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669 results for “ATOM”
Sampled ΔH/Δλ and ΔH data from ABFE calculations (using standard atomic masses) of 10 ligands bound to Cyclophilin D
<p>Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process"</p> <p>Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands to bound Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike other datasets in this work, which employed hydrogen mass repartitioning, the ligands here were calculated using standard atomic masses.</p> <p>All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information.</p> <p>Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders).</p> <p>Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).</p>
Dataset 2 for: Multi-eGO: an in-silico lens to look into protein aggregation kinetics at atomic resolution
<p><strong>Dataset</strong></p> <p>Molecular dynamics simulation trajectories of TTR peptide aggregation kinetics:</p> <ul> <li>multi-eGO-XXmM-Y: aggregation kinetics simulations of TTR using the multi-eGO force field at XXmM concentration replicate Y.</li> </ul>
Hydrogen atom recombination on Pt(111) and Pt(332)
<p>Experimantal transient rates of HD formation, Molecular beam parameters, Experimental isotopic branching, Experimental H+H rate constants, Modeled dissociative adsorption and recombinative desorption rate constants, Coverage dependent adsorption energy, Quantum mechanical entropy of H-atoms at 598K.</p>
Data of "Efficient generation of entangled multi-photon graph states from a single atom"
<p>Data published in "<em>Efficient generation of entangled multi-photon graph states from a single atom</em>"</p>
Influence of Titan's Variable Electromagnetic Environment on the Global Distribution of Energetic Neutral Atoms
<p>Data for the manuscript "Influence of Titan's Variable Electromagnetic Environment on the Global Distribution of Energetic Neutral Atoms" by Tippens et al., (2022). See README.txt for a description of the data files included here.</p>
Data set for the journal article Structural Analysis of Metal Coordination Sites in Single-Atom Catalysts Based on Carbon Nitrides
<p>The data is organized according to the figure in the manuscript. </p>
All-atom molecular dynamics simulations of phenylalanine-4-hydroxylase (PAH) tetramer to investigate the impact of two novel heterozygous mutations, p.Y198N and p.Y204F, observed in a classical phenylketonuria patient
<p>Phenylalanine-4-hydroxylase (PAH) tetramer system (Robetta modelling to complete the structure with template PDB ID: 6hyc) with parametrised BH<sub>4</sub> ligand (parameters are available in the dataset) and Fe(II) metal ions in a TIP3P water box ionised with 0.15 M KCl were presented as wild-type and carrying two novel mutations as Y198N on dimeric chains A and B, and Y204F on dimeric chains C and D. In addition, E353 and E422 are protonated as predicted by PROPKA. BH<sub>4</sub> molecule parametrization was performed by using GAFF, Antechamber and “amb2chm_par.py” program of Amber2018.</p> <p>5,000-step minimization and 1 ns equilibration were performed by fixing the protein to relax the system. Then, another 5,000-step minimization and 1 ns equilibration were performed without any constraints, except the SHAKE algorithm on water molecules, to relax the protein and system. The production simulations were performed along 100 ns trajectory at 310 K collected under NpT ensemble.</p> <p>All system preparation and simulation details for this dataset is available with the related background, results and conclusions in the following article:</p> <p>Tolga Aslan, Aslı Yenenler-Kutlu, Umut Gerlevik, Ayşe Çiğdem Aktuğlu Zeybek, Ertuğrul Kıykım, Osman Uğur Sezerman & Necla Birgul Iyison (2021) Identifying and elucidating the roles of Y198N and Y204F mutations in the PAH enzyme through molecular dynamic simulations, Journal of Biomolecular Structure and Dynamics, DOI: <a href="https://doi.org/10.1080/07391102.2021.1921619">10.1080/07391102.2021.1921619</a></p>
Flight demonstration of a miniature atomic scalar magnetometer based on a microfabricated rubidium vapor cell
<p>Data acquired by the Miniature Absolute Scalar Magnetometer (MASM) on the low-flying sounding rocket of the Twin Rockets to Investigate Cusp Electrodynamics 2 (TRICE-2) mission. The data columns are as follows:</p> <p>epoch time: CDF Epoch Time</p> <p>time: year, month, day, hour, minute, second</p> <p>lfreq [Hz]: Larmor frequency in Hertz</p> <p>Bt [nT]: Measured total magnetic field in nano-Tesla</p> <p>Btm [nT]: Total magnetic field of the IGRF model in nano-Tesla</p> <p>Bxm [nT]: Magnetic field Bx-component of the IGRF model in ECEF coordinates and nano-Tesla</p> <p>Bym [nT]: Magnetic field By-component of the IGRF model in ECEF coordinates and nano-Tesla</p> <p>Bzm [nT]: Magnetic field Bz-component of the IGRF model in ECEF coordinates and nano-Tesla</p> <p>flight time: Flight time with respect to launch in seconds</p> <p>ecef x pos [m]: ECEF X coordinate in meters</p> <p>ecef y pos [m]: ECEF Y coordinate in meters</p> <p>ecef z pos [m]: ECEF Z coordinate in meters</p> <p>ecef x vel [m/s]: ECEF X velocity in meters per second</p> <p>ecef y vel [m/s]: ECEF Y velocity in meters per second</p> <p>ecef z vel [m/s]: ECEF Z velocity in meters per second</p> <p>lat [deg]: Geopgraphic latitude in degrees</p> <p>lon [deg]: Geographics longitude in degrees</p> <p>alt [km]: Altitude in kilometers</p> <p>vcsel temp: VCSEL temperature in engineering units</p> <p>gas cell temp: Rubidium vapor cell temperature in engineering units</p> <p>bx mag: Magnetic field Bx-component measured by the mission's science magnetometer in ECEF coordinates and nano-Tesla</p> <p>by mag: Magnetic field By-component measured by the mission's science magnetometer in ECEF coordinates and nano-Tesla</p> <p>bz mag: Magnetic field Bz-component measured by the mission's science magnetometer in ECEF coordinates and nano-Tesla</p> <p>bt mag: Total magnetic field measured by the mission's science magnetometer in ECEF coordinates and nano-Tesla</p> <p>btf mag: Filtered total magnetic field measured by the mission's science magnetometer in ECEF coordinates and nano-Tesla</p>
Research data for "Exploring the configurational space of amorphous graphene with machine-learned atomic energies"
<p>This dataset supports the paper: "Exploring the configurational space of amorphous graphene with machine-learned atomic energies" (<a href="https://doi.org/10.1039/D2SC04326B">https://doi.org/10.1039/D2SC04326B</a>).</p> <p>Trajectory data for the 200-atom structures (Fig. 3) and the final configurations for the 612-atom structures as well as the GAP-17-optimised 610-atom structure from Toh et al are provided (Fig. 4). Additionally, the structures used for data analysis in Fig. 5 are given.</p> <p>The files are in extended xyz (.xyz) format and contain the raw data for coordinates, forces, and atomic energies (labelled 'c_1'). The files also contain the atomic energies relative to pristine graphene, labelled "Energy_per_atom", and the locally averaged energy relative to pristine graphene, labelled "NN_Energy_per_atom". Topological information is included at the end of the .xyz file for the 612-atom structures ('fig_4'/) and for the structures in 'fig_5/'.</p> <p>All raw atomic energies were computed using LAMMPS default settings and were output with six significant figures, with the exception of the Toh et al. structure (for which ASE was used, outputting a higher number of significant figures). </p> <p>The data can be read using, for example, the Atomic Simulation Environment (ASE), or visualised using Ovito.</p> <p> </p>
Atomic Force Microscopy image of coagulation factor Va in liquid
<p>Original raw and corrected AFM images of isolated coagulation factor Va (FVa). The image was acquired in liquid with an OTR8 cantilever using the peak force tapping mode of a multimode V microscope. The image size is 1 x 1 µm² with 1024 x 1024 pixels². The corrected image was obtained using Gwyddion (.gwy file) from the raw image file (.spm). This image was the experimental data used to assemble the A trimer and the two C domains of FVa using the AFMAssembly pipeline described in Chaves et al. (2014): http://dx.doi.org/10.1160/TH14-06-0481. The paper can be downloaded from the HAL repository (https://hal.archives-ouvertes.fr/hal-01146300v1).</p>
Dataset: Atomera Incorporated (ATOM) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Optimized atomic structures of thin Ag films on Pt(111) and Pd(111) surfaces
<p>VASP coordinate files of thin Ag films on Pt(111) and Pd(111) surfaces and the summary spreadsheet of corresponding energies. </p>
Data for "Atomic-scale perspective on individual thiol-terminated molecules anchored to single S vacancies in MoS2"
<p>This repository provides the original datasets for the manuscript "Atomic-scale perspective on individual thiol-terminated molecules anchored to single S vacancies in MoS2". It includes the original experimental data as well as the iPython Notebooks used to treat it in "<a href="../api/records/10160204/draft/files/Data_and_Analysis.zip/content" target="_blank" rel="noopener noreferrer">Data_and_Analysis.zip</a>" (see readme in individual folders for precise information), the datasets for the structure search and molecular dynamics calculations in "<a href="../api/records/10160204/draft/files/structure_search_and_MD.zip/content" target="_blank" rel="noopener noreferrer">structure_search_and_MD.zip</a>", as well as the data for the DFT calculations for the projected electronic density of states (PDoS) and the orbital densities of Fig.5 and 8 in "<a href="../api/records/10160204/draft/files/fig5.zip/content" target="_blank" rel="noopener noreferrer">fig5.zip</a>" and "<a href="../api/records/10160204/draft/files/fig8.zip/content" target="_blank" rel="noopener noreferrer">fig8.zip</a>", respectively.</p> <p> </p>
METADATA for results of irradiation-induced complex DNA damage measurements using plasmid pBR322 along a typical Proton Treatment Plan at the MedAustron proton and carbon beam therapy facility (energy 137–198 MeV and Linear Energy Transfer (LET) range 1–9 keV/μm), by means of Agarose Gel Electrophoresis and DNA fragmentation using Atomic Force Microscopy (AFM)
Open the record for dataset details and reuse information.
Long-lived magnetization in an atomic spin chain tuned to a diabolic point
<p>This is the OpenData Folder for the paper under the same name.</p>
Modeling the Emission of Energetic Neutral Atoms in Titan's Dynamic Magnetospheric Environment
<p>Data for the manuscript "Modeling the Emission of Energetic Neutral Atoms in Titan's Dynamic Magnetospheric Environment" by Tippens et al., (2024). See README.txt for a description of the data files included here.</p>
Research data supporting "Fate of Liposomes in Presence of Phospholipase C and D: From Atomic to Supramolecular Lipid Arrangement"
<p>Raw research data for experimental work supporting the publication above.</p> <p>Raw data for MD simulation is available upon reasonable request from Irene Yarovsky (irene.yarovsky@rmit.edu.au).</p>
Figure 2 in High-Resolution Functional Imaging of Native Proteins using Force Distance Curve Based Atomic Force Microscopy
Figure 2. - Juvenile Trachipterus arcticus, 129 mm SL, collected at Faial Island, Azores, 14 May 2014, on the surface. A: Portrait with anterior black facet visible; B: Oblique lateral view with first spines erected; note orange bulbous outgrowths on the prolonged spine; C: Lateral view showing proportions, markings and orientation of fins. Scale bars: A = 1 cm; B, C = 5 cm.
Figure 1 in High-Resolution Functional Imaging of Native Proteins using Force Distance Curve Based Atomic Force Microscopy
Figure 1. - Adult Trachipterus arcticus, about 1.8 m long, observed south of Pico Island, Azores, 18 Aug. 2013, 950 m deep.
Data for "On the atomic structure of the β′′ precipitate by density functional theory"
<p>The dataset contains the DFT results which is the basis for the results and discussions in the related article, "On the atomic structure of the β′′ precipitate by density functional theory". The details of the DFT calculations are written in the article.</p> <p>The names of the OUTCAR files in enthalpy_study_OUTCARS.tar.gz are more or less self-explanatory, at least within the context of the journal article. The KPOINT tests have the following format for the KPOINTS "XYZ" where X is always a single digit, Y is first to get a double-digit, while Z gets a double-digit second. The max distance in reciprocal space is thus not a constant as the OUTCAR files would suggest.</p> <p> </p> <p>The LET_DATA is the linear-elastic theory displacement-field as explained in the article for different aspect ratios of the precipitate eye structure.</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
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