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Institute: search.filters.UBSInstitut.Institut für ComputerphysikStart date: 2010End date: 2019Publication Type: search.filters.UBSTyp.Zeitschriftenartikel

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    Efficient algorithms for electrostatic interactions including dielectric contrasts
    (2013) Arnold, Axel; Breitsprecher, Konrad; Fahrenberger, Florian; Kesselheim, Stefan; Lenz, Olaf; Holm, Christian
    Coarse grained models of soft matter are usually combined with implicit solvent models that take the electrostatic polarizability into account via a dielectric background. In biophysical or nanoscale simulations that include water, this constant can vary greatly within the system. Performing molecular dynamics or other simulations that need compute exact electrostatic interactions between charges in those systems is computationally demanding. We review here several algorithms developped by us that perform exactly this task. For planar dielectric surfaces in partial periodic boundary conditions, the arising image charges can be either treated with the MMM2D algorithm in a very efficient and accurate way, or with the ELC term that enables the user to use his favorite 3D periodic Coulomb solver . Arbitrarily shaped interfaces can be dealt with using induced surface charges with the ICC algorithm. Finally, the local electrostatics algorithm MEMD (Maxwell Equations Molecular Dynamics) allows even to employ a smoothly varying dielectric constant in the systems. We introduce the concepts of these three algorithms, and an extension for the inclusion of boundaries that are to be held fixed at constant potential (metal conditions). For each method, we present a showcase application to highlight the importance of dielectric interfaces.
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    Electronic features of vacancy, nitrogen, and phosphorus defects in nanodiamonds
    (2019) Hertkorn, Jens; Fyta, Maria
    Defective 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.
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    Probing DNA nucleobases with diamond (111) surfaces
    (2019) Putra, Miftahussurur Hamidi; Fyta, Maria
    DNA 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.
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    The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents : a computational study
    (2014) Smiatek, Jens; Wohlfarth, Andreas; Holm, Christian
    In contrast to the broad knowledge about aqueous polyelectrolyte solutions, less is known about the properties in aprotic and apolar solvents. We therefore investigate the behavior of sulfonated polyelectrolytes in sodium form in the presence of different solvents via all-atom molecular dynamics simulations. The results clearly reveal strong variations in ion condensation constants and polyelectrolyte conformations for different solvents like water, dimethyl sulfoxide (DMSO) and chloroform. The binding free energies of the solvent contacts with the polyelectrolyte groups validate the influence of different solvent qualities. With regard to the ion condensation behavior, the numerical findings show that the explicit values for the condensation constants depend on the preferential binding coefficient as derived by the evaluation of Kirkwood--Buff integrals. Surprisingly, the smallest ion condensation constant is observed for DMSO compared to water, whereas in the presence of chloroform, virtually no free ions are present, which is in good agreement to the donor number concept. In contrast to the results for the low condensation constants, the sodium conductivity in DMSO is smaller compared to water. We are able to relate this result to the observed smaller diffusion coefficient for the sodium ions in DMSO.
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    2D MoS2 nanopores : ionic current blockade height for clustering DNA events
    (2019) Diaz Carral, Angel; Shekar Sarap, Chandra; Liu, Ke; Radenovic, Aleksandra; Fyta, Maria
    2D 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.