Universität Stuttgart
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Item Open Access Collective variables in data-centric neural network training(2023) Nikolaou, KonstantinNeural Networks have become beneficial tools for physics research. While they provide a powerful tool for data-driven modeling, their success is accompanied by a lack of interpretability. This thesis aims to add transparency to the opaque nature of NNs by means of collective variables, a concept well-known in the field of statistical physics. Three collective variables are introduced that emerge from the interactions between neurons and data. These observables enable one to capture holistic behavior of the network and are used to conduct an analysis of neural network training, focusing on data. Through the investigations, the collective variables are applied to selections from a novel sampling method: Random Network Distillation (RND). Besides studying collective variables, the investigation of Random Network Distillation as a data selection method composes the second part of this thesis. The method is analyzed and optimized with respect to its components, aiming to understand and improve the data selection process. It is shown that RND can be used to select data sets that are beneficial for neural network training, giving rise to its application in fields like active learning. The collective variables are leveraged to further investigate the selection method and its effect on neural network training, revealing previously unknown properties of RND-selected data sets. The potential of the collective variables is demonstrated and discussed from a data-centric perspective. They are shown to be discriminative towards the information content of data and give rise to novel insights into the nature of neural network training. In addition to fundamental research on neural networks, the collective variables offer several potential applications including the identification of adversarial attacks and facilitating neural architecture search.Item Open Access Machine learning-driven investigation of the structure and dynamics of the BMIM-BF4 room temperature ionic liquid(2024) Zills, Fabian; Schäfer, Moritz René; Tovey, Samuel; Kästner, Johannes; Holm, ChristianRoom-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 tetrafluoroborate. 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.Item Open Access Water structuring induces nonuniversal hydration repulsion between polar surfaces : quantitative comparison between molecular simulations, theory, and experiments(2024) Schlaich, Alexander; Daldrop, Jan O.; Kowalik, Bartosz; Kanduč, Matej; Schneck, Emanuel; Netz, Roland R.Polar surfaces in water typically repel each other at close separations, even if they are charge-neutral. This so-called hydration repulsion balances the van der Waals attraction and gives rise to a stable nanometric water layer between the polar surfaces. The resulting hydration water layer is crucial for the properties of concentrated suspensions of lipid membranes and hydrophilic particles in biology and technology, but its origin is unclear. It has been suggested that surface-induced molecular water structuring is responsible for the hydration repulsion, but a quantitative proof of this water-structuring hypothesis is missing. To gain an understanding of the mechanism causing hydration repulsion, we perform molecular simulations of different planar polar surfaces in water. Our simulated hydration forces between phospholipid bilayers agree perfectly with experiments, validating the simulation model and methods. For the comparison with theory, it is important to split the simulated total surface interaction force into a direct contribution from surface-surface molecular interactions and an indirect water-mediated contribution. We find the indirect hydration force and the structural water-ordering profiles from the simulations to be in perfect agreement with the predictions from theoretical models that account for the surface-induced water ordering, which strongly supports the water-structuring hypothesis for the hydration force. However, the comparison between the simulations for polar surfaces with different headgroup architectures reveals significantly different decay lengths of the indirect water-mediated hydration-force, which for laterally homogeneous water structuring would imply different bulk-water properties. We conclude that laterally inhomogeneous water ordering, induced by laterally inhomogeneous surface structures, shapes the hydration repulsion between polar surfaces in a decisive manner. Thus, the indirect water-mediated part of the hydration repulsion is caused by surface-induced water structuring but is surface-specific and thus nonuniversal.Item Open Access Insights into Hildebrand solubility parameters : contributions from cohesive energies or electrophilicity densities?(2023) Miranda‐Quintana, Ramón Alain; Chen, Lexin; Smiatek, JensWe introduce certain concepts and expressions from conceptual density functional theory (DFT) to study the properties of the Hildebrand solubility parameter. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our results show that a revised expression allows the replacement of cohesive energy densities by electrophilicity densities, which are numerically accessible by simple DFT calculations. As an extension, the reformulated expression provides a deeper interpretation of the main contributions and, in particular, emphasizes the importance of charge transfer mechanisms. All calculated values of the Hildebrand parameters for a large number of common solvents are compared with experimental values and show good agreement for non‐ or moderately polar aprotic solvents in agreement with the original formulation of the Hildebrand solubility parameters. The observed deviations for more polar and protic solvents define robust limits from the original formulation which remain valid. Likewise, we show that the use of machine learning methods leads to only slightly better predictability.Item Open Access Hybrid molecules consisting of lysine dendrons with several hydrophobic tails : a SCF study of self-assembling(2023) Shavykin, Oleg V.; Mikhtaniuk, Sofia E.; Fatullaev, Emil I.; Neelov, Igor M.; Leermakers, Frans A. M.; Brito, Mariano E.; Holm, Christian; Borisov, Oleg V.; Darinskii, Anatoly A.In this article, we used the numerical self-consistent field method of Scheutjens-Fleer to study the micellization of hybrid molecules consisting of one polylysine dendron with charged end groups and several linear hydrophobic tails attached to its root. The main attention was paid to spherical micelles and the determination of the range of parameters at which they can appear. A relationship has been established between the size and internal structure of the resulting spherical micelles and the length and number of hydrophobic tails, as well as the number of dendron generations. It is shown that the splitting of the same number of hydrophobic monomers from one long tail into several short tails leads to a decrease in the aggregation number and, accordingly, the number of terminal charges in micelles. At the same time, it was shown that the surface area per dendron does not depend on the number of hydrophobic monomers or tails in the hybrid molecule. The relationship between the structure of hybrid molecules and the electrostatic properties of the resulting micelles has also been studied. It is found that the charge distribution in the corona depends on the number of dendron generations G in the hybrid molecule. For a small number of generations (up to G=3), a standard double electric layer is observed. For a larger number of generations (G=4), the charges of dendrons in the corona are divided into two populations: in the first population, the charges are in the spherical layer near the boundary between the micelle core and shell, and in the second population, the charges are near the periphery of the spherical shell. As a result, a part of the counterions is localized in the wide region between them. These results are of potential interest for the use of spherical dendromicelles as nanocontainers for drug delivery.Item Open Access Convolution on distribution spaces characterized by regularization(2023) Kleiner, Tillmann; Hilfer, RudolfLocally convex convolutor spaces are studied which consist of those distributions that define a continuous convolution operator mapping from the space of test functions into a given locally convex lattice of measures. The convolutor spaces are endowed with the topology of uniform convergence on bounded sets. Their locally convex structure is characterized via regularization and function‐valued seminorms under mild structural assumptions on the space of measures. Many recent generalizations of classical distribution spaces turn out to be special cases of the general convolutor spaces introduced here. Recent topological characterizations of convolutor spaces via regularization are extended and improved. A valuable property of the convolutor spaces in applications is that convolution of distributions inherits continuity properties from those of bilinear convolution mappings between the locally convex lattices of measures.Item Open Access Coarse-grained simulations of molecular catalysis in confined spaces(2023) Tischler, Ingo; Holm, Christian (Prof. Dr.)Item Open Access CO2-induced drastic decharging of dielectric surfaces in aqueous suspensions(2024) Vogel, Peter; Beyer, David; Holm, Christian; Palberg, ThomasWe study the influence of airborne CO2 on the charge state of carboxylate stabilized polymer latex particles suspended in aqueous electrolytes. We combine conductometric experiments interpreted in terms of Hessinger's conductivity model with Poisson-Boltzmann cell (PBC) model calculations with charge regulation boundary conditions. Without CO2, a minority of the weakly acidic surface groups are dissociated and only a fraction of the total number of counter-ions actually contribute to conductivity. The remaining counter-ions exchange freely with added other ions like Na+, K+ or Cs+. From the PBC-calculations we infer a corresponding pKa of 4.26 as well as a renormalized charge in reasonably good agreement with the number of freely mobile counter-ions. Equilibration of salt- and CO2-free suspensions against ambient air leads to a drastic de-charging, which exceeds by far the expected effects of to dissolved CO2 and its dissociation products. Further, no counter-ion-exchange is observed. To reproduce the experimental findings, we have to assume an effective pKa of 6.48. This direct influence of CO2 on the state of surface group dissociation explains our recent finding of a CO2-induced decrease of the ζ-potential and supports the suggestion of an additional charge regulation caused by molecular CO2. Given the importance of charged surfaces in contact with aqueous electrolytes, we anticipate that our observations bear substantial theoretical challenges and important implications for applications ranging from desalination to bio-membranes.Item Open Access Motile bacteria in complex environments(2024) Lohrmann, Christoph; Holm, Christian (Prof. Dr.)Item Open Access Unraveling the impact of acetylation patterns in chitosan oligomers on Cu2+ ion binding : insights from DFT calculations(2023) Singh, Ratna; Smiatek, Jens; Moerschbacher, Bruno M.Chitosans are partially acetylated polymers of glucosamine, structurally characterized by their degree of polymerization as well as their fraction and pattern of acetylation. These parameters strongly influence the physico-chemical properties and biological activities of chitosans, but structure-function relationships are only poorly understood. As an example, we here investigated the influence of acetylation on chitosan-copper complexation using density functional theory. We investigated the electronic structures of completely deacetylated and partially acetylated chitosan oligomers and their copper-bound complexes. Frontier molecular orbital theory revealed bonding orbitals for electrophiles and antibonding orbitals for nucleophiles in fully deacetylated glucosamine oligomers, while partially acetylated oligomers displayed bonding orbitals for both electrophiles and nucleophiles. Our calculations showed that the presence of an acetylated subunit in a chitosan oligomer affects the structural and the electronic properties of the oligomer by generating new intramolecular interactions with the free amino group of neighboring deacetylated subunits, thereby influencing its polarity. Furthermore, the band gap energy calculated from the fully and partially deacetylated oligomers indicates that the mobility of electrons in partially acetylated chitosan oligomers is higher than in fully deacetylated oligomers. In addition, fully deacetylated oligomers form more stable complexes with higher bond dissociation energies with copper than partially acetylated ones. Interestingly, in partially acetylated oligomers, the strength of copper binding was found to be dependent on the pattern of acetylation. Our study provides first insight into the influence of patterns of acetylation on the electronic and ion binding properties of chitosans. Depending on the intended application, the obtained results can serve as a guide for the selection of the optimal chitosan for a specific purpose.
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