publications

2024

1. matscipy: materials science at the atomic scale with Python

   Petr Grigorev, Lucas Frérot, Fraser Birks, and 17 more authors

   Journal of Open Source Software, Jan 2024

   Abs DOI

   Grigorev et al., (2024). matscipy: materials science at the atomic scale with Python. Journal of Open Source Software, 9(93), 5668, https://doi.org/10.21105/joss.05668

2. dtool and dserver: A flexible ecosystem for findable data

   Johannes L. Hörmann, Luis Yanes, Ashwin Vazhappilly, and 5 more authors

   PLOS ONE, Jun 2024

   Abs DOI

   Making data FAIR—findable, accessible, interoperable, reproducible—has become the recurring theme behind many research data management efforts. dtool is a lightweight data management tool that packages metadata with immutable data to promote accessibility, interoperability, and reproducibility. Each dataset is self-contained and does not require metadata to be stored in a centralised system. This decentralised approach means that finding datasets can be difficult. dtool’s lookup server, short dserver, as defined by a REST API, makes dtool datasets findable, hence rendering the dtool ecosystem fit for a FAIR data management world. Its simplicity, modularity, accessibility and standardisation via API distinguish dtool and dserver from other solutions and enable it to serve as a common denominator for cross-disciplinary research data management. The dtool ecosystem bridges the gap between standardisation-free data management by individuals and FAIR platform solutions with rigid metadata requirements.

2023

1. Molecular simulations of sliding on SDS surfactant films

   Johannes L. Hörmann, Chenxu (刘宸旭) Liu, Yonggang (孟永钢) Meng, and 1 more author

   The Journal of Chemical Physics, Jun 2023

   Abs DOI

   We use molecular dynamics simulations to study the frictional response of monolayers of the anionic surfactant sodium dodecyl sulfate and hemicylindrical aggregates physisorbed on gold. Our simulations of a sliding spherical asperity reveal the following two friction regimes: at low loads, the films show Amonton’s friction with a friction force that rises linearly with normal load, and at high loads, the friction force is independent of the load as long as no direct solid–solid contact occurs. The transition between these two regimes happens when a single molecular layer is confined in the gap between the sliding bodies. The friction force at high loads on a monolayer rises monotonically with film density and drops slightly with the transition to hemicylindrical aggregates. This monotonous increase of friction force is compatible with a traditional plowing model of sliding friction. At low loads, the friction coefficient reaches a minimum at the intermediate surface concentrations. We attribute this behavior to a competition between adhesive forces, repulsion of the compressed film, and the onset of plowing.

2022

1. Lightweight research data management with dtool : a use case

   Johannes L. Hörmann, and Lars Pastewka

   In Proceedings of the 7th bwHPC Symposium, Nov 2022

   Abs DOI

   With the dtool data management framework, we adhere to the FAIR principles – findability, accessibility, interoperability, reusability – beginning at an early stage of the data lifecycle without introducing overwhelming administrative overhead. We show how the use of dtool has been implemented within IMTEK Simulation. In particular, we make data accessible, interoperable and reusable by packaging data and descriptive metadata in dtool datasets. The dtool lookup server makes data on a group-wide S3 object storage repository findable. The dtool ecosystem has proven applicable both for manual research data management as well as rapid generation of thousands of datasets in automized workflows.

2021

1. Molecular Simulations of Electrotunable Lubrication: Viscosity and Wall Slip in Aqueous Electrolytes

   Christian Seidl, Johannes L. Hörmann, and Lars Pastewka

   Tribology Letters, Jan 2021

   Abs DOI

   We study the frictional response of water-lubricated gold electrodes subject to an electrostatic potential difference using molecular dynamics simulations. Contrary to previous studies on electrotunable lubrication that were carried out by fixing the charges, our simulations keep electrodes at fixed electrostatic potential using a variable charge method. For pure water and NaCl solutions, viscosity is independent of the polarization of the electrodes, but wall slip depends on the potential difference. Our findings are in agreement with previous analytical theories of how wall slip is affected by interatomic interactions. The simulations shed light on the role of electrode polarization for wall slip and illustrate a mechanism for controlling friction and nanoscale flow in simple aqueous lubricants.

2020

1. SDS adsorptions films at the H2O – Au(111) interface: molecular dynamics study of AFM tip–surface contact

   Johannes Hörmann, and Lars Pastewka

   In NIC Series, Jan 2020

   Abs

   On the example of the anionic model surfactant sodium dodecyl sulphate at the idealised watergold interface, our present molecular dynamics simulations illuminate the interdependence of adsorption film morphology and its mechanical properties at the nanoscale. Distinct film phases exhibit unique force response features in modelled atomic force microscopy experiments. Hörmann, Johannes; Pastewka, Lars