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- Research DataInfluence of graphene on the electronic and magnetic properties of an iron(III) porphyrin chloride complex2024-09-24Although iron-based single atom catalysts are regarded as a promising alternative to precious metal catalysts, their precise electronic structures during catalysis still pose challenges for computational descriptions. A particularly urgent question is the influence of the environment on the electronic structure, and how to describe this properly with computational methods. Here, we study an iron porphyrin chloride complex adsorbed on a graphene sheet using density functional theory calculations to probe how much the electronic structure is influenced by the presence of a graphene layer. Our results indicate that weak interactions due to van der Waals forces dominate between the porphyrin complex and graphene, and only a small amount of charge is transferred between the two entities. Furthermore, the interplay of the ligand field environment, strong p-d hybridization, and correlation effects within the complex are strongly involved in determining the spin state of the iron ion. By bridging molecular chemistry and solid state physics, this study provides first steps towards a joint analysis of the properties of iron-based catalysts from first principles.
1 7 - Research DataDNP-enhanced magic angle spinning solid-state NMR spec-troscopy to determine RNA-ligand interactions2025-10-10Understanding the molecular recognition underlying RNA-ligand complex formation is of key importance to explain RNA regulatory function of riboswitches and to support the development of low molecular weight RNA binders as starting points for RNA-targeting drugs. Here, we report magic-angle spinning solid-state NMR spectroscopic studies enhanced by dynamic nuclear polarization (MAS-DNP) to determine the molecular recognition of a ligand-RNA riboswitch complex. We benchmarked different labeling strategies for four large RNAs (70-86 nt) of the aptamer domain of a 2’deoxyguanosine-sensing riboswitch from Mesoplasma florum. Samples were either prepared by chemo-enzymatic approaches or by solid-phase chemical RNA synthesis employing different labeling schemes of riboswitches of up to 86 nucleotides. RNA-ligand complexes were prepared by addition of their cognate metabolite. We show that nucleotide- and ligand-selective labeling are a prerequisite for the MAS-DNP studies to reduce the NMR signal overlap present in such large RNAs. We further extend site-specific labeling to atom-specific labeling that allowed us to derive the structure of the ligand binding pocket extending the application of 2D-13C,15N-TEDOR experiments. The work described here opens the avenue for the investigation of large RNA-ligand complexes by MAS-DNP.
41 1 - Research DataArchitectural principles of transporter-chaperone coupling within the native MHC I peptide-loading complex2025Adaptive immune responses are initiated by major histocompatibility class I (MHC I) presentation of antigenic peptides on the cell surface. This process relies on the peptide-loading complex (PLC), a dynamic transporter-multichaperone assembly in the endoplasmic reticulum (ER), to ensure high-fidelity selection, editing, and loading of peptides onto MHC I heterodimers. The PLC is the primary target for viral immune evasion, elicited in particular by human cytomegalovirus (HCMV), causing lifelong infections with severe risks for immunocompromised individuals. While the overall architecture of the PLC is known, how its activity is jeopardized by viral immune evasins remains unclear. Here, we present the 2.59–2.88 Å cryogenic electron microscopy structure of native human PLC associated with the HCMV immune evasin US6. US6 inhibits the heterodimeric transporter associated with antigen processing (TAP1/2) by latching its transmembrane helix laterally onto TAP2 and using its central disulfide-rich domain to mimic a translocating peptide. This effectively plugs the ER-lumenal exit and locks TAP in an outward-facing open conformation with closed nucleotide-binding domains and asymmetrically occluded ATP and ADP. In addition, the structure highlights the role of the unique N-terminal transmembrane domains of TAP as dynamic scaffolds that recruit the MHC I-specific chaperone tapasin by clamping its transmembrane helix to the core transmembrane domain of each transporter subunit. Our findings uncover how structural dynamics within human PLC are modulated by US6-mediated viral immune evasion and reveal potential targets for therapeutic modulation of antigen presentation in cancer and infectious diseases.
32 3 - Research DataAnisotropic antiferromagnetic order in EuPd3Si22025-10-07Single crystals of EuPd$_3$Si$_2$ were grown using a high-temperature EuPd-flux method. The material was structurally and chemically characterized by single-crystal x-ray diffraction, powder x-ray diffraction, Laue method and energy-dispersive x-ray spectroscopy. The structural analysis confirmed the orthorhombic crystal structure (space group $Imma$) but revealed differences in the lattice parameters and bond distances in comparison to previous work by Sharma et al.. \\ The composition is close to the ideal 1:3:2 stoichiometry with an occupation of 7 \% of the Si sites by Pd. The heat capacity, electrical resistivity, and magnetic susceptibility show two magnetic transitions indicating antiferromagnetic ordering below $T_{\rm N1}=$ 61\,K and a spin reorientation at $T_{\rm N2}=$ 40\,K. The orthorhombic material shows magnetic anisotropy with field applied along the three main symmetry axes, which is summarized in the temperature-field phase diagrams. The susceptibility data hint to an alignment of the magnetic moments along $[100]$ between $T_{\rm N1}$ and $T_{\rm N2}$. Below $T_{\rm N2}$ the magnetic structure changes to an arrangement with moments canted away from $[100]$. In contrast to published workby Sharma et al., the single crystals investigated in this study show AFM order below $T_{\rm N1}$ instead of ferromagnetism that sets in at higher $T_{\rm C1}=78\,\rm K$ which might originate from certain differences in the structure, composition or defects that have an impact on the dominant coupling constants of the RKKY interaction.
2 7 - Research DataRNA•DNA:DNA Triplex Formation Modulates Individual Base Pair Stabilities in the DNA Target Duplex Revealed by NMR Observed Solvent Exchange2025-09-30Long non-coding RNAs (lncRNAs) play a key role in numerous biological processes, including gene regulation. One potential mechanism involves the formation of RNA•DNA:DNA triplex structures, where the lncRNA binds in the major groove of a target DNA via Hoogsteen base pairs. Here, we investigated the impact of the lncRNA binding on the stability of the DNA duplex target to gain more insights into the triplex formation process. Quantification of the temperature-dependent imino proton solvent exchange allows the determination of the changes of individual DNA duplex base pairs upon triplex formation. The data shown here demonstrate that triplex formation alters DNA structure and stability by affecting both hydrogen bonding and base-stacking interactions. These thermodynamic insights support the prediction of triplex stability and enhance the understanding of RNA•DNA:DNA triplex formation.
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- Research DataThe global water resources and use model WaterGAP v2.2e - model output driven by gswp3-w5e5 and historical setup of direct human impacts2023-10-20Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download model output for the time period 1901-2019 that was computed by driving WaterGAP v2.2e by four alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. For two climate datasets, model runs up to 2021 or 2022 are available. For comparison, output of a version of WaterGAP v2.2d that is calibrated to the same dataset of observed streamflow as WaterGAP v2.2e is provided. Each of the climate forcing-model version combinations is run in two socio-economic settings, histsoc and nosoc. In nosoc, human water use is set to zero and man-made reservoirs are assumed to be non-existant. In the paper connected to this dataset (to be submitted to Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. The most important and requested model outputs (total water storage variations, streamflow and water use) are evaluated against observation data. Standard model output is described as well as the specifics of the WaterGAP contribution within the ISIMIP framework. Müller Schmied, H., Cáceres, D., Eisner, S., Flörke, M., Herbert, C., Niemann, C., Peiris, T. A., Popat, E., Portmann, F. T., Reinecke, R., Schumacher, M., Shadkam, S., Telteu, C.-E., Trautmann, T., Döll, P. (2021): The global water resources and use model WaterGAP v2.2d: Model description and evaluation. Geosci. Model Dev., 14, 1037–1079. https://doi.org/10.5194/gmd-14-1037-2021
1051 608 - Research DataThe global water resources and use model WaterGAP v2.2e - model output driven by gswp3-era5 and historical setup of direct human impacts2023-10-20Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download model output for the time period 1901-2019 that was computed by driving WaterGAP v2.2e by four alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. For two climate datasets, model runs up to 2021 or 2023 are available. For comparison, output of a version of WaterGAP v2.2d that is calibrated to the same dataset of observed streamflow as WaterGAP v2.2e is provided. Each of the climate forcing-model version combinations is run in two socio-economic settings, histsoc and nosoc. In nosoc, human water use is set to zero and man-made reservoirs are assumed to be non-existant. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. The most important and requested model outputs (total water storage variations, streamflow and water use) are evaluated against observation data. Standard model output is described as well as the specifics of the WaterGAP contribution within the ISIMIP framework. Müller Schmied, H., Cáceres, D., Eisner, S., Flörke, M., Herbert, C., Niemann, C., Peiris, T. A., Popat, E., Portmann, F. T., Reinecke, R., Schumacher, M., Shadkam, S., Telteu, C.-E., Trautmann, T., Döll, P. (2021): The global water resources and use model WaterGAP v2.2d: Model description and evaluation. Geosci. Model Dev., 14, 1037–1079. https://doi.org/10.5194/gmd-14-1037-2021
608 729 - Research DataA j_eff 12 Kitaev material on the triangular lattice: The case of NaRuO22023-06-07Motivated by recent reports of a quantum disordered ground state in the triangular lattice compound NaRuO$_2$, we derive a $j_{\rm eff}=1/2$ magnetic model for this system by means of first-principles calculations. The pseudospin Hamiltonian is dominated by bond-dependent off-diagonal $\Gamma$ interactions, complemented by a ferromagnetic Heisenberg exchange and a notably \emph{antiferromagnetic} Kitaev term. In addition to bilinear interactions, we find a sizable four-spin ring exchange contribution with a \emph{strongly anisotropic} character, which has been so far overlooked when modeling Kitaev materials. The analysis of the magnetic model, based on the minimization of the classical energy and exact diagonalization of the quantum Hamiltonian, points toward the existence of a rather robust easy-plane ferromagnetic order, which cannot be easily destabilized by physically relevant perturbations.
352 39 - Research DataThe global water resources and use model WaterGAP v2.2e - daily water storage model output driven by gswp3-era5 and historical setup of direct human impacts2024-04-04Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download daily model output for water storage variables for the time period 1901-2019 (2023) that was computed by driving WaterGAP v2.2e by two alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. Here, the single water storage compartments and terrestrial (total) water storage are provided.
265 131 - Research DataSection-Type Constraints on the Choice of Linguistic Mechanisms in Research Articles: A Corpus-Based Approach2023This thesis investigates the structure of research articles in the field of Computational Linguistics with the goal of establishing that a set of distinctive linguistic features is associated with each section type. The empirical results of the study are derived from the quantitative and qualitative evaluation of research articles from the ACL Anthology Corpus. More than 20,000 articles were analyzed for the purpose of retrieving the target section types and extracting the predefined set of linguistic features from them. Approximately 1,100 articles were found to contain all of the following five section types: abstract, introduction, related work, discussion, and conclusion. These were chosen for the purpose of comparing the frequency of occurrence of the linguistic features across the section types. Making use of frameworks for Natural Language Processing, the Stanford CoreNLP Module, and the Python library SpaCy, as well as scripts created by the author, the frequency scores of the features were retrieved and analyzed with state-of-the-art statistical techniques. The results show that each section type possesses an individual profile of linguistic features which are associated with it more or less strongly. These section-feature associations are shown to be derivable from the hypothesized purpose of each section type. Overall, the findings reported in this thesis provide insights into the writing strategies that authors employ so that the overall goal of the research paper is achieved. The results of the thesis can find implementation in new state-of-the-art applications that assist academic writing and its evaluation in a way that provides the user with a more sophisticated, empirically based feedback on the relationship between linguistic mechanisms and text type. In addition, the potential of the identification of text-type specific linguistic characteristics (a text-feature mapping) can contribute to the development of more robust language-based models for disinformation detection.
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