Browsing by Author "Lohrmann, Christoph"

Now showing 1 - 4 of 4

Open Access
Influence of bacterial swimming and hydrodynamics on attachment of phages
(2024) Lohrmann, Christoph; Holm, Christian; Datta, Sujit S.
Bacteriophages (“phages”) are viruses that infect bacteria. Since they do not actively self-propel, phages rely on thermal diffusion to find target cells - but can also be advected by fluid flows, such as those generated by motile bacteria themselves in bulk fluids. How does the flow field generated by a swimming bacterium influence how it encounters phages? Here, we address this question using coupled molecular dynamics and lattice Boltzmann simulations of flagellated bacteria swimming through a bulk fluid containing uniformly-dispersed phages. We find that while swimming increases the rate at which phages attach to both the cell body and flagellar propeller, hydrodynamic interactions strongly suppress this increase at the cell body, but conversely enhance this increase at the flagellar bundle. Our results highlight the pivotal influence of hydrodynamics on the interactions between bacteria and phages, as well as other diffusible species, in microbial environments.
Open Access
MDSuite : comprehensive post-processing tool for particle simulations
(2023) Tovey, Samuel; Zills, Fabian; Torres-Herrador, Francisco; Lohrmann, Christoph; Brückner, Marco; Holm, Christian
Particle-Based (PB) simulations, including Molecular Dynamics (MD), provide access to system observables that are not easily available experimentally. However, in most cases, PB data needs to be processed after a simulation to extract these observables. One of the main challenges in post-processing PB simulations is managing the large amounts of data typically generated without incurring memory or computational capacity limitations. In this work, we introduce the post-processing tool: MDSuite. This software, developed in Python, combines state-of-the-art computing technologies such as TensorFlow, with modern data management tools such as HDF5 and SQL for a fast, scalable, and accurate PB data processing engine. This package, built around the principles of FAIR data, provides a memory safe, parallelized, and GPU accelerated environment for the analysis of particle simulations. The software currently offers 17 calculators for the computation of properties including diffusion coefficients, thermal conductivity, viscosity, radial distribution functions, coordination numbers, and more. Further, the object-oriented framework allows for the rapid implementation of new calculators or file-readers for different simulation software. The Python front-end provides a familiar interface for many users in the scientific community and a mild learning curve for the inexperienced. Future developments will include the introduction of more analysis associated with ab-initio methods, colloidal/macroscopic particle methods, and extension to experimental data.
Open Access
Motile bacteria in complex environments
(2024) Lohrmann, Christoph; Holm, Christian (Prof. Dr.)
Open Access
Permeability estimation of regular porous structures : a benchmark for comparison of methods
(2021) Wagner, Arndt; Eggenweiler, Elissa; Weinhardt, Felix; Trivedi, Zubin; Krach, David; Lohrmann, Christoph; Jain, Kartik; Karadimitriou, Nikolaos; Bringedal, Carina; Voland, Paul; Holm, Christian; Class, Holger; Steeb, Holger; Rybak, Iryna
The intrinsic permeability is a crucial parameter to characterise and quantify fluid flow through porous media. However, this parameter is typically uncertain, even if the geometry of the pore structure is available. In this paper, we perform a comparative study of experimental, semi-analytical and numerical methods to calculate the permeability of a regular porous structure. In particular, we use the Kozeny-Carman relation, different homogenisation approaches (3D, 2D, very thin porous media and pseudo 2D/3D), pore-scale simulations (lattice Boltzmann method, Smoothed Particle Hydrodynamics and finite-element method) and pore-scale experiments (microfluidics). A conceptual design of a periodic porous structure with regularly positioned solid cylinders is set up as a benchmark problem and treated with all considered methods. The results are discussed with regard to the individual strengths and limitations of the used methods. The applicable homogenisation approaches as well as all considered pore-scale models prove their ability to predict the permeability of the benchmark problem. The underestimation obtained by the microfluidic experiments is analysed in detail using the lattice Boltzmann method, which makes it possible to quantify the influence of experimental setup restrictions.