Universität Stuttgart
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Item Open Access Electronic features of vacancy, nitrogen, and phosphorus defects in nanodiamonds(2019) Hertkorn, Jens; Fyta, MariaDefective nanostructures with a surface termination are the focus of this work. In order to elucidate the influence of the defect on the properties of nanomaterials, we take hydrogen terminated nanodiamonds. Various vacancy defect centers are separately embedded in a nanodiamond at different positions. These include some of the known defects, such as the charged nitrogen-vacancy (NV-), the silicon-vacancy (SiV0), the germanium-vacancy (GeV0), the phosphorous-nitrogen (PN), and the nickel-vacancy (NiV-). For these defective nanodiamonds, we probe the influence of the defect type, its position, as well as the size of the nanodiamond through their structural and electronic features. A detailed and comparative analysis is provided here, based on quantum mechanical simulations. Our results shed light into the inherent differences of these defects in nanodiamonds, allowing for a better understanding of defective nanostructures. In the end, we discuss the potential of tuning their characteristics in view of novel nanotechnological applications.Item Open Access Probing DNA nucleobases with diamond (111) surfaces(2019) Putra, Miftahussurur Hamidi; Fyta, MariaDNA units, the nucleobases, are probed with diamond (111) surfaces. The nucleobases are placed on top of a diamond surface interacting in a very specific way with the surface atoms. Different elements, such as hydrogen, nitrogen, and fluorine are chosen for the termination of the diamond. The energetic features and electronic properties of the combined system ’nucleobase/diamond surface’ are thoroughly studied using quantum-mechanical calculations. These point to nucleobase- and termination-specific characteristics linking to the potential of using diamond surfaces for identifying the DNA nucleobases. Focus is further given on mixed surfaces with a varying nitrogen and hydrogen coverage. For these, we provide pathways for tuning the electronic band gap of the surface/nucleobase complex with the nitrogen content of the surface. The results could unravel a clear crossover in the surface electron affinity and its relation to a reversal in the positions of the electronic band extremes from the material to the molecule and vice versa. These features link to a further selective modulation of the electronic transport and the excitation properties of the complexes with a strong biosensing potential.Item Open Access Confined Ru‐catalysts in a two‐phase heptane/ionic liquid solution : modeling aspects(2020) Kobayashi, Takeshi; Kraus, Hamzeh; Hansen, Niels; Fyta, MariaA modeling approach for atomic‐resolution studies of sup‐ ported ionic liquid phase (SILP) catalytic systems in silica mesoporous confinement with surface hydroxyl and functional groups is proposed. First, a force field for the Ru‐based catalyst is developed. Second, its solvation behavior within a bulk two‐phase system of heptane and an IL is studied. Third, static and dynamic properties of the confined system are investigated. Using classical molecular dynamics simulations, experimentally inaccessible properties can thus be studied that are important for an optimization of a SILP system for performing a ring‐closing metathesis reaction.Item Open Access Functionalized nanogap for DNA read‐out : nucleotide rotation and current‐voltage curves(2020) Maier, Frank C.; Fyta, MariaFunctionalized nanogaps embedded in nanopores show a strong potential for enhancing the detection of biomolecules, their length, type, and sequence. This detection is strongly dependent on the features of the target biomolecules, as well as the characteristics of the sensing device. In this work, through quantum‐mechanical calculations, we elaborate on representative such aspects for the specific case of DNA detection and read‐out. These aspects include the influence of single DNA nucleotide rotation within the nanogap and the current‐voltage (I‐V) characteristics of the nanogap. The results unveil a distinct variation in the electronic current across the functionalized device for the four natural DNA nucleotides with the applied voltage. These also underline the asymmetric response of the rotating nucleotides on this applied voltage and the respective variation in the rectification ratio of the device. The electronic tunneling current across the nanogap can be further enhanced through the proper choice of an applied bias voltage. We were able to correlate the enhancement of this current to the nucleotide rotation dynamics and a shift of the electronic transmission peaks towards the Fermi level. This nucleotide specific shift further reveals the sensitivity of the device in reading‐out the identity of the DNA nucleotides for all different configurations in the nanogap. We underline the important information that can be obtained from both the I‐V curves and the rectification characteristics of the nanogap device in view of accurately reading‐out the DNA information. We show that tuning the applied bias can enhance this detection and discuss the implications in view of novel functionalized nanopore sequencers.Item Open Access 2D MoS2 nanopores : ionic current blockade height for clustering DNA events(2019) Diaz Carral, Angel; Shekar Sarap, Chandra; Liu, Ke; Radenovic, Aleksandra; Fyta, Maria2D nanopores can be used to electrophoretically drive DNA molecules, which can in turn be identified through measurable electronic current blockades. In this work, we use experimental data from molybdenum disulfide nanopores threading DNA nucleotides and propose a methodological approach to interpret DNA events. Specifically, the experimental ionic traces are used to train an unsupervised machine learning model for identifying distinct molecular events through the 2D nanopore. For the first time, we propose a clustering of experimental 2D nanopore data based on the ionic current blockade height and unrelated to the traditional dwell time for each DNA event. Within this approach, the blockade level information is implicitly included in the feature space analysis and does not need to be treated explicitly. We could show the higher efficiency of the blockade height over the traditional dwell time also in coping with sparse nanopore data sets. Our approach allows for a deep insight into characteristic molecular features in 2D nanopores and provides a feedback mechanism to tune these materials and interpret the measured signals. It has, thus, a high impact on the efficiency of 2D nanopore-based DNA sequencers.