PN 3

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

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1 to 10 of 19 Results

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 doub...
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...
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...
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...
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 mention...
Supplementary Material for 'Entropic barrier of water permeation through single-file channels' Jun 30, 2023 - PN 3-11 Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter; Siligan, Christine; Horner, Andreas, 2023, "Supplementary Material for 'Entropic barrier of water permeation through single-file channels'", https://doi.org/10.18419/darus-3390, DaRUS, V1 Facilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in h...
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...
Replication Data for: Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al Jun 30, 2023 - PN 3-10 Xu, Xiang, 2023, "Replication Data for: Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al", https://doi.org/10.18419/darus-3579, DaRUS, V1 Data for the publication " Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al", Acta Materialia, 255, doi: 10.1016/j.actamat.2023.118986. This data set contains the training sets (VASP files), the utilized moment-tensor-potentials...
PN3A-4(Universität Stuttgart) Oct 16, 2023 Materials 4.0
PN 3A-7(Universität Stuttgart) Mar 8, 2024 Advanced Learning Strategies for Machine Learned Interatomic Potentials

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 doub...

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...

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...

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...

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 mention...

Supplementary Material for 'Entropic barrier of water permeation through single-file channels'

Jun 30, 2023 - PN 3-11

Wachlmayr, Johann; Fläschner, Gotthold; Pluhackova, Kristyna; Sandtner, Walter; Siligan, Christine; Horner, Andreas, 2023, "Supplementary Material for 'Entropic barrier of water permeation through single-file channels'", https://doi.org/10.18419/darus-3390, DaRUS, V1

Facilitated water permeation through narrow biological channels is fundamental for all forms of life. This process involves dehydration of bulk water entering the single-file region and hydrogen bond formation with channel lining amino acid residues. Despite its significance in h...

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...

Replication Data for: Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al

Jun 30, 2023 - PN 3-10

Xu, Xiang, 2023, "Replication Data for: Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al", https://doi.org/10.18419/darus-3579, DaRUS, V1

Data for the publication " Strong impact of spin fluctuations on the antiphase boundaries of weak itinerant ferromagnetic Ni3Al", Acta Materialia, 255, doi: 10.1016/j.actamat.2023.118986. This data set contains the training sets (VASP files), the utilized moment-tensor-potentials...

PN3A-4(Universität Stuttgart)

Oct 16, 2023

Materials 4.0

PN 3A-7(Universität Stuttgart)

Mar 8, 2024

Advanced Learning Strategies for Machine Learned Interatomic Potentials

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