Browsing by Author "Holm, Christian (Prof. Dr.)"

Now showing 1 - 18 of 18

Open Access
Coarse grained hydrogels
(2017) Richter, Tobias; Holm, Christian (Prof. Dr.)
Open Access
Coarse-grained simulations of molecular catalysis in confined spaces
(2023) Tischler, Ingo; Holm, Christian (Prof. Dr.)
Open Access
Dielectric effects in complex fluids
(2022) Zeman, Johannes; Holm, Christian (Prof. Dr.)
Open Access
Dielectric variations in simulations of charged soft matter
(2016) Fahrenberger, Florian; Holm, Christian (Prof. Dr.)
In this thesis, an algorithm to calculate electrostatic interactions in molecular dynamics simulations is extended to include spatial and temporal variations in the dielectric permittivity of the system. The algorithm is implemented, verified, and parallelized. It is then applied to a number of systems containing charged soft matter. Noticeable quantitative and qualitative differences are found between simulations including and excluding dielectric variations. Particularly for the effective charge of colloids, and for the conductivity of polyelectrolytes in aqueous solution, major behavioral changes are shown.
Open Access
Electrokinetic transport phenomena in soft-matter systems
(2018) Rempfer, Georg; Holm, Christian (Prof. Dr.)
Open Access
The electrophoretic mobility of bare and soft spherical colloids : a molecular dynamics study
(2014) Raafatnia, Shervin; Holm, Christian (Prof. Dr.)
In this work, the electrophoretic mobility of colloids in salt solutions are studied by means of coarse-grained Molecular Dynamics simulations. Two different types of colloids are considered; bare colloids and polyelectrolyte-grafted colloids. A novel model for simulation of large bare colloids in the presence of explicit ions is developed. Comparison of the results with experimental data helps gain a better understanding of the mechanisms responsible for the interesting phenomenon of mobility reversal. Furthermore, a hitherto unknown electrokinetic behavior of polyelectrolyte-grafted colloids is found from simulations including full hydrodynamic interactions. The validity of the existing theories is verified via comparison with simulation results.
Open Access
From the inhomogeneous electron gas to classical force fields : a multi-scale model for ionic liquids
(2013) Dommert, Florian; Holm, Christian (Prof. Dr.)
Ionic liquids are a class of solvents that have attracted a broad interest in the recent decade. They are often liquid at room temperature, but consist only of cations and anions without any additional solvent. The characteristic properties of these liquids are the negligible volatility and their tunability. Thus they are often referred to as designer solvents, which can be adapted in order to increase the efficiency of many applications like catalysis, capturing of flue gases, or solar cells. The number of different ionic liquids is quite large and an experimental screening of all ionic liquids would be very expensive and time-consuming. At this stage, classical molecular dynamics simulations are a very suitable tool that allows one to study thermodynamic, structural, and dynamic properties of liquids, but they depend on an accurate force field. For ionic liquids, reliable and transferable force fields are rare. For this reason, the main object of this work is to establish a method to optimize or generate a set of force field parameters. This is achieved by mapping the electronic and geometric structure information of the liquid phase gathered on the DFT level to the classical scale. Apart from our test system dimethylimidazolium chloride [MMIM][Cl] , which was used to develop corresponding methods, we investigated a broad spectrum of imidazolium-based cations combined with the anions thiocyanate [SCN]-, dicyanamide [DCA]-, and chloride [Cl]-. These studies were based on CPMD simulation snapshots, which allowed one to gain insight into the electronic structure of ionic liquids, especially in mechanisms of partial charge distribution and the net—charge reduction, which has been identified as a model for implicit polarization and charge transfer. These features are not only characteristic for an IL, but it has also been shown, that they occur already on a very local scale, which is the reason for the good performance of partial charges that were derived from small ion pair clusters. It was shown that the predicted charge transfer and polarization is in agreement with NMR experiments and measurements of the refractive index. From the computational side, consistency of the dipole moments given by the partial charges or by a Wannier analysis of the CPMD results was achieved. Though the width of dipole moment distribution could not be completely reproduced by the static partial charges, the increase in the dipole moment for an increasing number of interacting ion pairs (IPs) coincides very well. This shows that the proposed set of partial charges is perfectly suitable for the bulk phase of an IL. Finally the short—range (SR) interactions were adapted in respect to our proposed set of partial charges. An algorithm was implemented that optimizes the SR parameters based on an iterative adaption to match static properties given by the experimental mass density and the radial distribution functions derived from CPMD simulations. The routine has been successfully tested for [MMIM][Cl] and it has been shown that the implicit consideration of polarization and charge transfer models the dynamics already well, such that one can rely on static properties during the SR parameter optimization. This alleviates the tuning process, because the amount of simulation time required to sample a highly viscous IL decreases and, apart from the experimental mass density, only computational results are required. The latter aspect is of great importance for ILs, because a broad spectrum of experimental knowledge is not a given. Thus, during this work, the technique and computational framework to optimize FF parameters for ionic liquids was established and a large data set was accumulated. Thus, a solid basis for future work is provided, the development of a generic and transferable force field for ILs.
Open Access
Lattice Boltzmann methods for microswimmers in complex environments
(2021) Kuron, Michael; Holm, Christian (Prof. Dr.)
Open Access
Magnetic microrobot collectives as a model system for self-organisation
(2023) Gardi, Gaurav; Holm, Christian (Prof. Dr.)
Open Access
Modeling of complex electrolytes : a numerical simulation study
(2021) Narayanan Krishnamoorthy, Anand; Holm, Christian (Prof. Dr.)
Open Access
Modeling the translocation of DNA structures through nanopores
(2021) Szuttor, Kai; Holm, Christian (Prof. Dr.)
Open Access
Motile bacteria in complex environments
(2024) Lohrmann, Christoph; Holm, Christian (Prof. Dr.)
Open Access
Multiscale simulations of soft and hard matter
(2015) Röhm, Dominic; Holm, Christian (Prof. Dr.)
The first part of this Thesis presents results of investigations of selected dynamical properties. Furthermore, die crystallization of colloidal suspensions has been investigated. We show that for charge-stabilized suspensions, where the colloids interact via the Yukawa potential, hydrodynamic interactions can have a remarkable impact on the crystallization of colloidal particles. The results are based on Molecular Dynamics (MD) simulations of heterogeneous crystallization in a suspension of charged colloids supported by the computation of the solvent dynamics by the Lattice-Boltzmann (LB) method. In order to investigate the role of hydrodynamic interactions mediated by the solvent, we modeled the solvent both implicitly and explicitly, using Langevin dynamics and the fluctuating LB method, respectively. Our simulations show a reduction of the crystal growth velocity due to hydrodynamic interactions even at moderate hydrodynamic coupling. The slow down of the crystallization is accompanied by narrowing of the pre-ordering region, which shows that the attachment to a crystal surface is not a purely long-time diffusive process, as commonly thought. The arrangement of the colloids in the early state of a new crystal layer seems to be affected by the short-time dynamics of the colloids, which is again affected by hydrodynamic interactions. Crystallization in suspensions therefore can differ strongly from that of pure melts. In the second part of this Thesis we will introduce an approach for the efficient computation of strain evolution in a copper crystal. Here, instead of attaching a continuum solver to an MD simulation, we used a method that combines a finite-volume solver and MD simulations by spawning independent MD simulations to include microscopic details into the stress computation, which serves as input for every finite volume at the macro level. We developed an adaptive sampling method called Distributed Database Kriging for Adaptive Sampling, which applies a prediction scheme known as kriging to the heterogeneous multiscale method (HMM) for stochastic data supported by a cloud database. We demonstrated by means of two elastodynamics test problems, that a speedup of a factor of 2.5 to 25 can be achieved.
Open Access
Physics meets machine learning : theory and application
(2024) Tovey, Samuel; Holm, Christian (Prof. Dr.)
The doctoral thesis of Samuel Tovey. In this work, I explore the role machine learning plays in computational physics, specifically, the fitting of potential for molecular dynamics simulations and control of microscopic active matter. Further, it is shown that physics concepts can be used to understand machine learning, particularly the role of data in neural network training and the evolution and learning mechanisms of neural networks while training.
Open Access
Simulation and modeling of polyelectrolyte gels
(2020) Landsgesell, Jonas; Holm, Christian (Prof. Dr.)
Diese Dissertation behandelt die Entwicklung von Computermodellen zur Beschreibung von Polyelektrolytnetzwerken. Basierend auf dem periodische Gelmodell entwickeln wir zwei aufeinander aufbauende Computermodelle, welche zur Beschreibung der elastischen Eigenschaften von Polyelektrolytgelen dienen: das Einzelketten-Zellen-Gelmodell (ZGM) und das Poisson-Boltzmann Zellen-Gelmodell (PB ZGM). Da viele Polyelektrolytgele aus Bausteinen bestehen, welche chemisch reaktiv sind, ist es wichtig diese Eigenschaft korrekt in Computermodellen abzubilden. Zur Untersuchung dieser schwachen Polyelektrolytgele führen wir eine Methode zur Simulation von Ionisationsgleichgewichten in solchen Systemen ein. Der pH-Wert und die Salzkonzentration werden durch die Zusammensetzung der Überstandslösung definiert. Unsere Implementierung des Teilchenaustausches mit der Überstandslösung vermeidet bekannte Artefakte und unphysikalische Parameterkombinationen.
Open Access
Simulation of novel magnetic materials in the field of soft matter
(2014) Weeber, Rudolf; Holm, Christian (Prof. Dr.)
This thesis has dealt with the tailoring of magnetic soft matter. Two strategies are available to achieve this goal. First, it is possible to alter the magnetic nanoparticles, in order to change their interactions. Second, it is possible to exchange the carrier fluid into which the magnetic particles are embedded by a more complex matrix. For each of these two possibilities, an example was studied, namely shifted-dipole particles and magnetic gels. Shifted-dipole particles (sd-particles) are a special kind of model magnetic particles which can be used to explain findings for particles with magnetic caps as well as for particles with magnetic inclusions. Magnetic gels, on the other hand, derive their particular properties from an interplay of the magnetic properties of the nanoparticles and the elastic behavior of the polymer matrix. In the thesis, the findings for these two systems will be discussed, and further research questions will be identified.
Open Access
Simulation studies on electrodes and electrolytes for electric double layer capacitors
(2018) Breitsprecher, Konrad; Holm, Christian (Prof. Dr.)
In this dissertation, different capacitor systems are investigated by means of computer simulations. The basic aim of the simulation studies is to contribute towards a better understanding of the interplay of carbon electrodes in various geometries with ionic liquid-based electrolytes. A large focus lies on electrode modeling with an applied external voltage. How these models and underlying methods affect the behavior of electrolyte molecules at the solid-liquid interface as well as the performance of the systems as energy storage devices is a central question of this study.
Open Access
Simulations of DNA translocation through nanopores
(2015) Kesselheim, Stefan; Holm, Christian (Prof. Dr.)
In the past two decades, experiments addressing the transport of single molecules, especially DNA, has attracted great attention. This technology is considered promising for the next generation of rapid in cheap DNA sequencing methods. In this theses, physical models and computer simulation methods for the simulation of DNA transport through these so-called nanopores are investigated. Modelling techniques with different result ions are compared and evaluated with special focus on their predictions regarding the current modulation caused by DNA molecules that are transported through these pores.