Browsing by Author "Koch, Timo"

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Open Access
Mixed-dimension models for flow and transport processes in porous media with embedded tubular network systems
(Stuttgart: Eigenverlag des Instituts für Wasser- und Umweltsystemmodellierung der Universität Stuttgart, 2020) Koch, Timo; Flemisch, Bernd (apl. Prof. Dr. rer. nat.)
Flow in vascularized biological tissue, root water uptake, or flow around injection or extraction wells can be modeled by coupled mixed-dimensional PDE systems. Conceptually, such systems can be described as porous media with embedded tubular transport networks. We describe numerical methods for the simulation of such systems. The compartments are spatially discretized by non-matching computational grids: a three-dimensional mesh for the porous medium domain, and a geometrically embedded mesh of connected line segments for the network domain. A generalized abstract form of mixed-dimension embedded models is presented which summarizes several existing methods. A particularity of solutions to mixed-dimensional PDEs with dimensional gap two (0D-2D or 1D-3D) is the occurrence of singularities where the network center-lines intersect the porous domain. We introduce a new numerical scheme which removes these singularities by smoothing kernels, and exhibits improved convergence behavior and accuracy for coarse grid resolutions. The method is developed for isotropic, as well as anisotropic porous media. Furthermore, a new mixed-dimension embedded model for tissue perfusion and NMR signal generation is presented. Detailed perfusion simulations on the capillary scale are shown to reproduce image contrast of clinical (organ-scale) MRI data from multiple sclerosis patients. Similar modeling techniques and methods are then used to simulate root water uptake. For the implementation of such applications, a common software framework is developed by use of the open-source simulator DuMux. The framework allows the implementation of coupled mixed- and equidimensional models in a unified way, using software abstractions. Possible framework applications go beyond the methods presented in this work.
Open Access
A new simulation framework for soil-root interaction, evaporation, root growth, and solute transport
(2018) Koch, Timo; Heck, Katharina; Schröder, Natalie; Class, Holger; Helmig, Rainer
We have developed a general model concept and a flexible software framework for the description of plant-scale soil-root interaction processes including the essential fluid mechanical processes in the vadose zone. The model was developed in the framework of non-isothermal, multiphase, multicomponent flow and transport in porous media. The software is an extension of the open-source porous media flow and transport simulator DuMux to embedded mixed-dimensional coupled schemes. Our coupling concept allows us to describe all processes in a strongly coupled form and adapt the complexity of the governing equations in favor of either accuracy or computational efficiency. We have developed the necessary numerical tools to solve the strongly coupled nonlinear partial differential equation systems that arise with a locally mass conservative numerical scheme even in the context of evolving root architectures. We demonstrate the model concept and its features, discussing a virtual hydraulic lift experiment including evaporation, root tracer uptake on a locally refined grid, the simultaneous simulation of root growth and root water uptake, and an irrigation scenario comparing different models for flow in unsaturated soil. We have analyzed the impact of evaporation from soil on the soil water distribution around a single plant’s root system. Moreover, we have shown that locally refined grids around the root system increase computational efficiency while maintaining accuracy. Finally, we demonstrate that the assumptions behind the Richards equation may be violated under certain conditions.
Open Access
Umgang mit Forschungssoftware an der Universität Stuttgart
(2020) Flemisch, Bernd; Hermann, Sibylle; Holm, Christian; Mehl, Miriam; Reina, Guido; Uekermann, Benjamin; Boehringer, David; Ertl, Thomas; Grad, Jean-Noël; Iglezakis, Dorothea; Jaust, Alexander; Koch, Timo; Seeland, Anett; Weeber, Rudolf; Weik, Florian; Weishaupt, Kilian
Wir empfehlen die Einrichtung einer Organisationseinheit Forschungssoftware-Entwicklung an der Universität Stuttgart und eines daran angegliederten Stellenpools von Research Software Engineers (RSEs). Dazu schlagen wir Maßnahmen zur Schaffung und Finanzierung entsprechender neuer RSE-Stellen, zur Integration bestehender Stellen sowie zur Gewinnung und Förderung geeigneter Personen vor. RSEs sind Personen, die sich um Konzeption, Organisation, Implementierung, Testen, Dokumentation und Wartung von Forschungssoftware kümmern. Die institutionelle Förderung von Forschungssoftware-Entwicklung ist notwendig, da die Bedeutung von Software für die Forschung und Anforderungen an die entsprechende Software, u.a. durch die DFG, stetig zunimmt.