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11,506 results for “Dynamics”
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, NaCl and KCl salt concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and Dang ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field and ff99 ions
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and ff99 ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS with the lipid17 force field, only counterions, and CaCl2 concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution at various NaCl, KCl and CaCl2 concentrations, with Na+ counterions (and K+ counterions when noted with "_KCl" suffix).</p> <p>Lipid17 force field parameters used for lipids, TIP3p water model and Dang ions.</p> <p>The file names report the number of additional cations.</p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (various mixtures) with ECC-lipids force field, and Na+ (K+) counterions
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with only Na+ counterions (or with K+ counterions when noted with "_KCl" suffix).</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various CaCl2 additional concentrations
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of CaCl2.</p> <p>The numbers in the file names denote the number of additional Ca2+ cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Supplementary movies of the Kaikoura dynamic rupture model published in Ulrich et al. (2019)
<p>Ulrich, T., Gabriel, A. A., Ampuero, J. P., & Xu, W. (2018). Dynamic viability of the 2016 Mw 7.8 Kaikōura earthquake cascade on weak crustal faults.</p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e8V/m, 2e8 V/m, 3e8 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_08.xtc">traj_centered_08.xtc </a>1e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_centered_3_08.xtc">traj_centered_3_08.xtc </a> 3e8 V/m<br> <a href="https://zenodo.org/api/files/8ee8fcea-f0b9-4f56-937c-53d6aba607f3/traj_ricentrata_2_08.xtc">traj_ricentrata_2_08.xtc </a> 2e8 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: no field, 2e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_no_field.xtc">traj_centered_no_field.xtc </a> no field</p> <p><a href="https://zenodo.org/api/files/81479d2b-9168-43d1-8573-9c979435b8f0/traj_centered_2_07.xtc">traj_centered_2_07.xtc </a> 2e7 V/m</p> <p> </p>
S6 molecular dynamics simulation trajectories of tubulin in electric field: 1e7V/m, 5e7 V/m, A1604
<p>Molecular dynamics simulation trajectories of tubulin in electric field</p> <p>t<a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_07.xtc?versionId=62da1fac-7265-4aeb-a239-481088fb396a">raj_centered_07.xtc </a> 1e7 V/m</p> <p><a href="https://zenodo.org/api/files/cba74eb5-a746-4cdf-80e4-1c06a1ec0462/traj_centered_5_07.xtc?versionId=c0b8015d-b977-4eda-b678-9d4b719a90e2">traj_centered_5_07.xtc </a> 5e7 V/m</p> <p> </p> <p><br> <br> <br> </p>
Molecular Dynamics Simulation of Aluminium Binding to Amyloid-beta and its Effect on Peptide Structure
<p>MD frames and highest populated clusters, in PDB format</p>
Morphodynamic modeling of sediment pulse dynamics: Raw code and output
<p>Fortran source code and raw output files (.csv) for a 1D morphodynamic model simulating sediment pulse evolution.</p> <p>This material is provided as is, with absolutely no warranty expressed or implied. Any use is at your own risk.</p>
Supplementary movies of the dynamic rupture and tsunami models published in Ulrich et al. (2019)
<p>Supplementary movies of the dynamic rupture and tsunami models published in Ulrich et al. (2019)</p> <p>movie_Sulawesi_SR-cp.mov: Absolute slip rate (m/s) across the fault network during the earthquake. Author: Thomas Ulrich</p> <p>movie_Sulawesi_wavefield-cp.mov: Absolute slip rate (m/s) and wavefield (absolute particle velocity in m/s) across the fault network during the earthquake. Author: Thomas Ulrich</p> <p>SulawesiTanioka.mp4: Sea surface height (m) predicted by the tsunami scenario. Author: Stefan Vater</p> <p>reference: Ulrich, T., Vater, S., Madden, E. H., Behrens, J., van Dinther, Y., van Zelst, I., Fielding, E. J., Liang, C. & Gabriel, A. A. (2019). Coupled, Physics-based Modeling Reveals Earthquake Displacements are Critical to the 2018 Palu, Sulawesi Tsunami. doi: 10.31223/osf.io/3bwqa.</p>
BSc thesis:"The dynamics and localization of three fluorescent fusions of the periplasmic chaperone Skp in Escherichia coli"
<p>This is the full data set containing all primary and derived data generated during this thesis. The title of this thesis is: "The dynamics and localization of three fluorescent fusions of the periplasmic chaperone Skp in Escherichia coli". The experimental work was conducted at the Bacterial Cell Biology & Physiology group of the University of Amsterdam.</p>
CT Data of a Pen-Spring: Application to Under-Sampled Dynamic X-ray Tomography
<p>This is the documentation of Computed Tomography (CT) data of a pen-spring. It can be freely used for scientific purposes with appropriate references to the data and to this document in https://arxiv.org/abs/1907.01871. The provided data set includes the X-ray sinograms finalSino of a single 2D slice from a different height of the spring. The finalSino was obtained from a measured 10-projection or 100-projection sinogram using fan-beam geometry<br> by down-sampling and taking logarithms. The data set includes also those original measured sinograms and corresponding measurement matrices.</p>
Data for the manuscript: TOWARDS AN INTEGRATED SOIL-PLANT-ATMOSPHERE MODELING ENVIRONMENT: IMPLEMENTATION OF A DYNAMIC PLANT UPTAKE MODULE FOR THE HYDRUS MODEL
<p>Data used in the manuscript for the theoretical and experimental validation, and for the Global Sensitivity Analysis. For a thorough description, please refer to the manuscript.</p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl.</p> <p>The numbers in the file names denote the number of additional cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Plasticity in Collective Decision-Making for Robots: Creating Global Reference Frames, Detecting Dynamic Environments, and Preventing Lock-ins
<p>Swarm robots operate as autonomous agents and a swarm as a whole gets autonomous by its capability of collective decision-making.<br> Despite intensive research on models of<br> collective decision-making, the implementation in multi-robot systems is still challenging.<br> Here, we advance the state of the art by introducing more plasticity to the decision-making process and by increasing the task difficulty.<br> Most studies on large-scale multi-robot decision-making are limited to one instance of an iterated exploration-dissemination phase followed by successful and permanent convergence.<br> We investigate a dynamic environment that requires constant collective monitoring of option qualities.<br> Once a significant change in qualities is detected by the swarm, it has to collectively reconsider its previous decision accordingly.<br> This is only possible by preventing lock-ins, a global consensus state of no return.<br> In addition, we introduce a task of increased difficulty as the robots must locate themselves to assess the quality of an option.<br> Using local communication, swarm robots propagate hop-count information throughout the swarm to form a global reference frame.<br> We successfully validate our implementation in many swarm robot experiments concerning robustness to disruptions of the reference frame, scalability, and adaptivity to a dynamic environment.</p>
Supplementary material for "Molecular dynamics gives new insights into the glucose tolerance and inhibition mechanisms on β-glucosidases" (2 video files)
<p>Video S1: MD of the glucose exit in a glucose-tolerant GH1 β-Glucosidase</p> <p>Video S2: Interactions among glucose, D228, K257, and N312 in a glucose-tolerant GH1 β-glucosidase</p>
Structural and functional dynamics of soil microbes following bark beetle infestation
<p>Provided are the bacterial and fungal phyloseq objects for Structural and functional dynamics of soil microbes following spruce beetle infestation". Authored by: Gordon Custer, Dr. Linda van Diepen, and Dr. William Stump. All of the University of Wyoming</p>
Dynamic 3D Tomographic X-ray Data of Ladybug
<p>This is the documentation of the 3D dynamic tomographic X-ray (CT) data of a ladybug.<br> It can be freely used for scientific purposes with appropriate references to the data and to this document in http://arxiv.org/.</p>
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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.