{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2e8c74229b92f832896c3db3218bdc3f2/simtech", "tags" : [ "EXC2075","PN3","PN3-15","PN3-3","curated" ], "intraHash" : "e8c74229b92f832896c3db3218bdc3f2", "interHash" : "46ca487717fe7a6375f4b00aceee2b09", "label" : "Intermittent molecular motion and first passage statistics for the NMR relaxation of confined water", "user" : "simtech", "description" : "", "date" : "2025-09-04 07:43:28", "changeDate" : "2025-11-03 12:10:54", "count" : 11, "pub-type": "article", "journal": "Physical Review E","publisher":"American Physical Society (APS)", "year": "2025", "url": "http://dx.doi.org/10.1103/1j21-bqdm", "author": [ "Simon Gravelle","Benoit Coasne","Christian Holm","Alexander Schlaich" ], "authors": [ {"first" : "Simon", "last" : "Gravelle"}, {"first" : "Benoit", "last" : "Coasne"}, {"first" : "Christian", "last" : "Holm"}, {"first" : "Alexander", "last" : "Schlaich"} ], "volume": "112","number": "3", "issn" : "2470-0053", "doi" : "10.1103/1j21-bqdm", "bibtexKey": "Gravelle_2025" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2144040b6b4a14e95b80e9fd3b8a97fa8/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "144040b6b4a14e95b80e9fd3b8a97fa8", "interHash" : "6540701198ee27bafd44ab861fa554d3", "label" : "Intermittent flow paths in biofilms grown in a microfluidic channel", "user" : "simtech", "description" : "", "date" : "2025-06-27 15:18:47", "changeDate" : "2026-02-16 15:06:37", "count" : 7, "pub-type": "article", "journal": "Advances in Water Resources","publisher":"Elsevier BV", "year": "2025", "url": "http://dx.doi.org/10.1016/j.advwatres.2025.105018", "author": [ "Kerem Bozkurt","Christoph Lohrmann","Felix Weinhardt","Daniel Hanke","Raphael Hopp","Robin Gerlach","Christian Holm","Holger Class" ], "authors": [ {"first" : "Kerem", "last" : "Bozkurt"}, {"first" : "Christoph", "last" : "Lohrmann"}, {"first" : "Felix", "last" : "Weinhardt"}, {"first" : "Daniel", "last" : "Hanke"}, {"first" : "Raphael", "last" : "Hopp"}, {"first" : "Robin", "last" : "Gerlach"}, {"first" : "Christian", "last" : "Holm"}, {"first" : "Holger", "last" : "Class"} ], "pages": "105018", "issn" : "0309-1708", "doi" : "10.1016/j.advwatres.2025.105018", "bibtexKey": "Bozkurt_2025" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/245b9563e17b3baae4c050eebbb8e189a/simtech", "tags" : [ "EXC2075","PN3","PN3-15","PN3-3","curated" ], "intraHash" : "45b9563e17b3baae4c050eebbb8e189a", "interHash" : "46ca487717fe7a6375f4b00aceee2b09", "label" : "Intermittent molecular motion and first passage statistics for the NMR relaxation of confined water", "user" : "simtech", "description" : "[2501.17596] Intermittent molecular motion and first passage statistics for the NMR relaxation of confined water", "date" : "2025-03-06 16:17:17", "changeDate" : "2026-02-16 15:06:37", "count" : 11, "pub-type": "misc", "year": "2025", "url": "https://arxiv.org/abs/2501.17596", "author": [ "Simon Gravelle","Benoit Coasne","Christian Holm","Alexander Schlaich" ], "authors": [ {"first" : "Simon", "last" : "Gravelle"}, {"first" : "Benoit", "last" : "Coasne"}, {"first" : "Christian", "last" : "Holm"}, {"first" : "Alexander", "last" : "Schlaich"} ], "eprint" : "2501.17596", "archiveprefix" : "arXiv", "primaryclass" : "cond-mat.soft", "bibtexKey": "gravelle2025intermittentmolecularmotionpassage" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2cf84eb5764cc1a803a303492eff66c13/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "cf84eb5764cc1a803a303492eff66c13", "interHash" : "0379720d52733037fed53f62ebb46e90", "label" : "Electrolytes in conducting nanopores: Revisiting constant charge and constant potential simulations", "user" : "simtech", "description" : "Electrolytes in conducting nanopores: Revisiting constant charge and constant potential simulations - PubMed", "date" : "2024-09-12 10:07:34", "changeDate" : "2025-02-28 16:08:06", "count" : 7, "pub-type": "article", "journal": "The Journal of chemical physics","address":"United States", "year": "2024", "url": "https://pubmed.ncbi.nlm.nih.gov/39248380", "author": [ "Alexander Reinauer","Svyatoslav Kondrat","Christian Holm" ], "authors": [ {"first" : "Alexander", "last" : "Reinauer"}, {"first" : "Svyatoslav", "last" : "Kondrat"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "161","number": "10","pages": "104101--","abstract": "Simulating electrolyte-electrode systems poses challenges due to the need to account for the electrode's response to ion movements in order to maintain a constant electrode potential, which slows down the simulations. To circumvent this, computationally more efficient constant charge (CC) simulations are sometimes employed. However, the accuracy of CC simulations in capturing the behavior of electrolyte-electrode systems remains unclear, especially for microporous electrodes. Herein, we consider electrolyte-filled slit nanopores and systematically analyze the in-pore ion structure and diffusivity using CC and constant potential simulations. Our results indicate that CC simulations provide comparable pore occupancies at high bulk ion densities and for highly charged pores, but they fail to accurately describe the ion structure and dynamics, particularly in quasi-2D (single-layer) pores and at low ion densities. We attribute these results to the superionic state emerging in conducting nanoconfinement and its interplay with excluded volume interactions.", "issn" : "10897690", "comment" : "39248380[pmid]", "doi" : "10.1063/5.0226959", "bibtexKey": "reinauer24" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/264b23c6f8b77424390dddd95190c6ba8/simtech", "tags" : [ "EXC2075","PN1","PN3","PN3-15","PN3-3","curated" ], "intraHash" : "64b23c6f8b77424390dddd95190c6ba8", "interHash" : "d4d17670b880d3729f5be14a2d36e1af", "label" : "Assessing the Validity of NMR Relaxation Rates Obtained from Coarse-Grained Simulations of PEG\u2013Water Mixtures", "user" : "simtech", "description" : "", "date" : "2024-07-17 10:52:57", "changeDate" : "2024-07-19 15:09:42", "count" : 6, "pub-type": "article", "journal": "The Journal of Physical Chemistry B","publisher":"American Chemical Society (ACS)", "year": "2023", "url": "https://doi.org/10.1021%2Facs.jpcb.3c01646", "author": [ "Simon Gravelle","David Beyer","Mariano Brito","Alexander Schlaich","Christian Holm" ], "authors": [ {"first" : "Simon", "last" : "Gravelle"}, {"first" : "David", "last" : "Beyer"}, {"first" : "Mariano", "last" : "Brito"}, {"first" : "Alexander", "last" : "Schlaich"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "127","number": "25","pages": "5601--5608", "doi" : "10.1021/acs.jpcb.3c01646", "bibtexKey": "Gravelle_2023" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/21f4e2fcfb7ac368c54891b15d7efe1d7/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "1f4e2fcfb7ac368c54891b15d7efe1d7", "interHash" : "8db4b9267a1353f5a43730809959a080", "label" : "Machine Learning-Driven Investigation of the Structure and Dynamics of the BMIM-BF\u2084 Room Temperature Ionic Liquid", "user" : "simtech", "description" : "Machine Learning-Driven Investigation of the Structure and Dynamics of the BMIM-BF\u2084 Room Temperature Ionic Liquid - Faraday Discussions (RSC Publishing) DOI:10.1039/D4FD00025K", "date" : "2024-03-26 08:51:07", "changeDate" : "2024-06-21 18:11:21", "count" : 6, "pub-type": "article", "journal": "Faraday Discuss.","publisher":"The Royal Society of Chemistry", "year": "2024", "url": "http://dx.doi.org/10.1039/D4FD00025K", "author": [ "Fabian Zills","Moritz René Schäfer","Samuel Tovey","Johannes Kästner","Christian Holm" ], "authors": [ {"first" : "Fabian", "last" : "Zills"}, {"first" : "Moritz René", "last" : "Schäfer"}, {"first" : "Samuel", "last" : "Tovey"}, {"first" : "Johannes", "last" : "Kästner"}, {"first" : "Christian", "last" : "Holm"} ], "abstract": "Room-temperature ionic liquids are an exciting group of materials with the potential to revolutionize energy storage. Due to their chemical structure and means of interaction, they are challenging to study computationally. Classical descriptions of their inter- and intra-molecular interactions require time intensive parametrization of force-fields which is prone to assumptions. While ab initio molecular dynamics approaches can capture all necessary interactions, they are too slow to achieve the time and length scales required. In this work, we take a step towards addressing these challenges by applying state-of-the-art machine-learned potentials to the simulation of 1-Butyl-3-methylimidazolium tetrafluoroborat. We demonstrate a learning-on-the-fly procedure to train machine-learned potentials from single-point density functional theory calculations before performing production molecular dynamics simulations. Obtained structural and dynamical properties are in good agreement with computational and experimental references. Furthermore, our results show that hybrid machine-learned potentials can contribute to an improved prediction accuracy by mitigating the inherent shortsightedness of the models. Given that room-temperature ionic liquids necessitate long simulations to address their slow dynamics, achieving an optimal balance between accuracy and computational cost becomes imperative. To facilitate further investigation of these materials, we have made our IPSuite-based training and simulation workflow publicly accessible, enabling easy replication or adaptation to similar systems.", "doi" : "10.1039/D4FD00025K", "bibtexKey": "zills24a" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2cb318819a15eed1c2114f80a89e7e4fd/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "cb318819a15eed1c2114f80a89e7e4fd", "interHash" : "3d8baf8eb7110535d043bc3f8b6c2e93", "label" : "Influence of bacterial swimming and hydrodynamics on infection by phages", "user" : "simtech", "description" : "Influence of bacterial swimming and hydrodynamics on infection by phages | bioRxiv", "date" : "2024-03-26 08:42:29", "changeDate" : "2024-06-21 18:11:21", "count" : 7, "pub-type": "article", "journal": "bioRxiv","publisher":"Cold Spring Harbor Laboratory", "year": "2024", "url": "https://www.biorxiv.org/content/early/2024/01/16/2024.01.15.575727", "author": [ "Christoph Lohrmann","Christian Holm","Sujit S. Datta" ], "authors": [ {"first" : "Christoph", "last" : "Lohrmann"}, {"first" : "Christian", "last" : "Holm"}, {"first" : "Sujit S.", "last" : "Datta"} ], "abstract": "Bacteriophages (\u201Cphages\u201D) are viruses that infect bacteria. Since they do not actively self-propel, phages rely on thermal diffusion to find target cells\u2014but 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 and is infected by 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 both the cell body and flagellar propeller are infected by phages, 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.", "elocation-id" : "2024.01.15.575727", "eprint" : "https://www.biorxiv.org/content/early/2024/01/16/2024.01.15.575727.full.pdf", "doi" : "10.1101/2024.01.15.575727", "bibtexKey": "lohrmann24a" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/249fcdaaaf0f131bd07dfc3421f0ed9ee/simtech", "tags" : [ "EXC2075","PN3","PN3-12","PN3-3","curated" ], "intraHash" : "49fcdaaaf0f131bd07dfc3421f0ed9ee", "interHash" : "3b0b8c6ac78b3bdc154adb1820accfde", "label" : "ESPResSo, a Versatile Open-Source Software Package for Simulating Soft Matter Systems", "user" : "simtech", "description" : "", "date" : "2024-03-14 11:00:47", "changeDate" : "2024-09-02 15:11:03", "count" : 9, "pub-type": "incollection", "booktitle": "Reference Module in Chemistry, Molecular Sciences and Chemical Engineering","publisher":"Elsevier", "year": "2023", "url": "https://www.sciencedirect.com/science/article/pii/B9780128219782001033", "author": [ "Rudolf Weeber","Jean-Noël Grad","David Beyer","Pablo M. Blanco","Patrick Kreissl","Alexander Reinauer","Ingo Tischler","Peter Košovan","Christian Holm" ], "authors": [ {"first" : "Rudolf", "last" : "Weeber"}, {"first" : "Jean-Noël", "last" : "Grad"}, {"first" : "David", "last" : "Beyer"}, {"first" : "Pablo M.", "last" : "Blanco"}, {"first" : "Patrick", "last" : "Kreissl"}, {"first" : "Alexander", "last" : "Reinauer"}, {"first" : "Ingo", "last" : "Tischler"}, {"first" : "Peter", "last" : "Košovan"}, {"first" : "Christian", "last" : "Holm"} ], "abstract": "Particle-based coarse-grained simulations bridge the scales between models with atomistic details and a continuum description. They are typically applied to systems ranging from the nanometer scale to the micron scale. Examples for these systems are polymers, colloids or biological cells. In this chapter we will first provide an overview of simulation techniques suitable for coarse-grained models, in particular molecular dynamics and Monte Carlo schemes. Afterwards the simulation package ESPResSo is shortly described, together with simulation models from different fields that illustrate its new capabilities. In particular, we highlight simulations of weak polyelectrolytes, hydrogels, soft magnetic materials and chemical reactions subject to a flow field.", "isbn" : "978-0-12-409547-2", "doi" : "https://doi.org/10.1016/B978-0-12-821978-2.00103-3", "bibtexKey": "weeber2023espresso" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f965023517814d651514617573e08ce5/simtech", "tags" : [ "EXC2075","PN3","PN3-3","PN3A-9","curated" ], "intraHash" : "f965023517814d651514617573e08ce5", "interHash" : "2c9d833f89279fbcb2c472ff16efdfb8", "label" : "Disentanglement of Surface and Confinement Effects for Diene Metathesis in Mesoporous Confinement", "user" : "simtech", "description" : "", "date" : "2024-01-12 13:53:06", "changeDate" : "2024-07-17 11:05:53", "count" : 8, "pub-type": "article", "journal": "ACS Omega","publisher":"American Chemical Society (ACS)", "year": "2023", "url": "http://dx.doi.org/10.1021/acsomega.3c06195", "author": [ "Ingo Tischler","Alexander Schlaich","Christian Holm" ], "authors": [ {"first" : "Ingo", "last" : "Tischler"}, {"first" : "Alexander", "last" : "Schlaich"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "9","number": "1","pages": "598\u2013606","abstract": "We study the effects of a planar interface and confinement on a generic catalytically activated ring-closing polymerization reaction near an unstructured catalyst. For this, we employ a coarse-grained polymer model using grand-canonical molecular dynamics simulations with a Monte Carlo reaction scheme. Inspired by recent experiments in the group of M. Buchmeiser that demonstrated an increase in ring-closing selectivity under confinement, we show that both the interface effects, i.e., placing the catalyst near a planar wall, and the confinement effects, i.e., locating the catalyst within a pore, lead to an increase of selectivity. We furthermore demonstrate that curvature effects for cylindrical mesopores (2 nm < d < 12.3 nm) influence the distribution of the chain ends, leading to a further increase in selectivity. This leads us to speculate that specially corrugated surfaces might also help to enhance catalytically activated polymerization processes.", "issn" : "2470-1343", "doi" : "10.1021/acsomega.3c06195", "bibtexKey": "Tischler_2023" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/21d8472878d75be7808fda58f70b66ee5/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "1d8472878d75be7808fda58f70b66ee5", "interHash" : "3e600ed6517090326c119d9399f38302", "label" : "A screening of results on the decay length in concentrated electrolytes", "user" : "simtech", "description" : "", "date" : "2023-11-29 12:15:32", "changeDate" : "2024-06-18 15:00:36", "count" : 13, "pub-type": "article", "journal": "Faraday Discuss.","publisher":"The Royal Society of Chemistry", "year": "2023", "url": "http://dx.doi.org/10.1039/D3FD00043E", "author": [ "Henrik Jäger","Alexander Schlaich","Jie Yang","Cheng Lian","Svyatoslav Kondrat","Christian Holm" ], "authors": [ {"first" : "Henrik", "last" : "Jäger"}, {"first" : "Alexander", "last" : "Schlaich"}, {"first" : "Jie", "last" : "Yang"}, {"first" : "Cheng", "last" : "Lian"}, {"first" : "Svyatoslav", "last" : "Kondrat"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "246","number": "0","pages": "520-539","abstract": "Screening of electrostatic interactions in room-temperature ionic liquids and concentrated electrolytes has recently attracted much attention as surface force balance experiments have suggested the emergence of unanticipated anomalously large screening lengths at high ion concentrations. Termed underscreening, this effect was ascribed to the bulk properties of concentrated ionic systems. However, underscreening under experimentally relevant conditions is not predicted by classical theories and challenges our understanding of electrostatic correlations. Despite the enormous effort in performing large-scale simulations and new theoretical investigations, the origin of the anomalously long-range screening length remains elusive. This contribution briefly summarises the experimental, analytical and simulation results on ionic screening and the scaling behaviour of screening lengths. We then present an atomistic simulation approach that accounts for the solvent and ion exchange with a reservoir. We find that classical density functional theory (DFT) for concentrated electrolytes under confinement reproduces ion adsorption at charged interfaces surprisingly well. With DFT, we study confined electrolytes using implicit and explicit solvent models and the dependence on the solvent's dielectric properties. Our results demonstrate how the absence vs. presence of solvent particles and their discrete nature affect the short and long-range screening in concentrated ionic systems.", "doi" : "10.1039/D3FD00043E", "bibtexKey": "D3FD00043E" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2c533a4762e8c76dcb663b552ecb3a362/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "c533a4762e8c76dcb663b552ecb3a362", "interHash" : "11450f5c0bcf7ed153f788a8d8661614", "label" : "Solvent Effects on Structure and Screening in Confined Electrolytes", "user" : "simtech", "description" : "", "date" : "2023-11-29 12:05:33", "changeDate" : "2024-06-18 15:00:36", "count" : 10, "pub-type": "article", "journal": "Phys. Rev. Lett.","publisher":"American Physical Society", "year": "2023", "url": "https://link.aps.org/doi/10.1103/PhysRevLett.131.118201", "author": [ "Jie Yang","Svyatoslav Kondrat","Cheng Lian","Honglai Liu","Alexander Schlaich","Christian Holm" ], "authors": [ {"first" : "Jie", "last" : "Yang"}, {"first" : "Svyatoslav", "last" : "Kondrat"}, {"first" : "Cheng", "last" : "Lian"}, {"first" : "Honglai", "last" : "Liu"}, {"first" : "Alexander", "last" : "Schlaich"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "131","number": "11","pages": "118201","abstract": "Using classical density functional theory, we investigate the influence of solvent on the structure and ionic screening of electrolytes under slit confinement and in contact with a reservoir. We consider a symmetric electrolyte with implicit and explicit solvent models and find that spatially resolving solvent molecules is essential for the ion structure at confining walls, excess ion adsorption, and the pressure exerted on the walls. Despite this, we observe only moderate differences in the period of oscillations of the pressure with the slit width and virtually coinciding decay lengths as functions of the scaling variable $\\sigma_ion/łambda_D$, where $\\sigma_ion$ is the ion diameter and $łambda_D$ the Debye length. Moreover, in the electrostatic-dominated regime, this scaling behavior is practically independent of the relative permittivity and its dependence on the ion concentration. In contrast, the crossover to the hard-core-dominated regime depends sensitively on all three factors.", "numpages" : "6", "doi" : "10.1103/PhysRevLett.131.118201", "bibtexKey": "PhysRevLett.131.118201" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2472164dad0e076a669624a400e5c2a46/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "472164dad0e076a669624a400e5c2a46", "interHash" : "952999cda585d7085b9bab8b87535944", "label" : "NMR Investigation of Water in Salt Crusts: Insights from Experiments and Molecular Simulations", "user" : "simtech", "description" : "", "date" : "2023-11-23 15:53:13", "changeDate" : "2024-06-18 15:00:36", "count" : 10, "pub-type": "article", "journal": "Langmuir","publisher":"American Chemical Society", "year": "2023", "url": "https://doi.org/10.1021/acs.langmuir.3c00036", "author": [ "Simon Gravelle","Sabina Haber-Pohlmeier","Carlos Mattea","Siegfried Stapf","Christian Holm","Alexander Schlaich" ], "authors": [ {"first" : "Simon", "last" : "Gravelle"}, {"first" : "Sabina", "last" : "Haber-Pohlmeier"}, {"first" : "Carlos", "last" : "Mattea"}, {"first" : "Siegfried", "last" : "Stapf"}, {"first" : "Christian", "last" : "Holm"}, {"first" : "Alexander", "last" : "Schlaich"} ], "volume": "39","number": "22","pages": "7548--7556","abstract": "The evaporation of water from bare soil is often accompanied by the formation of a layer of crystallized salt, a process that must be understood in order to address the issue of soil salinization. Here, we use nuclear magnetic relaxation dispersion measurements to better understand the dynamic properties of water within two types of salt crusts: sodium chloride (NaCl) and sodium sulfate (Na2SO4). Our experimental results display a stronger dispersion of the relaxation time T1 with frequency for the case of sodium sulfate as compared to sodium chloride salt crusts. To gain insight into these results, we perform molecular dynamics simulations of salt solutions confined within slit nanopores made of either NaCl or Na2SO4. We find a strong dependence of the value of the relaxation time T1 on pore size and salt concentration. Our simulations reveal the complex interplay between the adsorption of ions at the solid surface, the structure of water near the interface, and the dispersion of T1 at low frequency, which we attribute to adsorption\u2013desorption events.", "shorttitle" : "NMR Investigation of Water in Salt Crusts", "shortjournal" : "Langmuir", "file" : "/home/pstaerk/Zotero/storage/XQS6MXB2/Gravelle et al. - 2023 - NMR Investigation of Water in Salt Crusts Insight.pdf", "issn" : "0743-7463", "journaltitle" : "Langmuir", "doi" : "10.1021/acs.langmuir.3c00036", "urldate" : "2023-11-23", "bibtexKey": "gravelle23a" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2f6dc2065235f680a7a47985cda008a00/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "f6dc2065235f680a7a47985cda008a00", "interHash" : "cddcad68860456aa98aab6b28faa252c", "label" : "A novel model for biofilm initiation in porous media flow", "user" : "simtech", "description" : "", "date" : "2023-11-16 13:52:17", "changeDate" : "2023-12-06 08:55:18", "count" : 9, "pub-type": "article", "journal": "Soft Matter","publisher":"The Royal Society of Chemistry", "year": "2023", "url": "http://dx.doi.org/10.1039/D3SM00575E", "author": [ "Christoph Lohrmann","Christian Holm" ], "authors": [ {"first" : "Christoph", "last" : "Lohrmann"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "19","number": "36","pages": "6920-6928","abstract": "Bacteria often form biofilms in porous environments where an external flow is present, such as soil or filtration systems. To understand the initial stages of biofilm formation, one needs to study the interactions between cells, the fluid and the confining geometries. Here, we present an agent based numerical model for bacteria that takes into account the planktonic stage of motile cells as well as surface attachment and biofilm growth in a lattice Boltzmann fluid. In the planktonic stage we show the importance of the interplay between complex flow and cell motility when determining positions of surface attachment. In the growth stage we show the applicability of our model by investigating how external flow and biofilm stiffness determine qualitative colony morphologies as well as quantitative measurements of, e.g., permeability.", "doi" : "10.1039/D3SM00575E", "bibtexKey": "D3SM00575E" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/228f9e24b73a5a941e807f2495e5a7c5b/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "28f9e24b73a5a941e807f2495e5a7c5b", "interHash" : "9887600c4087f5fade9a96138a5aa84c", "label" : "Optimal motility strategies for self-propelled agents to explore porous media", "user" : "simtech", "description" : "", "date" : "2023-11-16 13:49:39", "changeDate" : "2023-12-06 08:55:18", "count" : 10, "pub-type": "article", "journal": "Phys. Rev. E","publisher":"American Physical Society", "year": "2023", "url": "https://link.aps.org/doi/10.1103/PhysRevE.108.054401", "author": [ "Christoph Lohrmann","Christian Holm" ], "authors": [ {"first" : "Christoph", "last" : "Lohrmann"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "108","number": "5","pages": "054401","abstract": "Microrobots for, e.g., biomedical applications, need to be equipped with motility strategies that enable them to navigate through complex environments. Inspired by biological microorganisms we re-create motility patterns such as run-and-reverse, run-and-tumble, or run-reverse-flick applied to active rodlike particles in silico. We investigate their capability to efficiently explore disordered porous environments with various porosities and mean pore sizes ranging down to the scale of the active particle. By calculating the effective diffusivity for the different patterns, we can predict the optimal one for each porous sample geometry. We find that providing the agent with very basic sensing and decision-making capabilities yields a motility pattern outperforming the biologically inspired patterns for all investigated porous samples.", "numpages" : "9", "doi" : "10.1103/PhysRevE.108.054401", "bibtexKey": "PhysRevE.108.054401" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2405c1a037993c6bdc88b629d78501b03/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "405c1a037993c6bdc88b629d78501b03", "interHash" : "40d9059df9ca0bfc363e577fbc9d9616", "label" : "A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems", "user" : "simtech", "description" : "", "date" : "2023-08-01 15:35:52", "changeDate" : "2023-11-08 16:37:05", "count" : 6, "pub-type": "article", "journal": "Journal of computational science","publisher":"Elsevier", "year": "2022", "url": "", "author": [ "Ingo Tischler","Florian Weik","Robert Kaufmann","Michael Kuron","Rudolf Weeber","Christian Holm" ], "authors": [ {"first" : "Ingo", "last" : "Tischler"}, {"first" : "Florian", "last" : "Weik"}, {"first" : "Robert", "last" : "Kaufmann"}, {"first" : "Michael", "last" : "Kuron"}, {"first" : "Rudolf", "last" : "Weeber"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "63","pages": "101770", "research-areas" : "Computer Science", "language" : "eng", "issn" : "1877-7503 and 1877-7511", "affiliation" : "Holm, C (Corresponding Author), Univ Stuttgart, Inst Computat Phys, Stuttgart, Germany.\r\n Tischler, Ingo; Weik, Florian; Kaufmann, Robert; Kuron, Michael; Weeber, Rudolf; Holm, Christian, Univ Stuttgart, Inst Computat Phys, Stuttgart, Germany.", "unique-id" : "WOS:000841960600005", "doi" : "10.1016/j.jocs.2022.101770", "bibtexKey": "tischler2022thermalized" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2fc352fb28287f411ac43eb2413c0c7b7/simtech", "tags" : [ "EXC2075","PN1","PN1-4","PN3","PN3-3","curated","merged" ], "intraHash" : "fc352fb28287f411ac43eb2413c0c7b7", "interHash" : "8ddc01e2e16dad7827ff3dcf2a814b50", "label" : "Permeability Estimation of Regular Porous Structures: A Benchmark for Comparison of Methods", "user" : "simtech", "description" : "", "date" : "2023-07-18 10:54:04", "changeDate" : "2023-12-06 08:55:18", "count" : 20, "pub-type": "article", "journal": "Transport in Porous Media","publisher":"Springer", "year": "2021", "url": "https://link.springer.com/article/10.1007%2Fs11242-021-01586-2", "author": [ "Arndt Wagner","Elissa Eggenweiler","Felix Weinhardt","Zubin Trivedi","David Krach","Christoph Lohrmann","Kartik Jain","Nikolaos Karadimitriou","Carina Bringedal","Paul Voland","Christian Holm","Holger Class","Holger Steeb","Iryna Rybak" ], "authors": [ {"first" : "Arndt", "last" : "Wagner"}, {"first" : "Elissa", "last" : "Eggenweiler"}, {"first" : "Felix", "last" : "Weinhardt"}, {"first" : "Zubin", "last" : "Trivedi"}, {"first" : "David", "last" : "Krach"}, {"first" : "Christoph", "last" : "Lohrmann"}, {"first" : "Kartik", "last" : "Jain"}, {"first" : "Nikolaos", "last" : "Karadimitriou"}, {"first" : "Carina", "last" : "Bringedal"}, {"first" : "Paul", "last" : "Voland"}, {"first" : "Christian", "last" : "Holm"}, {"first" : "Holger", "last" : "Class"}, {"first" : "Holger", "last" : "Steeb"}, {"first" : "Iryna", "last" : "Rybak"} ], "volume": "138","number": "1","pages": "1--23","abstract": "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\u2013Carman 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.", "doi" : "10.1007/s11242-021-01586-2", "bibtexKey": "wagner2021permeability" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/20bd1f5edbe0ddc83bde1a1a2544022eb/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated","merged" ], "intraHash" : "0bd1f5edbe0ddc83bde1a1a2544022eb", "interHash" : "fc735d5acafb83ca634b3831372c5079", "label" : "DFT accurate interatomic potential for molten NaCl from machine learning", "user" : "simtech", "description" : "", "date" : "2021-12-20 09:55:56", "changeDate" : "2023-11-08 16:37:05", "count" : 9, "pub-type": "article", "journal": "The Journal of Physical Chemistry C","publisher":"ACS Publications", "year": "2020", "url": "https://pubs.acs.org/doi/10.1021/acs.jpcc.0c08870", "author": [ "Samuel Tovey","Anand Narayanan Krishnamoorthy","Ganesh Sivaraman","Jicheng Guo","Chris Benmore","Andreas Heuer","Christian Holm" ], "authors": [ {"first" : "Samuel", "last" : "Tovey"}, {"first" : "Anand", "last" : "Narayanan Krishnamoorthy"}, {"first" : "Ganesh", "last" : "Sivaraman"}, {"first" : "Jicheng", "last" : "Guo"}, {"first" : "Chris", "last" : "Benmore"}, {"first" : "Andreas", "last" : "Heuer"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "124","number": "47","pages": "25760-25768", "doi" : "10.1021/acs.jpcc.0c08870", "bibtexKey": "tovey2020dft" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/29cb92af8a6424cc32d435e0c9c933f59/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "9cb92af8a6424cc32d435e0c9c933f59", "interHash" : "cb9ff1b8738c6d11b2ccf2711ab0a5ff", "label" : "An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids", "user" : "simtech", "description" : "", "date" : "2021-12-15 10:40:22", "changeDate" : "2023-11-08 16:37:05", "count" : 8, "pub-type": "article", "year": "2021", "url": "", "author": [ "Michael Kuron","Cameron Stewart","Joost de Graaf","Christian Holm" ], "authors": [ {"first" : "Michael", "last" : "Kuron"}, {"first" : "Cameron", "last" : "Stewart"}, {"first" : "Joost", "last" : "de Graaf"}, {"first" : "Christian", "last" : "Holm"} ], "doi" : "10.1140/epje/s10189-020-00005-6", "bibtexKey": "kuron2021extensible" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/29f5fa95b4a32953c47849a6ba8584778/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "9f5fa95b4a32953c47849a6ba8584778", "interHash" : "031b2a68497a37697fb5f67f488e623e", "label" : "Modeling the current modulation of bundled DNA structures in nanopores", "user" : "simtech", "description" : "", "date" : "2021-12-15 10:40:15", "changeDate" : "2023-11-08 16:37:05", "count" : 8, "pub-type": "article", "journal": "The Journal of Chemical Physics", "year": "2021", "url": "https://doi.org/10.1063/5.0038530", "author": [ "Kai Szuttor","Florian Weik","Jean-Noël Grad","Christian Holm" ], "authors": [ {"first" : "Kai", "last" : "Szuttor"}, {"first" : "Florian", "last" : "Weik"}, {"first" : "Jean-Noël", "last" : "Grad"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "154","number": "5","pages": "054901", "eprint" : "https://doi.org/10.1063/5.0038530", "doi" : "10.1063/5.0038530", "bibtexKey": "szuttor2021modeling" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2e94aa5cdb67e194631082c03f28408d5/simtech", "tags" : [ "EXC2075","PN3","PN3-3","curated" ], "intraHash" : "e94aa5cdb67e194631082c03f28408d5", "interHash" : "ab2771eef7a622668f8766da921041a4", "label" : "A numerical investigation of analyte size effects in nanopore sensing systems", "user" : "simtech", "description" : "", "date" : "2021-12-15 10:39:48", "changeDate" : "2023-11-08 16:37:05", "count" : 8, "pub-type": "article", "journal": "The Journal of Chemical Physics", "year": "2021", "url": "https://doi.org/10.1063/5.0065085", "author": [ "Kai Szuttor","Patrick Kreissl","Christian Holm" ], "authors": [ {"first" : "Kai", "last" : "Szuttor"}, {"first" : "Patrick", "last" : "Kreissl"}, {"first" : "Christian", "last" : "Holm"} ], "volume": "155","number": "13","pages": "134902", "eprint" : "https://doi.org/10.1063/5.0065085", "doi" : "10.1063/5.0065085", "bibtexKey": "szuttor2021numerical" } ] }