Projects
inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research

Heart failure (HF) is a huge and growing health problem in the industrialized world, and is subject of considerable ongoing research. Computer simulations based on detailed biophysical models hold the promise to shed light on many important questions, and to provide a valuable supplement to traditional biomedical research. To this date such in silico models have been used to a very limited degree in HF research, and this is most likely due to the considerable challenges associated with performing accurate computer simulations of heart physiology and pathology. The purpose of this project is to address the most important of these challenges, and to considerably advancing the current state of the art in the field.
Specifically, we want to improve on the robustness and efficiency of the computational models. We aim to achieve this by developing new mathematical models for describing the contracting heart muscle tissue, and by improving the computational methods used to solve the resulting equations. Furthermore, we want to link the computational framework with software that enables efficient construction of models from medical images, to allow building computer models of individual patients. Patient specific models have a huge potential for clinical use in diagnosis and treatment optimization, but their use is currently limited by the lack of robust and usable computational tools, and by the lack of proper validation.
Final goal:
The main goal for the project is to accelerate heart failure research by facilitating the widespread use of accurate and validated computer models. The main delivery will be a package of robust and well documented software tools, that facilitate an efficient workflow from medical images and patient recordings to detailed computer simulations. The software will be based on the Fenics finite element framework, and will be distributed under an open license. The first official release is planned for 2015.
Funding source:
Research Council of Norway
All partners:
No formal partners, but Oslo University Hospital is an important collaborator.
Publications for inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research
Journal Article
pulse: A python package based on FEniCS for solving problems in cardiac mechanics
Journal of Open Source Software 4, no. 41 (2019): 1539.Status: Published
pulse: A python package based on FEniCS for solving problems in cardiac mechanics
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Journal of Open Source Software |
Volume | 4 |
Issue | 41 |
Pagination | 1539 |
Date Published | Jan-09-2019 |
Publisher | The Journal of Open Source Software, Open Source Initiative |
URL | http://www.theoj.org/joss-papers/joss.01539/10.21105.joss.01539.pdf |
DOI | 10.21105/joss.01539 |
Journal Article
Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization
International Journal for Numerical Methods in Biomedical Engineering 34, no. 7 (2018).Status: Published
Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 34 |
Issue | 7 |
Publisher | John Wiley & Sons |
DOI | 10.1002/cnm.2982 |
PhD Thesis
Patient-Specific Computational Modeling of Cardiac Mechanics
In The University of Oslo. Vol. PhD. Norway: University of Oslo, 2018.Status: Published
Patient-Specific Computational Modeling of Cardiac Mechanics
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | PhD Thesis |
Year of Publication | 2018 |
Degree awarding institution | The University of Oslo |
Degree | PhD |
Publisher | University of Oslo |
Place Published | Norway |
URL | http://urn.nb.no/URN:NBN:no-64609 |
Journal Article
Estimating cardiac contraction through high resolution data assimilation of a personalized mechanical model
Journal of Computational Science 24 (2017): 85-90.Status: Published
Estimating cardiac contraction through high resolution data assimilation of a personalized mechanical model
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Journal of Computational Science |
Volume | 24 |
Pagination | 85-90 |
Publisher | Elsevier |
ISSN | 1877-7503 |
Keywords | Adjoint Method, Cardiac Mechanics, Contractility, Data assimilation, PDE-constrained optimization |
URL | http://www.sciencedirect.com/science/article/pii/S1877750317308190 |
DOI | 10.1016/j.jocs.2017.07.013 |
Poster
Mechanical Analysis of Pulmonary Hypertension via Adjoint based Data Assimilation of a Finite Element Model
Summer Biomechanics, Bioengineering, and Biotransport Conference, Tuscon, USA, 2017.Status: Published
Mechanical Analysis of Pulmonary Hypertension via Adjoint based Data Assimilation of a Finite Element Model
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research, Center for Biomedical Computing (SFF) |
Publication Type | Poster |
Year of Publication | 2017 |
Date Published | 06/2017 |
Place Published | Summer Biomechanics, Bioengineering, and Biotransport Conference, Tuscon, USA |
Talks, contributed
Assessment of regional myocardial work through adjoint-based data assimilation
In Oslo, Norway, 2017.Status: Published
Assessment of regional myocardial work through adjoint-based data assimilation
Assessment of regional myocardial work through adjoint-based data assimilation
Introduction
To achieve efficient pumping of blood to the body, the healthy heart contracts in a synchronous manner. However, heart disease can alter how the heart is activated during a beat, and dyssynchronous contraction can occur, reducing the overall pumping efficiency. Advanced treatments exist for such cases, but selecting patients likely to respond can be challenging. The existing selection criteria, based on organ level measures of activation and contraction, have relatively low specificity. It is therefore of interest to extract new biomarkers to help better identify potential responders. Here we explore one example of a potential biomarker, the regional myocardial work [1], a measure of cardiac efficiency, using a computational model of cardiac mechanics optimized to patient specific data using a high level adjoint based data assimilation method.
Methods
Left ventricular (LV) geometry was obtained from 4D echocardiography, and the segmented chamber was modelled as an incompressible, continuous hyperelastic body described via an transversely isotropic material law[2]. Active force development was modeled through additively decomposing stress into passive and active stresses, the latter added along the cardiac fiber direction, defined by a rule based architecture.
The model was fit to 4D imaging of the LV through the cardiac cycle using an adjoint-based data assimilation technique, which automatically solves for the gradient of the solution with respect to local active stress, for highly efficient minimization of model misfit against collected data. Simulations were optimized both globally and regionally in 17 delineated segments[3]. With these simulations, the amount of mechanical work performed between time point tm and tn could be regionally calculated through -
W(tm, tn) = ∫ S: ∂tE dt = ∑i S(ti-½): dE(ti-½)
where
S(ti-½) = 0.5*(S(ti)+S(ti-1))
and
dE(ti-½) = E(ti)-E(ti-1)
Here subscript t indicates the time point, S is the Second Piola-Kirchhoff stress tensor and E is the Green-Lagrange strain tensor.
Results
We tested the method on healthy control subjects and patients suffering from left bundle branch block (LBBB). The results show an excellent fit between measured and simulated strain (R^2 = 0.8) and volume (R^2 = 1.0). The estimated regional myocardial work, assessed in these segments, shows clear differences between the healthy and diseased patients (e.g Mid Septal longitudinal wasted work ratio[1]: 1.45 (LBBB), 0.24(Healthy)) and can potentially be used as a biomarker to map regional cardiac dysfunction.
References
[1] doi:10.1152/ajpheart.00191.2013
[2] doi:10.1098/rsta.2009.0091
[3] doi:10.1002/cnm.2863
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Talks, contributed |
Year of Publication | 2017 |
Location of Talk | Oslo, Norway |
Type of Talk | International Conference on Computational Science and Engineering, In memory of Hans Petter Langtangen |
URL | https://cseconf2017.files.wordpress.com/2017/09/2017-09-28-cseconf2017-c... |
AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations

Uncertainties and measurement errors permeate all fields of computational science. In the biomedical disciplines, the uncertainties inherent in data acquisition and processing pose a fundamental challenge in our era of patient-specific modelling and simulation. The quantification of such uncertainties and their implications is vital for the predictive capabilities of computer simulations. In spite of its importance, the role of uncertainty quantification is yet underdeveloped in these data-driven scientific fields. This can be attributed to a critical and problematic gap between clinicians, biomedical engineers, numerical method and algorithm designers, and scientific software developers. Such gaps are not restricted to the biomedical domain: indeed, these gaps present a generic challenge in the field of computational science.
The AUQ-PDE project aims to bridge this gap by developing and integrating generic software components featuring a high degree of automation for uncertainty quantification in computational models governed by partial differential equations (PDEs). The applicability and usability of the software will be anchored in the application domains by the central involvement of application domain specialists. In particular, the software components will be demonstrated on a select set of research questions stemming from the in silico study of cardiac electrophysiology and mechanics. The software developed will allow scientists and engineers to quickly build tailored PDE models and quickly equip these models with tailored uncertainty quantification methods. In the longer-term, the more widespread availability of biomedical simulation studies with quantified uncertainties will positively impact the use of such studies for clinical practice. For instance, the cardiac modelling study proposed in this project will strengthen the possibility of using patient-specific simulations as a diagnostic or treatment planning tool for cardiac diseases.
The project brings together three partners from the Nordic countries: the Biomedical Computing Department at Simula Research Laboratory, Norway; the Department of Mathematical Sciences at Chalmers University of Technology, Sweden; and Department of Mathematics and Statistics at the University of Helsinki, Finland.
Final goal:
The AUQ-PDE project aims to develop and integrate generic software featuring a high degree of automation for uncertainty quantification in computational models governed by partial differential equations, and to apply the developed tools to a select set of research questions stemming from the in silico study of physiological processes.
Funding source:

All partners:
- Simula Research Laboratory
- Chalmers University of Technology
- University of Helsinki
Project leader:
Joakim Sundnes
Publications for AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations
Journal Article
Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response
International Journal for Numerical Methods in Biomedical Engineering 35, no. 5 (2019): e3178.Status: Published
Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response
Afilliation | Scientific Computing |
Project(s) | AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations, Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 35 |
Issue | 5 |
Pagination | e3178 |
Publisher | Wiley |
Journal Article
Efficient white noise sampling and coupling for multilevel Monte Carlo with non-nested meshes
SIAM Journal on Uncertainty Quantification 6, no. 4 (2018).Status: Published
Efficient white noise sampling and coupling for multilevel Monte Carlo with non-nested meshes
Afilliation | Scientific Computing |
Project(s) | AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations, Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | SIAM Journal on Uncertainty Quantification |
Volume | 6 |
Issue | 4 |
Publisher | SIAM |
Center for Biomedical Computing (SFF)

Center for Biomedical Computing (CBC) aims to develop and apply novel simulation technologies to reach new understanding of complex physical processes affecting human health. We target selected medical problems where insight from mathematical modeling can contribute to changing clinical practice.
The approach comprises well-defined research projects with multi-disciplinary teams consisting of experts in physical modeling, mathematics, numerical methods, scientific software development, bioengineering, medical research, and clinical treatment. Our teams focus on publishing novel research results of high relevance and quality.
The challenging applications being addressed drive new developments in computational methodologies and scientific software. A key mission of the Center is to make these useful developments accessible to computational scientists and engineers at large through professional, open source software. This original software can help advancing many other scientific fields dealing with complex multi-physics problems.
Three main research tasks
The Center for Biomedical Computing is devoted to three main objectives:
- The development of computational middleware that can be used to model the flow of bodily fluids in the cardiovascular system and spinal cord,
- robust flow solvers, and
- applications to biomedical fluid flow problems - applying mathematical modelling to physiological issues.
These highly integrated topics represent a broad, a medium, and a specialized scope, respectively, of advancing the current state of computational fluid dynamics.
The computational middleware is meant to be a useful “Matlab-like” set of tools generally applicable to computational scientists for rapid prototyping of multi-physics software based on partial differential equations.
The flow solvers part aims to advance the computational middleware in the specific direction of robust adaptive implicit finite element methods for viscous and turbulent fluid flow.
The application part will use the flow solvers in combination with the computational middleware to attack challenging biomedical flow problems.
Different applications and results
The composition of three main themes ensures results of different flavor. First, the computational middleware will be generally useful and has the potential of achieving substantial impact in science. Second, the flow solver part continues research of outstanding quality and usefulness in fluid dynamics. Finally, the application part addresses a new and vital class of challenging physical problems where mathematical modeling is in its initial stages. The three parts also span the range of natural science research, from generic application-independent tools via methods for a wide class of applications (fluid flow) to specific physical problems.
The group behind this project has an excellent track record for developing computational middleware and numerical methods, and applying these tools to solve problems in natural science. For both the computational middleware and flow solver parts, we intend to invite very promising young researchers from outstanding groups for long-term stays in the center and thereby help to increase the scientific quality of our group. Biomedical flow investigations will be done in close collaboration with scientists with vast experience in this field.
For more information, please visit the CBC website.
Publications for Center for Biomedical Computing (SFF)
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 |
Book Chapter
Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow
In Computational Glioscience . Springer Series in Computational Neuroscience: Springer, 2019.Status: Published
Astrocytic Ion Dynamics: Implications for Potassium Buffering and Liquid Flow
Afilliation | Scientific Computing |
Project(s) | Waterscales: Mathematical and computational foundations for modeling cerebral fluid flow, Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2019 |
Book Title | Computational Glioscience |
Publisher | Springer |
Place Published | Springer Series in Computational Neuroscience |
Journal Article
The trade off between tidal-turbine array yield and environmental impact: a multi-objective optimisation problem
Renewable Energy 114 (2019): 390-403.Status: Published
The trade off between tidal-turbine array yield and environmental impact: a multi-objective optimisation problem
In the drive towards a carbon-free society, tidal energy has the potential to become a valuable part of the UK energy supply. Developments are subject to intense scrutiny, and potential environmental impacts must be assessed. Unfortunately many of these impacts are still poorly understood, including the implications that come with altering the hydrodynamics. Here, methods are proposed to quantify ecological impact and to incorporate its minimisation into the array design process. Four tidal developments in the Pentland Firth are modelled with the array optimisation tool OpenTidalFarm, that designs arrays to generate the maximum possible profit. Maximum entropy modelling is used to create habitat suitability maps for species that respond to changes in bed-shear stress. Changes in habitat suitability caused by an altered tidal regime are assessed. OpenTidalFarm is adapted to simultaneously optimise array design to maximise both this habitat suitability and to maximise the profit of the array. The problem is thus posed as a multi-objective optimisation problem, and a set of Pareto solutions found, allowing trade-offs between these two objectives to be identified. The methods proposed generate array designs that have reduced negative impact, or even positive impact, on the habitat suitability of specific species or habitats of interest.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF), OptCutCell: Simulation-based optimisation with dynamic domains |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Renewable Energy |
Volume | 114 |
Pagination | 390-403 |
Publisher | Elsevier |
DOI | 10.1016/j.renene.2019.04.141 |
Journal Article
Inversion and computational maturation of drug response using human stem cell derived cardiomyocytes in microphysiological systems
Nature Scientific Reports 8 (2018).Status: Published
Inversion and computational maturation of drug response using human stem cell derived cardiomyocytes in microphysiological systems
While cardiomyocytes differentiated from human induced pluripotent stems cells (hiPSCs) hold great promise for drug screening, the electrophysiological properties of these cells can be variable and immature, producing results that are significantly different from their human adult counterparts. Here, we describe a computational framework to address this limitation, and show how in silico methods, applied to measurements on immature cardiomyocytes, can be used to both identify drug action and to predict its effect in mature cells. Our synthetic and experimental results indicate that optically obtained waveforms of voltage and calcium from microphysiological systems can be inverted into information on drug ion channel blockage, and then, through assuming functional invariance of proteins during maturation, this data can be used to predict drug induced changes in mature ventricular cells. Together, this pipeline of measurements and computational analysis could significantly improve the ability of hiPSC derived cardiomycocytes to predict dangerous drug side effects.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | Nature Scientific Reports |
Volume | 8 |
Number | 17626 |
Date Published | 12/2018 |
Publisher | Springer Nature |
URL | https://doi.org/10.1038/s41598-018-35858-7 |
DOI | 10.1038/s41598-018-35858-7 |
Multivariate Polynomial Chaos Expansions with Dependent Variables
SIAM Journal on Scientific Computing 40, no. 1 (2018): A199-A223.Status: Published
Multivariate Polynomial Chaos Expansions with Dependent Variables
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | SIAM Journal on Scientific Computing |
Volume | 40 |
Issue | 1 |
Pagination | A199–A223 |
Date Published | 01/2018 |
Publisher | SIAM |
DOI | 10.1137/15M1020447 |
Computing stationary solutions of the two-dimensional Gross–Pitaevskii equation with deflated continuation
Communications in Nonlinear Science and Numerical Simulation 54 (2018): 482-499.Status: Published
Computing stationary solutions of the two-dimensional Gross–Pitaevskii equation with deflated continuation
In this work we employ a recently proposed bifurcation analysis technique, the deflated continuation algorithm, to compute steady-state solitary waveforms in a one-component, two-dimensional nonlinear Schrödinger equation with a parabolic trap and repulsive interactions. Despite the fact that this system has been studied extensively, we discover a wide variety of previously unknown branches of solutions. We analyze the stability of the newly discovered branches and discuss the bifurcations that relate them to known solutions both in the near linear (Cartesian, as well as polar) and in the highly nonlinear regimes. While deflated continuation is not guaranteed to compute the full bifurcation diagram, this analysis is a potent demonstration that the algorithm can discover new nonlinear states and provide insights into the energy landscape of complex high-dimensional Hamiltonian dynamical systems.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | Communications in Nonlinear Science and Numerical Simulation |
Volume | 54 |
Pagination | 482-499 |
Publisher | Elsevier |
DOI | 10.1016/j.cnsns.2017.05.024 |
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 |
Fast Dictionary Learning from Incomplete Data
EURASIP Journal on Advances in Signal Processing 2018, no. 1 (2018): 12.Status: Published
Fast Dictionary Learning from Incomplete Data
This paper extends the recently proposed and theoretically justified iterative thresholding and K residual means algorithm ITKrM to learning dicionaries from incomplete/masked training data (ITKrMM). It further adapts the algorithm to the presence of a low rank component in the data and provides a strategy for recovering this low rank component again from incomplete data. Several synthetic experiments show the advantages of incorporating information about the corruption into the algorithm. Finally, image inpainting is considered as application example, which demonstrates the superior performance of ITKrMM in terms of speed and/or reconstruction quality compared to its closest dictionary learning counterpart.
Afilliation | Scientific Computing |
Project(s) | FunDaHD: Function-driven Data Learning in High Dimension, Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | EURASIP Journal on Advances in Signal Processing |
Volume | 2018 |
Issue | 1 |
Pagination | 12 |
Date Published | 02/2018 |
Publisher | Springer |
URL | http://rdcu.be/HD8p |
DOI |
Book
Mesh dependence in PDE-constrained optimisation
In An Application in Tidal Turbine Array Layouts. Berlin / Heidelberg: Springer Research Brief, 2017.Status: Published
Mesh dependence in PDE-constrained optimisation
This book provides an introduction to PDE-constrained optimisation using finite elements and the adjoint approach. The practical impact of the mathematical insights presented here are demonstrated using the realistic scenario of the optimal placement of marine power turbines, thereby illustrating the real-world relevance of best-practice Hilbert space aware approaches to PDE-constrained optimisation problems.
Many optimisation problems that arise in a real-world context are constrained by partial differential equations (PDEs). That is, the system whose configuration is to be optimised follows physical laws given by PDEs. This book describes general Hilbert space formulations of optimisation algorithms, thereby facilitating optimisations whose controls are functions of space. It demonstrates the importance of methods that respect the Hilbert space structure of the problem by analysing the mathematical drawbacks of failing to do so. The approaches considered are illustrated using the optimisation problem arising in tidal array layouts mentioned above.
This book will be useful to readers from engineering, computer science, mathematics and physics backgrounds interested in PDE-constrained optimisation and their real-world applications.
Afilliation | Scientific Computing |
Project(s) | OptCutCell: Simulation-based optimisation with dynamic domains, Center for Biomedical Computing (SFF) |
Publication Type | Book |
Year of Publication | 2017 |
Secondary Title | An Application in Tidal Turbine Array Layouts |
Edition | 1 |
Number of Pages | 111 |
Publisher | Springer Research Brief |
Place Published | Berlin / Heidelberg |
ISBN Number | 978-3-319-59482-8 |
URL | http://www.springer.com/us/book/9783319594828 |
Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges
In 7th International Workshop, STACOM 2016, Held in Conjunction with MICCAI 2016, Athens, Greece, October 17, 2016, Revised Selected Papers. Berlin Heidelberg: Springer International Publishing, 2017.Status: Published
Statistical Atlases and Computational Models of the Heart. Imaging and Modelling Challenges
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book |
Year of Publication | 2017 |
Secondary Title | 7th International Workshop, STACOM 2016, Held in Conjunction with MICCAI 2016, Athens, Greece, October 17, 2016, Revised Selected Papers |
Publisher | Springer International Publishing |
Place Published | Berlin Heidelberg |
URL | http://www.springer.com/gp/book/9783319527178 |
DOI | 10.1007/978-3-319-52718-5 |
SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation

The aim of SysAFib is to integrate the existing sources of knowledge, using a systems medicine approach, into a focused decision support system, to determine which patients are good candidates for atrial ablation and which patients are at risk for arrhythmia recurrence.
Funding source:
ERA CoSysMed administration, funded in Norway via BIOTEK2021 program of the Norwegian Research Council
All partners:
- Simula Research Laboratory,
- Oslo University Hospital,
- Universiteit Maastricht,
- INRIA Sophia Antipolis,
- Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH),
- Center for Computational Medicine in Cardiology (Universitá della Svizzera italiana and CardioCentro Ticino)
Project leader:
Simula Research Laboratory
Publications for SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation
Journal Article
The impact of cardiovascular risk factors on cardiac structure and function: Insights from the UK Biobank imaging enhancement study
PLoS ONE 12, no. 10 (2017): e0185114.Status: Published
The impact of cardiovascular risk factors on cardiac structure and function: Insights from the UK Biobank imaging enhancement study
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | PLoS ONE |
Volume | 12 |
Issue | 10 |
Pagination | e0185114 |
Date Published | Mar-10-2017 |
Publisher | PLOS ONE |
DOI | 10.1371/journal.pone.018511410.1371/ |
The opportunities and challenges for biophysical modelling of adverse and beneficial drug actions on the heart
Current Opinion in Systems Biology 4 (2017): 29-34.Status: Published
The opportunities and challenges for biophysical modelling of adverse and beneficial drug actions on the heart
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation, Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Current Opinion in Systems Biology |
Volume | 4 |
Pagination | 29-34 |
Publisher | Elsevier |
DOI | 10.1016/j.coisb.2017.05.018 |
Proceedings, refereed
Cardiac Mesh Reconstruction from Sparse, Heterogeneous Contours
In Medical Image Understanding and Analysis. MIUA 2017. Communications in Computer and Information Science. Vol. 723. Cham: Springer International Publishing, 2017.Status: Published
Cardiac Mesh Reconstruction from Sparse, Heterogeneous Contours
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation |
Publication Type | Proceedings, refereed |
Year of Publication | 2017 |
Conference Name | Medical Image Understanding and Analysis. MIUA 2017. Communications in Computer and Information Science |
Volume | 723 |
Pagination | 169 - 181 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-319-60963-8 |
ISSN Number | 1865-0929 |
URL | https://link.springer.com/chapter/10.1007/978-3-319-60964-5_15 |
DOI | 10.1007/978-3-319-60964-510.1007/978-3-319-60964-5_15 |
MRI-Based Heart and Torso Personalization for Computer Modeling and Simulation of Cardiac Electrophysiology
In Imaging for Patient-Customized Simulations and Systems for Point-of-Care Ultrasound. International Workshops, BIVPCS 2017 and POCUS 2017.. Vol. 10549. Cham: Springer International Publishing, 2017.Status: Published
MRI-Based Heart and Torso Personalization for Computer Modeling and Simulation of Cardiac Electrophysiology
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation |
Publication Type | Proceedings, refereed |
Year of Publication | 2017 |
Conference Name | Imaging for Patient-Customized Simulations and Systems for Point-of-Care Ultrasound. International Workshops, BIVPCS 2017 and POCUS 2017. |
Volume | 10549 |
Pagination | 61 - 70 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-319-67551-0 |
ISSN Number | 0302-9743 |
URL | https://link.springer.com/chapter/10.1007/978-3-319-67552-7_8#citeas |
DOI | 10.1007/978-3-319-67552-7_8 |
Talks, contributed
A Computational Model for the Identification of Atrial Stunning Pathways
In 2017 EMI International Conference, 2017.Status: Published
A Computational Model for the Identification of Atrial Stunning Pathways
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation, Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2017 |
Location of Talk | 2017 EMI International Conference |
Talks, invited
A New Paradigm for the Assessment of Chronic Anthracycline Mitochondrial Cardiotoxicity
In Safety Pharmacology Society Meeting, Berlin, Germany, 2017.Status: Published
A New Paradigm for the Assessment of Chronic Anthracycline Mitochondrial Cardiotoxicity
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation |
Publication Type | Talks, invited |
Year of Publication | 2017 |
Location of Talk | Safety Pharmacology Society Meeting, Berlin, Germany |
PARIS

Atrial Fibrillation (AF) is a complex cardiac disease that can lead to blood clots and increase the risk of stroke. AF is gaining epidemic proportions and the majority of AF patients are prescribed anticoagulants, but at the cost of increased risk of severe bleedings. Individualized anticoagulation management, therefore, remains a major challenge but routinely available patient-specific clinical data are under-utilized. Computational models based on patient-specific medical images of the atria have reached a high level of sophistication, but remain insufficiently validated and tested to be used for individualized clinical predictions. PARIS will utilize existing medical records of AF patients with known clinical outcome, to validate computer models and predictive machine learning methods in an iterative process. The ambition is to identify biomarkers that correlate with stroke and to prospectively outperform the current risk score to reduce individual bleeds by optimizing personalized treatment and clinical follow-up.
Funding
ERA-Net on Systems Medicine under the EU Framework Programme Horizon2020.
Partners
Inria Epione (France)
University Heart Center Hamburg (Germany)
Publications for PARIS
Poster
Impact of Rigid Versus Dynamic Boundaries on Computational Fluid Dynamics Predictor of Left Atrial Appendage Thrombus Formation
Computing in Cardiology, 2022.Status: Published
Impact of Rigid Versus Dynamic Boundaries on Computational Fluid Dynamics Predictor of Left Atrial Appendage Thrombus Formation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, PARIS, Simulation of Cardiac Devices and Drugs for In-Silico Testing and Certification (SimCardioTest) |
Publication Type | Poster |
Year of Publication | 2022 |
Place Published | Computing in Cardiology |
Talks, invited
A mechanistic approach towards personalized treatment in patients with atrial fibrillation
In University Heart & Vascular Center Hamburg - UKE, 2022.Status: Published
A mechanistic approach towards personalized treatment in patients with atrial fibrillation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, PARIS |
Publication Type | Talks, invited |
Year of Publication | 2022 |
Location of Talk | University Heart & Vascular Center Hamburg - UKE |
Computational Fluid Dynamics Approaches to Predict Flow Physics of Left Atrium
In Universitat Pompeu Fabra - Barcelona, Spain, 2022.Status: Published
Computational Fluid Dynamics Approaches to Predict Flow Physics of Left Atrium
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, PARIS, Simulation of Cardiac Devices and Drugs for In-Silico Testing and Certification (SimCardioTest), PersonalizeAF |
Publication Type | Talks, invited |
Year of Publication | 2022 |
Location of Talk | Universitat Pompeu Fabra - Barcelona, Spain |
The Dynamic Heart - Computational Tools for Studying Cardiac Growth and Remodeling (DynaComp)
The heart is a dynamic organ that continuously adapts to the needs of the body. The adaptation is normally useful and necessary, for example when physical exercise causes the heart to grow larger and pump more powerfully, to increase blood flow and oxygen supply to the body. But in some chronic heart diseases, the heart's adaptability can work against its purpose, and contribute to aggravate the function rather than improve it. For instance, the heart wall may grow thicker, which can make the heart pump more forcefully and supply more blood to the body, but at the same time makes the heart stiffer. A stiffer heart may not be properly filled for each heartbeat, and reduced filling gives less blood to eject and therefore reduced performance. The heart can try to compensate for this by growing even bigger and thicker, which worsens the problem and may lead to a vicious cycle that over time leads to heart failure. To give optimal treatment for chronic heart patients it is important to understand the physiological processes that drive the heart's adaptation, and what makes these vital mechanisms turn harmful in some situations. In the DynaComp project, we will use mathematical models and computer simulations to compute the mechanical forces in the heart muscle during a heartbeat, both for healthy hearts and in disease. In addition, we will create models for how these forces make the heart grow
and adapt over time, and how the dynamics of this process is altered during disease. The results of the project can provide a better understanding of the physiology of the heart, and lead to better diagnosis and treatment of chronic heart disease.
Funding source:
Researcher Project for Scientific Renewal (The Research Council of Norway)
Partners:
Institute for Experimental Medical Research, The University of Oslo
Publications
Journal Article
A cell-based framework for modeling cardiac mechanics
Biomechanics and Modeling in Mechanobiology 10101010, no. 1137/11115/11109/101145/779359 (2023).Status: Published
A cell-based framework for modeling cardiac mechanics
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Biomechanics and Modeling in Mechanobiology |
Volume | 10101010 |
Issue | 1137/11115/11109/101145/779359 |
Date Published | 01/2023 |
Publisher | Springer |
ISSN | 1617-7959 |
Keywords | Cardiac Mechanics, cardiomyocyte contraction, cell geometries, intracellular and extracellular mechanics, microscale modeling |
URL | https://link.springer.com/article/10.1007/s10237-022-01660-8 |
DOI | 10.1007/s10237-022-01660-8 |
A cell-based framework for modeling cardiac mechanics
Biomechanics and Modeling in Mechanobiology (2023).Status: Published
A cell-based framework for modeling cardiac mechanics
Cardiomyocytes are the functional building blocks of the heart – yet most models developed to simulate cardiac mechanics do not represent the individual cells and their surrounding matrix. Instead, they work on a homogenized tissue level, assuming that cellular and subcellular structures and processes scale uniformly. Here we present a mathematical and numerical framework for exploring tissue level cardiac mechanics on a microscale given an explicit three-dimensional geometrical representation of cells embedded in a matrix. We defined a mathematical model over such a geometry, and parametrized our model using publicly available data from tissue stretching and shearing experiments. We then used the model to explore mechanical differences between the extracellular and the intracellular space. Through sensitivity analysis, we found the stiffness in the extracellular matrix to be most important for the intracellular stress values under contraction. Strain and stress values were observed to follow a normal-tangential pattern concentrated along the membrane, with substantial spatial variations both under contraction and stretching. We also examined how it scales to larger size simulations, considering multicellular domains. Our work extends existing continuum models, providing a new geometrical-based framework for exploring complex cell-cell and cell-matrix interactions.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Biomechanics and Modeling in Mechanobiology |
Date Published | 01/2023 |
Publisher | Springer |
Keywords | Cardiac Mechanics, cardiomyocyte contraction, cell geometries, intracellular and extracellular mechanics, microscale modeling |
Editorial: Computational models of cardiovascular growth and remodeling
Frontiers in Physiology 14 (2023): 56.Status: Published
Editorial: Computational models of cardiovascular growth and remodeling
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2023 |
Journal | Frontiers in Physiology |
Volume | 14 |
Pagination | 56 |
Publisher | Frontiers |
URL | https://www.frontiersin.org/articles/10.3389/fphys.2023.1130420/full |
DOI | 10.3389/fphys.2023.1130420 |
Book Chapter
A Bayesian Approach to Parameter Estimation in Cardiac Mechanics
In Solid (Bio) mechanics: Challenges of the Next Decade, 245-256. Cham: Springer, 2022.Status: Published
A Bayesian Approach to Parameter Estimation in Cardiac Mechanics
Computational models of cardiac mechanics have been shown to capture the general mechanical function of the heart, and have been parameterized based on in vivo patient data to accurately reproduce the heart function of individual patients. Pre- vious attempts for creating such patient-specific problem have typically been based on solving a deterministic inverse problem, which minimizes the misfit between cer- tain model outputs and measured values. While this approach is robust and efficient, and has shown good agreement between model results and patient data, it does not provide any information about the uncertainty in the resulting model parameters. We here present a parameter estimation framework based on a Bayesian approach, which estimates probability density functions (PDFs) of material parameters based on uncertain input values. The method is based on sampling the parameter space and solving the associated forward model for each sample, which may lead to a substantial computational problem if multiple parameters are considered. However, the model also offers additional information in the form of univariate or multivariate PDFs for the estimated parameters. We investigate the potential of the methodology by solving a simple parameter estimation problem in passive left ventricular mechan- ics, and show that the results are in agreement with previous results obtained with a deterministic parameter estimation method.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Book Chapter |
Year of Publication | 2022 |
Book Title | Solid (Bio) mechanics: Challenges of the Next Decade |
Pagination | 245–256 |
Date Published | 06/2022 |
Publisher | Springer |
Place Published | Cham |
ISBN | ISBN 978-3-030-92338-9 |
URL | https://doi.org/10.1007/978-3-030-92339-6_10 |
DOI | 10.1007/978-3-030-92339-6_10 |
Data aggregation and anonymization for mathematical modeling and epidemiological studies
In Smittestopp - A Case Study on Digital Contact Tracing, 121-141. Vol. 11. Cham: Springer International Publishing, 2022.Status: Published
Data aggregation and anonymization for mathematical modeling and epidemiological studies
An important secondary purpose of the Smittestopp development was to provide aggregated data sets describing mobility and social interactions in Norway's population. The data were to be used to monitor the effect of government regulations and recommendations, provide input to advanced computational models to predict the pandemic's spread, and provide input to fundamental epidemiology research. In this chapter we describe the challenges and technical solutions of Smittestopp's data aggregation, as well as preliminary results from the time period when the app was active.We first give a detailed overview of the requirements, specifying the types of data to be collected and the level of spatial and temporal aggregation. We then proceed to describe the concepts for anonymization via :-anonymity and Y-differential privacy (Y-DP ), and the technical solutions for collecting and aggregating data from the database. In particular, we present details of how GPS- and Bluetooth events were mapped to geographical regions and points of interest, and the solutions employed for efficient data retrieval and processing. The preliminary results demonstrate how the recorded GPS- and Bluetooth events match with expected temporal and spatial variations in mobility and social interactions, and indicate the usefulness of the aggregated data as a tool for pandemic monitoring and research. One of the main criticisms of Smittestopp concerns the centralized storage of individuals' movements, even if such data were used and presented only at an aggregated and anonymized level. In this chapter, we also outline a completely different approach, where the GPS data do not leave the user's phone but are, instead, pre-processed to a much higher level of privacy before being dispatched to a server-side data aggregation algorithm. This approach, which would make the app significantly less intrusive, is made possible by recent advances in determining close contacts from Bluetooth data, either by a revised Smittestopp algorithm or by means of the Google/Apple Exposure Notification framework.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Book Chapter |
Year of Publication | 2022 |
Book Title | Smittestopp - A Case Study on Digital Contact Tracing |
Volume | 11 |
Pagination | 121–141 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-031-05466-2 |
URL | https://doi.org/10.1007/978-3-031-05466-2_7 |
DOI | 10.1007/978-3-031-05466-2_7 |
Talks, invited
A cell-based framework for modeling cardiac mechanics
In International Symposium in honor of Professor Gerhard A. Holzapfel’s 60th birthday, Graz, Austria, 2022.Status: Published
A cell-based framework for modeling cardiac mechanics
The mechanical function of cardiac tissue results from the complex interplay of
contracting cardiomyocytes and the passive extracellular matrix. Most computational
models of cardiac mechanics are based on a continuum approach, where the tissue
is viewed as a continuous and homogeneous mix of cells and extracellular material.
This approach has been successfully applied in numerous studies,
and will undoubtedly remain a cornerstone of computational biomechanics.
However, the extensive homogenization limits the models' ability to give detailed
insight into the mechanical forces experienced by individual cardiac cells, and
to delineate the mechanical contributions of myocytes and the extracellular matrix.
More detailed models exist, in the form of continuum mechanics models
of individual myocytes, but these are typically limited to a single myocyte and
do not consider the extracellular matrix.
Computational models of cardiac electrophysiology are typically based on the
same continuous and homogenized concept as the mechanics model, with the
bidomain model being the reference model for several decades. More recently,
models have been developed that explicitly represent the cells, the membrane,
and the domain between the cells. The approach is commonly referred to as the EMI
(Extracellular-Membrane-Intracellular) model, and has been applied in
studies of cardiac and neuronal electrophysiology. Natural extensions of the
EMI framework include detailed models of intra- and extracellular ion concentrations
and electro-diffusion, as well as coupling to models for cell contraction and mechanics.
We present a mechanical analogue of the EMI model, i.e., a continuum based
cardiac mechanics model that explicitly represents a three-dimensional network
of cells embedded in an extracellular matrix. Both the intra- and extracellular domains
are modeled as hyperelastic, with constitutive models based based on
the Holzapfel-Ogden model for passive myocardium. The two domains
have different passive mechanical properties, and the intracellular domain is
actively contracting while the extracellular domain is completely passive.
The active contraction is incorporated through a so-called active strain model,
and in this first version of the model it is assumed to be synchronous and homogeneous
across the entire intracellular domain. The model was parameterized using
publicly available experimental data for stretching and shear experiments,
and was used in preliminary explorations of mechanical interactions between
the intra- and extracellular domains. In particular, we studied how myocyte
stress and strain are affected by the mechanical properties of the two domains,
during passive stretching and active contraction. The results show considerable
spatial variations in both stress and strain, and indicate that the detailed
geometrical representation of the cells may give improved insight into certain
mechanisms of biomechanics and mechano-biology. Further development of
the model should include a more detailed exploration of material parameters,
cell geometry, and the mechanical coupling between the cells and the surrounding
matrix, as well as extending the framework to consider inhomogeneous contraction
and potentially coupling of contraction to cell electrophysiology and calcium diffusion.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Talks, invited |
Year of Publication | 2022 |
Location of Talk | International Symposium in honor of Professor Gerhard A. Holzapfel’s 60th birthday, Graz, Austria |
A mechanistic approach towards personalized treatment in patients with atrial fibrillation
In University Heart & Vascular Center Hamburg - UKE, 2022.Status: Published
A mechanistic approach towards personalized treatment in patients with atrial fibrillation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, PARIS |
Publication Type | Talks, invited |
Year of Publication | 2022 |
Location of Talk | University Heart & Vascular Center Hamburg - UKE |
Poster
A computational model of right ventricular remodelling in the presence of pulmonary arterial hypertension
In Biophysical Journal. Biophysical Society Annual Meeting, San Francisco, California, USA: Elsevier, 2022.Status: Published
A computational model of right ventricular remodelling in the presence of pulmonary arterial hypertension
During early-stage pulmonary arterial hypertension (PAH), the right ventricle (RV) undergoes anatomical adaptation in the form of a thickened RV free wall, and material adaptation in the form of altered passive stiffness and contractility. The early-stage compensatory adaptations may help to preserve cardiac output but can later evolve into maladaptive remodelling and organ failure. The transition from compensatory to detrimental remodelling remains poorly understood.
Using in vivo hemodynamic and morphological data from normotensive and hypertensive rats, we built idealized bi-ventricular finite element models representing different disease stages. We built a total of eight models, with RV wall thickness based on ex vivo measurements and passive material properties prescribed based on planar biaxial mechanical data obtained from the same animals. A previously developed inverse finite element framework was then used to fit the biventricular models to the in-vivo hemodynamic data, resulting in passive stiffness and contractility optimized to provide the best possible fit with the combined hemodynamic and biaxial data.
Model simulations were then used to study how the presence of PAH affects the stress distribution in the right ventricular free wall, and how wall stress and RV function are altered by the induced changes in morphology, passive stiffness and contractility. Further numerical experiments were conducted to gain insight into the relative contribution of geometric and material adaptation to maintaining RV function in early-stage PAH, as well as the role of the septal wall. Such insights can facilitate a more comprehensive understanding of the compensatory remodeling that occurs during the disease progression.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Poster |
Year of Publication | 2022 |
Secondary Title | Biophysical Journal |
Date Published | 02/2022 |
Publisher | Elsevier |
Place Published | Biophysical Society Annual Meeting, San Francisco, California, USA |
Impact of Rigid Versus Dynamic Boundaries on Computational Fluid Dynamics Predictor of Left Atrial Appendage Thrombus Formation
Computing in Cardiology, 2022.Status: Published
Impact of Rigid Versus Dynamic Boundaries on Computational Fluid Dynamics Predictor of Left Atrial Appendage Thrombus Formation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, PARIS, Simulation of Cardiac Devices and Drugs for In-Silico Testing and Certification (SimCardioTest) |
Publication Type | Poster |
Year of Publication | 2022 |
Place Published | Computing in Cardiology |
Journal Article
Computational cardiac physiology for new modelers: origins, foundations, and future
Acta Physiologica 236 (2022): e13865.Status: Published
Computational cardiac physiology for new modelers: origins, foundations, and future
Mathematical models of the cardiovascular system have come a long way since they were first introduced in the early 19th century. Driven by a rapid development of experimental techniques, numerical methods, and computer hardware, detailed models that describe physical scales from the molecular level up to organs and organ systems have been derived and used for physiological research. Mathematical and computational models can be seen as condensed and quantitative formulations of extensive physiological knowledge and are used for formulating and testing hypotheses, interpreting and directing experimental research, and have contributed substantially to our understanding of cardiovascular physiology. However, in spite of the strengths of mathematics to precisely describe complex relationships and the obvious need for the mathematical and computational models to be informed by experimental data, there still exist considerable barriers between experimental and computational physiological research. In this review, we present a historical overview of the development of mathematical and computational models in cardiovascular physiology, including the current state of the art. We further argue why a tighter integration is needed between experimental and computational scientists in physiology, and point out important obstacles and challenges that must be overcome in order to fully realize the synergy of experimental and computational physiological research.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | Acta Physiologica |
Volume | 236 |
Number | 2 |
Pagination | e13865 |
Publisher | Wiley |
Computational models of ventricular mechanics and adaptation in response to right-ventricular pressure overload
Frontiers in Physiology (2022): 1774.Status: Published
Computational models of ventricular mechanics and adaptation in response to right-ventricular pressure overload
Pulmonary arterial hypertension (PAH) is associated with substantial remodeling of the right ventricle (RV), which may at first be compensatory but at a later stage becomes detrimental to RV function and patient survival. Unlike the left ventricle (LV), the RV remains understudied, and with its thin-walled crescent shape, it is often modeled simply as an appendage of the LV. Furthermore, PAH diagnosis is challenging because it often leaves the LV and systemic circulation largely unaffected. Several treatment strategies such as atrial septostomy, right ventricular assist devices (RVADs) or RV resynchronization therapy have been shown to improve RV function and the quality of life in patients with PAH. However, evidence of their long-term efficacy is limited and lung transplantation is still the most effective and curative treatment option. As such, the clinical need for improved diagnosis and treatment of PAH drives a strong need for increased understanding of drivers and mechanisms of RV growth and remodeling (G&R), and more generally for targeted research into RV mechanics pathology. Computational models stand out as a valuable supplement to experimental research, offering detailed analysis of the drivers and consequences of G&R, as well as a virtual test bench for exploring and refining hypotheses of growth mechanisms. In this review we summarize the current efforts towards understanding RV G&R processes using computational approaches such as reduced-order models, three dimensional (3D) finite element (FE) models, and G&R models. In addition to an overview of the relevant literature of RV computational models, we discuss how the models have contributed to increased scientific understanding and to potential clinical treatment of PAH patients.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | Frontiers in Physiology |
Pagination | 1774 |
Publisher | Frontiers |
Regional Left Ventricular Fiber Stress Analysis for Cardiac Resynchronization Therapy Response
Annals of Biomedical Engineering 51 (2022): 343-351.Status: Published
Regional Left Ventricular Fiber Stress Analysis for Cardiac Resynchronization Therapy Response
Cardiac resynchronization therapy (CRT) is an effective treatment for a subgroup of heart failure (HF) patients, but more than 30% of those selected do not improve after CRT implantation. Imperfect pre-procedural criteria for patient selection and optimization are the main causes of the high non-response rate. In this study, we evaluated a novel measure for assessing CRT response. We used a computational modeling framework to calculate the regional stress of the left ventricular wall of seven CRT patients and seven healthy controls. The standard deviation of regional wall stress at the time of mitral valve closure (SD_MVC) was used to quantify dyssynchrony and com- pared between patients and controls and among the patients. The results show that SD_MVC is significantly lower in controls than patients and correlates with long-term response in patients, based on end-diastolic volume reduction. In contrast to our initial hypothesis, patients with lower SD_MVC respond better to therapy. The patient with the highest SD_MVC was the only non-responder in the patient cohort. The distribution of fiber stress at the beginning of the isovolumetric phase seems to correlate with the degree of response and the use of this measurement could potentially improve selection criteria for CRT implantation. Further studies with a larger cohort of patients are needed to validate these results.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | Annals of Biomedical Engineering |
Volume | 51 |
Pagination | 343–351 |
Date Published | 07/2022 |
Publisher | Springer |
Keywords | Cardiac resynchronization therapy, Computational cardiology, electrophysiology, Heart failure |
URL | https://doi.org/10.1007/s10439-022-03030-y |
DOI | 10.1007/s10439-022-03030-y |
Talks, contributed
Modeling cardiac mechanics using a cell-based framework
In 15th World Congress on Computational Mechanics (WCCM-XV), Yokohama, Japan. 15th World Congress on Computational Mechanics (WCCM-XV), 2022.Status: Published
Modeling cardiac mechanics using a cell-based framework
Cardiac tissue primarily consists of interconnected cardiac cells which contract in a synchronized manner as the heart beats. Most computational models of cardiac tissue, however, homogenize out the individual cells and their surroundings. This approach has been immensely useful for describing cardiac mechanics on an overall level, but gives very limited understanding of the interaction between individual cells and their intermediate surroundings. Several models have been developed for single cells, see e.g. [1, 2]. In this work, we extend the mechanical part of these frameworks to a domain representing multiple cells, allowing us to investigate cell-matrix and cell-cell interactions. We present a mechanical model in which each cell and the extracellular matrix have an explicit geometrical representation, similar to the electrophysiological model presented in [3]. The strain energy functions are defined separately for each of the intracellular and extracellular subdomains, while we assume continuity of displacement and stresses along the membrane. Active tension is only assigned to the intracellular subdomain. For each state, we find an equilibrium solution using the finite element method. We explore passive and active mechanics for a single cell surrounded by an extracellular matrix and for small collections of cells combined into tissue blocks. The explicit geometric representation gives rise to highly varying strain and stress patterns. We show that the extracellular matrix stiffness highly influences the cardiomyocyte stresses during contraction. Through large-scale simulations enabled by high-performance computing, we also demonstrate that our model can be scaled to small collections of cells, resembling small cardiac tissue samples.
[1] Tracqui, T. and Ohayon, J. An integrated formulation of anisotropic force–calcium relations driving spatio-temporal contractions of cardiac myocytes. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences (2009).
[2] Ruiz-Baier, R. Gizzi, A., Rossi, S. Cherubini, C. Laadhari, A. Filippi, S. and Quarteroni, A. Mathematical modelling of active contraction in isolated cardiomyocytes. Mathematical Medicine and Biology (2014).
[3] Tveito, A., Jæger, KH. Kuchta, M. Mardal, K-A. and Rognes, ME. A cell-based framework for numerical modeling of electrical conduction in cardiac tissue. Frontiers in Physics (2017).
\end{thebibliography}
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Talks, contributed |
Year of Publication | 2022 |
Location of Talk | 15th World Congress on Computational Mechanics (WCCM-XV), Yokohama, Japan |
Publisher | 15th World Congress on Computational Mechanics (WCCM-XV) |
Type of Talk | Contributed |
Keywords | cardiomyocyte contraction, cell-based geometries, intracellular and extracellular mechanics, microscale cardiac mechanics |
URL | https://prezi.com/view/uGIK0kQvrZ6G1CNOkc73/ |
Journal Article
A computational study of the effects of tachycardia-induced remodelling on calcium wave propagation in rabbit atrial myocytes
Frontiers in Physiology 12 (2021).Status: Published
A computational study of the effects of tachycardia-induced remodelling on calcium wave propagation in rabbit atrial myocytes
In atrial cardiomyocytes without a well-developed T-tubule system, calcium diffuses from the periphery towards the center creating a centripetal wave pattern. During atrial fibrillation, rapid activation of atrial myocytes induces complex remodelling in diffusion properties that result in failure of calcium to propagate in a fully regenerative manner towards the center; a phenomenon termed ``calcium silencing''. This has been observed in rabbit atrial myocytes after exposure to prolonged rapid pacing. Although experimental studies have pointed to possible mechanisms underlying calcium silencing, their individual effects and relative importance remain largely unknown.
In this study we used computational modelling of the rabbit atrial cardiomyocyte to query the individual effects and combined effects of the proposed mechanisms leading to calcium silencing and abnormal calcium wave propagation. We employed a population of models obtained from a newly developed model of the rabbit atrial myocyte with spatial representation of intracellular calcium handling. We selected parameters in the model that represent experimentally observed cellular remodelling which have been implicated in calcium silencing, and scaled their values in the population to match experimental observations. In particular, we changed the maximum conductances of I_CaL I_NCX, and I_NaK, RyR open probability, RyR density, Serca2a density, and calcium buffering strength. We incorporated remodelling in a population of 16 models by independently varying parameters that reproduce experimentally observed cellular remodelling, and quantified the resulting alterations in calcium dynamics and wave propagation patterns.
The results show a strong effect of I_CaL in driving calcium silencing, with I_NCX, I_NaK, and RyR density also resulting in calcium silencing in some models. Calcium alternans was observed in some models where I_NCX and Serca2a density had been changed. Simultaneously incorporating changes in all remodelled parameters resulted in calcium silencing in all models, indicating the predominant role of decreasing I_CaL in the population phenotype.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | Frontiers in Physiology |
Volume | 12 |
Publisher | Frontiers |
Keywords | calcium waves, computational model, population of models, rabbit atrial cardiomyocyte, spatial calcium dynamics, tachypacing |
Computational Modeling Studies of the Roles of Left Ventricular Geometry, Afterload, and Muscle Contractility on Myocardial Strains in Heart Failure with Preserved Ejection Fraction
Journal of Cardiovascular Translational Research 14 (2021): 1131-1145.Status: Published
Computational Modeling Studies of the Roles of Left Ventricular Geometry, Afterload, and Muscle Contractility on Myocardial Strains in Heart Failure with Preserved Ejection Fraction
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | Journal of Cardiovascular Translational Research |
Volume | 14 |
Pagination | 1131–1145 |
Publisher | Springer |
Nationwide rollout reveals efficacy of epidemic control through digital contact tracing
Nature Communications 12 (2021).Status: Published
Nationwide rollout reveals efficacy of epidemic control through digital contact tracing
Afilliation | Communication Systems, Scientific Computing, Machine Learning |
Project(s) | The Center for Resilient Networks and Applications, Department of Data Science and Knowledge Discovery , Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2021 |
Journal | Nature Communications |
Volume | 12 |
Number | 5918 |
Publisher | Springer Nature |
DOI | 10.1038/s41467-021-26144-8 |
Poster
Assessment of left ventricular mechanics in right ventricular overload using in silico rat models
In European Heart Journal. ESC Congress 2021: Oxford University Press, 2021.Status: Published
Assessment of left ventricular mechanics in right ventricular overload using in silico rat models
Background
To preserve cardiac function in overload conditions, the RV adapts by developing muscular hypertrophy through progressive tissue remodelling. This process may lead to a vicious cycle with detrimental effects on RV diastolic and systolic function, as seen in pulmonary arterial hypertension (PAH) patients. However, how RV overload affects LV function and remodelling remains an open question. Computational models of cardiac physiology offer an opportunity for investigating mechanisms difficult or impossible to analyse otherwise due to the existence of overlapping factors and technical limitations.
Aim
This study aims to assess the acute effects of RV overload and increased myocardial passive stiffness on the LV mechanical properties in an anatomically-based computational model of healthy rat heart.
Methods
A computational simulation pipeline of cardiac mechanics based on the Holzapfel-Ogden model has been implemented using MR images from a healthy rat. Whereas LV function was modelled realistically using catheter measurements conducted on the same subject than the MR imaging, RV function was based on representative literature values for healthy and PAH rats with RV overload. The following cases were defined (Fig. 1): CTRL, with normal RV function; PAH1, with 30% increase in RV ESV (end-systolic volume) and 15% increase in RV ESP (end-systolic pressure) in comparison to CTRL; and PAH2, with 60% increase in RV ESV and 30% increase in RV ESP compared to CTRL. The cardiac cycle was simulated for all cases whilst fitting the experimentally measured LV pressure and volume values from a healthy rat, which allowed quantifying the effects of RV overload on LV function.
Results
The increase of average circumferential strain in the LV correlated with the degree of RV overload simulated (CTRL: −8.7%, PAH1: −8.9%, PAH2: −9.2%), whilst average radial (CTRL: 35.2%, PAH1: 34.8%, PAH2: 30.3%) and longitudinal strains decreased (CTRL: −7.7%, PAH1: −7.4%, PAH2: −6.6%), as seen in Fig.2. However, regional differences in strain were significant: under RV overload conditions, circumferential strain increased in the septum (−3.5% difference in PAH2 vs. CTRL) but lower values were observed in the lateral wall (+1.7% difference in PAH2 vs. CTRL). Cardiac function of case PAH2 was simulated also with increased myocardial passive stiffness (2.67 kPa instead of 1.34 kPa) which presented a mild strain increase in the mid LV ventricle in comparison to PAH2 with normal stiffness (circumferential strain: −0.8%, radial strain: +0.5%, longitudinal strain: −0.2%).
Conclusion
Our study provides mechanistic evidence on how RV overload and increased passive myocardial stiffness causes a redistribution of strain and fibre stress in the LV, which may play a significant role in LV remodelling and function.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Poster |
Year of Publication | 2021 |
Secondary Title | European Heart Journal |
Date Published | 08/2021 |
Publisher | Oxford University Press |
Place Published | ESC Congress 2021 |
URL | https://doi.org/10.1093/eurheartj/ehab724.3074 |
DOI | 10.1093/eurheartj/ehab724.3074 |
Book Chapter
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 |
Journal Article
A computational study on integrated mechanisms of mechano-electric feedback in ischemic arrhythmogenesis
SAGE (2020).Status: Submitted
A computational study on integrated mechanisms of mechano-electric feedback in ischemic arrhythmogenesis
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | SAGE |
Publisher | Clinical Medicine Insights: Cardiology |
A novel computational model of the rabbit atrial cardiomyocyte with spatial calcium dynamics
Frontiers in Physiology 11 (2020): 1205.Status: Published
A novel computational model of the rabbit atrial cardiomyocyte with spatial calcium dynamics
Afilliation | Scientific Computing |
Project(s) | AFib-TrainNet: EU Training Network on Novel Targets and Methods in Atrial Fibrillation, Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Frontiers in Physiology |
Volume | 11 |
Pagination | 1205 |
Publisher | Frontiers |
Multisite pacing and myocardial scars: a computational study
Computer Methods in Biomechanics and Biomedical Engineering 23, no. 6 (2020).Status: Published
Multisite pacing and myocardial scars: a computational study
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 23 |
Issue | 6 |
Date Published | 01/2020 |
Publisher | Taylor and Francis |
ISSN | 1025-5842 |
URL | https://www.tandfonline.com/doi/full/10.1080/10255842.2020.1711885 |
DOI | 10.1080/10255842.2020.1711885 |
Regional Left Ventricular Fiber Stress Analysis for Cardiac Resynchronization Therapy Response
Journal of Cardiovascular Electrophysiology (2020).Status: Submitted
Regional Left Ventricular Fiber Stress Analysis for Cardiac Resynchronization Therapy Response
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Journal of Cardiovascular Electrophysiology |
Publisher | Wiley |
Uncertainty quantification and sensitivity analysis of left ventricular function during the full cardiac cycle
Philosophical Transactions of the Royal Society A 378 (2020): 20190381.Status: Published
Uncertainty quantification and sensitivity analysis of left ventricular function during the full cardiac cycle
Patient-specific computer simulations can be a powerful tool in clinical applications, helping in diagnostics and the development of new treatments. However, its practical use depends on the reliability of the models. The construction of cardiac simulations involves several steps with inherent uncertainties, including model parameters, the generation of personalized geometry and fibre orientation assignment, which are semi-manual processes subject to errors. Thus, it is important to quantify how these uncertainties impact model predictions. The present work performs uncertainty quantification and sensitivity analyses to assess the variability in important quantities of interest (QoI). Clinical quantities are analysed in terms of overall variability and to identify which parameters are the major contributors. The analyses are performed for simulations of the left ventricle function during the entire cardiac cycle. Uncertainties are incorporated in several model parameters, including regional wall thickness, fibre orientation, passive material parameters, active stress and the circulatory model. The results show that the QoI are very sensitive to active stress, wall thickness and fibre direction, where ejection fraction and ventricular torsion are the most impacted outputs. Thus, to improve the precision of models of cardiac mechanics, new methods should be considered to decrease uncertainties associated with geometrical reconstruction, estimation of active stress and of fibre orientation.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2020 |
Journal | Philosophical Transactions of the Royal Society A |
Volume | 378 |
Number | 2173 |
Pagination | 20190381 |
Publisher | The Royal Society Publishing |
ISSN | 1364-503X |
DOI | 10.1098/rsta.2019.0381 |
Book
Introduction to scientific programming with Python
In Simula SpringerBriefs on Computing. Switzerland: Springer , 2020.Status: Published
Introduction to scientific programming with Python
The book provides a first introduction programming for scientific and computational applications using the Python programming language. The presentation is compact and example-based, and is suitable for students and researchers with little or no prior experience in programming. The book uses relevant examples from mathematics and natural sciences to introduce programming as a practical toolbox, that should quickly enable readers to write their own programs for data processing and mathematical modeling. These tools include file reading, plotting, simple text analysis, and using NumPy for numerical computations, which are fundamental building blocks of all programs in data science and computational science. At the same time, readers are introduced to the fundamental concepts of programming, including variables, functions, loops, classes, and object oriented programming. The book therefore gives a good foundation for further studies of computer science and programming.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Book |
Year of Publication | 2020 |
Secondary Title | Simula SpringerBriefs on Computing |
Series Volume | 6 |
Number of Pages | 148 |
Date Published | 08/2020 |
Publisher | Springer |
Place Published | Switzerland |
ISBN | 978-3-030-50356-7 |
ISBN Number | 978-3-030-50355-0 |
URL | springer.com/gp/book/9783030503550 |
DOI | 10.1007/978-3-030-50356-7 |
Talks, contributed
A one-dimensional computational study of mechano-electric feedback and arrhythmogenic current generation
In Gordon Research Conference "Cardiac Arrhythmia Mechanisms", Barga, Italy, 2019.Status: Published
A one-dimensional computational study of mechano-electric feedback and arrhythmogenic current generation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Talks, contributed |
Year of Publication | 2019 |
Location of Talk | Gordon Research Conference "Cardiac Arrhythmia Mechanisms", Barga, Italy |
Journal Article
Arrhythmogenic current generation by myofilament-triggered Ca2+ release and sarcomere heterogeneity
Biophysical Journal 117, no. 12 (2019): 2471-2485.Status: Published
Arrhythmogenic current generation by myofilament-triggered Ca2+ release and sarcomere heterogeneity
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Biophysical Journal |
Volume | 117 |
Issue | 12 |
Pagination | 2471-2485 |
Publisher | Cell Press |
Computational quantification of patient-specific changes in ventricular dynamics associated with pulmonary hypertension
American Journal of Physiology-Heart and Circulatory Physiology 31711911, no. 6 (2019): H1363-H1375.Status: Published
Computational quantification of patient-specific changes in ventricular dynamics associated with pulmonary hypertension
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | American Journal of Physiology-Heart and Circulatory Physiology |
Volume | 31711911 |
Issue | 6 |
Pagination | H1363 - H1375 |
Publisher | American Journal of Physiology |
Effects of left ventricle wall thickness uncertainties on cardiac mechanics
Biomechanics and Modeling in Mechanobiology 18 (2019): 1415-1427.Status: Published
Effects of left ventricle wall thickness uncertainties on cardiac mechanics
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Biomechanics and Modeling in Mechanobiology |
Volume | 18 |
Number | 5 |
Pagination | 1415-1427 |
Publisher | Springer |
Place Published | Berlin Heidelberg |
Sensitivity of stress and strain calculations to passive material parameters in cardiac mechanical models using unloaded geometries
Computer Methods in Biomechanics and Biomedical Engineering 22 (2019): 664-675.Status: Published
Sensitivity of stress and strain calculations to passive material parameters in cardiac mechanical models using unloaded geometries
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 22 |
Number | 6 |
Pagination | 664-675 |
Publisher | Taylor & Francis |
Notes | PMID: 30822148 |
URL | https://doi.org/10.1080/10255842.2019.1579312 |
DOI | 10.1080/10255842.2019.1579312 |
Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response
International Journal for Numerical Methods in Biomedical Engineering 35, no. 5 (2019): e3178.Status: Published
Uncertainty in cardiac myofiber orientation and stiffnesses dominate the variability of left ventricle deformation response
Afilliation | Scientific Computing |
Project(s) | AUQ-PDE: Automated uncertainty quantification for numerical solutions of partial differential equations, Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2019 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 35 |
Issue | 5 |
Pagination | e3178 |
Publisher | Wiley |
Proceedings, refereed
Mechano-electric feedback and arrhythmogenic current generation in a computational model of coupled myocytes
In ICBME2019--YC Fung 100th Birthday Conference. Tech Science Press, 2019.Status: Published
Mechano-electric feedback and arrhythmogenic current generation in a computational model of coupled myocytes
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Proceedings, refereed |
Year of Publication | 2019 |
Conference Name | ICBME2019--YC Fung 100th Birthday Conference |
Publisher | Tech Science Press |
Journal Article
A Centerline-Based Model Morphing Algorithm for Patient-Specific Finite Element Modeling of the Left Ventricle
IEEE Transactions on Biomedical Engineering 65 (2018): 1391-1398.Status: Published
A Centerline-Based Model Morphing Algorithm for Patient-Specific Finite Element Modeling of the Left Ventricle
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | IEEE Transactions on Biomedical Engineering |
Volume | 65 |
Number | 6 |
Pagination | 1391–1398 |
Publisher | IEEE |
DOI | 10.1109/TBME.2017.2754980 |
Computational Modeling of Electrophysiology and Pharmacotherapy of Atrial Fibrillation: Recent Advances and Future Challenges
Frontiers in Physiology 9 (2018): 1221.Status: Published
Computational Modeling of Electrophysiology and Pharmacotherapy of Atrial Fibrillation: Recent Advances and Future Challenges
Afilliation | Scientific Computing |
Project(s) | AFib-TrainNet: EU Training Network on Novel Targets and Methods in Atrial Fibrillation |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | Frontiers in Physiology |
Volume | 9 |
Pagination | 1221 |
Date Published | Apr-09-2018 |
Publisher | Frontiers in Physiology |
URL | https://www.frontiersin.org/article/10.3389/fphys.2018.01221/fullhttps:/... |
DOI | 10.3389/fphys.2018.01221 |
Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization
International Journal for Numerical Methods in Biomedical Engineering 34, no. 7 (2018).Status: Published
Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 34 |
Issue | 7 |
Publisher | John Wiley & Sons |
DOI | 10.1002/cnm.2982 |
In vivo estimation of elastic heterogeneity in an infarcted human heart
Biomechanics and Modeling in Mechanobiology 17, no. 5 (2018): 1317-1329.Status: Published
In vivo estimation of elastic heterogeneity in an infarcted human heart
In myocardial infarction, muscle tissue of the heart is damaged as a result of ceased or severely impaired blood flow. Survivors have an increased risk of further complications, possibly leading to heart failure. Material properties play an important role in determining post-infarction outcome. Due to spatial variation in scarring, material properties can be expected to vary throughout the tissue of a heart after an infarction. In this study we propose a data assimilation technique that can efficiently estimate heterogeneous elastic material properties in a personalized model of cardiac mechanics. The proposed data assimilation is tested on a clinical dataset consisting of regional left ventricular strains and in vivo pressures during atrial systole from a human with a myocardial infarction. Good matches to regional strains are obtained, and simulated equi-biaxial tests are carried out to demonstrate regional heterogeneities in stress–strain relationships. A synthetic data test shows a good match of estimated versus ground truth material parameter fields in the presence of no to low levels of noise. This study is the first to apply adjoint-based data assimilation to the important problem of estimating cardiac elastic heterogeneities in 3-D from medical images.
Afilliation | Scientific Computing |
Project(s) | Department of Numerical Analysis and Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | Biomechanics and Modeling in Mechanobiology |
Volume | 17 |
Issue | 5 |
Pagination | 1317–1329 |
Date Published | May-05-2019 |
Publisher | Springer |
Place Published | Berlin Heidelberg |
ISSN | 1617-7959 |
URL | http://link.springer.com/10.1007/s10237-018-1028-5 |
DOI | 10.1007/s10237-018-1028-5 |
Preconditioned augmented Lagrangian formulation for nearly incompressible cardiac mechanics
International Journal for Numerical Methods in Biomedical Engineering 34 (2018): e2948.Status: Published
Preconditioned augmented Lagrangian formulation for nearly incompressible cardiac mechanics
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2018 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 34 |
Number | 4 |
Pagination | e2948 |
Publisher | Wiley Online Library |
Talks, contributed
A computational study of the contribution of mechano-electric feedback to arrhythmogenic current generation
In Berlin, Germany. Heart by Numbers, Biophysical Society, 2018.Status: Published
A computational study of the contribution of mechano-electric feedback to arrhythmogenic current generation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Talks, contributed |
Year of Publication | 2018 |
Location of Talk | Berlin, Germany |
Publisher | Heart by Numbers, Biophysical Society |
Adjoint Based Data Assimilation for Quantification of Dynamic Mechanical Behavior of the Heart
In World Congress of Biomechanics, New York, USA, 2018.Status: Published
Adjoint Based Data Assimilation for Quantification of Dynamic Mechanical Behavior of the Heart
Afilliation | Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2018 |
Location of Talk | World Congress of Biomechanics, New York, USA |
Poster
A Novel Computational Model of the Rabbit Atrial Myocyte Offers Insight into Calcium Wave Propagation Failure
In Biophysical Journal. Cambridge, USA, 2018.Status: Published
A Novel Computational Model of the Rabbit Atrial Myocyte Offers Insight into Calcium Wave Propagation Failure
Atrial cardiomyocytes have a less well-developed T-tubule system than ventricular cells, resulting in intracellular calcium waves propagating from the membrane to the center via centripetal calcium diffusion. Failure of centripetal calcium-wave propagation (‘calcium silencing’) has been observed in a rabbit model of rapid atrial pacing and in patients with atrial fibrillation, but the underlying mechanisms remain incompletely understood. The goal of this study was to develop a novel computational model of the rabbit atrial cardiomyocyte that incorporates detailed compartmentalization of intracellular calcium dynamics, which can be used to investigate the mechanisms underpinning calcium silencing.
We incorporated ion-current formulations reflecting rabbit electrophysiology into a previously published human atrial cardiomyocyte model. The model was validated with published experimental data and the effects of altered rate of calcium diffusion between the calcium-release-unit space and the cytosol (τdiff) were investigated. τdiff modulates local calcium levels available to activate neighboring calcium-release sites, affecting wave propagation.
Simulation results showed that calcium-wave propagation was highly sensitive to τdiff during normal pacing at 2 Hz. We observed impaired calcium-wave propagation for a range of values of τdiff, with full calcium-wave propagation for values of τdiff exceeding 12.7 ms, and calcium silencing for values of τdiff below 10.6 ms due to insufficient local positive feedback for calcium-induced calcium release to maintain centripetal wave propagation. We also observed calcium alternans between propagating and non-propagating waves for intermediate values of τdiff.
This study provided new insight into the mechanisms of calcium-wave propagation failure in rabbit atrial cardiomyocytes and motivates further investigation of the effects of altered calcium diffusion on wave-propagation abnormalities and calcium-dependent arrhythmogenesis. Moreover, the newly developed model will be a useful tool for studying conditions which permit restoration of normal calcium wave propagation.
Afilliation | Scientific Computing |
Project(s) | AFib-TrainNet: EU Training Network on Novel Targets and Methods in Atrial Fibrillation |
Publication Type | Poster |
Year of Publication | 2018 |
Secondary Title | Biophysical Journal |
Date Published | Jan-02-2018 |
Place Published | Cambridge, USA |
ISSN Number | 00063495 |
URL | https://linkinghub.elsevier.com/retrieve/pii/S0006349517319124https://ap... |
DOI | 10.1016/j.bpj.2017.11.680 |
Adjoint Based Personalization of Mechanical Models for Quantification of Right Ventricular Failure in Pulmonary Hypertension
Heart by Numbers Conference, Berlin, Germany, 2018.Status: Published
Adjoint Based Personalization of Mechanical Models for Quantification of Right Ventricular Failure in Pulmonary Hypertension
Afilliation | Scientific Computing |
Publication Type | Poster |
Year of Publication | 2018 |
Place Published | Heart by Numbers Conference, Berlin, Germany |
Turning the Azimuthal Motions of Adjacent Tropomyosins into a Coupled N-body Problem in a Brownian Model of Cardiac Thin Filament Activation
In Biophysical Journal. San Francisco, California/U.S.A.: Elsevier, 2018.Status: Published
Turning the Azimuthal Motions of Adjacent Tropomyosins into a Coupled N-body Problem in a Brownian Model of Cardiac Thin Filament Activation
Afilliation | Scientific Computing |
Publication Type | Poster |
Year of Publication | 2018 |
Secondary Title | Biophysical Journal |
Publisher | Elsevier |
Place Published | San Francisco, California/U.S.A. |
Book Chapter
Abnormal Tissue Zone Detection and Average Active Stress Estimation in Patients with LV Dysfunction
In Medical and Biological Image Analysis. IntechOpen, 2018.Status: Published
Abnormal Tissue Zone Detection and Average Active Stress Estimation in Patients with LV Dysfunction
Afilliation | Scientific Computing |
Publication Type | Book Chapter |
Year of Publication | 2018 |
Book Title | Medical and Biological Image Analysis |
Publisher | IntechOpen |
Proceedings, refereed
Electromechanical Model to Predict Cardiac Resynchronization Therapy
In 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2018.Status: Published
Electromechanical Model to Predict Cardiac Resynchronization Therapy
Afilliation | Scientific Computing |
Project(s) | MI-RISK: Risk factors for sudden cardiac death during acute myocardial infarction |
Publication Type | Proceedings, refereed |
Year of Publication | 2018 |
Conference Name | 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) |
Pagination | 5446-5459 |
Publisher | IEEE |
DOI | 10.1109/EMBC.2018.8513539 |
Journal Article
A Centerline Based Model Morphing Algorithm for Patient-Specific Finite Element Modelling of the Left Ventricle
IEEE Transactions on Biomedical Engineering (2017).Status: Published
A Centerline Based Model Morphing Algorithm for Patient-Specific Finite Element Modelling of the Left Ventricle
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | IEEE Transactions on Biomedical Engineering |
Date Published | 09/2017 |
Publisher | IEEE |
ISSN | 0018-9294 |
DOI | 10.1109/TBME.2017.2754980 |
A computational framework for testing arrhythmia marker sensitivities to model parameters in functionally calibrated populations of atrial cells
Chaos 27, no. 9 (2017).Status: Published
A computational framework for testing arrhythmia marker sensitivities to model parameters in functionally calibrated populations of atrial cells
Afilliation | Scientific Computing |
Project(s) | AFib-TrainNet: EU Training Network on Novel Targets and Methods in Atrial Fibrillation, Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Chaos |
Volume | 27 |
Issue | 9 |
Publisher | AIP |
DOI | 10.1063/1.4999476 |
An Evaluation of the Accuracy of Classical Models for Computing the Membrane Potential and Extracellular Potential for Neurons
Frontiers in Computational Neuroscience 11 (2017): 27.Status: Published
An Evaluation of the Accuracy of Classical Models for Computing the Membrane Potential and Extracellular Potential for Neurons
Two mathematical models are part of the foundation of Computational neurophysiology; a) the Cable equation is used to compute the membrane potential of neurons, and, b) volume-conductor theory describes the extracellular potential around neurons. In the standard procedure for computing extracellular potentials, the transmembrane currents are computed by means of a) and the extracellular potentials are computed using an explicit sum over analytical point-current source solutions as prescribed by volume conductor theory. Both models are extremely useful as they allow huge simplifications of the computational efforts involved in computing extracellular potentials. However, there are more accurate, though
computationally very expensive, models available where the potentials inside and outside the neurons are computed simultaneously in a self-consistent scheme. In the present work we explore the accuracy of the classical models a) and b) by comparing them to these more accurate schemes.
The main assumption of a) is that the ephaptic current can be ignored in the derivation of the Cable equation. We find, however, for our examples with stylized neurons, that the ephaptic current is comparable in magnitude to other currents involved in the computations, suggesting that it may be significant – at least in parts of the simulation. The magnitude of the error introduced in the membrane potential is several millivolts, and this error also translates into errors in the predicted extracellular potentials. While the error becomes negligible if we assume the extracellular conductivity to be very large, this assumption is, unfortunately, not easy to justify a priori for all situations of interest.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Frontiers in Computational Neuroscience |
Volume | 11 |
Pagination | 27 |
Publisher | Frontiers Media SA |
ISSN | 1662-5188 |
URL | http://journal.frontiersin.org/article/10.3389/fncom.2017.00027 |
DOI | 10.3389/fncom.2017.00027 |
An integrative appraisal of mechano-electric feedback mechanisms in the heart
Progress in biophysics and molecular biology 130 (2017): 404-417.Status: Published
An integrative appraisal of mechano-electric feedback mechanisms in the heart
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Progress in biophysics and molecular biology |
Volume | 130 |
Pagination | 404–417 |
Publisher | Elsevier |
Estimating cardiac contraction through high resolution data assimilation of a personalized mechanical model
Journal of Computational Science 24 (2017): 85-90.Status: Published
Estimating cardiac contraction through high resolution data assimilation of a personalized mechanical model
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Journal of Computational Science |
Volume | 24 |
Pagination | 85-90 |
Publisher | Elsevier |
ISSN | 1877-7503 |
Keywords | Adjoint Method, Cardiac Mechanics, Contractility, Data assimilation, PDE-constrained optimization |
URL | http://www.sciencedirect.com/science/article/pii/S1877750317308190 |
DOI | 10.1016/j.jocs.2017.07.013 |
High resolution data assimilation of cardiac mechanics
International journal for numerical methods in biomedical engineering 33 (2017): e2863.Status: Published
High resolution data assimilation of cardiac mechanics
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | International journal for numerical methods in biomedical engineering |
Volume | 33 |
Number | 11 |
Pagination | e2863 |
Date Published | 04/2017 |
Publisher | John Wiley & Sons, Ltd |
DOI | 10.1002/cnm.2863 |
Talks, contributed
A Computational Model for the Identification of Atrial Stunning Pathways
In 2017 EMI International Conference, 2017.Status: Published
A Computational Model for the Identification of Atrial Stunning Pathways
Afilliation | Scientific Computing |
Project(s) | SysAFib: Systems medicine for diagnosis and stratification of atrial fibrillation, Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2017 |
Location of Talk | 2017 EMI International Conference |
Assessment of regional myocardial work through adjoint-based data assimilation
In Oslo, Norway, 2017.Status: Published
Assessment of regional myocardial work through adjoint-based data assimilation
Assessment of regional myocardial work through adjoint-based data assimilation
Introduction
To achieve efficient pumping of blood to the body, the healthy heart contracts in a synchronous manner. However, heart disease can alter how the heart is activated during a beat, and dyssynchronous contraction can occur, reducing the overall pumping efficiency. Advanced treatments exist for such cases, but selecting patients likely to respond can be challenging. The existing selection criteria, based on organ level measures of activation and contraction, have relatively low specificity. It is therefore of interest to extract new biomarkers to help better identify potential responders. Here we explore one example of a potential biomarker, the regional myocardial work [1], a measure of cardiac efficiency, using a computational model of cardiac mechanics optimized to patient specific data using a high level adjoint based data assimilation method.
Methods
Left ventricular (LV) geometry was obtained from 4D echocardiography, and the segmented chamber was modelled as an incompressible, continuous hyperelastic body described via an transversely isotropic material law[2]. Active force development was modeled through additively decomposing stress into passive and active stresses, the latter added along the cardiac fiber direction, defined by a rule based architecture.
The model was fit to 4D imaging of the LV through the cardiac cycle using an adjoint-based data assimilation technique, which automatically solves for the gradient of the solution with respect to local active stress, for highly efficient minimization of model misfit against collected data. Simulations were optimized both globally and regionally in 17 delineated segments[3]. With these simulations, the amount of mechanical work performed between time point tm and tn could be regionally calculated through -
W(tm, tn) = ∫ S: ∂tE dt = ∑i S(ti-½): dE(ti-½)
where
S(ti-½) = 0.5*(S(ti)+S(ti-1))
and
dE(ti-½) = E(ti)-E(ti-1)
Here subscript t indicates the time point, S is the Second Piola-Kirchhoff stress tensor and E is the Green-Lagrange strain tensor.
Results
We tested the method on healthy control subjects and patients suffering from left bundle branch block (LBBB). The results show an excellent fit between measured and simulated strain (R^2 = 0.8) and volume (R^2 = 1.0). The estimated regional myocardial work, assessed in these segments, shows clear differences between the healthy and diseased patients (e.g Mid Septal longitudinal wasted work ratio[1]: 1.45 (LBBB), 0.24(Healthy)) and can potentially be used as a biomarker to map regional cardiac dysfunction.
References
[1] doi:10.1152/ajpheart.00191.2013
[2] doi:10.1098/rsta.2009.0091
[3] doi:10.1002/cnm.2863
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research |
Publication Type | Talks, contributed |
Year of Publication | 2017 |
Location of Talk | Oslo, Norway |
Type of Talk | International Conference on Computational Science and Engineering, In memory of Hans Petter Langtangen |
URL | https://cseconf2017.files.wordpress.com/2017/09/2017-09-28-cseconf2017-c... |
Integrated Mechanisms of Mechano-Electric feedback in Ischemic Arrhythmogenesis
In Bergen, Norway, 2017.Status: Published
Integrated Mechanisms of Mechano-Electric feedback in Ischemic Arrhythmogenesis
Afilliation | Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2017 |
Location of Talk | Bergen, Norway |
Poster
Integrated Mechanisms of Mechano-Electric Feedback in Ischemic Arrhythmogenesis
Oslo, Norway, 2017.Status: Published
Integrated Mechanisms of Mechano-Electric Feedback in Ischemic Arrhythmogenesis
Afilliation | Scientific Computing |
Publication Type | Poster |
Year of Publication | 2017 |
Date Published | 09/2017 |
Place Published | Oslo, Norway |
Mechanical Analysis of Pulmonary Hypertension via Adjoint based Data Assimilation of a Finite Element Model
Summer Biomechanics, Bioengineering, and Biotransport Conference, Tuscon, USA, 2017.Status: Published
Mechanical Analysis of Pulmonary Hypertension via Adjoint based Data Assimilation of a Finite Element Model
Afilliation | Scientific Computing |
Project(s) | inHeart: In Silico Heart Failure - Tools for Accelerating Biomedical Research, Center for Biomedical Computing (SFF) |
Publication Type | Poster |
Year of Publication | 2017 |
Date Published | 06/2017 |
Place Published | Summer Biomechanics, Bioengineering, and Biotransport Conference, Tuscon, USA |
Journal Article
Adjoint Multi-Start Based Estimation of Cardiac Hyperelastic Material Parameters using Shear Data
Biomechanics and Modeling in Mechanobiology (2016): 1-13.Status: Published
Adjoint Multi-Start Based Estimation of Cardiac Hyperelastic Material Parameters using Shear Data
Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | Biomechanics and Modeling in Mechanobiology |
Pagination | 1-13 |
Date Published | 23.03.2013 |
Publisher | Springer |
An integrated electromechanical-growth heart model for simulating cardiac therapies
Biomechanics and modeling in mechanobiology 15 (2016): 791-803.Status: Published
An integrated electromechanical-growth heart model for simulating cardiac therapies
An emerging class of models has been developed in recent years to predict cardiac growth and remodeling. We recently developed a cardiac constitutive model that predicts remodeling in response to elevated hemodynamics loading, and a subsequent reversal of the remodeling process when the loading is reduced. Here, we describe the integration of this model to an existing strongly coupled electromechanical model of the heart.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | Biomechanics and modeling in mechanobiology |
Volume | 15 |
Number | 4 |
Pagination | 791–803 |
Publisher | {Springer Berlin Heidelberg |
Methodology for morphometric analysis of modern human contralateral premolars
Journal of Computer Assisted Tomography 40, no. 4 (2016): 617-625.Status: Published
Methodology for morphometric analysis of modern human contralateral premolars
Objective: This study aimed at developing a standard methodology for morphometric analysis and comparison of contralateral human premolar pulp space using microcomputed tomography (micro-CT) and semi- automated software. The primary objective was to establish a method to compare the complex and minute morphological internal volumes of con- tralateral premolar pulp spaces and determine their degree of similarity. The secondary aim was to introduce new methodology for selecting contra- lateral premolars for the study of biomaterials and techniques. Methods: Forty-one intact human premolar pairs (n = 82) extracted from 28 patients were scanned with micro-CT. Quantitative comparative evalua- tion was performed through geometric morphometric deviation analysis of the pulp spaces after mirroring, automatic alignment, and coregistration with semiautomated software. Geometric parameters compared included volume, surface, and surface over volume. Shape deviation analysis of transformed mean distances and root mean square errors was conducted. Results: The geometric parameters of the contralateral premolar pulp spaces had significantly higher similarity coefficients than random pairs (P < 0.001). The shape deviation analysis and transformed mean distances had significantly lower values for contralaterals compared with random pairs (P < 0.001). The contralateral geometries had a statistically signifi- cant narrower distribution in deviation when compared with random pairs (P < 0.001).
Conclusions: We present a methodology that sets a new standard for internal validation of the teeth to be used in ex vivo testing of endodon- tic materials and techniques. It also shows that the resolution of the CT scan is crucial and that studies using cone beam CT cannot be used for such studies.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | Journal of Computer Assisted Tomography |
Volume | 40 |
Issue | 4 |
Pagination | 617-625 |
Publisher | Wolters Kluwer Health |
Physics-based computer simulation of the long-term effects of cardiac regenerative therapies
Technology 4 (2016): 23-29.Status: Published
Physics-based computer simulation of the long-term effects of cardiac regenerative therapies
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2016 |
Journal | Technology |
Volume | 4 |
Number | 01 |
Pagination | 23–29 |
Publisher | {World Scientific Publishing Co./Imperial College Press |
Space-discretization error analysis and stabilization schemes for conduction velocity in cardiac electrophysiology
International Journal for Numerical Methods in Biomedical Engineering 32 (2016).Status: Published
Space-discretization error analysis and stabilization schemes for conduction velocity in cardiac electrophysiology
The paper discusses spatial discretization techniques for the bidomain model of cardiac electrophysiology. A detailed error analysis for the conduction velocity is presented, which shed light on several questions and previous result in the literature concerning mass lumping and current interpolation methodologies. Based on the results of the analysis, we introduce a stabilized scheme with artificial conductivity, which tends to correct the conduction velocity on coarse grids. Finally, a weighted mass lumping scheme is shown to be super-convergent on uniform grids.
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 |
Volume | 32 |
Number | 10 |
Publisher | Wiley |
DOI | 10.1002/cnm.2762 |
Proceedings, refereed
Comparison of tetrahedral and hexahedral meshes for finite element simulation of cardiac electro-mechanics
In VII European Congress on Computational Methods in Applied Sciences and Engineering. National Technical University of Athens, 2016.Status: Published
Comparison of tetrahedral and hexahedral meshes for finite element simulation of cardiac electro-mechanics
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2016 |
Conference Name | VII European Congress on Computational Methods in Applied Sciences and Engineering |
Publisher | National Technical University of Athens |
Personalized Cardiac Mechanical Model using a High Resolution Contraction Field
In VPH16 Translating VPH to the Clinic, 2016.Status: Published
Personalized Cardiac Mechanical Model using a High Resolution Contraction Field
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2016 |
Conference Name | VPH16 Translating VPH to the Clinic |
Talks, invited
Impact of material parameter uncertainty on stress in patient specific models of the heart
In SIAM Conference on uncertainty quantification, Lausanne, Switzerland, 2016.Status: Published
Impact of material parameter uncertainty on stress in patient specific models of the heart
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2016 |
Location of Talk | SIAM Conference on uncertainty quantification, Lausanne, Switzerland |
Talks, contributed
Impact of material parameter variations on stress in patient specific models of the heart
In World Congress on Computational Mechanics, Seoul, South Korea, 2016.Status: Published
Impact of material parameter variations on stress in patient specific models of the heart
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2016 |
Location of Talk | World Congress on Computational Mechanics, Seoul, South Korea |
Proceedings, non-refereed
Optimization of a Spatially Varying Cardiac Contraction parameter using the Adjoint Method
In FEniCS'16, 2016.Status: Published
Optimization of a Spatially Varying Cardiac Contraction parameter using the Adjoint Method
A cardiac computational model is constrained using clinical measurements such as pressure, volume and regional strain. The problem is formulated as a PDE-constrained optimisation problem where the objective functional represents the misfit between measured and simulated data. The control parameter for the active phase is a spatially varying contraction parameter defined at every vertex in the mesh. This makes gradient calculations using the adjoint approach computationally advantageous over standard finite difference approximations.
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, non-refereed |
Year of Publication | 2016 |
Conference Name | FEniCS'16 |
Keywords | Adjoint Method, Cardiac Mechanics, parameter estimation, PDE-constrained optimization |
Poster
Patient Specific Modeling of Cardiac Mechanics using the Active Strain Formulation
In Geilo Winter School, 2016.Status: Published
Patient Specific Modeling of Cardiac Mechanics using the Active Strain Formulation
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Poster |
Year of Publication | 2016 |
Secondary Title | Geilo Winter School |
Role of Electromechanical Feedback in Mitral Valve Prolapse Arrhythmia
Freiburg, Germany: Conference on Cardiac Mechano-Electric Couping and Arrhythmias, 2016.Status: Published
Role of Electromechanical Feedback in Mitral Valve Prolapse Arrhythmia
Afilliation | Scientific Computing |
Publication Type | Poster |
Year of Publication | 2016 |
Date Published | 09/2016 |
Publisher | Conference on Cardiac Mechano-Electric Couping and Arrhythmias |
Place Published | Freiburg, Germany |
Journal Article
An integrated electromechanical-growth heart model for simulating cardiac therapies
Biomechanics and Modeling in Mechanobiology 15, no. 4 (2015): 791-803.Status: Published
An integrated electromechanical-growth heart model for simulating cardiac therapies
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2015 |
Journal | Biomechanics and Modeling in Mechanobiology |
Volume | 15 |
Issue | 4 |
Pagination | 791-803 |
Publisher | Springer Berlin Heidelberg |
Increased Membrane Capacitance Is the Dominant Mechanism of Stretch-Dependent Conduction Slowing in the Rabbit Heart: a Computational Study
Cellular and Molecular Bioengineering 8, no. 2 (2015): 237-246.Status: Published
Increased Membrane Capacitance Is the Dominant Mechanism of Stretch-Dependent Conduction Slowing in the Rabbit Heart: a Computational Study
Volume loading of the cardiac ventricles is known to slow electrical conduction in the rabbit heart, but the mech- anisms remain unclear. Previous experimental and modeling studies have investigated some of these mechanisms, including stretch-activated membrane currents, reduced gap junctional conductance, and altered cell membrane capacitance. In order to quantify the relative contributions of these mechanisms, we combined a monomain model of rabbit ventricular electrophysiology with a hyperelastic model of passive ventricular mechanics. After a simplied geometric model with prescribed homogeneous deformation had been used to t model parameters and charcterize individual MEF mechanisms, a 3D model of the rabbit left and right ventricles was compared with experimental measurements from optical electrical mapping studies in the isolated rabbit heart. The model was in ated to an end-diastolic pressure of 30 mmHg, resulting in epicardial strains comparable to those measured in the anterior left ventricular free wall. While the e ects of stretch activated channels did alter epicardial conduction velocity, an increase in cellular capacitance was required to explain previously reported experimental results. The new results suggest that for large strains, various mechanisms can combine and produce a biphasic relationship between strain and conduction velocity. However, at the moderate strains generated by high end-diastolic pressure, a stretch- induced increase in myocyte membrane capacitance is the dominant driver of conduction slowing during ventricular volume loading.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2015 |
Journal | Cellular and Molecular Bioengineering |
Volume | 8 |
Issue | 2 |
Pagination | 237-246 |
Publisher |
Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour
Proceedings of the Royal Society A 471 (2015).Status: Published
Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour
Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2015 |
Journal | Proceedings of the Royal Society A |
Volume | 471 |
Date Published | 12/2015 |
Publisher | The Royal Society |
Book Chapter
Bidomain Model: Computation
In Encyclopedia of Applied and Computational Mathematics, 125-128. Springer Berlin Heidelberg, 2015.Status: Published
Bidomain Model: Computation
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2015 |
Book Title | Encyclopedia of Applied and Computational Mathematics |
Pagination | 125-128 |
Date Published | 11/2015 |
Publisher | Springer Berlin Heidelberg |
ISBN Number | 978-3-540-70528-4 |
URL | http://dx.doi.org/10.1007/978-3-540-70529-1_294 |
DOI | 10.1007/978-3-540-70529-1_294 |
Electro-Mechanical Coupling in Cardiac Tissue
In Encyclopedia of Applied and Computational Mathematics. Springer Berlin Heidelberg, 2015.Status: Published
Electro-Mechanical Coupling in Cardiac Tissue
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2015 |
Book Title | Encyclopedia of Applied and Computational Mathematics |
Publisher | Springer Berlin Heidelberg |
ISBN Number | 978-3-540-70528-4 |
URL | http://dx.doi.org/10.1007/978-3-540-70529-1_481 |
DOI | 10.1007/978-3-540-70529-1_481 |
Talks, invited
Computational models of electro-mechanical interactions in the heart
In University of Uppsala, 2015.Status: Published
Computational models of electro-mechanical interactions in the heart
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | University of Uppsala |
Dyssynchronous Left Ventricular Stress Estimation
In Workshop on Advanced Numerical Techniques in Biomedical Computing: Simula Research Laboratory, 2015.Status: Published
Dyssynchronous Left Ventricular Stress Estimation
The heart is a muscular pump that moves approximatly 8,000 litres per day through the human body. It manages to this by a combination of contraction/relaxation along muscle fibers and elastic recoil. These two effects are indistinguishable in a medical image, but can be estimated using a computational model.
In our work we use adjoint based optimization techniques in order to determine muscle contraction and elastic recoil in a patient specific left ventricular geometry based on echocardiography and pressure catheter data. Possible applications of the technique include mechanical stress estimation and hypothesis testing in cardiac resynchronization therapy research.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2015 |
Location of Talk | Workshop on Advanced Numerical Techniques in Biomedical Computing: Simula Research Laboratory |
Talks, contributed
Identifying the Parameters of the Heart: Variational Data Assimilation in Cardiac Mechanics Using Dolfin-Adjoint
In FEniCS '15, Imperial College London, UK, 2015.Status: Published
Identifying the Parameters of the Heart: Variational Data Assimilation in Cardiac Mechanics Using Dolfin-Adjoint
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2015 |
Location of Talk | FEniCS '15, Imperial College London, UK |
Type of Talk | Featured presentation |
Modeling growth and remodeling in heart muscle tissue
In SIAM Conference on Computational Science and Engineering, 2015.Status: Published
Modeling growth and remodeling in heart muscle tissue
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2015 |
Location of Talk | SIAM Conference on Computational Science and Engineering |
Type of Talk | Minisymposium |
Significance of passive material parameters in mechanical models of the heart
In Lugano, Switzerland, 2015.Status: Published
Significance of passive material parameters in mechanical models of the heart
Significance of passive material parameters in mechanical
models of the heart
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2015 |
Location of Talk | Lugano, Switzerland |
Type of Talk | Conference presentation at MALT 2015 |
Poster
Mechano-electric feedback as a source of ectopic activity
In Gordon Research Conference on Arrhythmia Mechanisms, Lucca, Italy. Gordon Research Conference on Arrhythmia Mechanisms, Lucca, Italy, 2015.Status: Published
Mechano-electric feedback as a source of ectopic activity
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Poster |
Year of Publication | 2015 |
Secondary Title | Gordon Research Conference on Arrhythmia Mechanisms, Lucca, Italy |
Date Published | 03/2015 |
Place Published | Gordon Research Conference on Arrhythmia Mechanisms, Lucca, Italy |
Proceedings, refereed
Patient–Specific Parameter Estimation for a Transversely Isotropic Active Strain Model of Left Ventricular Mechanics
In Statistical Atlases and Computational Models of the Heart-Imaging and Modelling Challenges. Springer International Publishing, 2015.Status: Published
Patient–Specific Parameter Estimation for a Transversely Isotropic Active Strain Model of Left Ventricular Mechanics
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2015 |
Conference Name | Statistical Atlases and Computational Models of the Heart-Imaging and Modelling Challenges |
Pagination | 93-104 |
Publisher | Springer International Publishing |
Proceedings, non-refereed
Personalization of a Cardiac Compuational Model using Clinical Measurements
In 28th Nordic Seminar on Computational Mechanics. Vol. 28. Tallin, Estonia: Proceedings of NSCM-28, 2015.Status: Published
Personalization of a Cardiac Compuational Model using Clinical Measurements
Important features in cardiac mechanics that cannot easily be measured in the clinic, can be computed using a computational model that is calibrated to behave in the same way as a patient’s heart. To construct such a model, clinical measurements such as strain, volume and cavity pressure are used to personalize the mechanics of a cardiac computational model. The problem is formulated as a PDE-constrained optimization problem where the minimization functional represents the misfit between the measured and simulated data. The target parameters are material parameters and a spatially varying contraction parameter. The minimization is carried out using a gradient based optimization algorithm and an automatically derived adjoint equation. The method has been tested on synthetic data, and is able to reproduce a prescribed contraction pattern on the left ventricle.
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, non-refereed |
Year of Publication | 2015 |
Conference Name | 28th Nordic Seminar on Computational Mechanics |
Volume | 28 |
Pagination | 47-50 |
Date Published | 10/2015 |
Publisher | Proceedings of NSCM-28 |
Place Published | Tallin, Estonia |
Miscellaneous
Simulations of Heart Function (editorial)
In BioMed Research International. Hindawi Publishing Corporation, 2015.Status: Published
Simulations of Heart Function (editorial)
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Miscellaneous |
Year of Publication | 2015 |
Publisher | Hindawi Publishing Corporation |
Talks, contributed
A Continuum Model for Active Cardiac Muscle
In World congress on Computational Mechanics, Barcelona, Spain, 2014.Status: Published
A Continuum Model for Active Cardiac Muscle
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2014 |
Location of Talk | World congress on Computational Mechanics, Barcelona, Spain |
Keywords | Conference |
Talk, keynote
Computational Models of Electro-Mechanical Interactions in the Heart
In The Nordic Seminar on Computational Mechanics, Stockholm, 2014.Status: Published
Computational Models of Electro-Mechanical Interactions in the Heart
Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talk, keynote |
Year of Publication | 2014 |
Location of Talk | The Nordic Seminar on Computational Mechanics, Stockholm |
Type of Talk | Keynote talk |
Talks, invited
Computational Models of Electro-Mechanical Interactions in the Heart
In Invited mini symposium presentation at the European Conference for Mathematics in Industry, Taormina, Italy., 2014.Status: Published
Computational Models of Electro-Mechanical Interactions in the Heart
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | Invited mini symposium presentation at the European Conference for Mathematics in Industry, Taormina, Italy. |
Keywords | Conference |
Patient Specific Models of Cardiac Electro-Mechanics
In Seminar at Ecole des Mines, St Etienne, France, 2014.Status: Published
Patient Specific Models of Cardiac Electro-Mechanics
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2014 |
Location of Talk | Seminar at Ecole des Mines, St Etienne, France |
Journal Article
Improved Discretisation and Linearisation of Active Tension in Strongly Coupled Cardiac Electro-Mechanics Simulations
Computer Methods in Biomechanics and Biomedical Engineering 17 (2014): 604-15.Status: Published
Improved Discretisation and Linearisation of Active Tension in Strongly Coupled Cardiac Electro-Mechanics Simulations
Mathematical models of cardiac electro-mechanics typically consist of three tightly coupled parts: systems of ordinary differential equations describing electro-chemical reactions and cross-bridge dynamics in the muscle cells, a system of partial differential equations modelling the propagation of the electrical activation through the tissue and a nonlinear elasticity problem describing the mechanical deformations of the heart muscle. The complexity of the mathematical model motivates numerical methods based on operator splitting, but simple explicit splitting schemes have been shown to give severe stability problems for realistic models of cardiac electro-mechanical coupling. The stability may be improved by adopting semi-implicit schemes, but these give rise to challenges in updating and linearising the active tension. In this paper we present an operator splitting framework for strongly coupled electro-mechanical simulations and discuss alternative strategies for updating and linearising the active stress component. Numerical experiments demonstrate considerable performance increases from an update method based on a generalised Rush-Larsen scheme and a consistent linearisation of active stress based on the first elasticity tensor.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2014 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 17 |
Number | 6 |
Pagination | 604-15 |
Publisher |
Stable Time Integration Suppresses Unphysical Oscillations in the Bidomain Model
Frontiers in Physics 2, no. 40 (2014).Status: Published
Stable Time Integration Suppresses Unphysical Oscillations in the Bidomain Model
The bidomain model is a popular model for simulating electrical activity in cardiac tissue. It is a continuum-based model consisting of non-linear ordinary differential equations (ODEs) describing spatially averaged cellular reactions and a system of partial differential equations (PDEs) describing electrodiffusion on tissue level. Because of this multi-scale, ODE/PDE structure of the model, operator-splitting methods that treat the ODEs and PDEs in separate steps are natural candidates as numerical solution methods. Second-order methods can generally be expected to be more effective than first-order methods under normal accuracy requirements. However, the simplest and the most commonly applied second-order method for the PDE step, the Crank-Nicolson (CN) method, may generate unphysical oscillations. In this paper, we investigate the performance of a two-stage, L-stable singly diagonally implicit Runge-Kutta method for solving the PDEs of the bidomain model. Numerical experiments show that the enhanced stability property of this method leads to more physically realistic numerical simulations compared to both the CN and backward Euler methods.
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2014 |
Journal | Frontiers in Physics |
Volume | 2 |
Issue | 40 |
Publisher |
Proceedings, non-refereed
Least Squares Fitting of a Cardiac Hyperelasticity Model Using an Automatically Derived Adjoint Equation
In Proceedings of NSCM-27: the 27th Nordic Seminar on Computational Mechanics. Vol. 27. Drottning Kristinas väg 53: KTH Stockholm Royal Institute of Technology, 2014.Status: Published
Least Squares Fitting of a Cardiac Hyperelasticity Model Using an Automatically Derived Adjoint Equation
A Cardiac hyperelasticity model is successfully calibrated using an adjoint based least squares minimization and synthetic data.
Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, non-refereed |
Year of Publication | 2014 |
Conference Name | Proceedings of NSCM-27: the 27th Nordic Seminar on Computational Mechanics |
Volume | 27 |
Pagination | 272-275 |
Date Published | October |
Publisher | KTH Stockholm Royal Institute of Technology |
Place Published | Drottning Kristinas väg 53 |
Keywords | Conference |
Book Chapter
Patient–Specific Parameter Estimation for a Transversely Isotropic Active Strain Model of Left Ventricular Mechanics
In Lecture Notes in Computer Science, 93-104. Vol. 8896. Springer International Publishing, 2014.Status: Published
Patient–Specific Parameter Estimation for a Transversely Isotropic Active Strain Model of Left Ventricular Mechanics
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2014 |
Book Title | Lecture Notes in Computer Science |
Volume | 8896 |
Pagination | 93–104 |
Publisher | Springer International Publishing |
Proceedings, refereed
3D Heart Modeling With Cellular Automata, Mass-Spring System and CUDA
In Parallel computing technologies. Vol. 7979. Lecture notes in computer science 7979. Springer, 2013.Status: Published
3D Heart Modeling With Cellular Automata, Mass-Spring System and CUDA
The mechanical behavior of the heart is guided by the propagation of an electrical wave, called action potential. Many diseases have multiple effects on both electrical and mechanical cardiac physiology. To support a better understanding of the multi-scale and multi-physics processes involved in physiological and pathological cardiac conditions, a lot of work has been done in developing computational tools to simulate the electro-mechanical behavior of the heart. In this work, we implemented an aplication to mimic the heart tissue behavior, based on cellular automaton, mass-spring system and parallel computing with CUDA. Our application performed 3D simulations in a very short time. In order to assess the simulation results, we compared them with another synthetic model based on well-known partial differential equations(PDE). Preliminary results suggest our application was able to reproduce the PDE results with much less computational effort.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2013 |
Conference Name | Parallel computing technologies |
Volume | 7979 |
Pagination | 296-309 |
Publisher | Springer |
Talks, contributed
Computational Models of Electro-Mechanical Interactions in the Heart
In SIAM conference on computational science and engineering, Boston, 2013.Status: Published
Computational Models of Electro-Mechanical Interactions in the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2013 |
Location of Talk | SIAM conference on computational science and engineering, Boston |
Keywords | Conference |
Evaluation of Cardiac Tissue Engineering Applications Using Strongly Coupled Electromechanical Models of the Left Ventricle
In Computer Methods in Biomechanics and Biomedical Engineering, Utah, 2013.Status: Published
Evaluation of Cardiac Tissue Engineering Applications Using Strongly Coupled Electromechanical Models of the Left Ventricle
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2013 |
Location of Talk | Computer Methods in Biomechanics and Biomedical Engineering, Utah |
Keywords | Internal Seminar, University of Oslo |
Patient-Specific Models of Cardiac Electro-Mechanics
In Federal University of Juiz de Fora, 2013.Status: Published
Patient-Specific Models of Cardiac Electro-Mechanics
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2013 |
Location of Talk | Federal University of Juiz de Fora |
Strongly Coupled Electromechanical Models of the Heart
In Biomechanics and Medical Imaging Mini-Symposium, UCSF, 2013.Status: Published
Strongly Coupled Electromechanical Models of the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2013 |
Location of Talk | Biomechanics and Medical Imaging Mini-Symposium, UCSF |
Keywords | Conference |
Journal Article
Effects of Deformation on Transmural Dispersion of Repolarization Using in Silico Models of Human Left Ventricular Wedge
International Journal for Numerical Methods in Biomedical Engineering 29 (2013): 1323-1337.Status: Published
Effects of Deformation on Transmural Dispersion of Repolarization Using in Silico Models of Human Left Ventricular Wedge
Mechanical deformation affects the electrical activity of the heart through multiple feedback loops. The purpose of this work is to study the effect of deformation on transmural dispersion of repolarization and on surface electrograms using an in silico human ventricular wedge. To achieve this purpose, we developed a strongly coupled electromechanical cell model by coupling a human left ventricle electrophysiology model and an active contraction model reparameterized for human cells. This model was then embedded in tissue simulations on the basis of bidomain equations and nonlinear solid mechanics. The coupled model was used to evaluate effects of mechanical deformation on important features of repolarization and electrograms. Our results indicate an increase in the T-wave amplitude of the surface electrograms in simulations that account for the effects of cardiac deformation. This increased T-wave amplitude can be explained by changes to the coupling between neighboring myocytes, also known as electrotonic effect. The thickening of the ventricular wall during repolarization contributes to the decoupling of cells in the transmural direction, enhancing action potential heterogeneity and increasing both transmural repolarization dispersion and T-wave amplitude of surface electrograms. The simulations suggest that a considerable percentage of the T-wave amplitude (15%) may be related to cardiac deformation.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2013 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 29 |
Number | 12 |
Pagination | 1323-1337 |
Poster
The Effects of Mechanoelectrical Feedback on Conduction Velocity: a Computational Study
Cardiac Physiome Workshop, 2013.Status: Published
The Effects of Mechanoelectrical Feedback on Conduction Velocity: a Computational Study
Mechanical deformation is know to have an influence on the velocity of the electrical conduction in cardiac tissue. Several experimental and computational studies have investigated this and a wide variety of different strain-conduction velocity relationships have been reported. In short, there are increasing, decreasing, constant and biphasic relationships reported. The objective of this study is to develop a computational model that includes multiple mechanoelectrical feedback mechanisms and is capable of reproducing the different strain-conduction velocity relationships reported.
Afilliation | Scientific Computing |
Publication Type | Poster |
Year of Publication | 2013 |
Publisher | Cardiac Physiome Workshop |
Talks, invited
Computational Models of Electro-Mechanical Interactions in the Infarct Injured Heart
In National PhD conference in medical Imaging, Trondheim, Norway, 2012.Status: Published
Computational Models of Electro-Mechanical Interactions in the Infarct Injured Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2012 |
Location of Talk | National PhD conference in medical Imaging, Trondheim, Norway |
Computer Models of Electro-Mechanical Interactions in the Contracting Heart
In Seminar at the Norwegian Defence Research Establishment, 2012.Status: Published
Computer Models of Electro-Mechanical Interactions in the Contracting Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2012 |
Location of Talk | Seminar at the Norwegian Defence Research Establishment |
Computer Models of Electro-Mechanical Interactions in the Contracting Heart
In Workshop on computational models in biomedicine, Federal University of Juiz de Fora, Brazil, 2012.Status: Published
Computer Models of Electro-Mechanical Interactions in the Contracting Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2012 |
Location of Talk | Workshop on computational models in biomedicine, Federal University of Juiz de Fora, Brazil |
Numerical Methods for Strongly Coupled Simulations of Cardiac Electro-Mechanics
In Workshop on efficient solvers in biomedical applications, Graz, Austria, 2012.Status: Published
Numerical Methods for Strongly Coupled Simulations of Cardiac Electro-Mechanics
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2012 |
Location of Talk | Workshop on efficient solvers in biomedical applications, Graz, Austria |
Towards Patient-Specific Models of Strongly Coupled Cardiac Electro-Mechanics
In Cardiac Physiome Workshop, San Diego, 2012.Status: Published
Towards Patient-Specific Models of Strongly Coupled Cardiac Electro-Mechanics
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2012 |
Location of Talk | Cardiac Physiome Workshop, San Diego |
Talks, contributed
Computer Simulations of Electro-Mechanical Interactions in the Heart
In CBC Workshop on Adjoint-Based Methods for Transient Problems: Software and Applications, 2012.Status: Published
Computer Simulations of Electro-Mechanical Interactions in the Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | CBC Workshop on Adjoint-Based Methods for Transient Problems: Software and Applications |
Impact of Mechanical Deformation on Conduction Velocity of Cardiac Tissue
In World Congress on Computational Mechanics, 2012.Status: Published
Impact of Mechanical Deformation on Conduction Velocity of Cardiac Tissue
Impact of mechanical deformation on conduction velocity of cardiac tissue The heart is an electromechanical pump responsible of circulating blood in the body. The contraction of the heart is initiated by an electrical wave which spreads through the tissue. This stimulus triggers a chain of reactions that generates active force and consequently contraction, the so-called excitation-contraction coupling. However, there are several feedback loops that enable mechanical deformation to regulate the electrical activity, commonly referred to as mechano-electric feedback. Some examples of these mechanisms are deformation dependent conductivities, length and tension dependent binding rates, and stretch-activation channels, among others. The relevance of each of these mechanisms and the relationships between them are still poorly understood and need to be further investigated. Computational models that account both excitation-contraction and mechano-electric feedback are called strongly coupled models. These models are very complex and have already demonstrated to be an important tool to test new hypothesis and enhance understanding. Studies have investigated the relations between mechanical deformation and changes on electrical conduction velocity on mammalian ventricles. Some models try to mimic this effect by including deformation dependent conductivity, but, there is no detailed experimental data to support these assumptions. In this work a strongly coupled cardiac electromechanics simulation framework was developed, based on bidomain equations and large deformation theory. The simulations were used to compare different approaches and develop a model capable of better representing the dependency of conduction velocity on mechanical deformation that was reported in recent experimental studies.
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | World Congress on Computational Mechanics |
Keywords | Conference |
Multiple Mechanoelectrical Feedback Mechanisms Affect Conduction Velocity
In CaMo/CMRG Workshop, San Diego, 2012.Status: Submitted
Multiple Mechanoelectrical Feedback Mechanisms Affect Conduction Velocity
Mechanical deformation is know to have an influence on the velocity of the electrical conduction in cardiac tissue. Although this is an acknowledged phenomenon, there is still controversy with respect to the underlying biophysical mechanisms. Several experimental and computational studies have investigated this and a wide variety of different strain-conduction velocity relationships have been reported. In short, there are increasing, decreasing, constant and biphasic relationships reported. The objective of this study is to develop a computational model that includes multiple mechanoelectrical feedback mechanisms and is capable of reproducing different strain-conduction velocity relationships reported on experiments.
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | CaMo/CMRG Workshop, San Diego |
On the Stability of Operator Splitting Schemes for Strongly Coupled Cardiac Electro-Mechanics
In World Congress on Computational Mechanics, Sao Paulo, Brazil, 2012.Status: Published
On the Stability of Operator Splitting Schemes for Strongly Coupled Cardiac Electro-Mechanics
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2012 |
Location of Talk | World Congress on Computational Mechanics, Sao Paulo, Brazil |
Strongly Coupled Simulations of Cardiac Electro-Mechanics
In CBC seminar, 2012.Status: Published
Strongly Coupled Simulations of Cardiac Electro-Mechanics
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 |
Journal Article
Electromechanical Feedback With Reduced Cellular Connectivity Alters Electrical Activity in an Infarct Injured Left Ventricle - a Finite Element Model Study
American Journal of Physiology - Heart and Circulatory Physiology (2012): H206-H214.Status: Published
Electromechanical Feedback With Reduced Cellular Connectivity Alters Electrical Activity in an Infarct Injured Left Ventricle - a Finite Element Model Study
Myocardial infarction (MI) significantly alters the structure and function of the heart. As abnormal strain may drive heart failure and the generation of arrhythmias, we used computational methods to simulate a left ventricle with an MI over the course of a heartbeat to investigate strains and their potential implications to electrophysiology. We created a fully coupled finite element model of myocardial electromechanics consisting of a cellular physiological model, a bidomain electrical diffusion solver, and a nonlinear mechanics solver. A geometric mesh built from magnetic resonance imaging (MRI) measurements of an ovine left ventricle suffering from a surgically induced anteroapical infarct was used in the model, cycled through the cardiac loop of inflation, isovolumic contraction, ejection, and isovolumic relaxation. Stretch-activated currents were added as a mechanism of mechanoelectric feedback. Elevated fiber and cross fiber strains were observed in the area immediately adjacent to the aneurysm throughout the cardiac cycle, with a more dramatic increase in cross fiber strain than fiber strain. Stretch-activated channels decreased action potential (AP) dispersion in the remote myocardium while increasing it in the border zone. Decreases in electrical connectivity dramatically increased the changes in AP dispersion. The role of cross fiber strain in MI-injured hearts should be investigated more closely, since results indicate that these are more highly elevated than fiber strain in the border of the infarct. Decreases in connectivity may play an important role in the development of altered electrophysiology in the high-stretch regions of the heart.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2012 |
Journal | American Journal of Physiology - Heart and Circulatory Physiology |
Number | 302 |
Pagination | H206-H214 |
Date Published | Jan |
Keywords | Workshop |
DOI | 10.1152/ajpheart.00272.2011 |
Uncertainty Analysis of Ventricular Mechanics Using the Probabilistic Collocation Method
IEEE Transactions on Biomedical Engineering 59 (2012): 2171-2179.Status: Published
Uncertainty Analysis of Ventricular Mechanics Using the Probabilistic Collocation Method
Uncertainty and variability in material parameters are fundamental challenges in computational biomechanics. Analyzing and quantifying the resulting uncertainty in computed results with parameter sweeps or Monte Carlo methods has become very computationally demanding. In this paper we consider a stochastic method named the probabilistic collocation method, and investigate its applicability for uncertainty analysis in computing the passive mechanical behaviour of the left ventricle. Specifically, we study the effect of uncertainties in material input parameters upon response properties such as the increase in cavity volume, the elongation of the ventricle, the increase in inner radius, the decrease in wall thickness and the rotation at apex. The numerical simulations conducted herein indicate that the method is well suited for the problem of consideration, and is far more efficient than the Monte Carlo simulation method for obtaining a detailed uncertainty quantification. The numerical experiments also give interesting indications on which material parameters are most critical for accurately determining various global responses.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2012 |
Journal | IEEE Transactions on Biomedical Engineering |
Volume | 59 |
Number | 8 |
Pagination | 2171-2179 |
Date Published | August |
Poster
Multiple Mechanoelectrical Feedback Mechanisms Affect Conduction Velocity
Cardiac Physiome Workshop, 2012.Status: Published
Multiple Mechanoelectrical Feedback Mechanisms Affect Conduction Velocity
Mechanical deformation is know to have an influence on the velocity of the electrical conduction in cardiac tissue. Although this is an acknowledged phenomenon, there is still controversy with respect to the underlying biophysical mechanisms. Several experimental and computational studies have investigated this and a wide variety of different strain-conduction velocity relationships have been reported. In short, there are increasing, decreasing, constant and biphasic relationships reported. The objective of this study is to develop a computational model that includes multiple mechanoelectrical feedback mechanisms and is capable of reproducing different strain-conduction velocity relationships reported on experiments.
Afilliation | Scientific Computing |
Publication Type | Poster |
Year of Publication | 2012 |
Publisher | Cardiac Physiome Workshop |
Talks, invited
Kan Vi Regne Ut Hvordan Hjertet Virker?
In Idefestivalen, University of Oslo, 2011.Status: Published
Kan Vi Regne Ut Hvordan Hjertet Virker?
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | Idefestivalen, University of Oslo |
Strongly Coupled Electro-Mechanics Simulations of the Infarct Injured Heart
In International Conference on Numerical Methods and Applied Mathematics, Greece, 2011.Status: Published
Strongly Coupled Electro-Mechanics Simulations of the Infarct Injured Heart
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | International Conference on Numerical Methods and Applied Mathematics, Greece |
Strongly Coupled Electro-Mechanics Simulations of the Infarct Injured Heart
In Computational Science Seminar, University of Basel, Switzerland, 2011.Status: Published
Strongly Coupled Electro-Mechanics Simulations of the Infarct Injured Heart
Afilliation | Scientific Computing |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | Computational Science Seminar, University of Basel, Switzerland |
Strongly Coupled Electro-Mechanics Simulations of the Infarct Injured Heart
In Workshop on cardiac modeling, Federal University of Juiz de Fora, Brazil, 2011.Status: Published
Strongly Coupled Electro-Mechanics Simulations of the Infarct Injured Heart
Afilliation | Scientific Computing |
Publication Type | Talks, invited |
Year of Publication | 2011 |
Location of Talk | Workshop on cardiac modeling, Federal University of Juiz de Fora, Brazil |
Keywords | Conference |
Proceedings, refereed
A Note on Discontinuous Rate Functions for the Gate Variables in Mathematical Models of Cardiac Cells
In Proceedings of the International Conference on Computational Science, ICCS. Procedia computer science. Elsevier, 2010.Status: Published
A Note on Discontinuous Rate Functions for the Gate Variables in Mathematical Models of Cardiac Cells
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2010 |
Conference Name | Proceedings of the International Conference on Computational Science, ICCS |
Pagination | 945-950 |
Publisher | Elsevier |
ISBN Number | 1877-0509 |
Biomedical and Bioinformatics Challenges to Computer Science
In Proceedings of the International Conference on Computational Science, ICCS. Procedia Computer Science. Elsevier, 2010.Status: Published
Biomedical and Bioinformatics Challenges to Computer Science
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2010 |
Conference Name | Proceedings of the International Conference on Computational Science, ICCS |
Publisher | Elsevier |
ISBN Number | 1877-0509 |
The Development of a New Computational Model for the Electromechanics of the Human Myocyte
In 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2010.Status: Published
The Development of a New Computational Model for the Electromechanics of the Human Myocyte
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2010 |
Conference Name | 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) |
Publisher | IEEE |
ISBN Number | 978-1-4244-4124-2 |
Talks, contributed
Discontinuous Rate Function in Cardiac Cell Models
2010.Status: Published
Discontinuous Rate Function in Cardiac Cell Models
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2010 |
Keywords | Conference |
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 |
Journal Article
A Computationally Efficient Method for Determining the Size and Location of Myocardial Ischemia
IEEE Transactions on Biomedical Engineering 56 (2009): 263-272.Status: Published
A Computationally Efficient Method for Determining the Size and Location of Myocardial Ischemia
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2009 |
Journal | IEEE Transactions on Biomedical Engineering |
Volume | 56 |
Number | 2 |
Pagination | 263-272 |
Date Published | February |
A Second Order Algorithm for Solving Dynamic Cell Membrane Equations
IEEE Transactions on Biomedical Engineering 56 (2009): 2546-2548.Status: Published
A Second Order Algorithm for Solving Dynamic Cell Membrane Equations
This paper describes an extension of the so-called Rush-Larsen scheme, which is a widely used numerical method for solving dynamic models of cardiac cell electrophysiology. The proposed method applies a local linearization of non-linear terms in combination with the analytical solution of linear ordinary differential equations, to obtain a second order accurate numerical scheme. We compare the error and computational load of the second order scheme to the original Rush-Larsen method. For a given error tolerance, the second order method is from nine to 500 times faster than the original scheme, depending on the choice of model and tolerance.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2009 |
Journal | IEEE Transactions on Biomedical Engineering |
Volume | 56 |
Number | 10 |
Pagination | 2546-2548 |
An Unconditionally Stable Second Order Method for the Luo-Rudy 1 Model Used in Simulations of Defibrillation
International Journal of Numerical Analysis and Modeling 6 (2009): 627-641.Status: Published
An Unconditionally Stable Second Order Method for the Luo-Rudy 1 Model Used in Simulations of Defibrillation
Simulations of cardiac defibrillation are associated with considerable numerical challenges. The cell models have traditionally been discretized by first order explicit schemes, which are associated with severe stability issues. The sharp transition layers in the solution call for stable and efficient solvers. We propose a second order accurate numerical method for the Luo-Rudy phase 1 model of electrical activity in a cardiac cell, which provides sequential update of each governing ODE. An \textit{a priori} estimate for the scheme is given, showing that the bounds of the variables typically observed during electric shocks constitute an invariant region for the system, regardless of the time step chosen. Thus the choice of time step is left as a matter of accuracy. Conclusively, we demonstrate the theoretical result by some numerical examples, illustrating second order convergence for the Luo-Rudy 1 model.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2009 |
Journal | International Journal of Numerical Analysis and Modeling |
Volume | 6 |
Number | 4 |
Pagination | 627-641 |
Aproaching Cardiac Modeling Challenges to Computer Science With CellMl-Based Web Tools
Future Generation Computer Systems 26 (2009): 462-470.Status: Published
Aproaching Cardiac Modeling Challenges to Computer Science With CellMl-Based Web Tools
Afilliation | Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2009 |
Journal | Future Generation Computer Systems |
Volume | 26 |
Number | 3 |
Pagination | 462-470 |
Publisher | Elsevier |
Numerical Solution of the Bidomain Equations
Philosophical Transactions of the Royal Society A 367 (2009): 1931-1951.Status: Published
Numerical Solution of the Bidomain Equations
Knowledge of cardiac electrophysiology is e{ffi}ciently formulated in terms of mathematical models. Most of these models are, however, very complex and thus denies direct mathematical reasoning founded on classical and analytical considerations. This is particularly the case for the celebrated bidomain model, developed almost 40 years ago for concurrent analysis of extra- and intracellular electrical activity. Numerical simulations represent an indispensible tool to study electrophysiology based on this model. However, both steep gradients in the solutions and complicated geometries lead to extremely challenging computational problems. The greatest achievement in scienti{fi}c computing over the past 50 year was to enable solution of linear systems of algebraic equations arising from discretizations of partial di{ff}erential equations in an optimal manner; i.e. such that the CPU-e{ff}orts increases linearly in the number of computational nodes. Over the past decade such optimal methods have been introduced in simulation of electrophysiology. This development, together with the development of a{ff}ordable parallel computers, has enabled the solution of the bidomain model combined with accurate cellular models de{fi}ned on realistic geometries. However, in spite of recent progress, the full potential of modern computational methods has yet to be exploited for solution of the bidomain model. It is the purpose of this paper to review the development of numerical methods for solving the bidomain model. The {fi}eld is huge, and we have to restrict our focus to the development after year 2000.
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2009 |
Journal | Philosophical Transactions of the Royal Society A |
Volume | 367 |
Number | 1895 |
Pagination | 1931-1951 |
Date Published | May |
Towards a Computational Method for Imaging the Extracellular Potassium Concentration During Regional Ischemia
Mathematical Biosciences 220 (2009): 118-130.Status: Published
Towards a Computational Method for Imaging the Extracellular Potassium Concentration During Regional Ischemia
Afilliation | Scientific Computing, , Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2009 |
Journal | Mathematical Biosciences |
Volume | 220 |
Number | 2 |
Pagination | 118-130 |
DOI | 10.1016/j.mbs.2009.05.004 |
Proceedings, refereed
A Two Dimensional Model of Coupled Electromechanics in Cardiac Tissue
In Proceedings of the World Congress on Medical Physics and Biomedical Engineering. Springer, 2009.Status: Published
A Two Dimensional Model of Coupled Electromechanics in Cardiac Tissue
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2009 |
Conference Name | Proceedings of the World Congress on Medical Physics and Biomedical Engineering |
Publisher | Springer |
ISBN Number | 978-3-642-03881-5 |
Bioinformatics' Challenges to Computer Science: Bioinformatics Tools and Biomedical Modeling
In Proceedings of the International Conference on Computational Science, ICCS. Lecture notes in computational science. Springer, 2009.Status: Published
Bioinformatics' Challenges to Computer Science: Bioinformatics Tools and Biomedical Modeling
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2009 |
Conference Name | Proceedings of the International Conference on Computational Science, ICCS |
Publisher | Springer |
ISBN Number | 978-3-642-01969-2 |
Uncertainty Analysis of the Mechanics of the Heart
In Proceedings of the Twenty Second Nordic Seminar on Computational Mechanics. DCE Technical Memorandum. Aalborg University. Department of Civil Engineering, 2009.Status: Published
Uncertainty Analysis of the Mechanics of the Heart
Afilliation | Scientific Computing, Scientific Computing, , Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2009 |
Conference Name | Proceedings of the Twenty Second Nordic Seminar on Computational Mechanics |
Publisher | Aalborg University. Department of Civil Engineering |
ISBN Number | 1901-7278 |
Talks, contributed
Computer Modeling of Cardiac Electro-Mechanics - Models and Numerical Methods
In Talk at Cardiac Modeling seminar, Simula Research Laboratory, 2009.Status: Published
Computer Modeling of Cardiac Electro-Mechanics - Models and Numerical Methods
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2009 |
Location of Talk | Talk at Cardiac Modeling seminar, Simula Research Laboratory |
Multiscale Models of Physiological Systems
In Guest lecture at the course Bioinformatics for molecular biology, University of Oslo, 2009.Status: Published
Multiscale Models of Physiological Systems
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2009 |
Location of Talk | Guest lecture at the course Bioinformatics for molecular biology, University of Oslo |
Simulation of Strongly Coupled Electro-Mechanics in an Infarcted Left Ventricle
In Invited talk at the workshop Bidomain 2009, University of Graz, 2009.Status: Published
Simulation of Strongly Coupled Electro-Mechanics in an Infarcted Left Ventricle
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2009 |
Location of Talk | Invited talk at the workshop Bidomain 2009, University of Graz |
Book Chapter
Computer Simulations of the Heart
In Simula Research Laboratory - by thinking constantly about it, 259-276. Heidelberg: Springer, 2009.Status: Published
Computer Simulations of the Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2009 |
Book Title | Simula Research Laboratory - by thinking constantly about it |
Chapter | 20 |
Pagination | 259-276 |
Publisher | Springer |
Place Published | Heidelberg |
ISBN Number | 978-3-642-01155-9 |
Scientific Computing: Why - How - What - What's Next
In Simula Research Laboratory - by thinking constantly about it, 237-248. Springer, 2009.Status: Published
Scientific Computing: Why - How - What - What's Next
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2009 |
Book Title | Simula Research Laboratory - by thinking constantly about it |
Chapter | 18 |
Pagination | 237-248 |
Publisher | Springer |
ISBN Number | 978-3-642-01155-9 |
Poster
Electromechanical Modeling of the Infarct Injured Failing Ovine Heart
2009.Status: Published
Electromechanical Modeling of the Infarct Injured Failing Ovine Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Poster |
Year of Publication | 2009 |
Journal Article
A Note on Discontinues Rate Functions for the Gate Variables in Mathematical Models of Cardiac Cells
Procedia Computer Science 1 (2008): 945-950.Status: Published
A Note on Discontinues Rate Functions for the Gate Variables in Mathematical Models of Cardiac Cells
The gating mechanism of ionic channels in cardiac cells is often modeled by ordinary differential equations (ODEs) with voltage dependent rates of change. Some of these rate functions contain discontinuities or singularities, which are not physiologically founded but rather introduced to fit experimental data. Such non-smooth right hand sides of ODEs are associated with potential problems when the equations are solved numerically, in the form of reduced order of accuracy and inconsistent convergence. In this paper we propose to replace the discontinuous rates with smooth versions, by fitting functions of the form introduced by Noble (1962) to the original data found by Ebihara and Johnson (1980). We find that eliminating the discontinuities in the rate functions enables the numerical method to obtain the expected order of accuracy, and has a negligible effect on the kinetics of the membrane model.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2008 |
Journal | Procedia Computer Science |
Volume | 1 |
Number | 1 |
Pagination | 945-950 |
On the Frequency of Automaticity During Ischemia in Simulations Based on Stochastic Perturbations of the Luo-Rudy 1 Model
Computers in Biology and Medicine 38 (2008): 1218-1227.Status: Published
On the Frequency of Automaticity During Ischemia in Simulations Based on Stochastic Perturbations of the Luo-Rudy 1 Model
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2008 |
Journal | Computers in Biology and Medicine |
Volume | 38 |
Pagination | 1218-1227 |
Proceedings, refereed
Bioinformatics' Challenges to Computer Science
In Proceedings of the 8th international conference on Computational Science, Part III. ICCS '08. Springer, 2008.Status: Published
Bioinformatics' Challenges to Computer Science
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2008 |
Conference Name | Proceedings of the 8th international conference on Computational Science, Part III |
Pagination | 67-69 |
Publisher | Springer |
ISBN Number | 978-3-540-69383-3 |
DOI | 10.1007/978-3-540-69389-5\_9 |
Talks, contributed
Computational Challenges in Mathematical Models of the Heart
In Talk at Norwegian University of Life Sciences, January 30th, 2008.Status: Published
Computational Challenges in Mathematical Models of the Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2008 |
Location of Talk | Talk at Norwegian University of Life Sciences, January 30th |
Journal Article
A Comparison of Non-Standard Solvers for ODEs Describing Cellular Reactions in the Heart
Computer Methods in Biomechanics and Biomedical Engineering 10 (2007): 317-326.Status: Published
A Comparison of Non-Standard Solvers for ODEs Describing Cellular Reactions in the Heart
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2007 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 10 |
Number | 5 |
Pagination | 317-326 |
Date Published | October |
A Linear System of Partial Differential Equations Modeling the Resting Potential of a Heart With Regional Ischemia
Mathematical Biosciences 210 (2007): 238-252.Status: Published
A Linear System of Partial Differential Equations Modeling the Resting Potential of a Heart With Regional Ischemia
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2007 |
Journal | Mathematical Biosciences |
Volume | 210 |
Number | 1 |
Pagination | 238-252 |
Date Published | November |
An Unconditionally Stable Numerical Method for the Luo-Rudy 1 Model Used in Simulations of Defibrillation
Mathematical Biosciences 208 (2007): 375-392.Status: Published
An Unconditionally Stable Numerical Method for the Luo-Rudy 1 Model Used in Simulations of Defibrillation
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2007 |
Journal | Mathematical Biosciences |
Volume | 208 |
Number | 2 |
Pagination | 375-392 |
Date Published | August |
Talks, contributed
A Finite Element Model of Cardiac Electrophysiology and Mechanics
In VII International conference on computational plasticity, 2007.Status: Published
A Finite Element Model of Cardiac Electrophysiology and Mechanics
Background Computer models of heart function has the potential to become a valuable tool both for medical research and clinical practice. Simulations based on accurate biophysical models increase our understanding of heart physiology and pathology, and may also predict the outcome of therapeutic interventions and drugs. This has been an active research area for decades, but the models, and in particular their application in clinical practice, are still in an early development stage. Unresolved challenges in the field include the extreme complexity of the biological processes involved, and the multiscale nature of the problem, covering processes from molecular level to the complete organ system. Models and methods Passive heart tissue is commonly modeled as a hyperelastic material, which undergoes large deformations during normal heart function. We apply an exponential stress-strain relation, resulting in a strongly non-linear elasticity equation describing the deformations of the muscle. In order to model the actively contracting muscle, the elasticity equation is coupled to systems of ordinary differential equations (ODEs) which describes the electrical activation and active force development in the muscle cells. These systems are in turn coupled to a system of partial differential equations (PDEs) known as the bidomain model, which describes propagation of the electrical signal through the heart muscle. We apply operator splitting to divide the complete model into two separate PDE systems, describing electrophysiology and mechanics on tissue level, and one system of ODEs that describes electro-mechanical coupling on cell level. These individual systems are then discretized in time with implicit schemes of first or second order, and in space with the finite element method. Simple no-flux boundary conditions are applied for the electrophysiology problem, but the mechanics problem is subject to fairly complex dynamic boundary conditions resulting from the interaction with the blood flow. To avoid solving a fluid-structure interaction problem involving the full Navier-Stokes equation for blood flow, we employ a lumped parameter model to describe the circulation. This model is a system of ODEs that describes pressures, volumes and flows through a simplified, closed loop vessel system. When this model is coupled to the finite element model for the heart muscle the result is an index one differential-algebraic (DAE) system, where the algebraic part contains the finite element based electro-mechanics model. We propose to solve the DAE system with a Runge-Kutta method of Radau type, where the time step is automatically adjusted to the different phases of the heart cycle. Results Combining the Radau solver with operator splitting and finite element discretization results in a fairly robust method, which is flexible with respect to changing or replacing individual parts of the model. Initial test results confirm the robustness and convergence of the algorithm, and verifies that the mechanics part of the problem can be solved with good accuracy. The elecrophysiology part, which contains very steep gradients, has still not been solved with the desired accuracy.
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2007 |
Location of Talk | VII International conference on computational plasticity |
Application of Symbolic Finite Element Tools to Nonlinear Hyperelasticity
In Talk at MekIT'07: Fourth National Conference on Computational Mechanics, 2007.Status: Published
Application of Symbolic Finite Element Tools to Nonlinear Hyperelasticity
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2007 |
Location of Talk | Talk at MekIT'07: Fourth National Conference on Computational Mechanics |
Computational Techniques for Heart Muscle Mechanics
In Minisymposium talk at ICIAM 07, Zurich, 2007.Status: Published
Computational Techniques for Heart Muscle Mechanics
The heart occupies the most central role of the cardiovascular system, with the crucial role of supplying a continuous flow of blood through the vast network of vessels composing the circulatory system. Mathematical models of the heart in health and disease is an increasingly important tool for improving our understanding of this vital organ, and thereby help to reduce health problems and costs related to cardiovascular disorders. In this talk we give an overview of computational challenges and techniques related to modelling the mechanical function of the heart muscle. Models applied for this purpose vary in complexity from the simplest pressure-volume relations based on a given time varying elastance, to systems of differential equations that give a detailed description of cardiac electro-mechanical interaction. The primary focus of the talk will be on finite element modeling of the heart muscle, which includes modeling the passive mechanical properties of the tissue as well as the active muscle contraction and its coupling to electrophysiology. The heart muscle is normally modeled as a hyper-elastic material, with strongly non-linear and anisotropic material behavior. The resulting mathematical model consists of a large-strain elasticity equation, which is coupled to DAE systems that describe electro-chemical reactions on cell level, and also to a system of PDEs that describe the conduction of the electrical signal in the tissue. We discuss some approaches for solving this system, which offer a varying degree of coupling and feedback between electrophysiology and mechanics. We also discuss different approaches for coupling the heart muscle models to the rest of the circulatory system. The latter topic will also be covered in more detail in the other talks of the minisymposium.
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2007 |
Location of Talk | Minisymposium talk at ICIAM 07, Zurich |
Software Components for Biomedical Flows
In National seminar on medical technology, NFA (Norsk forening for automatisering), 2007.Status: Published
Software Components for Biomedical Flows
Afilliation | , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2007 |
Location of Talk | National seminar on medical technology, NFA (Norsk forening for automatisering) |
Using Mathematical Models to Test Physiological Hypotheses
In Invited talk at the annual meeting of the Scandinavian Physiological Society, 2007.Status: Published
Using Mathematical Models to Test Physiological Hypotheses
Mathematical models have been used in physiological research for centuries, but they have so far played a less important role than in many other branches of science. Important reasons for this include the extreme complexity and multi-scale nature of biological systems, which makes it challenging both to derive accurate models and to solve the resulting mathematical equations. With the increasing availabilty of powerful computer hardware and numerical software, accompanied by a revolutionary increase of knowledge in molecular biology, this situation is currently about to change. The last ten years in particular, we have seen the advent of increasingly accurate mathematical models of physiological systems, linking biophysical processes across a wide range of spatial and temporal scales. An illustrative example is mathematical models of heart electrophysiology and mechanics, where models have been derived that link processes on cellular and sub-cellular level to the function of the complete organ. Although modeling of other components of the body lags behind that of the cardiovascular system, there is an ongoing development to model other organs and organ systems. Profiled initiatives in this direction include the IUPS Physiome project (http://www.physiome.org.nz) and the Virtual Physiological Human (http://www.europhysiome.org). Although slightly differing in focus, the vision of both these initiatives is to construct advanced computational models of the complete human body, which may be used both for clinical work and as test beds for new physiological hypotheses. In this talk we present a few examples of mathematical models describing physiological phenomena, and how they have been used to verify and quantify physiological and clinical knowledge. The focus will be on mathematical models of the cardiovascular system.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Talks, contributed |
Year of Publication | 2007 |
Location of Talk | Invited talk at the annual meeting of the Scandinavian Physiological Society |
Proceedings, refereed
Application of Symbolic Finite Element Tools to Nonlinear Hyperelasticity
In Fourth national conference on Computational Mechanics (MekIT'07). NO-7005 Trondheim: Tapir Academic Press, 2007.Status: Published
Application of Symbolic Finite Element Tools to Nonlinear Hyperelasticity
The present paper addresses the use of high level languages, symbolic mathematical tools and code generation in an implementation of the finite element method, using a nonlinear hyperelasticity equation as example. Advantages of the software development method that will be demonstrated include closeness to the mathematics, enabling high human efficiency with easy to use high level languages, while still keeping a high computational efficiency by generating tailored inner loop code for the problem at hand. The application we have in mind for the equations presented here is the simulation of the passive elastic properties of heart and blood vessel tissue.
Afilliation | Scientific Computing, , Scientific Computing, Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Proceedings, refereed |
Year of Publication | 2007 |
Conference Name | Fourth national conference on Computational Mechanics (MekIT'07) |
Pagination | 87-101 |
Date Published | May |
Publisher | Tapir Academic Press |
Place Published | NO-7005 Trondheim |
ISBN Number | 978-82-519-2235-7 |
Talks, contributed
Computational Issues in Heart Modeling
In Presented at the Johann Radon Institute for Computational and Applied Mathematics, Linz, Austria, 2006.Status: Published
Computational Issues in Heart Modeling
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2006 |
Location of Talk | Presented at the Johann Radon Institute for Computational and Applied Mathematics, Linz, Austria |
Introduction to Heart Muscle Mechanics-Basic Concepts of Muscle Contraction and Soft Tissue Mechanics.
In Lecture at Svalbard summer school, 2006.Status: Published
Introduction to Heart Muscle Mechanics-Basic Concepts of Muscle Contraction and Soft Tissue Mechanics.
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2006 |
Location of Talk | Lecture at Svalbard summer school |
Notes | European Mathematical Society Summer School Mathematical Modeling of the Heart, Longyearbyen, Svalbard, Norway. Presented by J. Sundnes. |
On the Use of the Bidomain Equations for Computing the Transmembrane Potential Throughout the Heart Wall: an Inverse Problem
In Presented at the Computers in Cardiology conference in Valencia, Spain, 2006.Status: Published
On the Use of the Bidomain Equations for Computing the Transmembrane Potential Throughout the Heart Wall: an Inverse Problem
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2006 |
Location of Talk | Presented at the Computers in Cardiology conference in Valencia, Spain |
Simulating Electrical Activity in the Heart
In Presented at St Jude Medical, Stockholm, Sweeden, 2006.Status: Published
Simulating Electrical Activity in the Heart
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talks, contributed |
Year of Publication | 2006 |
Location of Talk | Presented at St Jude Medical, Stockholm, Sweeden |
Simulations of Reentrant Arrhythmias in the Heart, and Defibrillation As a Treatment
In Presented at NADA, KTH, Sweeden, 2006.Status: Published
Simulations of Reentrant Arrhythmias in the Heart, and Defibrillation As a Treatment
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Talks, contributed |
Year of Publication | 2006 |
Location of Talk | Presented at NADA, KTH, Sweeden |
Book
Computing the Electrical Activity in the Heart
Berlin Heidelberg: Springer, 2006.Status: Published
Computing the Electrical Activity in the Heart
This book describes mathematical models and numerical techniques for simulating the electrical activity in the heart. The book gives an introduction to the most important models of the field, followed by a detailed description of numerical techniques for the models. Particular focus is on efficient numerical methods for large scale simulations on both scalar and parallel computers. The results presented in the book will be of particular interest to researchers in bioengineering and computational biology, who face the challenge of solving these complex mathematical models efficiently. The book will also serve as a valuable introduction to a new and exciting field for computational scientists and applied mathematicians.
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Book |
Year of Publication | 2006 |
Publisher | Springer |
Place Published | Berlin Heidelberg |
ISBN Number | 3-540-33432-7 |
Journal Article
On the Computational Complexity of the Bidomain and the Monodomain Models of Electrophysiology
Annals of Biomedical Engineering 34 (2006): 1088-1097.Status: Published
On the Computational Complexity of the Bidomain and the Monodomain Models of Electrophysiology
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2006 |
Journal | Annals of Biomedical Engineering |
Volume | 34 |
Number | 7 |
Pagination | 1088-1097 |
Date Published | July |
Proceedings, refereed
On the Use of the Bidomain Equations for Computing the Transmembrane Potential Throughout the Heart Wall: an Inverse Problem
In Computers in Cardiology 2006. Computers in Cardiology, 2006.Status: Published
On the Use of the Bidomain Equations for Computing the Transmembrane Potential Throughout the Heart Wall: an Inverse Problem
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2006 |
Conference Name | Computers in Cardiology 2006 |
Pagination | 797-800 |
Publisher | Computers in Cardiology |
ISBN Number | 0276-6547 |
Notes | ISSN 0276-6547 |
Talks, contributed
A Mixed FEM for Modeling the Passive Mechanical Properties of the Myocardium
In Talk at the SIAM Conference on Computational Science & Engineering, 2005.Status: Published
A Mixed FEM for Modeling the Passive Mechanical Properties of the Myocardium
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2005 |
Location of Talk | Talk at the SIAM Conference on Computational Science & Engineering |
An Unconditionally Stable Numerical Method for the Luo-Rudy I Model Used in Defibrillation
In Presented at Tulane University, New Orleans, 2005.Status: Published
An Unconditionally Stable Numerical Method for the Luo-Rudy I Model Used in Defibrillation
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2005 |
Location of Talk | Presented at Tulane University, New Orleans |
Notes | Computational science seminar, Tulane University, New Orleans, February 2005. |
Computing the Electrical Activity in the Heart
In Presented at the Department of Mathematics, University of Oslo, 2005.Status: Published
Computing the Electrical Activity in the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2005 |
Location of Talk | Presented at the Department of Mathematics, University of Oslo |
Notes | Popmat seminar, April 2005. |
Kan Man Simulere Et Hjerteslag?
In LAMIS - SOMMERKURS Matematikk - med røtter og vinger, Asker, 2005.Status: Submitted
Kan Man Simulere Et Hjerteslag?
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2005 |
Location of Talk | LAMIS - SOMMERKURS Matematikk - med røtter og vinger, Asker |
Journal Article
A Mixed Finite Element Formulation for a Nonlinear, Transversely Isotropic Material Model for the Cardiac Tissue
Computer Methods in Biomechanics and Biomedical Engineering 8 (2005): 369-379.Status: Published
A Mixed Finite Element Formulation for a Nonlinear, Transversely Isotropic Material Model for the Cardiac Tissue
In this paper we present a mixed finite element method for modeling the passive properties of the myocardium. The passive properties are described by a non-linear, transversely isotropic, hyperelastic material model, and the myocardium is assumed to be almost incompressible. Single-field, pure displacement-based formulations are known to cause numerical difficulties when applied to incompressible or slightly compressible material cases. This paper presents an alternative approach in the form of a mixed formulation, where a separately interpolated pressure field is introduced as a primary unknown in addition to the displacement field. Moreover, a constraint term is included in the formulation to enforce (almost) incompressibility. Numerical results presented in the paper demonstrate the difficulties related to employing a pure displacement-based method, applying a set of physically relevant material parameter values for the cardiac tissue. The same problems are not experienced for the proposed mixed method. We show that the mixed formulation provides reasonable numerical results for compressible as well as nearly incompressible cases, also in situations of large fiber stretches. There is good agreement between the numerical results and the underlying analytical models.
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2005 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 8 |
Number | 6 |
Pagination | 369-379 |
Date Published | December |
An Operator Splitting Method for Solving the Bidomain Equations Coupled to a Volume Conductor Model for the Torso
Mathematical Biosciences 194 (2005): 233-248.Status: Published
An Operator Splitting Method for Solving the Bidomain Equations Coupled to a Volume Conductor Model for the Torso
In this paper we present a numerical method for the bidomain model, which describes the electrical activity in the heart. The model consists of two partial differential equations (PDEs), which are coupled to systems of ordinary differential equations (ODEs) describing electrochemical reactions in the cardiac cells. Many applications require coupling these equations to a third PDE, describing the electrical fields in the torso surrounding the heart. The resulting system is challenging to solve numerically, because of its complexity and very strict resolution requirements in time and space. We propose a method based on operator splitting and a fully coupled discretization of the three PDEs. Numerical experiments show that for simple simulation cases and fine discretizations, the algorithm is second-order accurate in space and time.
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2005 |
Journal | Mathematical Biosciences |
Volume | 194 |
Number | 2 |
Pagination | 233-248 |
Date Published | April |
Simulation of ST Segment Changes During Subendocardial Ischemia Using a Realistic 3-D Cardiac Geometry
IEEE Transactions on Biomedical Engineering 52 (2005): 799-807.Status: Published
Simulation of ST Segment Changes During Subendocardial Ischemia Using a Realistic 3-D Cardiac Geometry
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2005 |
Journal | IEEE Transactions on Biomedical Engineering |
Volume | 52 |
Number | 5 |
Pagination | 799-807 |
Date Published | May |
Solving the Heart Mechanics Equations With Newton and Quasi Newton Methods - a Comparison
Computer Methods in Biomechanics and Biomedical Engineering 8 (2005): 1-8.Status: Published
Solving the Heart Mechanics Equations With Newton and Quasi Newton Methods - a Comparison
The non-linear elasticity equations of heart mechancis are solved while emulating the effects of a propagating activation wave. The dynamics of a 1 cm^3 slab of active cardiac tissue was simulated as the electrical wave traversed the muscular heart wall transmurally. The regular Newton (Newton-Raphson) method was compared to two modified Newton approaches, and also to a third approach that delayed update only of some selected Jacobian elements. In addition, the impact of changing the time step (0.01 ms, 0.1 ms and 1 ms) and the relative nonlinear convergence tolerance (10^-4, 10^-3 and 10^-2) was investigated. Updating the Jacobian only when slow convergence occured was by far the most efficient approach, giving time savings of 83-96%. For each of the four methods, CPU times were reduced by 48-90% when the time step was increased by a factor 10. Increasing the convergence tolerance by the same factor gave time savings of 3-71%. Different combinations of activation wave speed, stress rate and bulk modulus revealed that the fastest method became relatively even faster as stress rate and bulk modulus were decreased, while the activation speed had negligible influence in this respect.
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2005 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 8 |
Number | 1 |
Pagination | 1-8 |
Proceedings, refereed
A Mixed Formulation for Modeling the Mechanical Bahavior of the Heart
In MekIt05 - Third national conference om Computational Mechanics, Trondheim May 11-12. Tapir Academic Press, 2005.Status: Published
A Mixed Formulation for Modeling the Mechanical Bahavior of the Heart
In this paper we present a mixed finite element formulation for modeling the mechanical behavior of the cardiac tissue. The modeling may be divided into a passive and an active part. The passive properties are in this work described by a transversely isotropic, hyperelastic material model. Moreover, the myocardium is assumed to be almost incompressible. In advanced models the active contraction is strongly connected to electro-physiological processes in the muscle cells. In this paper we simplify the active stress contribution by modeling it as a linear function in time. Due to the fact that the heart muscle undergoes large deformations during contraction, both material and geometrical non-linearities must be taken into account in the analysis. Numerical results are presented for different activation patterns applied to a box-shaped test specimen, which represents a piece of the myocardial wall. The proposed mixed method offers reasonable results in the modeling of the mechanical behavior of the test specimen.
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2005 |
Conference Name | MekIt05 - Third national conference om Computational Mechanics, Trondheim May 11-12 |
Pagination | 327-341 |
Date Published | May |
Publisher | Tapir Academic Press |
Numerical Simulations of Cardiac Arrhythmias and Defibrillation
In MekIT'05 - Third national conference on Computational Mechanics, Trondheim, Norway May 11-12. Trondheim: Tapir Academic Press, 2005.Status: Published
Numerical Simulations of Cardiac Arrhythmias and Defibrillation
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2005 |
Conference Name | MekIT'05 - Third national conference on Computational Mechanics, Trondheim, Norway May 11-12 |
Pagination | 135-144 |
Publisher | Tapir Academic Press |
Place Published | Trondheim |
ISBN Number | 82-519-2052-3 |
Technical reports
Non-Linear Elasticity With Applications to Heart Mechanics
Simula Research Laboratory, 2005.Status: Published
Non-Linear Elasticity With Applications to Heart Mechanics
This report gives an introduction to mathematical and numerical modeling of large-deformation elasticity problems. Basic non-linear continuum mechanics is presented along with a set of hyperelastic material models. Two alternative finite element formulations are described for solving such problems, for compressible and almost incompressible materials. Simulation results are presented for both methods. The elasticity solver is employed in simulating the mechanical behavior of the heart. Mathematical models are presented for describing the passive behavior of cardiac tissue and the active force development. Moreover, we show mathematical models and numerical algorithms for simulating the large deformations of the left ventricle during a heart beat.
Afilliation | Scientific Computing |
Project(s) | No Simula project |
Publication Type | Technical reports |
Year of Publication | 2005 |
Number | 2005-16 |
Publisher | Simula Research Laboratory |
Talks, contributed
Challenges in Mathematical Models of the Heart
In Presented at the SIAM Annual meeting, Portland, Oregon, 2004.Status: Published
Challenges in Mathematical Models of the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2004 |
Location of Talk | Presented at the SIAM Annual meeting, Portland, Oregon |
Modelling ST Segment Changes During Myocardial Ischemia
In Presented at the SIAM Conference on the Life Sciences: Portland, Oregon, 2004.Status: Submitted
Modelling ST Segment Changes During Myocardial Ischemia
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2004 |
Location of Talk | Presented at the SIAM Conference on the Life Sciences: Portland, Oregon |
Technical reports
Numerical Modeling of Isotropic, Hyperelastic Materials Undergoing Large Deformations
Simula Research Laboratory, 2004.Status: Published
Numerical Modeling of Isotropic, Hyperelastic Materials Undergoing Large Deformations
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Technical reports |
Year of Publication | 2004 |
Number | 2004-06 |
Publisher | Simula Research Laboratory |
Book Chapter
Block Preconditioning and Systems of PDEs
In Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming, 199-236. Lecture Notes in Computational Science and Engineering. Springer, 2003.Status: Published
Block Preconditioning and Systems of PDEs
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Book Chapter |
Year of Publication | 2003 |
Book Title | Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming |
Secondary Title | Lecture Notes in Computational Science and Engineering |
Pagination | 199-236 |
Publisher | Springer |
Electrical Activity in the Human Heart
In Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming, 401-449. Lecture Notes in Computational Science and Engineering. Springer, 2003.Status: Published
Electrical Activity in the Human Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Book Chapter |
Year of Publication | 2003 |
Book Title | Advanced Topics in Computational Partial Differential Equations - Numerical Methods and Diffpack Programming |
Secondary Title | Lecture Notes in Computational Science and Engineering |
Chapter | 10 |
Pagination | 401-449 |
Publisher | Springer |
Talks, contributed
Computing the Electrical Activity in the Human Heart
In Presented at the European Conference on Numerical Mathematics and Advanced Applications, Prague, Czech Republic, 2003.Status: Published
Computing the Electrical Activity in the Human Heart
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2003 |
Location of Talk | Presented at the European Conference on Numerical Mathematics and Advanced Applications, Prague, Czech Republic |
Computing the Electrical Activity in the Human Heart
In Presented at the Centre of Mathematics for Applications, Oslo, 2003.Status: Published
Computing the Electrical Activity in the Human Heart
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2003 |
Location of Talk | Presented at the Centre of Mathematics for Applications, Oslo |
Computing the Heart
In Presented at the 21st CAD-FEM users' meeting 2003 - International congress on FEM technology, Potsdam, Germany, 2003.Status: Published
Computing the Heart
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2003 |
Location of Talk | Presented at the 21st CAD-FEM users' meeting 2003 - International congress on FEM technology, Potsdam, Germany |
Parallel Algorithms for Simulating the Electrical Activity of the Heart
In Presented at the Dagstuhl seminar Challenges in computational science and engineering, 2003.Status: Published
Parallel Algorithms for Simulating the Electrical Activity of the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2003 |
Location of Talk | Presented at the Dagstuhl seminar Challenges in computational science and engineering |
Notes | Presented by Joakim Sundnes, March 2003. |
Journal Article
Mathematical Models and Numerical Methods for the Forward Problem in Cardiac Electrophysiology
Computing and Visualization in Science 5 (2003): 215-239.Status: Published
Mathematical Models and Numerical Methods for the Forward Problem in Cardiac Electrophysiology
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2003 |
Journal | Computing and Visualization in Science |
Volume | 5 |
Number | 4 |
Pagination | 215-239 |
Proceedings, refereed
Modeling the Electro-Mechanical Behavior of an Infarcted Heart
In Proceedings from MekIT'03, Second national conference on Computational Mechanics. Trondheim, 2003.Status: Published
Modeling the Electro-Mechanical Behavior of an Infarcted Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Proceedings, refereed |
Year of Publication | 2003 |
Conference Name | Proceedings from MekIT'03, Second national conference on Computational Mechanics |
Date Published | 8-9 May |
Place Published | Trondheim |
Journal Article
A Domain Embedding Strategy for Solving the Bidomain Equations on Complicated Geometries
International Journal of Bioelectromagnetism 4 (2002): 53-54.Status: Published
A Domain Embedding Strategy for Solving the Bidomain Equations on Complicated Geometries
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2002 |
Journal | International Journal of Bioelectromagnetism |
Volume | 4 |
Number | 2 |
Pagination | 53-54 |
A Second Order Scheme for Solving the Bidomain and Forward Problem
International Journal of Bioelectromagnetism 4 (2002): 51-52.Status: Published
A Second Order Scheme for Solving the Bidomain and Forward Problem
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2002 |
Journal | International Journal of Bioelectromagnetism |
Volume | 4 |
Number | 2 |
Pagination | 51-52 |
Multigrid Block Preconditioning for a Coupled System of Partial Differential Equations Modeling the Electrical Activity in the Heart
Computer Methods in Biomechanics and Biomedical Engineering 5 (2002).Status: Published
Multigrid Block Preconditioning for a Coupled System of Partial Differential Equations Modeling the Electrical Activity in the Heart
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2002 |
Journal | Computer Methods in Biomechanics and Biomedical Engineering |
Volume | 5 |
Number | 6 |
ODE Solvers for a Stiff System Arising in the Modeling of the Electrical Activity of the Heart
International Journal of Nonlinear Sciences and Numerical Simulation 3 (2002).Status: Published
ODE Solvers for a Stiff System Arising in the Modeling of the Electrical Activity of the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2002 |
Journal | International Journal of Nonlinear Sciences and Numerical Simulation |
Volume | 3 |
Number | 3 |
Talks, contributed
Diffpack Simulation of the Electrical Activity in the Heart
In Invited minisymposium talk at the 20th CAD-FEM User's Meeting, Friedrichshafen, Germany, 2002.Status: Published
Diffpack Simulation of the Electrical Activity in the Heart
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2002 |
Location of Talk | Invited minisymposium talk at the 20th CAD-FEM User's Meeting, Friedrichshafen, Germany |
Notes | Presented by A. M. Bruaset |
PhD Thesis
Numerical Methods for Simulating the Electrical Activity of the Heart
Department of Informatics, University of Oslo, 2002.Status: Published
Numerical Methods for Simulating the Electrical Activity of the Heart
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | PhD Thesis |
Year of Publication | 2002 |
Publisher | Department of Informatics, University of Oslo |
Thesis Type | phd |
Journal Article
Efficient Solution of Ordinary Differential Equations Modeling Electrical Activity in Cardiac Cells
Mathematical Biosciences (2001): 55-72.Status: Published
Efficient Solution of Ordinary Differential Equations Modeling Electrical Activity in Cardiac Cells
Afilliation | Scientific Computing, Scientific Computing |
Publication Type | Journal Article |
Year of Publication | 2001 |
Journal | Mathematical Biosciences |
Pagination | 55-72 |
Talks, contributed
On Numerical Techniques for the Bidomain Model
In Presented at the SIAM Annual meeting, San Diego, California, 2001.Status: Published
On Numerical Techniques for the Bidomain Model
Afilliation | Scientific Computing, Scientific Computing, Scientific Computing |
Publication Type | Talks, contributed |
Year of Publication | 2001 |
Location of Talk | Presented at the SIAM Annual meeting, San Diego, California |
Technical reports
An Investigation of Different Solvers for Stiff ODE Systems
Department of Informatics, University of Oslo, 2000.Status: Published
An Investigation of Different Solvers for Stiff ODE Systems
Publication Type | Technical reports |
Year of Publication | 2000 |
Publisher | Department of Informatics, University of Oslo |
Talks, contributed
Efficient Solution of ODEs Modeling Electrical Activity in Cardiac Cells
In DIFTA seminar, Norwegian University of Science and Technology, 2000.Status: Published
Efficient Solution of ODEs Modeling Electrical Activity in Cardiac Cells
Publication Type | Talks, contributed |
Year of Publication | 2000 |
Location of Talk | DIFTA seminar, Norwegian University of Science and Technology |
Notes | Presented by Joakim Sundnes, October 2000. |
Journal Article
Organ-level validation of a cross-bridge cycling descriptor in a left ventricular finite element model: effects of ventricular loading on myocardial strains
Physiological Reports 5: e13392.Status: Published
Organ-level validation of a cross-bridge cycling descriptor in a left ventricular finite element model: effects of ventricular loading on myocardial strains
Abstract Although detailed cell-based descriptors of cross-bridge cycling have been applied in finite element (FE) heart models to describe ventricular mechanics, these multiscale models have never been tested rigorously to determine if these descriptors, when scaled up to the organ-level, are able to reproduce well-established organ-level physiological behaviors. To address this void, we here validate a left ventricular (LV) FE model that is driven by a cell-based cross-bridge cycling descriptor against key organ-level heart physiology. The LV FE model was coupled to a closed-loop lumped parameter circulatory model to simulate different ventricular loading conditions (preload and afterload) and contractilities. We show that our model is able to reproduce a linear end-systolic pressure volume relationship, a curvilinear end-diastolic pressure volume relationship and a linear relationship between myocardial oxygen consumption and pressureâvolume area. We also show that the validated model can predict realistic LV strain-time profiles in the longitudinal, circumferential, and radial directions. The predicted strain-time profiles display key features that are consistent with those measured in humans, such as having similar peak strains, time-to-peak-strain, and a rapid change in strain during atrial contraction at late-diastole. Our model shows that the myocardial strains are sensitive to not only LV contractility, but also to the LV loading conditions, especially to a change in afterload. This result suggests that caution must be exercised when associating changes in myocardial strain with changes in LV contractility. The methodically validated multiscale model will be used in future studies to understand human heart diseases.
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Journal | Physiological Reports |
Volume | 5 |
Number | 21 |
Pagination | e13392 |
Publisher | Wiley |
Keywords | Cardiac energetics, finite element modeling, left ventricle, myocardial strain |
URL | https://physoc.onlinelibrary.wiley.com/doi/abs/10.14814/phy2.13392 |
DOI | 10.14814/phy2.13392 |
Preconditioned augmented Lagrangian formulation for nearly incompressible cardiac mechanics
International journal for numerical methods in biomedical engineering 34: e2948.Status: Published
Preconditioned augmented Lagrangian formulation for nearly incompressible cardiac mechanics
Afilliation | Scientific Computing |
Publication Type | Journal Article |
Journal | International journal for numerical methods in biomedical engineering |
Volume | 34 |
Number | 4 |
Pagination | e2948 |
Publisher | Wiley |