Publications
Journal Article
CSF circulation and dispersion yield rapid clearance from intracranial compartments
TBA (2022).Status: Submitted
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 | TBA |
Publisher | TBA |
URL | https://doi.org/10.1101/2022.05.02.490257 |
Robust approximation of generalized Biot-Brinkman problems
TBA (2022).Status: Submitted
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 | TBA |
Publisher | TBA |
URL | https://arxiv.org/abs/2112.13618 |
Robust Preconditioning and Error Estimates for Optimal Control of the Convection--Diffusion--Reaction Equation with Limited Observation in Isogeometric Analysis
SIAM Journal on Numerical Analysis 602740, no. 1 (2022): 195-221.Status: Published
Robust Preconditioning and Error Estimates for Optimal Control of the Convection--Diffusion--Reaction Equation with Limited Observation in Isogeometric Analysis
Afilliation | Scientific Computing |
Project(s) | SciML - Scientific Machine Learning |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | SIAM Journal on Numerical Analysis |
Volume | 602740 |
Issue | 1 |
Pagination | 195 - 221 |
Date Published | Jan-02-2022 |
Publisher | SIAM |
ISSN | 0036-1429 |
URL | https://epubs.siam.org/doi/10.1137/21M139147Xhttps://epubs.siam.org/doi/... |
DOI | 10.1137/21M139147X |
Twofold saddle-point formulation of Biot poroelasticity with stress-dependent diffusion
arXiv (2022).Status: Submitted
Twofold saddle-point formulation of Biot poroelasticity with stress-dependent diffusion
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | arXiv |
Publisher | arXiv |
URL | https://arxiv.org/pdf/2109.15006.pdf |
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 |
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 |
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 |
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 |
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 |
Analysis and approximation of mixed-dimensional PDEs on 3D-1D domains coupled with Lagrange multipliers
SIAM Journal on Numerical Analysis 59, no. 1 (2021): 558-582.Status: Published
Analysis and approximation of mixed-dimensional PDEs on 3D-1D domains coupled with Lagrange multipliers
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | SIAM Journal on Numerical Analysis |
Volume | 59 |
Issue | 1 |
Pagination | 558–582 |
Publisher | SIAM |
DOI | 10.1137/20M1329664 |
Direction and magnitude of cerebrospinal fluid flow vary substantially across central nervous system diseases
Fluids and Barriers of the CNS 18, no. 1186–193 (2021).Status: Published
Direction and magnitude of cerebrospinal fluid flow vary substantially across central nervous system diseases
Afilliation | Scientific Computing |
Project(s) | SciML - Scientific Machine Learning |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | Fluids and Barriers of the CNS |
Volume | 18 |
Issue | 1186–193 |
Date Published | Jan-12-2021 |
Publisher | Springer |
URL | https://fluidsbarrierscns.biomedcentral.com/articles/10.1186/s12987-021-... |
DOI | 10.1186/s12987-021-00251-6 |
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 |
Robust Preconditioners for Perturbed Saddle-Point Problems and Conservative Discretizations of Biot's Equations Utilizing Total Pressure
SIAM Journal on Scientific Computing 43, no. 4 (2021): B961-B983.Status: Published
Robust Preconditioners for Perturbed Saddle-Point Problems and Conservative Discretizations of Biot's Equations Utilizing Total Pressure
Afilliation | Scientific Computing |
Project(s) | SciML - Scientific Machine Learning |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | SIAM Journal on Scientific Computing |
Volume | 43 |
Issue | 4 |
Pagination | B961 - B983 |
Date Published | Jan-01-2021 |
Publisher | SIAM |
ISSN | 1064-8275 |
URL | https://epubs.siam.org/doi/10.1137/20M1379708https://epubs.siam.org/doi/... |
DOI | 10.1137/20M1379708 |
Sleep deprivation impairs molecular clearance from the human brain
Brain 144, no. 3 (2021): 863-874.Status: Published
Sleep deprivation impairs molecular clearance from the human brain
It remains an enigma why human beings spend one-third of their life asleep. Experimental data suggest that sleep is required for clearance of waste products from brain metabolism. This has, however, never been verified in humans. The primary aim of the present study was to examine in vivo whether one night of total sleep deprivation affects molecular clearance from the human brain. Secondarily, we examined whether clearance was affected by subsequent sleep. Multiphase MRI with standardized T1 sequences was performed up to 48 h after intrathecal administration of the contrast agent gadobutrol (0.5 ml of 1 mmol/ml), which served as a tracer molecule. Using FreeSurfer software, we quantified tracer enrichment within 85 brain regions as percentage change from baseline of normalized T1 signals. The cerebral tracer enrichment was compared between two cohorts of individuals; one cohort (n = 7) underwent total sleep deprivation from Day 1 to Day 2 (sleep deprivation group) while an age and gender-matched control group (n = 17; sleep group) was allowed free sleep from Day 1 to Day 2. From Day 2 to 3 all individuals were allowed free sleep. The tracer enriched the brains of the two groups similarly. Sleep deprivation was the sole intervention. One night of sleep deprivation impaired clearance of the tracer substance from most brain regions, including the cerebral cortex, white matter and limbic structures, as demonstrated on the morning of Day 2 after intervention (sleep deprivation/sleep). Moreover, the impaired cerebral clearance in the sleep deprivation group was not compensated by subsequent sleep from Day 2 to 3. The present results provide in vivo evidence that one night of total sleep deprivation impairs molecular clearance from the human brain, and that humans do not catch up on lost sleep.
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | Brain |
Volume | 144 |
Issue | 3 |
Pagination | 863-874 |
Date Published | 04/2021 |
Publisher | Oxford Academic |
Place Published | Brain |
DOI | 10.1093/brain/awaa443 |
Variations in the cerebrospinal fluid dynamics of the American alligator (Alligator mississippiensis)
Fluids and Barriers of the CNS 18, no. 1205 (2021).Status: Published
Variations in the cerebrospinal fluid dynamics of the American alligator (Alligator mississippiensis)
Afilliation | Scientific Computing |
Project(s) | SciML - Scientific Machine Learning |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | Fluids and Barriers of the CNS |
Volume | 18 |
Issue | 1205 |
Date Published | Jan-12-2021 |
Publisher | Springer |
URL | https://fluidsbarrierscns.biomedcentral.com/articles/10.1186/s12987-021-... |
DOI | 10.1186/s12987-021-00248-1 |
Book
Mathematical modeling of the human brain: from magnetic resonance images to finite element simulation
.: Springer, 2021.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 | 2021 |
Publisher | Springer |
Place Published | . |
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 |
Proceedings, refereed
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
An observation on the uniform preconditioners for the mixed Darcy problem
Numerical Methods for Partial Differential Equations 36 (2020): 1718-1734.Status: Published
An observation on the uniform preconditioners for the mixed Darcy problem
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Numerical Methods for Partial Differential Equations |
Volume | 36 |
Number | 6 |
Pagination | 1718–1734 |
Publisher | Wiley |
Apparent diffusion coefficient estimates based on 24 hours tracer movement support glymphatic transport in human cerebral cortex
Scientific Reports 10, no. 1 (2020).Status: Published
Apparent diffusion coefficient estimates based on 24 hours tracer movement support glymphatic transport in human cerebral cortex
Afilliation | Scientific Computing |
Project(s) | DataSim: Data-driven Algorithms for Physical Simulations |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Scientific Reports |
Volume | 10 |
Issue | 1 |
Date Published | Jan-12-2020 |
Publisher | Nature |
URL | http://www.nature.com/articles/s41598-020-66042-5http://www.nature.com/a... |
DOI | 10.1038/s41598-020-66042-5 |
Dynamics of a neuron–glia system: the occurrence of seizures and the influence of electroconvulsive stimuli: A mathematical and numerical study
Journal of computational neuroscience 48 (2020): 229-251.Status: Published
Dynamics of a neuron–glia system: the occurrence of seizures and the influence of electroconvulsive stimuli: A mathematical and numerical study
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Journal of computational neuroscience |
Volume | 48 |
Number | 2 |
Pagination | 229-251 |
Publisher | Springer |
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 |
Robust preconditioners for perturbed saddle-point problems and conservative discretizations of Biot's equations utilizing total pressure
arXiv preprint arXiv:2011.05236 (2020).Status: Submitted
Robust preconditioners for perturbed saddle-point problems and conservative discretizations of Biot's equations utilizing total pressure
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | arXiv preprint arXiv:2011.05236 |
Publisher | SIAM |
Robust preconditioning for coupled Stokes–Darcy problems with the Darcy problem in primal form
Computers & Mathematics with Applications (2020).Status: Published
Robust preconditioning for coupled Stokes–Darcy problems with the Darcy problem in primal form
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Computers & Mathematics with Applications |
Publisher | Elsevier |
ISSN | 0898-1221 |
URL | http://www.sciencedirect.com/science/article/pii/S0898122120303291 |
DOI | 10.1016/j.camwa.2020.08.021 |
Robust preconditioning of monolithically coupled multiphysics problems
arXiv preprint arXiv:2001.05527 (2020).Status: Submitted
Robust preconditioning of monolithically coupled multiphysics problems
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | arXiv preprint arXiv:2001.05527 |
Publisher | SIAM |
Slope limiting the velocity field in a discontinuous Galerkin divergence-free two-phase flow solver
Computers & Fluids 196 (2020): 104322.Status: Published
Slope limiting the velocity field in a discontinuous Galerkin divergence-free two-phase flow solver
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Computers & Fluids |
Volume | 196 |
Pagination | 104322 |
Date Published | Jan-01-2020 |
Publisher | Elsevier |
ISSN | 00457930 |
DOI | 10.1016/j.compfluid.2019.104322 |
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, invited
Mathematical modeling of the g-lymphatic system – preconditioning of Darcy - Stokes systems
In IMG 2019, Kunming, China, 2019.Status: Published
Mathematical modeling of the g-lymphatic system – preconditioning of Darcy - Stokes systems
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talks, invited |
Year of Publication | 2019 |
Location of Talk | IMG 2019, Kunming, China |
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 |
Mathematical modeling of the glymphatic system
In ICIAM, Valencia, Spain, 2019.Status: Published
Mathematical modeling of the glymphatic system
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talks, invited |
Year of Publication | 2019 |
Location of Talk | ICIAM, Valencia, Spain |
Parameter Identification of Brain Cleaning
In ICIAM, Valencia, Spain, 2019.Status: Published
Parameter Identification of Brain Cleaning
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talks, invited |
Year of Publication | 2019 |
Location of Talk | ICIAM, Valencia, Spain |
Preconditioning of multi-physics problems with applications to the biomechanics of the brain
In MOX, Milan, Italy, 2019.Status: Published
Preconditioning of multi-physics problems with applications to the biomechanics of the brain
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talks, invited |
Year of Publication | 2019 |
Location of Talk | MOX, Milan, Italy |
Preconditioning with some application to brain modeling
In Symposium on the occasion of Ragnar Winther's 70th birthday, Oslo, Norway, 2019.Status: Published
Preconditioning with some application to brain modeling
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talks, invited |
Year of Publication | 2019 |
Location of Talk | Symposium on the occasion of Ragnar Winther's 70th birthday, Oslo, Norway |
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 |
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 |
How does the presence of neural probes affect extracellular potentials?
Journal of Neural Engineering 16 (2019): 026030.Status: Published
How does the presence of neural probes affect extracellular potentials?
{Objective. Mechanistic modeling of neurons is an essential component of computational neuroscience that enables scientists to simulate, explain, and explore neural activity. The conventional approach to simulation of extracellular neural recordings first computes transmembrane currents using the cable equation and then sums their contribution to model the extracellular potential. This two-step approach relies on the assumption that the extracellular space is an infinite and homogeneous conductive medium, while measurements are performed using neural probes. The main purpose of this paper is to assess to what extent the presence of the neural probes of varying shape and size impacts the extracellular field and how to correct for them. Approach. We apply a detailed modeling framework allowing explicit representation of the neuron and the probe to study the effect of the probes and thereby estimate the effect of ignoring it. We use meshes with simplified neurons and different types of probe and compare the extracellular action potentials with and without the probe in the extracellular space. We then compare various solutions to account for the probes’ presence and introduce an efficient probe correction method to include the probe effect in modeling of extracellular potentials. Main results. Our computations show that microwires hardly influence the extracellular electric field and their effect can therefore be ignored. In contrast, multi-electrode arrays (MEAs) significantly affect the extracellular field by magnifying the recorded potential. While MEAs behave similarly to infinite insulated planes, we find that their effect strongly depends on the neuron-probe alignment and probe orientation. Significance. Ignoring the probe effect might be deleterious in some applications, such as neural localization and parameterization of neural models from extracellular recordings. Moreover, the presence of the probe can improve the interpretation of extracellular recordings, by providing a more accurate estimation of the extracellular potential generated by neuronal models.
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Journal of Neural Engineering |
Volume | 16 |
Number | 2 |
Pagination | 026030 |
Date Published | feb |
Publisher | IOP} Publishing |
URL | https://doi.org/10.1088%2F1741-2552%2Fab03a1 |
DOI | 10.1088/1741-2552/ab03a1 |
Laplacian Preconditioning of Elliptic PDEs: Localization of the Eigenvalues of the Discretized Operator
SIAM Journal on Numerical Analysis 57, no. 3 (2019): 1369-1394.Status: Published
Laplacian Preconditioning of Elliptic PDEs: Localization of the Eigenvalues of the Discretized Operator
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | SIAM Journal on Numerical Analysis |
Volume | 57 |
Issue | 3 |
Pagination | 1369 - 1394 |
Date Published | Feb-01-2019 |
Publisher | SIAM |
Place Published | SIAM Journal of Numerical Analysis |
ISSN | 0036-1429 |
URL | https://epubs.siam.org/doi/10.1137/18M1212458https://epubs.siam.org/doi/... |
DOI | 10.1137/18M1212458 |
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 |
Multi-resolution Bayesian CMB component separation through Wiener filtering with a pseudo-inverse preconditioner
Astronomy & Astrophysics 627 (2019): A98.Status: Published
Multi-resolution Bayesian CMB component separation through Wiener filtering with a pseudo-inverse preconditioner
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Astronomy & Astrophysics |
Volume | 627 |
Pagination | A98 |
Date Published | Jan-07-2019 |
Publisher | EDP Sciences |
ISSN | 0004-6361 |
URL | https://www.aanda.org/10.1051/0004-6361/201732037https://www.aanda.org/1... |
DOI | 10.1051/0004-6361/201732037 |
Multigrid Methods for Discrete Fractional Sobolev Spaces
SIAM Journal on Scientific Computing 41 (2019): A948-A972.Status: Published
Multigrid Methods for Discrete Fractional Sobolev Spaces
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | SIAM Journal on Scientific Computing |
Volume | 41 |
Number | 2 |
Pagination | A948–A972 |
Publisher | {SIAM |
On the singular Neumann problem in linear elasticity
Numerical Linear Algebra with Applications 26, no. 1 (2019): e2212.Status: Published
On the singular Neumann problem in linear elasticity
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Numerical Linear Algebra with Applications |
Volume | 26 |
Issue | 1 |
Pagination | e2212 |
Date Published | Aug-08-2019 |
Publisher | Wiley |
Place Published | Numerical Linear Algebra with Applications |
URL | http://doi.wiley.com/10.1002/nla.2212http://onlinelibrary.wiley.com/wol1... |
DOI | 10.1002/nla.2212 |
Preconditioning trace coupled 3D-1D systems using fractional Laplacian
Numerical Methods for Partial Differential Equations 35, no. 1 (2019): 375-393.Status: Published
Preconditioning trace coupled 3D-1D systems using fractional Laplacian
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Numerical Methods for Partial Differential Equations |
Volume | 35 |
Issue | 1 |
Pagination | 375-393 |
Date Published | Apr-09-2019 |
Publisher | Wiley |
Place Published | Numerical Methods for Partial Differential Equations |
URL | http://doi.wiley.com/10.1002/num.22304http://onlinelibrary.wiley.com/wol... |
DOI | 10.1002/num.22304 |
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 |
Miscellaneous
An Observation On The Uniform Preconditioners For The Mixed Darcy Problem
https://arxiv.org/abs/1812.00653: arXive, 2019.Status: Submitted
An Observation On The Uniform Preconditioners For The Mixed Darcy Problem
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Miscellaneous |
Year of Publication | 2019 |
Publisher | arXive |
Place Published | https://arxiv.org/abs/1812.00653 |
Book
Introduction to Numerical Methods for Variational Problems
Vol. 21. Cham: Springer International Publishing, 2019.Status: Published
Introduction to Numerical Methods for Variational Problems
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book |
Year of Publication | 2019 |
Volume | 21 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN | 1611-0994 |
ISBN Number | 978-3-030-23787-5 |
URL | http://link.springer.com/10.1007/978-3-030-23788-2http://link.springer.c... |
DOI | 10.1007/978-3-030-23788-2 |
Talks, contributed
Mathematical modeling of the g - lymphatic system – preconditioning of Darcy - Stokes systems
In Biomechanics of living systems, Tøyen hovedgård, Norway, 2019.Status: Published
Mathematical modeling of the g - lymphatic system – preconditioning of Darcy - Stokes systems
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talks, contributed |
Year of Publication | 2019 |
Location of Talk | Biomechanics of living systems, Tøyen hovedgård, Norway |
Robust preconditioners for multiphysics problems involving porous flow in physiology modeling
In ICIAM 2019, Valencia, Spain, 2019.Status: Published
Robust preconditioners for multiphysics problems involving porous flow in physiology modeling
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talks, contributed |
Year of Publication | 2019 |
Location of Talk | ICIAM 2019, Valencia, Spain |
Talk, keynote
Robust Preconditioners for Multiscale Systems in Biomechanics
In 12th International Conference on Large-Scale Scientific Computations, Sozopol, Bulgaria, 2019.Status: Published
Robust Preconditioners for Multiscale Systems in Biomechanics
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talk, keynote |
Year of Publication | 2019 |
Location of Talk | 12th International Conference on Large-Scale Scientific Computations, Sozopol, Bulgaria |
Type of Talk | contributed |
Proceedings, refereed
Sub-voxel Perfusion Modeling in Terms of Coupled 3d-1d Problem
In Numerical Mathematics and Advanced Applications ENUMATH 2017. Cham: Springer International Publishing, 2019.Status: Published
Sub-voxel Perfusion Modeling in Terms of Coupled 3d-1d Problem
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Proceedings, refereed |
Year of Publication | 2019 |
Conference Name | Numerical Mathematics and Advanced Applications ENUMATH 2017 |
Pagination | 35 - 47 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-319-96414-0 |
ISSN Number | 1439-7358 |
URL | http://link.springer.com/content/pdf/10.1007/978-3-319-96415-7.pdf |
DOI | 10.1007/978-3-319-96415-710.1007/978-3-319-96415-7_2 |
Talks, contributed
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 |
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 |
Journal Article
Brain-wide glymphatic enhancement and clearance in humans assessed with MRI
JCI insight 3 (2018).Status: Published
Brain-wide glymphatic enhancement and clearance in humans assessed with MRI
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | JCI insight |
Volume | 3 |
Number | 13 |
Publisher | American Society for Clinical Investigation |
DOI | 10.1172/jci.insight.121537 |
Cerebrospinal fluid volumetric net flow rate and direction in idiopathic normal pressure hydrocephalus
NeuroImage: Clinical 20 (2018): 731-741.Status: Published
Cerebrospinal fluid volumetric net flow rate and direction in idiopathic normal pressure hydrocephalus
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | NeuroImage: Clinical |
Volume | 20 |
Pagination | 731-741 |
Publisher | Elsevier |
Comparison of phase-contrast MR and flow simulations for the study of CSF dynamics in the cervical spine
The Neuroradiology Journal 31, no. 3 (2018): 292-298.Status: Published
Comparison of phase-contrast MR and flow simulations for the study of CSF dynamics in the cervical spine
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | The Neuroradiology Journal |
Volume | 31 |
Issue | 3 |
Pagination | 292-298 |
Publisher | SAGE Publications |
DOI | 10.1177/1971400918759812 |
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 |
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, no. 2 (2018): 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 | 2018 |
Journal | Acta Neurochirurgica |
Volume | 161 |
Issue | 2 |
Pagination | 247–256 |
Date Published | Mar-11-2019 |
Publisher | Springer |
Place Published | Vienna |
ISSN | 0001-6268 |
URL | http://link.springer.com/10.1007/s00701-018-3730-6http://link.springer.c... |
DOI | 10.1007/s00701-018-3730-6 |
Real-World Variability in the Prediction of Intracranial Aneurysm Wall Shear Stress: The 2015 International Aneurysm CFD Challenge
Cardiovascular Engineering and Technology 9, no. 4 (2018): 544-564.Status: Published
Real-World Variability in the Prediction of Intracranial Aneurysm Wall Shear Stress: The 2015 International Aneurysm CFD Challenge
Purpose
Image-based computational fluid dynamics (CFD) is widely used to predict intracranial aneurysm wall shear stress (WSS), particularly with the goal of improving rupture risk assessment. Nevertheless, concern has been expressed over the variability of predicted WSS and inconsistent associations with rupture. Previous challenges, and studies from individual groups, have focused on individual aspects of the image-based CFD pipeline. The aim of this Challenge was to quantify the total variability of the whole pipeline.
Methods
3D rotational angiography image volumes of five middle cerebral artery aneurysms were provided to participants, who were free to choose their segmentation methods, boundary conditions, and CFD solver and settings. Participants were asked to fill out a questionnaire about their solution strategies and experience with aneurysm CFD, and provide surface distributions of WSS magnitude, from which we objectively derived a variety of hemodynamic parameters.
Results
A total of 28 datasets were submitted, from 26 teams with varying levels of self-assessed experience. Wide variability of segmentations, CFD model extents, and inflow rates resulted in interquartile ranges of sac average WSS up to 56%, which reduced to < 30% after normalizing by parent artery WSS. Sac-maximum WSS and low shear area were more variable, while rank-ordering of cases by low or high shear showed only modest consensus among teams. Experience was not a significant predictor of variability.
Conclusions
Wide variability exists in the prediction of intracranial aneurysm WSS. While segmentation and CFD solver techniques may be difficult to standardize across groups, our findings suggest that some of the variability in image-based CFD could be reduced by establishing guidelines for model extents, inflow rates, and blood properties, and by encouraging the reporting of normalized hemodynamic parameters.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | Cardiovascular Engineering and Technology |
Volume | 9 |
Issue | 4 |
Pagination | 544–564 |
Date Published | 10/2018 |
Publisher | Springer |
Place Published | US |
ISSN | 1869-408X |
Keywords | Intracranial aneurysm, Patient-specific modeling, Rupture risk, Uncertainty quantification, Wall shear stress |
URL | https://goo.gl/mG9u9t |
DOI | 10.1007/s13239-018-00374-2 |
Variational data assimilation for transient blood flow simulations
International Journal for Numerical Methods in Biomedical Engineering 35, no. 1 (2018): e3152.Status: Published
Variational data assimilation for transient blood flow simulations
Several cardiovascular diseases are caused from localised abnormal blood flow such as in the case of stenosis or aneurysms. Prevailing theories propose that the development is caused by abnormal wall-shear stress in focused
areas. Computational fluid mechanics have arisen as a promising tool for a more precise and quantitative analysis, in particular because the anatomy is often readily available even by standard imaging techniques such as magnetic resolution and computed tomography angiography. However, computational fluid mechanics rely on accurate initial and boundary conditions which is difficult to obtain. In this paper we address the problem of recovering high resolution information from noisy, low-resolution measurements of blood flow using variational data assimilation based on a transient Navier-Stokes model. Numerical experiments are performed in both 2D and 3D and with pulsatile flow relevant for physiological flow in cerebral aneurysms. The results demonstrate that, with suitable regularisation, the model accurately reconstructs flow, even in the presence of significant noise.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF), OptCutCell: Simulation-based optimisation with dynamic domains |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 35 |
Issue | 1 |
Pagination | e3152 |
Date Published | 10/2018 |
Publisher | John Wiley & Sons |
Keywords | adjoint equations, blood flow, Finite element method, Navier-Stokes, optimal control, variational data assimilation |
“Bucket” cerebrospinal fluid bulk flow: when the terrain disagrees with the map
Acta Neurochirurgica 161, no. 2 (2018): 259-261.Status: Published
“Bucket” cerebrospinal fluid bulk flow: when the terrain disagrees with the map
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | Acta Neurochirurgica |
Volume | 161 |
Issue | 2 |
Pagination | 259–261 |
Date Published | May-12-2019 |
Publisher | Springer |
ISSN | 0001-6268 |
URL | http://link.springer.com/10.1007/s00701-018-3775-6 |
DOI | 10.1007/s00701-018-3775-6 |
Talk, keynote
Mathematical modeling of the glymphatic system – the physics of Alzheimer’s disease ?
In Mathematical models in health sciences, Nantes, France, 2018.Status: Published
Mathematical modeling of the glymphatic system – the physics of Alzheimer’s disease ?
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talk, keynote |
Year of Publication | 2018 |
Location of Talk | Mathematical models in health sciences, Nantes, France |
Type of Talk | Invited Plenary |
Mathematical modeling of the glymphatic system – the physics of Alzheimer’s disease?
In INdAM, Rome, Italy, 2018.Status: Published
Mathematical modeling of the glymphatic system – the physics of Alzheimer’s disease?
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talk, keynote |
Year of Publication | 2018 |
Location of Talk | INdAM, Rome, Italy |
Talks, invited
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 |
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 |
Preconditioners for PDE constrained optimization problems (coarse observations, boundary control)
In SIAM ALA, Hong Kong, China, 2018.Status: Published
Preconditioners for PDE constrained optimization problems (coarse observations, boundary control)
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talks, invited |
Year of Publication | 2018 |
Location of Talk | SIAM ALA, Hong Kong, China |
Poster
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/... |
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 |
A numerical investigation of intrathecal isobaric drug dispersion within the cervical subarachnoid space
PLoS ONE 12, no. 3 (2017): e0173680.Status: Published
A numerical investigation of intrathecal isobaric drug dispersion within the cervical subarachnoid space
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 | PLoS ONE |
Volume | 12 |
Issue | 3 |
Pagination | e0173680 |
Publisher | PLOS |
DOI | 10.1371/journal.pone.0173680 |
Interstitial Solute Transport in 3D Reconstructed Neuropil Occurs by Diffusion Rather than Bulk Flow
Proceedings of the National Academy of Sciences 114, no. 37 (2017): 9894-9899.Status: Published
Interstitial Solute Transport in 3D Reconstructed Neuropil Occurs by Diffusion Rather than Bulk Flow
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF), Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Proceedings of the National Academy of Sciences |
Volume | 114 |
Issue | 37 |
Pagination | 9894-9899 |
Publisher | National Academy og Sciences |
DOI | 10.1073/pnas.1706942114 |
Non-invasive Assessment of Pulsatile Intracranial Pressure with Phase-Contrast Magnetic Resonance Imaging
PLoS ONE 12, no. 11 (2017): e0188896.Status: Published
Non-invasive Assessment of Pulsatile Intracranial Pressure with Phase-Contrast Magnetic Resonance Imaging
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 | PLoS ONE |
Volume | 12 |
Issue | 11 |
Pagination | e0188896 |
Publisher | PLOS ONE |
DOI | 10.1371/journal.pone.0188896 |
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 |
Parameter-robust discretization and preconditioning of Biot's consolidation model
SIAM Journal of Scientific Computing 39 (2017): 1-24.Status: Published
Parameter-robust discretization and preconditioning of Biot's consolidation model
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | SIAM Journal of Scientific Computing |
Volume | 39 |
Pagination | 1-24 |
Publisher | SIAM |
DOI | 10.1137/15M1029473 |
Robustness of common hemodynamic indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms.
PLoS ONE 12, no. 6 (2017): e0177566.Status: Published
Robustness of common hemodynamic indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms.
BACKGROUND:
Using computational fluid dynamics (CFD) to compute the hemodynamics in cerebral aneurysms has received much attention in the last decade. The usability of these methods depends on the quality of the computations, highlighted in recent discussions. The purpose of this study is to investigate the convergence of common hemodynamic indicators with respect to numerical resolution.
METHODS:
38 middle cerebral artery bifurcation aneurysms were studied at two different resolutions (one comparable to most studies, and one finer). Relevant hemodynamic indicators were collected from two of the most cited studies, and were compared at the two refinements. In addition, correlation to rupture was investigated.
RESULTS:
Most of the hemodynamic indicators were very well resolved at the coarser resolutions, correlating with the finest resolution with a correlation coefficient >0.95. The oscillatory shear index (OSI) had the lowest correlation coefficient of 0.83. A logarithmic Bland-Altman plot revealed noticeable variations in the proportion of the aneurysm under low shear, as well as in spatial and temporal gradients not captured by the correlation alone.
CONCLUSION:
Statistically, hemodynamic indicators agree well across the different resolutions studied here. However, there are clear outliers visible in several of the hemodynamic indicators, which suggests that special care should be taken when considering individual assessment.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | PLoS ONE |
Volume | 12 |
Issue | 6 |
Pagination | e0177566 |
Publisher | Public Library of Science |
Talks, invited
Biographical note on biomedical applications
In International Conference on Computational Science and Engineering, Oslo, Norway, 2017.Status: Published
Biographical note on biomedical applications
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talks, invited |
Year of Publication | 2017 |
Location of Talk | International Conference on Computational Science and Engineering, Oslo, Norway |
Blood flow in cerebral aneurysms, water flow clearance in Alzheimer and operator preconditioning
In Prague, Czech Republic, 2017.Status: Published
Blood flow in cerebral aneurysms, water flow clearance in Alzheimer and operator preconditioning
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talks, invited |
Year of Publication | 2017 |
Location of Talk | Prague, Czech Republic |
Type of Talk | Invited |
Coupling CSF flow, perfusion and glymphatics (?)
In 2nd Workshop on computational aspects of perfusion and flow in live tissue, Bergen, Norway, 2017.Status: Published
Coupling CSF flow, perfusion and glymphatics (?)
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
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 |
Type of Talk | invited |
Experimental investigation of transitional effects at low Reynolds number in blood vessels - X-ray, microphones and simulations
In CMBE 2017, Pittsburgh, USA, 2017.Status: Published
Experimental investigation of transitional effects at low Reynolds number in blood vessels - X-ray, microphones and simulations
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2017 |
Location of Talk | CMBE 2017, Pittsburgh, USA |
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 |
Simulating the fluid flow of the lymphatic system - extracellular fluid flow
In The 4th CSF symposium, Atlanta, USA, 2017.Status: Published
Simulating the fluid flow of the lymphatic system - extracellular 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 | 2017 |
Location of Talk | The 4th CSF symposium, Atlanta, USA |
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 |
Talk, keynote
Computational modeling of the glymphatic system: how is waste cleared from the brain?
In HPCSE 2017, Ostrava, Czech Republic, 2017.Status: Published
Computational modeling of the glymphatic system: how is waste cleared from the brain?
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
Publication Type | Talk, keynote |
Year of Publication | 2017 |
Location of Talk | HPCSE 2017, Ostrava, Czech Republic |
Type of Talk | Invited, plenary |
Computational modeling of the glymphatic system: how is waste cleared from the brain?
In Interpore 2017, Rotterdam, the Netherlands, 2017.Status: Published
Computational modeling of the glymphatic system: how is waste cleared from the brain?
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talk, keynote |
Year of Publication | 2017 |
Location of Talk | Interpore 2017, Rotterdam, the Netherlands |
Type of Talk | Invited, plenary |
Physics of oscillatory CSF Flow
In ASSR, San Diego, USA, 2017.Status: Published
Physics of oscillatory CSF Flow
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
Publication Type | Talk, keynote |
Year of Publication | 2017 |
Location of Talk | ASSR, San Diego, USA |
The operator preconditioning framework with various applications to interstitial fluid flow and the aging human brain
In Enumath, Voss, Norway, 2017.Status: Published
The operator preconditioning framework with various applications to interstitial fluid flow and the aging human brain
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Talk, keynote |
Year of Publication | 2017 |
Location of Talk | Enumath, Voss, Norway |
Talks, contributed
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 |
Journal Article
Association of pulse pressure gradient across cranio-cervical junction as derived from phase-contrast magnetic resonance imaging and invasively measured pulsatile intracranial pressure in symptomatic patients with Chiari malformation type 1
Acta Neurochirurgica 158, no. 12 (2016).Status: Published
Association of pulse pressure gradient across cranio-cervical junction as derived from phase-contrast magnetic resonance imaging and invasively measured pulsatile intracranial pressure in symptomatic patients with Chiari malformation type 1
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | Acta Neurochirurgica |
Volume | 158 |
Issue | 12 |
Publisher | Springer |
Computational Investigation of Cerebrospinal Fluid Dynamics in the Posterior Cranial Fossa and Cervical Subarachnoid Space in Patients with Chiari I Malformation
PLOS ONE 11 (2016).Status: Published
Computational Investigation of Cerebrospinal Fluid Dynamics in the Posterior Cranial Fossa and Cervical Subarachnoid Space in Patients with Chiari I Malformation
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | PLOS ONE |
Volume | 11 |
Number | 10 |
Publisher | PLOS ONE |
Direct numerical simulations of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation – the role of cranio-vertebral junction
International Journal for Numerical Methods in Biomedical Engineering (2016).Status: Published
Direct numerical simulations of transitional hydrodynamics of the cerebrospinal fluid in Chiari I malformation – the role of cranio-vertebral junction
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Publisher | John Wiley & Sons |
Preconditioners for saddle point systems with trace constraints coupling 2D and 1D domains
SIAM Journal of Scientific Computing 38, no. 6 (2016).Status: Published
Preconditioners for saddle point systems with trace constraints coupling 2D and 1D domains
Afilliation | Scientific Computing |
Project(s) | Waterscape: The Numerical Waterscape of the Brain, Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | SIAM Journal of Scientific Computing |
Volume | 38 |
Issue | 6 |
Publisher | SIAM |
Robust preconditioners for PDE-constrained optimization with limited observations
BIT Numerical Mathematics 57 (2016): 405-431.Status: Published
Robust preconditioners for PDE-constrained optimization with limited observations
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | BIT Numerical Mathematics |
Volume | 57 |
Number | 2 |
Pagination | 405-431 |
Publisher | Springer |
Transitional hemodynamics in intracranial aneurysms - Comparative velocity investigations with high resolution Lattice Boltzmann simulations, normal resolution ANSYS simulations and MR imaging
Medical Physics 43, no. 11 (2016).Status: Published
Transitional hemodynamics in intracranial aneurysms - Comparative velocity investigations with high resolution Lattice Boltzmann simulations, normal resolution ANSYS simulations and MR imaging
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | Medical Physics |
Volume | 43 |
Issue | 11 |
Publisher | Medical Physics Online |
Talks, invited
Brain & Water:computational modeling of the aging brain
In MedViz conference, Bergen, 2016.Status: Published
Brain & Water:computational modeling of the aging 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 | MedViz conference, Bergen |
Experimental investigation of transitional effects at low Reynolds number in blood vessels: X-ray, Microphones and Simulations
In EarthFlows Workshop, UiO, Oslo, 2016.Status: Published
Experimental investigation of transitional effects at low Reynolds number in blood vessels: X-ray, Microphones and Simulations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2016 |
Location of Talk | EarthFlows Workshop, UiO, Oslo |
Overview of the modeling of water flow in and surrounding the central nervous system
In Istituto Italiano di Tecnologia, Piza, Italy, 2016.Status: Published
Overview of the modeling of water flow in and surrounding the central nervous system
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 | Istituto Italiano di Tecnologia, Piza, Italy |
Poroelastic modeling of the central nervous system: Chiari and dementia
In Workshop on modeling of flow in live tissue: Methodological interaction between geo and life-sciences, CMR, Fantoft, Bergen, 2016.Status: Published
Poroelastic modeling of the central nervous system: Chiari and dementia
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 | Workshop on modeling of flow in live tissue: Methodological interaction between geo and life-sciences, CMR, Fantoft, Bergen |
Robustness of common hemodynamics indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms
In MS at WCCM16, Seoul, 2016.Status: Published
Robustness of common hemodynamics indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2016 |
Location of Talk | MS at WCCM16, Seoul |
Variational data assimilation for blood flow simulations
In MS at SIAM UQ, Zurich, 2016.Status: Published
Variational data assimilation for blood flow simulations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2016 |
Location of Talk | MS at SIAM UQ, Zurich |
Book Chapter
Cerebrospinal fluid flow in adults.
In Handbook of clinical neurology, 591-603. Vol. 135. Elsevier, 2016.Status: Published
Cerebrospinal fluid flow in adults.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2016 |
Book Title | Handbook of clinical neurology |
Volume | 135 |
Pagination | 591-603 |
Publisher | Elsevier |
ISBN Number | 978-0-444-53485-9 |
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... |
Solving singular problems. The right way.
In FEniCS'16 Workshop, Simula Research Laboratory, Oslo, Norway, 2016.Status: Published
Solving singular problems. The right way.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2016 |
Location of Talk | FEniCS'16 Workshop, Simula Research Laboratory, Oslo, Norway |
Type of Talk | contributed |
Proceedings, refereed
BEND|P|Y: Python framework for computing bending of complex plate-beam systems
In MekIT'15 8th National Conference on Computational Mechanics. Barcelona, Spain: International Center for Numerical Methods in Engineering (CIMNE), 2015.Status: Published
BEND|P|Y: Python framework for computing bending of complex plate-beam systems
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2015 |
Conference Name | MekIT'15 8th National Conference on Computational Mechanics |
Pagination | 307-320 |
Date Published | 11/2015 |
Publisher | International Center for Numerical Methods in Engineering (CIMNE) |
Place Published | Barcelona, Spain |
ISBN Number | 978-84-944244-9-6 |
Characterization of the space of rigid motions in arbitrary domains
In MekIT'15 8th National Conference on Computational Mechanics. Barcelona, Spain: International Center for Numerical Methods in Engineering (CIMNE), 2015.Status: Published
Characterization of the space of rigid motions in arbitrary domains
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2015 |
Conference Name | MekIT'15 8th National Conference on Computational Mechanics |
Pagination | 259-274 |
Publisher | International Center for Numerical Methods in Engineering (CIMNE) |
Place Published | Barcelona, Spain |
ISBN Number | 978-84-944244-9-6 |
Exploring The Critical Reynolds Number For Transition In Intracranial Aneurysms–highly Resolved Simulations Below Kolmogorov Scales
In 4th International Conference on Computational and Mathematical Biomedical Engineering - CMBE2015, 2015.Status: Published
Exploring The Critical Reynolds Number For Transition In Intracranial Aneurysms–highly Resolved Simulations Below Kolmogorov Scales
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2015 |
Conference Name | 4th International Conference on Computational and Mathematical Biomedical Engineering - CMBE2015 |
Journal Article
Computational fluid dynamics evaluation of flow reversal treatment of giant basilar tip aneurysm
Interventional Neuroradiology 21, no. 5 (2015): 586-591.Status: Published
Computational fluid dynamics evaluation of flow reversal treatment of giant basilar tip aneurysm
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2015 |
Journal | Interventional Neuroradiology |
Volume | 21 |
Issue | 5 |
Pagination | 586-591 |
Publisher | SAGE Publications |
Other Numbers | PMID: 26253111 |
DOI | 10.1177/1591019915597415 |
Poro-elastic modeling of Syringomyelia – a systematic study of the effects of pia mater, central canal, median fissure, white and gray matter on pressure wave propagation and fluid movement within the cervical spinal cord
Computer Methods in Biomechanics and Biomedical Engineering 19, no. 6 (2015): 686-698.Status: Published
Poro-elastic modeling of Syringomyelia – a systematic study of the effects of pia mater, central canal, median fissure, white and gray matter on pressure wave propagation and fluid movement within the cervical spinal cord
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2015 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 19 |
Issue | 6 |
Pagination | 686-698 |
Publisher | Taylor & Francis Online |
Other Numbers | PMID: 26176823 |
DOI | 10.1080/10255842.2015.1058927 |
Transitional flow in intracranial aneurysms–a space and time refinement study below the Kolmogorov scales using Lattice Boltzmann Method
Computers & Fluids (2015).Status: Published
Transitional flow in intracranial aneurysms–a space and time refinement study below the Kolmogorov scales using Lattice Boltzmann Method
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2015 |
Journal | Computers & Fluids |
Publisher | Elsevier |
Talks, invited
Computational modelling of the biomechanics in the central nervous system – Chiari and syringomyelia
In Complex materials; Mathematical models and numerical methods, Oslo, 2015.Status: Published
Computational modelling of the biomechanics in the central nervous system – Chiari and syringomyelia
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | Complex materials; Mathematical models and numerical methods, Oslo |
Computational modelling of the biomechanics in the central nervous system – Chiari and syringomyelia
In Simpla meeting, Oslo, 2015.Status: Published
Computational modelling of the biomechanics in the central nervous system – Chiari and syringomyelia
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | Simpla meeting, Oslo |
Type of Talk | Invited talk |
Flows in complex geometries such as blood vessels and the central nervous system
In EarthFlows kick-off meeting, Oslo, 2015.Status: Published
Flows in complex geometries such as blood vessels and the central nervous system
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | EarthFlows kick-off meeting, Oslo |
Type of Talk | Invited talk |
On the complexity of the Cerebrospinal fluid flow in the upper spinal column – is the assumption of laminar flow appropriate?
In Cerebrospinal Fluid Dynamics Society Meeting, Amiens, 2015.Status: Published
On the complexity of the Cerebrospinal fluid flow in the upper spinal column – is the assumption of laminar flow appropriate?
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | Cerebrospinal Fluid Dynamics Society Meeting, Amiens |
Type of Talk | Invited talk |
Poroelastic modeling of Syringomyelia - the effects of pia mater, central canal, median fissure, white and grey matter on pressure wave propagation and fluid movement within the cervical spinal cord
In International Hydrocephalus Imaging Working Group, Chicago, 2015.Status: Published
Poroelastic modeling of Syringomyelia - the effects of pia mater, central canal, median fissure, white and grey matter on pressure wave propagation and fluid movement within the cervical spinal cord
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | International Hydrocephalus Imaging Working Group, Chicago |
Role of CSF flow in the pathogenesis of Syringomyelia
In ASNR 53rd Annual Meeting & The Foundation of the ASNR Symposium 2015, April 25 – 30, 2015; Chicago, Illinois, 2015.Status: Published
Role of CSF flow in the pathogenesis of Syringomyelia
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | ASNR 53rd Annual Meeting & The Foundation of the ASNR Symposium 2015, April 25 – 30, 2015; Chicago, Illinois |
Type of Talk | Plenary talk |
Talks, contributed
Computational modelling of the biomechanics in the central nervous system – Chiari and syringomyelia
In Simula Research Laboratory, Oslo, 2015.Status: Published
Computational modelling of the biomechanics in the central nervous system – Chiari and syringomyelia
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2015 |
Location of Talk | Simula Research Laboratory, Oslo |
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 |
Robust preconditioners for PDE-constrained optmization with limited data
In 2015 SIAM CSE, Salt Lake City, 2015.Status: Published
Robust preconditioners for PDE-constrained optmization with limited data
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2015 |
Location of Talk | 2015 SIAM CSE, Salt Lake City |
Type of Talk | Minisymposium |
Book Chapter
On the Assumption of Laminar Flow in Physiological Flows: Cerebral Aneurysms As an Illustrative Example
In Modeling the Heart and the Circulatory System, 177-195. MS&A. Springer International Publishing, 2015.Status: Published
On the Assumption of Laminar Flow in Physiological Flows: Cerebral Aneurysms As an Illustrative Example
In physiological fluid flows, except for in the heart and the aorta, the Reynolds numbers are moderate (below 1000). This is far below the typical point of transition in pipe flow, which occurs around Reynolds number 2300. Because of this, laminar flow is commonly assumed in the modelling of these flows, resulting in computational methods tailored for this flow regime.
This chapter presents a critical review of this assumption, and both clinical and numerical evidence of transitional physiological flows are presented. The pulsatility and complex geometries in physiological flow are highlighted as the main reasons for a lower transition point in physiological flows.
Furthermore, we discuss the threshold of transition in a particular case of an aneurysm with respect to resolution, Reynolds number and non-Newtonian viscosity modelling.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2015 |
Book Title | Modeling the Heart and the Circulatory System |
Secondary Title | MS&A |
Chapter | 7 |
Series Volume | 14 |
Pagination | 177-195 |
Publisher | Springer International Publishing |
Journal Article
A Multilevel Solver for Gaussian Constrained CMB Realizations
The Astrophysical Journal Supplement Series 210 (2014).Status: Published
A Multilevel Solver for Gaussian Constrained CMB Realizations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2014 |
Journal | The Astrophysical Journal Supplement Series |
Volume | 210 |
Number | 2 |
Publisher |
Effect of Cranio-Vertebral Decompression on CSF Dynamics in Chiari I Malformation Studied With Computational Fluid Dynamics
Journal of Neurosurgery 21, no. 4 (2014): 559-564.Status: Published
Effect of Cranio-Vertebral Decompression on CSF Dynamics in Chiari I Malformation Studied With Computational Fluid Dynamics
Object. The effect of craniovertebral decompression surgery on CSF flow dynamics in Chiari I patients has been incompletely characterized. We used computational fluid dynamics to calculate the effect of decompression surgery on CSF flow dynamics in the posterior fossa and upper cervical spinal canal.
Methods. Oscillatory flow was simulated in idealized 3D models of the normal adult and the Chiari I subarachnoid spaces (both previously described) and in three models of the Chiari malformation post cranio-vertebral decompressions. The three postoperative models were created from the Chiari model by virtually modifying the Chiari model subarachnoid space to simulate surgical decompressions of different magnitudes. Velocities and pressures were computed with the Navier-Stokes equations in Star-CD for multiple cycles of CSF flow oscillating at 80 cycles per minute. Pressure gradients and velocities were compared for 8 levels extending from the posterior fossa to the C3/4 level. Relative pressures and peak velocities were plotted by level from the posterior fossa to C3/4. The heterogeneity of flow velocity distribution around the spinal cord was compared between models.
Results. Peak systolic velocities were generally lower in the post-operative models, than in the pre-operative Chiari model. The two larger surgical defects had peak systolic velocities that were closer to normal model velocities than the smallest surgical defect and equal to those in the normal model at the C3 and C4 levels. For the smallest defect, peak velocities were decreased, but not to levels in the normal model. In the postoperative models, heterogeneity in flow velocity distribution around the spinal cord increased from normal model levels as the degree of decompression increased. Pressures in the 5 models differed in magnitude and in pattern. Pressures gradients along the spinal canal in the normal and Chiari models were non-linear with steeper gradients below C3/4 than above. The Chiari model had a steeper pressure gradient than the normal model above C3/4 and the same gradient below. The postoperative models had lower pressure gradients than the Chiari model above C2/3. The most conservative decompression had smaller than normal model pressure gradients above C2/3 The two larger decompression defects had CSF pressure gradients below those in the normal model above C2/3. These two models had a less steep gradient above C3 and a steeper gradient below.
Conclusions. In computer simulations, cranio-vertebral surgical defects generally diminished CSF velocities and CSF pressures.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2014 |
Journal | Journal of Neurosurgery |
Volume | 21 |
Issue | 4 |
Pagination | 559-564 |
Date Published | 10/2014 |
Publisher | AANS |
Numerical Simulations of the Pulsating Flow of Cerebrospinal Fluid Flow in the Cervical Spinal Canal of a Chiari Patient
Journal of Biomechanics 47, no. 5 (2014): 1082-90.Status: Published
Numerical Simulations of the Pulsating Flow of Cerebrospinal Fluid Flow in the Cervical Spinal Canal of a Chiari Patient
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2014 |
Journal | Journal of Biomechanics |
Volume | 47 |
Issue | 5 |
Number | 47(5) |
Pagination | 1082-90 |
Date Published | 03/2014 |
Publisher |
Spinal Fluid Biomechanics and Imaging: an Update for Neuroradiologists
American Journal of Neuroradiology 35, no. 10 (2014): 1864-1869.Status: Published
Spinal Fluid Biomechanics and Imaging: an Update for Neuroradiologists
Flow imaging with cardiac-gated phase-contrast MR has applications in the management of neurologic disorders. Together with computational fluid dynamics, phase-contrast MR has advanced our understanding of spinal CSF flow. Phase-contrast MR is used to evaluate patients with Chiari I malformation who are candidates for surgical treatment. In theory, abnormal CSF flow resulting from the abnormal tonsil position causes syringomyelia and other neurologic signs and symptoms in patients with Chiari I. CSF flow imaging also has research applications in syringomyelia and spinal stenosis. To optimize MR acquisition and interpretation, neuroradiologists must have familiarity with healthy and pathologic patterns of CSF flow. The purpose of this review is to update concepts of CSF flow that are important for the practice of flow imaging in the spine.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2014 |
Journal | American Journal of Neuroradiology |
Volume | 35 |
Issue | 10 |
Pagination | 1864-1869 |
Date Published | 10/2014 |
Publisher | American Society of Neuroradiology |
URL | http://www.ncbi.nlm.nih.gov/pubmed/25012674 |
DOI | 10.3174/ajnr.A4023 |
Talks, invited
Cerebrospinal Fluid Flow in Association With the Central Nervous System - Chiari and Drug Delivery
In MS on Computational Biomechanics, WCCM-ECCM-ECCOM, 2014.Status: Published
Cerebrospinal Fluid Flow in Association With the Central Nervous System - Chiari and Drug Delivery
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | MS on Computational Biomechanics, WCCM-ECCM-ECCOM |
CSF Flow at Foramen Magnum
In International Hydrocephalus Imaging Working Group,Montreal, Canada, 2014.Status: Published
CSF Flow at Foramen Magnum
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | International Hydrocephalus Imaging Working Group,Montreal, Canada |
Er Zombier En Trussel Mot Menneskeheten?
In Upop aften - Det norske student samfund, 2014.Status: Published
Er Zombier En Trussel Mot Menneskeheten?
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | Upop aften - Det norske student samfund |
On Numerical Methods for Transitional Flow - Application to Blood Flow in Aneurysms
In Quality and Validation of Computational Cardio-vascular Biomechanics, WCCM-ECCM-ECCOM, 2014.Status: Published
On Numerical Methods for Transitional Flow - Application to Blood Flow in Aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | Quality and Validation of Computational Cardio-vascular Biomechanics, WCCM-ECCM-ECCOM |
On the Assumption of Laminar Flow in the Modeling of Physiological Flow
In Anvendt og beregningsorientert matematikk, Bergen, 2014.Status: Published
On the Assumption of Laminar Flow in the Modeling of Physiological Flow
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | Anvendt og beregningsorientert matematikk, Bergen |
On the Assumption of Laminar Flow of CSF in Chiari Patients
In international Chiari Research Group, 2014.Status: Published
On the Assumption of Laminar Flow of CSF in Chiari Patients
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | international Chiari Research Group |
Talk, keynote
On the Modeling of the Central Nervous System in Chiari Patients - Transitional Flow, Poroelasticity and Porous-Viscus Flow Couplings
In Gordon Conference on Flow & Transport in Permeable Media, 2014.Status: Published
On the Modeling of the Central Nervous System in Chiari Patients - Transitional Flow, Poroelasticity and Porous-Viscus Flow Couplings
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talk, keynote |
Year of Publication | 2014 |
Location of Talk | Gordon Conference on Flow & Transport in Permeable Media |
Preliminary study of the impact of spinal cord nerve roots and denticulate ligaments on drug movement in the cervical spinal subarachnoid space
In 21 July, Barcelona, Spain, 2014.Status: Published
Preliminary study of the impact of spinal cord nerve roots and denticulate ligaments on drug movement in the cervical spinal subarachnoid space
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talk, keynote |
Year of Publication | 2014 |
Location of Talk | 21 July, Barcelona, Spain |
Type of Talk | Keynote |
URL | http://www.wccm-eccm-ecfd2014.org/admin/files/fileabstract/a2880.pdf |
Technical reports
A Multilevel Solver for Gaussian Constrained CMB Realizations
2013.Status: Published
A Multilevel Solver for Gaussian Constrained CMB Realizations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Technical reports |
Year of Publication | 2013 |
Proceedings, refereed
A Second Order Fast Sweeping Method for the Eikonal Equation Based on Minimization
In The Nordic Seminar on Computational Mechanics, 2013.Status: Published
A Second Order Fast Sweeping Method for the Eikonal Equation Based on Minimization
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2013 |
Conference Name | The Nordic Seminar on Computational Mechanics |
A Stabilized Nitsche Fictitious Domain Formulation for the Three-Field Stokes Problem
In The 26th Nordic Seminar on Computational Mechanics, 2013.Status: Published
A Stabilized Nitsche Fictitious Domain Formulation for the Three-Field Stokes Problem
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2013 |
Conference Name | The 26th Nordic Seminar on Computational Mechanics |
ISBN Number | 978-82-92593-12-7 |
Effect of Oscillatory Cerebrospinal Fluid Pressure on Fluid Movement in the Spinal Cord
In Seventh National Conference on Computational Mechanics (MekIT'13). Tapir Akademisk Forlag, 2013.Status: Published
Effect of Oscillatory Cerebrospinal Fluid Pressure on Fluid Movement in the Spinal Cord
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2013 |
Conference Name | Seventh National Conference on Computational Mechanics (MekIT'13) |
Publisher | Tapir Akademisk Forlag |
Preliminary Study of the Impact of Spinal Cord Nerve Roots and Denticulate Ligaments on Drug Movement in the Cervical Spinal Subarachnoid Space
In The Nordic Seminar on Computational Mechanics, 2013.Status: Published
Preliminary Study of the Impact of Spinal Cord Nerve Roots and Denticulate Ligaments on Drug Movement in the Cervical Spinal Subarachnoid Space
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2013 |
Conference Name | The Nordic Seminar on Computational Mechanics |
Preliminary Study of the Impact of Spinal Cord Nerve Roots and Denticulate Ligaments on Drug Movement in the Cervical Spinal Subarachnoid Space
In The Nordic Seminar on Computational Mechanics, 2013.Status: Published
Preliminary Study of the Impact of Spinal Cord Nerve Roots and Denticulate Ligaments on Drug Movement in the Cervical Spinal Subarachnoid Space
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2013 |
Conference Name | The Nordic Seminar on Computational Mechanics |
Journal Article
A Study of Wall Shear Stress in 12 Aneurysms With Respect to Different Viscosity Models and Flow Conditions
Journal of Biomechanics 46 (2013): 2802-2808.Status: Published
A Study of Wall Shear Stress in 12 Aneurysms With Respect to Different Viscosity Models and Flow Conditions
Recent computational fluid dynamics (CFD) studies relate abnormal blood flow to rupture of cerebral aneurysms. However, it is still debated how to model blood flow with sufficient accuracy. Common assumptions made include Newtonian behavior of blood, traction free outlet boundary conditions and inlet boundary conditions based on available literature. These assumptions are often required since the available patient specific data is usually restricted to the geometry of the aneurysm and the surrounding vasculature. However, the consequences of these assumptions have so far been inadequately addressed. This study investigates the effects of 4 different viscosity models, 2 different inflow conditions and 2 different outflow conditions in 12 middle cerebral artery aneurysms. The differences are quantified in terms of 3 different wall shear stress (WSS) metrics, involving maximal WSS, average WSS, and proportion of aneurysm sac area with low WSS. The results were compared with common geometrical metrics such as volume, aspect ratio, size ratio and parent vessel diameter and classifications in terms of sex and aneurysm type. The results demonstrate strong correlations between the different viscosity models and boundary conditions. The correlation between the different WSS metrics range from weak to medium. No strong correlations were found between the different WSS metrics and the geometrical metrics or classifications.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | Journal of Biomechanics |
Volume | 46 |
Number | 16 |
Pagination | 2802-2808 |
Date Published | November |
A Uniformly Stable Fortin Operator for the Taylor-Hood Element
Numerische Mathematik 123 (2013): 537-551.Status: Published
A Uniformly Stable Fortin Operator for the Taylor-Hood Element
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | Numerische Mathematik |
Volume | 123 |
Number | 3 |
Pagination | 537-551 |
DOI | 10.1007/s00211-012-0492-6 |
Analysis of the Minimal Residual Method Applied to Ill-Posed Optimality Systems
SIAM Journal on Scientific Computing 35 (2013): A785-A814.Status: Published
Analysis of the Minimal Residual Method Applied to Ill-Posed Optimality Systems
Afilliation | Scientific Computing, , 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 | 2 |
Pagination | A785-A814 |
CSF Pressure and Velocity in Obstructions of the Subarachnoid Spaces
The Neuroradiology Journal 26 (2013).Status: Published
CSF Pressure and Velocity in Obstructions of the Subarachnoid Spaces
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | The Neuroradiology Journal |
Volume | 26 |
Number | 2 |
Effect of the Central Canal in the Spinal Cord on Fluid Movement Within the Cord
The Neuroradiology Journal 26 (2013): 585-590.Status: Published
Effect of the Central Canal in the Spinal Cord on Fluid Movement Within the Cord
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | The Neuroradiology Journal |
Volume | 26 |
Number | 5 |
Pagination | 585-590 |
Estimation of CSF Flow Resistance in the Upper Cervical Spine
The Neuroradiology Journal 3 (2013): 49-53.Status: Published
Estimation of CSF Flow Resistance in the Upper Cervical Spine
Afilliation | , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | The Neuroradiology Journal |
Volume | 3 |
Number | 2 |
Pagination | 49-53 |
High-Resolution Computational Fluid Dynamics Detects High-Frequency Velocity Fluctuations in Bifurcation, But Not Sidewall, Aneurysms of the Middle Cerebral Artery
Journal of Biomechanics 46, no. 2 (2013): 402-407.Status: Published
High-Resolution Computational Fluid Dynamics Detects High-Frequency Velocity Fluctuations in Bifurcation, But Not Sidewall, Aneurysms of the Middle Cerebral Artery
High-frequency flow fluctuations in intracranial aneurysms have previously been reported in vitro and in vivo. On the other hand, the vast majority of image-based computational fluid dynamics (CFD) studies of cerebral aneurysms report periodic, laminar flow. We have previously demonstrated that transitional flow, consistent with in vivo reports, can occur in a middle cerebral artery (MCA) bifurcation aneurysm when ultra-high-resolution direct numerical simulation methods are applied. The object of the present study was to investigate if such high-frequency flow fluctuations might be more widespread in adequately-resolved CFD models. A sample of N=12 anatomically realistic MCA aneurysms (five unruptured, seven ruptured), was digitally segmented from CT angiograms. Four were classified as sidewall aneurysms, the other eight as bifurcation aneurysms. Transient CFD simulations were carried out assuming a steady inflow velocity of 0.5 m/s, corresponding to typical peak systolic conditions at the MCA. To allow for detection of clinically-reported high-frequency flow fluctuations and resulting flow structures, temporal and spatial resolutions of the CFD simulations were in the order of 0.1 ms and 0.1 mm, respectively. A transient flow response to the stationary inflow conditions was found in five of the 12 aneurysms, with energetic fluctuations up to 100 Hz, and in one case up to 900 Hz. Incidentally, all five were ruptured bifurcation aneurysms, whereas all four sidewall aneurysms, including one ruptured case, quickly reached a stable, steady state solution. Energetic, rapid fluctuations may be overlooked in CFD models of bifurcation aneurysms unless adequate temporal and spatial resolutions are used. Such fluctuations may be relevant to the mechanobiology of aneurysm rupture, and to a recently reported dichotomy between predictors of rupture likelihood for bifurcation vs. sidewall aneurysms.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | Journal of Biomechanics |
Volume | 46 |
Issue | 2 |
Pagination | 402-407 |
Publisher | Elsevier |
Simulating CSF Flow Dynamics in the Normal and the Chiari I Subarachnoid Space During Rest and Exertion
American Journal of Neuroradiology 34 (2013): 41-15.Status: Published
Simulating CSF Flow Dynamics in the Normal and the Chiari I Subarachnoid Space During Rest and Exertion
Purpose: CSF fluid dynamics in normal subjects and Chiari I patients have been characterized during rest with Phase contrast MR and Computational Fluid Dynamics (CFD). CSF flow velocities and pressures in the non-resting state have not been adequately characterized. We used computer simulations to study CSF dynamics during increased heart rate in the normal and the Chiari I subarachnoid space. Materials and Methods: Cyclic CSF flow was simulated for multiple cycles in idealized 3D models of the subarachnoid space for normal and Chiari I malformation subarachnoid spaces, with flow cycles corresponding to 80 or 120 heart beats per minute. Flow velocities and pressures were computed by the Navier-Stokes equations. Synchronous bidirectional flow and flow patterns were displayed in Star-CD and inspected visually. Peak velocities and pressure differences in the two models were compared for the two cycle frequencies. Results: Elevating the cycle rate from 80 to 120 cpm increased peak superior-inferior pressure gradients (top-bottom) by just 0.01% in the normal model and 2% in the Chiari model. Corresponding average pressure gradients increased by 92% and 100%, respectively. Also, in both models, the range of synchronous bidirectional flow velocities increased. Systolic velocities had smaller increases with faster cycling. For each cycle rate, peak and average pressure gradients in the Chiari model were greater than in the normal by 11% - 16%. Conclusions: Rising the cycle rate from 80 to 120 cpm increased superior-inferior average pressure gradients and the range of synchronous bidirectional flow velocities in the normal and Chiari I models.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | American Journal of Neuroradiology |
Volume | 34 |
Number | 1 |
Pagination | 41-15 |
Manuals
Combining FEniCS With Your Favorite Software in C, C++, Fortran, Or MATLAB
2013.Status: Published
Combining FEniCS With Your Favorite Software in C, C++, Fortran, Or MATLAB
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Manuals |
Year of Publication | 2013 |
Talks, invited
Efficient Preconditioning of Optimality Systems With Non-Self-Adjoint State Operators
In IFIP 2013, minisymposia Preconditioning for PDE-Constrained Optimization, Linz, Austria, 2013.Status: Published
Efficient Preconditioning of Optimality Systems With Non-Self-Adjoint State Operators
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2013 |
Location of Talk | IFIP 2013, minisymposia Preconditioning for PDE-Constrained Optimization, Linz, Austria |
Book Chapter
Escaping the Zombie Threat by Mathematics
In Zombies in the Academy: Living Death in Higher Education. University of Chicago Press, 2013.Status: Published
Escaping the Zombie Threat by Mathematics
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2013 |
Book Title | Zombies in the Academy: Living Death in Higher Education |
Chapter | 18 |
Publisher | University of Chicago Press |
Talk, keynote
On the Assumption of Laminar Flow in the Modeling of Physiological Flow
In Modelling of physiological flows (MPF 2013), 2013.Status: Published
On the Assumption of Laminar Flow in the Modeling of Physiological Flow
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talk, keynote |
Year of Publication | 2013 |
Location of Talk | Modelling of physiological flows (MPF 2013) |
Operator Preconditioning for Well-Posed and Ill-Posed Problems
In Preconditioning 2013, 2013.Status: Published
Operator Preconditioning for Well-Posed and Ill-Posed Problems
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talk, keynote |
Year of Publication | 2013 |
Location of Talk | Preconditioning 2013 |
Talks, contributed
Patient-Specific Simulations of Vasospasm in 3 Different Cases
In Modelling Physiological Flows, 2013.Status: Published
Patient-Specific Simulations of Vasospasm in 3 Different Cases
Background: Subarachnoid hemorrhage from a ruptured intracranial aneurysm may give rise to cerebral vasospasm. Cerebral vasospasm is an inflammatory response that may develop from day 4 after the ictus and persists for a variable time period. The inflammation causes vessel wall thickening and accordingly a decrease in inner vessel diameter, potentially causing cerebral malperfusion. Cerebral vasospasm represents a feared complication and is a common cause of poor outcome after aneurysmal hemorrhage. Due to the risk for cerebral ischemia, the aneurysm cannot be secured surgically until the vasospasm resolves. In addition, the risk for re-rupture of the aneurysm is considered very high during the phase where the vasospasms resolve. It is unknown how the geometry and flow into an aneurysm changes through a phase of vasospasm of the parent artery, and which risk factors for rupture those changes may effect. By use of computational fluid dynamics (CFD), hemodynamics have previously been shown to correlate with aneurysm growth and rupture, and may be a factor in the development of this disease. The vasospasm may severely affect the geometry of the blood vessels, and thus also the hemodynamics. In this study, we will simulate 3 different cases of vasospasm and discuss the subsequent hemodynamic consequences and development of associated aneurysms. Methods: In three different cases, CT angiography scans were performed to determine the severity of the vasospasms. In addition, Doppler velocity measurements were made in relevant arteries. Based on these data, we performed CFD simulations to investigate the hemodynamic changes in patients only a few days apart. In addition to qualitative studies of the flow patterns, we will calculate the wall shear stress and known hemodynamic indicators of aneurysm development, and analyse for any variations Results: Case A: Rupture in an ICA sidewall aneurysm caused vasospasms. The vasospasms appeared to cause large variations in flow velocity. At day 1 the flow rate was large, and CFD revealed severely disturbed flow patterns around the aneurysm. At day 5, at approximately one third of the flow rate, CFD showed a largely undisturbed flow pattern. However, the CT data showed a clear growth of the aneurysm. Case B: Rupture of a large right ICA sidewall aneurysm caused vasospasms in the left parts of the circle of Willis, where aneurysms were located in the ICA (sidewall) and MCA (bifurcation). In the ICA, the vasospasms caused the most severe constriction immediately downstream of the aneurysm. This appeared to have little effect on the flow patterns around the aneurysm. Just prior to the MCA bifurcation aneurysm, a constriction in the artery caused the concentration of a flow jet into the aneurysm. The CT images showed aneurysm growth. Case C: Rupture of an ACA (A2) aneurysm. Doppler measurements indicated changing flow ratio between left and right ACA. CFD showed that this caused direction change in the anterior communicating artery, and CT images showed aneurysm growth. Conclusions: Cerebral vasospasm may cause severe temporary changes in the vasculature, and thus effect the hemodynamics in and around cerebral aneurysms. Indications are found that the hemodynamic consequences of vasospams may cause growth or re-growth of aneurysms, potentially increasing the risk of rupture.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2013 |
Location of Talk | Modelling Physiological Flows |
Edited books
Proceedings of the 26th Nordic Seminar on Computational Machanics
Simula Research Laboratory, 2013.Status: Published
Proceedings of the 26th Nordic Seminar on Computational Machanics
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Edited books |
Year of Publication | 2013 |
Date Published | October |
Publisher | Simula Research Laboratory |
ISBN Number | 978-82-92593-12-7 |
Book Chapter
A Comparison of Some Common Finite Element Schemes for the Incompressible Navier-Stokes Equations
In Automated Solution of Differential Equations by the Finite Element Method, 395-418. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
A Comparison of Some Common Finite Element Schemes for the Incompressible Navier-Stokes Equations
Afilliation | Scientific Computing, , 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 | 21 |
Pagination | 395-418 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
A Comparison of Some Common Finite Element Schemes for the Incompressible Navier-Stokes Equations
In Automated Solution of Differential Equations by the Finite Element Method, 395-418. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
A Comparison of Some Common Finite Element Schemes for the Incompressible Navier-Stokes Equations
Afilliation | Scientific Computing, , 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 | 21 |
Pagination | 395-418 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
A Computational Framework for Nonlinear Elasticity
In Automated Solution of Differential Equations by the Finite Element Method, 527-544. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
A Computational Framework for Nonlinear Elasticity
Afilliation | , 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 | 27 |
Pagination | 527-544 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
A Coupled Stochastic and Deterministic Model of Ca2+ Dynamics in the Dyadic Cleft
In Automated Solution of Differential Equations by the Finite Element Method, 611-627. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
A Coupled Stochastic and Deterministic Model of Ca2+ Dynamics in the Dyadic Cleft
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 | 33 |
Pagination | 611-627 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
A FEniCS Tutorial
In Automated Solution of Differential Equations by the Finite Element Method, 1-70. Springer, 2012.Status: Published
A FEniCS Tutorial
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 |
Chapter | 1 |
Pagination | 1-70 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
An Adaptive Finite Element Solver for Fluid-structure Interaction Problems
In Automated Solution of Differential Equations by the Finite Element Method, 554-572. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
An Adaptive Finite Element Solver for Fluid-structure Interaction Problems
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 | 29 |
Pagination | 554-572 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
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 |
Block Preconditioning of Systems of PDEs
In Automated Solution of Differential Equations by the Finite Element Method, 643-654. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Block Preconditioning of Systems of PDEs
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 | 35 |
Pagination | 643-654 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Block Preconditioning of Systems of PDEs
In Automated Solution of Differential Equations by the Finite Element Method, 643-654. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Block Preconditioning of Systems of PDEs
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 | 35 |
Pagination | 643-654 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Cerebrospinal Fluid Flow
In Automated Solution of Differential Equations by the Finite Element Method, 455-470. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Cerebrospinal Fluid Flow
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 | 24 |
Pagination | 455-470 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Cerebrospinal Fluid Flow
In Automated Solution of Differential Equations by the Finite Element Method, 455-470. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Cerebrospinal Fluid Flow
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 | 24 |
Pagination | 455-470 |
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 |
Computational Hemodynamics
In Automated Solution of Differential Equations by the Finite Element Method, 439-454. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Computational Hemodynamics
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 | 23 |
Pagination | 439-454 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Computational Hemodynamics
In Automated Solution of Differential Equations by the Finite Element Method, 439-454. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Computational Hemodynamics
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 | 23 |
Pagination | 439-454 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Constructing General Reference Finite Elements
In Automated Solution of Differential Equations by the Finite Element Method, 117-128. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Constructing General Reference 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 | 4 |
Pagination | 117-128 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Constructing General Reference Finite Elements
In Automated Solution of Differential Equations by the Finite Element Method, 117-128. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Constructing General Reference 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 | 4 |
Pagination | 117-128 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Discrete Optimization of Finite Element Matrix Evaluation
In Automated Solution of Differential Equations by the Finite Element Method, 161-168. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Discrete Optimization of Finite Element Matrix Evaluation
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 | 9 |
Pagination | 161-168 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
DOLFIN: a C++/Python Finite Element Library
In Automated Solution of Differential Equations by the Finite Element Method, 173-225. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
DOLFIN: a C++/Python Finite Element Library
Afilliation | Scientific Computing, , 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 | 10 |
Pagination | 173-225 |
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 |
FErari: an Optimizing Compiler for Variational Forms
In Automated Solution of Differential Equations by the Finite Element Method, 235-243. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
FErari: an Optimizing Compiler for Variational Forms
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 | 12 |
Pagination | 235-243 |
Publisher | Springer |
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 |
Finite Element Assembly
In Automated Solution of Differential Equations by the Finite Element Method, 137-142. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Finite Element Assembly
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 | 6 |
Pagination | 137-142 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Finite Element Assembly
In Automated Solution of Differential Equations by the Finite Element Method, 137-142. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Finite Element Assembly
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 | 6 |
Pagination | 137-142 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Finite Element Variational Forms
In Automated Solution of Differential Equations by the Finite Element Method, 129-136. Vol. 84. Lec 84. Springer, 2012.Status: Published
Finite Element Variational Forms
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 | Lec |
Volume | 84 |
Chapter | 5 |
Pagination | 129-136 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Instant: Just-in-Time Compilation of C/C++ in Python
In Automated Solution of Differential Equations by the Finite Element Method, 253-268. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Instant: Just-in-Time Compilation of C/C++ in Python
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 | 14 |
Pagination | 253-268 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Instant: Just-in-Time Compilation of C/C++ in Python
In Automated Solution of Differential Equations by the Finite Element Method, 253-268. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Instant: Just-in-Time Compilation of C/C++ in Python
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 | 14 |
Pagination | 253-268 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Lessons Learned in Mixed Language Programming
In Automated Solution of Differential Equations by the Finite Element Method, 363-381. Vol. 84. Springer, 2012.Status: Published
Lessons Learned in Mixed Language Programming
Afilliation | Scientific Computing, , 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 |
Volume | 84 |
Chapter | 19 |
Pagination | 363-381 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Lessons Learned in Mixed Language Programming
In Automated Solution of Differential Equations by the Finite Element Method, 363-381. Vol. 84. Springer, 2012.Status: Published
Lessons Learned in Mixed Language Programming
Afilliation | Scientific Computing, , 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 |
Volume | 84 |
Chapter | 19 |
Pagination | 363-381 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Simulation of Transitional Flows
In Automated Solution of Differential Equations by the Finite Element Method, 419-438. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Simulation of Transitional Flows
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 | 22 |
Pagination | 419-438 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Simulation of Transitional Flows
In Automated Solution of Differential Equations by the Finite Element Method, 419-438. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Simulation of Transitional Flows
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 | 22 |
Pagination | 419-438 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
SyFi and SFC: Symbolic Finite Elements and Form Compilation
In Automated Solution of Differential Equations by the Finite Element Method, 269-278. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
SyFi and SFC: Symbolic Finite Elements and Form Compilation
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 | 15 |
Pagination | 269-278 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
SyFi and SFC: Symbolic Finite Elements and Form Compilation
In Automated Solution of Differential Equations by the Finite Element Method, 269-278. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
SyFi and SFC: Symbolic Finite Elements and Form Compilation
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 | 15 |
Pagination | 269-278 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Tensor Representation of Finite Element Variational Forms
In Automated Solution of Differential Equations by the Finite Element Method, 157-167. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
Tensor Representation of Finite Element Variational Forms
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 | 8 |
Pagination | 157-167 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
The Finite Element Method
In Automated Solution of Differential Equations by the Finite Element Method, 73-90. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
The Finite Element Method
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 | 2 |
Pagination | 73-90 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
UFC: a Finite Element Code Generation Interface
In Automated Solution of Differential Equations by the Finite Element Method, 279-298. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
UFC: a Finite Element Code Generation Interface
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 | 16 |
Pagination | 279-298 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
UFC: a Finite Element Code Generation Interface
In Automated Solution of Differential Equations by the Finite Element Method, 279-298. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
UFC: a Finite Element Code Generation Interface
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 | 16 |
Pagination | 279-298 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
UFL: a Finite Element Form Language
In Automated Solution of Differential Equations by the Finite Element Method, 299-334. Vol. 84. Lecture Notes in Computational Science and Engineering 84. Springer, 2012.Status: Published
UFL: a Finite Element Form Language
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 | 17 |
Pagination | 299-334 |
Publisher | Springer |
ISBN Number | 978-3-642-23098-1 |
Technical reports
A Uniform Inf-Sup Condition With Applications to Preconditioning
Simula, 2012.Status: Published
A Uniform Inf-Sup Condition With Applications to Preconditioning
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Technical reports |
Year of Publication | 2012 |
Publisher | Simula |
Talks, contributed
Are Zombies a Threat to Mankind?
In Invited talk for the opening of RF kjelleren at the University of Oslo, 2012.Status: Published
Are Zombies a Threat to Mankind?
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | Invited talk for the opening of RF kjelleren at the University of Oslo |
CSF Flow Dynamics: Effects of Viscosity and Inertia
In ANSR 2012, New York, 2012.Status: Published
CSF Flow Dynamics: Effects of Viscosity and Inertia
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | ANSR 2012, New York |
Efficient Preconditioning of Optimality Systems
In EMG 2012, 2012.Status: Published
Efficient Preconditioning of Optimality Systems
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | EMG 2012 |
Non-Newtonian Effects in Cerebral Aneurysms. a Computational Study on 12 Patient Specific Aneurysms
In ICS '12, 2012.Status: Published
Non-Newtonian Effects in Cerebral Aneurysms. a Computational Study on 12 Patient Specific Aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | ICS '12 |
On Well-Posedness and Stability
In CBC Seminar series, 2012.Status: Published
On Well-Posedness and Stability
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 |
The Finite Element Library FEniCS
In Steinman's lab, University of Toronto, 2012.Status: Published
The Finite Element Library FEniCS
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | Steinman's lab, University of Toronto |
The Finite Element Library FEniCS + Blood Flow Simulations in Cerebral Aneurysms
In Marsden's lab at UCSD, 2012.Status: Published
The Finite Element Library FEniCS + Blood Flow Simulations in Cerebral Aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | Marsden's lab at UCSD |
The Minimal Residual Method Applied to Ill-Posed Optimality Systems; Eigenvalues and Convergence Properties
In Numerical Methods for Optimal Control and Inverse Problems workshop, Munich, Germany, 2012.Status: Published
The Minimal Residual Method Applied to Ill-Posed Optimality Systems; Eigenvalues and Convergence Properties
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | Numerical Methods for Optimal Control and Inverse Problems workshop, Munich, Germany |
Will FEniCS Fly?
In FEniCS 12 workshop, 2012.Status: Published
Will FEniCS Fly?
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | FEniCS 12 workshop |
Edited books
Automated Solution of Differential Equations by the Finite Element Method
Springer, 2012.Status: Published
Automated Solution of Differential Equations by the Finite Element Method
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Edited books |
Year of Publication | 2012 |
Publisher | Springer |
ISBN Number | 3642230989 |
Talks, invited
Blood Flow in Cerebral Aneurysms - Can Turbulence Be a Risk Indicator?
In SDU workshop, 2012.Status: Published
Blood Flow in Cerebral Aneurysms - Can Turbulence Be a Risk Indicator?
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2012 |
Location of Talk | SDU workshop |
Poster
On Non-Newtonian Effects in Cerebral Aneurysms: a Computational Study on 12 Patient Specific Aneurysms
2012.Status: Published
On Non-Newtonian Effects in Cerebral Aneurysms: a Computational Study on 12 Patient Specific Aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Poster |
Year of Publication | 2012 |
Revisiting 'Turbulence' in Cerebral Aneurysms
2012.Status: Published
Revisiting 'Turbulence' in Cerebral Aneurysms
One of the commonly made assumptions in Computational Fluid Dynamics (CFD) is that cerebral blood flow is laminar, i.e., viscous forces are dominating and the flow is smooth. The numerical methods that are used, are chosen or tailored accordingly, i.e., to converge to such a laminar flow solution with the minimal amount of work1-2. The flow is modeled with a temporal resolution far below the clinically reported frequencies3 and thus any potential flow disturbances, if physically present, are being numerically suppressed. Since no potential disturbances are resolved, no disturbances are observed and the assumption of laminar flow is therefore a self-fulfilling prophecy. Even though recent laminar CFD studies can discriminate between ruptured and unruptured aneurysms better than, e.g. aneurysm size, the link between the proposed hemodynamic agonists and the mechanisms of rupture is unclear. However, the literature contains much evidence which supports that certain aneurysms exhibit energetic high frequency flow fluctuations. For example, high frequency flow fluctuations are known to produce sound, and clinicians have reported such sound or 'bruits' from aneurysms during craniotomy.3 The predominant frequencies were at 460 Hz, which is consistent with the energy peaks at higher frequencies recorded acoustically on the eyes in patients with aneurysms.4 Unstable flow has also been reported in glass model studies of aneurysms.5 This evidence seems to have been ignored, or at least has not received much attention in computational modeling studies. The goal of the present study was to investigate if such high-frequency flow fluctuations in intracranial aneurysms might be a common occurrence, by using thousands of time steps in contrast to, e.g., one hundred2.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Poster |
Year of Publication | 2012 |
Keywords | Conference |
Journal Article
Patient-Specific 3D Simulation of Cyclic CSF Flow at the Cranio-Cervical Region
American Journal of Neuroradiology 33 (2012): 1756-1762.Status: Published
Patient-Specific 3D Simulation of Cyclic CSF Flow at the Cranio-Cervical Region
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2012 |
Journal | American Journal of Neuroradiology |
Volume | 33 |
Number | 9 |
Pagination | 1756-1762 |
Publisher | American Society of Neuroradiology |
Talks, contributed
'Turbulence' in Cerebral Aneurysms
In CBC Workshop on Biomechanics, 17-18 November, 2011.Status: Published
'Turbulence' in Cerebral Aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2011 |
Location of Talk | CBC Workshop on Biomechanics, 17-18 November |
Computational Cerebral Hemodynamics
In The Norwegian Defence Research Establishment, 2011.Status: Published
Computational Cerebral Hemodynamics
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2011 |
Location of Talk | The Norwegian Defence Research Establishment |
Direct Numerical Simulation of Transitional Flow in Patient-Specific Intracranial Aneurysms
In ASME 2011 Summer Bioengineering Conference, 2011.Status: Published
Direct Numerical Simulation of Transitional Flow in Patient-Specific Intracranial Aneurysms
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2011 |
Location of Talk | ASME 2011 Summer Bioengineering Conference |
Efficient Preconditioning of Optimality Systems
In Precond 11, 2011.Status: Published
Efficient Preconditioning of Optimality Systems
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2011 |
Location of Talk | Precond 11 |
On the Construction of Preconditioners for Systems of PDEs
In SIAM Conference on Computational Science and Engineering, MS2, 2011.Status: Published
On the Construction of Preconditioners for Systems of PDEs
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2011 |
Location of Talk | SIAM Conference on Computational Science and Engineering, MS2 |
Simulation Methodology for Cerebral Blood Flow
In Biomedical Simulation Lab, Institute of Biomaterials and Biomedical Engineering at the University of Toronto, 2011.Status: Published
Simulation Methodology for Cerebral Blood Flow
In experiments turbulence has previously been shown to occur in intracranial aneurysms, but the turbulent effects on the arterial wall have not been investigated. The effects of turbulence induced oscillatory wall stresses could be of great importance in understanding aneurysm rupture due to the local arterial wall response to such hemodynamical forces. To investigate the effects of turbulence on blood flow in an intracranial aneurysm, we performed a high resolution computational fluid dynamics (CFD) simulations in a patient specific middle cerebral artery (MCA) aneurysm using a realistic, pulsatile inflow velocity. The flow showed transition to turbulence just after peak systole, and the turbulent fluctuations increased in intensity until mid deceleration, before relaminarization occurred during diastole. The flow impinged with an angle nearly normal onto the aneurysm dome, and the turbulence structures greatly affected both the frequency of change of wall shear stress (WSS) direction and WSS magnitude, which reached a maximum value of 41.5 Pa. The recorded frequencies were predominantly in the range of 1-500 Hz. The current study confirms, through properly resolved CFD simulations, that turbulence can occur in intracranial aneurysms. Because of the local arterial wall response to hemodynamical forces, the effects of oscillatory WSS caused by turbulence, could be correlated with aneurysm rupture, and should be investigated experimentally.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2011 |
Location of Talk | Biomedical Simulation Lab, Institute of Biomaterials and Biomedical Engineering at the University of Toronto |
Why Blood Flow in the Vicinity of Aneurysms Is Difficult to Compute
In Talk at CBC Workshop on CBC Key Topics, 2011.Status: Submitted
Why Blood Flow in the Vicinity of Aneurysms Is Difficult to Compute
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 CBC Key Topics |
Journal Article
A Quantitative Characterization of Differences in Flow Patterns in Ruptured Versus Unruptured MCA Aneurysms
journal (2011).Status: Submitted
A Quantitative Characterization of Differences in Flow Patterns in Ruptured Versus Unruptured MCA Aneurysms
The rupture of an intracranial aneurysm is often associated with death or severe neurological deficits. When detected, the physician has to evaluate the risk of rupture and determine the optimal treatment. Risk estimation based on computational fluid dynamics (CFD) and wall shear stress (WSS) has recently been the focus of many studies. Here, we introduce new indicators for assessing risk of aneurysm rupture based on fluid mechanical properties such as the kinetic energy, vorticity and pressure drop over the aneurysm.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | journal |
CSF Flow in Chiari I and Syringomyelia From the Perspective of Computational Fluid Dynamics
The Neuroradiology Journal 24 (2011): 20-23.Status: Published
CSF Flow in Chiari I and Syringomyelia From the Perspective of Computational Fluid Dynamics
Phase contrast MR in patients with the Chiari I malformation demonstrates abnormal CSF flow in the foramen magnum and upper cervical spinal canal, related to abnormal pressure gradients. The purpose of this study was to analyze the role of CSF pressure in the pathogenesisof syringomyelia, with computational models. The spinal cord was modeled as a cylindrical poro-elastic structure with homogenous and isotropic permeability. The permeability was then made heterogeneous and anisotropic to represent the different properties of the central canal, gray and white matter. Fluid with a defined pressure, varying both in time and space, was prescribed in the SAS. Simulations were performed to quantify deformations and fluid movement within the cord. In the simulations with uniform permeability fluid moved into the cord in regions of higher pressure and out of the cord in regions of lower pressure. With permeability differences simulating gray and white matter the pattern was more complex, but similar. Adding the central spinal canal, fluid moved into the cord as in the previous case. However, preferential flow along the central canal hindered fluid from flowing back into the SAS. Pressure gradients in the SAS produce movement of fluid in the spinal cord. Assuming different relative permeability in gray matter, white matter and the central spinal canal, abnormal CSF gradients lead to accumulation of fluid within and adjacent to the spinal cord central canal.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | The Neuroradiology Journal |
Volume | 24 |
Number | 1 |
Pagination | 20-23 |
Date Published | February |
Direct Numerical Simulation of Transitional Flow in a Patient-Specific Intracranial Aneurysm
Journal of Biomechanics 44 (2011): 2826-2832.Status: Published
Direct Numerical Simulation of Transitional Flow in a Patient-Specific Intracranial Aneurysm
In experiments turbulence has previously been shown to occur in intracranial aneurysms, but the turbulent effects on the arterial wall have not been investigated. The effects of turbulence induced oscillatory wall stresses could be of great importance in understanding aneurysm rupture due to the local arterial wall response to such hemodynamical forces. To investigate the effects of turbulence on blood flow in an intracranial aneurysm, we performed a high resolution computational fluid dynamics (CFD) simulations in a patient specific middle cerebral artery (MCA) aneurysm using a realistic, pulsatile inflow velocity. The flow showed transition to turbulence just after peak systole, and the turbulent fluctuations increased in intensity until mid deceleration, before relaminarization occurred during diastole. The flow impinged with an angle nearly normal onto the aneurysm dome, and the turbulence structures greatly affected both the frequency of change of wall shear stress (WSS) direction and WSS magnitude, which reached a maximum value of 41.5 Pa. The recorded frequencies were predominantly in the range of 1-500 Hz. The current study confirms, through properly resolved CFD simulations, that turbulence can occur in intracranial aneurysms. Because of the local arterial wall response to hemodynamical forces, the effects of oscillatory WSS caused by turbulence, could be correlated with aneurysm rupture, and should be investigated experimentally. Keywords: Computational fluid dynamics, Blood flow, Direct Numerical Simulation, Turbulence, Middle cerebral artery aneurysm
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | Journal of Biomechanics |
Volume | 44 |
Number | 16 |
Pagination | 2826-2832 |
DOI | 10.1016/j.jbiomech.2011.08.015 |
Effect of Tonsilar Herniation on Cyclic CSF Flow Studied With Computational Flow Analysis
American Journal of Neuroradiology 32 (2011): 1474-1481.Status: Published
Effect of Tonsilar Herniation on Cyclic CSF Flow Studied With Computational Flow Analysis
Purpose: The Chiari I malformation, characterized by tonsils extending below the foramen magnum, has increased cerebrospinal fluid (CSF) velocities compared to normal subjects. Measuring the effect of tonsilar herniation on CSF flow in humans is confounded by inter-individual variation. The goal of this study was to determine the effect of herniated tonsils on flow velocity and pressure dynamics. Materials and Methods: A previously described 3D mathematical model of the normal subarachnoid space was modified by extending the tonsils inferiorly. The chamber created was compared with the anatomy of the subarachnoid space. Pressures and velocities were calculated by Computational Fluid Analysis (CFA) methods for sinusoidal flow of a Newtonian fluid. Results were displayed as 2D color-coded plots and 3D animations. Pressure gradients and flow velocities were compared with those in the normal model. Velocity distributions were also compared with those in clinical images of CSF flow. Results: The model represented grossly the subarachnoid space of a Chiari patient. Fluid flow patterns in the Chiari model were complex with jets in some locations and stagnant flow in others. Flow jets, synchronous bi-directional flow, and pressure gradients were greater in the Chiari model than in the normal model. The distribution of flow velocities in the model corresponded well with those observed in clinical images of CSF flow in Chiari I patients. Conclusions: Tonsilar herniation per se increases the pressure gradients and the complexity of flow patterns associated with oscillatory CSF flow.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | American Journal of Neuroradiology |
Volume | 32 |
Number | 5 |
Pagination | 1474-1481 |
Flow Characteristics in a Canine Aneurysm Model: A Comparison of 4-D Accelerated Phase-Contrast MR Measurements and Computational Fluid Dynamics Simulations
Medical Physics 38 (2011): 6300-6313.Status: Published
Flow Characteristics in a Canine Aneurysm Model: A Comparison of 4-D Accelerated Phase-Contrast MR Measurements and Computational Fluid Dynamics Simulations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | Medical Physics |
Volume | 38 |
Number | 11 |
Pagination | 6300-6313 |
Publisher | Med Phys |
Order Optimal Preconditioners for Fully Implicit Runge-Kutta Schemes Applied to the Bidomain Equations
Numerical Methods for Partial Differential Equations 27, no. 5 (2011): 1290-1312.Status: Published
Order Optimal Preconditioners for Fully Implicit Runge-Kutta Schemes Applied to the Bidomain Equations
The partial differential equation part of the bidomain equations is discretized in time with fully implicit Runge-Kutta methods, and the resulting block systems are preconditioned with a block diagonal preconditioner. By studying the time-stepping operator in the proper Sobolev spaces, we show that the preconditioned systems have bounded condition numbers given that the Runge-Kutta scheme is A-stable and irreducible with an invertible coefficient matrix. A new proof of order optimality of the preconditioners for the one-leg discretization in time of the bidomain equations is also presented. The theoretical results are verified by numerical experiments. Additionally, the concept of weakly positive-definite matrices is introduced and analyzed.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | Numerical Methods for Partial Differential Equations |
Volume | 27 |
Issue | 5 |
Pagination | 1290-1312 |
Publisher | Wiley Subscription Services, Inc., A Wiley Company |
Notes | Listed in annual report 2010. Published online june 2010. |
DOI | 10.1002/num.20582 |
Preconditioning Discretizations of Systems of Partial Differential Equations
Numerical Linear Algebra with Applications 18 (2011): 1-40.Status: Published
Preconditioning Discretizations of Systems of Partial Differential Equations
This survey paper is based on three talks given by the second author at the London Mathematical Society Durham Symposium on Computational Linear Algebra for Partial Differential Equations in the summer of 2008. The main focus will be on an abstract approach to the construction of preconditioners for symmetric linear systems in a Hilbert space setting. Typical examples that are covered by this theory are systems of partial differential equations which correspond to saddle point problems. We will argue that the mapping properties of the coefficient operators suggest that block diagonal preconditioners are natural choices for these systems. To illustrate our approach a number of examples will be considered. In particular, parameter-dependent systems arising in areas like incompressible flow, linear elasticity, and optimal control theory will be studied. The paper contains analysis of several models which have previously been discussed in the literature. However, here each example is discussed with reference to a more unified abstract approach.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2011 |
Journal | Numerical Linear Algebra with Applications |
Volume | 18 |
Number | 1 |
Pagination | 1-40 |
Notes | Listed in annual report 2010. Appeared online April 2010. |
DOI | 10.1002/nla.716 |
Proceedings, refereed
Cerebrospinal Fluid Flow Characteristics at Double Heart Rate
In Neuroradiology, 53 (Suppl. 1), S33, 35th European Soc of Neuroradiology ann. meeting, Antwerpen, Belgium. Proc. of the 35th European Society of Neuroradiology Ann. Meeting, Antwerpen, Belgium, 21-25 Sept, Springer Verlag, 2011.Status: Published
Cerebrospinal Fluid Flow Characteristics at Double Heart Rate
Purpose. Cerebrospinal fluid (CSF) flow has been much studied for human beings at rest, i.e. with a correspondingly low heart rate. Current measurement procedures, e.g. with MRI, can not easily collect data at higher heart rates. However, such restrictions may be circumvented by computer simulations. The goal of the present study was to characterize CSF flow at double heart rate for the cranio-vertebral region of a healthy subject though computer simulations. Methods. Several cycles of CSF flow were simulated with a 3D idealized model of the relevant region at a heart rate of 120 bpm. Velocity and pressure were calculated by solving the Navier-Stokes equations numerically. Velocity and pressure characteristics from different times and locations were then compared to corresponding data achieved from the same model with normal heart rate (defined as 60 bpm here). For simplicity, prescribed flow velocities at model boundaries were defined as sinusoidal. Results. It was found that flow velocities and pressure gradients increased substantially. Maximum velocities at the cranio-vertebral junction doubled (to more than 4 cm/s), while pressure gradients along the flow channel increased by a factor 4. Synchronous bidirectional flow also became much more prominent. Conclusions. Our findings suggest that CSF flow velocities and pressure gradients are substantially higher during typical day to day activities than during rest, which is the state commonly reported on in the literature. Our finding may have implications for our understanding of how, e.g., Chiari malformation and Syringomyelia develop.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2011 |
Conference Name | Neuroradiology, 53 (Suppl. 1), S33, 35th European Soc of Neuroradiology ann. meeting, Antwerpen, Belgium |
Publisher | Proc. of the 35th European Society of Neuroradiology Ann. Meeting, Antwerpen, Belgium, 21-25 Sept, Springer Verlag |
ISBN Number | 0028-3940 |
Cyclic Cerebrospinal Fluid Flow (I): Towards the Understanding of Cerebrospinal Fluid Flow Dynamics in Chiari I Malformation
In ASNR 49th Annual Meeting & the Foundation of the ASNR Symposium, June 4 - 9, 2011., 2011.Status: Published
Cyclic Cerebrospinal Fluid Flow (I): Towards the Understanding of Cerebrospinal Fluid Flow Dynamics in Chiari I Malformation
Purpose Chiari I malformation leads to abnormal cerebrospinal fluid (CSF) flow dynamics and often is accompanied by syrinx formation. Phase constrast MR investigations reveal that peak flow velocities increase, whereas the altered pressure gradients are much more difficult to assess noninvasively. In this study, we use computer simulations to investigate how tonsil herniation changes pressure dynamics and flow in the cervical subarachnoid space. Materials and Methods. A 3D mathematical model of the cervical subarachnoid space, with and without herniated tonsils, was used to simulate CSF flow dynamics over several cycles of sinusoidal flow. Simulation results for the case with herniated tonsils were compared with corresponing results for normally positioned tonsils, while keeping all other parameters the same. Results Tonsil herniation caused pressure gradients to increse both in the superior-inferior direction and in axial planes of the model. The change in pressure dynamics caused a more complex flow velocity pattern with higher peak velocities, pronounced synchronous bi-directional flow, and larger velocity components within axial planes. Conclusion Chiari I malformation increases pressure gradients and flow complexity in the cervical subarachnoid space. This implies, e.g., that the spinal cord-CSF interaction dynamics changes following tonsil herniation, something which might have a role to play in syrinx formation.
Afilliation | , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2011 |
Conference Name | ASNR 49th Annual Meeting & the Foundation of the ASNR Symposium, June 4 - 9, 2011. |
ISBN Number | XXXX |
Investigations of Transistional Flows Using Image Based Hemodynamics
In 8th International Conference on CFD in Oil & Gas, Metallurgical and Process Industries, 2011.Status: Published
Investigations of Transistional Flows Using Image Based Hemodynamics
We investigated the complexity of blood flow in intracranial aneurysms in terms of the frequency spectrum of pointwise velocity and pressure fluctuations. The investigations were performed using high-resolution computational fluid dynamics (CFD) simulations for patient-specific middle cerebral artery (MCA) aneurysms, using realistic inflow profile. Through these simulations, the study confirmed that complex transitional flow can occur in intracranial aneurysms. In particular, we found fluctuations of the order of 500- 1000 Hz.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2011 |
Conference Name | 8th International Conference on CFD in Oil & Gas, Metallurgical and Process Industries |
Date Published | June |
On the Complexity of Stationary Flow in Patient-Specific Aneurysms
In MekIT'11 Sixth national conference on Computational Mechanics. tapir academic press, 2011.Status: Published
On the Complexity of Stationary Flow in Patient-Specific Aneurysms
Summary Sound or bruits in the vasculatory system at the range of 1Hz-1kHz is known to occur, and frequency peaks at high frequencies are associated with sick blood vessels. The exact reason for these sounds are not known, but the sound may be generated by turbulence. Turbulence generated sound is typically associated with high frequencies but also with low energy levels. Unfortunately, most blood flow simulations are performed with space and time resolutions where rapid fluctuations typ- ically associated with non-laminar flow cannot be captured. Complex non-laminar flow and the subsequent oscillatory wall stresses can po- tentially be of importance in understanding aneurysm rupture through the local arterial wall response. To investigate the possible presence of complex non-laminar blood flow in intracranial aneurysms, we per- formed high resolution computational fluid dynamics (CFD) simulations for patient specific middle cerebral artery (MCA) aneurysms with sta- tionary inflow conditions. The current study confirms, through high resolution simulations, that complex oscillatory flow may occur in in- tracranial aneurysms. CFD practitioners should therefore be aware of the potentially strong demands to space-time computational resolution in blood flow simulations.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2011 |
Conference Name | MekIT'11 Sixth national conference on Computational Mechanics |
Pagination | 379-392 |
Publisher | tapir academic press |
ISBN Number | 978-82-519-2798-7 |
Porous and Viscous Flow Modeling on the Study of Cyst Development in the Human Spinal Cord
In 8th International Conference on CFD in Oil & Gas, Metallurgical and Process Industries, 2011.Status: Published
Porous and Viscous Flow Modeling on the Study of Cyst Development in the Human Spinal Cord
In this study, we apply an incremental pressure correction scheme to a coupled Navier-Stokes-Darcy problem in order to model porous and viscous flow in and around the human spinal cord. Simulations show that the central canal, a narrow channel in the spinal cord which is usually only partly present in most adults, has a profound effect on pressure distributions within the spinal cord - an effect that can be of importance in the study of cyst formation in the cord. The numerical method was verified using the method of manufactured solutions, showing that the simple operator splitting scheme produces reliable results in this complex case.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2011 |
Conference Name | 8th International Conference on CFD in Oil & Gas, Metallurgical and Process Industries |
The Effect of Varying Cross-Sectional Areas on Cerebrospinal Fluid Flow and Pressure in the Cervical Spine
In MekIT'11. Sixth national conference on Computational Mechanics. Tapir Academic Press, 2011.Status: Published
The Effect of Varying Cross-Sectional Areas on Cerebrospinal Fluid Flow and Pressure in the Cervical Spine
The aim of this study was to determine CSF pressure and velocities in idealized geometries representing the stenosed spinal canal found in Chiari patients.We applied the Navier-Stokes equation to simulate the cyclic CSF flow during one cardiac cycle. Hereby, we have illuminated a well-established medical hypothesis for the relation between the Chiari I malformation and syringomyelia: namely that spinal cord cysts are caused by the so-called Venturi effect (predicted by Bernoulli's law) appearing in fluids that flow through obstructed areas. The results showed that the pressure gradient in geometries with obstructions comparable to Chiari patients may be 10 times as high as under normal flow conditions. The results also showed that the pressure gradients at the level of an obstruction may be twice as large as that predicted from steady flow or Bernoulli's law.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2011 |
Conference Name | MekIT'11. Sixth national conference on Computational Mechanics |
Publisher | Tapir Academic Press |
ISBN Number | 978-82-519-2798-7 |
Talks, invited
Cerebrospinal Fluid Flow in the Upper Cervical Canal in Patients With the Chiari I Malformation
In 1ST CSF Hydrodynamics Symposium, 2011.Status: Published
Cerebrospinal Fluid Flow in the Upper Cervical Canal in Patients With the Chiari I Malformation
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | 1ST CSF Hydrodynamics Symposium |
FEniCS: an Attempt to Combine Simplicity, Generality, Efficiency and Reliability
In Python-based Software for Solving Partial Differential Equations Minisymposium at SIAM Conference on Computational Science and Engineering, 2011.Status: Published
FEniCS: an Attempt to Combine Simplicity, Generality, Efficiency and Reliability
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | Python-based Software for Solving Partial Differential Equations Minisymposium at SIAM Conference on Computational Science and Engineering |
Simulating Blood Flow in Cerebral Aneurysm
In Minisymposium Numerical Methods for Biomedical Problems on Enumath, 2011.Status: Published
Simulating Blood Flow in Cerebral Aneurysm
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | Minisymposium Numerical Methods for Biomedical Problems on Enumath |
The Finite Element Library FEniCS and Simulation of Blood Flow in Cerebral Aneurysms
In Talk at CSB Seminar, University of Stuttgart, 2011.Status: Published
The Finite Element Library FEniCS and Simulation of Blood Flow in Cerebral Aneurysms
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 CSB Seminar, University of Stuttgart |
Book Chapter
Construction of Preconditioners by Mapping Properties for Systems of Partial Differential Equations
In Efficient preconditioning methods for elliptic partial differential equations, 65-84. Bentham Science Publishers, 2011.Status: Published
Construction of Preconditioners by Mapping Properties for Systems of Partial Differential Equations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2011 |
Book Title | Efficient preconditioning methods for elliptic partial differential equations |
Chapter | 4 |
Pagination | 65-84 |
Publisher | Bentham Science Publishers |
ISBN Number | 978-1-60805-291-2 |
Talks, contributed
An Operator Theoretical Approach to Preconditioning Optimality Systems
In Talk at European Multi-Grid Conference, EMG, 2010, 2010.Status: Published
An Operator Theoretical Approach to Preconditioning Optimality Systems
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | Talk at European Multi-Grid Conference, EMG, 2010 |
Cerebrospinal Fluid (CSF) - Oscillating Flow and Pressure
In CBC Workshop on Aerosols: Dispersion, Transport and Effects, Simula, November 10, 2010.Status: Published
Cerebrospinal Fluid (CSF) - Oscillating Flow and Pressure
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | CBC Workshop on Aerosols: Dispersion, Transport and Effects, Simula, November 10 |
Cerebrospinal Fluid (CSF) - Oscillating Flow and Pressure
In Selected Topics Seminar IWS Stuttgart, 2010.Status: Published
Cerebrospinal Fluid (CSF) - Oscillating Flow and Pressure
Afilliation | Scientific Computing, , Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | Selected Topics Seminar IWS Stuttgart |
CSF Hydrodynamic in Patients With Syringomyelia and Chiari I Malformations
In Annual NUPUS meeting in Freudenstadt, 2010.Status: Published
CSF Hydrodynamic in Patients With Syringomyelia and Chiari I Malformations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | Annual NUPUS meeting in Freudenstadt |
CSF Strømning I Forbindelse Med Chiari Malformasjon Og Syringomyelia
In CBC Workshop on Clinical Issues Related to the Cerebrospinal Fluid, 2010.Status: Published
CSF Strømning I Forbindelse Med Chiari Malformasjon Og Syringomyelia
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | CBC Workshop on Clinical Issues Related to the Cerebrospinal Fluid |
From a Physical Problem to Computer Simulations
In CBC Workshop on Cerebrospinal Fluid Flow in the Brain and Spinal Canal - Clinical, Experimental and Mathematical Models and Problems, Simula, May 28, 2010.Status: Published
From a Physical Problem to Computer Simulations
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | CBC Workshop on Cerebrospinal Fluid Flow in the Brain and Spinal Canal - Clinical, Experimental and Mathematical Models and Problems, Simula, May 28 |
Is Zombies a Threat to Mankind?
In Talk presented at FEniCS 2010. FEniCS 2010, 2010.Status: Published
Is Zombies a Threat to Mankind?
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | Talk presented at FEniCS 2010 |
Place Published | FEniCS 2010 |
The Baby Justicia Project: Biomechanical Investigations of the Shaken Baby Syndrome (SBS)
In WCB2010, Seminar session, Head/Brain Injury - Models, 2010.Status: Published
The Baby Justicia Project: Biomechanical Investigations of the Shaken Baby Syndrome (SBS)
Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Location of Talk | WCB2010, Seminar session, Head/Brain Injury - Models |