Universität Stuttgart
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Item Open Access MDSuite : comprehensive post-processing tool for particle simulations(2023) Tovey, Samuel; Zills, Fabian; Torres-Herrador, Francisco; Lohrmann, Christoph; Brückner, Marco; Holm, ChristianParticle-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.Item 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, IrynaThe 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.Item Open Access PDADMAC/PSS oligoelectrolyte multilayers : internal structure and hydration properties at early growth stages from atomistic simulations(2020) Sánchez, Pedro A.; Vögele, Martin; Smiatek, Jens; Qiao, Baofu; Sega, Marcello; Holm, ChristianWe analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter 2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.Item Open Access Zero shot molecular generation via similarity kernels(2025) Elijošius, Rokas; Zills, Fabian; Batatia, Ilyes; Norwood, Sam Walton; Kovács, Dávid Péter; Holm, Christian; Csányi, GáborGenerative modelling aims to accelerate the discovery of novel chemicals by directly proposing structures with desirable properties. Recently, score-based, or diffusion, generative models have significantly outperformed previous approaches. Key to their success is the close relationship between the score and physical force, allowing the use of powerful equivariant neural networks. However, the behaviour of the learnt score is not yet well understood. Here, we analyse the score by training an energy-based diffusion model for molecular generation. We find that during the generation the score resembles a restorative potential initially and a quantum-mechanical force at the end, exhibiting special properties in between that enable the building of large molecules. Building upon these insights, we present Similarity-based Molecular Generation (SiMGen), a new zero-shot molecular generation method. SiMGen combines a time-dependent similarity kernel with local many-body descriptors to generate molecules without any further training. Our approach allows shape control via point cloud priors. Importantly, it can also act as guidance for existing trained models, enabling fragment-biased generation. We also release an interactive web tool, ZnDraw, for online SiMGen generation ( https://zndraw.icp.uni-stuttgart.de ).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 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 Triggered dissolution of electrostatically crosslinked hydrogels from star‐shaped polyampholytic block copolymers(2026) Grün, Jonas Julius; Beyer, David; Mons, Peter Johannes; Seitel, Sebastian; Fribiczer, Nora; Poudel, Purushottam; Könemann, Nicklas; Zank, Lynn Kendra Renate Jagna; Zylla, Paul Fabio; Košovan, Peter; Seiffert, Sebastian; Holm, Christian; Schacher, Felix HelmutWe explore the possible reversible formation of hydrogels through electrostatic interactions between four‐arm star‐shaped block copolymers, consisting of a polyethylene glycol (PEG) inner block and either an anionic polystyrene sulfonate [PEG27‐b‐PSS108]4 or a zwitterionic polybetaine [PEG27‐b‐PCBMAAm110]4 as outer block. The combination of both can induce attractive or repulsive electrostatic interactions depending on the solution pH value and ionic strength. The polymers were synthesized using controlled atom transfer radical polymerization (ATRP). The charge of [PEG27‐b‐PCBMAAm110]4 was further investigated by potentiometric titration and zeta potential measurements. Using oscillatory shear rheology, we demonstrated the required conditions for hydrogel formation. Stable hydrogel formation is observed within a wide pH range (6.8 -9.5), corresponding to the protonation states of the carboxylic acid groups that facilitate electrostatic interactions. We also showed how the hydrogel stability is influenced by parameters like block copolymer concentration and ionic strength. Coarse‐grained simulations provided molecular‐scale insights, revealing charge regulation effects and the energetic favorability of electrostatic complexation up to high pH values. Overall, our results demonstrated the key design principles, as the polyelectrolyte length, ionic strength, and charge regulation effects, for the formation of partially reversible hydrogels, triggered by changes in the solution pH. Furthermore, we showed that understanding the desired conditions for hydrogel formation requires a combination of experimental characterization with modeling approaches.Item Open Access An extensible lattice Boltzmann method for viscoelastic flows : complex and moving boundaries in Oldroyd-B fluids(2021) Kuron, Michael; Stewart, Cameron; de Graaf, Joost; Holm, ChristianMost biological fluids are viscoelastic, meaning that they have elastic properties in addition to the dissipative properties found in Newtonian fluids. Computational models can help us understand viscoelastic flow, but are often limited in how they deal with complex flow geometries and suspended particles. Here, we present a lattice Boltzmann solver for Oldroyd-B fluids that can handle arbitrarily shaped fixed and moving boundary conditions, which makes it ideally suited for the simulation of confined colloidal suspensions. We validate our method using several standard rheological setups and additionally study a single sedimenting colloid, also finding good agreement with the literature. Our approach can readily be extended to constitutive equations other than Oldroyd-B. This flexibility and the handling of complex boundaries hold promise for the study of microswimmers in viscoelastic fluids.Item Open Access A sequence-specific theory for charge-regulating IDPs(2026) Beyer, David; Holm, Christian; Wang, Zhen-GangIntrinsically disordered proteins are a notable class of biological polymers whose physicochemical properties and biological functions are determined by an intricate interplay of chain connectivity, electrostatic interactions, the sequence of residues, and nonuniversal short-range interactions. An important phenomenon in these molecules is charge regulation, which arises from weakly acidic and basic residues, but is often neglected in theoretical descriptions. In this work, we use the Edwards-Singh variational method to derive an approximate theory that describes sequence effects in the charge regulation and chain conformation of intrinsically disordered proteins. The main result of our theory is a set of coupled algebraic equations yielding a renormalized Kuhn length and residue-specific mean-fields that determine the respective ionization states of the residues. We discuss limiting cases of these equations that underline the internal consistency of our theory and connect our results to earlier studies. To solve the full set of equations, we propose a simple numerical scheme. As test cases, we calculate the conformation and ionization state of a weak polyelectrolyte and of 30 sequence variants of the polypeptide (EK)25. For the weak polyelectrolyte, we show that the theory predicts phenomena such as the overall suppressed ionization due to electrostatic interactions and the enhanced ionization at the chain ends. In the case of the polypeptide (EK)25, we find strong effects of the sequence on ionization, with well-mixed sequences exhibiting a broad pH range where the polypeptide is net neutral, while blockier sequences exhibit a steeper ionization response. Moreover, we also observe pronounced sequence effects on the swelling behavior of the chains.Item Open Access Implicit-solvent coarse-grained simulations of linear-dendritic block copolymer micelles(2023) Brito, Mariano E.; Mikhtaniuk, Sofia E.; Neelov, Igor M.; Borisov, Oleg V.; Holm, ChristianThe design of nanoassemblies can be conveniently achieved by tuning the strength of the hydrophobic interactions of block copolymers in selective solvents. These block copolymer micelles form supramolecular aggregates, which have attracted great attention in the area of drug delivery and imaging in biomedicine due to their easy-to-tune properties and straightforward large-scale production. In the present work, we have investigated the micellization process of linear–dendritic block copolymers in order to elucidate the effect of branching on the micellar properties. We focus on block copolymers formed by linear hydrophobic blocks attached to either dendritic neutral or charged hydrophilic blocks. We have implemented a simple protocol for determining the equilibrium micellar size, which permits the study of linear–dendritic block copolymers in a wide range of block morphologies in an efficient and parallelizable manner. We have explored the impact of different topological and charge properties of the hydrophilic blocks on the equilibrium micellar properties and compared them to predictions from self-consistent field theory and scaling theory. We have found that, at higher degrees of branching in the corona and for short polymer chains, excluded volume interactions strongly influence the micellar aggregation as well as their effective charge.