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2,208 results for “coupling”
Data for Transient 2D IR spectroscopy and multiscale simulations reveal vibrational couplings in the Cyanobacteriochrome Slr1393-g3
<p>Data used in the Manuscript Transient 2D IR spectroscopy and multiscale simulations reveal vibrational couplings in the Cyanobacteriochrome Slr1393-g3</p>
Data underlying the article: 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors
<p>This repository contains the datasets and results supporting the conclusions of the manuscript "<strong>3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors</strong>". </p> <p>Publicly available data is not included in this repository. The source code to generate the results gathered here can be found on GitHub (https://github.com/CDDLeiden/3ddpd). </p>
Dataset for Strong electron-phonon coupling and bipolarons in Sb2S3
<p>VASP ground state relaxed unit cell structure for Sb2S3 at HSE06 and optB86b level. Relaxed electron and hole bipolaron supercell structures using HSE06. VASP input files needed to relax a perturbed supercell to obtained the electron and hole bipolaron.</p>
PALM Model System v 6.0 input and configuration files for coupled large eddy simulations of land surface heterogeneity effects and diurnal evolution of late summer and early autumn atmospheric boundary layers during the CHEESEHEAD19 field campaign
<p>Namelist, configuration and forcing files for the PALM Model System 6.0 revision number 21.10-rc.2 used for the numerical simulations Coupled Large Eddy Simulations of land surface heterogeneity induced atmospheric boundary layer response during the CHEESEHEAD19 field campaign.</p>
Dataset: Formulation and Implementation of Frequency-Dependent Linear Response Properties with Relativistic Coupled Cluster Theory for GPU-accelerated Computer Architectures
<p>This dataset collects the data (outputs, coordinate files) for the calculations presented in the manuscript "Formulation and Implementation of Frequency-Dependent Linear Response Properties with Relativistic Coupled<br> Cluster Theory for GPU-accelerated Computer Architectures".</p>
Over-coupled resonator for broadband surface enhanced infrared absorption (SEIRA)
<p>This repository contains all datasets and MATLAB codes used in the paper "Over-coupled resonator for broadband surface enhanced infrared absorption (SEIRA)"</p> <p>3 folders can be found</p> <ul> <li>BMM contains a main python script that reproduces the electromagnetic computations of the article</li> <li>CMT : contains 3 scripts <ul> <li><strong>Absorption2D.m</strong> computes a 2D map of the absorption from the resonator from eq.1 of the main text as a function of f and (ω − ωr )/γnr .</li> <li><strong>DeltaRm.m</strong> plots the analytical expression of Delta Rm computed in the SI as a function of f.</li> <li><strong>DRanalytics.m</strong> plots the reflexion with the absorber as a function of omega. The expression is derived from the coupled mode formalism as described in the supplemental information.</li> </ul> </li> <li>Data_exp: contains raw experimental datasets of the figures.</li> <li>over_coupling_package : contains scripts to reproduce the electromagnetic simulations presented in the paper</li> </ul> <p>===============================</p> <p>PAPER ABSTRACT:</p> <p>Detection of molecules is a key issue for many applications. Surface enhanced infrared absorption (SEIRA) uses arrays of resonant nanoantennas with good quality factors which can be used to locally enhance the illumination of molecules. The technique has proved to be an effective tool to detect small amount of material. However nanoresonators can detect molecules on a narrow bandwidth so that a set of resonators is necessary to identify a molecule fingerprint. Here, we introduce an alternative paradigm and use low quality factor resonators with large radiative losses (over-coupled resonators). The bandwidth enables to detect all absorption lines between 5 and 10 µm, reproducing the molecular absorption spectrum. Counterintuitively, despite a lower quality factor, the system sensitivity is improved and we report a reflectivity variation as large as one percent per nanometer of molecular layer of PMMA. This paves the way to specific identification of molecules. We illustrate the potential of the technique with the detection of the explosive precursor 2,4-dinitrotoluene (DNT). There is a fair agreement with electromagnetic simulations and we also introduce an analytic model of the SEIRA signal obtained in the over-coupling regime.</p>
Parasitoid–host eavesdropping reveals temperature coupling of preferences to communication signals without genetic coupling
<p>Receivers of acoustic communication signals evaluate signal features to identify conspecifics. Changes in the ambient temperature can alter these features, rendering species recognition a challenge. To maintain effective communication, temperature coupling—changes in receiver signal preferences that parallel temperature-induced changes in signal parameters—occurs among genetically coupled signallers and receivers. Whether eavesdroppers of communication signals exhibit temperature coupling is unknown. Here, we investigate if the parasitoid fly Ormia ochracea , an eavesdropper of cricket calling songs, exhibits song pulse rate preferences that are temperature coupled. We use a high-speed treadmill system to record walking phonotaxis at three ambient temperatures (21, 25, and 30°C) in response to songs that varied in pulse rates (20 to 90 pulses per second). Total walking distance, peak steering velocity, angular heading, and the phonotaxis performance index varied with song pulse rates and ambient temperature. The peak of phonotaxis performance index preference functions became broader and shifted to higher pulse rate values at higher temperatures. Temperature-related changes in cricket songs between 21 and 30°C did not drastically affect the ability of flies to recognize cricket calling songs. These results confirm that temperature coupling can occur in eavesdroppers that are not genetically coupled with signallers.</p>
Dataset: Frequency-Dependent Quadratic Response Properties and Two-photon Absorption from Relativistic Equation-of-Motion Coupled Cluster Theory
<p>This dataset comprises outputs and post-processing results related to the paper "Frequency-Dependent Quadratic Response Properties and Two-photon Absorption from Relativistic Equation-of-Motion Coupled Cluster Theory", by Xiang Yuan, Loic Halbert, Lucas Visscher and Andre Severo Pereira Gomes.</p>
Supplementary material for 3D Acoustic-Elastic Coupling with Gravity: The Dynamics of the 2018 Palu, Sulawesi Earthquake and Tsunami
<p>This repository contains the supplementary files for our SC21 submission: "3D Acoustic-Elastic Coupling with Gravity: The Dynamics of the 2018 Palu, Sulawesi Earthquake and Tsunami".</p> <p>It contains the input data for all simulations. For more details, please refer to the included README.md files.</p> <p> </p> <p>The directory "seissol-sc21-revision-source-code" contains the version of SeisSol that we used.</p> <p> </p>
Inductively coupled plasma mass spectrometry of ions released from the coating into LB and DMEM medium
<p>several coatings from the ternary alloy of Zr-Cu-Ag metallic glasses (fabricated by PVD magnetron co-sputtering) were tested by the mass spectroscopy to evaluate their ion release in LB and DMEM. LB is the common medium for bacterial culture while DMEM is common for cells. coated samples have the name SP in them, while the non-coated one is PBT. They were in orbital shaker at 37˚C, 120 rpm for 1 day, 3 days and 7 days. </p>
Data for The importance of cloud phase when assessing surface melting in an offline coupled firn model over Ross Ice shelf, West Antarctica
<p>This is the data used in the paper "The importance of cloud phase when assessing surface melting in an offline coupled firn model over Ross Ice shelf, West Antarctica"</p>
Insights on the coupling between vibronically active molecular vibrations and lattice phonons in molecular nanomagnets
<p>Spin–lattice relaxation is a key open problem to understand the spin dynamics of single-molecule magnets and molecular spin qubits. While modelling the coupling between spin states and local vibrations allows to determine the more relevant molecular vibrations for spin relaxation, this is not sufficient to explain how energy is dissipated towards the thermal bath. Herein, we employ a simple and efficient model to examine the coupling of local vibrational modes with long-wavelength longitudinal and transverse phonons in the clock-like spin qubit [Ho(W<sub>5</sub>O<sub>18</sub>)<sub>2</sub>]<sup>9−</sup>. We find that in crystals of this polyoxometalate the vibrational mode previously found to be vibronically active at low temperature does not couple significantly to lattice phonons. This means that further intramolecular energy transfer <em>via</em> anharmonic vibrations is necessary for spin relaxation in this system. Finally, we discuss implications for the spin–phonon coupling of [Ho(W<sub>5</sub>O<sub>18</sub>)<sub>2</sub>]<sup>9−</sup> deposited on a MgO (001) substrate, offering a simple methodology that can be extrapolated to estimate the effects on spin relaxation of different surfaces, including 2D materials.</p>
Simulation data of Schmidt et al., A three-dimensional finite element formulation coupling electrochemistry and solid mechanics on resolved microstructures of all-solid-state lithium-ion batteries, DOI: https://doi.org/10.1016/j.cma.2023.116468
<p>This data set includes the simulation results of the relevant simulations published in the paper: "Schmidt et al., A three-dimensional finite element formulation coupling electrochemistry and solid mechanics on resolved microstructures of all-solid-state lithium-ion batteries, DOI: https://doi.org/10.1016/j.cma.2023.116468".</p> <p>Please refer to the paper for the details of the model as well as the parameterization of the model for the respective simulations.</p> <p>The provided lzip archive is structured into separate folders, one per simulation. Each folder contains the output data and a short README.txt with further hints. For information on the compression algorithm and how to uncompress it lzip please refer to https://en.wikipedia.org/wiki/Lzip.</p>
Data for "Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis"
<p>Raw data associated with the publication "Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis". Data associated with individual figures and corresponding analyses are uploaded as separate tabs in the Excel file. Radecker_etal_NanoSIMS.zip contains the individual NanoSIMS images (names according to treatment). Radecker_etal_Chlorophyll_Fluorescence_Images.zip contains exemplary photographs of chlorophyll fluorescence of Aiptasia (names according to treatment).</p> <p> </p> <p> </p>
In silico data for: Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling
<p>Directory layout and description for deposited data, scripts, and results associated with</p> <p><strong>Folding correctors can restore CFTR post-translational folding landscape by allosteric domain-domain coupling</strong></p> <p>Naoto Soya, Haijin Xu, Ariel Roldan, Zhengrong Yang, Haoxin Ye, Fan Jiang, Aiswarya Premchandar, Guido Veit, Susan P.C. Cole, John Kappes, Tamas Hegedus, and Gergely L. Lukacs</p> <p> </p> <p>Two files are provided:</p> <ol> <li><strong>soya_md_trajectories.tar</strong> - This file contains the trajectories merged from the last part (450-500 ns) of the parallel simulations: md_450000_500000.xtc</li> <li><strong>soya_insilico_data.zip</strong> - This file contains all other deposited files including input data, scripts, results files.<br> The content of this file can be found below:</li> </ol> <p><strong>README.md </strong>- the content of this description</p> <p><strong>homo - Homology modeling</strong></p> <ul> <li>run*.py, myloopmodel.py, and mymodel.py files are separated for technical reasons, for running model-building in parallel mode</li> <li><strong>cftr-loop</strong> - Demonstrates the removal of the RI and seeling the break with loopmodeling</li> <li><strong>mrp1</strong> - Scripts and input files for human MRP1 homology modeling; the large unresolved loop in NBD1 was not modeled but sealed for MD; this required renumbering of the ouput</li> <li><strong>mrp6</strong> - Scripts, input, and output files for human MRP1 homology modeling; output: mrp6_human_closed.pdb; the selected CFTR and MRP1 models were the input for MD simulaitons; to see these energy minimized structures, please see the corresponding 'md' directory below.</li> </ul> <p><strong>md - Moldecular dynamics</strong></p> <ul> <li>The <strong>md_system_info.xlsx</strong> file contains the basic properties of simulation boxes</li> <li>MD parameter files: step6*.mdp for minimization and equilibration; step7_production.mdp for production run</li> <li>wordom.dat is the wordom configuration file</li> <li>cmap_mda.mp.py is a script for contact map calculation</li> <li><strong>cftr-*, mrp1-*</strong> <ul> <li>the simulation system generated by CHARMM-GUI: step5_charmm2gmx.pdb</li> <li>the output gro file of parallel simulations (the last state of the sysmtems): md_[1-6].gro</li> <li>! the trajectory merged from the last part (450-500 ns) of the parallel simulations: trajectories md_450000_500000.xtc are in a separte file (soya_md_trajectories.tar) with the same directory structure</li> <li>the merged trajectory contains only the SOLU; the corresponding structure file: prot.pdb</li> <li>index.ndx</li> </ul> </li> </ul> <p><strong>figures</strong></p> <ul> <li><strong>figure-3a</strong> <ul> <li>pdb files are the output of gmx rmsf</li> <li>pse file is saved visualization of the pdb files for PyMOL<br> </li> </ul> </li> <li><strong>figure-3c-s4b</strong> <ul> <li>You can run color_all.tcl in VMD to reproduce the network communities in structural context; this is dependent on the .pdb and .vmd files also deposited in this directory</li> <li>Network community members (residues) are listed in the Word files</li> <li>dri in file names and in scripts refers to 6ss<br> </li> </ul> </li> <li><strong>figure-s3a</strong> <ul> <li>tmd1_structures.pse contains the structures for PyMOL</li> <li>Please see the Source Data file for plotting RMSF</li> <li>Contact map data are in the tmd1_wt.npy and tmd1_r170g.npy file<br> </li> </ul> </li> <li><strong>figure-s3e</strong> <ul> <li>PyMOL pse files to visualise the dynamics of NBD1/2 structures<br> </li> </ul> </li> <li><strong>figure-s4a</strong> <ul> <li>Contains the calculated betweenness.txt files</li> <li>betweenness_plots.py for plotting</li> <li>wt_prot.pdb: required for plotting with resi thick-labels<br> </li> </ul> </li> <li><strong>figure-s5c</strong> <ul> <li>PyMOL pse files to visualise the dynamics of NBD1/2 structures<br> </li> </ul> </li> <li><strong>figure-s8d</strong> <ul> <li>Data for MRP1/ABCC1</li> <li>You can run color_all.tcl in VMD to reproduce the network communities in structural context; this is dependent on the .pdb and .vmd files also deposited in this directory</li> <li>Network community members (residues) are listed in the Word files</li> </ul> </li> </ul>
Solving Coupled Differential Equation Groups Using PINO-CDE (VTCD)
<p>Early version for this paper can be found at arXiv (<a href="https://doi.org/10.48550/arXiv.2210.00222">https://doi.org/10.48550/arXiv.2210.00222</a>).</p> <p>The paper conducts experiment on three different examples. This dataset contains necessary data to replicate results in the paper for the Vehicle-Track Coupled Dynamics (VTCD).</p> <p>Corresponding code and instructions can be found at Github (https://github.com/WenHaoDing/PINO-CDE.git).</p>
"I was on vacation in Mala, living in a self-catering holiday cottage, together with my girlfriend (we're together for 11 years now), recovering from a heavy workload in the second half of 2008. We were sitting outside, probably sipping a beer, when we heard the sound of bells approaching. Stepping on the stones that enclose the little forecourt of the cottage, we could just see the goat herd being driven by. Idashed for my R09 (recording equipment) to get that impression – but too slowly too late, it seemed, the herd had disappeared and with it the sound. When Iwas about to pack my R09 again the sound appeared to come back, so Idashed down the driveway, just in time to see the herd pass, and then Ifollowed it a couple of hundred meters, walking behind the herd, trying not to breathe or make stepping sounds, eventually, when dogs started barking and a car approached from behind, I stopped and let the goats go on, the car passes, honks ... and Icut the recording and walk back to the cottage." [Peter/ptroxler]13 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"I was on vacation in Mala, living in a self-catering holiday cottage, together with my girlfriend (we're together for 11 years now), recovering from a heavy workload in the second half of 2008. We were sitting outside, probably sipping a beer, when we heard the sound of bells approaching. Stepping on the stones that enclose the little forecourt of the cottage, we could just see the goat herd being driven by. Idashed for my R09 (recording equipment) to get that impression – but too slowly too late, it seemed, the herd had disappeared and with it the sound. When Iwas about to pack my R09 again the sound appeared to come back, so Idashed down the driveway, just in time to see the herd pass, and then Ifollowed it a couple of hundred meters, walking behind the herd, trying not to breathe or make stepping sounds, eventually, when dogs started barking and a car approached from behind, I stopped and let the goats go on, the car passes, honks ... and Icut the recording and walk back to the cottage." [Peter/ptroxler]13
Full-scale MBR coupled with PAC for the removal of 232 OMPs: operating conditions, conventional pollutants, concentration of OMPs, UHPLC-QTOF-MS analysis
<p>The spreadsheet contains data regarding the operation and performance of a full-scale MBR coupled with powdered activated carbon (PAC) added inside the reactor. This hybrid system is chosen to evaluate the removal of 232 organic micropollutants (OMPs) and the potential enhancement in the removal efficiencies with the addition of PAC at a concentration of 0.1 g/L and 0.2 g/L</p><ul><li>First worksheet contains minimum, maximum, and average concentrations of conventional pollutants (COD, BOD, SST, SSV, DOC, UV254, nitrogen compounds, phosphorous, <i>E. coli</i>) in the influent and effluent of the WWTP. Methodologies adopted are also reported.</li><li>Second worksheet reports the operating conditions of the full-scale MBR as well as information about the tubular UF membranes installed. Characteristics of the PAC purchased to perform the experiments regarding the removal of OMPs are also described.</li><li>Third worksheet reports minimum, maximum and average concentration of 232 OMPs in the influent and effluent during:<ol><li>The monitoring period considering only the MBR</li><li>The experimental periods where PAC is added and maintained at a concentration of 0.1g/L and 0.2g/L inside the MBR</li></ol></li><li>Fourth worksheet contains metadata regarding the UHPLC–QTOF–MS analysis performed to evaluate the occurrence of OMPs in the influent and effluent of the WWTP. Sampling, storage and sample preparation is described, followed to LC-ESI-tandem MS analysis. LOD and LOQ are reported.</li></ul>
Large mass hierarchies from strongly-coupled dynamics---Recombined data release
<p>This release contains data associated with the publication <a href="https://arxiv.org/abs/1605.04258">Large mass hierarchies from strongly-coupled dynamics</a> (<a href="https://doi.org/10.1007/JHEP06(2016)114">JHEP 06 (2016) 114</a>).</p> <p>Compared to <a href="https://doi.org/10.5281/zenodo.13128485">the raw data release</a>, it makes the following changes:</p> <ul> <li>The two CSV files present in <a href="https://doi.org/10.5281/zenodo.13128485">the raw data release</a> are combined, with a common column schema. Since not all data were retained from all steps of the original computation, some of these data have been recomputed.</li> <li>The lattice data plotted in Figs. 2 and 3 of <a href="https://doi.org/10.1007/JHEP06(2016)114">the paper</a> are also included, and plotted by the Mathematica notebook.</li> </ul> <p>It comprises five files:</p> <ul> <li><code>README.md</code>: containing this summary and further details of the contents of each file.</li> <li><code>su2_adjoint_lattice_data.csv</code>: the data for the points plotted in Figures 2 and 3 of <a href="https://doi.org/10.1007/JHEP06(2016)114">the paper</a>. Masses of the scalar and tensor glueball, extracted from Monte Carlo ensembles of SU(2) with adjoint fermions.</li> <li><code>sigmamodel.csv</code>: the data shown in Figures 4 and 5 of <a href="https://doi.org/10.1007/JHEP06(2016)114">the paper</a>. The mass of the composite spin-0 and spin-2 states, computed for , as a function of , normalised to the mass of the lightest scalar or tensor.</li> <li><code>DataRelease.nb</code>: A Mathematica notebook that will take the above three files and generate plots similar to thsoe shown in <a href="https://doi.org/10.1007/JHEP06(2016)114">the paper</a>. This has been tested using Mathematica 14.0.</li> <li><code>unify_lmh_2016.zip</code>: A Snakemake and Python workflow to take the data from <a href="https://doi.org/10.5281/zenodo.13128485">the raw data release</a>, some data released as part of <a href="https://doi.org/10.5281/zenodo.12802810">the analysis workflow for arXiv:2408.00171</a>, and some previously unpublished data included in the archive, and generate the two CSV files above. Includes a <code>README.md</code> file containing more information about how to run the workflow.</li> </ul>
A Couple Support Intervention for Prostate Cancer
ClinicalTrials.gov study NCT01842438. IPD Sharing: NO. Countries: 1. Publications: 1.
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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.