C04: Pore-scale and REV-scale approaches to biological and chemical pore-space alteration in porous media

Porosity and permeability are two major hydraulic properties that govern flow through porous media. Different kinds of processes can lead to alterations of the pore space which eventually change the hydraulic properties. This project focuses primarily on fluid-solid interfaces that are prone to change as a result of microbial activity. The alterations need to be measured experimentally and interpreted on the scales of interest by means of numerical simulations. It is also required to improve the efficiency of corresponding complex numerical simulation methods.

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1 to 10 of 25 Results

Effects of Surface Chemistry and Substrate Material on Bacterial Attachment and Biomineralization in Microfluidic Flow Cells Jun 18, 2026 Bozkurt, Kerem; Marquis, James; Avci, Recep; Heinemann, Joshua; Lingley, Andrew; Neubauer, Michael; Class, Holger; Gerlach, Robin, 2026, "Effects of Surface Chemistry and Substrate Material on Bacterial Attachment and Biomineralization in Microfluidic Flow Cells", https://doi.org/10.18419/DARUS-5845, DaRUS, V1 This dataset includes images captured during the experiments, processed images obtained through image analysis, the MATLAB code used for image processing, and detailed analysis results in .csv format. The dataset contains seven experimental folders. Each experimental folder includes two imaging periods: Pre-Biomineralization (PB) and Post-biominera...
Data for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog May 27, 2026 Wendel, Kai; Keim, Leon; Strauch, Bettina; Zimmer, Martin; Class, Holger, 2026, "Data for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog", https://doi.org/10.18419/DARUS-4818, DaRUS, V2, UNF:6:CzusT72hkTaH4buUKZ/+Iw== [fileUNF] This dataset contains laboratory-experiment data and simulation data for the publication Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog. The structure of the dataset is as follows: experimentalDataset – Contains the relevant experimental data set. ftb – Contains the simulation data organized in f...
Code for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog May 27, 2026 Wendel, Kai; Keim, Leon; Strauch, Bettina; Zimmer, Martin; Class, Holger, 2026, "Code for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog", https://doi.org/10.18419/DARUS-4819, DaRUS, V2 This dataset contains the DuMux code for the simulations in paper "Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog" To run the simulations at your own computer, please conduct the following steps: Install docker for (example in ubuntu)[https://docs.docker.com/engine/install/ubuntu/] Make sure you...
Code and benchmarks for a vertically averaged drag term for pseudo-3D Stokes simulations Mar 24, 2026 - Publication: Rigorous vertical averaging for pseudo-3D modeling of precipitation obstructed fluid flow Krach, David; Weinhardt, Felix; Class, Holger; Steeb, Holger; Schneider, Martin, 2026, "Code and benchmarks for a vertically averaged drag term for pseudo-3D Stokes simulations", https://doi.org/10.18419/DARUS-5624, DaRUS, V1 Content: This data set includes snapshots of the code used to compute the benchmarks and applications in Krach et al (2026). The included software tools allow users to conduct pseudo-3D Stokes simulations with a geometry-informed drag term as well as analytical drag terms using DuMux. Users can determine permeability, volumetric flux, and local pre...
Results for pseudo-3D Stokes simulations using a vertically averaged drag term Mar 24, 2026 - Publication: Rigorous vertical averaging for pseudo-3D modeling of precipitation obstructed fluid flow Krach, David; Weinhardt, Felix; Class, Holger; Steeb, Holger; Schneider, Martin, 2026, "Results for pseudo-3D Stokes simulations using a vertically averaged drag term", https://doi.org/10.18419/DARUS-5626, DaRUS, V1 Content: This data set includes all the necessary input data to fully replicate the benchmarks and applications in Krach et al.(2026). In addition, the results for all solvers are provided as raw simulation output as well as in condense form. Complete datasets: 01_SINGLE_PRECIPITATE, 02_SEGMENT1, 03_SEGMENT2, 04_SEGMENT3, 05_WHOLE_DOMAIN Each data...
Publication: Rigorous vertical averaging for pseudo-3D modeling of precipitation obstructed fluid flow(Universität Stuttgart) Mar 13, 2026
Data used in and produced during calibration and validation of the model for bioconcrete production Sep 15, 2025 Hommel, Johannes; Bozkurt, Kerem; Nething, Christoph; Smirnova, Maiia, 2025, "Data used in and produced during calibration and validation of the model for bioconcrete production", https://doi.org/10.18419/DARUS-4814, DaRUS, V1 Data used in and produced during calibration and validation of the model for bioconcrete production in the paper "A numerical 1D reactive flow and transport model for cementation processes in bio-concrete production". Experimental data is derived from Smirnova et al. 2023. The experiment TR1-2 was used to calibrate the developed model for bioconcre...
Model for Bioconcrete Production Sep 15, 2025 Hommel, Johannes; Bozkurt, Kerem; Wang, Yue; Class, Holger, 2025, "Model for Bioconcrete Production", https://doi.org/10.18419/DARUS-4813, DaRUS, V1 This dataset contains the code for the REV-scale model for "A numerical 1D reactive flow and transport model for cementation processes in bio-concrete production". The model was (and can be) applied for various experimental setups, for which input files are provided as well. The setup of these is described in the Readme. Related datasets and reposi...
Data for: Intermittent flow paths in biofilms grown in a microfluidic channel Jul 2, 2025 - Publication: Intermittent flow paths in biofilms grown in a microfluidic channel Bozkurt, Kerem; Lohrmann, Christoph; Weinhardt, Felix; Hanke, Daniel; Hopp, Raphael; Gerlach, Robin; Holm, Christian; Class, Holger, 2025, "Data for: Intermittent flow paths in biofilms grown in a microfluidic channel", https://doi.org/10.18419/DARUS-4314, DaRUS, V1 Content: This dataset includes images of 10 different biofilm growth experiments to observe intermittent flow paths in a microfluidic channel. All images taken by optical microscopy per five minutes. The experiments took in avarage 4-5 days. The published data is the raw images of the experiments. The images names were related to the timestamps as...
Publication: Intermittent flow paths in biofilms grown in a microfluidic channel(Universität Stuttgart) Jul 1, 2025 TODO

Effects of Surface Chemistry and Substrate Material on Bacterial Attachment and Biomineralization in Microfluidic Flow Cells

Jun 18, 2026

Bozkurt, Kerem; Marquis, James; Avci, Recep; Heinemann, Joshua; Lingley, Andrew; Neubauer, Michael; Class, Holger; Gerlach, Robin, 2026, "Effects of Surface Chemistry and Substrate Material on Bacterial Attachment and Biomineralization in Microfluidic Flow Cells", https://doi.org/10.18419/DARUS-5845, DaRUS, V1

This dataset includes images captured during the experiments, processed images obtained through image analysis, the MATLAB code used for image processing, and detailed analysis results in .csv format. The dataset contains seven experimental folders. Each experimental folder includes two imaging periods: Pre-Biomineralization (PB) and Post-biominera...

Data for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog

May 27, 2026

Wendel, Kai; Keim, Leon; Strauch, Bettina; Zimmer, Martin; Class, Holger, 2026, "Data for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog", https://doi.org/10.18419/DARUS-4818, DaRUS, V2, UNF:6:CzusT72hkTaH4buUKZ/+Iw== [fileUNF]

This dataset contains laboratory-experiment data and simulation data for the publication Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog. The structure of the dataset is as follows: experimentalDataset – Contains the relevant experimental data set. ftb – Contains the simulation data organized in f...

Code for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog

May 27, 2026

Wendel, Kai; Keim, Leon; Strauch, Bettina; Zimmer, Martin; Class, Holger, 2026, "Code for: Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog", https://doi.org/10.18419/DARUS-4819, DaRUS, V2

This dataset contains the DuMux code for the simulations in paper "Validating a Numerical Model for Calco-Carbonic Reactive Flow in a Laboratory Scale Fracture Analog" To run the simulations at your own computer, please conduct the following steps: Install docker for (example in ubuntu)[https://docs.docker.com/engine/install/ubuntu/] Make sure you...

Code and benchmarks for a vertically averaged drag term for pseudo-3D Stokes simulations

Mar 24, 2026 - Publication: Rigorous vertical averaging for pseudo-3D modeling of precipitation obstructed fluid flow

Krach, David; Weinhardt, Felix; Class, Holger; Steeb, Holger; Schneider, Martin, 2026, "Code and benchmarks for a vertically averaged drag term for pseudo-3D Stokes simulations", https://doi.org/10.18419/DARUS-5624, DaRUS, V1

Content: This data set includes snapshots of the code used to compute the benchmarks and applications in Krach et al (2026). The included software tools allow users to conduct pseudo-3D Stokes simulations with a geometry-informed drag term as well as analytical drag terms using DuMux. Users can determine permeability, volumetric flux, and local pre...

Results for pseudo-3D Stokes simulations using a vertically averaged drag term

Mar 24, 2026 - Publication: Rigorous vertical averaging for pseudo-3D modeling of precipitation obstructed fluid flow

Krach, David; Weinhardt, Felix; Class, Holger; Steeb, Holger; Schneider, Martin, 2026, "Results for pseudo-3D Stokes simulations using a vertically averaged drag term", https://doi.org/10.18419/DARUS-5626, DaRUS, V1

Content: This data set includes all the necessary input data to fully replicate the benchmarks and applications in Krach et al.(2026). In addition, the results for all solvers are provided as raw simulation output as well as in condense form. Complete datasets: 01_SINGLE_PRECIPITATE, 02_SEGMENT1, 03_SEGMENT2, 04_SEGMENT3, 05_WHOLE_DOMAIN Each data...

Publication: Rigorous vertical averaging for pseudo-3D modeling of precipitation obstructed fluid flow(Universität Stuttgart)

Mar 13, 2026

Data used in and produced during calibration and validation of the model for bioconcrete production

Sep 15, 2025

Hommel, Johannes; Bozkurt, Kerem; Nething, Christoph; Smirnova, Maiia, 2025, "Data used in and produced during calibration and validation of the model for bioconcrete production", https://doi.org/10.18419/DARUS-4814, DaRUS, V1

Data used in and produced during calibration and validation of the model for bioconcrete production in the paper "A numerical 1D reactive flow and transport model for cementation processes in bio-concrete production". Experimental data is derived from Smirnova et al. 2023. The experiment TR1-2 was used to calibrate the developed model for bioconcre...

Model for Bioconcrete Production

Sep 15, 2025

Hommel, Johannes; Bozkurt, Kerem; Wang, Yue; Class, Holger, 2025, "Model for Bioconcrete Production", https://doi.org/10.18419/DARUS-4813, DaRUS, V1

This dataset contains the code for the REV-scale model for "A numerical 1D reactive flow and transport model for cementation processes in bio-concrete production". The model was (and can be) applied for various experimental setups, for which input files are provided as well. The setup of these is described in the Readme. Related datasets and reposi...

Data for: Intermittent flow paths in biofilms grown in a microfluidic channel

Jul 2, 2025 - Publication: Intermittent flow paths in biofilms grown in a microfluidic channel

Bozkurt, Kerem; Lohrmann, Christoph; Weinhardt, Felix; Hanke, Daniel; Hopp, Raphael; Gerlach, Robin; Holm, Christian; Class, Holger, 2025, "Data for: Intermittent flow paths in biofilms grown in a microfluidic channel", https://doi.org/10.18419/DARUS-4314, DaRUS, V1

Content: This dataset includes images of 10 different biofilm growth experiments to observe intermittent flow paths in a microfluidic channel. All images taken by optical microscopy per five minutes. The experiments took in avarage 4-5 days. The published data is the raw images of the experiments. The images names were related to the timestamps as...

Publication: Intermittent flow paths in biofilms grown in a microfluidic channel(Universität Stuttgart)

Jul 1, 2025

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