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11,506 results for “Dynamics”
Ion-Pair Dynamics upon Photoinduced Electron Transfer Monitored by Pump-Pump-Probe Spectroscopy
<p>The files contain all the data that are shown in the figures of the main text and of the supporting information of the article:</p> <p>Beckwith, J.; Lang, B.; Grilj, J.; Vauthey, E. Ion-Pair Dynamics upon Photoinduced Electron Transfer Monitored by Pump-Pump-Probe Spectroscopy. J. Phys. Chem. Lett. 10 (2019), 10.1021/acs.jpclett.9b01431</p>
Dynamics of Surface Deformation Induced By Dikes and Cone Sheets in a Cohesive Brittle Coulomb Crust Data
<p>Two files containing raw surface monitoring data from two experimental series and one file containing the analysis of the processed surface monitoring data.<br> <br> </p>
Dynamics of the Young Solar Wind: Weakened Magnetization and Onset of Large Scale Turbulence (Simulation Data)
<p>Simulation data used in "Dynamics of the Young Solar Wind: Weakened Magnetization and Onset of Large Scale Turbulence", submitted to Geophysical Research Letters.</p>
Data from: Diphthong Synthesis using the Dynamic 3D Digital Waveguide Mesh
<p>This dataset comprises the data and MATLAB scripts associated with the paper "Diphthong Synthesis using the Dynamic 3D Digital Waveguide Mesh" published in <em>IEEE/ACM Transactions on Audio, Speech and Language Processing</em>.</p> <p>The dataset contains:</p> <ul> <li>Audio files in .wav format including simulation outputs and recorded microphone and electrolaryngograph signals</li> <li>MATLAB files for simulation (requires GPU device) and plotting results, including volume matrices for 6 English monophthongs, obtained from MRI images as described in the paper</li> <li>Plots of results in .png and MATLAB .fig format</li> </ul> <p><strong>Contact: amelia.gully@york.ac.uk</strong></p>
Effective ergodicity in single-spin-flip dynamics
<p>Dataset and plotting routines to reproduce the results from Physical Review E 90, 032141 (2014). </p> <p>A quantitative measure of convergence to effective ergodicity, the Thirumalai-Mountain (TM) metric, is applied to Metropolis and Glauber single-spin-flip dynamics. In computing this measure, finite lattice ensemble averages are obtained using the exact solution for a one dimensional Ising model, whereas the time averages are computed with Monte Carlo simulations. The time evolution of the effective ergodic convergence of Ising magnetization is monitored. By this approach, diffusion regimes of the effective ergodic convergence of magnetization are identified for different lattice sizes, nonzero temperature, and nonzero external field values. Results show that caution should be taken when using the TM metric at system parameters that give rise to strong correlations.</p> <p> </p>
Data from "Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family."
<p>This data accompanies the paper entitled Allostery and evolution: a molecular journey throught the structural and dynamical landscape of an enzyme super family.</p> <p>The zip archive contains: </p> <p>1- Starting configurations of the proteins after equilibration in PDB format and trajectories of unrestrained molecular dynamics simulations with the positions of the proteins every 100 ps in XTC gromacs format are provided for all systems. </p> <p>2- The free energy profiles and histograms are provided for all umbrella sampling simulations and the scripts used to run it with gromacs.</p>
Data from: Rate of permafrost thaw and associated plant community dynamics in peatlands of northwestern Canada
<p>This dataset was collected to document the changing plant community, and associated environmental factors, as warming climate conditions accelerate permafrost thaw in northern peatland environments. Due to the insulative properties of dry, surface peat layers, discontinuous permafrost is preferentially found in peatlands, termed peat plateaux, where the volumetric expansion of ice-rich permafrost has resulted in a raised, dry ground surface dominated by lichens and, often, stunted black spruce forests. As ground temperatures warm, and the ice-rich permafrost thaws, the ground surface sinks to, or below, the water table, and these peat plateau environments change dramatically from black spruce and lichen-dominated peat plateaux to treeless moss- and sedge-dominated collapse scar environments. Data are from a set of 17 sites distributed along a latitudinal gradient in the Mackenzie Valley of Northwestern Canada. At each site, a transect of five to nine contiguous 1x1m quadrats was sampled, spanning the transition from peat plateau to collapse scar environments and, thus, capturing the zone of active permafrost thaw within peat plateaux as they transition to collapse scars. Fourteen of these sites were sampled at two time periods: 2007 and 2008 (T1: time 1), and 2017 and 2018 (T2: time 2) enabling an assessment of 10-year changes (9 years for one site). This dataset includes quadrat-level measurements of plant community composition (percent cover by species), frost depth, water table depth, peat depth, soil moisture, and canopy cover. Site level measurements consist of maximum peat depth, along with pH and electrical conductivity of collapse scar water samples, as well as the annual rate of lateral permafrost thaw. We also include basic site location parameters, as well as several climatic parameters, interpolated for each site using BioSIM software.</p>
Temporal dynamics of canopy properties and carbon and water fluxes in a temperate evergreen angiosperm forest
<p>Dataset and code for the Manuscript "<span>Temporal dynamics of canopy properties and carbon and water fluxes in a temperate evergreen angiosperm forest"</span></p>
Uncovering kinesin dynamics in neurites with MINFLUX - Repository
<p><strong>Data repository for the publication Uncovering kinesin dynamics in neurites with MINFLUX and corresponding matlab scripts to evaluate the data</strong>. </p> <p>.zip file contains:</p> <ol> <li>Data repository</li> <li>Matlab scripts</li> </ol> <p>Please do not change the contained folders or rename them, otherwise the matlab scripts will stop working.</p> <p>Matlab scripts were prepared in matlab 2022b.</p>
Enhancing Full Waveform Inversion of Field GPR Data: A Source-Independent Approach with Dynamic Reference Selection via SE-Wave-U-Net
<p>Data presented in the manuscript titled 'Enhancing Full Waveform Inversion of Field GPR Data: A Source-Independent Approach with Dynamic Reference Selection via SE-Wave-U-Net'</p>
Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures
<p>This data contains all necessary input file to construct the micro fibril.</p>
Reinforcing Tunnel Network Exploration in Proteins using Gaussian Accelerated Molecular Dynamics (parameters, trajectories)
<ul> <li>00_LinB-Wt.tar.gz - LinB-Wt simulation files:</li> </ul> <p> 1.cMD(Classical MD simulation):<br> <br> 1. Stripped parameter file *.parm7.<br> 2. Simulation file after removing ions and water and merging last 5us of production run in amber *.nc format.<br> <br> <br> 2.GaMD(Gaussian Accelerated MD simulation): <br> <br> 1. Stripped parameter file *.parm7.<br> 2. Simulation file after removing ions and water and merging last 5us of production run in amber *.nc format.</p> <ul> <li>01_LinB-Open.tar.gz - LinB Open mutant simulation files:</li> </ul> <p> 1.cMD(Classical MD simulation):<br> <br> 1. Stripped parameter file *.parm7. <br> 2. Simulation file after removing ions and water and merging last 5us of production run in amber *.nc format.<br> <br> <br> 2.GaMD(Gaussian Accelerated MD simulation): <br> 1. Stripped parameter file *.parm7.<br> 2. Simulation file after removing ions and water and merging last 5us of production run in amber *.nc format.</p> <ul> <li>02_LinB-Closed.tar.gz - LinB Closed mutant simulation files:</li> </ul> <p> 1.cMD(Classical MD simulation):<br> 1. Stripped parameter file *.parm7.<br> 2. Simulation file after removing ions and water and merging last 5us of production run in amber *.nc format.<br> <br> <br> 2.GaMD(Gaussian Accelerated MD simulation): <br> 1. Stripped parameter file *.parm7.<br> 2. Simulation file after removing ions and water and merging last 5us of production run in amber *.nc format.</p>
Data for: Microbiome and metabolic dynamics shape coral post-stress recovery
<p>This is the data underlying the analysis for the coral experiment described in the article: "Microbiome and metabolic dynamics shape coral post-stress recovery"</p> <p>It contains:</p> <ul> <li>The endosymbiotic symbiodiniaceae density calculated to surface area per sample and analytical replicate 4-6.</li> <li>Bactiral taxa identfied and the number of sequence reads assign to that ID (ASV) for each sample.</li> <li>Meta data for the samples collected, linking the sample number to experimental treatments and replicates.</li> <li>Lipid data including the concentration of fatty acids in each sample collected.</li> <li>Protein concentrations in each sample including sample (coral nubin) surface area </li> </ul> <p> </p>
Molecular Dynamics (MD) Simulation Data for Dynamics Underlie the Drug Recognition Mechanism by the Efflux Transporter EmrE
<p>MD simulations on the proton bound (PDB 8UWU), deprotonated on E14A (PDB 8UWU), TPP Bound (PDB 8UWU) on our NMR derived structures.</p> <p> </p> <p>MD simulations on the proton bound (7MH6) and deprotonated on E14A (7MH6) on X-ray structures. </p> <p> </p> <p>Total raw simulation data would be too large for uploading to repositories. To reduce size of file, starting structure and tpr files are uploaded. Final structure at 2.5 μs are also uploaded. </p>
Assembly, persistence, and disassembly dynamics of Quaternary Caribbean frugivore communities
<p>How communities assemble and restructure is of critical importance to ecological theory, evolutionary theory, and conservation, but long-term perspectives on the patterns and processes of community assembly are rarely integrated into traditional community ecology, and the utility of communities as an ecological concept has been repeatedly questioned in part due to a lack of temporal perspective. Through a synthesis of paleontological and neontological data, I reconstruct Caribbean frugivore communities over the Quaternary (2.58 mya – present). Numerous Caribbean frugivore lineages arise during periods coincident with the global origins of plant-frugivore mutualisms. The persistence of many of these lineages into the Quaternary is indicative of long-term community stability, but an analysis of Quaternary extinctions reveals a non-random loss of large-bodied mammalian and reptilian frugivores. Anthropogenic impacts, including human niche construction, underlie the recent reorganization of frugivore communities, setting the stage for continued declines and evolutionary responses in plants that have lost mutualistic partners. These impacts also support ongoing and future introductions of invader complexes: introduced plants and frugivores that further exacerbate native biodiversity loss by interacting more strongly with one another than with native plants or frugivores. This work illustrates the importance of paleontological data and perspectives in conceptualizing ecological communities, which are dynamic and important entities.</p>
Closed-loop microstimulations of the orbitofrontal cortex during real-life gaze interaction enhance dynamic social attention
Open the record for dataset details and reuse information.
Subset of global model sea level data for "Challenges, Advances and Opportunities in Regional Sea Level Projections: the Role of Ocean-shelf Dynamics"
<p>Monthly sea surface height above the geoid data in NW European seas from six global simulations using the NEMO ocean model (https://www.nemo-ocean.eu/) for 1990 to 2009</p> <p><strong>ORCA0083_DFS_NWS_ssh_1990_2009, ORCA025_DFS_NWS_ssh_1990_2009, ORCA1_DFS_NWS_ssh_1990_2009,</strong> are the N006 simulation set created by Andrew Coward and the NOC Marine Systems Modelling team as used by:</p> <p>Baker et al 2022 Biological Carbon Pump Sequestration Efficiency in the North Atlantic: A Leaky or a Long-Term Sink? Global Biogeochemical Cycles <a href="https://doi.org/10.1029/2021GB007286">https://doi.org/10.1029/2021GB007286</a>,</p> <p>Wilson, C. <em>et al.</em> 2021 Significant variability of structure and predictability of Arctic Ocean surface pathways affects basinwide connectivity. <em>Commun. Earth Environ.</em> <strong>2</strong>, 164. <a href="https://doi.org/10.1038/s43247-021-00237-0">https://doi.org/10.1038/s43247-021-00237-0</a> (2021).</p> <p>These simulations are forced by the Drakkar Forcing Set 5.2 (DFS) and initialised at 1958, with a nominal 1/12, 1/4 and 1 degree resolution. See references for further model details.</p> <p><strong>ORCA025_JRA_NWS_ssh_1990_2009, ORCA025_JRA_tides_NWS_ssh_1990_2009, ORCA025_JRA_ShelfPhysics_NWS_ssh_1990_2009, </strong>are new simulations produced by Chris Wilson, James Harle and the Shelf Enabled NEMO team. All are forced by the JRA reanalysis, initialised in 1976.</p> <p><strong>ORCA025_JRA_NWS_ssh_1990_2009</strong> is a reference run based on GO9, an evolution of the Joint Marine Modelling Programme configuration described by Storkey et al 2018 UK Global Ocean GO6 and GO7: a traceable hierarchy of model resolutions, Geoscientific Model Development https://gmd.copernicus.org/articles/11/3187/2018/</p> <p><strong>ORCA025_JRA_tides_NWS_ssh_1990_2009</strong> adds explicit tides to this.</p> <p><strong>ORCA025_JRA_ShelfPhysics_NWS_ssh_1990_2009</strong> adds tides, Generic Length Scale Mixing and Multi-envelope vertical coordinates</p> <p>Details of these simulations can be found here:</p> <p>https://github.com/NOC-MSM/SE-NEMO </p>
Seasonal dynamics in the mammalian microbiome between disparate environments
<p>Host-associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption; but we also observed similarities in the urban and exurban grey squirrel microbiome during the autumn, which we attribute to engrained seed caching instincts in preparation for the winter. Host behaviour and diet selection may therefore be capable of maintaining similarities in microbiome structure between disparate environments. However, the depletion of an obligate host mucin glycan specialist (Akkermansia) during the winter in both urban and exurban squirrels was among the strongest differential abundance patterns we observed. In summary, urban grey squirrels showed different seasonal patterns in their microbiome than squirrels from exurban forests, however, in some instances host behaviour and physiological responses might be capable of maintaining similar microbiome responses across seasons. </p>
Moving in the landscape: omnidirectional connectivity dynamics in China from 1985 to 2020
<p><span>Global changes in human land use have profoundly transformed natural landscapes, leading to significant habitat fragmentation and threatening key ecosystem functions. To address this issue, we employed morphological methods and circuit theory to evaluate the dynamics of ecological corridors and their connectivity in China from 1985 to 2020.</span></p>
Annual dynamics and metagenomics of marine vesicles: a layer of complexity in the dissolved organic fraction
<p>The data consists of Illumina raw reads obtained from prokaryotes from coastal Mediterranean seawaters in Alicante, Spain, over the course of one year. Illumina DNA prep kit (IDT, Ref. 20026930) was used following the manufacturer's protocol to generate and sequence the libraries for the obtained DNA samples from prokaryotic metagenomes. Subsequently, these libraries were sequenced using HiSeq X technology (150 PE, 1 lane) by two different facilities: Macrogen in Seoul, Republic of Korea, and the Genomics Unit of the Center for Genomic Regulation (CRG) in Barcelona, Spain. The dataset was used in order to ascertain the main microbial producers involved in the release of DNA packaged in EVs in our annual sampling.</p> <p>The samples are named according to the convention 'prokmeta[Month], where 'prokmeta' signifies prokaryotic metagenome, '[Month]' indicates the month of sampling, and "1" represents the forward , while (2) represent the reverse read. For instance, 'prokmetaDEC.1' denotes the prokaryotic metagenome for sample of December, with '1' indicating the forward read, while 'prokmetaDEC.2' represents the corresponding reverse read. This naming scheme is consistent across all samples in the dataset from sample of November 2021 to sample of June 2022.</p> <p> </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.