Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
312
datasets available to search
ShareScore release 0.9.0
Dataset results
312 results for “Confinement”
Freeform topology optimized, dispersive nanostructures for field confinement
<p>Provides the 3D topology optimized nanostructures as STL files, as well as the Lumerical files used to validate their performance presented in the article "Time-Domain Topology Optimization of Arbitrary Dispersive Materials for Broadband 3D Nanophotonics Inverse Design" (https://doi.org/10.1021/acsphotonics.3c00572).</p>
Data set related to the manuscript "Ionic liquids under confinement: From systematic variations of the ion and pore sizes towards an understanding of structure and dynamics in complex porous carbons"
<p>Graphical files in the agr format for all the figures in the main text of the manuscript entitled "Ionic liquids under confinement: From systematic variations of the ion and pore sizes towards an understanding of structure and dynamics in complex porous carbons" (10.1021/acsami.9b16740). Example of input file for one of the systems simulated.</p>
Supplementary data for "Molecular dynamics study of confined water in the periclase-brucite system under conditions of reaction-induced fracturing"
<p>In this dataset you can find sample data from periclase and brucite simulations and python scripts that can be used to confirm the plots in the paper.</p> <ul> <li>"bruciteSimualtions" and "periclaseSimualtions" contains the simulations where the mineral in contact with water is either brucite or periclase. Within each of these two folders, there are two subfolders, "waterProperties" and "waterThickness". <ul> <li>The data in "waterProperties" is used to calculate water properties. Each folder inside "simulations" represent one simulation.</li> <li>The data in "waterThickness" is used to calculate the change in water film thickness with time under different conditions. The simulations are run for either 3 ns or 10 ns. Each folder inside "simulations_Xns" represent one simulation.</li> </ul> </li> <li>For each folder containing one simulations, we provide: <ul> <li>NAME.run: The input script</li> <li>NAME.data: The input data</li> <li>job.sh: Script to run the simulation</li> <li>log.lammps: Thermodynamic output from the simulation</li> <li>Note that the pressures given in the folder names and in the simulations are in atm, not MPa.</li> </ul> </li> </ul> <p> </p> <ul> <li>"bruciteSimulations" and "periclaseSimualtions" are in zip containers. In order to use them, please unzip them and leave the resulting folders in the same directory as this README file. </li> </ul> <p> </p> <ul> <li>The python scripts shows how to extract the relevant data from the lammps log files, which enables reproduction of the figures in the paper. See instructions below to use the scripts.</li> </ul> <p><br> Installation instructions to make the python plot scripts working, assuming you already have numpy and matplotlib:</p> <p>> pip3 install git+https://github.com/henriasv/regex-file-collector.git</p> <p>> pip3 install git+https://github.com/henriasv/lammps-logfile.git<br> </p> <p>If this does not work, please contact Marthe Grønlie Guren, m.g.guren@geo.uio.no</p>
Microfluidic monitoring of the growth of individual hyphae in confined environments
Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass, and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of Talaromyces helicus, a soil isolate, and of the model fungus Neurospora crassa through parallel microchannels. The distributions of growth velocity obtained for each strain were compared to measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, N. crassa was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for T. helicus. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behavior of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to adress its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.
Temperature response of water-saturated compact Longmenshan limestone and porous Rajasthan sandstone to changes in confining pressure
<p>Three data sets are stored in this data submission. The first data set includes the temperature response of water-saturated compact Longmenshan limestone (L27) and porous Rajasthan sandstone (RJS) to changes in confining pressure under drained/undrained conditions. The second data set includes the thermal properties of rock-forming minerals and estimations of thermal characteristic time/distance. The third data set includes the internal temperature evolution of the water-saturated sample within 1 s after instantaneous loading in models M-01, M-02 and M03, in which the thermal properties of the solid grains are set to be that of gypsum, average values of the main rock-minerals and <em>α</em>-quartz, respectively.</p>
Dataset and simulation files for article: "Designing of strongly confined short-wave Brillouin phonons in silicon waveguide periodic lattices"
<p>Dataset and simulation files for article: "Designing of strongly confined short-wave Brillouin phonons in silicon waveguide periodic lattices"</p>
Data set related to the manuscript "Simulations of ionic liquids confined in surface-functionalized nanoporous carbons: Implications for energy storage"
<p>Graphical files in the agr format for all the figures in the manuscript entitled "Simulations of ionic liquids confined in surface-functionalized nanoporous carbons: Implications for energy storage". Examples of input files for the three systems simulated.</p>
Data for the article "Commensurability between element symmetry and the number of skyrmions governing skyrmion diffusion in confined geometries"
<p>Data for the article "Commensurability between element symmetry and the number of skyrmions governing skyrmion diffusion in confined geometries" (<a href="https://arxiv.org/abs/2009.03995">[2009.03995] Commensurability governing skyrmion diffusion in confined geometries (arxiv.org)</a>)</p>
Entropy Poduction in a Box: Analysis of Instabilities in Confined Hydrothermal Systems
<p>This data set was generated using the numerical tool SHEMAT suite. All relevant input and output files are given here for the scenarios discussed in our manuscript: (1) onset of convection, varying box geometry for (2) homogeneous models, and (3) heterogeneous models.</p> <p>Additionally, some Matlab files show how the simulation results are analyses d in terms of the entropy production.</p>
Ultrasonic velocity measurements of lunar regolith simulant at low confining pressures with variable ice content
<p>This dataset was created by Christopher Chance Amos during completion of a PhD degree in Space Resources</p><p>at Colorado School of Mines. This data was collected during Spring 2023.</p><p> </p><p>This dataset includes compressional and shear raw collected waveforms as well as interpreted velocities</p><p>from first-break picking. See the README files in subdirectories for explanations of individual files.</p><p> </p><p>The purpose of this dataset is to serve as a foundation and calibration for seismic modeling of the lunar</p><p>near-surface. These models will be used to determine if seismic methods are feasible for characterizing</p><p>the quantity and form of lunar subsurface ice deposits.</p>
Microchamber slide design for cell confinement during imaging- Tetrahymena rostrata timelapse data
<p>We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 10× 0.45 Plan Apo Air or a Plan Apo λD 100x OIL OFN25 DIC N2 objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 file.<br><br><i>Tetrahymena rostrata</i> was provided by Andrzej Kaczanowski, who isolated the cells from the small snail <i>Cohlicopa lubrica</i> near Warsaw. The cells were cultured in medium consisting 0.5% yeast extract and 0.5% of proteose peptone supplemented with 250 ug/ml streptomycin sulphate and 250 ug/ml penicillin G to maintain sterility.</p>
Microchamber slide design for cell confinement during imaging- Colpoda steinii in 384 well or microwells
<p>We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 10× 0.45 Plan Apo Air objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 file. The repository contains timelapse series data at irregular intervals between the beginning of data collection and after two hours. Wells on a glass-bottom 384 well plate or microwells contained <i>Colpoda steinii</i> cells.</p>
Microchamber slide design for cell confinement during imaging- early encystment
<p>The data shows an early stage of <i>Colpoda steinii</i> encystment.</p><p>We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 10× 0.45 Plan Apo Air objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 files. The repository contains timelapse data.</p>
Microchamber slide design for cell confinement during imaging- reanimation experiment
<p>We dried slides with 1000 <i>Colpoda steinii</i> cysts per well over a weekend. We reanimated the slides with either 1 mM Tris pH 7.5 or hay medium + K. aerogenes (1ul of preculture + 1ml hay medium). We rehydrated the cells for 10 minutes in 1 mM Tris pH 7.5 on an orbital shaker (100 rpm). We washed the cells in 0.1% SDS for 10 minutes on the shaker. The cells were washed with 1 mM Tris three times for 1 minute before adding Tris or the experimental medium and imaging.</p><p>Plate 1: Tris</p><p>Plate 2: hay medium + K.a.</p><p>At time point 26, active cells are visible in plate 2 at B6, C6, D6, E6. There were no reanimation events observed on the plate treated with Tris alone.</p>
Anisotropic molecular diffusion in confinement II (Dataset)
<p>This archive contains the simulation settings for the bulk and S-L-V system configurations used in the associated paper "Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films" (DOI: 10.5281/zenodo.7446070).</p><p>We here provide two different archives: </p><ul><li>One with the gromacs simulation configuration used for the simulation ("il_sim_settings_data.zip")</li><li>One with the raw extracted diffusion (parallel+perpendicular) and interface-normal density data ("graph_raw_data.zip"), which is the data underlying all plots in our associated publication.</li></ul><p>In "il_sim_settings_data.zip" there are folders for the bulk- and S-L-V- systems respectively, each containing folder for the systems with n=2,4,6,8.10 carbon atoms in the cation alkyl chain. These folders are labeled c<n> (i.e., for example: c2). Within these folders you will find the respective top and tpr files for the simulation.</p><p>In "graph_raw_data.zip" you can also find a folder for the bulk and the slv systems in the top level directory.</p><p>In "bulk", you can again find the folders c2,c4,c6,c8,c10 labeled as described above. Each folder contains a folder "diffusion_msd", which contains the gromacs (gmx msd) results for cations and anions in xvg format respectively. Also it contains a folder "diffusion_epm", which contains the epm model analysis results in these systems. Each file contains a header explaining the detailed data format. The file name depicts whether the data pertains to cations or anions within the respective system.</p><p>In "slv", you first find the c2,c4,c6,c8,c10 level of folders and within each folder two files describing the perpendicular diffusivity according to EPM analysis for cations and anions respectively in that respective SLV system ("D_perp_anion.txt"/"D_perp_cation.txt") the results of the parallel MSD-based analysis ("D_parallel_anion.txt"/"D_parallel_cation.txt") as well as the interface-normal number density profiles ("innd_anion.txt"/"innd_cation.txt")</p>
Rock indentation tests with lateral confinement on Gildehaus Bentheim sandstone
<p>This dataset records the test results for rock indentation on Gildehaus Bentheim sandstone with a lateral confinement up to 20 MPa and is associated with the study named 'On the effect of lateral confinement on rock-cutting tool interactions' . </p><p>The original test results for rock indentation with lateral confinement are in files of .csv format. Each file is named according to 'rock type-sample ID-lateral confinement'. For example, 'GBS-AD2-20MPa.csv' refers to a test on a Gildehaus Bentheim sandstone specimen with sampleID AD2 tested at 20 MPa confinement. In each data file, there are four columns of data, that are 'Confining pressure, MPa', 'Displacement of oil cylinder, mm', 'Force, kN' and 'Displacement, mm'. The sample height has also been included and cylinder/actuator for supplying oil has a diameter of 10 mm. For test where acoustic emission data is available, the test date and time has been included.</p><p>Files started with 'event data' are acoustic emission data. In each file, the first to fifth column is 'Number of Event', 'Data','Time','Decimal second' and 'Local Time'.</p>
Experimentally probing the effect of confinement geometry on lipid diffusion
<p>Dataset accompanying the J. Phys. Chem. B paper: "<span>Experimentally probing the effect of confinement geometry on lipid diffusion". Contains raw and processed FCS data, processed FRAP data, and VCell simulations, and Jupyter notebooks to generate the figures in the associated manuscript.</span></p>
Data for 'Confined vacuum resonances as artificial atoms with tunable lifetime'
<p>This folder contains all the raw data needed to generate the figures in the paper '<em>Confined vacuum resonances as artificial<br> atoms with tunable lifetime</em><em>.</em>' The data are seperated by the figures in which they appear, with a text folder in each folder that contains any relevant additional information. </p>
Data for the paper "Optimization of quasisymmetric stellarators with self-consistent bootstrap current and energetic particle confinement"
<p>Data for the paper "Optimization of quasisymmetric stellarators with self-consistent bootstrap current and energetic particle confinement"</p>
Microchamber slide design for cell confinement during imaging- measurements
<p>Spreadsheet of measurements of cells using CellProfiler.</p>
ScienceDex guides
Understand access before you commit
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.