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87 results for “Structure solution”
Dataset of "From Gas to Solution: The Changing Neutral Structure of Proline Upon Solvation"
Liquid-jet photoelectron spectroscopy (LJ-PES) and electronic-structure theory were employed to investigate the chemical and structural properties of the amino acid L-proline in aqueous solution for its three ionized states (protonated, zwitterionic, deprotonated). This is the first PES study of this amino acid in its most biologically relevant environment. Proline's structure in the aqueous phase under neutral conditions is zwitterionic, distinctly different from the non-ionic neutral form in the gas phase. By analyzing the carbon 1s and nitrogen 1s core-levels as well as the valence spectra of aqueous-phase proline, we found that the electronic structure is dominated by the protonation state of each constituent molecular site (the carboxyl and amine) with small yet noticeable interference across the molecule. The site-specific nature of the core-level spectra enables probing of individual molecular constituents. The valence photoelectron spectra are more difficult to interpret because of overlapping signals of proline with the solvent and pH-adjusting agents (HCl and NaOH). Yet we are able to reveal subtle effects of specific (hydrogen-bonding) interaction with the solvent on the electronic structure. We also demonstrate that the relevant conformational space is much smaller for aqueous-phase proline than it is for its gas phase analogue. This study suggests that caution must be taken when comparing photoelectron spectra for gaseous and aqueous-phase molecules, particularly if those molecules are readily protonated / deprotonated in solution.
Quantitative electronic structure and work-function changes of liquid water induced by solute - data
<p>Data set pertaining to the article "Quantitative electronic structure and work-function changes of liquid water induced by solute" | Physical Chemistry Chemical Physics, 24, 1310 (2022).</p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard v2022.07 using the NXmpes user contributed format suggested by the Fairmat consortium, see<br> https://www.nexusformat.org/<br> https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html<br> A few extensions specific to liquid jet-experiments were added to the standard, and are explained in the notes-group on the top level of each file.<br> NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format:<br> * nexpy (distributed with python)<br> * https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)</p> <p>In each NeXus file-entry, two types of spectra are shown:<br> 1. Sweep-averaged spectra, integrated over the non-dispersive coordinate of our detector ('data').<br> 2. As-measured data ('raw').</p> <p>Files with extension .txt are comma-separated ascii-files.<br> The following files are provided:</p> <p>Photoemission data pertaining to solute measurements using the cut-off as energy reference:<br> NaI_data.h5<br> tbai_data.h5</p> <p>Biased spectra were typically recorded in the following order:<br> [cut-off (fine), cut-off (coarse), (valence band)*(N repeats)]*(M repeats)<br> To avoid the saving of overly complex hdf5-files, these data were saved in a different order, namely:<br> [cut-off (fine)*(M repeats), cut-off (coarse)*(M repeats), (valence band)*(N*M repeats)].</p> <p>Numeric representations of the traces shown in the article's figures:<br> Figure_1a-data.txt<br> Figure_1b-data.txt<br> Figure_2a-data.txt<br> Figure_2b-data.txt<br> Figure_2c-data.txt<br> Figure_3-data.txt<br> Figure_4-data.txt<br> Figure_5a-data.txt<br> Figure_5b-data.txt<br> Figure_6a-data.txt<br> Figure_6b-data.txt<br> Figure_6c-data.txt<br> Figure_7_diff_spectra-data.txt<br> Figure_8-data.txt</p> <p>Traces shown in several figures are included only in the data file pertaining to the figure in which they occur first.</p> <p> </p> <p>Contact: Uwe Hergenhahn, uhe@fhi.mpg.de .</p>
Integrative structure determination of PTBP1-viral IRES complex in solution
<p>Ensemble structure model of the RNA-binding protein PTBP1 in complex with the internal ribosome entry site (IRES) of encephalomyocarditis virus (EMCV) RNA and data underlying these models.</p> <ul> <li>Main ensemble based on all restraints (corresponding to Figure 2 in the associated paper)</li> <li>Ensemble obtained with only DEER distance distribution restraints corresponding to Figure S7(A) in the Supplementary Material of the associated paper</li> <li>Validation ensemble obtained with all restraints after removing the conformers of the main ensemble from the raw ensemble corresponding to Figure S7(B) inthe Supplementary Material of the associated paper</li> <li>Ensemble obtianed with all restraints by fitting populations with a non-negative linear least squares (NNLLSQ) approach corresponding to Figure S8(A) in ths Supplementary Material of the associated paper</li> <li>Primary DEER-EPR data underlying site-to-site distance distributions for 35 spin-label pairs and corresponding distanace distributions</li> <li>Small-angle neutron scattering (SANS) curves a two detector distances with corresponding resolution files and a small-angle x-ray scattering (SAXS) curve</li> <li>Restraint file for the ensemble fit with MMMx software, specifying the mean distances and standrad deviations of distance distributions that were also used for specifying lower and upper distance bounds in CYANA generation of the raw ensemble</li> <li>Source data for the figures in the associated paper</li> <li>Source data for the tables in the associated paper</li> </ul> <p>All ensembles are ZIP files containing single PDB files for all conformers and an ensemble specification that reports populations for all conformers.</p>
Data for "Atomic structure of solute clusters in Al-Zn-Mg alloys"
<p>This dataset contains the data used in the publication entitled "<a href="https://www.sciencedirect.com/science/article/abs/pii/S1359645420310119"><strong>Atomic structure of solute clusters in Al-Zn-Mg alloys</strong></a>", published in Acta Materialia 17. December 2020.</p> <p>The data contained herein are:</p> <ul> <li>As-acquired transmission electron microscopy (TEM) images.</li> <li>Atom probe tomography data.</li> <li>All structural models used in density functional theory (DFT) calculations.</li> <li>Structures used for simulating scanning-TEM (STEM) images and nanobeam diffraction (NBD) patterns.</li> </ul> <p> </p> <p>The TEM images includes high angle annular dark field (HAADF) images and selected area diffraction patterns. These are given in .dm3/.dm4 files, and can be opened in e.g. the "<a href="https://www.gatan.com/products/tem-analysis/gatan-microscopy-suite-software">Gatan Microscopy Suite" </a>software. The images are also given as .tif images. The files are names after the "Figx_alloy_condition_xxx". "Figx" refers to the figure in the main article, "alloy" describes the alloy used and "condition" describes from what ageing condition. The uncorrected image series used for Fig. 6c (in the article) is included and requires the <a href="http://lewysjones.com/software/smart-align/">SmartAlign </a>plugin in the Gatan Microscopy Suite to analyse the dataset. SmartAlign allows for correcting rigid and non-rigid distortions in the STEM images in order to reduce effect of specimen drift and scan noise during acquisition. </p> <p>The ATP data is given as a .xlsx file. The data here is the processed data after applying the maximum separation algorithm. The data here is used to produce Figs. 2b and 2c in the paper. <br> <br> The structures used in the DFT calculations are given here as .cif files. These are separated into "Single_clusters" and "Stacked_clusters" and named according to Tabs. 1 and 2 in the Supplementary material of the paper.</p> <p>The two structures used for simulating STEM-HAADF and NBD patterns are given in the folder "TEM_simulations". "Mg32Zn124D_94x94" was used for NBD and "Mg32Zn124D_X_Zn4" was used for HAADF-STEM. The stack used for Supplementary Fig. 7c is labeled "Mg32Zn124D_94x94_slab_1Allayerop.cif".</p> <p> </p> <p> </p> <p> </p>
Atomic coordinates used in the solution of a TDRD2 crystal structure
<p>These coordinates were referred to as "Coordinates from [...] an unpublished TDRD2 crystal structure" in Supporting Information of our manuscript <em>Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2</em>. This model has not been validated for any other use.</p>
From Gas to Solution: The Changing Neutral Structure of Proline Upon Solvation - data
<p>Data set pertaining to the manuscript "From Gas to Solution: The Changing Neutral Structure of Proline Upon Solvation", submitted for peer review.</p> <p>In this work, Liquid-jet photoelectron spectroscopy (LJ-PES) and electronic-structure theory were employed to investigate the chemical and structural properties of the amino acid L-proline in aqueous solution for its three ionized states (protonated, zwitterionic, deprotonated). Experimental data were recorded by photoemission spectroscopy from a liquid jet source using synchrotron radiation. The data set documents the experimentally recorded spectra, including the proline photoelectron spectra and spectra of the zero energy cut-off, that were used to calibrate the binding energy scale.</p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard, see the<br>NeXus Data Format definition (v2024.02), https://manual.nexusformat.org/index.html<br>NXmpes expansion for FAIRmat data (v.2024.07), https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXmpes.html<br>NXmpes_liquid expansion to NXmpes (v.2024.07), https://fairmat-nfdi.github.io/nexus_definitions/mpes-liquid/classes/contributed_definitions/NXmpes_liquid.html<br>NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format:<br>* nexpy (distributed with python)<br>* https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)</p> <p>In each NeXus file-entry, two types of spectra are shown:<br>1. Sweep-averaged spectra, integrated over the non-dispersive coordinate of our detector ('data'). <br>2. As-measured data ('raw').</p> <p>If you use these data for your scientific work we kindly ask you to send us an electronic version or the citation of your work.</p> <p>Contact: Uwe Hergenhahn, uhe@fhi.mpg.de .</p>
Dataset From: Oscillatory structural forces between charged interfaces in solutions of oppositely charged polyelectrolytes
<p>The dataset for the publication "Oscillatory structural forces between charged interfaces in solutions of oppositely charged polyelectrolytes". DOI: 10.1039/d0sm01257b.</p> <p>Files containing data have .dat extension and are in text format.</p>
Tensile2d: 2D quasistatic non-linear structural mechanics solutions, under geometrical variations
<p>This dataset contains 2D quasistatic non-linear structural mechanics solutions, under geometrical variations. </p> <p>A Description is provided in <a href="https://arxiv.org/pdf/2305.12871.pdf">the MMGP paper</a> Sections 4.1 and A.2.</p> <p>The file format is PLAID, see <a href="https://plaid-lib.readthedocs.io/ ">the plaid documentation</a>.</p> <p>The variablity in the samples are 6 input scalars and the geometry (mesh). Outputs of interest are 4 scalars and 6 fields.</p> <p>Seven nested training sets of sizes 8 to 500 are provided, with complete input-output data. A testing set of size 200, as well as two out-of-distribution sample, are provided, for which outputs are not provided. </p> <p> </p> <p>Tips to access the data:</p> <p>After decompressing the downloaded file:</p> <p>from plaid.containers.dataset import Dataset<br>from plaid.problem_definition import ProblemDefinition</p> <p>dataset = Dataset()<br>problem = ProblemDefinition()</p> <p>problem._load_from_dir_(os.path.join(/path/to/data,'problem_definition'))<br>dataset._load_from_dir_(os.path.join(/path/to/data,'dataset'), verbose = True)</p> <p>print("problem =", problem)<br>print("dataset =", dataset)</p> <p>sample = dataset[0]<br>print("sample =", sample)</p> <p>for fn in sample.get_field_names():<br> print(f"{fn} =", sample.get_field(fn))<br>for sn in sample.get_scalar_names():<br> print(f"{sn} =", sample.get_scalar(sn))</p> <p>print("nodes =", sample.get_nodes())<br>print("elements =", sample.get_elements())<br>print("nodal_tags =", sample.get_nodal_tags())</p> <p> </p>
USP5 zinc-finger ubiquitin binding domain with L-cysteine(residue195)-glutathione disulfide structure solution
<p>USP5 zinc-finger ubiquitin binding domain with L-cysteine(residue195)-glutathione disulfide structure solution to 1.6 Å resolution</p>
Figure 2 in Solution structure of the first RRM domain of human spliceosomal protein SF3b49
Figure 2. – Fresh specimen of Lutjanus madras (UPVMI 1084, 211.3 mm SL, Panay Island, Republic of the Philippines).
Figure 3 in Solution structure of the first RRM domain of human spliceosomal protein SF3b49
Figure 3. – Diagrams of the first gill arch of the right side of Lutjanus madras. A: UPVMI 1084; B: MUFS 46214 (226.0 mm SL, Beruwala, Sri Lanka). Arrowhead and arrows indicate soft flesh-like mass and rudimentary gill rakers, respectively.
T1234: A distortion-matched structural scan solution to misregistration of high resolution fMRI data, Part 1
<p>Raw and processed MRI data of the study entiled: T1234-Part 1</p> <p>Authors: Chung (Kenny) Kan1, Rüdiger Stirnberg2, Marcela Montequin1, Omer Faruk Gulban3,4, A Tyler Morgan1, Peter Bandettini1, Laurentius (Renzo) Huber1</p> <ol> <li>NIMH, NIH, Bethesda, United States,</li> <li>German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany,</li> <li>CN, FPN, University of Maastricht, The Netherlands,</li> <li>Brain Innovation, Maastricht, The Netherlands</li> </ol> <p><strong>Purpose</strong>: High-resolution fMRI at 7T is limited by limited registration quality between functional data with structural scans. We aim to provide a fast acquisition method that provides distortion-matched, artifact mitigated structural reference data.</p> <p><strong>Methods</strong>: We developed an efficient sequence approach with adjustable distortions, termed T1234: T1-weighted 2-inversion 3D-EPI with 4 directions for high-resolution fMRI. A forward Bloch model is implemented for T1 quantification and protocol optimization. 20 participants were scanned on 7T with structural and functional protocols to evaluate the utility of T1234.</p> <p><strong>Results</strong>: We find that a fast protocol provides reliable data for whole-brain segmentations in EPI-space in 3:00-3:40 min). It is robust across sessions, participants, and three 7T SIEMENS scanners. T1234 allows layer fMRI signal analysis with higher laminar precision.</p> <p><strong>Conclusion: </strong>This structural mapping approach allows precise registration with fMRI data. T1234 is implemented, validated, and tested to serve users of our sequence (locally and >50 centers worldwide). </p>
Crystal Structure Solution and High Temperature Thermal Expansions of NaZr2(PO4)3-type Materials
<p>The NaZr<sub>2</sub>P<sub>3</sub>O<sub>12 </sub>(NZP) family<sub> </sub>of materials have shown low and tailorable thermal expansion properties. This dataset includes SrZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub>, CaZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub>, NaTi<sub>2</sub>P<sub>3</sub>O<sub>12</sub>, NaZr<sub>2</sub>P<sub>3</sub>O<sub>12</sub>, MgZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub>, and related solid solutions. These materials were synthesized using the organic-inorganic steric entrapment method. The samples were characterized with in-situ high-temperature x-ray diffraction at the Advanced Photon Source and National Synchrotron Light Source II from 25 to 1500 ℃. The average linear thermal expansion of SrZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> and CaZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> was between -1 x10<sup>-6</sup>/℃ and 6 x10<sup>-6</sup>/℃ from 25 to 1500 ℃. High temperature polymorphs of CaZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> and SrZr<sub>4</sub>P<sub>6</sub>O<sub>24</sub> were solved by Fourier difference mapping and Rietveld refinement. This polymorph is present above about 1250 ℃. This work measured thermal expansion coefficients to 1500 ℃ for all samples and investigated the differences in thermal expansion mechanisms between polymorphs and between compositions. </p>
GEOLAB Project CTP-ISSR: monotonic and cyclic Centrifuge Tests on Piles in sand proving Innovative Solutions to enhance Structural Resilience
<p>The existing structures are facing continuous changes in the loading conditions during their life span. These changes can be caused by weather and geo-hazards events and affect the structural response which is often already weakened by aging.</p> <p>A clear understanding of the interaction between the superstructure, the foundation and the surrounding soil is one of the crucial aspects to deal with to adapt the design and maintenance to enhance the resilience of new and existing Critical Infrastructures (CI) often used way beyond their life expectancy. Besides the loading components already considered in engineering practice, CI endure loads having cyclic nature acting continuously during service life (e.g., wind) which are often disregarded in foundation design and may trigger collapse mechanisms. Indeed, they are usually modelled as equivalent-static actions thus neglecting the accumulation of generalized permanent displacements of piled foundations in terms of settlement, sliding and rotation. This lack in design approach can be attributed to very limited research contributions dealing with cyclic loads. </p> <p>The CTP-ISSR (monotonic and cyclic Centrifuge Tests on Piles in sand proving Innovative Solutions to enhance Structural Resilience) project aims at investigating via centrifuge tests the behaviour of piled foundations under different loading types. Two series of centrifuge experiments on annular shaped pile groups and isolated piles embedded in Hostun sand were carried out at an increased gravity of 50 g in the Turner Beam Centrifuge at Schofield Centre, University of Cambridge. </p> <p>To simulate prototype reinforced concrete piles, model piles, made up of cement and metal wires, were manufactured in laboratory by means of an ad-hoc mould and manual mortar pouring. Such modelling is necessary to replicate the strong dependency of pile cross-sectional moment capacity on the axial force. Piles were installed in an 850 mm steel tub filled with manually poured Hostun sand prepared with a low-to-medium relative density. </p> <p>The first test included 2 single piles ad 2 groups of 8 piles connected by a circular rigid cap clear from the soil. The model foundations were subjected to monotonic vertical loads or vertical eccentric cyclic loads of different amplitudes and frequencies. In a similar fashion, the second test included 3 single piles ad 2 pile groups. In this case, the model foundations were subjected to monotonic vertical or horizontal loads or to cyclic horizontal loads of different amplitudes and frequencies. The response of the foundation system, in terms of loads and displacements, was monitored through loads cells, Linear Variable Differential Transformers (LVDTs) and Micro-Electro-Mechanical-Systems (MEMS). A miniaturized Cone Penetration Test (mini-CPT) was used to characterize the soil before the test execution. The experimental campaign was accomplished in 10 working days (including, among the others, model preparation, execution, data acquisition and dismantle). </p> <p>The results of the experiments will serve as benchmarks for the development of a non-linear macroelement for piled foundation. Adopting this innovative approach allows the strengthening of CI resilience by adapting the traditional design and maintenance to properly consider changing loading conditions in a simple yet reliable manner. </p> <p>Researchers and practitioners will be the beneficiaries of the outcome of this research, expecting the following advantages: <br> - Innovation in design, with the possibility to properly consider cyclic loading;<br> - Improvement in identifying possible failure mechanisms and the required maintenance to enhance reliability and resilience of existing CI.</p>
UltraScan Solution Modeler (US-SOMO) hydrodynamic parameter, structural small angle scattering and SESCA circular dichroism (CD) calculations on AlphaFold predicted structures
Open the record for dataset details and reuse information.
Data from: NOVOWrap: an automated solution for plastid genome assembly and structure standardization
<p>Plastid genomes play an important role in genomics and evolutionary biology. Next-generation sequencing has revolutionized plastid genomic data acquisition to the point that genome assembly has become a bottlenecks for widespread utilization of plastid genome data. To solve this problem, we developed an open-source, cross-platform tool known as, NOVOWrap, which includes both command-line and graphical interfaces for automatically assembling plastid genomes on personal computers. With minimal inputs, settings, and user intervention, NOVOWrap can automatically assemble plastid genomes, validate results and standardize the structure using affordable computer resources. The performance of this software has been successfully benchmarked against the plastid genomes of 11 species belonging to lycopods, gymnosperms, and angiosperms. This program is expected to liberate researchers from laborious and cumbersome computer manipulations and create reliable and standardized genomic data.</p>
Data and Scripts for the Article: Structural Sensitivity of N1s Excitations in N-methylacetamide Solutions
<p>Data and scripts for the article titled: Structural Sensitivity of N1s Excitations in N-methylacetamide Solutions.</p> <p>For further details on the contents, see the "readme.md"-file.</p>
Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data
<p>guided walkthrough of poster at <a href="https://doi.org/10.5281/zenodo.6821815">https://doi.org/10.5281/zenodo.6821815</a></p> <p>which provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata and the techniques for structuring this data as Linked Data.</p> <p>You can also watch the video in the browser on the <a href="https://gerbi-gmb.de/i3dbio/i3dbio-resources/metadata-guide/">I3D:bio website</a>.</p>
Apo USP5 zinc-finger ubiquitin binding domain structure solution 2018/03/30
<p>USP5 zinc-finger ubiquitin binding domain structure solution to 1.55 Å resolution</p>
Figure 1 in Solution structure of the first RRM domain of human spliceosomal protein SF3b49
Figure 1. – Sampling locality of the present specimen of Lutjanus madras.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.