Stuttgart Center for Simulation Science (SC SimTech)

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231 to 240 of 376 Results

In situ micro-XRCT data sets of an open-cell polyurethane foam sample under combined loading conditions (compression + torsion, tension) Apr 4, 2023 - Publication: Foams Ruf, Matthias; Steeb, Holger, 2023, "In situ micro-XRCT data sets of an open-cell polyurethane foam sample under combined loading conditions (compression + torsion, tension)", https://doi.org/10.18419/DARUS-2834, DaRUS, V1, UNF:6:mBGU8dC4irutNHDUz0h2Kg== [fileUNF] This dataset contains eight micro X-ray Computed Tomography (micro-XRCT) scan data sets (projection, reconstructed, and binarized images, respectively) of the identical open-cell reticulated polyurethane (PUR) foam sample with 10 pores per inch under different loads. The initial diameter and length of the unloaded cylindrical sample were 50 mm and...
Registered Cars and Motorized Two- and Three-wheelers in Worldwide Countries Mar 22, 2023 - PN 7-6 Steffen, Maier, 2023, "Registered Cars and Motorized Two- and Three-wheelers in Worldwide Countries", https://doi.org/10.18419/DARUS-3378, DaRUS, V1 Interactive plot of registered cars and motorized two- and three-wheelers in worldwide countries based the data set from the "WHO Global Status Report on Road Safety 2018" of the World Health Organization.
Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations" Mar 13, 2023 - Holm group Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2023, "Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"", https://doi.org/10.18419/DARUS-3313, DaRUS, V1 Simulations and data analysis scripts for the publication "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations". The dataset contains two types of simulation scripts: all-atom simulation (GROMACS) and coarse-grained simulations (ESPRESSO). In both cases, the system is a polymer PEG bulk system. See the README fil...
Molecular simulation scripts for slit nanopores Mar 9, 2023 - NMR investigation of water confined by salt interface Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for slit nanopores", https://doi.org/10.18419/DARUS-3180, DaRUS, V1 GROMACS molecular simulation input files for slit nanopores made of NaCl and Na2SO4 solid walls, and filled with respectively NaCl and Na2SO4 solutions. Initial configuration with a given salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash...
Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death' Mar 9, 2023 - PN 3-11 Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/DARUS-3373, DaRUS, V1 Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether...
Molecular simulation scripts for bulk solutions Mar 8, 2023 - NMR investigation of water confined by salt interface Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/DARUS-3179, DaRUS, V1 GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash script.
Interface Preserving Moving Mesh (Code) Mar 8, 2023 - Projects without PN Affiliation Alkämper, Maria; Magiera, Jim M., 2022, "Interface Preserving Moving Mesh (Code)", https://doi.org/10.18419/DARUS-1671, DaRUS, V2 Open source implementation in C++ for an interface preserving moving mesh in 2d and 3d using CGAL Delaunay triangulations. The time-dependent computational mesh allows for large point deformations while preserving a lower dimensional interface surface. See README.md for more information.
Replication Data for phase-field contributions in level-set comparison study Mar 2, 2023 - PN 1-6 Kelm, Mathis; Bringedal, Carina; Flemisch, Bernd, 2023, "Replication Data for phase-field contributions in level-set comparison study", https://doi.org/10.18419/DARUS-3359, DaRUS, V1, UNF:6:MsNXqcARspF5yuVdFLKT0Q== [fileUNF] Primary and post-processed simulation data and visualization tools to reproduce the phase-field results presented in the related publication. The folders "simulation" and "effective_quantities" contain primary simulation results obtained with the code published in the DuMux-pub module Kelm2022a and post-processed effective quantities obtained using...
PN 3-11(Universität Stuttgart) Feb 28, 2023PN 3 Biological Molecular Dynamics Simulations
Pre-trained and fine-tuned ANI models for: Transfer learning for chemically accurate interatomic neural network potentials Feb 20, 2023 - PN 6 Zaverkin, Viktor; Holzmüller, David; Bonfirraro, Luca; Kästner, Johannes, 2023, "Pre-trained and fine-tuned ANI models for: Transfer learning for chemically accurate interatomic neural network potentials", https://doi.org/10.18419/DARUS-3299, DaRUS, V1 Pre-trained and fine-tuned ANI models using the Gaussian Moments Neural Network (GM-NN) approach. Code for GM-NN implemented within the Tensorflow framework, including the respective documentation and tutorials, can be found on GitLab. The data represents TensorFlow v2 checkpoints and stores the metadata for the checkpoint and parameters for the mo...

In situ micro-XRCT data sets of an open-cell polyurethane foam sample under combined loading conditions (compression + torsion, tension)

Apr 4, 2023 - Publication: Foams

Ruf, Matthias; Steeb, Holger, 2023, "In situ micro-XRCT data sets of an open-cell polyurethane foam sample under combined loading conditions (compression + torsion, tension)", https://doi.org/10.18419/DARUS-2834, DaRUS, V1, UNF:6:mBGU8dC4irutNHDUz0h2Kg== [fileUNF]

This dataset contains eight micro X-ray Computed Tomography (micro-XRCT) scan data sets (projection, reconstructed, and binarized images, respectively) of the identical open-cell reticulated polyurethane (PUR) foam sample with 10 pores per inch under different loads. The initial diameter and length of the unloaded cylindrical sample were 50 mm and...

Registered Cars and Motorized Two- and Three-wheelers in Worldwide Countries

Mar 22, 2023 - PN 7-6

Steffen, Maier, 2023, "Registered Cars and Motorized Two- and Three-wheelers in Worldwide Countries", https://doi.org/10.18419/DARUS-3378, DaRUS, V1

Interactive plot of registered cars and motorized two- and three-wheelers in worldwide countries based the data set from the "WHO Global Status Report on Road Safety 2018" of the World Health Organization.

Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"

Mar 13, 2023 - Holm group

Gravelle, Simon; Beyer, David; Brito, Mariano E.; Schlaich, Alexander; Holm, Christian, 2023, "Scripts for "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations"", https://doi.org/10.18419/DARUS-3313, DaRUS, V1

Simulations and data analysis scripts for the publication "Assessing the validity of NMR relaxation rates obtained from coarse-grained simulations". The dataset contains two types of simulation scripts: all-atom simulation (GROMACS) and coarse-grained simulations (ESPRESSO). In both cases, the system is a polymer PEG bulk system. See the README fil...

Molecular simulation scripts for slit nanopores

Mar 9, 2023 - NMR investigation of water confined by salt interface

Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for slit nanopores", https://doi.org/10.18419/DARUS-3180, DaRUS, V1

GROMACS molecular simulation input files for slit nanopores made of NaCl and Na2SO4 solid walls, and filled with respectively NaCl and Na2SO4 solutions. Initial configuration with a given salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash...

Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'

Mar 9, 2023 - PN 3-11

Degen, Morris; Santos, José Carlos; Pluhackova, Kristyna; Cebrero, Gonzalo; Ramos, Saray; Jankevicius, Gytis; Hartenian, Ella; Guillerm, Undina; Mari, Stefania A.; Kohl, Bastian; Müller, Daniel J.; Schanda, Paul; Maier, Timm; Perez, Camilo; Sieben, Christian; Broz, Petr; Hiller, Sebastian, 2023, "Supplementary material for 'Structural basis for ninjurin-1 mediated plasma membrane rupture in lytic cell death'", https://doi.org/10.18419/DARUS-3373, DaRUS, V1

Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture (PMR) as the defining terminal event. PMR was long thought to be driven by osmotic pressure, until it was recently shown to be in many cases an active process, mediated by the protein ninjurin-1 (NINJ1). Here, we studied whether...

Molecular simulation scripts for bulk solutions

Mar 8, 2023 - NMR investigation of water confined by salt interface

Gravelle, Simon; Holm, Christian; Schlaich, Alexander, 2023, "Molecular simulation scripts for bulk solutions", https://doi.org/10.18419/DARUS-3179, DaRUS, V1

GROMACS molecular simulation input files for bulk solutions of NaCl and Na2SO4. Initial configuration with different salt concentration can be generated using the Python script ConfigurationGenerator.py, and successive GROMACS runs can be performed by running the runall.sh Bash script.

Interface Preserving Moving Mesh (Code)

Mar 8, 2023 - Projects without PN Affiliation

Alkämper, Maria; Magiera, Jim M., 2022, "Interface Preserving Moving Mesh (Code)", https://doi.org/10.18419/DARUS-1671, DaRUS, V2

Open source implementation in C++ for an interface preserving moving mesh in 2d and 3d using CGAL Delaunay triangulations. The time-dependent computational mesh allows for large point deformations while preserving a lower dimensional interface surface. See README.md for more information.

Replication Data for phase-field contributions in level-set comparison study

Mar 2, 2023 - PN 1-6

Kelm, Mathis; Bringedal, Carina; Flemisch, Bernd, 2023, "Replication Data for phase-field contributions in level-set comparison study", https://doi.org/10.18419/DARUS-3359, DaRUS, V1, UNF:6:MsNXqcARspF5yuVdFLKT0Q== [fileUNF]

Primary and post-processed simulation data and visualization tools to reproduce the phase-field results presented in the related publication. The folders "simulation" and "effective_quantities" contain primary simulation results obtained with the code published in the DuMux-pub module Kelm2022a and post-processed effective quantities obtained using...

PN 3-11(Universität Stuttgart)

Feb 28, 2023PN 3

Biological Molecular Dynamics Simulations

Pre-trained and fine-tuned ANI models for: Transfer learning for chemically accurate interatomic neural network potentials

Feb 20, 2023 - PN 6

Zaverkin, Viktor; Holzmüller, David; Bonfirraro, Luca; Kästner, Johannes, 2023, "Pre-trained and fine-tuned ANI models for: Transfer learning for chemically accurate interatomic neural network potentials", https://doi.org/10.18419/DARUS-3299, DaRUS, V1

Pre-trained and fine-tuned ANI models using the Gaussian Moments Neural Network (GM-NN) approach. Code for GM-NN implemented within the Tensorflow framework, including the respective documentation and tutorials, can be found on GitLab. The data represents TensorFlow v2 checkpoints and stores the metadata for the checkpoint and parameters for the mo...

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