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689 results for “crystals”
Data and code for figures: Dynamics of soliton crystals in optical microresonators
<p>This dataset contains the data presented in the figures of the paper Dynamics of soliton crystals in optical microresonators.</p> <p>The data for figure X (X = 1, 2, 3, 4, S1, S2, S3, S4, S5) is gathered in one matlab dataset file Fig_X.mat, which contains structure variable figX whose fields are the panels of the figure in the manuscript (a,b,c,...). In each of the panel field, you find subfields containing the data arrays for all the lines presented in the panel.</p> <p><br> A minimal script znd_FigX_plot.m is provided for each figure in order to plot all the panels.</p> <p>The datasets and scripts were generated and tested using Matlab 2018b.</p>
Crystal structure of olive flounder [Paralichthys olivaceus] interferon gamma at 2.3 Angstrom resolution - diffraction data
<p>Diffraction images, Bessy II (Berlin), MX 14.1, 12.5.2017, PDB ID 6F1E</p>
Rare Nature of Crystals of the Novel Multimeric Haloalkane Dehalogenase DpaA from Paraglaciecola agarilytica NO2.
<p>Manuscript reports on novel haloalkane dehalogenase DpaA isolated from a psychrophilic and halophilic bacterium <em>Paraglaciecola agarilytica</em> NO2 that was crystallized and two independent crystallization and data collection experiments resulted in several data sets with a resolution ranging from 2.2 to 3.7 Å. X-ray diffraction data analysis hinted at oligomeric nature of DpaA leading to certain issues with the solution of structure. Our results unveil a rare example of an oligomeric dehalogenase belonging the subfamily I as well as highlight new findings in the solution of crystallographic data with unusual crystal packing. The crystal structures of HLD-I subfamily already deposited into the PDB database are monomeric. There are only a few examples of oligomeric haloalkane dehalogenases from the other subfamilies HLD-II and HLD-III that can form dimers and tetramers. The crystal structures of enzymes from the HLD-III subfamily showing oligomeric properties in gel-filtration experiments have not been solved to date. DpaA’s propensity to oligomerization likely causes the problems with solution of the structure, such as pseudo-translation, in a wide range of crystallization conditions and across various crystal lattices. Our results contribute to explaining new findings in solving the structures of oligomeric proteins that exhibit unusual crystal packing and mark the DpaA enzyme as an uncommon oligomeric example of the HLD-I subfamily.</p>
Supplementary information to "Rainbow in the dark. The identification of diagnostic projectile impact features on rock crystal"
<p>Images of the experimental projectiles (pre-hafting, hafted before and after shooting), Hirox (Low magnification) pictures of pre-hafting and post-shooting projectiles and selection of fractures smoked with magnesium.</p>
BIR-MicroED: TEM image series revealing bend contour motion in static microcrystals (biotin, Zn(II)-methionine, Co(II)-porphyrin, AVAAGA) and diffraction patterns acquired from the same crystals at 200 kV
<p>This deposition contains a series zip files each containing TEM image series and electron diffraction images in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). Zip files are named according to the format: <em>"CompoundName</em>_bendcontour_imageseries_<em>AcceleratingVoltage</em>_<em>Temperature</em>.zip"</p> <p>Data is further divided into sub-directories according to the particular crystal studied (crystal1, crystal2, crystal3), each containing a TEM image series (name format: "<em>CompoundName</em>_static_imageseries_<em>AcceleratingVoltage</em>_<em>Temperature</em>_crystal#.mrc") and 10 diffraction snapshots (2 frames each, each convering 1 second of electron beam exposure) acquired at equally spaced time intervals throughout the image series. These are named according to the format:</p> <p>"CompoundName_bendcontour_crystal#_diffraction_snap#.mrc"</p>
Robust and efficient reranking in crystal structure prediction: a data driven method for real-life molecules
<p>The content of this repository accompanies the publication "Robust and efficient reranking in crystal structure prediction: a data driven method for real-life molecules" and contains the complete dataset produced for the fentanyl CSP. </p> <p>Three types of datasets are present : Generation, ML-Reranker and GRACE. <br>Generation refers to all the molecular crystal structures that GRACE has generated using the tailor made force field. It's the starting pool of the reranking exercise, and it contains all the structures that will be selected by the reranking processes.<br>ML-Reranker refers to the data generated by the algorithm proposed in our manuscript. The configurations and energies are obtained by selecting from structures from the generation pool and relaxing their coordinates.<br>GRACE dataset contains the configurations which a user obtains at the end of a standard GRACE reranking procedure. Since GRACE follows differet convergence and minimization critera, the structures obtained in this dataset can differ (non-substantially) from the equivalents found in the ML-Reranker. </p> <p>*.data : contains the indices, energy of the crystal structure (kcal/mol) and, in case of the ml-reranker dataset, the indices mapping the obtained landscape to their generating pool.</p> <p>*.xyz : contains ASE formatted, extended-xyz list of structures corresponding to each exercise.</p> <p>Authors:</p> <p>Andrea Anelli, Hanno Dietrich, Philipp Ectors, Frank Stowasser, Tristan Bereau, Marcus Neumann, Joost van den Ende</p>
Data for Responsive Soft Interface Liquid Crystal Microfluidics
<p>The data used in the article entitled Responsive Soft Interface Liquid Crystal Microfluidics.</p>
Dataset for Low temperature electron spin resonance study of an MnPS3 antiferromagnetic single crystal
<p>This is a dataset for a paper "Low temperature electron spin resonance study of an MnPS3 antiferromagnetic single crystal". All details about the data are included in the readme file.</p>
Microscopic mechanism of the L1_2–D0_19 phase transformation in a Co-base single crystal superalloy
<p>This record contains datasets related to the publication:</p> <p>N. Karpstein et al., Microscopic mechanism of the L1<sub>2</sub>-D0<sub>19</sub> phase transformation in a Co-base single crystal superalloy, Acta Materialia (2024), <a href="https://doi.org/10.1016/j.actamat.2024.120416" target="_blank" rel="noopener">doi:10.1016/j.actamat.2024.120416</a>.</p> <p>A readme file containing descriptions of datatypes can be found in the main folder.</p> <p> </p> <p>Abstract:</p> <p>In γ′-strengthened superalloys based on the Co-Al-W system, the stability of the γ′ phase is often limited, as it is found to transform into other phases such as B2 and D0<sub>19</sub> after long-term annealing. To explore the details behind the annealing-induced transformation from the metastable L1<sub>2</sub>-γ′ phase to the thermodynamically stable D0<sub>19</sub>-χ phase in the single-crystalline Co-base superalloy ERBOCo-VF60 (Co<sub>79.8</sub>Al<sub>8.9</sub>W<sub>9.0</sub>Ta<sub>2.3</sub> in at.%), scanning transmission electron microscopy and atom probe tomography are employed. Due to the structural similarity between the L1<sub>2</sub> and D0<sub>19</sub> structures, coherent plate-shaped χ precipitates are formed in the γ/γ′ microstructure parallel to {111} planes through a shear-based transformation mechanism. While the χ phase precipitates slowly during isothermal aging, its formation can be significantly accelerated locally by coating the superalloy with a Cr-rich layer, which indirectly stabilizes the χ phase as revealed by thermodynamic calculations. This procedure allowed us to obtain an intermediate (incomplete) state of χ-phase formation in terms of both crystal structure and composition. By characterizing the partial dislocations at the tip of growing χ precipitates, the microscopic details of the shear-based cubic-to-hexagonal transformation from L1<sub>2</sub> to D0<sub>19</sub> are uncovered. The compositional aspect of the transformation involves a significant diffusion-mediated enrichment of W in the χ phase, accompanied by a simultaneous W depletion in the γ′ phase, leading to its transformation to the γ phase.</p>
Supporting data for 'Rapid quantification of methane in water with parts-per-billion sensitivity using a metal-organic framework-functionalized quartz crystal resonator'
<p>Supporting data for the preprint 'Rapid quantification of methane in water with parts-per-billion sensitivity using a metal-organic framework-functionalized quartz crystal resonator' published at ChemRxiv (doi://10.26434/chemrxiv-2024-x62zz)</p> <p> </p>
Dataset for Next-Generation Self-Powered Photodetectors using 2D Bismuth Oxide Selenide Crystals
<p>The dataset contains relevant data and figures regarding the manuscript "Next-Generation Self-Powered Photodetectors using 2D Bismuth Oxide Selenide Crystals".</p> <p>All Figures are in jpg/tiff format and all relevant data are in csv formats. </p> <p>The data in csv format are labelled as specified in the corresping images (e.g. Figure 1a csv file corresponds to data used to plot graphs from Figure 1a etc.). </p> <p>Axis labeling and units are always specified at the beginning of individual columns. If more than one curve was plotted from the csv file, the conditions can also be found at the beginning of corresponding columns.</p>
3D ED dataset of co-crystal of GRGDS peptide with trifluoroacetic acid (TFA)
<p>EPU-D electron diffraction dataset of the GRGDS TFA co-crystal. The original diffraction data is in MRC format, with all metadata stored in the PETS2 pts2 file. JANA files for absolute structure determination and dynamical refinement are also included.</p>
X-ray diffraction data on the crystal structures of Tris-bound β-glucosidase from Thermoanaerobacterium saccharolyticum
<p>X-ray diffraction data of Tris-bound β-glucosidase from Thermoanaerobacterium saccharolyticum</p> <p>Data type: raw data<br>Data format: cbf</p> <p>Data <br>1. TsaBgl-Tris Data I <br>2. TsaBgl-Tris Data II<br>3. TsaBgl-Tris Data III </p>
Associated coordinate and mtz files for "Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio- selective oxidation of antifungal macrolides"
<p>Coordinate and mtz files for the associated protein structures reported in "Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio- selective oxidation of antifungal macrolides".</p>
Atomic Structure of Amyloid Crystals
<p>3D ED/MicroED data collected on micro-crystals of a fragment of amyloid-beta peptide. The specimen was prepared using the Preassis method (Zhao et. al. Nature Communications 2021) on Quantifoil R2/1 (300 mesh) grid. 3D ED/MicroED data were collected on a 200kV JEOL JEM-2100 LaB<sub>6 </sub>TEM equipped with a Timepix hybrid pixel detector. A Gatan 914 cryo-transfer holder was used to keep the specimen at liquid nitrogen temperature during data collection. The rotation speed of goniometer, exposure time, electron dose rate and camera length were 0.23 degree/s, 0.5 s, 0.1 e<sup>-</sup>/Å<sup>2</sup>/s and 30cm, respectively. The software <em>Instamatic </em>was used for electron diffraction data collection. The rotation range of individual dataset was limited between 40 degree and 50 degree due to beam damage.</p> <p>The data was saved in TIFF, SMV, and DM3 (for REDp processing) format. Information of the individual data collection can be found in the cRED_log file. Input files for PETS processing and XDS processing (automatically generated) are also included.</p> <p> </p>
Critical prethermal discrete time crystal created by two-frequency driving
<p>We report the observation of long-lived Floquet prethermal discrete time crystalline (PDTC) order in a three-dimensional position-disordered lattice of interacting dipolar-coupled 13C nuclei in diamond at room temperature. We demonstrate a novel strategy of "two-frequency" driving, involving an interleaved application of slow and fast drives that simultaneously prethermalize the spins with an emergent quasi-conserved magnetization along the x-axis, while enabling continuous and highly resolved observation of their dynamic evolution when periodically kicked away from x. The PDTC order manifests itself in a robust period doubling response of this drive-induced quasi-conserved spin magnetization interchanging between x and -x; our experiments allow a unique means to study the formation and melting of PDTC order. This dataset contains the raw data for the main text of the paper "Critical prethermal discrete time crystal created by two-frequency driving" found at <em>arXiv</em>:2201.02162, DOI: https://arxiv.org/abs/2201.02162. The authors encourage anyone to reach out with any questions or further help interpreting our results.</p>
Data supporting the publication "Enhanced nonlinear optomechanics in a coupled-mode photonic crystal device"
<p>Data supporting the publication "Enhanced nonlinear optomechanics in a coupled-mode photonic crystal device". Set contains raw measured data and plotted data points for all figures in the main text.</p>
Data from: Gardner-like crossover from variable to persistent force contacts in granular crystals
<p>We report experimental evidence of a Gardner-like crossover from variable to persistent force contacts in a two-dimensional, bidisperse granular crystal by analyzing the variability of both particle positions and force networks formed under uniaxial compression. Starting from densities just above the freezing transition, and for variable amounts of additional compression, we compare configurations to both their own initial state, and to an ensemble of equivalent, reinitialized states. This protocol shows that force contacts are largely undetermined when the density is below a Gardner-like crossover, after which they gradually transition to being persistent, being fully so only above the jamming point. We associate the disorder that underlies this effect to the size of the microscopic asperities of the photoelastic disks used, by analogy to other mechanisms that have been previously predicted theoretically.</p>
Spontaneous crystallization of a large Pt nanoparticle
<p>This is a video of a "large" (16384 atoms) Pt nanoparticle solidifying from 3000 K down to 300 K over 1 ns of molecular dynamics, modeled with a GAP interatomic potential for platinum [1]. One can observe how the formation of the stable bulk fcc motifs is nucleated inward from the surface. A paper reference will be added when available.</p> <p><strong>References</strong></p> <ol> <li>J. Kloppenburg and M.A. Caro. General-purpose GAP potential for platinum. DOI: <a href="https://doi.org/10.5281/zenodo.7415219">10.5281/zenodo.7415219</a>.</li> </ol>
A database of synthetic inelastic neutron scattering spectra from molecules and crystals
<p>This database contains simulated inelastic neutron scattering (INS) spectra for 10,000+ inorganic crystals and 20,000+ organic molecules. The INS database for inorganic crystals is based on the phonon database at Kyoto University by Atsushi Togo (http://phonondb.mtl.kyoto-u.ac.jp/). The INS database for organic molecules is based on the QM8 dataset (http://quantum-machine.org/datasets/).</p> <p>Entry lists can be found in crystals.dat and molecules.dat. After unzipping the tar.gz files, data for each structure model can be found in a subfolder. </p> <p>For the inorganic crystal database, each subfolder contains five files: a structure.cif file for the crystal structure, a vis_inc_0K.csv file containing the simulated VISION/TOSCA spectra, a powder_2Dmesh_coh_0K.csv file containing the simulated powder S(Q,E), a vis_nwdos.csv file containing the neutron weighted PDOS, a vis_dos.csv file containing the true PDOS, and a gamma_modes.xyz file containing the displacements of gamma point phonons for visualization (with Jmol, http://jmol.sourceforge.net/).</p> <p>For the QM8 molecular database, there are five files in each subfolder: an INFO-* file containing the SMILES string as well as the IUPAC name (if available) for this molecule, a *.com file containing the input for Gaussian simulation (which also contains the atomic coordinates), a *vis_inc_0K.csv file containing the simulated INS spectra, a *.xyz file containing the atomic displacement of each vibrational modes (can be visualized with Jmol), and a *modes.csv file containing the calculated INS intensity for each normal mode. </p> <p>A python script (plot_ins.py) to plot the INS data files is provided<br> Usage: plot_ins.py *.csv {-s [1,2] -x [0:100] -y [0:100] -z [0:2.5]}<br> -s : spectrum index, -x/y/z : range to plot </p> <p><br> The manual for the OCLIMAX software used for INS simulations is also provided for reference.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.