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Subject: Chemistry Subject: Computer and Information Science Deposit Date: 2022

1 to 10 of 10 Results

Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models' Sep 21, 2023 - Molecular Simulation Kraus, Hamzeh; Högler, Marc; Hansen, Niels, 2023, "Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'", https://doi.org/10.18419/darus-3067, DaRUS, V1 This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for bulk phase simulations as well as for pore simulations with 14 different compounds. The pore simulations are...
Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation Mar 14, 2023 - MD Simulations Jeltsch, Albert; Schnee, Philipp; Saad, Mina; Weirich, Sara; Pleiss, Jürgen; Bashtrykov, Pavel, 2023, "Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation", https://doi.org/10.18419/darus-3263, DaRUS, V1 This data collection contains additional data related to Khella et al.: "The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation". This includes Movie 1: Example of a successful docking of AdoMet to the NSD2 T1150A - H3K36me2 pepti...
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 s...
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 s...
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 checkpoint...
QSDB - a graphical Quorum Sensing Database: VANTED add-on source code Nov 21, 2022 - SFB-TRR 161 D04 "Quantitative Aspects of Immersive Analytics for the Life Sciences" Klein, Karsten; Garkov, Dimitar; Rütschlin, Sina; Böttcher, Thomas; Schreiber, Falk, 2022, "QSDB - a graphical Quorum Sensing Database: VANTED add-on source code", https://doi.org/10.18419/darus-3242, DaRUS, V1 The add-on had been designed for the VANTED framework and used to create QSDB Database's collection of clickable networks. Each network is laid out according to SBGN standards, showing quorum sensing and quorum quenching interactions between organisms and signaling molecules. Thi...
Data for: FAIR and scalable management of small-angle X-ray scattering data Jun 9, 2022 - SFB 1333 A4 - Bruckner group Giess, Torsten; Itzigehl, Selina; Range, Jan Peter; Bruckner, Johanna R.; Pleiss, Jürgen, 2022, "Data for: FAIR and scalable management of small-angle X-ray scattering data", https://doi.org/10.18419/darus-2842, DaRUS, V1 This dataset contains small-angle X-ray scattering (SAXS) measurements on various octyltrimethylammonium bromide (OTAB)/water and octyltrimethylammonium chloride (OTAC)/water mixtures at different mass fractions and temperatures, as well as analysis and visualization data thereof...
Movies of thin film water on rough NaCl surface Mar 25, 2022 - Thin Film Water on NaCl(100) Gravelle, Simon, 2022, "Movies of thin film water on rough NaCl surface", https://doi.org/10.18419/darus-2770, DaRUS, V1 Videos showing water molecules at a rough sodium chloride solid surface for different roughness and different water chemical potential. The force field for the water is TIP4P/epsilon (https://doi.org/10.1021/jp410865y), and the force field for the ions is from Loche et al. (https...
Molecular simulation scripts for thin film water on NaCl surface Mar 25, 2022 - Thin Film Water on NaCl(100) Gravelle, Simon, 2022, "Molecular simulation scripts for thin film water on NaCl surface", https://doi.org/10.18419/darus-2726, DaRUS, V1 LAMMPS and GROMACS molecular simulation input files. The system consists of thin film water confined in a 7 nm NaCl slit pore, and can be generated using the Python scripts in SystemGeneration. The simulation is either equilibrium molecular dynamics (EMD), non equilibrium molecul...
Movies of thin film water on NaCl(100) surface Mar 25, 2022 - Thin Film Water on NaCl(100) Gravelle, Simon, 2022, "Movies of thin film water on NaCl(100) surface", https://doi.org/10.18419/darus-2697, DaRUS, V1 Videos showing water molecules at a sodium chloride (NaCl) solid surface for different water content. The force field for the water is TIP4P/epsilon (https://doi.org/10.1021/jp410865y), and the force field for the ions is from Loche et al. (https://doi.org/10.1021/acs.jpcb.1c0530...

Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'

Sep 21, 2023 - Molecular Simulation

Kraus, Hamzeh; Högler, Marc; Hansen, Niels, 2023, "Supplementary material for 'Axial Diffusion in Liquid-Saturated Cylindrical Silica Pore Models'", https://doi.org/10.18419/darus-3067, DaRUS, V1

This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter files are provided for bulk phase simulations as well as for pore simulations with 14 different compounds. The pore simulations are...

Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

Mar 14, 2023 - MD Simulations

Jeltsch, Albert; Schnee, Philipp; Saad, Mina; Weirich, Sara; Pleiss, Jürgen; Bashtrykov, Pavel, 2023, "Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation", https://doi.org/10.18419/darus-3263, DaRUS, V1

This data collection contains additional data related to Khella et al.: "The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation". This includes Movie 1: Example of a successful docking of AdoMet to the NSD2 T1150A - H3K36me2 pepti...

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 s...

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 s...

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 checkpoint...

QSDB - a graphical Quorum Sensing Database: VANTED add-on source code

Nov 21, 2022 - SFB-TRR 161 D04 "Quantitative Aspects of Immersive Analytics for the Life Sciences"

Klein, Karsten; Garkov, Dimitar; Rütschlin, Sina; Böttcher, Thomas; Schreiber, Falk, 2022, "QSDB - a graphical Quorum Sensing Database: VANTED add-on source code", https://doi.org/10.18419/darus-3242, DaRUS, V1

The add-on had been designed for the VANTED framework and used to create QSDB Database's collection of clickable networks. Each network is laid out according to SBGN standards, showing quorum sensing and quorum quenching interactions between organisms and signaling molecules. Thi...

Data for: FAIR and scalable management of small-angle X-ray scattering data

Jun 9, 2022 - SFB 1333 A4 - Bruckner group

Giess, Torsten; Itzigehl, Selina; Range, Jan Peter; Bruckner, Johanna R.; Pleiss, Jürgen, 2022, "Data for: FAIR and scalable management of small-angle X-ray scattering data", https://doi.org/10.18419/darus-2842, DaRUS, V1

This dataset contains small-angle X-ray scattering (SAXS) measurements on various octyltrimethylammonium bromide (OTAB)/water and octyltrimethylammonium chloride (OTAC)/water mixtures at different mass fractions and temperatures, as well as analysis and visualization data thereof...

Movies of thin film water on rough NaCl surface

Mar 25, 2022 - Thin Film Water on NaCl(100)

Gravelle, Simon, 2022, "Movies of thin film water on rough NaCl surface", https://doi.org/10.18419/darus-2770, DaRUS, V1

Videos showing water molecules at a rough sodium chloride solid surface for different roughness and different water chemical potential. The force field for the water is TIP4P/epsilon (https://doi.org/10.1021/jp410865y), and the force field for the ions is from Loche et al. (https...

Molecular simulation scripts for thin film water on NaCl surface

Mar 25, 2022 - Thin Film Water on NaCl(100)

Gravelle, Simon, 2022, "Molecular simulation scripts for thin film water on NaCl surface", https://doi.org/10.18419/darus-2726, DaRUS, V1

LAMMPS and GROMACS molecular simulation input files. The system consists of thin film water confined in a 7 nm NaCl slit pore, and can be generated using the Python scripts in SystemGeneration. The simulation is either equilibrium molecular dynamics (EMD), non equilibrium molecul...

Movies of thin film water on NaCl(100) surface

Mar 25, 2022 - Thin Film Water on NaCl(100)

Gravelle, Simon, 2022, "Movies of thin film water on NaCl(100) surface", https://doi.org/10.18419/darus-2697, DaRUS, V1

Videos showing water molecules at a sodium chloride (NaCl) solid surface for different water content. The force field for the water is TIP4P/epsilon (https://doi.org/10.1021/jp410865y), and the force field for the ions is from Loche et al. (https://doi.org/10.1021/acs.jpcb.1c0530...

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