PN 3

SimTech EXC 2075 Project Network 3 "Data-integrated model reduction for particles and continua"

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21 to 30 of 30 Results

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.
Data for: High-accuracy thermodynamic properties to the melting point from ab initio calculations aided by machine-learning potentials Jan 11, 2023 - Materials Design Jung, Jong Hyun; Srinivasan, Prashanth; Forslund, Axel; Grabowski, Blazej, 2023, "Data for: High-accuracy thermodynamic properties to the melting point from ab initio calculations aided by machine-learning potentials", https://doi.org/10.18419/DARUS-3239, DaRUS, V1 Data for the publication High-accuracy thermodynamic properties to the melting point from ab initio calculations aided by machine-learning potentials, npj Comput. Mater., DOI: 10.1038/s41524-022-00956-8 (2023) This data set contains - the training sets (VASP files), - the low moment-tensor-potentials (MTPs) and high-MTPs, - the effective quasiharmo...
Supplementary material for 'Predicting and rationalizing the Soret coefficient of binary Lennard-Jones mixtures in the liquid state' Aug 26, 2022 - Institute of Thermodynamics and Thermal Process Engineering Zimmermann, Nils Edvin Richard; Guevara-Carrion, Gabriela; Vrabec, Jadran; Hansen, Niels, 2022, "Supplementary material for 'Predicting and rationalizing the Soret coefficient of binary Lennard-Jones mixtures in the liquid state'", https://doi.org/10.18419/DARUS-2996, DaRUS, V2 Supplementary material for 'Predicting and rationalizing the Soret coefficient of binary Lennard-Jones mixtures in the liquid state' (N. E. R. Zimmermann, G. Guevara-Carrion, J. Vrabec, N. Hansen, Adv. Theory Simul., 2022) containing scripts, packages, and files to re-create and to submit LAMMPS simulations performed for non-equilibrium molecular d...
Publication data for: "The presence of a wall enhances the probability for ring-closing metathesis: insights from classical polymer theory and atomistic simulations - data from C6 group" Jul 20, 2022 - SFB 1333 C6 - Holm group, ICP Tischler, Ingo; Holm, Christian; Schlaich, Alexander, 2022, "Publication data for: "The presence of a wall enhances the probability for ring-closing metathesis: insights from classical polymer theory and atomistic simulations - data from C6 group"", https://doi.org/10.18419/DARUS-1371, DaRUS, V1 All primary data files and processed data of the journal article from C6 group. It contains the simulation and analysis scripts, the ESPResSo commit and a patch to it, with which the data was produced.
Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction' May 4, 2022 - Institute of Thermodynamics and Thermal Process Engineering Fleck, Maximilian; Markthaler, Daniel; Stankiewicz, Bartosz; Hansen, Niels, 2022, "Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction'", https://doi.org/10.18419/DARUS-2132, DaRUS, V1, UNF:6:8wyFNcxoOTcKA+4ZpSWLAg== [fileUNF] Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction' containing files to (re-)execute GROMACS simulations performed during the mutation study. This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files ar...
Supplementary material for 'Influence of Layer Slipping on Adsorption of Light Gases in Covalent Organic Frameworks: A Combined Experimental and Computational Study' Apr 26, 2022 - Institute of Thermodynamics and Thermal Process Engineering Kessler, Christopher; Schuldt, Robin; Emmerling, Sebastian; Lotsch, Bettina; Kästner, Johannes; Gross, Joachim; Hansen, Niels, 2022, "Supplementary material for 'Influence of Layer Slipping on Adsorption of Light Gases in Covalent Organic Frameworks: A Combined Experimental and Computational Study'", https://doi.org/10.18419/DARUS-2308, DaRUS, V1, UNF:6:ifmtNZEZHi+MkSvB5rd1dw== [fileUNF] This dataset contains results from Grand Canonical Monte Carlo (GCMC) Simulation (data/isotherms_sim/) and experiment (data/isotherms/exp). All Data is presented in a jupyter notebook and for a fast overview without executing the notebook also as pdf-file. Furthermore the dataset contains the modified cif files of COF LZU-1, including partial charg...
Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange' Jan 16, 2022 - Institute of Thermodynamics and Thermal Process Engineering Markthaler, Daniel; Kraus, Hamzeh; Hansen, Niels, 2022, "Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'", https://doi.org/10.18419/DARUS-2109, DaRUS, V1 Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the recent SAMPL8 CB8 "Drugs of Abuse" challenge using the GROMACS MD package. To compare with experimental data, a scheme for correcting the raw simulation estimates was propose...
Supplementary material for 'Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B' Nov 25, 2021 - Molecular Simulation Markthaler, Daniel; Hansen, Niels, 2021, "Supplementary material for 'Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B'", https://doi.org/10.18419/DARUS-2104, DaRUS, V1 This dataset contains all relevant simulation input files (topologies, coordinates, simulation parameters), generated simulation output (final configurations, time series of collective variables) together with scripts used for set-up and analysis of the umbrella sampling and double decoupling simulations.
2d microstructure data Feb 15, 2021 - Data Analytics in Engineering Lißner, Julian, 2020, "2d microstructure data", https://doi.org/10.18419/DARUS-1151, DaRUS, V2 The hdf5 file contains image data of inclusion based microstructured material and the homogenized effective heat conductivity thereof. The microstructure is defined with a representative volume element with periodic boundary conditions. 30.000 images are contained and split into two inclusion subclasses of circular and rectangular inclusions. Featu...

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.

Data for: High-accuracy thermodynamic properties to the melting point from ab initio calculations aided by machine-learning potentials

Jan 11, 2023 - Materials Design

Jung, Jong Hyun; Srinivasan, Prashanth; Forslund, Axel; Grabowski, Blazej, 2023, "Data for: High-accuracy thermodynamic properties to the melting point from ab initio calculations aided by machine-learning potentials", https://doi.org/10.18419/DARUS-3239, DaRUS, V1

Data for the publication High-accuracy thermodynamic properties to the melting point from ab initio calculations aided by machine-learning potentials, npj Comput. Mater., DOI: 10.1038/s41524-022-00956-8 (2023) This data set contains - the training sets (VASP files), - the low moment-tensor-potentials (MTPs) and high-MTPs, - the effective quasiharmo...

Supplementary material for 'Predicting and rationalizing the Soret coefficient of binary Lennard-Jones mixtures in the liquid state'

Aug 26, 2022 - Institute of Thermodynamics and Thermal Process Engineering

Zimmermann, Nils Edvin Richard; Guevara-Carrion, Gabriela; Vrabec, Jadran; Hansen, Niels, 2022, "Supplementary material for 'Predicting and rationalizing the Soret coefficient of binary Lennard-Jones mixtures in the liquid state'", https://doi.org/10.18419/DARUS-2996, DaRUS, V2

Supplementary material for 'Predicting and rationalizing the Soret coefficient of binary Lennard-Jones mixtures in the liquid state' (N. E. R. Zimmermann, G. Guevara-Carrion, J. Vrabec, N. Hansen, Adv. Theory Simul., 2022) containing scripts, packages, and files to re-create and to submit LAMMPS simulations performed for non-equilibrium molecular d...

Publication data for: "The presence of a wall enhances the probability for ring-closing metathesis: insights from classical polymer theory and atomistic simulations - data from C6 group"

Jul 20, 2022 - SFB 1333 C6 - Holm group, ICP

Tischler, Ingo; Holm, Christian; Schlaich, Alexander, 2022, "Publication data for: "The presence of a wall enhances the probability for ring-closing metathesis: insights from classical polymer theory and atomistic simulations - data from C6 group"", https://doi.org/10.18419/DARUS-1371, DaRUS, V1

All primary data files and processed data of the journal article from C6 group. It contains the simulation and analysis scripts, the ESPResSo commit and a patch to it, with which the data was produced.

Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction'

May 4, 2022 - Institute of Thermodynamics and Thermal Process Engineering

Fleck, Maximilian; Markthaler, Daniel; Stankiewicz, Bartosz; Hansen, Niels, 2022, "Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction'", https://doi.org/10.18419/DARUS-2132, DaRUS, V1, UNF:6:8wyFNcxoOTcKA+4ZpSWLAg== [fileUNF]

Supplementary material for 'Exploring the Effect of Enhanced Sampling on Protein Stability Prediction' containing files to (re-)execute GROMACS simulations performed during the mutation study. This dataset contains simulation input files in GROMACS format accompanying the mentioned publication. Structure, topology, and simulation parameter-files ar...

Supplementary material for 'Influence of Layer Slipping on Adsorption of Light Gases in Covalent Organic Frameworks: A Combined Experimental and Computational Study'

Apr 26, 2022 - Institute of Thermodynamics and Thermal Process Engineering

Kessler, Christopher; Schuldt, Robin; Emmerling, Sebastian; Lotsch, Bettina; Kästner, Johannes; Gross, Joachim; Hansen, Niels, 2022, "Supplementary material for 'Influence of Layer Slipping on Adsorption of Light Gases in Covalent Organic Frameworks: A Combined Experimental and Computational Study'", https://doi.org/10.18419/DARUS-2308, DaRUS, V1, UNF:6:ifmtNZEZHi+MkSvB5rd1dw== [fileUNF]

This dataset contains results from Grand Canonical Monte Carlo (GCMC) Simulation (data/isotherms_sim/) and experiment (data/isotherms/exp). All Data is presented in a jupyter notebook and for a fast overview without executing the notebook also as pdf-file. Furthermore the dataset contains the modified cif files of COF LZU-1, including partial charg...

Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'

Jan 16, 2022 - Institute of Thermodynamics and Thermal Process Engineering

Markthaler, Daniel; Kraus, Hamzeh; Hansen, Niels, 2022, "Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'", https://doi.org/10.18419/DARUS-2109, DaRUS, V1

Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the recent SAMPL8 CB8 "Drugs of Abuse" challenge using the GROMACS MD package. To compare with experimental data, a scheme for correcting the raw simulation estimates was propose...

Supplementary material for 'Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B'

Nov 25, 2021 - Molecular Simulation

Markthaler, Daniel; Hansen, Niels, 2021, "Supplementary material for 'Umbrella sampling and double decoupling data for methanol binding to Candida antarctica lipase B'", https://doi.org/10.18419/DARUS-2104, DaRUS, V1

This dataset contains all relevant simulation input files (topologies, coordinates, simulation parameters), generated simulation output (final configurations, time series of collective variables) together with scripts used for set-up and analysis of the umbrella sampling and double decoupling simulations.

2d microstructure data

Feb 15, 2021 - Data Analytics in Engineering

Lißner, Julian, 2020, "2d microstructure data", https://doi.org/10.18419/DARUS-1151, DaRUS, V2

The hdf5 file contains image data of inclusion based microstructured material and the homogenized effective heat conductivity thereof. The microstructure is defined with a representative volume element with periodic boundary conditions. 30.000 images are contained and split into two inclusion subclasses of circular and rectangular inclusions. Featu...

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