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11,506 results for “Dynamics”
Simulation Input Data for "Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics"
<p>This is the reduced data behind an upcoming manuscript investigating impact of acetylation on plant secondary cell wall. The data is taken directly from the directory structure that contains both the simulation and analysis, with excluded trajectory files and intermediate products to fit within the zenodo upload limit. The tar command used to generate this tarball was: </p> <p> </p> <pre><code>tar -zcvf Acetylatedcellwall.tar.gz --exclude="*BAK" --exclude="*dcd" --exclude="*poster*" --exclude="*old" --exclude="*out" --exclude="*vel" --exclude="*ppm" --exclude="*mp4" --exclude="*txt" --exclude="*tga" --exclude="*vmd" --exclude="*log" --exclude="fixed*png" --exclude="frame*png" --exclude="nonacetylation*png" . </code></pre>
Supplementary material for "Comprehensive framework for dynamic energy assessment of building systems using IFC graphs and Modelica"
<p>The provided files include the following:</p> <ul> <li>The IFC model of the demo building used in Section 2.</li> <li>The parsed space boundaries graph.</li> <li>The resulting fragmented space boundaries graph.</li> </ul>
Data for 'Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations'
<h2>Melike Berksoz, Canan Atilgan* </h2> <h3>Faculty of Engineering and Natural Sciences, Sabanci University </h3> <p><strong>*Correspondance:</strong> Canan Atilgan, Faculty of Natural Sciences and Engineering, Sabancı University, Tuzla 34956 Istanbul, Türkiye, E-mail: canan@sabanciuniv.edu</p> <p>Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes <em>in</em> <em>vivo.</em> A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which effect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.</p> <p>Hydrogen bond occupancies were calculated with merging_bonds.py script. Double counted hydrogen bonds where a residue acts both as acceptor and donor are merged into a single entry with merge_files.py. To run sasa.tcl, you need VMD software. Trajectories were created with NAMD2 with a dcdfrequency of 5000 timesteps (every 10 ps) and strided in a 1:100 ratio (every 1 ns=1 frame in dcd). </p>
Vancomycin Molecular Dynamics
<p>Vancomycin Molecular Dynamics. Solvated in water for 10 nanoseconds in UCSF Chimera software. By Victor Padilla Sanchez, PhD Email: drvictorpadilla@aol.com Website: https://www.drvictorpadillasanchez.com</p>
StateSwitch (dynamic) BIDS dataset
<div> <div>Raw BIDS data for StateSwitch (dynamic)</div> <div> </div> <div>The data are distributed as nested DataLad datasets that are hosted on gin. Please see the repository URL for access.</div> <div> </div> <div> <div> <div>Please cite the following references if you use these data:</div> <br> <div>Kosciessa, J. Q., Lindenberger, U. & Garrett, D. D. Thalamocortical excitability modulation guides human perception under uncertainty. Nat. Commun. 12, 2430 (2021).</div> <div> </div> <div>Kosciessa, J. Q., Mayr, U., Lindenberger, U. & Garrett, D. D. Broadscale dampening of uncertainty adjustment in the aging brain. Nat. Commun. (in press, 2024).</div> <br> <div>A static copy of the data for younger adults is also provided at https://osf.io/mgxqr/.</div> <br> <div>In case of questions, contact kosciessa@mpib-berlin.mpg.de or [MPIB Research Data Management](<rdm@mpib-berlin.mpg.de>).</div> </div> </div> </div>
Ciclosporin Molecular Dynamics
<p>Ciclosporin Molecular Dynamics. By Victor Padilla Sanchez, PhD. President, Washington Metropolitan University. Email: drvictorpadilla@aol.com Website: https://www.drvictorpadillasanchez.com </p>
Antibody Molecular Dynamics
<p>Antibody Molecular Dynamics. By Victor Padilla Sanchez, PhD Email: drvictorpadilla@aol.com Website: https://www.drvictorpadillasanchez.com</p>
Rapid microfluidic perfusion system enables controlling dynamics of intracellular pH regulated by Na+/H+ exchanger NHE1
<p>Dataset for manuscript titled "Rapid microfluidic perfusion system enables controlling dynamics of intracellular pH regulated by Na+/H+ exchanger NHE1."</p> <p>Version 2: additional data for Figure 2(e) and (f).</p>
Free Energy of Membrane Pore Formation and Stability from Molecular Dynamics Simulations
Open the record for dataset details and reuse information.
Perpendicular Crossing Chains Enable High Mobility in a Non-Crystalline Conjugated Polymer: Molecular Dynamics Forcefields and Structures
<p>This repository contains molecular dynamics forcefields and structures used to produce results described in the research article: "<em>Perpendicular Crossing Chains Enable High Mobility in a Non-Crystalline Conjugated Polymer</em>" published in <em>Proceedings of the National Academy of Sciences</em> (DOI:10.1073/pnas.2403879121)</p> <p>The following data is available:</p> <ul> <li>Coarse-grained forcefields of the conjugated polymer C16-IDTBT (12mer and 24mer).</li> <li>Coarse-grained structures of single chains of C16-IDTBT (12mer and 24mer).</li> <li>Atomistic forcefields of the conjugated polymer C16-IDTBT (12mer and 24mer).</li> <li>Atomistic structures of single chains of C16-IDTBT (12mer and 24mer).</li> <li>Bonded and non-bonded parameter files for the atomistic C16-IDTBT forcefields.</li> <li>Coarse-grained structures of thin film models (1 x C16-IDTBT 24mers, 3 x C16-IDTBT 12mers, 3 x P3HT 48mers, 3 x PffBT4T-2OD 12mers).</li> <li>Backmapped (atomistic) structures of thin film models (1 x C16-IDTBT 24mers, 3 x C16-IDTBT 12mers, 3 x P3HT 48mers, 3 x PffBT4T-2OD 12mers).</li> </ul> <p>Coarse-grained models are based on the Martini 3 forcefield: Souza, P. et al., <em>Nature Methods</em>, 2021, (https://doi.org/10.1038/s41592-021-01098-3). The bonded and nonbonded parameters may be sourced from the Martini website: https://cgmartini.nl/</p> <p>Atomistic models are based on the OPLS-AA forcefield: Kaminski, G. A. et al.,<em> J. Phys. Chem. B</em>, 2001, (https://doi.org/10.1021/jp003919d). The required bonded and nonbonded parameters have been included in this repository for convenience.</p> <p>Please note that the C16-IDTBT atomistic forcefields and single chain structures have previously been published in another repository (https://doi.org/10.11583/DTU.c.5254236.v1). They are included here for completeness.</p> <p>For any further data related to this research article, please contact the authors.</p>
[Dataset] Intensity and Dimensionality-Dependent Dynamics of Laser-Proton Acceleration in 1D, 2D, and 3D Particle-in-Cell Simulations
<p>The included Jupyter Notebooks (.ipynb) were used to generate figures and make calculations for the work. The resulting image files are saved in Figure_Outputs.tar.gz. The other archives (1D.tar.gz, 2DS.tar.gz, 2DP.tar.gz, 3D.tar.gz, laser_focus.tar.gz, and EField.tar.gz) are compressed directories containing EPOCH PIC simulation outputs for the paper (relevant directories should be extracted to replicate analysis with provided files). </p> <p>Since the last version, a new figure (Figure 6, an ion phase space) has been added. Notebooks for later figures have been renumbered and the figure outputs have been updated. </p>
Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure Data and Code
<p>This dataset includes all data used for the creation of "Including dynamic population and environmental heterogeneity in continuum models of collective behaviour with applications to locust foraging and group structure" as well as a snapshot of the code used.<br><br>Each zip should be unzippable and the code should operate with only the contents of the zip file.</p>
Molecular dynamics of LYVE-1 and CD44 in complex with hyaluronan
<p>Input and output data for MD of mouse/human LYVE-1 and mouse CD44, both, as apo proteins (PDB codes 8ORX, 8OS2, 2JCP, respectively) and in complex with hyaluronan hexasaccharide (HA6; PDB codes 8OX3, 8OXD, 2JCR, respectively). AMBER parm7 topology (.top), restart (.rst), minimisation and MD inputs (.tin, .in), binary NETCDF trajectories (.netcdf) and volumetric maps (.dx) are shared.</p> <p>LYVE-1/CD44 input structures in their apo forms or with HA6 bound were immersed in an octahedral box of TIP3P water molecules and 150 mM NaCl was added. Hydrogen mass repartitioning to 3Da enabled us to use a time step of 4 fs. A stepwise relaxation protocol using sander.MPI of AMBER20 was followed by 1 µs MD production run using pmemd.cuda of AMBER20. Trajectories were first analysed for structural stability using RMSD metrics by use of cpptraj of AMBER20. Due to the high flexibility of the systems, we analysed only portions of 500 ns length of residues 29 to 138, 24 to 133 and 25 to 134 for mLYVE-1/hLYVE-1/CD44, respectively. The following hydrogen-bonding criteria were used: 3.6 Å cutoff for acceptor‧‧‧donor distance and 120-180º range for acceptor‧‧‧H-donor angle. Bridging water molecule occupancies were calculated by summing up binary, ternary and quaternary interactions (the cutoff for each was set to a minimum of 10 %).</p>
Evidence that metapopulation dynamics maintain a species' range limit
<p>This zip folder includes both raw data from a multi-year (2019 and 2022) survey of coastal dune habitat and occupancy by <em>Camissoniopsis cheiranthifolia</em>, as well as an R project and associated scripts for an analysis of variation in metapopulation dynamics towards a species' range limit.</p>
Data for "The Massive and Distant Clusters of WISE Survey. XII. Exploring X-ray AGN in Dynamically Active Massive Galaxy Clusters at z~1"
<p>This dataset corresponds to the manuscript titled "The Massive and Distant Clusters of <em>WISE</em> Survey. XII. Exploring X-ray AGN in Dynamically Active Massive Galaxy Clusters at z~1" (<span>DOI: 10.3847/1538-4357/adbae4)</span>, accepted for publication in <em>The Astrophysical Journal</em> on February 24, 2025. To replicate the plots and access the catalogs used in the paper, download and extract all the zip folders along with the Jupyter Notebook "<a href="https://zenodo.org/api/records/14928038/draft/files/madcows_notebook.ipynb/content">madcows_notebook.ipynb</a>" into the same directory. Open the notebook and follow the instructions provided. For any issues, please contact the corresponding author.</p>
Benchmarking Different QP Formulations and Solvers for Dynamic Quadrupedal Walking
Open the record for dataset details and reuse information.
Simulated winter snow, soil thermal regime, and artificial drainage dynamics under climate change.
<p>This dataset provides simulated winter subsurface drainage outputs from the calibrated Root Zone Water Quality Model–Simultaneous Heat and Water (RZ-SHAW) and four machine-learning models (Cubist, LSTM, Multilinear, SVM) for five agricultural research sites across Eastern Canada (Alfred, Harrow, Kentville, Ottawa-Greenbelt, and St-Emmanuel). The simulations span from 1950 to 2100 under the high-emission climate change scenario RCP8.5, derived from the Canadian Regional Climate Model Large Ensemble (CANRCM4 LE).</p> <p>Included in this repository are:</p> <ul> <li> <p>Winter drainage volume's future projections from 1950 to 2100 the RZ-SHAW and machine-learning models.</p> </li> <li> <p>RZ-SHAW simulated future projections from 1950 to 2100 in snow cover, soil thermal conditions, subsurface drainage volume and frequency, evaporation, surface runoff, and soil water storage.</p> </li> </ul> <p>This dataset also contains simulated annual crop yield projections (kg/hectare) from 1950 to 2100 the five sites Alfred (corn), Harrow (corn and soybean), Kentville (corn), Ottawa (corn), St-Emmanuel (corn). Simulations were performed using the RZ-SHAW model under RCP8.5 climate change scenario. Each site's data includes annual grain yield values and Sen's slope trend analysis with Mann-Kendall significance test results.</p> <p>Users should note the following important limitations when interpreting these yield projections:</p> <ol> <li>Simplified Crop Growth Parameters: The crop module was implemented primarily to account for crop residue effects on winter soil conditions, not for yield prediction. No calibration was performed for crop growth parameters.</li> <li>No Nutrient Stress: Simulations were run without nitrogen or phosphorus limitations for simplicity, which may overestimate yields in scenarios where nutrient availability would be constraining.</li> <li>Fixed Management Practices: Planting and harvest dates were held constant throughout the simulation period (1950-2100) based on historical averages, which becomes increasingly unrealistic under future climate conditions.</li> <li>No CO₂ Fertilization Effect: Atmospheric CO₂ concentration changes were not incorporated, potentially underestimating photosynthetic responses in future climate scenarios.</li> <li>Limited Stress Responses: The model's representation of heat stress, drought tolerance, and other physiological responses to extreme conditions may not fully capture crop responses under future climate scenarios.</li> <li>No Adaptation Strategies: The simulations do not account for potential adaptations such as cultivar changes, shifting planting dates, or irrigation implementation that would likely occur in response to changing conditions.</li> </ol>
Illuminating Tycho's Rays: Automated Crater Census Uncovers Equilibrium Dynamics and Regolith Stratification on the Lunar Surface
<p>Excel files containing all crater data are output from ArcMap.</p> <p><br>DATA_HUMA_craters_raw contains two files for the *186 and *808 NAC images as coordinates and diameter (km). These are all the manual labelling for the NACs, with not-included data. Full set.</p> <p>DATA_YOLO_craters_raw contains several files for each sub-area, coordinates, diameter, and additional information</p> <p>DATA_selected_craters is a table that formed the <strong>basis for the analysis</strong>. It lists the crater sizes for each area (summed) and gives the surface area of the regions under investigation.</p>
Data and Code for "Drift velocity of bacterial chemotaxis in dynamic chemical environments"
<p>Datasets and code required to recreate all results from "Drift velocity of bacterial chemotaxis in dynamic chemical environments"</p>
Population dynamics of the sea snake Emydocephalus annulatus
<p>For sea snakes as for many types of animals, long-term studies on population biology are rare and hence, we do not understand the degree to which annual variation in population sizes is driven by density-dependent regulation versus by stochastic abiotic factors. We monitored three populations of turtle-headed sea snakes (<i>Emydocephalus annulatus</i>) in New Caledonia over an 18-year period. Annual recruitment (% change in numbers) showed negative density-dependence: that is, recruitment increased when population densities were low, and decreased when densities were high. Windy weather during winter increased survival of neonates, perhaps by shielding them from predation; but those same weather conditions reduced body condition and the reproductive output of adult snakes. The role for density-dependence in annual dynamics of these populations is consistent with the slow, K-selected life-history attributes of the species; and the influence of weather conditions on reproductive output suggests that females adjust their allocation to reproduction based on food availability during vitellogenesis.</p>
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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.