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1,548 results for “Trajectories”
MD simulation trajectory of a fully hydrated POPG bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated POPG bilayer [288 POPG, 10664 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=298K. 250 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DPPE bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPE bilayer [288 DPPE, 9386 WAT]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=336K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DPPG bilayer @314K: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DPPG bilayer [288 DPPG, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=314K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a fully hydrated DOPS bilayer: SLIPIDS, Gromacs 5.0.4. 2017.
<p>MD simulation trajectory files, for fully hydrated DOPS bilayer [288 DOPS, 11232 WAT and 288 NA ions]. The SLIPIDS force field was used with Gromacs 5.0.4. Conditions: T=303K. 200 ns trajectory, last 100 ns uploaded for analysis.</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M CsCl, Berger force field for lipids, Dang's for Cs+ and ffgmx for Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M CsCl (102 POPC, 26 POPS, 4290 WAT, 106 Cs+, 80 Cl-). Additional Cs+ cations added to neutralize the negative charge of POPS. Berger force field for lipids, Dang's for Cs+ (), ffgmx for Cl- are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here).<br> K+ nonbonding parameters (from Dang's Cs+ from JPC B 1999, 103, 8195):<br> sig=0.383086, eps=0.41840</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M KCl, Berger force field for lipids, Dang's for K+ and ffgmx for Cl-
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M KCl (102 POPC, 26 POPS, 4290 WAT, 106 K+, 80 Cl-). Additional K+ cations added to neutralize the negative charge of POPS. Berger force field for lipids, Dang's for K+ (), ffgmx for Cl- are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here).K+ nonbonding parameters (from Dang's JPC B 1999, 103, 8195 based on Vacha et al. Biophys. J 2009, 96, 4493.):<br> sig=0.3048655 eps=0.418400</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p>
MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl, Berger force field for lipids and ffgmx for ions
<p>MD simulation trajectory of a POPC/POPS (4:1) bilayer with 1M NaCl (102 POPC, 26 POPS, 4290 WAT, 106 Na+, 80 Cl-). Additional Na+ cations added to neutralize the negative charge of POPS. Berger force field for lipids and ffgmx for ions are employed. Gromacs 4.0.7, T=310K, 200 ns trajectories were calculated with the last 50 ns stored here.</p> <p>Used in:</p> <p>P. Jurkiewicz, L. Cwiklik, A. Vojtiskova, P. Jungwirth, M. Hof, Structure, Dynamics, and Hydration of POPC/POPS Bilayers Suspended in NaCl, KCl, and CsCl <br> <em>BBA Biomembranes </em>2012<em>, 1818, 609-616.</em><br> DOI: 10.1016/j.bbamem.2011.11.033</p> <p> </p>
Energy and time optimal trajectories in exploratory jumps of the spider Phidippus regius
<p>Supplementary files S1 from the paper Energy and time optimal trajectories in exploratory jumps of the spider <em>Phidippus regius</em>. CT Scan files - A repository with files from CT scanning, composed of: 1. The volume from the CT scan in VGI/VOL format. 2. A VAXML model of the spider (stl meshes tied together with an XML file). 3. A Drishti Prayog model of the volume</p>
MimiIWG FAIRv162 Temperature Trajectories
<h3>1. Introduction</h3><p>These files represent the source code and input files for the temperature trajectories used for the pairing of the MimiIWG integrated assessment model with the MimiFAIRv162 climate model. They serve as inputs for <strong>sensitivity analysis</strong> in Tan, Rennels, and Parthum 2023 "The Social Costs of Hydrofluorocarbons and the Benefits from Their Expedited Phasedown" with replication code for that paper <a href="https://github.com/bryanparthum/schfc-paper">here</a>. </p><p>They are used as automatically downloaded inputs to the <a href="https://github.com/lrennels/MimiIWG_FAIRv162">MimiIWG_FAIRv162</a> repository, a dependency of the paper replication code.</p><p>Please see the publication and repositories for important details about methodology and assumptions <strong>before considering use </strong>and feel free to be in touch with the authors with any further questions or clarifications.</p><h3>2. temp_trajectory_replication.zip</h3><p>This folder holds all code and data to replicate the data outputs. Note that the <i>Manifest.toml </i>and <i>Project.toml</i> files are accessed by the source code to define the Julia environment and should not be modified.</p><h4>data folder (data)</h4><p>Data input files that define the emissions for the IWG EMF-22 scenarios including</p><ul><li>dice_inputs_ch4 - <a href="https://github.com/rffscghg/MimiIWG.jl">https://github.com/rffscghg/MimiIWG.jl</a> repository at path MimiIWG/data/IWG_inputs/DICE/CH4N20emissions_annualversion.xls in CH4annual Tab Units of MtCH4</li><li>dice_inputs_n2o - <a href="https://github.com/rffscghg/MimiIWG.jl">https://github.com/rffscghg/MimiIWG.jl</a> repository at path MimiIWG/data/IWG_inputs/DICE/CH4N20emissions_annualversion.xls in N2Oannual Tab Units of MtN2O</li><li>dice_inputs_land_co2 - <a href="https://github.com/rffscghg/MimiIWG.jl">https://github.com/rffscghg/MimiIWG.jl</a> repository at path MimiIWG/data/IWG_inputs/DICE/SCC_input_EMFscenarios.xls in LandCO2 tab Units of GtC per decade</li><li>dice_inputs_industrial_co2 - <a href="https://github.com/rffscghg/MimiIWG.jl">https://github.com/rffscghg/MimiIWG.jl</a> repository at path MimiIWG/data/IWG_inputs/DICE/SCC_input_EMFscenarios.xls in IndustrialCO2 tab Units of GtC per decade</li></ul><h4>src folder (src)</h4><p>Source code files to produce files in <i>mimiiwg_fairv162_temp_trajectories</i> folder. To produce the output use Julia to run <i>main.jl</i> to produce the output files (~12GB) in an <i>output</i> folder created in the parent directory of <i>main.jl</i>.</p><h3>3. mimiiwg_fairv162_temp_trajectories.zip</h3><p>This folder holds input data files as produced by the src source code above. These are used as inputs for running the MimiIWG-FAIRv162 model.</p><p>There is one file per gas (CO2 and 11 HFCs) - socioeconomic scenario (5 EMF-22 scenarios) making 60 files, plus a key file. All files are in Arrow format for efficiency.</p><p>Each gas-scenario input file has the following specifications:</p><ul><li>2237 sets of temperature trajectories, one for each FAIR constrained parameter set to be used in a Monte Carlo Analysis</li><li>within each set, one baseline temperature trajectory and one trajectory for a pulse of emissions (1GtC or 1 MtHFC) in a given year from 2005 to 2105 in five-year intervals</li><li>units are anomaly from pre-industrial in degrees Celsius</li></ul>
Cortical somatostatin long-range projection neurons and interneurons exhibit divergent developmental trajectories
<p>Spatial transcriptomic data with 94 gene panels on P5 mouse neocortex. Files here include raw tiff files, results/spot counts, DAPI files for ROI segmentation, ROI segmented, final measurement with annotated region and counts. </p>
MD files (psf, pdb, and toppar) for the trajectories of the glycoprotein receptors FSHR and LHCGR.
<p>PSF and PDB files for trajectories on FSHR and LHCGR in SDPC lipids. Top and par parameters for charmm36m included.</p><p>PDB files and trr files include only backbone atoms. All frames were fitted to the to the transmembrane domains.</p>
Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023
<p>Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023</p> <p> </p> <p> </p>
Backward trajectories from AMOC lower limb
<p>Backward trajectory run from the AMOC lower limb using TRACMASS. This is a part of the previous upload https://doi.org/10.5281/zenodo.7924420 . </p>
Iron particles oxidation measurements - trajectories, cracking and temperature
<p>Data collected in Miniatura 6 project no 2022/06/X/ST8/01753 "Experimental investigation of combustion kinetics and cracking intensity of iron particles in high heating rate conditions" financed by National Science Centre, Poland</p>
Data from: facial growth and development trajectories based on 3D images: geometric morphometrics with a deformation perspective
<p>Developmental changes of facial shape are commonly investigated through geometric morphometrics. A limitation with this approach is the inability to investigate patterns of morphological changes at local scale. This could be addressed through quantifying the deformation required to deform one shape to another. This study aimed to investigate changes in mean, rate, and variance of facial shape at local scale using geometric morphometrics through deformation perspective. 2112 Europeans 3 to 40 years-old from the 3D Facial Norms project were included. Shape and rate trajectories from partial least-squares regressions revealed that the developmentally protrusive nasal bridge was due to local expansion in surrounding tissues as opposed to shape changes in nasal bridge per-ser. Local expansion of the supraorbital region, in particular the medial part in males, resulted in the sloping forehead and deep-situated eyes with development. Facial shape variation increased non-linearly with age (p < 0.05), with features having larger rate of change becoming more developmentally diversified. In summary, our deformation perspective facilitates unravelling morphogenetic processes underlying shape changes. Our extended analytical scope inspires novel measures worthy of consideration while establishing facial growth charts. The analytical framework in this study is broadly applicable for analysis of shape changes in general.</p>
Input parameters and output trajectory files for manuscript "Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLPro: Insights from the Computational and Experimental Investigations"
<p>Input parameters used for molecular dynamics simulations on GROMACS 2022 software and the output trajectory files for calculating binding free energy, in the manuscript with the title: "Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CL<sup>Pro</sup>: Insights from the Computational and Experimental Investigations"</p>
Molecular Dynamics Trajectories for the D3 receptor (D3R) complexes bound with a GαOβγ heterotrimer and 1) FOB02-04A bitopic agonist; 2) pramipexole.
<p>Molecular Dynamics Data for publication "Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket". Sandra Arroyo-Urea, Antonina L. Nazarova, Ángela Carrión-Antolí et al., Nat. Comm., revision (2024). https://doi.org/10.21203/rs.3.rs-3433207/v1</p> <p><br>This directory includes the PDB (Protein Data Bank) format file detailing the topology and the XTC (eXtended Trajectory) format file outlining the trajectories for two distinct complexes: 1) the FOB02-04A-bound structure of D3 receptor (D3R) complexes in association with a GαOβγ heterotrimer, and 2) the pramipexole-bound structures of D3R complexes also coupled to a GαOβγ heterotrimer. The data is organized in a strided trajectory with a timestep of 0.5 nanoseconds per frame. To reapply periodic boundary conditions, users can employ the standard periodic boundary condition commands available in Visual Molecular Dynamics (VMD) package.</p> <p> </p> <p>The MD trajectory data for this study was acquired as well as uploaded by Antonina L. Nazarova.</p>
Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling
<p>Scripts associated with the analysis and plotting of data for the Cell paper: Charting the cellular biogeography in colitis reveals fibroblast trajectories and coordinated spatial remodeling</p>
GPS trajectories of tourists on Torsö and Brommö 2021 from INCULTUM Sweden Pilot
<div>This dataset is part of ongoing work about tourist behaviour changes on Torsö and Brommö. It was collected using GPS trackers. </div> <div> <div> <p> </p> </div> </div>
Results from simulated drift trajectories of driting Fish Aggregating Devices used in Figures for paper Escalle et al., (2024) Simulating drifting fish aggregating device trajectories to identify potential interactions with endangered sea turtles
<p>Escalle et al., (2024) Simulating drifting fish aggregating device trajectories to identify potential interactions with endangered sea turtles<br><span><a href="../doi/10.5281/zenodo.10815559">https://zenodo.org/doi/10.5281/zenodo.10815559</a></span></p> <p>Results data description<br>The above doi contains simulation output data generated from passive drift simulations of drifting FADs in the Pacific ocean. We refer the reader to the main text of the paper for details and definitions of the different zones and simulation experiments.</p> <p>All data files are matrices stored in comma-delimited files (.csv), where the first provides the column names of the matrix, and the first column provides the row names. The first cell in row 1, column 1 is simply a placement value that describes the nature of the matrix. </p> <p>When this value is a hash symbol (#), it denotes that the matrix represents a spatial density of virtual particles under a particular drift scenario and over a particular period of time. Column names provide the latitude indices of each cell, and row names are the longitude indices. Values are the proportion of all particules in the domain that passed through this cell, during the drift-time window of this results file (see below).</p> <p>When the first cell value is a hash followed by a code (e.g. # EqZ), it denotes that the file represents a connectivity matrix between the zones given by the code (e.g. Equatorial Zones EqZ or Fishing Zones FZ) and defined in the row names of the matrix, and the turtle zones defined by the column names. Values are the proportion of particules beginning the zone defined by the row name at the start of the simulation, which are now present in the zone defined by the column name.</p> <p>Files name follow a convention describing the deployment and drift-time scenario they represent.</p> <p>For spatial density matrices:<br>[Origin Zones]_[Subset]_Density_[Drift Time]_....csv</p> <p>For connectivity/transition matrices:<br>[Origin Zones]_[Drift Time]_[Number of Simulations Run]_TransitionMatrix_....csv</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.