Department of Computational Physiology
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Publications at Department of Computational Physiology
Book Chapter
A Bayesian Approach to Parameter Estimation in Cardiac Mechanics
In Solid (Bio) mechanics: Challenges of the Next Decade, 245-256. 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 |
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. 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 |
Pagination | 121–141 |
Publisher | Springer International Publishing |
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 |
Ordinary Differential Equation-based Modeling of Cells in Human Cartilage
In Computational Physiology, 25-39. Vol. 12. Cham: Springer International Publishing, 2022.Status: Published
Ordinary Differential Equation-based Modeling of Cells in Human Cartilage
Chondrocytes produce the extracellular cartilage matrix required for smooth joint mobility. As cartilage is not vascularised, and chondrocytes are not innervated by the nervous system, chondrocytes are therefore generally considered non-excitable. However, chondrocytes do express a range of ion channels, ion pumps, and receptors involved in cell homeostasis and cartilage maintenance. Dysfunction in these ion channels and pumps has been linked to degenerative disorders such as arthritis. Because the electrophysiological properties of chondrocytes are difficult to measure experimentally, mathematical modelling can instead be used to investigate the regulation of ionic currents. Such models can provide insight into the finely tuned parameters underlying fluctuations in membrane potential and cell behaviour in healthy and pathological conditions. Here, we introduce an open-source, intuitive, and extendable mathematical model of chondrocyte electrophysiology, implementing key proteins involved in regulating the membrane potential. Because of the inherent biological variability of cells and their physiological ranges of ionic concentrations, we describe a population of models that provides a robust computational representation of the biological data. This permits parameter variability in a manner mimicking biological variation, and we present a selection of parameter sets that suitably represent experimental data. Our mathematical model can be used to efficiently investigate the ionic currents underlying chondrocyte behaviour.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Book Chapter |
Year of Publication | 2022 |
Book Title | Computational Physiology |
Volume | 12 |
Pagination | 25 - 39 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-031-05163-0 |
ISBN | 2512-1677 |
URL | https://link.springer.com/chapter/10.1007/978-3-031-05164-7_3#chapter-info |
DOI | 10.1007/978-3-031-05164-7_3 |
3D Simulations of Fetal and Maternal Ventricular Excitation for Investigating the Abdominal ECG
In Computational Physiology Simula Summer School 2021 - Student Reports, 13-24. Vol. 12. Cham: Springer International Publishing, 2022.Status: Published
3D Simulations of Fetal and Maternal Ventricular Excitation for Investigating the Abdominal ECG
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Book Chapter |
Year of Publication | 2022 |
Book Title | Computational Physiology Simula Summer School 2021 - Student Reports |
Volume | 12 |
Pagination | 13 - 24 |
Date Published | 05/2022 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-031-05163-0 |
ISBN | 2512-1677 |
URL | https://doi.org/10.1007/978-3-031-05164-7_2 |
DOI | 10.1007/978-3-031-05164-7_2 |
Conduction Velocity in Cardiac Tissue as Function of Ion Channel Conductance and Distribution
In Computational Physiology - Simula Summer School 2021 − Student Reports, 41-50. Vol. 12. Cham: Springer International Publishing, 2022.Status: Published
Conduction Velocity in Cardiac Tissue as Function of Ion Channel Conductance and Distribution
Ion channels on the membrane of cardiomyocytes regulate the propagation of action potentials from cell to cell and hence are essential for the proper function of the heart. Through computer simulations with the classical monodomain model for cardiac tissue and the more recent extracellular-membrane-intracellular (EMI) model where individual cells are explicitly represented, we investigated how conduction velocity (CV) in cardiac tissue depends on the strength of various ion currents as well as on the spatial distribution of the ion channels. Our simulations show a sharp decrease in CV when reducing the strength of the sodium (Na+) currents, whereas independent reductions in the potassium (K1 and Kr) and L-type calcium currents have negligible effect on the CV. Furthermore, we find that an increase in number density of Na+ channels towards the cell ends increases the CV, whereas a higher number density of K1 channels slightly reduces the CV. These findings contribute to the understanding of ion channels (e.g. Na+ and K+ channels) in the propagation velocity of action potentials in the heart.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Book Chapter |
Year of Publication | 2022 |
Book Title | Computational Physiology - Simula Summer School 2021 − Student Reports |
Volume | 12 |
Chapter | 4 |
Pagination | 41 - 50 |
Date Published | 05/2022 |
Publisher | Springer International Publishing |
Place Published | Cham |
ISBN Number | 978-3-031-05163-0 |
ISBN | 2512-1677 |
Keywords | conduction velocity, EMI model, ion channels |
URL | https://link.springer.com/chapter/10.1007/978-3-031-05164-7_4 |
DOI | 10.1007/978-3-031-05164-7_4 |
Journal Article
Regional Left Ventricular Fiber Stress Analysis for Cardiac Resynchronization Therapy Response
Annals of Biomedical Engineering (2022).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 |
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 |
Resource-efficient use of modern processor architectures for numerically solving cardiac ionic cell models
Frontiers in Physiology 13 (2022).Status: Published
Resource-efficient use of modern processor architectures for numerically solving cardiac ionic cell models
A central component in simulating cardiac electrophysiology is the numerical solution of nonlinear ordinary differential equations, also called cardiac ionic cell models, that describe cross-cell-membrane ion transport. Biophysically detailed cell models often require a considerable amount of computation, including calls to special mathematical functions. This paper systematically studies how to efficiently use modern multicore CPUs for this costly computational task. We start by investigating the code restructurings needed to effectively enable compiler- supported SIMD vectorisation, which is the most important performance booster in this context. It is found that suitable OpenMP directives are sufficient for achieving both vectorisation and parallelisation. We then continue with an evaluation of the performance optimisation technique of using lookup tables. Due to increased challenges for automated vectorisation, the obtainable benefits of lookup tables are dependent on the hardware platforms chosen. Throughout the study, we report detailed time measurements obtained on Intel Xeon, Xeon Phi, AMD Epyc and two ARM processors including Fujitsu A64FX, while attention is also paid to the impact of SIMD vectorisation and lookup tables on the computational accuracy. As a realistic example, the benefits of performance enhancement are demonstrated by a 10^9-run ensemble on the OakForest-PACS system, where code restructurings and SIMD vectorisation yield an 84% reduction in computing time, corresponding to 63,270 node hours.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology, MicroCard: Numerical modeling of cardiac electrophysiology at the cellular scale |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | Frontiers in Physiology |
Volume | 13 |
Date Published | 06/2022 |
Publisher | Frontiers |
ISSN | 1664-042X |
URL | https://www.frontiersin.org/article/10.3389/fphys.2022.904648 |
DOI | 10.3389/fphys.2022.904648 |
Arrhythmogenic influence of mutations in a myocyte‑based computational model of the pulmonary vein sleeve
Nature Scientific Reports 12 (2022): 7040.Status: Published
Arrhythmogenic influence of mutations in a myocyte‑based computational model of the pulmonary vein sleeve
In the heart, electrophysiological dysregulation arises from defects at many biological levels (from point mutations in ion channel proteins to gross structural abnormalities). These defects disrupt the normal pattern of electrical activation, producing ectopic activity and reentrant arrhythmia. To interrogate mechanisms that link these primary biological defects to macroscopic electrophysiologic dysregulation most prior computational studies have utilized either (i) detailed models of myocyte ion channel dynamics at limited spatial scales, or (ii) homogenized models of action potential conduction that reproduce arrhythmic activity at tissue and organ levels. Here we apply our recent model (EMI), which integrates electrical activation and propagation across these scales, to study human atrial arrhythmias originating in the pulmonary vein (PV) sleeves. These small structures initiate most supraventricular arrhythmias and include pronounced myocyte‑to‑myocyte heterogeneities in ion channel expression and intercellular coupling. To test EMI’s cell‑based architecture in this physiological context we asked whether ion channel mutations known to underlie atrial fibrillation are capable of initiating arrhythmogenic behavior via increased excitability or reentry in a schematic PV sleeve geometry. Our results illustrate that EMI’s improved spatial resolution can directly interrogate how electrophysiological changes at the individual myocyte level manifest in tissue and as arrhythmia in the PV sleeve.
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | Nature Scientific Reports |
Volume | 12 |
Pagination | 7040 |
Publisher | Springer Nature |
URL | https://rdcu.be/cMntU |
DOI | 10.1038/s41598-022-11110-1 |
A deep generative model of 3D single-cell organization
PLOS Computational Biology 18 (2022): e1009155.Status: Published
A deep generative model of 3D single-cell organization
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | PLOS Computational Biology |
Volume | 18 |
Number | 1 |
Pagination | e1009155 |
Publisher | {Public Library of Science San Francisco, CA USA |
Artificial intelligence for the detection, prediction, and management of atrial fibrillation
Herzschrittmachertherapie+ Elektrophysiologie (2022): 1-8.Status: Published
Artificial intelligence for the detection, prediction, and management of atrial fibrillation
Afilliation | Scientific Computing |
Project(s) | Department of Computational Physiology |
Publication Type | Journal Article |
Year of Publication | 2022 |
Journal | Herzschrittmachertherapie+ Elektrophysiologie |
Pagination | 1–8 |
Publisher | {Springer Medizin |