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1,294 results for “reactions”
"The current-voltage characteristics and partial pressure dependence of defect controlled electrochemical reactions on mixed conducting oxides"
<p>Oxygen exchange reaction rates on mixed conducting perovskite electrodes are described as a function of defect concentrations, see <a href="http://elchinfo.cta.tuwien.ac.at/pmwiki/uploads/Profiles/Schmid_JESoc.pdf">The current-voltage characteristics and partial pressure dependence of defect controlled electrochemical reactions on mixed conducting oxides</a> for a detailed description.</p> <p>Here, (exchange) currents, polarization resistances, <span class="math-tex">\(p_{\rm{O_2}}\)</span> dependencies and Tafel-slopes are calculated as function of <span class="math-tex">\(p_{\rm{O_2}}\)</span> and overpotential for different possible reaction mechnisms. The defect concentrations are taken from the model material La<sub>0.6</sub>Sr<sub>0.4</sub>FeO<sub>3-<span class="math-tex">\(\delta\)</span></sub>, and listed in Brouwer_Bias.csv as a function of <span class="math-tex">\(p_{\rm{O_2}}\)</span> and overpotential.</p> <p>Model 7 describes a molecular mechanisms wothout adsorption limitation, model 8 includes adsorption limitation. Likewise Models 10 and 11 describe atomic mechanisms without and with adsorption limitation, respectively.</p> <p>Overpotentials are listed in V, oxygen partial pressures in bar, defect concentrations in defects per unit cell and currents are in arbitrary units as are resistances.</p> <p>Partial pressure and overpotential dependencies (p and n slopes) are given as <span class="math-tex">\(\frac{\partial \ln j}{\partial\ln p_{\rm{O_2}}}\)</span>(unitless) and <span class="math-tex">\(\frac{\partial \ln j}{\partial\eta}\)</span>(/V), and likewise with resistances instead of currents (rp and rn slopes), respectively.</p> <p>The source code for this project is available at: https://github.com/AlexSchmid22191/EIS_R_Sim</p>
Dataset for state-specific reaction of OCS+Ne* from "A novel crossed-molecular-beam experiment for investigating reactions of state- and conformationally selected strong-field-seeking molecules"
<p><strong>Data and analysis for all figures containing experimental data of the paper:</strong></p> <p>•Title: A novel crossed-molecular-beam experiment for investigating reactions of state- and conformationally selected strong-field-seeking molecules</p> <p>•Authors: L. Ploene, P. Straňák, H. Gao, J. Küpper and S.Willitsch</p> <p>•Journal: Molecular Physics</p> <p>DOI: https://doi.org/10.1080/00268976.2021.1965234</p> <p> </p> <p><strong>The PDF contains three flow-chart diagrams, describing how the data has been analysed:</strong></p> <p>•Diagram 1: Deflection profiles of OCS by femtosecond-ionisation compared to MC trajectory simulations for Paper-Figure 3</p> <p>•Diagram 2: Typical TOF-MS trace of Ne* + OCS for Paper-Figure 4 and Experimental deflection profile of OCS+ and S+ from chemi-ionisation reaction Ne* + OCS for Paper-Figure 5</p> <p>•Diagram 3: Least-square fitting of experimental deflection profiles of OCS+and S+ with state-specific simulated deflection profiles for Paper-Figure 6a and 6b</p>
Data for "A Surface-Promoted Redox Reaction Occurs Spontaneously on Solvating Inorganic Aerosol Surfaces"
<p>Dataset for "A Surface-Promoted Redox Reaction Occurs Spontaneously on Solvating Inorganic Aerosol Surfaces"</p>
The moisture plasticizing effect on enzyme-catalyzed reactions in model and real systems in view of legume ageing and their hard to cook development
<p>Data used for the figures in the article</p>
Supporting data for "Correlations between precipitation reactions and electrochemical performance of lithium-sulfur batteries"
<p>This is the dataset of electrochemical and operando small-angle and wide-angle scattering experiments for our publication "Correlations between precipitation reactions and electrochemical performance of lithium-sulfur batteries probed by operando scattering techniques". The title of the article was changed in the revision process while this dataset was already published. This archive contains the raw data and scripts written in R used in the analysis and presentation of the results in this manuscript.</p> <p><strong>Abstract for the manuscript:</strong></p> <p>A comprehensive description of electrochemical processes in the positive electrode of lithium-sulfur batteries is crucial for the utiliza- tion of active material. However, the discharge mechanisms are complicated due to various reactions in multiple phases and the tor- tuosity of the highly porous carbon matrix. In this work, simulta- neous measurements of small-angle and wide-angle scattering and cell resistance are performed on operating lithium-sulfur cells. Re- sults indicate that precipitates grow mostly in number, not in size, and that the structure of the carbon matrix is not affected. The com- parison of the small-angle and wide-angle scattering reveals the amorphous discharge products found at a low discharge rate. Further analysis demonstrates the correlation between the diffusion resistance and the compositional change of electrolyte in the meso- pores at the end of discharge, which suggests that Li-ion deficiency is the limiting factor for sulfur utilization at a medium discharge rate.</p>
Do genetic differences in growth thermal reaction norms maintain genetic variation in timing of diapause induction?
<ol> <li>An optimal timing for diapause induction through the sexual production of dormant propagules is expected in organisms with temporary populations. Yet, empirical studies often find high within-population genetic variation in the sexual production of such propagules, suggesting that this is a common feature of such organisms.</li> <li>Here, we hypothesize that genetic variation in the propensity to produce dormant propagules, <i>P<sub>d</sub></i>, is maintained by a genotype-by-environment interaction in clonal reproductive rates, where fast-growing genotypes within an environment should delay diapause relative to slow-growing genotypes. From this, we derive two predictions. First, if reaction norms of clonal reproduction cross between two environments, the genetic correlation of <i>P<sub>d</sub></i> between these environments should be negative. Second, the correlation between plasticity values of clonal reproduction and <i>P<sub>d</sub></i> should be negative.</li> <li>We tested these predictions by quantifying ephippia production in genotypes of a population of the facultative sexual cladoceran <i>Daphnia magna</i> at two temperatures. The population biomass at the onset of ephippia production was used as a measure of <i>P<sub>d</sub></i>, whereas juvenile somatic growth rate was used as a proxy for clonal reproductive rate. Plasticity for both measurements was derived from thermal reaction norms.</li> <li>Our results did not support either prediction, as neither the genetic correlation of <i>P<sub>d</sub></i> between environments, nor the correlation between plasticity values of growth and <i>P<sub>d</sub></i> were found to be significant.</li> <li>Our results suggest that genetic variation in the timing of diapause is not maintained by genetic differences in thermal clonal reproduction reaction norms. We propose as an alternative hypothesis that if there is across year variation in how stochastically the environment deteriorates, fluctuating selection may favor genotypes with different <i>P<sub>d</sub></i> between years.</li> </ol>
Input files and dataset for CD3CN+F Reaction sampling in CHARMM
<p>The input files and resulting trajectory data for the CD3CN application described in:</p> <p><a href="https://pubs.rsc.org/en/content/articlelanding/2016/fd/c6fd00138f#!divAbstract">Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics</a>, by O'Connor et al.</p>
Data to support "Physics-based representations for machine learning properties of chemical reactions
<p>4 datasets of reaction data: </p> <p>1. SN2-20 dataset adapted from https://iopscience.iop.org/article/10.1088/2632-2153/aba822/meta</p> <p>2. Proparg-21-TS dataset from https://pubs.rsc.org/en/content/articlehtml/2021/sc/d1sc00482d</p> <p>3. GDB7-22-TS dataset from https://www.nature.com/articles/s41597-020-0460-4</p> <p>4. Our Hydroform-22-TS dataset of 2,350 structures of reactant and product structures and associated barriers</p> <p>In all cases, there are xyz files of reactant(s) and product(s) structures, and a csv file of associated properties (reaction energies for the first case, e.e. values for the second, and barriers for the third and fourth).</p> <p>For example usage see https://github.com/lcmd-epfl/b2r2-reaction-rep</p>
Structures for article: "The reactivity of pyridine in cold interstellar environments: The reaction of pyridine with the CN radical"
<p>Set of cartesian structures supporting the article: "The reactivity of pyridine in cold interstellar environments: The reaction of pyridine with the CN radical"</p> <p> </p>
Data supplement for: Validating the Nernst--Planck transport model under reaction-driven flow conditions using RetroPy v1.0
<p>This is the repository for the publication's supplementary data and plotting scripts: Validating the Nernst–Planck transport model under reaction-driven flow conditions using RetroPy v1.0.</p> <p>The dependency of the scripts can be installed using conda and pip:</p> <pre><code>conda create -n plot numpy matplotlib==3.6.1 h5py python=3.9 conda activate plot pip install palettable</code></pre> <p>To reproduce the figures, execute the files using python:</p> <pre><code>python figure03.py</code></pre> <p> </p>
Supplementary Information for "Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications"
<p>This is the external Supplementary Information for our publication "Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications".</p> <p>The .zip files contains the raw data and metadata for all items (supplementary and main text) as well as the calculation results. This includes UV, HPLC, NMR, DFT and MD results. This revised version presents extended DFT results (now including dispersion contributions) as well as additional NMR data (now including analytical data for isolated 1f, among other data).</p> <p>To some extent, this work builds on and borrows from our previous publications on spectral unmixing (https://doi.org/10.3390/mps2030060, https://doi.org/10.1002/cbic.202000204), continuous reaction monitoring (https://doi.org/10.1021/acs.analchem.1c05356), and thermodynamic reaction control (https://doi.org/10.1002/adsc.201901230, https://doi.org/10.5281/zenodo.3568858, https://doi.org/10.1002/cphc.202000901, https://doi.org/10.1021/acscatal.1c02589).</p>
Stereodynamical control of the H+HD→H2+D reaction through HD reagent alignment
<p><span>Prealigning nonpolar reacting molecules leads to large stereodynamical effects because of their weak steering interaction en route to the reaction barrier. However, experimental limitations in preparing aligned molecules efficiently have hindered the investigation of steric effects in bimolecular reactions involving hydrogen. Here we report a high-resolution crossed-beam study of the reaction H+HD(<em>ν</em>=1, <em>j</em>=2)→H<sub>2</sub>(<em>ν</em>', <em>j'</em>)+D at collision energies of 0.50, 1.20, and 2.07 electron volts, in which the vibrationally excited hydrogen deuteride(HD) molecules were prepared in two collision configurations, with their bond, preferentially aligned parallel and perpendicular to the relative velocity of collision partners. Notable stereodynamical effects in differential cross-sections were observed. Quantum dynamics calculations revealed that strong constructive interference in the perpendicular configuration plays an important role in the stereodynamical effects observed.</span></p>
Raw dataset for "Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time"
<p>The dataset contains raw diffraction images in .tiff format. Each image file name contains three numbers, separated by "_". The first number refers to the order in which the images were taking in laboratory time. The second number refers to the absolute translation stage position in millimeters in the optical beam path of the pump beam. The stage position can be converted into a pump-probe delay time (taking into account the speed of light and a factor of 2 for the beam path, since the pulses move back and forth on the stage). Larger stage position values correspond to the optical pump pulse arriving later with respect to the probe pulse. Time zero was determined to be at 156.26 mm using a solid reference sample.</p>
Source data of Safety Assessment by Differential Prefrontal Circuits Mediates Flexibility in Fear Reactions
<p>The processed data of <strong>Safety Assessment by Differential Prefrontal Circuits Mediates Flexibility in Fear Reactions</strong></p>
Replication package for our TOSEM paper entitled "An Empirical Study on GitHub Pull Requests' Reactions"
<p>This package contains our dataset and the source code used to collect data from the the top 10,000 most starred GitHub repositories, and the selected six repositories (i.e., Cataclysm-DDA, Julia, Laravel, Node, RPCS3 and Rust), as well as the source code to analyze the data and generate all the figures in the paper. </p> <p>Please carefully read the README.md file for more details.</p>
Data for: Effects of domestication and captive breeding on reaction to moving objects: Implications for avoidance behaviors of obstacles and predators by masu salmon Oncorhynchus masou
<p>Domestication and captive breeding can compromise obstacle- and predator-avoidance of animals in the wild. Whereas previous studies only examined these effects in combination, here we examine them individually by comparing the abilities of wild, F1 (offspring of wild parents), and captive-bred (approx. F15) masu salmon (<em>Oncorhynchus</em> <em>masou</em>) to avoid a falling object under experimental conditions. Rates of avoidance failure were low (wild, 12.5%; F1, 10.7%; captive-bred, 8%) under light conditions but increased under dark conditions (wild, 11.1%; F1, 32.1%; captive-bred, 60.0%). We attribute the elevated avoidance-failure rate among F1 fish to the lack of learning opportunities in hatchery environments, and the further elevation of avoidance-failure rate among captive-bred fish to the degradation of sensory organ function. These results imply reduced survival rates for F1 and captive-bred fish in the wild and are consistent with the low stocking efficiencies reported for captive-bred masu salmon.</p>
Ultrafast formation dynamics of D3+ from the light-driven bimolecular reaction of the D2-D2 dimer
<p>All the raw data for the main figures of our literature of "Ultrafast formation dynamics of D<sub>3</sub><sup>+</sup> from the light-driven bimolecular reaction of the D<sub>2</sub>-D<sub>2</sub> dimer". Molecular dynamics trajectories and the initial configurations are supplied.</p>
Transfer reaction induced fission 238U(d,p-fission) with HELIOS
<p>Upload includes:</p> <ol> <li><strong>Pre-sorted data with built physics events. </strong>All experimental data in the files "gen_run###.root"</li> <li><strong>Link to GutHub containing all relevant codes to sort the data and produce physics histograms. </strong>Analysis code at <a href="https://github.com/calemhoffman/digios/tree/h074_238U">https://github.com/calemhoffman/digios/tree/h074_238U</a>. README files describe the usage.</li> <li><strong>Copy of electronic logbook containing experimental matters.</strong> "ELOG_H074_238U.pdf" in reverse chronological order.</li> <li><strong>Document with detector distances and details on the setup.</strong> "h074_238U-setup.pptx"</li> <li><strong>Absolute transfer (d,p) and transfer induced fission (d,pf) cross sections.</strong> "238U-dpf-supplemental-data.xlxs"</li> </ol> <ul> </ul>
Ab initio multiple spawning simulations for "Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time"
<p>60 ICs a(0.82)-2SA-cas(6,4)-SCF/6-31G* using AIMS/uPBE0-D3 for 1st ps of alpha-terpinene photochemistry. 20 for each<br> conformer upon rotation around the isopropyl group. Each initial condition (IC) is saved in a<br> separate folder labeled after conformers m, p, t, and with the index number of the initial condition.<br> The folder contains the positions and amplitudes of all trajectory basis functions (TBF) arising from<br> the initial condition as well as information about their coupling. The TBF index 1 always refers to<br> the TBF launched in the Franck-Condon region of the excited state based on an initial condition<br> sampled from a ground state Wigner distribution. </p> <p>Description of the folders and subsequent files in each IC folder:</p> <p>Simulation_data <br> X-YYYY : X is the isomer and YYYY is the initial condition number<br> "Positions.x.xyz" : Files containing the geometries of each TBF in cartesian coordinates in Angstroms<br> at each time step. The "x" in the filename corresponds to the index of the TBF.<br> "Amp.x" : Files containing the TBF amplitudes for each timestep.<br> "Spawn.log" : File containing timing information about the spawning events.<br> "S.dat" : File containing coupling matrices between the TBFs for every time step.<br> "ext_x" : Folders containing extensions of TBFs on DFT level. Each folder contains a file<br> "coors.xyz" with cartesian coordinates in Angstroms at each time step. The<br> timestep size of the DFT trajectories is uniformly 0.5 femtoseconds. Only TBFs in<br> the groundstate are extended on DFT level. Therefore, there is no folder "ext_1".</p> <p>Simulation_Parameters : Parameters for FMS and TeraChem nonadiabatic dynamics <br> X-rotamer : x is isomer containing parameter files for all X rotamers<br> "c0.casscf" : Binary file with the alpha(0.82)-SA2-CAS(6,4)-SCF/6-31G* orbitals<br> "Geometry.dat" : Initial condition (position and momentum) to start the FMS/TeraChem nonadiabatic dynamics<br> "Control.dat" : Parameter file for running FMS<br> "misc_options" : Parameter file for running TeraChem <br> "DFT-tc.in" : TeraChem adiabatic dynamics on ground electronic state (ext_x)<br> </p>
Data and code to create figures of "Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time"
<p>Instruction of making Fig 4 in the main text:<br> 04/07/2023, SLAC, CA<br> Yusong (Liu), on behalf of Thomas (Wolf)</p> <p>1. Making Figure 1:<br> Figure 1 is fully vectorized with file 'Figure-1.svg', also saved in a png version, 'Figure-1.png'</p> <p>2. Making Figure 2:<br> The data plots in panels a and b are produced from a Matlab script: 'MakingFig2MainText.m'<br> This script loads data saved in 'TerpNatCommFig2.mat' and produce several files if using the saving condition:<br> 'PDFStaticTwoDelaysExpSim_22.fig'<br> 'PDFStaticTwoDelaysExpSim_22.png'<br> 'PDFStaticTwoDelaysExpSim_22.svg'<br> The final Figure 2, 'Figure-2.svg', then was assembled using 'PDFStaticTwoDelaysExpSim_22.svg' and 'Molskeleton.svg'.</p> <p>3. Making Figure 3:<br> The data plots in panels a, b, and c are produced from a Matlab script: 'MakingFig3MainText.m'<br> This script loads data saved in 'TerpNatCommFig3.mat' and produce several files if using the saving condition:<br> 'Fig3PDFFalseCMapLineOutExpSim_V10.fig'<br> 'Fig3PDFFalseCMapLineOutExpSim_V10.png'<br> 'Fig3PDFFalseCMapLineOutExpSim_V10.svg'<br> The final Figure 3, 'Figure-3.svg', then was assembled using 'Fig3PDFFalseCMapLineOutExpSim_V10.svg' and 'MolCartoonsFig3.svg'.</p> <p>4. Making Figure 4:<br> (1). Drawing the signal in Fig. 4 panel a<br> Fig. 4a was generated from a py script: 'MakingFig4aMainText.ipynb'<br> Run this script and it will load the data set 'MainFig4aData.npy'generate a figure showing Fig. 4a.<br> Change the figure saving condition to decide whether or not save the figure to both .svg and .png files as below:<br> 'Figure-4a.png'<br> 'Figure-4a.svg'<br> (2). Drawing the signals in Fig. 4 panels b and c<br> These two panels, the signals are drew from a Matlab script: 'MakingFig4bcMainText.m'<br> Run this script and it will load data set 'TerpNatCommFig4.mat' and plot panels b and c<br> Change the figure saving conditions to decide whether or not save to both .svg and .png files as below:<br> 'Fig4DataPanelsbc_v11.fig'<br> 'Fig4DataPanelsbc_v11.png'<br> 'Fig4DataPanelsbc_v11.svg'<br> (3). Fig 4 is then assembled with the 3 data plot panels, molecular cartoons, and equations:<br> Data plot panels:<br> 'Figure-4a.svg'<br> 'Fig4DataPanelsbc_v11.svg'<br> Molecular cartoons:<br> 'Fig4aCartoon.svg' 'Fig4bCartoon.svg' 'Fig4cCartoon.svg'<br> And equations:<br> 'Fig4bEquPhi.svg' 'Fig4cEquPsi.svg'<br> Fig 4 is fully vectorized with file: 'Figure-4.svg' and also saved as a .png version 'Figure-4.png'</p> <p>5. Making Figure-5:<br> The whole Fig. 5 is produced from a single .py script: 'MakingFig5MainText.ipynb'<br> Run the script and it will plot Figure-5. If choosing the save conditions, then it will save Figure-5 to 'Figure-5.svg' and 'Figure-5.png'.</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.