Universität Stuttgart
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Item Open Access Entropic segregation of polymers under confinement(2016) Minina, Elena; Holm, Christan (Prof. Dr.)Overlapping polymers confined in a cylinder experience strong repulsion that drives them towards segregation. This has biological relevance to chromosome segregation in single-celled elongated bacteria such as Escherichia coli because in principle, chromosomes can segregate for purely entropic reasons without any help from active mechanisms. In this thesis, we investigated entropic segregation of polymers under cylindrical confinement of infinite length where the confining cylinder is so narrow that its diameter is significantly smaller than the radius of gyration of the unconfined polymers.Item 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.Item Open Access Electronic, adsorption, and transport properties of diamondoid-based complexes(2017) Adhikari, Bibek; Fyta, Maria (Jun. Prof. Dr.)Quantum simulation is an invaluable tool to researchers from various fields of scientific research. It allows the investigation of various complex condensed matter in the regimes of physics, chemistry, and biology. In this work, we focused our attention in unraveling the physical, chemical, electronic, transport, and optical properties of diamondoids and their complexes through quantum simulations. We have implemented a bottom-up approach where we move from the doping and functionalization of single diamondoids up to the diamondoid-based molecular devices. Naturally, diamondoids have been extracted from petroleum and also have been synthesized in the lab. These diamondoids are hydrogen terminated carbon cage-like structures which have lattice structure similar to diamond. As a result, they are found to be as rigid and stiff as diamonds and are comparable to the stiffness of graphite and carbon nanotubes. In addition to their strong physical properties, they are also the building blocks for important drugs. Furthermore, because they have a negative electron affinity, they are potentially useful in molecular electronics and electron-emitting devices.Item 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.Item Open Access Coarse grained hydrogels(2017) Richter, Tobias; Holm, Christian (Prof. Dr.)Item 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.Item 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.Item Open Access Electronic transport properties of DNA sensing nanopores : insight from quantum mechanical simulations(2017) Sivaraman, Ganesh; Fyta, Maria (Jun.-Prof. Dr.)The translocation of DNA through nanopores is an intensively studied field as it can lead to a new perspective in DNA sequencing. During this process the DNA is electrophoretically driven through a nanoscale hole in a membrane, and use different sensing schemes to read out the sequence. Within the scope of nanopore sequencing two important sensing schemes relevant to this thesis are: 1.) Tunneling sequencers based on solid state nanopores embedded with gold electrodes 2.) 2D materials beyond graphene For scheme 1, an obvious improvement is to coat the gold electrode with molecules that have high conductance and can form instantaneous hydrogen bond bridges with the translocating polynucleotide thereby improving the transverse current signal. The molecule that we propose is the so called diamondoid which are diamond caged molecules with hydrogen termination. Before applying such a molecule to a nanopore electrode set up, one would like to understand their interaction with DNA and its nucleobases. For this purpose, hydrogen bonded complexes formed between nitrogen doped derivatives of smallest diamondoids (i.e. adamantane derivatives) and nucleobases were investigated using dispersion corrected density functional theory (DFT). Mutated and methylated nucleobases are also taken into consideration in these investigations. DFT calculations revealed that hydrogen bonds are of moderate strength. In addition, starting from the DFT predicted hydrogen bonding configuration for each complex, rotations, and translations along a reference axis was performed to capture variations in the interaction energies along the donor-acceptor groups of the hydrogen bonds. The electronic density of states analysis for the hydrogen bonded complexes revealed distinguishable signatures for each nucleobase, thereby showing the suitability for application in electrodes functionalised with such probe molecules. In the next step, an adamantane derivative is placed on one of the electrode and nucleotides are introduced in such a way that nucleobases form hydrogen bonds with the of the nitrogen group of the adamantane derivatives. Electronic transport calculations were performed for gold electrodes functionalised with 3 different adamantane derivatives. Four pristine nucleotides, one mutated, and one methylated nucleotides were considered. Analysis of the transmission spectra reveal that each of the nucleotides has a unique resonance peak far below the Fermi level. We have also proposed a gating voltage window to sample the resonance peaks of the nucleotide so that they can be distinguished from each other. An alternative to tunneling sequencers would be to use nanopores built in to ultra thin metallic nanoribbons such as graphene. The sequence can be read out from the in-plane current modulation resulting from the local field effect of the translocating nucleotides in the vicinity of the metallic pore edges. But the hydrophobicity of graphene makes it a difficult candidate in aqueous environment. Hence in scheme 2, the aim is to model an ultra thin material that can rectify the hydrophobicity of graphene and can be a very good candidate for current modulation sequencing. Ultra thin MoS2 (2H) monolayer exist as direct band gap semiconductor. Nanopores based on 2H phases have been reported in the literature and are not hydrophobic. By means of chemical exfoliation of the 2H phase, a meta stable 1T phase of MoS2 has also been synthesized by various experimental groups. The 1T phase of MoS2 is metallic. The aim of this thesis is to model a nano-biosensor template based on a hybrid MoS2 monolayer made up of a metallic (1T) phase sandwiched between semiconducting (2H) phase. The sensor that we propose, should have only metallic nanopore edges. As a first step, we have modeled the semiconductor-metal interface, and compared them with experiments. Then an investigation to understand the influence of the increase of the metallic unit on the electronic properties is performed. Since, point defects are highly relevant to electrochemical pore growth, a point sulfur defect analysis is provided to ascertain the weakest point in the sheet. Finally to understand the effect of the interface electronic transport calculations are performed. The transmission spectra reveals a clear asymmetry in the current flow across the interface by means of gating. In the end, the relevance of such a hybrid MoS2 material for nanopore sequencing is discussed.Item Open Access Electrokinetic transport phenomena in soft-matter systems(2018) Rempfer, Georg; Holm, Christian (Prof. Dr.)