timokoch

• Poulain, Stephane; Koch, Timo; Mahadevan, L. & Carlson, Andreas (2026). Viscous adhesion in vibrating sheets: elastohydrodynamics with inertia and compressibility effects. Journal of Fluid Mechanics. ISSN 0022-1120. 1031. doi: 10.1017/jfm.2026.11231. Full text in Research Archive Show summary

  Inspired by recent experiments demonstrating that vibrating elastic sheets can function as seemingly contactless suction cups, we investigate the elastohydrodynamic hovering of a thin elastic sheet vibrating near a wall. Previous theoretical work suggests that the hovering height results from a balance between the active forcing that triggers the vibrations, the bending stresses associated with the sheet’s deformation, the viscous lubrication flow between the sheet and the wall, and the sheet’s weight. Here, we extend this analysis beyond the asymptotic regime of weak forcing and explore the regime of strong forcing through numerical simulations. We identify the scalings for the equilibrium hovering height and the maximum load that can be supported. We further quantify the influence of fluid inertia and compressibility: both effects are found to introduce repulsive contributions to the net force on the sheet, which can significantly reduce its adhesive strength. Beyond providing insights into soft contactless grippers and swimming near surfaces, our analysis is relevant to the elastohydrodynamics of squeeze films and near-field acoustic levitation.

• Riseth, Jørgen Nilsen; Koch, Timo; Lian, Sofie Lysholm; Storås, Tryggve Holck; T., Zikatanov, Ludmil & Valnes, Lars Magnus [Show all 8 contributors for this article] (2026). Human brain MRI data of intrathecally injected tracer evolution over 72 hours for data-integrated simulations. Scientific Data. 13. doi: 10.1038/s41597-026-06564-1. Full text in Research Archive Show summary

  We present the Gonzo dataset: Brain MRI with processed and derivative data from one healthy male human volunteer ("Gonzo”) before and during the 72 hours after intrathecal injection of the contrast agent gadobutrol into the cerebrospinal fluid (CSF) of the spinal canal. The MRI data records include images highlighting the temporal and spatial evolution of the contrast agent in CSF, brain, and adjacent structures. In addition to raw MRI, we provide derivatives that enable numerical simulations of the transport process under study. Derivatives include T1 maps, tracer concentration maps, diffusion tensor maps, and unstructured triangulated volume meshes of the brain geometry. We also provide brain region markers obtained by image segmentation. A regional statistical analysis of the concentration data complements the image data. The presented data can be used to study the transport behavior and the underlying processes of a tracer in the brain. It is intended to contribute to and inspire new studies on the understanding of tracer transport, method development for image analysis, and simulation of brain fluid transport processes.

• Poulain, Stephane; Koch, Timo; Mahadevan, L. & Carlson, Andreas (2025). Hovering of an Actively Driven Fluid-Lubricated Foil. Physical Review Letters. ISSN 0031-9007. 135(21). doi: 10.1103/bs69-16nj. Full text in Research Archive Show summary

  Inspired by recent experimental observations of a harmonically excited elastic foil hovering near a wall while supporting substantial weight, we develop a theoretical framework that describes the underlying physical effects. Using elastohydrodynamic lubrication theory, we quantify how the dynamic deformation of the soft foil couples to the viscous fluid flow in the intervening gap. Our analysis shows that the soft foil rectifies the reversible forcing, breaking time-reversal symmetry; the spatial distribution of the forcing determines whether the sheet is attracted to or repelled from the wall. A simple scaling law predicts the time-averaged equilibrium hovering height and the maximum weight the sheet can sustain before detaching. Numerical simulations of the governing equation corroborate our theoretical predictions, are in qualitative agreement with experiments, and might explain the behavior of organisms while providing design principles for soft robotics.

• Nordbotten, Jan M.; Fernø, Martin; Flemisch, Bernd; Kovscek, Anthony R.; Lie, Knut-Andreas & Both, Jakub W. [Show all 41 contributors for this article] (2025). Benchmarking CO₂ storage simulations: Results from the 11th Society of Petroleum Engineers Comparative Solution Project. International Journal of Greenhouse Gas Control. ISSN 1750-5836. 148. doi: 10.1016/j.ijggc.2025.104519. Full text in Research Archive Show summary

  The 11th Society of Petroleum Engineers Comparative Solution Project (shortened SPE11 herein) benchmarked simulation tools for geological carbon dioxide (CO2) storage. A total of 45 groups from leading research institutions and industry across the globe signed up to participate, with 18 ultimately contributing valid results that were included in the comparative study reported here. This paper summarizes the SPE11 results. A comprehensive introduction and qualitative discussion of the submitted data are provided, together with an overview of online resources for accessing the full depth of data. A global metric for analyzing the relative distance between submissions is proposed and used to conduct a quantitative analysis of the submissions. This analysis attempts to statistically resolve the key aspects influencing the variability between submissions. The study shows that the major qualitative variation between the submitted results is related to thermal effects, dissolution-driven convective mixing, and resolution of facies discontinuities. Moreover, a strong dependence on grid resolution is observed across all three versions of the SPE11. However, our quantitative analysis suggests that the observed variations are predominantly influenced by factors not documented in the technical responses provided by the participants. We therefore identify that unreported variations due to human choices within the process of setting up, conducting, and reporting on the simulations underlying each SPE11 submission are at least as impactful as the computational choices reported.

• Koch, Timo & Mardal, Kent-Andre (2025). Estimation of fluid flow velocities in cortical brain tissue driven by the microvasculature. Interface Focus. ISSN 2042-8898. 15(1). doi: 10.1098/rsfs.2024.0042. Full text in Research Archive Show summary

  We present a modelling framework for describing bulk fluid flow in brain tissue. Within this framework, using computational simulation, we estimate bulk flow velocities in the grey matter parenchyma due to static or slowly varying water potential gradients—hydrostatic pressure gradients and osmotic pressure gradients. Working with the situation that experimental evidence and some model parameter estimates, as we point out, are presently insufficient to estimate velocities precisely, we explore feasible parameter ranges resulting in a range of estimates. We consider the effect of realistic microvascular architecture (extracted from mouse cortical grey matter). Although the estimated velocities are small in magnitude (e.g. in comparison to blood flow velocities), the passive transport of solutes with the bulk fluid can be a relevant process when considering larger molecules transported over larger distances. We compare velocity magnitudes resulting from filtration and pulsations. Filtration can lead to continuous directed fluid flow in the parenchyma, while pulsation-driven flow is (at least partly) reversible. For the first time, we consider the effect of the vascular architecture on the velocity distribution in a tissue sample of ca 1 mm3 cortical grey matter tissue. We conclude that both filtration and pulsations are potentially potent drivers for fluid flow.

• Schneider, Martin & Koch, Timo (2024). Stable and locally mass- and momentum-conservative control-volume finite-element schemes for the Stokes problem. Computer Methods in Applied Mechanics and Engineering. ISSN 0045-7825. 420. doi: 10.1016/j.cma.2023.116723. Full text in Research Archive Show summary

  We introduce new control-volume finite-element discretization schemes suitable for solving the Stokes problem. Within a common framework, we present different approaches for constructing such schemes. The first and most established strategy employs a non-overlapping partitioning into control volumes. The second represents a new idea by splitting into two sets of control volumes, the first set yielding a partition of the domain and the second containing the remaining overlapping control volumes required for stability. The third represents a hybrid approach where finite volumes are combined with finite elements based on a hierarchical splitting of the ansatz space. All approaches are based on typical finite element function spaces but yield locally mass and momentum conservative discretization schemes that can be interpreted as finite volume schemes. We apply all strategies to the inf-sub stable MINI finite-element pair. Various test cases, including convergence tests and the numerical observation of the boundedness of the number of preconditioned Krylov solver iterations, as well as more complex scenarios of flow around obstacles or through a three-dimensional vessel bifurcation, demonstrate the stability and robustness of the schemes.

• Schot, Maik; Becker, Malin; Paggi, Carlo Alberto; Gomes, Francisca; Koch, Timo & Gensheimer, Tarek [Show all 12 contributors for this article] (2023). Photoannealing of Microtissues Creates High-Density Capillary Network Containing Living Matter in a Volumetric-Independent Manner. Advanced Materials. ISSN 0935-9648. doi: 10.1002/adma.202308949. Full text in Research Archive Show summary

  The vascular tree is crucial for the survival and function of large living tissues. Despite breakthroughs in 3D bioprinting to endow engineered tissues with large blood vessels, there is currently no approach to engineer high-density capillary networks into living tissues in a scalable manner. We here present photo-annealing of living microtissues(PALM) as a scalable strategy to engineer capillary-rich tissues. Specifically, in-air microfluidics was used to produce living microtissues composed of cell-laden microgels in ultra-high throughput, which could be photo-annealed into a monolithic living matter. Annealed microtissues inherently give rise to an open and interconnected pore network within the resulting living matter. Interestingly, utilizing soft microgels enables microgel deformation, which leads to the uniform formation of capillary-sized pores. Importantly, the ultra-high throughput nature underlying the microtissue formation uniquely facilitates scalable production of living tissues of clinically relevant sizes (>1 cm3 ) with an integrated high-density capillary network. In short, PALM generates monolithic, microporous, modular tissues that meet the previously unsolved need for large engineered tissues containing high-density vascular networks, which is anticipated to advance the fields of engineered organs, regenerative medicine, and drug screening

• Gläser, Dennis; Koch, Timo & Flemisch, Bernd (2023). GridFormat: header-only C++-library for grid file I/O. Journal of Open Source Software (JOSS). 8(90). doi: 10.21105/joss.05778. Full text in Research Archive
• Schnepf, Andrea; Black, Christopher K; Couvreur, Valentin; Delory, Benjamin M; Doussan, Claude & Heymans, Adrien [Show all 20 contributors for this article] (2023). Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake. in silico Plants (isP). 5(1). doi: 10.1093/insilicoplants/diad005. Full text in Research Archive Show summary

  Abstract Functional-structural root architecture models have evolved as tools for the design of improved agricultural management practices and for the selection of optimal root traits. In order to test their accuracy and reliability, we present the first benchmarking of root water uptake from soil using five well-established functional-structural root architecture models: DuMux, CPlantBox, R-SWMS, OpenSimRoot and SRI. The benchmark scenarios include basic tests for water flow in soil and roots as well as advanced tests for the coupled soil-root system. The reference solutions and the solutions of the different simulators are available through Jupyter Notebooks on a GitHub repository. All of the simulators were able to pass the basic tests and continued to perform well in the benchmarks for the coupled soil-plant system. For the advanced tests, we created an overview of the different ways of coupling the soil and the root domains as well as the different methods used to account for rhizosphere resistance to water flow. Although the methods used for coupling and modelling rhizosphere resistance were quite different, all simulators were in reasonably good agreement with the reference solution. During this benchmarking effort, individual simulators were able to learn about their strengths and challenges, while some were even able to improve their code. Some now include the benchmarks as standard tests within their codes. Additional model results may be added to the GitHub repository at any point in the future and will be automatically included in the comparison.

• Busek, Mathias; Aizenshtadt, Aleksandra; Koch, Timo; Frank, Anna; Delon, Ludivine Sylvie Claude & Martinez, Mikel Amirola [Show all 12 contributors for this article] (2023). Pump-less, recirculating organ-on-a-chip (rOoC) platform. Lab on a Chip. ISSN 1473-0197. doi: 10.1039/D2LC00919F. Full text in Research Archive
• Koch, Timo; Vinje, Vegard & Mardal, Kent-Andre (2023). Estimates of the permeability of extra-cellular pathways through the astrocyte endfoot sheath. Fluids and Barriers of the CNS. 20(1). doi: 10.1186/s12987-023-00421-8. Full text in Research Archive Show summary

  Background Astrocyte endfoot processes are believed to cover all micro-vessels in the brain cortex and may play a significant role in fluid and substance transport into and out of the brain parenchyma. Detailed fluid mechanical models of diffusive and advective transport in the brain are promising tools to investigate theories of transport. Methods We derive theoretical estimates of astrocyte endfoot sheath permeability for advective and diffusive transport and its variation in microvascular networks from mouse brain cortex. The networks are based on recently published experimental data and generated endfoot patterns are based on Voronoi tessellations of the perivascular surface. We estimate corrections for projection errors in previously published data. Results We provide structural-functional relationships between vessel radius and resistance that can be directly used in flow and transport simulations. We estimate endfoot sheath filtration coefficients in the range Lp = 2 × 10−11 mPa−1 s−1 to 3 × 10−11 mPa−1 s−1 , diffusion membrane coefficients for small solutes in the range CM = 5 × 102 m−1 to 6 × 102 m−1 , and gap area fractions in the range 0.2–0.6%, based on a inter-endfoot gap width of 20 nm. Conclusions The astrocyte endfoot sheath surrounding microvessels forms a secondary barrier to extra-cellular transport, separating the extra-cellular space of the parenchyma and the perivascular space outside the endothelial layer. The filtration and membrane diffusion coefficients of the endfoot sheath are estimated to be an order of magnitude lower than those of the extra-cellular matrix while being two orders of magnitude higher than those of the vessel wall.

• Gläser, Dennis; Koch, Timo; Peters, Sören; Marcus, Sven & Bernd, Flemisch (2023). fieldcompare: A Python package for regression testing simulation results. Journal of Open Source Software (JOSS). 8(81). doi: 10.21105/joss.04905. Full text in Research Archive Show summary

  In various research areas such as engineering, physics, and mathematics, numerical simulations play an important role. A number of research software simulation frameworks have been established, for instance, Dune (Bastian et al., 2008, 2021), Dumux (Flemisch et al., 2011; Koch et al., 2021), Deal.II (Arndt et al., 2022), FEniCS (A. Logg, 2012; FEniCS, 2023), and VirtualFluids (Kutscher et al., 2022). Numerical software typically has a high inherent complexity as it aims at solving complex physical model equations by using advanced mathematical methods for solving partial differential equations. Beyond this, the model equations often involve parameters that are described by means of empirical constitutive relationships. Thus, a numerical simulation usually brings together various software components: for the domain discretization, the discretization method for the equations, the physics, and a non-linear and/or linear solver to obtain a solution for the discretized equations. While each of these components can be unit tested, it is important to have system tests that verify that a particular type of simulation can be carried out successfully. By successful we mean here that the simulation produces the correct results. As sufficiently complex problems often lack analytical solutions, determining correctness of numerical simulations poses a significant challenge. In the absence of an analytical solution, a common strategy is to use a trusted reference for comparison (e.g., data measured in experiments or results from previous publications). From the perspective of software quality assurance, it suffices to define a reference result as the correct one and continuously verify that the code still reproduces it. In numerical software, such regression tests play a vital role at the level of system tests (Kempf & Koch, 2017). They make sure that developers notice when a certain change to the code affects the results produced by the simulations. Whether the new results are better or worse has to be decided by the developers, and in the case of the former, the reference results may be updated. In order to carry out regression tests, one must be able to detect significant deviations between newly-computed and reference results. What a significant deviation is has to be decided by the developers as well, and adequate tolerances have to be chosen that are big enough to avoid false negatives from machine precision issues, but small enough to ensure that physically relevant deviations in the results are detected. Some numerical software packages as, for instance, DUNE and DuMux (Flemisch et al., 2011), provide mechanisms to detect such deviations. However, the functionality is not provided independent of the frameworks themselves and is therefore only available to their users. Besides this, only those mesh file formats that are used by the frameworks are supported. Very recently, DuMux incorporated fieldcompare into its test suite in place of its in-house solutions.

• Koch, Timo (2022). Projection-based resolved interface 1D-3D mixed-dimension method for embedded tubular network systems. Computers and Mathematics with Applications. ISSN 0898-1221. 109, p. 15–29. doi: 10.1016/j.camwa.2022.01.021. Full text in Research Archive Show summary

  We present a novel numerical technique for computational models of thin tubular networks embedded in a bulk domain, for example a porous medium. These systems occur in the simulation of fluid flow in vascularized biological tissue, root water and nutrient uptake in soil, hydrological or petroleum wells in rock formations, or heat transport in micro-cooling devices. The key processes, such as heat and mass transfer, are often dominated by the exchange between the network system and the embedding domain. By explicitly resolving the interface between these domains with the computational mesh, we can accurately describe these processes. The network is efficiently described by a network of line segments. Coupling terms are evaluated by projection of the interface variables. The new method is naturally applicable for nonlinear and time-dependent problems and can therefore be used as a reference method in the development of novel implicit interface 1D-3D methods and in the design of verification benchmarks for embedded tubular network methods. Implicit interface models, not resolving the bulk-network interface explicitly have proven to be very efficient but have only been mathematically analyzed for linear elliptic problems so far. Using two application scenarios, fluid perfusion of vascularized tissue and root water uptake from soil, we investigate the effect of some common modeling assumptions of implicit interface methods numerically.

• Boon, Wietse; Koch, Timo; Kuchta, Miroslav & Mardal, Kent-Andre (2022). Robust Monolithic Solvers for the Stokes--Darcy Problem with the Darcy Equation in Primal Form. SIAM Journal on Scientific Computing. ISSN 1064-8275. 44(4), p. B1148–B1174. doi: 10.1137/21M1452974. Full text in Research Archive Show summary

  We construct mesh-independent and parameter-robust monolithic solvers for the coupled primal Stokes--Darcy problem. Three different formulations and their discretizations in terms of conforming and nonconforming finite element methods and finite volume methods are considered. In each case, robust preconditioners are derived using a unified theoretical framework. In particular, the suggested preconditioners utilize operators in fractional Sobolev spaces. Numerical experiments demonstrate the parameter-robustness of the proposed solvers.

• Busek, Mathias; Aizenshtadt, Aleksandra; Koch, Timo; Frank, Anna; Delon, Ludivine Sylvie Claude & Martinez, Mikel Amirola [Show all 12 contributors for this article] (2022). Pump-less, recirculating organ-on-a-chip (rOoC) platform. Lab on a Chip. ISSN 1473-0197. p. 345–361. doi: 10.1039/d2lc00919f. Full text in Research Archive Show summary

  We developed a novel, pump-less directional flow recirculating organ-on-a-chip (rOoC) platform that creates controlled unidirectional gravity-driven flow by a combination of a 3D-tilting system and an optimized microfluidic layout. The rOoC platform was assembled utilizing a layer-to-layer fabrication technology based on thermoplastic materials. It features two organoid compartments supported by two independent perfusion channels and separated by a hydrogel barrier. We developed a computational model to predict wall shear stress values and then measured the flow rate in the microfluidic channels with micro-Particle-Image-Velocimetry (μPIV). The suitability of the rOoC for functional culture of endothelial cells was tested using HUVECs seeded in the perfusion channels. HUVECs aligned in response to the directional flow, formed a barrier and were able to sprout into the organoid compartments. Next, we demonstrated the viability of human stem-cell derived liver organoids in the organoid compartments. Finally, we show the possibility to circulate immune cells in the microfluidic channels that retain viability without being trapped or activated. The rOoC platform allows growing and connecting of two or more tissue or organ representations on-chip with the possibility of applying gradients, endothelial barriers, microvasculature and circulating cells independent of external tubing and support systems.

• Koch, Timo; Wu, Hanchuan & Schneider, Martin (2021). Nonlinear mixed-dimension model for embedded tubular networks with application to root water uptake. Journal of Computational Physics. ISSN 0021-9991. 450. doi: 10.1016/j.jcp.2021.110823. Full text in Research Archive Show summary

  We present a numerical scheme for the solution of nonlinear mixed-dimensional PDEs describing coupled processes in embedded tubular network system in exchange with a bulk domain. Such problems arise in various biological and technical applications such as in the modeling of root-water uptake, heat exchangers, or geothermal wells. The nonlinearity appears in form of solution-dependent parameters such as pressure-dependent permeability or temperature-dependent thermal conductivity. We derive and analyze a numerical scheme based on distributing the bulk-network coupling source term by a smoothing kernel with local support. By the use of local analytical solutions, interface unknowns and fluxes at the bulk-network interface can be accurately reconstructed from coarsely resolved numerical solutions in the bulk domain. Numerical examples give confidence in the robustness of the method and show the results in comparison to previously published methods. The new method outperforms these existing methods in accuracy and efficiency. In a root water uptake scenario, we accurately estimate the transpiration rate using only a few thousand 3D mesh cells and a structured cube grid whereas other state-of-the-art numerical schemes require millions of cells and local grid refinement to reach comparable accuracy.

• Weishaupt, Kilian; Koch, Timo & Helmig, Rainer (2021). A fully implicit coupled pore-network/free-flow model for the pore-scale simulation of drying processes. Drying Technology. ISSN 0737-3937. doi: 10.1080/07373937.2021.1955706. Full text in Research Archive Show summary

  We present a fully coupled pore-network/free-flow model providing pore-scale insight into drying processes. We solve the Navier–Stokes equations with component transport in the free-flow region, coupled to a dynamic two-phase, two-component pore-network model (PNM) in the porous domain. The dynamic multi-physics model allows to temporally resolve drying processes in-between capillary equilibrium states. All simulations are non-isothermal and use pressure- and temperature-depended fluid properties. Carefully chosen coupling conditions and a monolithic solver ensure local conservation of mass, momentum, and energy fluxes, in particular at the interface between both model domains. We solve for wetting and non-wetting fluid pressure fields and consider advective gas transport in the network. Numerical examples demonstrate that the coupled model is able to cover a wide range of physical processes relevant for drying and show the mutual interaction of the two subregions. The model is implemented in the modular open-source framework DuMux such that extensions are straight-forward.

• Koch, Timo; Weishaupt, Kilian; Müller, Johannes; Weigand, Bernhard & Helmig, Rainer (2021). A (Dual) Network Model for Heat Transfer in Porous Media. Transport in Porous Media. ISSN 0169-3913. 140, p. 107–141. doi: 10.1007/s11242-021-01602-5. Full text in Research Archive Show summary

  Abstract We present a dual network model to simulate coupled single-phase flow and energy transport in porous media including conditions under which local thermal equilibrium cannot be assumed. The models target applications such as the simulation of catalytic reactors, micro-fluidic experiments, or micro-cooling devices. The new technique is based on a recently developed algorithm that extracts both the pore space and the solid grain matrix of a porous medium from CT images into an interconnected network representation. We simulate coupled heat and mass transfer in these networks simultaneously, allowing naturally to model scenarios with heterogeneous temperature distributions in both void space and solid matrix. The model is compared with 3D conjugate heat transfer simulations for both conduction- and convection-dominated scenarios. It is shown to reproduce effective thermal conductivities over a wide range of fluid to solid thermal conductivity ratios with a single parameter set. Morevoer, it captures local thermal nonequilibrium effects in a micro-cooling device scenario.

• Koch, Timo; Gläser, Dennis; Weishaupt, Kilian; Ackermann, Sina; Beck, Martin & Becker, Beatrix [Show all 23 contributors for this article] (2021). DuMux 3–an open-source simulator for solving flow and transport problems in porous media with a focus on model coupling. Computers and Mathematics with Applications. ISSN 0898-1221. doi: 10.1016/j.camwa.2020.02.012. Full text in Research Archive
• Schnepf, Andrea; Black, Christopher K; Couvreur, Valentin; Delory, Benjamin M; Doussan, Claude & Koch, Axelle [Show all 20 contributors for this article] (2020). Call for participation: collaborative benchmarking of functional-structural root architecture models. The case of root water uptake. Frontiers in Plant Science. 11. doi: 10.3389/fpls.2020.00316. Full text in Research Archive Show summary

  Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models, such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore, defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute toward improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.

• Koch, Timo; Flemisch, Bernd; Rainer, Helmig; Wiest, Roland & Obrist, Dominik (2020). A multiscale subvoxel perfusion model to estimate diffusive capillary wall conductivity in multiple sclerosis lesions from perfusion MRI data. International Journal for Numerical Methods in Biomedical Engineering. ISSN 2040-7939. 36(2). doi: 10.1002/cnm.3298. Full text in Research Archive Show summary

  We propose a new mathematical model to learn capillary leakage coefficients from dynamic susceptibility contrast MRI data. To this end, we derive an embedded mixed-dimension flow and transport model for brain tissue perfusion on a subvoxel scale. This model is used to obtain the contrast agent concentration distribution in a single MRI voxel during a perfusion MRI sequence. We further present a magnetic resonance signal model for the considered sequence including a model for local susceptibility effects. This allows modeling MR signal-time curves that can be compared with clinical MRI data. The proposed model can be used as a forward model in the inverse modeling problem of inferring model parameters such as the diffusive capillary wall conductivity. Acute multiple sclerosis lesions are associated with a breach in the integrity of the blood-brain barrier. Applying the model to perfusion MR data of a patient with acute multiple sclerosis lesions, we conclude that diffusive capillary wall conductivity is a good indicator for characterizing activity of lesions, even if other patient-specific model parameters are not well-known.

• Koch, Timo; Schneider, Martin; Rainer, Helmig & Jenny, Patrick (2020). Modeling tissue perfusion in terms of 1d-3d embedded mixed-dimension coupled problems with distributed sources. Journal of Computational Physics. ISSN 0021-9991. 410. doi: 10.1016/j.jcp.2020.109370. Full text in Research Archive
• Koch, Timo; Rainer, Helmig & Schneider, Martin (2020). A new and consistent well model for one-phase flow in anisotropic porous media using a distributed source model. Journal of Computational Physics. ISSN 0021-9991. 410. doi: 10.1016/j.jcp.2020.109369. Full text in Research Archive
• Vidotto, Ettore; Koch, Timo; Köppl, Tobias; Helmig, Rainer & Wohlmuth, Barbara Irmgard (2019). Hybrid models for simulating blood flow in microvascular networks. Multiscale Modeling & simulation. ISSN 1540-3459. doi: 10.1137/18M1228712. Full text in Research Archive
• Koch, Timo; Heck, Katharina; Schröder, Natalie; Class, Holger & Rainer, Helmig (2018). A new simulation framework for soil-root interaction, evaporation, root growth, and solute transport. Vadose Zone Journal. 17(1), p. 1–21. doi: 10.2136/vzj2017.12.0210. Full text in Research Archive
• Kempf, Dominic & Koch, Timo (2017). System testing in scientific numerical software frameworks using the example of DUNE. Archive of Numerical Software. 5(1). doi: 10.11588/ans.2017.1.27447. Full text in Research Archive
• Sander, Oliver; Koch, Timo; Schröder, Natalie & Flemisch, Bernd (2017). The Dune FoamGrid implementation for surface and network grids. Archive of Numerical Software. 5(1). doi: 10.11588/ans.2017.1.28490. Full text in Research Archive

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• Skjelanger, Kristoffer; Veyskarami, Maziar; Kostelecky, Anna Mareike & Koch, Timo (2026). Pore-network modeling of buoyancy-driven bubbles at intermediate Bond-numbers. doi: https:/cmwrconference.org/wp-content/uploads/2026/07/CMWR2026_abstract_book.pdf. Full text in Research Archive Show summary

  Gravity effects cannot be neglected in two-phase flow in porous media at intermediate Bond-numbers. At the pore scale, such conditions may arise when the density difference is very large, the pore sizes are large, or in the presence of an artificial gravity field (as in a rotating system). In our case, efforts to reduce hydrogen production costs have suggested rotating electrolyzers, necessitating a deeper understanding of pore-scale phenomena at intermediate Bond numbers. In this talk, we present a pore-network model with discrete bubble tracking to more accurately capture mass transport in the intermediate-Bond-number regime. In addition to capillary-driven phase transport, we will allow buoyancy-driven bubbles to move through the pore network. This bubble transport can occur if bubbles smaller than the typical pore size detach from the walls of the porous medium, which is readily achieved in a rotating system with large apparent G-forces. We then track their motion and behavior within the pore network. To this end, we numerically derive appropriate local rules for bubble transport from Stokes simulations of rising bubbles in simple pore-throat geometries. The model is implemented in DuMux . Finally, we discuss the observed flow patterns in the pore-network model and the effects of micro-bubble flow on the overall system dynamics. The relative importance of continuous-phase capillarity-dominated transport and bubble-like buoyancy-driven transport is then evaluated for different Bond numbers.

• Skjelanger, Kristoffer; Veyskarami, Maziar; Kostelecky, Anna Mareike & Koch, Timo (2026). Pore-network modeling of buoyancy-driven microbubbles in a supergravity field. doi: https:/events.interpore.org/event/58/contributions/8626/. Full text in Research Archive Show summary

  Decreasing the production cost of hydrogen is a key challenge in the hydrogen economy, and one of the obstacles is the overpotential caused by bubble effects. Experimental studies have shown that rotating an electrolyzer promotes bubble detachment from the electrode surface of an alkaline electrolyzer; however, the mechanism within the porous medium remains largely unknown. In this talk, we will present a pore-network model with discrete bubble tracking as a way of understanding the bubble transport within a porous medium under the influence of a supergravity field. The pore-network model is chosen for its discrete mass conservation, well-defined geometry, and computational efficiency. In addition to the capillary-driven phase transport, we will allow buoyancy driven microbubbles to move through the pore-network. This buoyancy-driven bubble transport can appear in strong gravitational fields where the bubble detachment radius is smaller than the average pore-size. In a rotating system, the supergravity field can easily exceed 100 G. Using classical nucleation theory and bubble detachment sizes, we can estimate the minimum size of a mobile bubble in the porous medium. We can then track their movement and behavior through the pore-network by formulating suitable rules for bubble transport and numerically determining the rising velocity of bubbles in simple pore-throat geometries. The model is implemented in DuMux. Finally, we discuss the observed flow-patterns in the pore-network model and how this microbubble flow impacts the overall system. The respective importance of continuous phase capillarity-dominated transport and bubble-like transport driven by buoyancy is then evaluated for different gravitational fields.

• Poulain, Stephane Albert Jules; Koch, Timo; Mahadevan, L. & Carlson, Andreas (2025). Hovering of active fluid-lubricated foil. Full text in Research Archive
• Poulain, Stephane Albert Jules; Koch, Timo; Mahadevan, L. & Carlson, Andreas (2025). Hovering of an actively driven fluid-lubricated foil. Full text in Research Archive
• Haugen, Håvard Jostein; Carlson, Andreas & Koch, Timo (2024). Nå kan forskere lage vev med blodårer. Et gjennombrudd på veien mot kunstige organer. [Internet]. Forskning.no. Full text in Research Archive Show summary

  Fra én enkelt celle til et lite barn: Når fosteret vokser i mors mage skjer det komplekse reaksjoner. Så langt er forskerne langt unna å kopiere denne prosessen, men målet er å kunne lage kunstige organer. Det er flere steg på veien dit. Forskere har klart å printe celler på en overflate og lage todimensjonale strukturer. Det jobbes også med å lage organoider – miniorganer som gjør det mulig å teste medisiner. Likevel er det et godt stykke igjen til hele tredimensjonale organer som for eksempel kan brukes til organtransplantasjon. – Det er vanskelig å konkurrere med naturen. Den har mange tusen års evolusjon forsprang og har gjort så mye prøving og feiling for å få prosessen til å gå så fort som mulig, sier professor i biomaterialer, Håvard Haugen, ved Universitetet i Oslo. Hva er organoider? En organoide er vev fra et organ som dyrkes på et laboratorium. For eksempel kan vev fra leveren brukes til å se hvordan leveren bryter ned enkelte stoffer. Organoider brukes i medisinsk forskning, blant annet for å teste hvordan en medisin virker på et organ. Når forskerne skal prøve å gjøre det samme på lab, gjerne raskere og mer effektivt enn i kroppen, er det en stor utfordring. Det er så mange faktorer som de ikke kan kontrollere som spiller en rolle.

• Koch, Timo; Vinje, Vegard & Mardal, Kent-Andre (2023). Correction to: Estimates of the permeability of extra-cellular pathways through the astrocyte endfoot sheath (Fluids and Barriers of the CNS, (2023), 20, 1, (20), 10.1186/s12987-023-00421-8). Fluids and Barriers of the CNS. 20(1). doi: 10.1186/s12987-023-00456-x. Full text in Research Archive
• Koch, Timo; Weishaupt, Kilian & Müller, Johannes (2023). Spatial Variance of Pore-Scale Fluid Velocities. In Médici, Ezequiel F. & Otero, Alejandro D. (Ed.), Album of Porous Media. Springer. ISSN 9783031238000. p. 128–128. doi: 10.1007/978-3-031-23800-0_105. Full text in Research Archive
• Koch, Timo; Mardal, Kent-Andre & Valnes, Lars Magnus (2023). The Complex Pore Spaces of Our Brain: A Challenge and Opportunity for Computer Simulations. In Médici, Ezequiel F. & Otero, Alejandro D. (Ed.), Album of Porous Media. Springer. ISSN 9783031238000. p. 29–29. doi: 10.1007/978-3-031-23800-0_20. Full text in Research Archive
• Kuchta, Miroslav; Boon, Wietse; Hornkjøl, Martin; Koch, Timo; Mardal, Kent-Andre & Ruiz-Baier, Ricardo (2022). Parameter-robust Methods for Biot-Stokes and Darcy-Stokes Interfacial Coupling without Lagrange Multipliers. Full text in Research Archive
• Kuchta, Miroslav; Boon, Wietse; Koch, Timo; Mardal, Kent-Andre & Ruiz-Baier, Ricardo (2022). Parameter-robust monolithic solvers for coupled Biot/Darcy-Stokes models. Full text in Research Archive
• Kuchta, Miroslav; Boon, Wietse; Holter, Karl; Hornkjøl, Martin; Koch, Timo & Mardal, Kent-Andre [Show all 7 contributors for this article] (2022). Fractional operators in coupled multiphysics problems with implicit coupling. Full text in Research Archive
• Kuchta, Miroslav; Boon, Wietse; Holter, Karl; Hornkjøl, Martin; Koch, Timo & Mardal, Kent-Andre [Show all 7 contributors for this article] (2022). Parameter-robust monolithic solvers for Stokes-Darcy/Biot systems. Full text in Research Archive
• Sande, Espen; Koch, Timo; Kuchta, Miroslav & Mardal, Kent-Andre (2025). On a robust inf-sup condition for the Stokes problem in slender domains - with application to preconditioning. arxiv.org. doi: https:/arxiv.org/abs/2510.24590. Full text in Research Archive

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