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689 results for “crystals”
Crystal structure of d(CCGGGGTACCCCGG)2 at 1.4 Å resolution.
<p>The X-ray crystal structure of the DNA tetradecamer sequence d(CCGGGGTACCCCGG)<sub>2</sub> is reported at 1.4 Å resolution in the tetragonal space group P4<sub>1</sub>2<sub>1</sub>2. The sequence was designed to fold as a four-way junction. However, it forms an A-type double helix in the presence of barium chloride. The metal ion could not be identified in the electron-density map. The crystallographic asymmetric unit consists of one A-type double helix with 12 base pairs per turn, in contrast to 11 base pairs per turn for canonical A-DNA. A large number of solvent molecules have been identified in both the grooves of the duplex and around the backbone phosphate groups.</p>
Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution.
<p>We presented a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)<sub>2 </sub>all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. Crystals did not have any metal ion in the crystallization solution apart from the sodium in the buffer. However, the sequence does not take up the junction structure, but forms an A-type double helix in P4<sub>1</sub>2<sub>1</sub>2 space group.</p>
Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution.
<p>We presented a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)<sub>2 </sub>all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of magnesium, it does not take up the junction structure, but forms an A-type double helix in P4<sub>1</sub>2<sub>1</sub>2 space group. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Though the crystallization condition has magnesium chloride, it was not observed in the electron density map.</p>
X-ray diffraction images of Anti-CD20 crystals
<p>Original X-ray diffraction images from Pilatus detector taken at Diamond Light Source Synchrotron (I04 beamline).</p> <p>Images can be read by AXDV (or similar) software.</p> <p>These datasets were used for diffraction and crystallographic analyses reported in Yang et al., Crystals 2019, 9, 230.</p> <p> </p>
Serial synchrotron crystallography dataset and 3D-ED dataset - HEWL crystals obtained by instant crystallization with TbXo4
<h2>Data sets related to the publication "Nucleating Agent Crystallophore Induces Instant Protein Crystallization" by Sauter et al.</h2> <p><em><strong>3D-Electron Diffraction data</strong></em>: The raw data obtained on the protein Hen Egg-White Lysozyme is contained in the file <em>RAW-Data_3D-ED_deposition.tar.bz2</em>.</p> <p>Results of first rounds of model refinement are contained in <em>3D-ED-affi_4-5sets</em> files</p> <p><em><strong>Synchrotron Serial Crystallography data</strong></em>: The raw SSX data obtained on the protein Hen Egg-White Lysozyme can be accessed through <a href="https://doi.org/10.15151/ESRF-DC-1823716276">https://doi.org/10.15151/ESRF-DC-1823716276</a>.</p> <p>Results of first rounds of model refinement are contained in <em>SSX-Xo4-supernatent</em> files</p>
cif files and VASP files for Li6PS5X crystals and a set of isovalent analogs
<p>This dataset is meant as supplementary material to the research paper titled "The Devil in the Details: Lessons from Li6PS5X for Robust High-Throughput Workflows" authored by Asif Iqbal Bhatti, Sandeep Kumar, Catharina Jaeken, Michael Sluydts, Danny E.P. Vanpoucke and Stefaan Cottenier. At the time of writing this description, the manuscript is under peer review (publication info will be added here once published). </p> <p>The data set contains cif files as well as VASP input and output for all crystals that are being discussed in this paper.</p>
Crystallization behavior and structural build-up of palm stearin - wax hybrid fat blends
<p>This dataset was used in the publication <em>"Crystallization behavior and structural build-up of palm stearin - wax hybrid fat blends"</em>. An overview of the abbreviations and the dataset can be found below.</p>
Dataset for the article "Influence of oxidative and consequential reductive annealing on the photoluminescence intensity, decay time and morphology of ZnO single-crystal faces".
<p>Dataset for the article "Influence of oxidative and consequential reductive annealing on the photoluminescence intensity, decay time and morphology of ZnO single-crystal facets".</p> <p>David John1,2, Zdeněk Remeš1, Radim Novák1, Štěpán Remeš1, Jakub Volf1,3,4, Oleg Babčenko1, Egor Ukraintsev5, Bohuslav Rezek5, and Maksym Buryi3</p> <p>1 Institute of Physics of the Czech Academy of Sciences, Cukrovarnická 10/112, 162 00, Prague, Czech Republic<br>2 Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Břehová 7, 115019, Prague, Czech Republic<br>3 Institute of Plasma Physics of the Czech Academy of Sciences, U Slovanky 2525/1a, 182 00, Prague, Czech Republic <br>4 Department of Inorganic Chemistry, University of Chemistry and Technology, Technická 5, Prague 6, 166 28, Czech Republic<br>5 Faculty of Electrical Engineering of the Czech Technical University, Technická 2, 160 00, Prague, Czech Republic</p> <p> </p> <p>Dataset description:</p> <p>08_08_2024_ZnO_41a_700C_O_CF4_Multi75_10x10um.0_00000 AFM data<br>08_08_2024_ZnO_41a_700C_O_CF4_Multi75_10x10um.0_00003 AFM data<br>16_08_2024_ZnO_700C_O_CF4Multi_10x10um.0_00001 AFM data<br>16_08_2024_ZnO_700C_O_CF4Multi_10x10um.0_00003 AFM data<br>afm zn AFM data<br>data phase shift fit phase shift data<br>grafy phase shift fit phase shift data<br>ZnO faces optical images</p>
Stress-Strain Analysis of Polycrystalline Copper with Goss Texture Using Crystal Plasticity FEM
<pre>Stress-strain analysis of single-phase polycrystalline copper with a Goss texture using a cubic representative volume element (RVE) and periodic boundary conditions, performed with Abaqus through the crystal plasticity finite element method.</pre>
Surfalex HF formability study - Workflow 2 - Fit single crystal parameters
<p>This MatFlow workflow is the second in a set of eight workflows developed during our formability study of the Surfalex HF (AA6016A) material. In this workflow, we calibrated crystal plasticity (CP) parameters using experimental data. The hardening coefficient, the initial and maximum CRSS values, and the hardening exponent, as defined in the CP phenomenological power law adopted by DAMASK were optimised. Starting from trial guesses for these parameters, we optimised the parameters with respect to the experimental stress-strain curve of the Surfalex HF material, using a Levenberg-Marquardt procedure. At each iteration of the process, N+1 CP simulations were performed (for N fitting parameters). Five iterations were used in total.</p> <p>This workflow can be downloaded and explored in a Jupyter notebook, as explained in the <a href="https://github.com/LightForm-group/surfalex_data_explorer">GitHub repository here</a>.</p>
Research data supporting "Tin phosphide anodes for potassium-ion batteries: insights from crystal structure prediction"
<p>This dataset contains the output files of crystal structure prediction calculations (density-functional theory relaxations, bandstructures, phonon calculations, GIPAW-NMR calculations) on the ternary K-Sn-P phase diagram. All calculations were performed with the CASTEP DFT package (https://www.castep.org/) and the "matador" Python library (https://github.com/ml-evs/matador).</p> <p><strong>Contents:</strong></p> <ul> <li>"convergence_tests.zip": contains the results of convergence tests on the K-P system at two levels of accuracy "polish" and "searches" on the corresponding edge of the K-Sn-P ternary system</li> <li>"phonons.zip": contains CASTEP output files for phonon calculations on the predicted low-lying phases on the corresponding edge of the K-Sn-P phase diagram</li> <li>"polish.zip": contains CASTEP output files of relaxations on the corresponding edge of the K-Sn-P system at the "polish" level of accuracy using various different xc-functionals or external pressures.</li> <li>"searches.zip": contains ".res" files that provide the relaxed structure from each different crystal structure prediction method on the corresponding edge of the K-Sn-P system.</li> <li>"bulk_modulus.zip" contains CASTEP output files for calculation of E(V) curves for low-lying KP phases with different xc-functionals.</li> <li>"nmr.zip" contains CASTEP output files for GIPAW-NMR calculations of chemical shifts for low-lying K-Sn-P phases.</li> <li>"spectral.zip" contains CASTEP and OptaDOS output files for projected bandstructure and DOS calculations of low-lying K-Sn-P phases.</li> <li>"digests.zip" contains JSON representations of all the structures from polish and searches, broken down into K-P and K-Sn-P specific digests.</li> </ul>
Dataset for Link between Anisotropic Electrochemistry and Surface Transformations at Single Crystal Silicon Electrodes: Implications for Lithium Ion Batteries
<p>This dataset provides the raw data to the manuscript</p> <p>"<strong>Link between Anisotropic Electrochemistry and Surface Transformations at Single Crystal Silicon Electrodes: Implications for Lithium Ion Batteries"</strong></p> <p>Specifically, the following measurements are provided:</p> <ul> <li>Electrochemical measurements as cyclic voltammetry using scanning electrochemical cell microscopy for three different Si crystallographic orientations (100, 110, 311) in 1 M LiPF6 in ethylene carbonate - ethyl methyl carbonate ("SECCM/")</li> <li>Scanning electron microscopy and transmission electron microscopy imaging of pristine and cycled samples ("Images/")</li> </ul>
Polymorphism and Perfection in Crystallization of Hard Sphere Polymers
<p>Data archive corresponding to the publications "Polymorphism and Perfection in Crystallization of Hard Sphere Polymers" by M. Herranz et al., Polymers 14, 4435 (2022); DOI: https://doi.org/10.3390/polym14204435</p> <p>Please see README.txt for instructions on how to access and read the files from the crystallographic analysis based on the CCE norm descriptor.</p> <p>All snapshots have been generated and successively analyzed by the Simu-D software.</p>
Photonic crystals with rainbow colors by centrifugation-assisted assembly of colloidal lignin nanoparticles
<p>Source data (CSV files) associated with the publication titled <strong>Photonic crystals with rainbow colors by </strong><strong>centrifugation-assisted assembly </strong><strong>of colloidal lignin nanoparticles</strong>.</p>
Temperature-Dependent THz Properties and Emission of Organic Crystal BNA
<p>This dataset is accompanying the paper "Temperature-Dependent THz Properties and Emission of Organic Crystal BNA"</p> <p><strong>General data acquisition:</strong></p> <p>The data was acquired with a modified Menlo Tera K-15 THz-TDS, consisting of a photoconductive emitter/receiver and four off-axis-parabolic mirrors (OAP). The second and third OAP, focusing and collecting the THz, are with a longer focus length to have enough space for the cryostat (Janis ST-100), which is equipped with 3 mm z-cut quartz windows for entry and exit of the THz beam. The delay line offers delays up to 1600 ps but the range was restricted to cut out the reflections from the z-cut quartz windows. Instead of averaging with Menlo’s own software ScanControl, each single trace is read out. 10 000 traces are saved for each unique measurement condition (crystal orientation, temperature) and saved in a single HDF-5 file. HDF-5 is an efficient (binary), cross-platform data format and can be read easily by i.e. Python or Matlab.</p> <p> </p> <p><strong>The structure is as follows:</strong></p> <p><strong>raw_data </strong></p> <p>The folder raw_data contains four folders. The folder “dark” contains a single file since this is independent of crystal orientation and temperature of the cryostat. For this measurement, the THz beam was blocked but all electronics, selected delay range etc. kept the same, to measure the noise-floor of the system.</p> <p>The folder reference was captured with the cryostat incl. windows, vacuum and crystal holder in place. Even though there should be no change in the transfer function by changing the temperature (due to the large aperture of the crystal holder), we still recorded reference traces for each temperature.</p> <p>The folder “BNA_orientation_001” contains the data with the organic crystal BNA in vertical orientation (<001>).</p> <p>The folder “BNA_orientation_100” contains the data with the organic crystal BNA in horizontal orientation (<100>).</p> <p><strong>averaged_corrected_data</strong></p> <p>The folder “averaged_corrected_data” reduces the large amount of raw data due to averaging. The program “Correct@TDS” (developed in the group of Dr. Romain Peretti, Terahertz Photonics Group @ IEMN - CNRS (UMR 8520), publication in preparation), is used to fit specific correction parameters for the delay, dilatation, amplitude noise and periodic sampling. The mean data is saved for each temperature in a text file called “mean.txt”. The other output of “Correct@TDS” is diagnostic information about the correction parameters and about the standard deviation in frequency- and time-domain.</p> <p><strong>extracted_n_alpha</strong></p> <p>The folder “extracted_n_alpha” contains the refractive index, absorption coefficient and more in a single HDF-5 file, extracted by the program phoeniks (<a href="https://github.com/TimVog/phoeniks">https://github.com/TimVog/phoeniks</a>), which is developed in our group. All results for the paper are saved in the internal folder structure of the HDF-5 file (for crystal orientation and temperature).</p> <p>The folder “nelly” shows the extraction of n and alpha done with Nelly [1] (<a href="https://github.com/YaleTHz/nelly">https://github.com/YaleTHz/nelly</a>) for the vertical orientation, which was used for the supplementary document.</p> <p> </p> <p>[1] Nelly: A User-Friendly and Open-Source Implementation of Tree-Based Complex Refractive Index Analysis for Terahertz Spectroscopy</p> <p>Uriel Tayvah, Jacob A. Spies, Jens Neu, and Charles A. Schmuttenmaer</p> <p>Analytical Chemistry 2021 93 (32), 11243-11250</p> <p>DOI: 10.1021/acs.analchem.1c02132</p> <p> </p>
Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation
<p>Data archive corresponding to the manuscript "Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation" by M. Herranz et al., Phys. Rev. E 107, 064605 (2023); DOI: 10.1103/PhysRevE.107.064605</p> <p>Please see README.txt for instructions on how to access and read the files from the crystallographic analysis based on the CCE norm descriptor.</p> <p>All snapshots have been generated and successively analyzed by the Simu-D software.</p>
Phononic crystals dataset for supervised training of surrogate deep learning model
<p>The dataset contains shapes of unit cells of phononic crystals (inputs) in the form of images and corresponding dispersion diagrams (outputs). The dataset is used for deep learning (DL) model training.<br> Outputs are in the form of .mat files which contain vectors of reduced wavevector and corresponding frequencies, and also displacements u, v, w which can be used for polarization calculation.</p> <p>The dataset contains 11000 cases.</p> <p>Note: Ignore names "labels" as these are actually inputs to the DL model, not labels.</p>
Raw Data for the Article "Cyclopentadienone triisocyanide iron complexes: general synthesis and crystal structures of tris(2,6-dimethylphenyl isocyanide)(η4-tetraphenylcyclopentadienone)iron and tris(naphthalen-2-yl isocyanide)(η4-tetraphenylcyclopentadienone)iron acetone hemisolvate"
<p>This data set contains the raw data (NMR, HRMS, Elemental analysis) for the article "Cyclo­penta­dienone triisocyanide iron complexes: general synthesis and crystal structures of tris­­(2,6-di­methyl­phenyl isocyanide)(η<sup>4</sup>-tetra­phenyl­cyclo­penta­dienone)iron and tris­­(naphthalen-2-yl iso­cyanide)(η<sup>4</sup>-tetra­phenyl­cyclo­penta­dienone)iron acetone hemisolvate" published in <em>Acta Crystallographica Section E: Crystallographic Communications</em>, DOI:</p> <p><a href="https://doi.org/10.1107/S205698902300498X">https://doi.org/10.1107/S205698902300498X</a></p>
Dataset for Nanoscale Growth Mechanisms of Gypsum: Implications for Environmental Control of Crystal Habits
<p>This dataset collected here has been used in the paper "Nanoscale Growth Mechanisms of Gypsum: Implications for Environmental Control of Crystal Habits".</p> <p>The files are in .dat format and each one corresponds to the images indicated in the file name.</p>
Datasets supporting the publication "Technical Note: in-situ measurements and modelling of the oxidation kinetics in films of a cooking aerosol proxy using a Quartz Crystal Microbalance with Dissipation monitoring (QCM-D)" by Milsom et al.
<p>Supporting experimental and modelling data for the manuscript entitled "Technical Note: Modelling and in-situ measurements of the oxidation kinetics in films of a cooking aerosol proxy using a Quartz Crystal Microbalance with Dissipation monitoring (QCM-D)" by Adam Milsom et al. 2023. </p> <p>Includes raw QCM-D data with the numbers at the beginning of the files corresponding to the experiment numbers in the manuscript. </p> <p>Normalised Raman peak area data for modelling and model ensemble outputs, including uptake coefficients. </p>
ScienceDex guides
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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.