Timo Koch

• 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.
• 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). ISSN 2475-9066. 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). ISSN 2517-5025. 5(1). doi: 10.1093/insilicoplants/diad005. 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. ISSN 2045-8118. 20(1). doi: 10.1186/s12987-023-00421-8. Full text in Research Archive
• 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). ISSN 2475-9066. 8(81). doi: 10.21105/joss.04905. Full text in Research Archive
• Busek, Mathias; Aizenshtadt, Aleksandra; Koch, Timo; Frank, Anna; Delon, Ludivine Sylvie Claude & Amirola Martinez, Mikel [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
• 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.
• 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
• 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
• 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.
• 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
• 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
• 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. ISSN 1664-462X. 11. doi: 10.3389/fpls.2020.00316. Full text in Research Archive
• 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
• 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.
• 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.
• 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.
• 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. ISSN 1539-1663. 17(1), p. 1–21. doi: 10.2136/vzj2017.12.0210.
• Sander, Oliver; Koch, Timo; Schröder, Natalie & Flemisch, Bernd (2017). The Dune FoamGrid implementation for surface and network grids. Archive of Numerical Software. ISSN 2197-8263. 5(1). doi: 10.11588/ans.2017.1.28490.
• Kempf, Dominic & Koch, Timo (2017). System testing in scientific numerical software frameworks using the example of DUNE. Archive of Numerical Software. ISSN 2197-8263. 5(1). doi: 10.11588/ans.2017.1.27447.

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• 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. ISSN 2045-8118. 20(1). doi: 10.1186/s12987-023-00456-x.
• 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 978-3-031-23800-0. p. 128–128. doi: 10.1007/978-3-031-23800-0_105.
• 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 978-3-031-23800-0. p. 29–29. doi: 10.1007/978-3-031-23800-0_20.

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