliation | Scientific Computing |
| Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2022 |
| Location of Talk | Simula Research Laboratory, Oslo, Norway |
| Type of Talk | Invited lecture |
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 adaptivity for human brain mechanics
In FEniCS'22, University of California San Diego, La Jolla, US, 2022.Status: Published
Finite element adaptivity for human brain mechanics
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2022 |
| Location of Talk | FEniCS'22, University of California San Diego, La Jolla, US |
| Type of Talk | Invited presentation |
Finite elements and brain multiphysics
In MAE 207: Finite element analysis in coupled problems, UCSD, La Jolla, US, 2022.Status: Published
Finite elements and brain multiphysics
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2022 |
| Location of Talk | MAE 207: Finite element analysis in coupled problems, UCSD, La Jolla, US |
| Type of Talk | Invited guest lecture |
Mathematical modelling of human brain transport: from medical images to biophysical simulation
In Laboratoire Mechnique des Solides, École Polytechnique, Paris, France, 2022.Status: Published
Mathematical modelling of human brain transport: from medical images to biophysical simulation
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2022 |
| Location of Talk | Laboratoire Mechnique des Solides, École Polytechnique, Paris, France |
Mathematical modelling of human brain transport: from medical images to biophysical simulation
In UCSD Institute for Neural Computation seminar series, La Jolla, CA, USA, 2022.Status: Published
Mathematical modelling of human brain transport: from medical images to biophysical simulation
| 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, invited |
| Year of Publication | 2022 |
| Location of Talk | UCSD Institute for Neural Computation seminar series, La Jolla, CA, USA |
Mathematical modelling of human brain transport: from medical images to biophysical simulation
In Pretty Porous Science Seminar, University of Stuttgart, Stuttgart, Germany, 2022.Status: Published
Mathematical modelling of human brain transport: from medical images to biophysical simulation
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2022 |
| Location of Talk | Pretty Porous Science Seminar, University of Stuttgart, Stuttgart, Germany |
Such stuff as dreams are made on: a computational tale of optimal transport and brain clearance
In IEEE Brain Discovery Workshop on Brain, Mind and Body: Cognitive Neuroengineering for Health and Wellness, 2022.Status: Published
Such stuff as dreams are made on: a computational tale of optimal transport and brain clearance
| 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, invited |
| Year of Publication | 2022 |
| Location of Talk | IEEE Brain Discovery Workshop on Brain, Mind and Body: Cognitive Neuroengineering for Health and Wellness |
Book
Mathematical modeling of the human brain: from magnetic resonance images to finite element simulation
In Simula SpringerBriefs on Computing. Vol. 10. Cham: Springer, 2022.Status: Published
Mathematical modeling of the human brain: from magnetic resonance images to finite element simulation
| 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 |
| Year of Publication | 2022 |
| Secondary Title | Simula SpringerBriefs on Computing |
| Volume | 10 |
| Number of Pages | 118 |
| Publisher | Springer |
| Place Published | Cham |
Talk, keynote
Mathematical modelling of human brain transport: from medical images to biophysical simulation
In ECCOMAS Conference, Oslo, Norway, 2022.Status: Published
Mathematical modelling of human brain transport: from medical images to biophysical simulation
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talk, keynote |
| Year of Publication | 2022 |
| Location of Talk | ECCOMAS Conference, Oslo, Norway |
| Date Published | 06/2022 |
| Type of Talk | Semi-plenary lecture |
Such stuff as dreams are made on: a finite element tale of optimal transport and brain clearance
In Acta Numerica 30th Birthday Conference, Banach Centre at Bedlewo, Poland, 2022.Status: Published
Such stuff as dreams are made on: a finite element tale of optimal transport and brain clearance
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talk, keynote |
| Year of Publication | 2022 |
| Location of Talk | Acta Numerica 30th Birthday Conference, Banach Centre at Bedlewo, Poland |
| Date Published | 06/2022 |
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 |
Talks, contributed
Modeling fluid flow in perivascular networks
In ECCOMAS22, Oslo (Norway), 2022.Status: Accepted
Modeling fluid flow in perivascular networks
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, contributed |
| Year of Publication | 2022 |
| Location of Talk | ECCOMAS22, Oslo (Norway) |
| DOI | 10.5281/zenodo.7848945 |
The pulsating brain: an interface-coupled fluid-poroelastic model of the cranial cavity
In ECCOMAS Congress 2022, Oslo, Norway. ECCOMAS CONGRESS 2022, 2022.Status: Accepted
The pulsating brain: an interface-coupled fluid-poroelastic model of the cranial cavity
Driven by cardiac and respiratory pulsations, our brain and the cerebrospinal (CSF) fluid
surrounding it exhibit complex fluid flow and displacement patterns. Despite being essen-
tial to normal brain function, our understanding of intracranial dynamics is still limited,
and various diseases are associated with impaired CSF flow and elevated intracranial pres-
sure [1]. Computational models offer further insights into pulsatile intracranial dynamics,
but are complicated by the close interplay of arterial inflow, venous outflow, CSF motion
and brain tissue movement inside the rigid cranial cavity.
In this talk, I will present a new computational model of cardiac-induced pulsatile motion
inside the human cranial cavity. The CSF flow in the subarachnoid space and ventricular
system is modelled using the time-dependent Stokes equations, and coupled with Biot’s
poroelasticity equations in the brain tissue, thus integrating all major intracranial con-
stituents into the modelling approach. Employing the pulsatile inflow of blood into brain
tissue as a driver of motion, the model enables us to study the dynamics of the entire
intracranial system.
The model is discretized using a coupled/monolithic approach with a mixed
Taylor-Hood type finite element scheme and implemented with the finite element frame-
work FEniCS. Numerical results obtained with a detailed 3D human head model and
physiological material parameters are presented and compared with experimental data.
The new model faithfully replicates the main aspects of intracranial pulsatile motion.
| Afilliation | Scientific Computing |
| Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, contributed |
| Year of Publication | 2022 |
| Location of Talk | ECCOMAS Congress 2022, Oslo, Norway |
| Publisher | ECCOMAS CONGRESS 2022 |
| Keywords | brain mechanics, Finite element method, interface coupling, multiphysics problems |
Miscellaneous
Software and Data for "Human intracranial pulsatility during the cardiac cycle: a computational modelling framework"
Zenodo, 2022.Status: Published
Software and Data for "Human intracranial pulsatility during the cardiac cycle: a computational modelling framework"
This repository contains the code, meshes and data required to reproduce the results of the article "Human intracranial pulsatility during the cardiac cycle: a computational modelling framework", M. Causemann, V. Vinje and M.E. Rognes (2022).
The easiest way of getting the code running is based on snakemake and singularity: Installing both (using .e.g conda: conda create -c bioconda -c conda-forge -n snakemake snakemake singularity) and running snakemake --cores N will run pull a docker image (mcause/brainsim:openblas) and execute all steps on N cores. Note however, that the required computational resources are quite large and unlikely to be met by a desktop computer. Snakemake also supports submitting jobs on a SLURM cluster via the --profile profile_folder_name option. An example of a profile configuration can be found in the ex3 folder.
The complete workflow is defined in the Snakefile, which hence also provides documentation of the individual steps.
| Afilliation | Scientific Computing |
| Project(s) | Exciting times: Extreme modelling of excitable tissue (EMIx), Department of Numerical Analysis and Scientific Computing |
| Publication Type | Miscellaneous |
| Year of Publication | 2022 |
| Publisher | Zenodo |
| URL | {https://doi.org/10.5281/zenodo.6553790 |
| DOI | 10.5281/zenodo.6553790 |
Public outreach
Waterscales: Mathematical and computational foundations for modelling cerebral fluid flow
In European Mathematical Society Magazine. Vol. 126. European Mathematical Society, 2022.Status: Accepted
Waterscales: Mathematical and computational foundations for modelling cerebral fluid flow
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Public outreach |
| Year of Publication | 2022 |
| Secondary Title | European Mathematical Society Magazine |
| Volume | 126 |
| Pagination | 1-10 |
| Date Published | 01/2022 |
| Publisher | European Mathematical Society |
| Type of Work | Magazine article |
Talks, invited
Numerical foundations of the brain's waterscape
In Séminaire du Laboratoire Jacques-Louis Lions (invited), Sorbonne University, Paris, France, 2021.Status: Published
Numerical foundations of the brain's waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2021 |
| Location of Talk | Séminaire du Laboratoire Jacques-Louis Lions (invited), Sorbonne University, Paris, France |
Brain modelling: from magnetic resonance images to finite element simulation - a lecture series
In Porous Media Math Seminar Series, University of Bergen, Norway, 2021.Status: Published
Brain modelling: from magnetic resonance images to finite element simulation - a lecture series
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2021 |
| Location of Talk | Porous Media Math Seminar Series, University of Bergen, Norway |
| Type of Talk | Invited short course |
| Notes | 6 x 45 min lectures |
| URL | https://github.com/meg-simula/mri2fem-lectures |
Depressed brain cells - a numerical perspective
In 6th Oxford International Neuron and Brain Mechanics Workshop, Oxford, UK, 2021.Status: Published
Depressed brain cells - a numerical perspective
| 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, invited |
| Year of Publication | 2021 |
| Location of Talk | 6th Oxford International Neuron and Brain Mechanics Workshop, Oxford, UK |
Mixed-dimensional coupled finite elements in FEniCS.
In Indo-Norwegian workshop on computational challenges and modelling of coupled processes in porous media, University of Bergen (Norway), 2021.Status: Accepted
Mixed-dimensional coupled finite elements in FEniCS.
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2021 |
| Location of Talk | Indo-Norwegian workshop on computational challenges and modelling of coupled processes in porous media, University of Bergen (Norway) |
| DOI | 10.5281/zenodo.7849094 |
Modeling fluid flow in perivascular networks
In Oslo glymphatics symposium, Oslo (Norway), 2021.Status: Published
Modeling fluid flow in perivascular networks
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2021 |
| Location of Talk | Oslo glymphatics symposium, Oslo (Norway) |
| DOI | 10.5281/zenodo.7848945 |
Modelling intracranial pressure, fluid flow and solute transport in surface perivascular space
In Brain H20 Symposium, Copenhagen, Denmark (virtual), 2021.Status: Published
Modelling intracranial pressure, fluid flow and solute transport in surface perivascular space
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2021 |
| Location of Talk | Brain H20 Symposium, Copenhagen, Denmark (virtual) |
Understanding the mechanisms of the brain's waterscape
In 2021 InterPore Conference (online), 2021.Status: Published
Understanding the mechanisms of the brain's waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2021 |
| Location of Talk | 2021 InterPore Conference (online) |
| Type of Talk | Invited lecture |
| URL | https://www.youtube.com/watch?v=U3X_KVz1O4M&t=82s |
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 |
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 |
Derivation of a Cell-Based Mathematical Model of Excitable Cells
In Modeling Excitable Tissue: The EMI Framework, 1-13. Vol. 7. Cham: Springer International Publishing, 2021.Status: Published
Derivation of a Cell-Based Mathematical Model of Excitable Cells
Excitable cells are of vital importance in biology, and mathematical models have contributed significantly to understand their basic mechanisms. However, classical models of excitable cells are based on severe assumptions that may limit the accuracy of the simulation results. Here, we derive a more detailed approach to modeling that has recently been applied to study the electrical properties of both neurons and cardiomyocytes. The model is derived from first principles and opens up possibilities for studying detailed properties of excitable cells. We refer to the model as the EMI model because both the extracellular space (E), the cell membrane (M) and the intracellular space (I) are explicitly represented in the model, in contrast to classical spatial models of excitable cells. Later chapters of the present text will focus on numerical methods and software for solving the model. Also, in the next chapter, the model will be extended to account for ionic concentrations in the intracellular and extracellular spaces.
| Afilliation | Scientific Computing |
| Project(s) | Department of Computational Physiology |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Volume | 7 |
| Chapter | 1 |
| Pagination | 1-13 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
| ISBN Number | 978-3-030-61157-6 |
| ISBN | 2512-1677 |
| URL | https://link.springer.com/content/pdf/10.1007%2F978-3-030-61157-6_1.pdf |
| DOI | 10.1007/978-3-030-61157-6_1 |
Improving Neural Simulations with the EMI Model
In Modeling Excitable Tissue: The EMI Framework, 87-98. Cham: Springer International Publishing, 2021.Status: Published
Improving Neural Simulations with the EMI Model
Mathematical modeling of neurons is an essential tool to investigate neuronal activity alongside with experimental approaches. However, the conventional modeling framework to simulate neuronal dynamics and extracellular potentials makes several assumptions that might need to be revisited for some applications. In this chapter we apply the EMI model to investigate the ephaptic effect and the effect of the extracellular probes on the measured potential. Finally, we introduce reduced EMI models, which provide a more computationally efficient framework for simulating neurons with complex morphologies.
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Pagination | 87–98 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
| ISBN Number | 978-3-030-61157-6 |
| URL | https://doi.org/10.1007/978-3-030-61157-6_7 |
| DOI | 10.1007/978-3-030-61157-6_7 |
Iterative Solvers for EMI Models
In Modeling Excitable Tissue: The EMI Framework, 70-86. Cham: Springer International Publishing, 2021.Status: Published
Iterative Solvers for EMI Models
This chapter deals with iterative solution algorithms for the four EMI formulations derived in (17, Chapter 5). Order optimal monolithic solvers robust with respect to material parameters, the number of degrees of freedom of discretization as well as the time-stepping parameter are presented and compared in terms of computational cost. Domain decomposition solver for the single-dimensional primal formulation is discussed.
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Pagination | 70–86 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
| ISBN Number | 978-3-030-61157-6 |
| URL | https://doi.org/10.1007/978-3-030-61157-6_6 |
| DOI | 10.1007/978-3-030-61157-6_6 |
Modeling Cardiac Mechanics on a Sub-Cellular Scale
In Modeling Excitable Tissue: The EMI Framework, 28-43. Vol. 7. Cham: Springer International Publishing, 2021.Status: Published
Modeling Cardiac Mechanics on a Sub-Cellular Scale
We aim to extend existing models of single-cell mechanics to the EMI framework, to define spatially resolved mechanical models of cardiac myocytes embedded in a passive extracellular space. The models introduced here will be pure mechanics models employing fairly simple constitutive laws for active and passive mechanics. Future extensions of the models may include a coupling to the electrophysiology and electro-diffusion models described in the other chapters, to study the impact of spatially heterogeneous ion concentrations on the cell and tissue mechanics.
| Afilliation | Scientific Computing |
| Project(s) | Department of Computational Physiology |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Volume | 7 |
| Edition | 1 |
| Chapter | 3 |
| Pagination | 28-43 |
| Date Published | 11/2020 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
Operator Splitting and Finite Difference Schemes for Solving the EMI Model
In Modeling Excitable Tissue: The EMI Framework, 44-55. Vol. 7. Cham: Springer International Publishing, 2021.Status: Published
Operator Splitting and Finite Difference Schemes for Solving the EMI Model
We want to be able to perform accurate simulations of a large number of cardiac cells based on mathematical models where each individual cell is represented in the model. This implies that the computational mesh has to have a typical resolution of a few µm leading to huge computational challenges. In this paper we use a certain operator splitting of the coupled equations and showthat this leads to systems that can be solved in parallel. This opens up for the possibility of simulating large numbers of coupled cardiac cells.
| Afilliation | Scientific Computing |
| Project(s) | Department of Computational Physiology, Department of High Performance Computing |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Volume | 7 |
| Chapter | 4 |
| Pagination | 44 - 55 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
| ISBN Number | 978-3-030-61156-9 |
| ISBN | 2512-1677 |
| URL | http://link.springer.com/content/pdf/10.1007/978-3-030-61157-6_4 |
| DOI | 10.1007/978-3-030-61157-6_4 |
Solving the EMI Equations using Finite Element Methods
In Modeling Excitable Tissue: The EMI Framework, 56-69. Cham: Springer International Publishing, 2021.Status: Published
Solving the EMI Equations using Finite Element Methods
This chapter discusses 2 X 2 symmetric variational formulations and associated finite element methods for the EMI equations. We demonstrate that the presented methods converge at expected rates, and compare the approaches in terms of approximation of the transmembrane potential. Overall, the choice of which formulation to employ for solving EMI models becomes largely a matter of desired accuracy and available computational resources.
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Pagination | 56–69 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
| ISBN Number | 978-3-030-61157-6 |
| URL | https://doi.org/10.1007/978-3-030-61157-6_5 |
| DOI | 10.1007/978-3-030-61157-6_5 |
Solving the EMI Equations using Finite Element Methods
In Modeling Excitable Tissue: The EMI Framework, 56-69. Cham: Springer International Publishing, 2021.Status: Published
Solving the EMI Equations using Finite Element Methods
This chapter discusses 2 X 2 symmetric variational formulations and associated finite element methods for the EMI equations. We demonstrate that the presented methods converge at expected rates, and compare the approaches in terms of approximation of the transmembrane potential. Overall, the choice of which formulation to employ for solving EMI models becomes largely a matter of desired accuracy and available computational resources.
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing |
| Publication Type | Book Chapter |
| Year of Publication | 2021 |
| Book Title | Modeling Excitable Tissue: The EMI Framework |
| Pagination | 56–69 |
| Publisher | Springer International Publishing |
| Place Published | Cham |
| ISBN Number | 978-3-030-61157-6 |
| URL | https://doi.org/10.1007/978-3-030-61157-6_5 |
| DOI | 10.1007/978-3-030-61157-6_5 |
Proceedings, refereed
A mixed framework for topological model reduction of coupled PDEs
In 9th edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering. CIMNE, 2021.Status: Published
A mixed framework for topological model reduction of coupled PDEs
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2021 |
| Conference Name | 9th edition of the International Conference on Computational Methods for Coupled Problems in Science and Engineering |
| Publisher | CIMNE |
| URL | https://www.scipedia.com/public/Gjerde_Rognes_2021a |
| DOI | 10.23967/coupled.2021.005 |
Parameter robust preconditioning for multi-compartmental Darcy equations
In Numerical Mathematics and Advanced Applications ENUMATH 2019. Vol. 139. Springer International Publishing, 2021.Status: Published
Parameter robust preconditioning for multi-compartmental Darcy equations
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2021 |
| Conference Name | Numerical Mathematics and Advanced Applications ENUMATH 2019 |
| Volume | 139 |
| Edition | 1 |
| Pagination | 794–797 |
| Publisher | Springer International Publishing |
| DOI | 10.1007/978-3-030-55874-1 |
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 discretization of poroelasticity without Darcy stability – Stokes-Biot revisited
BIT Numerical Mathematics 61 (2021): 941-976.Status: Published
Accurate discretization of poroelasticity without Darcy stability – Stokes-Biot revisited
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing, Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2021 |
| Journal | BIT Numerical Mathematics |
| Volume | 61 |
| Pagination | 941-976 |
| Publisher | Springer |
| DOI | 10.1007/s10543-021-00849-0 |
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 |
Brain solute transport is more rapid in periarterial than perivenous spaces
Scientific Reports 11 (2021).Status: Published
Brain solute transport is more rapid in periarterial than perivenous spaces
| 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 | Scientific Reports |
| Volume | 11 |
| Number | 16085 |
| Date Published | 08/2021 |
| Publisher | Nature |
| URL | https://www.nature.com/articles/s41598-021-95306-x |
| DOI | 10.1038/s41598-021-95306-x |
Parameter robust preconditioning by congruence for multiple-network poroelasticity
SIAM Journal of Scientific Computing 43, no. 4 (2021): B984-B1007.Status: Published
Parameter robust preconditioning by congruence for multiple-network poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Department of Numerical Analysis and Scientific Computing, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2021 |
| Journal | SIAM Journal of Scientific Computing |
| Volume | 43 |
| Issue | 4 |
| Pagination | B984–B1007 |
| Publisher | SIAM |
| DOI | 10.1137/20M1326751 |
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 |
Talk, keynote
Computational brainphatics
In 2021 SIAM Conference on Computational Science and Engineering, 2021.Status: Published
Computational brainphatics
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talk, keynote |
| Year of Publication | 2021 |
| Location of Talk | 2021 SIAM Conference on Computational Science and Engineering |
| Date Published | 03/2021 |
| Type of Talk | Plenary keynote |
Edited books
Modeling Excitable Tissue: The EMI Framework
Springer, 2021.Status: Published
Modeling Excitable Tissue: The EMI Framework
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Edited books |
| Year of Publication | 2021 |
| Publisher | Springer |
Journal Article
Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo
International Journal for Numerical Methods in Biomedical Engineering 37, no. 1 (2020): e3412.Status: Published
Fast uncertainty quantification of tracer distribution in the brain interstitial fluid with multilevel and quasi Monte Carlo
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Waterscape: The Numerical Waterscape of the Brain, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Journal Article |
| Year of Publication | 2020 |
| Journal | International Journal for Numerical Methods in Biomedical Engineering |
| Volume | 37 |
| Issue | 1 |
| Pagination | e3412 |
| Date Published | 11/2020 |
| Publisher | Wiley |
| URL | https://onlinelibrary.wiley.com/doi/full/10.1002/cnm.3412 |
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 |
Intracranial pressure elevation alters CSF clearance pathways
Fluids and Barriers of the CNS 17 (2020).Status: Published
Intracranial pressure elevation alters CSF clearance pathways
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, 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 | Fluids and Barriers of the CNS |
| Volume | 17 |
| Number | 29 |
| Date Published | 04/2020 |
| Publisher | Springer Nature BMC |
| Keywords | brain mechanics, Cerebrospinal Fluid, Intracranial pressure |
| DOI | 10.1186/s12987-020-00189-1 |
The mechanisms behind perivascular fluid flow
PLOS ONE 15 (2020): 1-20.Status: Published
The mechanisms behind perivascular fluid flow
Flow of cerebrospinal fluid (CSF) in perivascular spaces (PVS) is one of the key concepts involved in theories concerning clearance from the brain. Experimental studies have demonstrated both net and oscillatory movement of microspheres in PVS (Mestre et al. (2018), Bedussi et al. (2018)). The oscillatory particle movement has a clear cardiac component, while the mechanisms involved in net movement remain disputed. Using computational fluid dynamics, we computed the CSF velocity and pressure in a PVS surrounding a cerebral artery subject to different forces, representing arterial wall expansion, systemic CSF pressure changes and rigid motions of the artery. The arterial wall expansion generated velocity amplitudes of 60–260 μm/s, which is in the upper range of previously observed values. In the absence of a static pressure gradient, predicted net flow velocities were small (<0.5 μm/s), though reaching up to 7 μm/s for non-physiological PVS lengths. In realistic geometries, a static systemic pressure increase of physiologically plausible magnitude was sufficient to induce net flow velocities of 20–30 μm/s. Moreover, rigid motions of the artery added to the complexity of flow patterns in the PVS. Our study demonstrates that the combination of arterial wall expansion, rigid motions and a static CSF pressure gradient generates net and oscillatory PVS flow, quantitatively comparable with experimental findings. The static CSF pressure gradient required for net flow is small, suggesting that its origin is yet to be determined.
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2020 |
| Journal | PLOS ONE |
| Volume | 15 |
| Number | 12 |
| Pagination | 1-20 |
| Publisher | Public Library of Science |
| URL | https://doi.org/10.1371/journal.pone.0244442 |
| DOI | 10.1371/journal.pone.0244442 |
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 |
Talks, invited
The brain's (numerical) waterscape
In Springer Partial Differential Equations and Applications webinar, 2020.Status: Published
The brain's (numerical) waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2020 |
| Location of Talk | Springer Partial Differential Equations and Applications webinar |
The brain's numerical waterscape
In Oxford Industrial and Applied Mathematics Seminar, Oxford, UK, 2020.Status: Published
The brain's numerical waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Talks, invited |
| Year of Publication | 2020 |
| Location of Talk | Oxford Industrial and Applied Mathematics Seminar, Oxford, UK |
Journal Article
A mixed finite element method for nearly incompressible multiple-network poroelasticity
SIAM Journal on Scientific Computing 41, no. 2 (2019): A722-A747.Status: Published
A mixed finite element method for nearly incompressible multiple-network poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | SIAM Journal on Scientific Computing |
| Volume | 41 |
| Issue | 2 |
| Pagination | A722–A747 |
| Date Published | 03/2019 |
| Publisher | SIAM |
| URL | https://epubs.siam.org/doi/10.1137/18M1182395 |
| DOI | 10.1137/18M1182395 |
Automated adjoints of coupled PDE-ODE systems
SIAM Journal on Scientific Computing 41, no. 3 (2019).Status: Published
Automated adjoints of coupled PDE-ODE systems
| Afilliation | Scientific Computing |
| Project(s) | OptCutCell: Simulation-based optimisation with dynamic domains, Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | SIAM Journal on Scientific Computing |
| Volume | 41 |
| Issue | 3 |
| Publisher | SIAM |
| URL | http://epubs.siam.org/toc/sjoce3/41/3 |
| DOI | 10.1137/17M1144532 |
Respiratory influence on cerebrospinal fluid flow – a computational study based on long-term intracranial pressure measurements
Scientific Reports 9, no. 1 (2019): 9732.Status: Published
Respiratory influence on cerebrospinal fluid flow – a computational study based on long-term intracranial pressure measurements
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | Scientific Reports |
| Volume | 9 |
| Issue | 1 |
| Pagination | 9732 |
| Date Published | 07/2019 |
| Publisher | Springer Nature |
| DOI | 10.1038/s41598-019-46055-5 |
Towards personalized computer simulation of breast cancer treatment: a multi-scale pharmacokinetic and pharmacodynamic model informed by multi-type patient data
Cancer Research 79, no. 16 (2019): 4293-4304.Status: Published
Towards personalized computer simulation of breast cancer treatment: a multi-scale pharmacokinetic and pharmacodynamic model informed by multi-type patient data
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | Cancer Research |
| Volume | 79 |
| Issue | 16 |
| Pagination | 4293-4304 |
| Date Published | 05/2019 |
| Publisher | American Association for Cancer Research |
| URL | http://cancerres.aacrjournals.org/content/early/2019/05/22/0008-5472.CAN... |
| DOI | 10.1158/0008-5472.CAN-18-1804 |
Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response
International Journal for Numerical Methods in Biomedical Engineering 35, no. 5 (2019): e3178.Status: Published
Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response
| Afilliation | Scientific Computing |
| Project(s) | AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | International Journal for Numerical Methods in Biomedical Engineering |
| Volume | 35 |
| Issue | 5 |
| Pagination | e3178 |
| Publisher | Wiley |
Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields
Fluids and Barriers of the Central Nervous System 16 (2019): 32.Status: Published
Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Journal | Fluids and Barriers of the Central Nervous System |
| Volume | 16 |
| Number | 1 |
| Pagination | 32 |
| Date Published | 09/2019 |
| Publisher | BMC |
| URL | https://europepmc.org/articles/pmc6767654 |
| DOI | 10.1186/s12987-019-0152-7 |
Talks, invited
Advances in conformal finite element methods for generalized poroelasticity: A-posteriori error estimates for the two-field generalized poroelasticity equations and an elliptic-parabolic framework
In Interpore 2019, Valencia, Spain, 2019.Status: Published
Advances in conformal finite element methods for generalized poroelasticity: A-posteriori error estimates for the two-field generalized poroelasticity equations and an elliptic-parabolic framework
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2019 |
| Location of Talk | Interpore 2019, Valencia, Spain |
Intracranial pressure elevation alters CSF clearance pathways
In The 2019 CSF Symposium, Oslo, Norway, 2019.Status: Published
Intracranial pressure elevation alters CSF clearance pathways
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2019 |
| Location of Talk | The 2019 CSF Symposium, Oslo, Norway |
Nearly incompressible generalized poroelasticity - discretization and preconditioning
In International workshop in connection with Ragnar Winther's 70th birthday, Oslo, Norway, 2019.Status: Published
Nearly incompressible generalized poroelasticity - discretization and preconditioning
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2019 |
| Location of Talk | International workshop in connection with Ragnar Winther's 70th birthday, Oslo, Norway |
UQ of parenchymal tracer distribution using random diffusion and convective velocity fields
In 5th biennial CSF Dynamics Symposium, Oslo, Norway, 2019.Status: Published
UQ of parenchymal tracer distribution using random diffusion and convective velocity fields
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2019 |
| Location of Talk | 5th biennial CSF Dynamics Symposium, Oslo, Norway |
Book Chapter
Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow
In Computational Glioscience . Springer Series in Computational Neuroscience: Springer, 2019.Status: Published
Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Center for Biomedical Computing (SFF) |
| Publication Type | Book Chapter |
| Year of Publication | 2019 |
| Book Title | Computational Glioscience |
| Publisher | Springer |
| Place Published | Springer Series in Computational Neuroscience |
Talks, contributed
Mixed-dimensional coupled finite elements in FEniCS
In ENUMATH 2019, Egmond aan Zee, The Netherlands, 2019.Status: Published
Mixed-dimensional coupled finite elements in FEniCS
| 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 | ENUMATH 2019, Egmond aan Zee, The Netherlands |
Mixed-dimensional coupled finite elements in FEniCS
In FEniCS'19, Washington DC, USA, 2019.Status: Published
Mixed-dimensional coupled finite elements in FEniCS
| 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'19, Washington DC, USA |
Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields
In International congress on industrial and applied mathematics, Valencia, Spain. ICIAM, 2019.Status: Published
Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, contributed |
| Year of Publication | 2019 |
| Location of Talk | International congress on industrial and applied mathematics, Valencia, Spain |
| Publisher | ICIAM |
Master's thesis
A posteriori error estimation for multiple-network poroelasticity
In The University of Oslo. Oslo, Norway: The University of Oslo, 2018.Status: Published
A posteriori error estimation for multiple-network poroelasticity
The multiple network poroelasticity equations (MPET) describe mechanical deformation and fluid flow in porous media and can be used to understand various biological processes in a physiological setting. Modeling transportation of fluid within the brain is essential to discover the underlying mechanisms that are currently being investigated concerning various neurodegenerative diseases such as Alzheimer's disease. Mathematical modeling is considered to be more accessible and less expensive than performing advanced medical tests and experiments; however, numerical simulations are still prone to error, making it essential to control and minimize. Physiological frameworks often include complex geometries which may produce complex error distributions. A posterior error estimation presents a framework to measure and control the error in specific regions of the computational domain. This thesis presents the derivation of a posteriori error estimates for MPET with two interacting fluid networks, extending the analysis from on fluid network. The presented estimates can be extended to the MPET model with an arbitrary number of networks, which is demonstrated with a computational experiment using four networks on a brain mesh with physiologically inspired parameters.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Master's thesis |
| Year of Publication | 2018 |
| Degree awarding institution | The University of Oslo |
| Date Published | 08/2018 |
| Publisher | The University of Oslo |
| Place Published | Oslo, Norway |
| Keywords | a posteriori error estimates, generalized poroelasticity, MPET |
Talks, contributed
A Robust 3-Field formulation for Generalized Poroelasticity
In FEniCS 18, Oxford, United Kingdom, 2018.Status: Published
A Robust 3-Field formulation for Generalized Poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | FEniCS 18, Oxford, United Kingdom |
A Stokes-Biot Stable H(div)-based mixed method for generalized poroelasticity
In SIAM Life Sciences 2018, Minneapolis, Minnesota, USA, 2018.Status: Published
A Stokes-Biot Stable H(div)-based mixed method for generalized poroelasticity
| Afilliation | Software Engineering |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | SIAM Life Sciences 2018, Minneapolis, Minnesota, USA |
Fluid dynamics in syringomyelia cavities
In Vancouver, Canada, 2018.Status: Published
Fluid dynamics in syringomyelia cavities
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | Vancouver, Canada |
| Type of Talk | Parallel paper session at the 56th annual meeting of the American Society of Neuroradiology |
Mixed-dimensional coupled finite elements in FEniCS
In FEniCS18, Oxford, UK, 2018.Status: Published
Mixed-dimensional coupled finite elements in FEniCS
| Afilliation | Software Engineering, Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | FEniCS18, Oxford, UK |
| Notes | Best postdoctoral presentation award at the FEniCS’18 |
Mixed-dimensional coupled finite elements in FEniCS
In ECCM-ECFD 2018, Glasgow (UK), 2018.Status: Published
Mixed-dimensional coupled finite elements in FEniCS
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | ECCM-ECFD 2018, Glasgow (UK) |
Mixed-dimensional models of the brain's waterscape with FEniCS
In InterPore 2018, New-Orleans (USA), 2018.Status: Published
Mixed-dimensional models of the brain's waterscape with FEniCS
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | InterPore 2018, New-Orleans (USA) |
The Influence of Breathing on Cerebrospinal Fluid Movement in the Brain
In Glasgow, United Kingdom, 2018.Status: Published
The Influence of Breathing on Cerebrospinal Fluid Movement in the Brain
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, contributed |
| Year of Publication | 2018 |
| Location of Talk | Glasgow, United Kingdom |
| Type of Talk | Minisymposium at the ECCOMAS: ECCM - ECFD conference |
Talks, invited
A robust mixed finite element method for generalized poroelasticity
In Glasgow, UK, 2018.Status: Published
A robust mixed finite element method for generalized poroelasticity
The classical Biot and Terzaghi soil models, describing flow through a single fluid network in a porous and elastic medium, were generalized to equations describing multiple fluid network poroelasticity (MPET) by Barenblatt and Aifantis. The MPET equations have been utilized in geomechanics to simulate multiple fractured strata for a few decades, but are now also beginning to find their application in biomechanics. Indeed, the multiple network poroelasticity theory aptly models the multiple fluid networks encountered in e.g. the brain: such as extracellular spaces, vasculature and paravasculature.
In this talk, we propose a new mixed finite element formulation for the multiple-network poroelasticity equations. The key idea is to introduce the network fluid fluxes as additional variable targeting a finite element formulation that is robust with respect to low hydraulic conductivities and storage coefficients. We will present both theoretical and numerical results regarding the robustness and convergence of the new method, together with numerical demonstrations relating to the topic of cerebral interstitial and
paravascular fluid flow.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | Glasgow, UK |
| Type of Talk | Technical Talk: Numerical Analysis, Scientific Computing |
| Keywords | brain mechanics, mixed finite element methods, multiple-network poroelasticity |
A Stokes-Biot Stable Hdiv-Based Mixed Method for Generalized Poroelasticity’
In ECCM-ECFD. Glasgow, United Kingdom, 2018.Status: Published
A Stokes-Biot Stable Hdiv-Based Mixed Method for Generalized Poroelasticity’
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | ECCM-ECFD. Glasgow, United Kingdom |
Mixed-dimensional modeling of the brain’s waterscape
In Workshop on solvers for materials with high-aspect-ratio inclusions, Finse, Norway, 2018.Status: Published
Mixed-dimensional modeling of the brain’s waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | Workshop on solvers for materials with high-aspect-ratio inclusions, Finse, Norway |
Parameter-robust discretization and preconditioning of multiple-network poroelasticity equations
In University of Oxford, UK, 2018.Status: Published
Parameter-robust discretization and preconditioning of multiple-network poroelasticity equations
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | University of Oxford, UK |
Parameter-robust discretization and preconditioning of multiple-network poroelasticity equations
In Glasgow, UK, 2018.Status: Published
Parameter-robust discretization and preconditioning of multiple-network poroelasticity equations
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | Glasgow, UK |
Stokes Biot Stability and a Mixed Formulation for Generalized Poroelasticity
In Lorentz Center, Leiden, Netherlands, 2018.Status: Published
Stokes Biot Stability and a Mixed Formulation for Generalized Poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | Lorentz Center, Leiden, Netherlands |
Stokes-Biot Stability and a Mixed Formulation For Generalized Poroelasticity
In SIAM Life Sciences. Minneapolis, Minnesota, 2018.Status: Published
Stokes-Biot Stability and a Mixed Formulation For Generalized Poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | SIAM Life Sciences. Minneapolis, Minnesota |
Waterscape of the Brain: Mathematics and Scientific Computing Enabling Clinical Simulation
In Simula Research Conference, Son, Norway, 2018.Status: Published
Waterscape of the Brain: Mathematics and Scientific Computing Enabling Clinical Simulation
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2018 |
| Location of Talk | Simula Research Conference, Son, Norway |
Journal Article
Efficient white noise sampling and coupling for multilevel Monte Carlo with non-nested meshes
SIAM Journal on Uncertainty Quantification 6, no. 4 (2018).Status: Published
Efficient white noise sampling and coupling for multilevel Monte Carlo with non-nested meshes
| Afilliation | Scientific Computing |
| Project(s) | AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations, Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Journal Article |
| Year of Publication | 2018 |
| Journal | SIAM Journal on Uncertainty Quantification |
| Volume | 6 |
| Issue | 4 |
| Publisher | SIAM |
Fluid dynamics in syringomyelia cavities: Effects of heart rate, CSF velocity, CSF velocity waveform and craniovertebral decompression
The Neuroradiology Journal 31, no. 5 (2018): 482-489.Status: Published
Fluid dynamics in syringomyelia cavities: Effects of heart rate, CSF velocity, CSF velocity waveform and craniovertebral decompression
Purpose: How fluid moves during the cardiac cycle within a syrinx may affect its development. We measured syrinx fluid velocities before and after craniovertebral decompression in a patient and simulated syrinx fluid velocities for different heart rates, syrinx sizes and CSF flow velocities in a model of syringomyelia.
Materials and Methods: With Phase Contrast MR we measured CSF and syrinx fluid velocities in a Chiari patient before and after craniovertebral decompression. With an idealized 2D model of the subarachnoid space (SAS), cord and syrinx, we simulated fluid movement in the SAS and syrinx with the Navier-Stokes equations for different heart rates, inlet velocities and syrinx diameters.
Results: In the patient, fluid oscillated in the syrinx at 200 to 210 cycles per minute before and after craniovertebral decompression. Velocities peaked at 3.6 and 2.0 cm/sec respectively in the SAS and the syrinx before surgery and at 2.7 and 1.5 cm/sec after surgery. In the model, syrinx velocity varied between 0.91 and 12.70 cm/sec. Increasing CSF inlet velocities from 1.56 to 4.69 cm/sec increased peak syrinx fluid velocities in the syrinx by 151 to 299% for the three cycle rates. Increasing cycle rates from 60 to 120 cpm, increased peak syrinx velocities by 160 to 312% for the three inlet velocities. Peak velocities changed inconsistently with syrinx size.
Conclusions: CSF velocity, heart rate and syrinx diameter affect syrinx fluid velocities, but not the frequency of syrinx fluid oscillation. Craniovertebral decompression decreases both CSF and syrinx fluid velocities.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Department of Numerical Analysis and Scientific Computing |
| Publication Type | Journal Article |
| Year of Publication | 2018 |
| Journal | The Neuroradiology Journal |
| Volume | 31 |
| Issue | 5 |
| Pagination | 482-489 |
| Date Published | 09/2018 |
| Publisher | SAGE Publications |
| URL | http://journals.sagepub.com/doi/10.1177/1971400918795482 |
In vivo estimation of elastic heterogeneity in an infarcted human heart
Biomechanics and Modeling in Mechanobiology 17, no. 5 (2018): 1317-1329.Status: Published
In vivo estimation of elastic heterogeneity in an infarcted human heart
In myocardial infarction, muscle tissue of the heart is damaged as a result of ceased or severely impaired blood flow. Survivors have an increased risk of further complications, possibly leading to heart failure. Material properties play an important role in determining post-infarction outcome. Due to spatial variation in scarring, material properties can be expected to vary throughout the tissue of a heart after an infarction. In this study we propose a data assimilation technique that can efficiently estimate heterogeneous elastic material properties in a personalized model of cardiac mechanics. The proposed data assimilation is tested on a clinical dataset consisting of regional left ventricular strains and in vivo pressures during atrial systole from a human with a myocardial infarction. Good matches to regional strains are obtained, and simulated equi-biaxial tests are carried out to demonstrate regional heterogeneities in stress–strain relationships. A synthetic data test shows a good match of estimated versus ground truth material parameter fields in the presence of no to low levels of noise. This study is the first to apply adjoint-based data assimilation to the important problem of estimating cardiac elastic heterogeneities in 3-D from medical images.
| Afilliation | Scientific Computing |
| Project(s) | Department of Numerical Analysis and Scientific Computing |
| Publication Type | Journal Article |
| Year of Publication | 2018 |
| Journal | Biomechanics and Modeling in Mechanobiology |
| Volume | 17 |
| Issue | 5 |
| Pagination | 1317–1329 |
| Date Published | May-05-2019 |
| Publisher | Springer |
| Place Published | Berlin Heidelberg |
| ISSN | 1617-7959 |
| URL | http://link.springer.com/10.1007/s10237-018-1028-5 |
| DOI | 10.1007/s10237-018-1028-5 |
I am a computer scientist with a background in artificial intelligence and biophysics. I previously developed methods for determining the risk of sudden cardiac death based on MRI analysis, and models of electrical propagation in damaged heart tissue at King's College London. Afterwards, I worked with bioinformatics and machine learning for two years at the University of Oslo. In 2017, I completed my PhD at Simula Research Laboratory/UiO on the topic of cardiac mechanics.
Poster
Mixed-dimensional modeling of the brain’s waterscape
InterPore 2018, New-Orleans (USA), 2018.Status: Published
Mixed-dimensional modeling of the brain’s waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Poster |
| Year of Publication | 2018 |
| Place Published | InterPore 2018, New-Orleans (USA) |
Respiratory influence on intracranial pressure gradients and aqueductal flow in normal pressure hydrocephalus
Dublin, Ireland, 2018.Status: Published
Respiratory influence on intracranial pressure gradients and aqueductal flow in normal pressure hydrocephalus
Phase contrast MRI does not take into account the role of respiration on cerebrospinal fluid (CSF) flow. We used in vivo pressure measurements from two locations in the intracranial space to calculate a pulsatile pressure gradient. This pressure data was used as input to an idealized model of the aqueduct to calculate CSF flow. We found the cardiac and respiratory cycle to contribute equally to CSF flow. The total flow volume was dominated by respiration, and all subjects showed variability in pressure gradients over time resulting also in variability in CSF flow.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Poster |
| Year of Publication | 2018 |
| Date Published | 07/2018 |
| Place Published | Dublin, Ireland |
| Type of Work | Poster Presentation at World Congress of Biomechanics |
| URL | https://app.oxfordabstracts.com/stages/123/programme-builder/submission/... |
Stokes-Biot stability and a mixed formulation for generalized proelasticity
Lorentz Center, Leiden, Netherlands, 2018.Status: Published
Stokes-Biot stability and a mixed formulation for generalized proelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Poster |
| Year of Publication | 2018 |
| Date Published | 05/2018 |
| Place Published | Lorentz Center, Leiden, Netherlands |
| Type of Work | Workshop poster presentation |
Journal Article
A cell-based framework for numerical modelling of electrical conduction in cardiac tissue
Frontiers in Physics, Computational Physics 5 (2017).Status: Published
A cell-based framework for numerical modelling of electrical conduction in cardiac tissue
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2017 |
| Journal | Frontiers in Physics, Computational Physics |
| Volume | 5 |
| Date Published | 10/2017 |
| Publisher | Frontiers |
| URL | https://www.frontiersin.org/articles/10.3389/fphy.2017.00048/full?&utm_s... |
| DOI | 10.3389/fphy.2017.00048 |
cbcbeat: an adjoint-enabled framework for computational cardiac electrophysiology
Journal of Open Source Software 2, no. 13 (2017).Status: Published
cbcbeat: an adjoint-enabled framework for computational cardiac electrophysiology
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2017 |
| Journal | Journal of Open Source Software |
| Volume | 2 |
| Issue | 13 |
| Date Published | 06/2017 |
| Publisher | The Journal of Open Source Software, Open Source Initiative |
| URL | http://dx.doi.org/10.21105/joss.00224 |
| DOI | 10.21105/joss.00224 |
High resolution data assimilation of cardiac mechanics
International journal for numerical methods in biomedical engineering 33 (2017): e2863.Status: Published
High resolution data assimilation of cardiac mechanics
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2017 |
| Journal | International journal for numerical methods in biomedical engineering |
| Volume | 33 |
| Number | 11 |
| Pagination | e2863 |
| Date Published | 04/2017 |
| Publisher | John Wiley & Sons, Ltd |
| DOI | 10.1002/cnm.2863 |
Inverse estimation of cardiac activation times via gradient-based optimization
International Journal for Numerical Methods in Biomedical Engineering 34, no. 2 (2017): e2919.Status: Published
Inverse estimation of cardiac activation times via gradient-based optimization
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2017 |
| Journal | International Journal for Numerical Methods in Biomedical Engineering |
| Volume | 34 |
| Issue | 2 |
| Pagination | e2919 |
| Date Published | 08/2017 |
| Publisher | John Wiley & Sons |
| URL | http://onlinelibrary.wiley.com/doi/10.1002/cnm.2919/abstract |
| DOI | 10.1002/cnm.2919 |
Numerical study of intrathecal drug delivery to a permeable spinal cord: effect of catheter position and angle
Computer Methods in Biomechanics and Biomedical Engineering 20, no. 15 (2017): 1599-1608.Status: Published
Numerical study of intrathecal drug delivery to a permeable spinal cord: effect of catheter position and angle
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2017 |
| Journal | Computer Methods in Biomechanics and Biomedical Engineering |
| Volume | 20 |
| Issue | 15 |
| Pagination | 1599-1608 |
| Publisher | Taylor & Francis Online |
| DOI | 10.1080/10255842.2017.1393805 |
Talks, contributed
Accurate numerical modelling of small collections of cardiac cells
In FEniCS'17, Luxembourg City, Luxembourg, 2017.Status: Published
Accurate numerical modelling of small collections of cardiac cells
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2017 |
| Location of Talk | FEniCS'17, Luxembourg City, Luxembourg |
Modelling pulsatility in the context of Normal-Pressure Hydrocephalus via multiple-network poroelasticity
In 5th International Conference on Computational and Mathematical Biomedical Engineering, Pittsburgh, US, 2017.Status: Published
Modelling pulsatility in the context of Normal-Pressure Hydrocephalus via multiple-network poroelasticity
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2017 |
| Location of Talk | 5th International Conference on Computational and Mathematical Biomedical Engineering, Pittsburgh, US |
Towards coupled mixed dimensional finite elements in FEniCS
In FEniCS17 conference, University of Luxembourg, Luxembourg, 2017.Status: Published
Towards coupled mixed dimensional finite elements in FEniCS
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, contributed |
| Year of Publication | 2017 |
| Location of Talk | FEniCS17 conference, University of Luxembourg, Luxembourg |
Talk, keynote
Compatible discretizations in our hearts and minds
In ENUMATH, Voss, Norway, 2017.Status: Published
Compatible discretizations in our hearts and minds
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talk, keynote |
| Year of Publication | 2017 |
| Location of Talk | ENUMATH, Voss, Norway |
Impact of high abstraction/high performance finite element software in biomedical computing
In 24th International Conference on Domain Decomposition Methods, Svalbard, Norway, 2017.Status: Published
Impact of high abstraction/high performance finite element software in biomedical computing
The development of numerical software in general and finite element
software in particular is recognized as a challenging and error-prone
process -- traditionally requiring in-depth expertise from a number of
scientific fields. The FEniCS and Dolfin-adjoint projects target this
challenge by developing generic algorithms and open source software
for the automated solution of partial differential equations using
finite element methods. The FEniCS Project is described by in the
FEniCS book [1] and a number of research papers, see e.g. [2].
The related Dolfin-adjoint software, winner of the 2015 Wilkinson
Prize for Numerical Software, automatically derives discrete adjoint
and tangent linear models from a forward FEniCS model[3]. These
adjoint and tangent linear models are key ingredients in many
important algorithms, such as data assimilation, optimal control,
sensitivity analysis, design optimisation, and error estimation.
In this presentation, I'll give an overview of the FEniCS and
Dolfin-adjoint projects focusing on current developments and
applications in biomedical computing.
[1] A. Logg, K.-A. Mardal, G. N. Wells et al. (2012). Automated
Solution of Differential Equations by the Finite Element Method,
Springer. [doi:10.1007/978-3-642-23099-8]
[2] M. S. Alnæs, J. Blechta, J. Hake, A. Johansson, B. Kehlet,
A. Logg, C. Richardson, J. Ring, M. E. Rognes and G. N. Wells
(2015). The FEniCS Project Version 1.5, Archive of Numerical Software,
3(100), [doi:10.11588/ans.2015.100.20553].
[3] P. E. Farrell, D. A. Ham, S. W. Funke and M. E. Rognes
(2013). Automated derivation of the adjoint of high-level transient
finite element programs, SIAM Journal on Scientific Computing 35.4,
pp. C369-C393. doi:10.1137/120873558.
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talk, keynote |
| Year of Publication | 2017 |
| Location of Talk | 24th International Conference on Domain Decomposition Methods, Svalbard, Norway |
The PDEs of our hearts and minds
In Women in PDEs, Karlsruhe, Germany, 2017.Status: Published
The PDEs of our hearts and minds
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Center for Biomedical Computing (SFF) |
| Publication Type | Talk, keynote |
| Year of Publication | 2017 |
| Location of Talk | Women in PDEs, Karlsruhe, Germany |
| Date Published | 04/2017 |
Poster
FEniCS: Sustainable Software Development Practices
SIAM CSE17 PP108 Minisymposterium: Software Productivity and Sustainability for CSE and Data Science, 2017.Status: Published
FEniCS: Sustainable Software Development Practices
The FEniCS project aims to provide a high productivity environment for development of finite element based simulation software. Techniques applied to achieve this goal include mixed language programming and code generation, which enables writing high performance programs in a high level language. End-user productivity is a high priority goal in our software designs. To sustain the productivity of the multinational team of part-time developers (mainly researchers and students) is paramount to the long term survival of the project. To minimize the developer workload while making the process open and accessible to new contributors and users, we regularly question which tools are the best available for our needs. On this poster we will present our current tool choices and work flows for developers and the wider FEniCS community. This list includes version control, build systems, testing, release management, team communication, documentation, and end user support. The most recent addition to our toolbox are developer curated Docker images. We are investigating their usefulness in testing infrastructure, end user deployment, HPC cluster deployment, and as reproducible software environments to accompany journal publications. We welcome discussion on alternatives that can simplify our lives.
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Poster |
| Year of Publication | 2017 |
| Date Published | 03/2017 |
| Place Published | SIAM CSE17 PP108 Minisymposterium: Software Productivity and Sustainability for CSE and Data Science |
| Keywords | FEniCS, Poster, Sofware Development |
| DOI | 10.6084/m9.figshare.4696318.v1 |
Talks, invited
Is Respiration the main driver of CSF Flow?
In International Convention Center, Kobe, Japan, 2017.Status: Published
Is Respiration the main driver of CSF Flow?
Recent studies using magnetic resonance imaging (MRI) have suggested cerebrospinal fluid (CSF) motion caused by respiration to play a more important role than previously thought. The cardiac cycle of CSF motion is used clinically, often to predict which hydrocephalus patients will respond to shunting and who will not.
This talk asks the question whether CSF flow could also be regulated by the longer respiratory cycle. To assess this question we applied in vivo pressure measurements to a simplification of the spinal canal and the aqueduct. From this we can measure the amplitude of the flow components induced by the cardiac and respiratory cycle respectively.
In our study the amplitude of CSF motion was higher for respiration in the spinal canal, and in the aqueduct cardiac the two amplitudes were approximately equal.
This is a starting work, so no conclusions can be made yet. We emphasize the point that it is possible for small and long pressure waves in respiration to cause greater flow than a short cardiac pressure wave with a greater amplitude.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2017 |
| Location of Talk | International Convention Center, Kobe, Japan |
| Type of Talk | Seminar, Annual Meeting (IHIWG group) |
| Keywords | Brain, Cerebrospinal Fluid, Computational Fluid Dynamics, Pulsation, Respiration, Spinal Cord |
The Brain as a Poroelastic Medium - Simulating pulsatile motion and flow
In Hamburg, Germany, 2017.Status: Published
The Brain as a Poroelastic Medium - Simulating pulsatile motion and flow
This talk presents a general overview of the numerical work at the Waterscape group at Simula. First, I present the governing equations, together with standard solving schemes and how to handle discretization in FEniCS. The total pressure formulation is introduced, and an optimal preconditioner for the total pressure formulation is presented.
In the last five-ten years, fluid flow and solute transport in the human brain has gained rapid interest in the research community. The discoveries by Iliff and Nedergaard describing a glyphatic network washing solutes out of the brain through a bulk flow of fluid, followed by Xie et al.'s study claiming that sleep enhances this mechanism was discoveries that also gained significant media attention.
The brain has several more or less separated networks allowing for fluid flow; Blood vessels, paravascular spaces and interstitial fluid. The relation between fluid flow in these networks to each other and to the macroscoping displacement of brain tissue can be explained with the multiple network poroelastic theory (MPET). Because there are no consensus of the value of all material parameters the models we use need to be robust within a given parameter regime. In addition, as the number of networks grow, the system of equations becomes larger and the solvers we use must also be fast and efficient within the given range of the parameters.
The total pressure formulation, presented in this talk, restores convergence related to the problem of "locking", and allows for a parameter robust preconditioner. Proof that the scheme is stable has been given earlier, and the current work aims to extend this proof to a general number of networks.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain |
| Publication Type | Talks, invited |
| Year of Publication | 2017 |
| Location of Talk | Hamburg, Germany |
| Keywords | Brain, Poroelasticity, Porous media, Total pressure, Waterscape |
The numerical waterscape of the brain
In Workshop on Biomechanics of living systems, from cells to organisms, Oslo, Norway, 2017.Status: Published
The numerical waterscape of the brain
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2017 |
| Location of Talk | Workshop on Biomechanics of living systems, from cells to organisms, Oslo, Norway |
The numerical waterscape of the brain
In 2nd Workshop on computational aspects of perfusion and flow in live tissue, Bergen, Norway, 2017.Status: Published
The numerical waterscape of the brain
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2017 |
| Location of Talk | 2nd Workshop on computational aspects of perfusion and flow in live tissue, Bergen, Norway |
The numerical waterscape of the brain
In Université libre du Bruxelles, Bruxelles, Belgium, 2017.Status: Published
The numerical waterscape of the brain
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Talks, invited |
| Year of Publication | 2017 |
| Location of Talk | Université libre du Bruxelles, Bruxelles, Belgium |
Public outreach
Making models of your brain's waterscape
2017 Cutting Edge Festival, 2017.Status: Published
Making models of your brain's waterscape
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow |
| Publication Type | Public outreach |
| Year of Publication | 2017 |
| Publisher | 2017 Cutting Edge Festival |
Mathematics that cures us
Oslo: TEDxOslo 2017, 2017.Status: Published
Mathematics that cures us
| Afilliation | Scientific Computing |
| Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Public outreach |
| Year of Publication | 2017 |
| Publisher | TEDxOslo 2017 |
| Place Published | Oslo |
Talks, invited
A 2-day training course in FEniCS and dolfin-adjoint
In NGCM Summer Academy, University of Southampton, 2016.Status: Published
A 2-day training course in FEniCS and dolfin-adjoint
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | NGCM Summer Academy, University of Southampton |
Developing simulation technology to solve biomedical problems: analysis, implementation and applications
In University of Uppsala, 2016.Status: Published
Developing simulation technology to solve biomedical problems: analysis, implementation and applications
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | University of Uppsala |
High-level abstractions, algorithms and applications in forward and inverse finite element solution of PDEs
In Nordic Seminar on Computational Mechanics, Chalmers University of Technology, Sweden, 2016.Status: Published
High-level abstractions, algorithms and applications in forward and inverse finite element solution of PDEs
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | Nordic Seminar on Computational Mechanics, Chalmers University of Technology, Sweden |
The FEniCS and dolfin-adjoint projects
In Higher-order DG methods and finite element software for modern architectures, University of Bath, UK, 2016.Status: Published
The FEniCS and dolfin-adjoint projects
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | Higher-order DG methods and finite element software for modern architectures, University of Bath, UK |
The FEniCS and Dolfin-adjoint Projects
In NGCM Summer Academy, University of Southampton, 2016.Status: Published
The FEniCS and Dolfin-adjoint Projects
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | NGCM Summer Academy, University of Southampton |
The Numerical Waterscape of the Brain
In Norway-Russia workshop on Biot's equations and error estimation, Voss, Norway, 2016.Status: Published
The Numerical Waterscape of the Brain
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | Norway-Russia workshop on Biot's equations and error estimation, Voss, Norway |
| Type of Talk | Invited |
Time scales of mathematics: from basic research to societal application
In RCN Workshop on the Importance of Mathematics for Value Creation, Lysaker, Norway, 2016.Status: Published
Time scales of mathematics: from basic research to societal application
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | RCN Workshop on the Importance of Mathematics for Value Creation, Lysaker, Norway |
Waterscales: mathematical and computational foundations for modelling cerebral fluid flow
In OBCE-Simula Workshop, Simula Research Laboratory, Norway, 2016.Status: Published
Waterscales: mathematical and computational foundations for modelling cerebral fluid flow
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2016 |
| Location of Talk | OBCE-Simula Workshop, Simula Research Laboratory, Norway |
Journal Article
Adjoint Multi-Start Based Estimation of Cardiac Hyperelastic Material Parameters using Shear Data
Biomechanics and Modeling in Mechanobiology (2016): 1-13.Status: Published
Adjoint Multi-Start Based Estimation of Cardiac Hyperelastic Material Parameters using Shear Data
| Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing, Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2016 |
| Journal | Biomechanics and Modeling in Mechanobiology |
| Pagination | 1-13 |
| Date Published | 23.03.2013 |
| Publisher | Springer |
Talks, contributed
Modelling and simulation of viscous and poroelastic fluid flow in the brain
In FEniCS16, Simula Research Laboratory, 2016.Status: Published
Modelling and simulation of viscous and poroelastic fluid flow in the brain
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2016 |
| Location of Talk | FEniCS16, Simula Research Laboratory |
| Keywords | Finite elements, Numerical Simulations, Poroelasticity |
On accurate and efficient simulations of multiple-network poroelastic modelling with applications to interstitial fluid flow in the human brain
In WCCM XII & APCOM VI, Seoul , 2016.Status: Published
On accurate and efficient simulations of multiple-network poroelastic modelling with applications to interstitial fluid flow in the human brain
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2016 |
| Location of Talk | WCCM XII & APCOM VI, Seoul |
| Keywords | Numerical Simulations, Poroelasticity, Preconditioner |
Simulating Cerebrospinal Fluid Flow and Spinal Cord Movement Associated with Syringomyelia
In Chalmers Institute of Technology. Website: Chalmers Publication Library, 2016.Status: Published
Simulating Cerebrospinal Fluid Flow and Spinal Cord Movement Associated with Syringomyelia
In this study, we tested the hypothesis that fluid velocities within syringes in the spinal cord related to syringomyelia can be explained by fluid-structure interaction (FSI), and that spinal cord movements alter cerebrospinal fluid (CSF) dynamics in the subarachnoid space (SAS). We formulate the coupled fluid-structure interaction problem with an Arbitrary-Lagrangian-Eulerian formulation based on Eulerian coordinates in a moving domain. Our implementation is based on the FEniCS software. The model is then used to investigate FSI effects of syringomyelia in idealized geometries of the spinal cord and SAS.
Our results indicate that FSI in a model of a healthy subject yields results quantitatively and qualitatively similar to computational fluid dynamics. In contrast, in the presence of a syrinx, FSI predicts greater displacements of the cord, and a nonlinear pressure distribution is introduced in the CSF along the cord. With a sinusoidally pulsating flow of CSF in the SAS, an opposing sinusoidal flow is seen within the syrinx. With CSF pulsation closer to the natural environment in the SAS, higher frequencies of oscillatory fluid flow are observed within the syrinx.
| Afilliation | Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2016 |
| Location of Talk | Chalmers Institute of Technology |
| Publisher | Chalmers Publication Library |
| Place Published | Website |
| Other Numbers | S2-2-b |
| Keywords | Finite elements |
| URL | http://publications.lib.chalmers.se/publication/244480-proceedings-of-29... |
Proceedings, non-refereed
Optimization of a Spatially Varying Cardiac Contraction parameter using the Adjoint Method
In FEniCS'16, 2016.Status: Published
Optimization of a Spatially Varying Cardiac Contraction parameter using the Adjoint Method
A cardiac computational model is constrained using clinical measurements such as pressure, volume and regional strain. The problem is formulated as a PDE-constrained optimisation problem where the objective functional represents the misfit between measured and simulated data. The control parameter for the active phase is a spatially varying contraction parameter defined at every vertex in the mesh. This makes gradient calculations using the adjoint approach computationally advantageous over standard finite difference approximations.
| Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Proceedings, non-refereed |
| Year of Publication | 2016 |
| Conference Name | FEniCS'16 |
| Keywords | Adjoint Method, Cardiac Mechanics, parameter estimation, PDE-constrained optimization |
Poster
Patient Specific Modeling of Cardiac Mechanics using the Active Strain Formulation
In Geilo Winter School, 2016.Status: Published
Patient Specific Modeling of Cardiac Mechanics using the Active Strain Formulation
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Poster |
| Year of Publication | 2016 |
| Secondary Title | Geilo Winter School |
I currently work on the IdentiPhy project where I am hired as a senior research engineer to develop tools and software to analyse and model heart-on-chip systems.
The waterscape of the brain
2016.Status: Published
The waterscape of the brain
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
| Publication Type | Poster |
| Year of Publication | 2016 |
| Date Published | 09/2016 |
| Keywords | Neuroscience, Numerical Simulations, Waterscape |
Proceedings, refereed
Personalized Cardiac Mechanical Model using a High Resolution Contraction Field
In VPH16 Translating VPH to the Clinic, 2016.Status: Published
Personalized Cardiac Mechanical Model using a High Resolution Contraction Field
| Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2016 |
| Conference Name | VPH16 Translating VPH to the Clinic |
I currently work on the IdentiPhy project where I am hired as a senior research engineer to develop tools and software to analyse and model heart-on-chip systems.
Talks, invited
A 2-day training course in FEniCS and dolfin-adjoint
In NGCM Summer Academy, University of Southampton, 2015.Status: Published
A 2-day training course in FEniCS and dolfin-adjoint
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2015 |
| Location of Talk | NGCM Summer Academy, University of Southampton |
| Type of Talk | Invited |
Dyssynchronous Left Ventricular Stress Estimation
In Workshop on Advanced Numerical Techniques in Biomedical Computing: Simula Research Laboratory, 2015.Status: Published
Dyssynchronous Left Ventricular Stress Estimation
The heart is a muscular pump that moves approximatly 8,000 litres per day through the human body. It manages to this by a combination of contraction/relaxation along muscle fibers and elastic recoil. These two effects are indistinguishable in a medical image, but can be estimated using a computational model.
In our work we use adjoint based optimization techniques in order to determine muscle contraction and elastic recoil in a patient specific left ventricular geometry based on echocardiography and pressure catheter data. Possible applications of the technique include mechanical stress estimation and hypothesis testing in cardiac resynchronization therapy research.
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2015 |
| Location of Talk | Workshop on Advanced Numerical Techniques in Biomedical Computing: Simula Research Laboratory |
Introduction to dolfin-adjoint and its applications in cardiac electrophysiology
In 2015 Summer School in Computational Physiology: Models, Tools, and Techniques for Cardiac Applications, 2015.Status: Published
Introduction to dolfin-adjoint and its applications in cardiac electrophysiology
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2015 |
| Location of Talk | 2015 Summer School in Computational Physiology: Models, Tools, and Techniques for Cardiac Applications |
The FEniCS and Dolfin-adjoint Projects
In NGCM Summer Academy, University of Southampton, 2015.Status: Published
The FEniCS and Dolfin-adjoint Projects
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2015 |
| Location of Talk | NGCM Summer Academy, University of Southampton |
| Type of Talk | Invited |
Towards a Unified Framework for Automated a Posteriori Error Estimation and Adaptivity in Space-Time
In SIAM CSE, Salt Lake City, USA, 2015.Status: Published
Towards a Unified Framework for Automated a Posteriori Error Estimation and Adaptivity in Space-Time
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2015 |
| Location of Talk | SIAM CSE, Salt Lake City, USA |
| Type of Talk | Invited |
Journal Article
A Nitsche-based Cut Finite Element Method for a Fluid-Structure Interaction Problem
Communications in Applied Mathematics and Computational Science 10 (2015): 97-120.Status: Published
A Nitsche-based Cut Finite Element Method for a Fluid-Structure Interaction Problem
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2015 |
| Journal | Communications in Applied Mathematics and Computational Science |
| Volume | 10 |
| Number | 2 |
| Pagination | 97-120 |
| Publisher | Mathematical Sciences Publishers |
| DOI | 10.2140/camcos.2015.10.97 |
The FEniCS Project Version 1.5
Archive of Numerical Software 3, no. 100 (2015).Status: Published
The FEniCS Project Version 1.5
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2015 |
| Journal | Archive of Numerical Software |
| Volume | 3 |
| Issue | 100 |
| Date Published | 12/2015 |
| Publisher | Open Journal Systems, sponsored by the University of Heidelberg |
Talks, contributed
Biomedical Computing at Simula Research Laboratory
In UNICAT Kick-off meeting, Porto, Portugal (Invited), 2015.Status: Published
Biomedical Computing at Simula Research Laboratory
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2015 |
| Location of Talk | UNICAT Kick-off meeting, Porto, Portugal (Invited) |
Effect of Spinal Cord Viscoelasticity on Its Response to CSF Pressure Waves: a Computational Study
In ASNR 53rd Annual Meeting & The Foundation of the ASNR Symposium 2015, April 25 – 30, Chicago, Illinois, 2015.Status: Published
Effect of Spinal Cord Viscoelasticity on Its Response to CSF Pressure Waves: a Computational Study
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2015 |
| Location of Talk | ASNR 53rd Annual Meeting & The Foundation of the ASNR Symposium 2015, April 25 – 30, Chicago, Illinois |
Identifying the Parameters of the Heart: Variational Data Assimilation in Cardiac Mechanics Using Dolfin-Adjoint
In FEniCS '15, Imperial College London, UK, 2015.Status: Published
Identifying the Parameters of the Heart: Variational Data Assimilation in Cardiac Mechanics Using Dolfin-Adjoint
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2015 |
| Location of Talk | FEniCS '15, Imperial College London, UK |
| Type of Talk | Featured presentation |
New simulation technology driven by medical challenges: the Biomedical Computing Department @ Simula
In Oslo, Simula Research Laboratory, 2015.Status: Published
New simulation technology driven by medical challenges: the Biomedical Computing Department @ Simula
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2015 |
| Location of Talk | Oslo, Simula Research Laboratory |
Non-Manifold Manifold Simulations Using FEniCS
In FEniCS '15, Imperial College London, UK, 2015.Status: Published
Non-Manifold Manifold Simulations Using FEniCS
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2015 |
| Location of Talk | FEniCS '15, Imperial College London, UK |
Poster
Dolfin-adjoint, automated adjoint models for FEniCS
Salt Lake City, USA: SIAM Conference on Computational Science and Engineering, 2015.Status: Published
Dolfin-adjoint, automated adjoint models for FEniCS
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Poster |
| Year of Publication | 2015 |
| Publisher | SIAM Conference on Computational Science and Engineering |
| Place Published | Salt Lake City, USA |
| Notes | Winner of the Best Poster Award |
Dolfin-adjoint: Automatic adjoint models for FEniCS
In The 8th International Congress on Industrial and Applied Mathematics. Beijing, China: The 8th International Congress on Industrial and Applied Mathematics, 2015.Status: Published
Dolfin-adjoint: Automatic adjoint models for FEniCS
Adjoint and tangent linear models form the basis of many numerical techniques, including sensitivity
analysis, optimization and stability analysis. The implementation of adjoint models for nonlinear or time-
dependent models are notoriously challenging: the manual approach is time-consuming and traditional
automatic differentiation tools lack robustness and performance.
dolfin-adjoint solves this problem by automatically analyzing the high-level mathematical structure
inherent in finite element methods. It raises the traditional abstraction of algorithmic differentiation
from the level of individual floating point operations to that of whole systems of differential equations.
This approach delivers a number of advantages over the previous state-of-the-art: robust hands-off
automation of adjoint model derivation, optimal computational efficiency, and native parallel support.
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Poster |
| Year of Publication | 2015 |
| Secondary Title | The 8th International Congress on Industrial and Applied Mathematics |
| Publisher | The 8th International Congress on Industrial and Applied Mathematics |
| Place Published | Beijing, China |
Proceedings, non-refereed
Personalization of a Cardiac Compuational Model using Clinical Measurements
In 28th Nordic Seminar on Computational Mechanics. Vol. 28. Tallin, Estonia: Proceedings of NSCM-28, 2015.Status: Published
Personalization of a Cardiac Compuational Model using Clinical Measurements
Important features in cardiac mechanics that cannot easily be measured in the clinic, can be computed using a computational model that is calibrated to behave in the same way as a patient’s heart. To construct such a model, clinical measurements such as strain, volume and cavity pressure are used to personalize the mechanics of a cardiac computational model. The problem is formulated as a PDE-constrained optimization problem where the minimization functional represents the misfit between the measured and simulated data. The target parameters are material parameters and a spatially varying contraction parameter. The minimization is carried out using a gradient based optimization algorithm and an automatically derived adjoint equation. The method has been tested on synthetic data, and is able to reproduce a prescribed contraction pattern on the left ventricle.
| Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Proceedings, non-refereed |
| Year of Publication | 2015 |
| Conference Name | 28th Nordic Seminar on Computational Mechanics |
| Volume | 28 |
| Pagination | 47-50 |
| Date Published | 10/2015 |
| Publisher | Proceedings of NSCM-28 |
| Place Published | Tallin, Estonia |
I currently work on the IdentiPhy project where I am hired as a senior research engineer to develop tools and software to analyse and model heart-on-chip systems.
Journal Article
A Stabilized Nitsche Fictitious Domain Method for the Stokes Problem
Journal of Scientific Computing 61, no. 3 (2014): 604-628.Status: Published
A Stabilized Nitsche Fictitious Domain Method for the Stokes Problem
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2014 |
| Journal | Journal of Scientific Computing |
| Volume | 61 |
| Issue | 3 |
| Number | online |
| Pagination | 604-628 |
| Date Published | March |
| Publisher | |
| DOI | 10.1007/s10915-014-9838-9 |
A Stabilized Nitsche Overlapping Mesh Method for the Stokes Problem
Numerische Mathematik 128, no. 1 (2014): 73-101.Status: Published
A Stabilized Nitsche Overlapping Mesh Method for the Stokes Problem
We develop a Nitsche-based formulation for a general class of stabilized finite element methods for the Stokes problem posed on a pair of overlapping, non- matching meshes. By extending the least-squares stabilization to the overlap region, we prove that the method is stable, consistent, and optimally convergent. To avoid an ill-conditioned linear algebra system, the scheme is augmented by a least-squares term measuring the discontinuity of the solution in the overlap region of the two meshes. As a consequence, we may prove an estimate for the condition number of the resulting stiffness matrix that is independent of the location of the interface. Finally, we present numerical examples in three spatial dimensions illustrating and confirming the theoretical results.
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2014 |
| Journal | Numerische Mathematik |
| Volume | 128 |
| Issue | 1 |
| Number | online |
| Pagination | 73-101 |
| Date Published | January |
| Publisher | |
| DOI | 10.1007/s00211-013-0603-z |
Unified Form Language: a Domain-Specific Language for Weak Formulations of Partial Differential Equations
ACM Transactions on Mathematical Software 40, no. 2 (2014).Status: Published
Unified Form Language: a Domain-Specific Language for Weak Formulations of Partial Differential Equations
We present the Unified Form Language (UFL), which is a domain-specific language for representing weak formulations of partial differential equations with a view to numerical approximation. Features of UFL include support for variational forms and functionals, automatic differentiation of forms and expressions, arbitrary function space hierarchies for multi-field problems, general differential operators and flexible tensor algebra. With these features, UFL has been used to effortlessly express finite element methods for complex systems of partial differential equations in near-mathematical notation, resulting in compact, intuitive and readable programs. We present in this work the language and its construction. An implementation of UFL is freely available as an open-source software library. The library generates abstract syntax tree representations of variational problems, which are used by other software libraries to generate concrete low-level implementations. Some application examples are presented and libraries that support UFL are highlighted.
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2014 |
| Journal | ACM Transactions on Mathematical Software |
| Volume | 40 |
| Issue | 2 |
| Number | 9 |
| Publisher | ACM |
Talks, invited
Adaptive Finite Elements: Practice and Implementation
In Centre for Mathematics for Applications, University of Oslo, 2014.Status: Published
Adaptive Finite Elements: Practice and Implementation
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2014 |
| Location of Talk | Centre for Mathematics for Applications, University of Oslo |
Automated Goal-Oriented Error Control and Adaptivity
In RCN site visit to the CBC, Simula Research Laboratory, Fornebu, 2014.Status: Published
Automated Goal-Oriented Error Control and Adaptivity
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2014 |
| Location of Talk | RCN site visit to the CBC, Simula Research Laboratory, Fornebu |
High-Level Advanced Abstractions and Techniques in Finite Element Software
In CBC Workshop on Computational Modeling with Applications in Biomedicine and Geophysics at Simula Research Laboratory, 2014.Status: Published
High-Level Advanced Abstractions and Techniques in Finite Element Software
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2014 |
| Location of Talk | CBC Workshop on Computational Modeling with Applications in Biomedicine and Geophysics at Simula Research Laboratory |
In Silico Physiological Flows
In Seminar in connection with Villani visit at Simula Research Laboratory, Fornebu, 2014.Status: Published
In Silico Physiological Flows
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2014 |
| Location of Talk | Seminar in connection with Villani visit at Simula Research Laboratory, Fornebu |
Talks, contributed
An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology
In FEniCS'14 Workshop, University of Chicago center in Paris, France, 2014.Status: Published
An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2014 |
| Location of Talk | FEniCS'14 Workshop, University of Chicago center in Paris, France |
An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology
In CBC and CCI Workshop on Cardiac Modelling at Simula Research Laboratory, Fornebu, 2014.Status: Published
An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2014 |
| Location of Talk | CBC and CCI Workshop on Cardiac Modelling at Simula Research Laboratory, Fornebu |
Perspectives on the Current State of the Art of Computational Modelling of Fluid Flow in the Brain Parenchyma
In CBC and CINPLA Workshop on Modelling Liquid Transport in the Brain, Simula Research Laboratory, Fornebu, 2014.Status: Published
Perspectives on the Current State of the Art of Computational Modelling of Fluid Flow in the Brain Parenchyma
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2014 |
| Location of Talk | CBC and CINPLA Workshop on Modelling Liquid Transport in the Brain, Simula Research Laboratory, Fornebu |
Proceedings, non-refereed
Least Squares Fitting of a Cardiac Hyperelasticity Model Using an Automatically Derived Adjoint Equation
In Proceedings of NSCM-27: the 27th Nordic Seminar on Computational Mechanics. Vol. 27. Drottning Kristinas väg 53: KTH Stockholm Royal Institute of Technology, 2014.Status: Published
Least Squares Fitting of a Cardiac Hyperelasticity Model Using an Automatically Derived Adjoint Equation
A Cardiac hyperelasticity model is successfully calibrated using an adjoint based least squares minimization and synthetic data.
| Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Proceedings, non-refereed |
| Year of Publication | 2014 |
| Conference Name | Proceedings of NSCM-27: the 27th Nordic Seminar on Computational Mechanics |
| Volume | 27 |
| Pagination | 272-275 |
| Date Published | October |
| Publisher | KTH Stockholm Royal Institute of Technology |
| Place Published | Drottning Kristinas väg 53 |
| Keywords | Conference |
Talks, contributed
An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology
In CBC/CCI workshop Advancing numerical technologies in the cardiac domain, 2013.Status: Published
An Adjoint-Enabled Simulation Framework for Cardiac Electrophysiology
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2013 |
| Location of Talk | CBC/CCI workshop Advancing numerical technologies in the cardiac domain |
| Keywords | Workshop |
FEniCS on a Moebius Strip
In CBC seminar series, 2013.Status: Published
FEniCS on a Moebius Strip
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2013 |
| Location of Talk | CBC seminar series |
Solving PDEs Over Manifolds With FEniCS
In FEniCS'13, Cambridge, 2013.Status: Published
Solving PDEs Over Manifolds With FEniCS
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2013 |
| Location of Talk | FEniCS'13, Cambridge |
| Keywords | Conference |
| Notes | Presentation at FEniCS '13, Cambridge, UK. |
Journal Article
Automated Derivation of the Adjoint of High-Level Transient Finite Element Programs
SIAM Journal on Scientific Computing 35 (2013): 369-393.Status: Published
Automated Derivation of the Adjoint of High-Level Transient Finite Element Programs
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2013 |
| Journal | SIAM Journal on Scientific Computing |
| Volume | 35 |
| Number | 4 |
| Pagination | 369-393 |
Automated Goal-Oriented Error Control I: Stationary Variational Problems
SIAM Journal on Scientific Computing 35 (2013): 173-193.Status: Published
Automated Goal-Oriented Error Control I: Stationary Variational Problems
This article presents a general and novel approach to automated goal-oriented error control in the solution of nonlinear stationary finite element variational problems. The approach is based on automated linearization to obtain the linearized dual problem, automated derivation and evaluation of a\~posteriori error estimates, and automated adaptive mesh refinement to control the error in a given goal functional to within a given tolerance. Numerical examples representing a variety of different discretizations of linear and nonlinear partial differential equations are presented, including Poisson's equation, a mixed formulation of linear elasticity, and the incompressible Navier-Stokes equations.
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2013 |
| Journal | SIAM Journal on Scientific Computing |
| Volume | 35 |
| Number | 3 |
| Pagination | 173-193 |
| Date Published | June |
Automating the Solution of PDEs on the Sphere and Other Manifolds in FEniCS 1.2
Geoscientific Model Development (2013): 2099-2119.Status: Published
Automating the Solution of PDEs on the Sphere and Other Manifolds in FEniCS 1.2
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2013 |
| Journal | Geoscientific Model Development |
| Number | 6 |
| Pagination | 2099-2119 |
| Date Published | June |
Benchmarking FEniCS for Mantle Convection Simulations
Computers & Geosciences 50 (2013): 95-105.Status: Published
Benchmarking FEniCS for Mantle Convection Simulations
| Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2013 |
| Journal | Computers & Geosciences |
| Volume | 50 |
| Number | 1 |
| Pagination | 95-105 |
| Date Published | January |
| Publisher | Elsevier |
| Notes | Special issue entitled Benchmark problems, datasets and methodologies for the computational geosciences |
Proceedings, refereed
A Newton Method for Fluid-Structure Interaction Using Full Jacobians Based on Automatic Form Differentiation
In 6th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS 2012, 2012.Status: Published
A Newton Method for Fluid-Structure Interaction Using Full Jacobians Based on Automatic Form Differentiation
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2012 |
| Conference Name | 6th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS 2012 |
Automatically Generated Solvers for Variational Formulations of Time-Dependent Partial Differential Equations
In 6th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS 2012, 2012.Status: Published
Automatically Generated Solvers for Variational Formulations of Time-Dependent Partial Differential Equations
| Afilliation | Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Proceedings, refereed |
| Year of Publication | 2012 |
| Conference Name | 6th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS 2012 |
Journal Article
An Analysis of the Shock Strength Needed to Achieve Defibrillation in a Simplified Mathematical Model of Cardiac Tissue
International Journal of Numerical Analysis and Modeling 9 (2012): 644-657.Status: Published
An Analysis of the Shock Strength Needed to Achieve Defibrillation in a Simplified Mathematical Model of Cardiac Tissue
| Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Journal Article |
| Year of Publication | 2012 |
| Journal | International Journal of Numerical Analysis and Modeling |
| Volume | 9 |
| Number | 3 |
| Pagination | 644-657 |
Talks, invited
Automated FEniCS Frameworks for Adjoint Models and Their Applications
In KAUST, 2012.Status: Published
Automated FEniCS Frameworks for Adjoint Models and Their Applications
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2012 |
| Location of Talk | KAUST |
Automatically Generated Solvers for Variational Formulations of Time-Dependent Partial Differential Equations
In ECCOMAS, 2012.Status: Published
Automatically Generated Solvers for Variational Formulations of Time-Dependent Partial Differential Equations
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2012 |
| Location of Talk | ECCOMAS |
The FEniCS Project: a Modern Framework for the Automated Solution of PDEs by FEM
In Computational Geoscience Workshop, 2012.Status: Published
The FEniCS Project: a Modern Framework for the Automated Solution of PDEs by FEM
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2012 |
| Location of Talk | Computational Geoscience Workshop |
The FEniCS Project: a Short Course
In KAUST, 2012.Status: Published
The FEniCS Project: a Short Course
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2012 |
| Location of Talk | KAUST |
The FEniCS Project: a Tutorial
In Imperial College, 2012.Status: Published
The FEniCS Project: a Tutorial
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2012 |
| Location of Talk | Imperial College |
Book Chapter
Automated Testing of Saddle Point Stability Conditions
In Automated Solution of Differential Equations by the Finite Element Method, 655-670. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Automated Testing of Saddle Point Stability Conditions
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Book Chapter |
| Year of Publication | 2012 |
| Book Title | Automated Solution of Differential Equations by the Finite Element Method |
| Secondary Title | Lecture Notes in Computational Science and Engineering |
| Volume | 84 |
| Chapter | 36 |
| Pagination | 655-670 |
| Publisher | Springer |
| ISBN Number | 978-3-642-23098-1 |
Common and Unusual Finite Elements
In Automated Solution of Differential Equations by the Finite Element Method, 91-116. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Common and Unusual Finite Elements
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Book Chapter |
| Year of Publication | 2012 |
| Book Title | Automated Solution of Differential Equations by the Finite Element Method |
| Secondary Title | Lecture Notes in Computational Science and Engineering |
| Volume | 84 |
| Chapter | 3 |
| Pagination | 91-116 |
| Publisher | Springer |
| ISBN Number | 978-3-642-23098-1 |
Dynamic Simulations of Convection in the Earth's Mantle
In Automated Solution of Differential Equations by the Finite Element Method, 587-602. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Berlin Heidelberg: Springer, 2012.Status: Published
Dynamic Simulations of Convection in the Earth's Mantle
In this chapter, we model dynamic convection processes in the Earth's mantle: linking the geodynamical equations, numerical implementation and Python code tightly together. The convection is generated by heating from below with a compositionally distinct and denser layer at the bottom. The time-dependent nonlinear partial differential equations to be solved are the quasi-static Stokes equations with depth- and temperature-dependent viscosity and advection-diffusion equations for the composition and temperature. We present a numerical algorithm for the simulation of these equations as well as an implementation of this algorithm using the DOLFIN Python interface. The results show the compositional heterogeneities persist, but interact strongly with the convecting system, generating upwellings and moving as material from the surface displaces them. This chapter will be of interest to those seeking to model fluid discontinuities using field methods as well as those interested in mantle convection simulations.
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Book Chapter |
| Year of Publication | 2012 |
| Book Title | Automated Solution of Differential Equations by the Finite Element Method |
| Secondary Title | Lecture Notes in Computational Science and Engineering |
| Volume | 84 |
| Chapter | 31 |
| Pagination | 587-602 |
| Publisher | Springer |
| Place Published | Berlin Heidelberg |
| ISBN Number | 978-3-642-23098-1 |
FFC: the FEniCS Form Compiler
In Automated Solution of Differential Equations by the Finite Element Method, 223-234. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
FFC: the FEniCS Form Compiler
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Book Chapter |
| Year of Publication | 2012 |
| Book Title | Automated Solution of Differential Equations by the Finite Element Method |
| Secondary Title | Lecture Notes in Computational Science and Engineering |
| Volume | 84 |
| Chapter | 11 |
| Pagination | 223-234 |
| Publisher | Springer |
| ISBN Number | 978-3-642-23098-1 |
Talks, contributed
Techniques for Automated Treatment of Variational Forms Over Arbitrary Dimension Tensor Product Finite Elements
In CBC Seminar series, 2012.Status: Published
Techniques for Automated Treatment of Variational Forms Over Arbitrary Dimension Tensor Product Finite Elements
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2012 |
| Location of Talk | CBC Seminar series |
Talks, contributed
Automated Goal-Oriented Error Control
In Talk at CBC workshop on Biomechanics, November 2011, 2011.Status: Published
Automated Goal-Oriented Error Control
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2011 |
| Location of Talk | Talk at CBC workshop on Biomechanics, November 2011 |
Error Control and Adaptivity for the Non-Expert
In Talk at CBC Workshop on Biomedical Modeling, 2011.Status: Published
Error Control and Adaptivity for the Non-Expert
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2011 |
| Location of Talk | Talk at CBC Workshop on Biomedical Modeling |
FEniCS After 1.0: Current Trends at CBC@Simula
In Talk at FEniCS'11 / Red Raider Minisymposium 2011, Texas Tech University, Lubbock, November 2011, 2011.Status: Published
FEniCS After 1.0: Current Trends at CBC@Simula
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2011 |
| Location of Talk | Talk at FEniCS'11 / Red Raider Minisymposium 2011, Texas Tech University, Lubbock, November 2011 |
More Or Less Shocking: Using Energy Estimates to Answer Scientific Questions
In Talk at Biocomp Seminar, Simula Research Laboratory, October 2011, 2011.Status: Published
More Or Less Shocking: Using Energy Estimates to Answer Scientific Questions
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2011 |
| Location of Talk | Talk at Biocomp Seminar, Simula Research Laboratory, October 2011 |
Talks, invited
Automated Goal-Oriented Error Control a Posteriori Error Estimation and Adaptivity in Finite Element Exterior Calculus
In Talk at USNCCM '11, Minneapolis, 2011.Status: Published
Automated Goal-Oriented Error Control a Posteriori Error Estimation and Adaptivity in Finite Element Exterior Calculus
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2011 |
| Location of Talk | Talk at USNCCM '11, Minneapolis |
Bringing Error Control to the Non-Expert - Automation of a Posteriori Error Estimation
In Talk at CBC Workshop on Multiscale Problems and Methods, 2011.Status: Published
Bringing Error Control to the Non-Expert - Automation of a Posteriori Error Estimation
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2011 |
| Location of Talk | Talk at CBC Workshop on Multiscale Problems and Methods |
FEniCS: the Next Generation PDE Software
In Talk at CBC Workshop on Biomedical Modeling, 2011.Status: Published
FEniCS: the Next Generation PDE Software
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2011 |
| Location of Talk | Talk at CBC Workshop on Biomedical Modeling |
Goal-Oriented Error Control Automated!
In Talk at SIAM CSE Reno, Nevada, USA, 2011.Status: Published
Goal-Oriented Error Control Automated!
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2011 |
| Location of Talk | Talk at SIAM CSE Reno, Nevada, USA |
The FEniCS Project
In Talk at Imperial College, 2011.Status: Published
The FEniCS Project
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, invited |
| Year of Publication | 2011 |
| Location of Talk | Talk at Imperial College |
Talks, contributed
A Framework for Automated Goal-Oriented Error Control
In Talk at BIT 50 - Trends in Numerical Computing, 2010.Status: Published
A Framework for Automated Goal-Oriented Error Control
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2010 |
| Location of Talk | Talk at BIT 50 - Trends in Numerical Computing |
Automated Goal-Oriented Error Control
In China-Norway-Sweden Workshop on Computational Mathematics, 2010.Status: Published
Automated Goal-Oriented Error Control
| Afilliation | Scientific Computing, , Scientific Computing |
| Project(s) | Center for Biomedical Computing (SFF) |
| Publication Type | Talks, contributed |
| Year of Publication | 2010 |
| Location of Talk | China-Norway-Sweden Workshop on Computational Mathematics |