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2,194 results for “Diffusers”
Data for Diffusion phase-imaging in anisotropic media using non-linear gradients for diffusion encoding
<p>Diffusion MRI data for experiments on anisotropic synthetic fibre phantom and isotropic agar phantom. </p>
Reaction-diffusion systems simulations
<p>Simulations of different reaction-diffusion systems. 2D models are 100x100 nodes grid. 1D model 100 nodes chain.</p> <p> </p> <p>biomass_{BIFPARAM} = biomass model</p> <p>fn_{BIFTYPE}_{BIFPARAM} = fitzhugh-nagumo model</p> <p>gl_{BIFTYPE}_{BIFPARAM} = ginzburg-landau model</p> <p>nonlinear_1d_{BIFPARAM} = nonlinear dynamical model, 1D chain of reactive systems</p> <p> </p> <p>Note that fn_turing is not really a turing bifurcation, but rather a travelling wave emission.</p>
Dataset for Unrolled-DOT: An Interpretable Deep Network for Diffuse Optical Tomography
<p>Official dataset repository for Unrolled-DOT: An Interpretable Deep Network for Diffuse Optical Tomography. The repository contains both the experimental dataset (allTrainingDat_30-Sep-2021.mat) as well as data that is a dependency for running our code (5_29_21_src-det_10x10_scene_4cm.zip).</p>
Dataset for 'A microscopic diffusion-induced discrete element model for swellable particles'
<p>This dataset contains both numerical simulation data and experimental data describing the swelling behaviour of binary particle systems. Detailed study on the swelling behaviour is presented in a journal paper entitled "A microscopic diffusion-induced discrete element model for swellable particles ". We provide all the essential data in a single excel file with the description below:</p> <p>Dataset 1-Evolution of the radius of core zone obtained from experiments (used in Fig.7c of the associated paper): Experimental data for the measured radius of core zone and associated standard deviation at various time.</p> <p>Dataset 2-Calibration procedures for the microscopic swelling model from DEM simulation (used in Fig8 of the associated paper).</p> <p>Dataset 3 - Evolutions of the normalised average diameter d/d_0 (used in Fig.9) obtained from experiments and DEM simulations.</p> <p>Dataset 4 - Evolutions of normalised water concentration (used in Fig.10a) and Young’s modulus (used in Fig.10b) of the swollen particle obtained with different swelling models.</p> <p>Dataset 5 - Evolution of core zone obtained from DEM simulations with the microscopic swelling model (used in Fig.10b).</p> <p>Dataset 6 - Evolution of the height of the particle bed obtained from experiments and simulations (used in Fig.13 of the associated paper): Experimental data for the measured hight and associated standard deviation at various time, as well as the numerical data.</p> <p>Dataset 7 -Evolutions of (a) The ratio of average normal contact force to the initial gravity of the dry particle (used in Fig.14a of the associated paper) and (b) the ratio of average normal contact force to the instantaneous gravity(used in Fig.14b of the associated paper) obtained from DEM simulations with the microscopic swelling model.</p> <p>Dataset 8 - Evolution of the dimensionless height of the bilayer particle bed and randomly mixed particle bed obtained from experiments and simulations (used in Fig.17 of the associated paper): Experimental data for the measured hight and associated standard deviation at various time, as well as the numerical data.</p> <p>Dataset 9 - Evolution of the dimensionless height of the pure SAP particle bed obtained from simulations with different water concentration in the liquid (used in Fig.18 of the associated paper):</p> <p>Dataset 10 -Evolution of dimensionless heights of SAP particle bed and (b) the dimensionless diameter of the particle obtained from DEM simulations during shrinkage with different water concentrations in the liquid (used in Fig.19 of the associated paper).</p> <p>Dataset 11 -Comparison of the dimensionless height of SAP particle bed, dimensionless diameter and the standard deviation of dimensionless diameter obtained from DEM simulations with different values of diffusivity for particle-particle diffusion (used in Fig.20 of the associated paper).</p>
Thermal and percolative analysis of 3D diffuse-interface composite microstructure
<p>This dataset contains supplementary data and utilities of the publication "Data-driven thermal and percolative analysis of 3D diffuse-interface composite microstructure" (<a href="https://doi.org/10.1016/j.matdes.2023.111746">Fathidoost, 2023</a>).</p> <p>This dataset documents homogenized anisotropic thermal conductivity of the corresponding microstructure (identified by volume fraction (Vf) and aspect ratio (Ar)) as a tensor with normalized interface thermal resistance (see Table 1). Voxelized digital microstructures and utilities are also attached for visualizing the overall thermal anisotropy.</p> <p><em>Table 1: The geometrical and thermal parameters employed in the generated microstructures.</em></p> <table> <thead> <tr> <th>Parameters</th> <th>Value (Unit)</th> <th>Type</th> <th>Increment</th> </tr> </thead> <tbody> <tr> <td>Minor principal axes length</td> <td>5 (nm)</td> <td>Constant</td> <td>-</td> </tr> <tr> <td>Aspect ratio, <span class="math-tex">\(A_\mathrm{r}\)</span></td> <td>[1 ,6]</td> <td>Linear</td> <td>1</td> </tr> <tr> <td>Inclusion volume fraction, <span class="math-tex">\(V_\mathrm{f}\)</span></td> <td>[5, 60]</td> <td>Linear</td> <td>5</td> </tr> <tr> <td>Thermal conductivity ratio, <span class="math-tex">\(K_\mathrm{r}\)</span></td> <td>[15, 100]</td> <td>Linear</td> <td>15</td> </tr> <tr> <td>Normalized interface resistance, <span class="math-tex">\(\tilde{R}_\mathrm{s} \)</span></td> <td>[1e-6, 1e10]</td> <td>Logarithmic</td> <td>1e2</td> </tr> </tbody> </table> <p><strong>Notice:</strong> The digital microstructure has been voxelized and stored in the ExodusII format, which can be loaded and visualized by the post-processing software, such as ParaView. In order to perform the homogenization, interface smoothening is required, i.e., to generate diffuse interfaces. In this work, we smoothened the interface by operating transient Allen-Cahn calculation with finite timesteps. Sec. 2.1 of the publication for more information).</p>
Ex vivo 100 μm isotropic diffusion MRI‐based tractography of connectivity changes in the end‐stage R6/2 mouse model of Huntington's disease
<div> <div> <div> <div> <p><strong>Background</strong>: Huntington's disease is a progressive neurodegenerative disorder. Brain atrophy, as measured by volumetric magnetic resonance imaging (MRI), is a downstream consequence of neurodegeneration, but microstructural changes within brain tissue are expected to precede this volumetric decline. The tissue microstructure can be assayed non-invasively using diffusion MRI, which also allows a tractographic analysis of brain connectivity.</p> <p><strong>Methods</strong>: We here used ex vivo diffusion MRI (11.7T) to measure microstructural changes in different brain regions of end‐stage (14 weeks of age) wild type and R6/2 mice (male and female) modeling Huntington's disease. To probe the microstructure of different brain regions, reduce partial volume effects and measure connectivity between different regions, a 100 μm isotropic voxel resolution was acquired.</p> <p><strong>Results</strong>: Although fractional anisotropy did not reveal any difference between wild‐type controls and R6/2 mice, mean, axial, and radial diffusivity were increased in female R6/2 mice and decreased in male R6/2 mice. Whole brain streamlines were only reduced in male R6/2 mice, but streamline density was increased. Region‐to‐region tractography indicated reductions in connectivity between the cortex, hippocampus, and thalamus with the striatum, as well as within the basal ganglia (striatum—globus pallidus—subthalamic nucleus—substantia nigra—thalamus).</p> <p><strong>Conclusions</strong>: Biological sex and left/right hemisphere affected tractographic results, potentially reflecting different stages of disease progression. This proof‐of‐principle study indicates that diffusion MRI and tractography potentially provide novel biomarkers that connect volumetric changes across different brain regions. In a translation setting, these measurements constitute a novel tool to assess the therapeutic impact of interventions such as neuroprotective agents in transgenic models, as well as patients with Huntington's disease.</p> </div> </div> </div> </div>
Data and Software for "Numerical diffusion and Turbulent mixing in convective self-aggregation"
<p>This folder contain the python scripts and the data necessary for reproducing figures and results reported in the paper " Numerical diffusion and turbulent mixing in convective self-aggregation" (in preparation for submission for the Journal of Advances in Modeling Earth System)</p>
Pitch-angle and energy diffusion coefficients calculated for ions interacting with kinetic Alfven waves near the magnetopause
<p>In each file:<br> the first row (starting with the second column) contains pitch-angle grid in degrees<br> the first column (starting with the second row) contains the energy grid in keV<br> "x_to_L" value in the file name denotes the position in space along the normal to the magnetopause relative to the current sheet center (see description file).<br> energy diffusion coefficients are measured in keV^2/s, and pitch-angle coefficients are measured in rad^2/s.</p>
Hydrogen Diffusion in Silicate Glasses
<p>This repository contains all data and MATLAB(c) scripts that were used to calculate diffusion profiles in the associated publication.</p>
The role of chloroplast movement in C4 photosynthesis: A theoretical analysis using a 3-D reaction-diffusion model for maize
<p>Chloroplast movement within mesophyll (M) cells in C<sub>4</sub> plants is hypothesized to enhance the CO<sub>2</sub> concentrating mechanism (CCM), but this is difficult to verify experimentally. A three-dimensional (3-D) leaf model can help analyze how chloroplast movement influences the operation of CCM. The first volumetric reaction-diffusion model of C<sub>4</sub> photosynthesis that incorporates: detailed 3-D leaf anatomy, light propagation, ATP and NADPH production and CO<sub>2</sub>, O<sub>2</sub> and bicarbonate concentration driven by diffusional and assimilation/emission processes, was developed and implemented for maize leaves to simulate various chloroplast movement scenarios within M cells: the movement of all M chloroplasts towards bundle-sheath (BS) cells (aggregative movement) and movement of only those of interveinal M cells towards BS cells (avoidance movement). Light absorbed by bundle-sheath (BS) chloroplasts relative to M chloroplasts increased in both cases. Avoidance movement decreased light absorption by M chloroplasts considerably. Consequently, total ATP and NADPH production and net photosynthesis rate increased for aggregative movement and decreased for avoidance movement case compared to the default case of no chloroplast movement at high light intensities. Leakiness increased in both chloroplast movement scenarios due to the imbalance in energy production and demand in M and BS cells. These results suggest the need to design strategies for coordinated increases in electron transport and Rubisco activities for an efficient CCM at very high light intensities.</p>
Data set related to the manuscript "Investigating particle size effects on NMR spectra of ions diffusing in porous carbons through a mesoscopic model"
<p>Graphical files in the agr format for all the figures in the manuscript entitled "Investigating particle size effects on NMR spectra of ions diffusing in porous carbons through a mesoscopic model". Examples of input files for the lattice simulations are also provided.</p>
Dataset for "DEM-CFD analysis of swelling behaviours of binary particle systems with a microscopic diffusion model"
<p>This dataset contains both numerical simulation data and experimental data describing the swelling behaviour of binary particle systems. Detailed study on the swelling behaviour is presented in a journal paper entitled "DEM-CFD analysis of swelling behaviours of binary particle systems with a microscopic diffusion mode". We provide all the essential data in a single excel file with the description below:</p> <p>Dataset 1- Evolution of the height of the particle bed obtained from experiments and simulations (used in Fig.6 of the associated paper): Experimental data for the measured hight and associated standard deviation at various time, as well as the numerical data.</p> <p>Dataset 2 - Evolutions of the normalised average radius r/r_0 (used in Fig.7a) and the coefficient of variation CV (used in Fig.7b) for SAP particles obtained from DEM-CFD simulations.</p> <p>Dataset 3 - Radial distribution Functions (RDFs) for (Fig.9a) SAP particles and (Fig.9b) POM particles at different time instants.</p> <p>Dataset 4 - Positions of POM particles projected into the x-y plane at different time instants (the red dots are particle centres), (a) t = 0 min; (b) t = 3 min; (c) t = 6 min; (d) t = 10 min.</p> <p>Dataset 5 - Evolution of Lacey mixing index for the binary particles during the swelling process.</p> <p>Dataset 6 - Average normal stress distribution of particles in x-y and x-z planes at t = 2 min.</p> <p>DataSet 7 - Velocity vectors of particles projected in x-z planes at different time instants: (a) t = 1 min; (b) t= 2 min (Data for Fig.13)</p> <p>Dataset 8 - Positions of POM particles projected into x-y plane at time t= 10 min (the red dots are particle centres) with different coefficient of frictions (a) μ=0.1; (b) μ=0.2; (c) μ=0.3; (d) μ=0.4; (e) μ=0.5.(Data for Fig.15)</p> <p>Dataset 9 - RDFs for POM particles at time t= 10 min with different coefficients of friction.(Data for Fig.16)</p>
Investigating the fast spectral diffusion of a quantum emitter in hBN using resonant excitation and photon correlations
<p>Data from the article "Investigating the fast spectral diffusion of a quantum emitter in hBN using resonant excitation and photon correlations" (<a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.107.195304">Phys. Rev. B <strong>107</strong>, 195304 (2023)</a> – [<a href="https://arxiv.org/abs/2303.05315">arXiv</a>])</p>
modeled and measured diffuse and diffuse fraction of PAR range
<p>Csv file with the diffuse fraction of PAR (modeled and measured), diffuse component of PAR (modeled and measured), and clearness index in the PAR and Total ranges.</p>
Dataset used in the paper "Verifying the parameterization of vertical eddy viscosity and diffusivity in the bottom boundary layer"
<p>This dataset is created from the data obtained over the continental shelf of the East China Sea in July 2020 during a cruise of the training ship Nagasaki-maru of Nagasaki University (NN055), and used in the manuscript entitled "Verifying the parameterization of vertical eddy viscosity and diffusivity in the bottom boundary layer" by Takahiro Endoh, Takuya Hirooka, and Yoshinobu Wakata, which will be submitted to Journal of Physical Oceanography.</p>
Painting a more complete picture of white matter microstructure with myelin water and tensor valued diffusion
<p>Data supporting the publication <strong>Painting a more complete picture of white matter microstructure with myelin water and tensor valued diffusion. </strong></p> <p>V1.0: Includes atlases of MRI measures described in the paper, tracts generated specifically for the study, and a sample subject's data.</p> <p>Processing code available at: https://github.com/sharadab/microstructure_processing_paper </p>
Data from: Minority-group incubators and majority-group reservoirs for the diffusion of climate change adaptations
<p>These data are part of a data portal that accompanies the special issue 'Climate change adaptation needs a science of culture,' published in Philosophical Transactions of the Royal Society B in 2023. To access the data portal, please visit <a href="https://doi.org/10.5061/dryad.bnzs7h4h4"><strong>10.5061/dryad.bnzs7h4h4</strong></a>.</p> <p>This repository contains code and supporting documentation for the agent-based model analyzed in our paper, "Minority-group incubators and majority-group reservoirs for climate change adaptation". We performed and analyzed a suite of agent-based models that simulated the spread of an adaptation, i.e., a beneficial behavior, in a population with a minority and majority group, defined by group size and tendency to interact with others from one's own group versus another group (homophily). We ran 1000 trials per parameter setting, where parameters were systematically varied to test different homophily levels in each group, and the effect of whether the minority group, majority group, or both groups start with one member knowing the adaptation. The adaptation either spread from one agent in one or both groups to the rest of the members of both groups in the case of adaptation success, or the adaptation disappeared from the entire population (adaptation failure). We then calculated the success rate across all 1000 trials. We also measured the mean time to either adaptive success or failure.</p>
Data-driven characterization and correction of the orientation dependence of magnetization transfer measures using diffusion MRI
<p>These are the produced plots for every subjects and every sessions of the study. Here are the characterization plots, the corrected plots, and the tractometry plots.</p>
Simulation data for Enhanced Diffusion through Multivalency
<p>Simulation Monte Carlo data for manuscript Enhanced Diffusion through Multivalency</p>
Raw data of "Aggregation of adult parasitic nematodes in sex-mixed groups analyzed by transient anomalous diffusion formalism."
<p>Manuscript abstract:</p> <p>Intestinal parasitic worms are widespread throughout the world, causing chronic infections in humans and animals. However, very little is known about the locomotion of the worms in the host gut. We studied the movement of <em>Heligmosomoides bakeri, </em>naturally infecting mice and used as animal model for roundworm infections. We investigated the locomotion of <em>H.bakeri</em> in simplified environments mimicking key physical features of the intestinal lumen, i.e. medium viscosity and intestinal villi topography. We found that the motion sequence of these nematodes is non-periodic, but the migration could be described by transient anomalous diffusion. Aggregation as a result of biased, enhanced-diffusive locomotion of nematodes in sex-mixed groups was detected. This locomotion is probably stimulated by mating and reproduction, while single nematodes moved randomly (diffusive). Natural physical obstacles as high mucus-like viscosity or villi topography, slowed down but did not entirely prevent nematodes aggregation. Additionally, the mean displacement rate of nematodes in sex-mixed groups of 3.0·10<sup>-3</sup> mm/s in mucus-like medium is in good agreement with estimates of migration velocities of 10<sup>-4</sup> to 10<sup>-3</sup> mm/s in the gut. Our data indicate <em>H.bakeri</em> motion to be non-periodic and their migration random (diffusive-like), but triggerable by the presence of kin.</p> <p>These are our raw data as well as our Python source code of the analysis algorithm.</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.