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43 results on '"Nägel, Arne"'

6. Parareal convergence for 2D unsteady flow around a cylinder

Author

Kreienbuehl, Andreas, Naegel, Arne, Ruprecht, Daniel, Vogel, Andreas, Wittum, Gabriel, and Krause, Rolf

Subjects
Computer Science - Computational Engineering, Finance, and Science, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Numerical Analysis, Mathematics - Numerical Analysis
Abstract

In this technical report we study the convergence of Parareal for 2D incompressible flow around a cylinder for different viscosities. Two methods are used as fine integrator: backward Euler and a fractional step method. It is found that Parareal converges better for the implicit Euler, likely because it under-resolves the fine-scale dynamics as a result of numerical diffusion., Comment: 16 pages, 7 figures

Published
2015

7. Numerical simulation of skin transport using Parareal

Author

Kreienbuehl, Andreas, Naegel, Arne, Ruprecht, Daniel, Speck, Robert, Wittum, Gabriel, and Krause, Rolf

Subjects
Computer Science - Computational Engineering, Finance, and Science, Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Numerical Analysis, Computer Science - Performance, Mathematics - Numerical Analysis
Abstract

In-silico investigation of skin permeation is an important but also computationally demanding problem. To resolve all scales involved in full detail will not only require exascale computing capacities but also suitable parallel algorithms. This article investigates the applicability of the time-parallel Parareal algorithm to a brick and mortar setup, a precursory problem to skin permeation. The C++ library Lib4PrM implementing Parareal is combined with the UG4 simulation framework, which provides the spatial discretization and parallelization. The combination's performance is studied with respect to convergence and speedup. It is confirmed that anisotropies in the domain and jumps in diffusion coefficients only have a minor impact on Parareal's convergence. The influence of load imbalances in time due to differences in number of iterations required by the spatial solver as well as spatio-temporal weak scaling is discussed., Comment: 11 pages, 8 figures

Published
2015
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13. Space and Time Parallel Multigrid for Optimization and Uncertainty Quantification in PDE Simulations

Author

Grasedyck, Lars, Löbbert, Christian, Wittum, Gabriel, Nägel, Arne, Schulz, Volker, Siebenborn, Martin, Krause, Rolf, Benedusi, Pietro, Küster, Uwe, Dick, Björn, Barth, Timothy J., Series editor, Griebel, Michael, Series editor, Keyes, David E., Series editor, Nieminen, Risto M., Series editor, Roose, Dirk, Series editor, Schlick, Tamar, Series editor, Bungartz, Hans-Joachim, editor, Neumann, Philipp, editor, and Nagel, Wolfgang E., editor

Published
2016
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14. Automated Performance Modeling of the UG4 Simulation Framework

Author

Vogel, Andreas, Calotoiu, Alexandru, Nägel, Arne, Reiter, Sebastian, Strube, Alexandre, Wittum, Gabriel, Wolf, Felix, Barth, Timothy J., Series editor, Griebel, Michael, Series editor, Keyes, David E., Series editor, Nieminen, Risto M., Series editor, Roose, Dirk, Series editor, Schlick, Tamar, Series editor, Bungartz, Hans-Joachim, editor, Neumann, Philipp, editor, and Nagel, Wolfgang E., editor

Published
2016
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17. 10,000 Performance Models per Minute – Scalability of the UG4 Simulation Framework

Author

Vogel, Andreas, Calotoiu, Alexandru, Strube, Alexandre, Reiter, Sebastian, Nägel, Arne, Wolf, Felix, Wittum, Gabriel, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Träff, Jesper Larsson, editor, Hunold, Sascha, editor, and Versaci, Francesco, editor

Published
2015
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21. An efficient algorithm for biomechanical problems based on a fully implicit nested Newton solver

Author

Knodel, Markus, Di Stefano, Salvatore, Nägel, Arne, and Grillo, Alfio

Subjects
Applied Mathematics, Mechanical Engineering, Computational Mechanics
Abstract

Numerical simulations of the dynamics of soft biological tissues are highly non-trivial because tissues generally exhibit complex biological response to external and internal actions, including large deformations and remodeling. Combining the advantages of globally implicit approach (GIA) solvers with the general applicability of the semi-implicit General Plasticity Algorithm (GPA), introduced by some of us some years ago, we present a new, efficient plasticity algorithm, which we call Bio Mechanics Basis Plasticity Algorithm (BMBPA). This is fully implicit, based on a nested Newton solver, and naturally suited for massively parallel computations. The Bilby?Kr?ner?Lee (BKL) multiplicative decomposition of the deformation gradient tensor is employed to introduce the unknowns of our model. We distinguish between global and local unknowns, associated with local and global equations, which are connected by means of a resolution function. The BMBPA asks for very few conditions to be applied and thus can be easily employed to solve several types of biological and biomechanical problems. We demonstrate the efficacy of BMBPA by performing two numerical experiments of a monophasic model of fiber-reinforced tissues. In one case, we consider the shear-compression test of a cubic specimen of tissue, while, in the other case, we focus on the unconfined compression test of a cylinder. The BMBPA is capable of solving the deformation and the remodeling of anisotropic biological tissues by employing a computation time of hours, while the GPA, applied to the same problems as the BMBPA, needs a substantially longer amount of time. All computations were performed in parallel and, within all tests, the performance of the BMBPA displayed substantially higher than the one of the GPA. The results of our simulations permit to study the overall mechanical behavior of the considered tissue and enable further investigations in the field of tissue biomechanics.

Published
2022
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29. Editorial

Author

Grillo, Alfio, Krause, Rolf, Lemke, Babett, Nägel, Arne, and Queisser, Gillian

Published
2019
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40. Quantitative analysis of hepatitis C NS5A viral protein dynamics on the ER surface

Author

Knodel, Markus Michael, Nägel, Arne, Reiter, Sebastian, Vogel, Andreas, Targett-Adams, Paul, McLauchlan, John, Herrmann, Eva, Wittum, Gabriel, Knodel, Markus Michael, Nägel, Arne, Reiter, Sebastian, Vogel, Andreas, Targett-Adams, Paul, McLauchlan, John, Herrmann, Eva, and Wittum, Gabriel

Abstract

Exploring biophysical properties of virus-encoded components and their requirement for virus replication is an exciting new area of interdisciplinary virological research. To date, spatial resolution has only rarely been analyzed in computational/biophysical descriptions of virus replication dynamics. However, it is widely acknowledged that intracellular spatial dependence is a crucial component of virus life cycles. The hepatitis C virus-encoded NS5A protein is an endoplasmatic reticulum (ER)-anchored viral protein and an essential component of the virus replication machinery. Therefore, we simulate NS5A dynamics on realistic reconstructed, curved ER surfaces by means of surface partial differential equations (sPDE) upon unstructured grids. We match the in silico NS5A diffusion constant such that the NS5A sPDE simulation data reproduce experimental NS5A fluorescence recovery after photobleaching (FRAP) time series data. This parameter estimation yields the NS5A diffusion constant. Such parameters are needed for spatial models of HCV dynamics, which we are developing in parallel but remain qualitative at this stage. Thus, our present study likely provides the first quantitative biophysical description of the movement of a viral component. Our spatio-temporal resolved ansatz paves new ways for understanding intricate spatial-defined processes central to specfic aspects of virus life cycles.

Published
2018

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