Browsing by Author "Maier, Benjamin"

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    Die Finite-Elemente-Methode mit dynamisch-adaptiven kartesischen Gittern
    (2015) Maier, Benjamin
    In dieser Arbeit wird ein zweidimensionales Strömungsproblem, beschrieben durch die Navier-Stokes-Gleichungen, auf einem dynamisch adaptiven Gitter mithilfe der Finite-Elemente-Methode berechnet. Es wird der komplette Ablauf der Berechnung anhand einer Implementierung vorgestellt. Als Datenstruktur werden Quadtrees verwendet, die mit einem bottom-up-Algorithmus nach Sundar et al. parallel erzeugt werden können. Basierend auf der Vorticity wird das Gitter während der Simulation verfeinert oder vergröbert. Es wird die parallele Skalierbarkeit untersucht und für ein reguläres Gitter ein Laufzeitvergleich mit einer Referenzimplementierung ohne Quadtrees durchgeführt.
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    Scalable biophysical simulations of the neuromuscular system
    (2021) Maier, Benjamin; Schulte, Miriam (Prof. Dr.)
    The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer simulations with detailed biophysical models provide a non-invasive tool to interpret EMG signals and gain new insights into the system. The numerical solution of such multi-scale models imposes high computational work loads, which restricts their application to short simulation time spans or coarse resolutions. We tackled this challenge by providing scalable software employing instruction-level and task-level parallelism, suitable numerical methods and efficient data handling. We implemented a comprehensive, state-of-the-art, multi-scale multi-physics model framework that can simulate surface EMG signals and muscle contraction as a result of neuromuscular stimulation. This work describes the model framework and its numerical discretization, develops new algorithms for mesh generation and parallelization, covers the use and implementation of our software OpenDiHu, and evaluates its computational performance in numerous use cases. We obtain a speedup of several hundred compared to a baseline solver from the literature and demonstrate, that our distributed-memory parallelization and the use of High Performance Computing resources enables us to simulate muscular surface EMG of the biceps brachii muscle with realistic muscle fiber counts of several hundred thousands. We find that certain model effects are only visible with such high resolution. In conclusion, our software contributes to more realistic simulations of the neuromuscular system and provides a tool for applied researchers to complement in vivo experiments with in-silico studies. It can serve as a building block to set up comprehensive models for more organs in the musculoskeletal system.