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.
45
datasets available to search
ShareScore release 0.9.0
Dataset results
45 results for “channel dynamics”
The dynamics of marsh-channel slump blocks: an observational study using repeated drone imagery
We analyzed the spatial and temporal dynamics of slump blocks within Dean Creek, a creek located on Sapelo Island (GA) and surrounded by salt marsh. To accomplish this, we utilized 11 images of Dean Creek captured between March 2020 and March 2021, which were acquired by using a DJI Matrice 210 UAV. For each image, we manually digitized the perimeters of slump blocks, which have the distance from intact marsh boundary exceeding 0.3 m. These digitized perimeters were subsequently converted into polygons to determine the size, number and cumulative area of slump blocks in each image. Temporal changes to the slump blocks between subsequent images were also analysed. The coordinate system of these polygon data is WGS 1984 UTM Zone 17N.
SBC LTER: Kelp blade characteristics to support turnover dynamics of giant kelp, Macrocystis pyrifera in the Santa Barbara Channel
These data describe the age-specific changes in the size and related traits of giant kelp (Macrocystis pyrifera) blades in the Santa Barbara Channel (Isla Vista Reef) during the spring and summer of 2012-2013. Data are contained in three tables: 1) a time series of change in blade size with age due to growth and senescence for blades growing at different depths and locations in the kelp forest, 2) physical traits of blades (biomass density, nitrogen, chlorophyll a) of different ages collected at different depths and locations in the kelp forest, and 3) photosynthetic performance (Pmax, alpha) of blades of different ages collected at different depths and locations in the kelp forest. These data were used to test whether spatial variation in the turnover dynamics of giant kelp blades could be could be explained by leaf life span theory developed for higher plants. The data were also used in a mathematical model of frond growth and senescence to investigate the relative and absolute magnitude of blade senescence in a kelp forest, and to examine how these losses were affected by light availability. Analyses using these data were published in Rodriguez, G. E. 2014. Turnover dynamics of the giant kelp, Macrocystis pyrifera. Ph.D., University of California, Santa Barbara. ProQuest, UMI Dissertations Publishing, 2014. 3682967.
Molecular Dynamics simulations suggest possible activation and deactivation pathways in hERG channel
<ol> <li>equil_gating_4_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 4 equilibration trajectory</li> <li>equil_gating_6_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 6 equilibration trajectory</li> <li>equil_gating_8_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 8 equilibration trajectory</li> <li>equil_gating_4.dcd: 100 ns NPT trajectory of the hERG closed state with gating charge 4</li> <li>equil_gating_6.dcd: 100 ns NPT trajectory of the hERG closed state with gating charge 6</li> <li>equil_gating_8.dcd: 100 ns NPT trajectory of the hERG closed state with gating charge 8</li> <li>equil_open_assembly_xleap.prmtop: file topology of the hERG open state equilibration trajectory</li> <li>equil_open.dcd: 100 ns NPT trajectory of the hERG open state</li> <li>herg_closed_gating_4.pdb: PDB file of hERG closed state with gating charge 4 after Steered MD simulations</li> <li>herg_closed_gating_6.pdb: PDB file of hERG closed state with gating charge 6 after Steered MD simulations</li> <li>herg_closed_gating_8.pdb: PDB file of hERG closed state with gating charge 8 after Steered MD simulations</li> <li>TMD_O-C_closed_gating_8_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 8 TMD trajectory</li> <li>TMD_O-C_closed_gating_6_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 6 TMD trajectory</li> <li>TMD_O-C_closed_gating_4_assembly_xleap.prmtop: file topology of the hERG closed state with gating charge 4 TMD trajectory</li> <li>TMD_O-C_closed_gating_8.dcd: TMD trajectory of the hERG closed state with gating charge 8</li> <li>TMD_O-C_closed_gating_6.dcd: TMD trajectory of the hERG closed state with gating charge 6</li> <li>TMD_O-C_closed_gating_4.dcd: TMD trajectory of the hERG closed state with gating charge 4</li> </ol> <p>MD trajectories (equilibration and Targeted MD trajectories) in dcd format can be visualized using visualization tools such as VMD or PyMol after uploading the topology file.</p> <p>The directory data_supplementary-note-4.tar.bz2 contains the files related to the Supplementary Notes 4: "A practical example of pathway calculation".</p>
Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains
<p>Provided are reduced trajectories (.dcd) of the MD simulations -- each trajectory has 100 ps/frame with only protein and ion atoms remaining. Each set of trajectories are accompanied by a protein structure file (.psf) which is required to visualize the trajectories in VMD. Additionally, the z-trajectories of each intracellular ion (2 ps/frame) are provided in zipped files.<br> <br> To re-create the potentials of mean force (PMF) in Yue & Haddad et al., use the scripts provided with the paper (https://github.com/reichow-lab/Yue-Haddad_et-al.JPhysiol2021):<br> <br> </p> <pre><code class="language-bash">python3 GapJ_Analysis.py "Cx46_Ace_Produc-1_POT_*"</code></pre> <ul> <li>Choose a bin size in Å (3)</li> <li>Choose an output name (Cx46_Ace)</li> <li>Choose option (M)</li> <li>Choose time (ps) / frame (2)</li> <li>Choose column from file (1)</li> <li>Choose bin<sub>min</sub>/bin<sub>max </sub>(auto)</li> </ul>
Classifying the generation and formation channels of dynamically-formed gravitational-wave events
<p>This dataset contains all the simulations of dynamically-formed binaries performed with the software <a href="https://github.com/Kkritos/Rapster">rapster</a>, together with trained machine-learning classification models from (Antonelli, Kritos et al, in prep.), see <a href="https://github.com/aantonelli94/TheBHClassifier">the public codes online</a>.</p> <p>All items starting with "mergers_*" are simulations of clusters and they follow the structure reported in the documentation of <a href="https://github.com/Kkritos/Rapster">rapster</a>. The simulations differ in the choice of the hyperparameters for the distribution of the cluster mass, half-mass radius and initial spin distribution for the binaries.</p> <p>All items starting from "RFClassifier_*" are machine-learning classification models that use a Random Forest Classifier and that are trained with the simulations above. The models ending with "*_gen" predict the generation of the black holes, those with "*_form" predict their formation channels. </p> <p> </p>
Molecular dynamics simulation data 1: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 gap junction channel</p>
Investigation on Dynamic Characteristics of Lightning Return Stroke Channel
<p>The dynamic characteristics in lightning discharge plasma channel are of great significance in studying the micro-physical mechanism of the discharge process. This paper established a simplified radiation-hydrodynamic model (RHM) of the return stroke channel radial expansion based on the fluid dynamics theory, and for the first time, considered the affect of the light radiation loss in the discharge process. The temporal evolutions of the characteristic parameters, such as temperature, pressure and expansion rate for return stroke channel were analyzed. The results indicated that the current peak value and the risetime are important factors in determining the channel dynamics characteristics. At the initial stage of return stroke, the light radiation loss has a distinct influence on channel temperature, which leads to a transitory drop in temperature forming a bimodal waveform structure. Following the peak current, the channel reaches peak pressure, which leads to a subsequent secondary temperature peak and accelerates the expansion of the channel. Peak current and the risetime are the indicator parameters of strong discharge and the main factors of lightning disaster. This work provides reference data for further research on the radial energy transport of lightning return stroke channel and the formation mechanism of shock waves.The dynamic characteristics in lightning discharge plasma channel are of great significance in studying the micro-physical mechanism of the discharge process. This paper established a simplified radiation-hydrodynamic model (RHM) of the return stroke channel radial expansion based on the fluid dynamics theory, and for the first time, considered the affect of the light radiation loss in the discharge process. The temporal evolutions of the characteristic parameters, such as temperature, pressure and expansion rate for return stroke channel were analyzed. The results indicated that the current peak value and the risetime are important factors in determining the channel dynamics characteristics. At the initial stage of return stroke, the light radiation loss has a distinct influence on channel temperature, which leads to a transitory drop in temperature forming a bimodal waveform structure. Following the peak current, the channel reaches peak pressure, which leads to a subsequent secondary temperature peak and accelerates the expansion of the channel. Peak current and the risetime are the indicator parameters of strong discharge and the main factors of lightning disaster. This work provides reference data for further research on the radial energy transport of lightning return stroke channel and the formation mechanism of shock waves.</p>
Data from: Interactions of wood accumulations, channel dynamics, and geomorphic heterogeneity within a river corridor
<p>Natural rivers are inherently dynamic. Spatial and temporal variations in water, sediment, and wood fluxes both cause and respond to an increase in geomorphic heterogeneity within the river corridor. We analyze 16 two-kilometer river corridor segments of the Swan River in Montana, USA to examine relationships between wood accumulations (wood accumulation distribution density, count, and persistence), channel dynamism (total sinuosity and average channel migration), and geomorphic heterogeneity (density, aggregation, interspersion, and evenness of patches in the river corridor). We hypothesize that i) more dynamic river segments correlate with a greater presence, persistence, and distribution of wood accumulations; ii) years with higher peak discharge correspond with greater channel dynamism and wood accumulations; and iii) all river corridor variables analyzed play a role in explaining river corridor spatial heterogeneity. Our results suggest that decadal-scale channel dynamism, as reflected in total sinuosity, corresponds to greater numbers of wood accumulations per surface area and greater persistence of these wood accumulations through time. Second, higher peak discharges correspond to greater values of wood distribution density, but not to greater channel dynamism. Third, persistent values of geomorphic heterogeneity, as reflected in the heterogeneity metrics of aggregation, interspersion, patch density, and evenness, are explained by potential predictor variables analyzed here. Our results reflect the complex interactions of water, sediment, and large wood in river corridors; the difficulties of interpreting causal relationships among these variables through time; and the importance of spatial and temporal analyses of past and present river processes to understand future river conditions</p>
Molecular Dynamics Simulations of Hydrophilic (QTY) Potassium Ion Channels in Water
<p>You can find here the molecular dynamics (MD) trajectories of QTY proteins in water performed for the "Computational engineering of water-soluble potassium ion channels through QTY transformation" manuscript. Please cite our paper and the previous Zenodo dataset when referring to or using this data. If you have any questions, please contact me (Eva Smorodina) at ribes.ev@gmail.com. Thank you!<br><br>Smorodina, E. (2024). Molecular Dynamics Simulations of Hydrophobic (cryo-EM and Native) and Hydrophilic (QTY) Potassium Ion Channels [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10592842</p>
X-ray scattering datasets associated with the publication "Side chain length dependent dynamics and conductivity in self assembled ion channels"
<p>X-ray scattering datasets for samples described in the 2022 publication "Side chain length dependent dynamics and conductivity in self assembled ion channels". This dataset includes both raw and processed X-ray scattering data for samples ILC8, ILC10, ILC12, ILC14 and ILC16 alongside background measurement files (BKG).</p>
Molecular dynamics simulation data 3: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes: Production run gromacs trajectories for the Cx43 gap junction channel (500 mV)</p>
Molecular dynamics simulation data 2: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 hemichannel</p>
Data from: Interactions of wood accumulations, channel dynamics, and geomorphic heterogeneity within a river corridor
Open the record for dataset details and reuse information.
Data from: Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid
TRPV1 channels support the detection of noxious and nociceptive input. Currently available functional and structural data suggest that TRPV1 channels have two gates within their permeation pathway: one formed by a ′bundle-crossing′ at the intracellular entrance and a second constriction at the selectivity filter. To describe conformational changes associated with channel gating, the fluorescent non-canonical amino acid coumarin-tyrosine was genetically encoded at Y671, a residue proximal to the selectivity filter. Total internal reflection fluorescence microscopy was performed to image the conformational dynamics of the channels in live cells. Photon counts and optical fluctuations from coumarin encoded within TRPV1 tetramers correlates with channel activation by capsaicin, providing an optical marker of conformational dynamics at the selectivity filter. In agreement with the fluorescence data, molecular dynamics simulations display alternating solvent exposure of Y671 in the closed and open states. Overall, the data point to a dynamic selectivity filter that may serve as a gate for permeation.
Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics
<p>Dataset of molecular dynamics trajectories described in the "Chanalyzer: a computational geometry approach for the analysis of protein channel shape and dynamics" work.</p> <p>Trajectories of differently functionalized MscL channel forms. </p> <p>The *_xyzr.tar.gz files contain the processed frames in the xyzr format, which is a compatible input for NanoShaper</p> <p>The conf.prm file is the parameter file that has been used for the NanoShaper tool</p>
Interaction of the inhibitory peptides ShK and HmK with the voltage-gated potassium channel KV1.3: Role of conformational dynamics
<p><strong>ABSTRACT: </strong>Peptide toxins that adopt the ShK fold can inhibit the voltage-gated potassium channel K<sub>V</sub>1.3 with IC<sub>50</sub> values in the pM range, and are therefore potential leads for drugs targeting autoimmune and neuroinflammatory diseases. NMR relaxation measurements and pressure-dependent NMR have shown that, despite being cross-linked by disulfide bonds, ShK itself is flexible in solution. This flexibility affects the local structure around the pharmacophore for K<sub>V</sub>1.3 channel blockade and, in particular, the relative orientation of the key Lys and Tyr side chains (Lys22 and Tyr23 in ShK), and has implications for the design of K<sub>V</sub>1.3 inhibitors. In this study, we have performed molecular dynamics (MD) simulations on ShK and a close homolog, HmK, in order to probe the conformational space occupied by the Lys and Tyr residues, and docked the different conformations with a recently determined cryo-EM structure of the K<sub>V</sub>1.3 channel. Although ShK and HmK have 60% sequence identity, their dynamic behaviors are quite different, with ShK sampling a broad range of conformations over the course of a 5 μs MD simulation, while HmK is relatively rigid. We also investigated the importance of conformational dynamics, in particular the distance between the side chains of the key dyad Lys22 and Tyr23, for binding to K<sub>V</sub>1.3. Although these peptides have quite different dynamics, the dyad in both adopts a similar configuration upon binding, revealing a conformational selection upon binding to K<sub>V</sub>1.3 in the case of ShK. Intriguingly, the more flexible peptide, ShK, binds with nearly 300-fold higher affinity than HmK.</p>
Model output: Unraveling the mechanisms that cause cyclic channel-shoal dynamics of ebb-tidal deltas: a numerical modeling study
<p>Output from model runs for Lenstra et al., “Unraveling the mechanisms that cause cyclic channel-shoal dynamics of ebb-tidal deltas: a modeling study”. The dataset contains two types of model output, namely (1) the default model runs and (2) the sensitity runs with waves+tides, waves only, and tides only.</p> <p>The files covering the default model runs contain:</p> <p>ModeledDays - time vector for the depth series [days]</p> <p>XT - east-west location of grid points high resolution domains [m]</p> <p>YT - north-south location of grid points high resolution domains [m]</p> <p>depth - depth series for the high resolution domains [m]</p> <p>XSea - east-west location of grid points outer sea domain [m]</p> <p>YSea - north-south location of grid points outer sea domain [m]</p> <p>depthSea - depth series for the outer sea domain [m]</p> <p>XBasin - east-west location of grid points basin domain [m]</p> <p>YBasin - north-south location of grid points basin domain [m]</p> <p>depthBasin - depth series for the basin domain [m]</p> <p>ST_Days - time vector for the sediment transport series [days]</p> <p>ST_Inlet - tidally-averaged total sediment transport through the inlet (positive seaward) [10<sup>6</sup> m<sup>3</sup>/year]</p> <p>ST_Up - tidally-averaged total sediment transport through the cross-section at the updrift coast (positive eastward) [10<sup>6</sup> m<sup>3</sup>/year]</p> <p>ST_Down - tidally-averaged total sediment transport through the cross-section at the downdrif coast (positive eastward) [10<sup>6</sup> m<sup>3</sup>/year]</p> <p>The files covering the sensitivity runs contain for the high resolution domains:</p> <p>XT - east-west location of grid points [m]</p> <p>YT - north-south location of grid points [m]</p> <p>TA_STX - east-west component of the tidally-averaged total sediment transport [m<sup>3</sup>/s/m]</p> <p>TA_STY - north-south component of the tidally-averaged total sediment transport [m<sup>3</sup>/s/m]</p> <p>TA_U - east-west component of the tidally-averaged flow velocities [m/s]</p> <p>TA_V - north-south component of the tidally-averagedf low velocities [m/s]</p> <p>M2 - amplitude of the semi-diurnal tidal flow velocities (not for wave only runs) [m/s] </p>
Experimental data for Dynamic cover effects in lateral bedrock channel bank abrasion: Experiment and model comparison
<p>Experimental data for bank erosion.xlsx contains the data used for the figures in the paper, and the distribution of bedrock bank erosion in the longitudinal direction in Run 1 - Run 18.</p>
Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms: Molecular dynamics coordinate and trajectory files
<p>Molecular dynamics files associated with the publication: Spliced isoforms of the cardiac Nav1.5 channel modify channel activation by distinct structural mechanisms</p>
Vascular KATP channel structural dynamics reveal regulatory mechanism by Mg-nucleotides
<p>MD simulation data for vascular KATP channel focusing on Kir6.1-pore and SUR2B in the presence and absence of MgADP. </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.