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26 results for “interaction energies”
Adsorption free energies and potentials of mean-force for interactions between amino acids, lipid fragments, and nanoparticles
<p>This dataset contains tabulated potentials of mean force (PMFs) and associated adsorption (binding) free energies for interactions of amino acids side chain analogues and lipid fragments (LF) with a range of materials: titanium dioxide, iron oxide, amorphous silica, quartz, and a range of carbon-based materials including amorphous carbon, graphene and carbon nanotubes both in a pristine form and functionalized by certain chemical groups. All data were computed from atomistic molecular dynamics simulations as a part of the SmartNanoTox project 2016-2020. Version 2 of the dataset includes additional materials: zink oxide, zink sulfate in pristine and PMMA-coated forms computed within NanoSolveIt project (2019-2023). The data are intended to be used in coarse-grained models describing interactions of nanomaterials with nanoparticles, for the prediction of the binding affinity of proteins and lipids to nanoparticles, and as biological "fingerprints" of nanomaterials characterizing behavior of the nanomaterials in biological environments. </p>
Mining API Interactions to Analyze SoftwareRevisions for the Evolution of Energy Consumption (MSR'2021 Dataset)
<p><strong>Motivation</strong></p> <p>This repository contains the data-set used as a basis for our MSR'2021 paper <em>Mining API Interactions to Analyze Software Revisions for the Evolution of Energy Consumption</em>.</p> <p><strong>Description of the dataset</strong></p> <p>The dataset is stored in a file <em>msr_2021_dataset.csv</em> and contains the following data:</p> <ul> <li>id - an individual identifier</li> <li>sampleNr - a number identifying the group this sample relates to</li> <li>name - the name of the library examined</li> <li>className - the class name as an abbreviation</li> <li>method - the name of the executed method</li> <li>duration - duration of method execution</li> <li>durationAdjusted - duration after alignment between method trace and energy profile</li> <li>energyConsumption - computed energy consumption</li> <li>watts - recorded wattage</li> <li>`package-names` - per package uAPI profile</li> <li>uApi - the computed uAPI profile value</li> </ul> <p>The files <em>joule_anova_posthoc_result.csv</em> and <em>uAPI_anova_posthoc_result.csv</em> contain the results of the ANOVA and Tukey HSD posthoc analysis to determine accuracy and F1-score of the presented approach.</p> <p> </p> <p><strong>License</strong></p> <p>Creative Commons CC-BY</p>
PhytoNodes for Environmental Monitoring: Stimulus Classification based on Natural Plant Signals in an Interactive Energy-efficient Bio-hybrid System
<p>Cities worldwide are growing, putting bigger populations at risk due to urban pollution. Environmental monitoring is essential and requires a major paradigm shift. We need green and inexpensive means of measuring at high sensor densities and with high user acceptance. We propose using phytosensing: using natural living plants as sensors. In plant experiments we gather electrophysiological data with sensor nodes. We expose the plant <em>Zamioculcas zamiifolia</em> to five different stimuli: wind, temperature, blue light, red light, or no stimulus. Using that data we train ten different types of artificial neural networks to classify measured time series according to the respective stimulus. We achieve good accuracy and succeed in running trained classifying artificial neural networks online on the microcontroller of our small energy-efficient sensor node. To indicate later possible use cases, we showcase the system by sending a notification to a smartphone application once our continuous signal analysis detects a given stimulus.</p> <p> </p> <p>Data repository for our paper "PhytoNodes for Environmental Monitoring: Stimulus Classification based on<br> Natural Plant Signals in an Interactive Energy-efficient Bio-hybrid System", submitted to the GoodIT conference. Please refer to the paper for more information.</p> <p> </p> <p><strong>Contents of this repository</strong></p> <ul> <li><em>mu_interface:</em> Code for our data collection plant experiments, based on Raspberry Pis and the <a href="http://cybertronica.co/?q=products/phytosensor">Cybertronica phytosensing and phytoactuating system</a>.</li> <li><em>raw_data: </em>The datasets from our plant experiments for the stimuli wind, temperature, red light, blue light, and no stimulus.</li> <li><em>dl-4-tsc:</em> Deep learning framework developed by <a href="https://doi.org/10.1007/s10618-019-00619-1">Fawaz et. al (Deep learning for time series classification: a review)</a> and adapted to our use case. Find the training and testing datasets in the archives folder as well as the trained classifiers in the results folder.</li> <li><em>classification_results.ods: </em>Overview of the results from the deep learning framework (accuracy, precision, recall, training time).</li> <li><em>TFLite_Models: </em>The trained classifiers in TensorFlow Lite Format.</li> <li><em>00_AI_BLE_MeasuringOnlyWind: </em>Source code for classification on STM-based PhytoNodes (using MCDCNN two-class classifier) and Bluetooth communication. The code is written for the STM32WB55 Nucleo board and can be transferred to the dongle.</li> <li><em>zavrsniProjekt_iOS: </em>Source code of the iOS app used to receive data from the STM-based PhytoNodes.</li> <li><em>Watchplant_application_documentation.pdf: </em>Instructions to build and use the iOS app.</li> </ul>
Data Set For Efficient Calculation of Dispersion Energy for Multireference Systems with Cholesky Decomposition. Application to Excited-state Interactions
<p>Data Set to Accompany:</p> <p>"Efficient Calculation of Dispersion Energy for Multireference Systems with Cholesky Decomposition. Application to Excited-state Interactions"</p>
Plane waves versus correlation-consistent basis sets: A comparison of MP2 non-covalent interaction energies in the complete basis set limit
<p>Supporting data and analysis scripts for the work</p> <p><a href="https://doi.org/10.26434/chemrxiv-2023-203z9">Plane waves versus correlation-consistent basis sets: A comparison of MP2 non-covalent interaction energies in the complete basis set limit</a></p>
Hotspots in the grid: Avian sensitivity and vulnerability to collision risk from energy infrastructure interactions in Europe and North Africa
<p>Wind turbines and power lines can cause bird mortality due to collision or electrocution. The biodiversity impacts of energy infrastructure (EI) can be minimised through effective landscape-scale planning and mitigation. The identification of high-vulnerability areas is urgently needed to assess potential cumulative impacts of EI while supporting the transition to zero-carbon energy.</p> <p>We collected GPS location data from 1,454 birds from 27 species susceptible to collision within Europe and North Africa and identified areas where tracked birds are most at risk of colliding with existing EI. Sensitivity to EI development was estimated for wind turbines and power lines by calculating the proportion of GPS flight locations at heights where birds were at risk of collision and accounting for species' specific susceptibility to collision. We mapped the maximum collision sensitivity value obtained across all species, in each 5x5 km grid cell, across Europe and North Africa. Vulnerability to collision was obtained by overlaying the sensitivity surfaces with density of wind turbines and transmission power lines.</p> <p>Results: Exposure to risk varied across the 27 species, with some species flying consistently at heights where they risk collision. For areas with sufficient tracking data within Europe and North Africa, 13.6% of the area was classified as high sensitivity to wind turbines and 9.4% was classified as high sensitivity to transmission power lines. Sensitive areas were concentrated within important migratory corridors and along coastlines. Hotspots of vulnerability to collision with wind turbines and transmission power lines (2018 data) were scattered across the study region with highest concentrations occurring in central Europe, near the strait of Gibraltar and the Bosporus in Turkey.</p> <p>Synthesis and Applications: We identify the areas of Europe and North Africa that are most sensitive for the specific populations of birds for which sufficient GPS tracking data at high spatial resolution were available. We also map vulnerability hotspots where mitigation at existing EI should be prioritised to reduce collision risks. As tracking data availability improves our method could be applied to more species and areas to help reduce bird-EI conflicts.</p>
Data release for the paper "Measurements of protons and charged pions emitted from the $\nu_{\mu}$ charged-current interactions on iron at a mean neutrino energy of 1.49 GeV using a nuclear emulsion detector"
<p>This data release is associated with the paper "Measurements of protons and charged pions emitted from the <span class="math-tex">\(\nu_{\mu}\)</span> charged-current interactions on iron at a mean neutrino energy of 1.49 GeV using a nuclear emulsion detector". It is currently available on <a href="http://arxiv.org/abs/2203.08367">arXiv:2203.08367</a> and to be submitted to Phys. Rev. D.</p> <p><strong>When citing this data release, please cite as well the paper.</strong></p> <p>The provided zip file contains the data as below.</p> <ol> <li>event.root: Event by event information of 183 iron-target interactions.</li> <li>plot.root: Plot information as shown in the paper.</li> <li>detector_efficiency.root: Detectrion efficiencies for muons, charged pions, and protons.</li> <li>momentum_resolution.root: Relation between true and reconstructed momentum for muons, charged pions, and protons.</li> <li>misPID.root: Mis-PID rates of protons and pions.</li> <li>syscov.root: Covariance matrices of systematic uncertainties.</li> <li>flux.root: The neutrino flux and the covariance matrix of the flux error.</li> </ol> <p>The zip file also contains a README.pdf file with detailed information on the included files. Please read it.</p>
Data release for the "First measurement of muon neutrino charged-current interactions on hydrocarbon without pions in the final state using multiple detectors with correlated energy spectra at T2K"
<p>### On-/Off-Axis Data Release<br>#### (Version 1.0.1, dated 2024/08/12)</p> <p>This tar archive contains the data release for ‘First measurement of muon neutrino charged-current interactions on hydrocarbon without pions in the final state using multiple detectors with correlated energy spectra at T2K’. It contains the cross-section data points and supporting information in ROOT and text format, which are detailed below:</p> <p>+ `onoffaxis_xsec_data.root`<br>This ROOT file contains the extracted cross section and the nominal MC prediction as TH1D histograms for both the flattened 1D array of bins and in the angle binning for the analysis. The ROOT file also contains both the covariance and inverted covariance matrix for the result stored as TH2D histograms. The angle bin numbering and the corresponding bin edges are detailed at the end of the README.</p> <p>+ `flux_analysis.root`<br>This ROOT file contains the nominal and post-fit flux histograms for ND280 and INGRID. Two different binnings are included: a fine binned histogram (220 bins) and a coarse binned histogram (20 bins). The coarse binned histogram corresponds to the flux parameters detailed in the paper (and bin edges listed in the appendix).</p> <p>+ `xsec_data_mc.csv`<br>The extracted cross-section data points and the nominal MC prediction for each bin is stored as a comma-separated value (CSV) file with header row.</p> <p>+ `cov_matrix.csv` and `inv_matrix.csv`<br>The covariance matrix and the inverted covariance matrix are both stored as CSV files with each row stored as a single line and columns separated by commas (there is no header row). Matrix element (0,0) corresponds to the first number in the file.</p> <p>+ `nd280_analysis_binning.csv` and `ingrid_analysis_binning.csv`<br>The analysis bin edges are included as CSV files. The columns are labeled with a header row and denote the linear bin index and the lower and upper bin edge for the angle and momentum bins. The units are in cos(angle) for the angle bins and in MeV/c for the momentum bins.</p> <p>+ `calc_chisq.cxx`<br>This is an example ROOT script to calculate the chi-square between the data and the nominal MC prediction using the ROOT file in the data release. To run, open ROOT and load the script (`.L calc_chisq.cxx`) and execute the function `calc_chisq("/path/to/file.root")`.</p> <p>+ `calc_chisq.py`<br>This is an example Python script to calculate the chi-square between the data and the nominal MC prediction using the text/CSV files in the data release. The code requires NumPy as an external dependency, but otherwise uses built-in modules. To run, execute using a Python3 interpreter and give the file paths to the data/MC text file and the inverse covariance text file as the first and second arguments respectively -- e.g. `python3 calc_chisq.py /path/to/xsec_data_mc.csv /path/to/inv_matrix.csv`</p> <p>+ ND280 angle bin numbering<br> - 0: `-1.0 < cos(#theta) < 0.20`<br> - 1: `0.20 < cos(#theta) < 0.60`<br> - 2: `0.60 < cos(#theta) < 0.70`<br> - 3: `0.70 < cos(#theta) < 0.80`<br> - 4: `0.80 < cos(#theta) < 0.85`<br> - 5: `0.85 < cos(#theta) < 0.90`<br> - 6: `0.90 < cos(#theta) < 0.94`<br> - 7: `0.94 < cos(#theta) < 0.98`<br> - 8: `0.98 < cos(#theta) < 1.00`</p> <p>+ INGRID angle bin numbering<br> - 0: `0.50 < cos(#theta) < 0.82`<br> - 1: `0.82 < cos(#theta) < 0.94`<br> - 2: `0.94 < cos(#theta) < 1.00`<br> <br>### Changelog</p> <p>#### v1.0.1<br>Fix transcription error in INGRID momentum binning. The lowest momentum bin edge is at 350 MeV/c, not 300 MeV/c.</p>
Data Set "Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions"
<p>This data set accompanies the publication "Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions" by Johannes Vornweg and Christoph R. Jacob (TU Braunschweig, Germany) </p> <p>It contains the following files:</p> <p><br>Directory 1_structures:</p> <p> PDB files of all structures used for the test calculations. <br> The PDB files correspond to the protonated structures obtained <br> as described in the main text.</p> <p><br>Directory 02_figure_scripts:</p> <p> Jupyter Notebook for generating all plots included in the manuscript, <br> including raw numerical data.</p> <p><br>Directory 03_input_scripts:</p> <p> - min_congrad.mdp: input file for partial optimization of protonated <br> protein--ligand complexes with Gromacs</p> <p> PyADF input scripts:</p> <p> - sp_single.pyadf: single-point calculations of separate protein and ligand<br> - sp_complex.pyadf: single-point calculation of protein-ligand complex<br> - mfccmbe3.pyadf: MFCC and MFCC-MBE(2) calculations of P-L interaction energy</p> <p> These scripts can be used with PyADF v1.5 (DOI: 10.5281/zenodo.13236550)</p>
Pitch-angle and energy diffusion coefficients calculated for ions interacting with kinetic Alfven waves near the magnetopause
<p>In each file:<br> the first row (starting with the second column) contains pitch-angle grid in degrees<br> the first column (starting with the second row) contains the energy grid in keV<br> "x_to_L" value in the file name denotes the position in space along the normal to the magnetopause relative to the current sheet center (see description file).<br> energy diffusion coefficients are measured in keV^2/s, and pitch-angle coefficients are measured in rad^2/s.</p>
Analysis of Safety and Tissue Interaction of Injectable and Energy-based Biosmulators
ClinicalTrials.gov study NCT06993558. IPD Sharing: UNDECIDED. Countries: 1. Publications: 8.
Hotspots in the grid: Avian sensitivity and vulnerability to collision risk from energy infrastructure interactions in Europe and North Africa
Open the record for dataset details and reuse information.
High resolution, interactive, or animated versions of illustrations used in the paper "Quantifying the Dunkelflaute: An analysis of variable renewable energy droughts in Europe"
Open the record for dataset details and reuse information.
CoUDlabs_WP8_T811_UOS_001. Investigating geometrical effects on hydraulic energy losses during sewer to surface flow interactions during urban floods
<p>This document describes the dataset used in CO UD-labs JRA3 (WP 8) Task 8.1.1. This considers the hydraulic exchange (surcharge) from a piped drainage system to surface flood flow through a manhole. The dataset includes measurements of pressure, flow rate and depth from a physical scale model. The effect of changing the manhole lid properties on flow exchange (surcharge) and pressure in the experimental system is quantified over a range of flow rates. </p>
Molecular docking analysis was performed to assess the affinity of onalespib for their targets LOX, elucidating binding poses, protein interactions, and associated binding energies.
<p>To analyze the binding affinities and interaction modes between the drug candidates and their targets, we employed the Autodock Vina software [21]. Molecular structures of the candidate drugs and targets of hub genes were retrieved from Pubchem (https://pubchem.ncbi.nlm.nih.gov/) and Protein Data Bank database (http://www.rcsb.org/), respectively. <span>In the analysis of docking, the files for all proteins and molecules were converted to PDBQT format. Water molecules were removed and polar hydrogen atoms were added. The grid box was positioned at the center to encompass the protein domain, allowing for unrestricted movement of molecules.</span></p>
Reference and ESPF-DRF QM/MM data for bimolecular interaction energies
<p>Reference QM data and ESPF-DRF QM/MM (generated with PyESPF + PySCF https://github.com/tomfay/PyESPF ) interaction energy data for a set of test bimolecular systems.</p>
Results and plotting scripts for the manuscript 'SuCCESs – a global IAM for exploring the interactions between energy, materials, land-use and climate systems in long-term scenarios'
<p><br>This archives the results for the manuscript 'SuCCESs – a global IAM for exploring the interactions between energy, materials, land-use and climate systems in long-term scenarios'</p> <p>For the model version used to create these results, please see: https://doi.org/10.5281/zenodo.13981520</p> <p>Files to reproduce the figures, in R language:<br>SuCCESs validation.R - Reads GDX files and produces plots for energy and emissions.<br>SuCCESs validation MC.R - The same, but with the Monte Carlo GDXs.</p> <p>External data sources:</p> <p>***<br>GHG emissions are from IGCC and PRIMAP</p> <p>IGCC: https://climatechangetracker.org/igcc (CC-BY license)</p> <p>PRIMAP:<br>Gütschow, Johannes; Jeffery, M. Louise; Gieseke, Robert; Gebel, Ronja; Stevens, David; Krapp, Mario; Rocha, Marcia (2016): The PRIMAP-hist national historical emissions time series, Earth Syst. Sci. Data, 8, 571-603, https://doi.org/10.5194/essd-8-571-2016<br>Gütschow, Johannes ; Busch, Daniel ; Pflüger, Mika (2024): The PRIMAP-hist national historical emissions time series (1750-2023) v2.6. Zenodo. https://doi.org/10.5281/zenodo.13752654<br>https://primap.org/primap-hist/ (CC-BY-4.0 license)</p> <p>***<br>Historical energy production and use data are from IEA Energy Statistics Data Browser (CC BY 4.0 licence).<br>https://www.iea.org/data-and-statistics/data-tools/energy-statistics-data-browser?country=WORLD&fuel=CO2%20emissions&indicator=CO2BySource</p> <p>***<br>IAM results are from the SSP database: https://tntcat.iiasa.ac.at/SspDb </p> <p>Keywan Riahi, Detlef P. van Vuuren, Elmar Kriegler, Jae Edmonds, Brian C. O’Neill, Shinichiro Fujimori, Nico Bauer, Katherine Calvin, Rob Dellink, Oliver Fricko, Wolfgang Lutz, Alexander Popp, Jesus Crespo Cuaresma, Samir KC, Marian Leimbach, Leiwen Jiang, Tom Kram, Shilpa Rao, Johannes Emmerling, Kristie Ebi, Tomoko Hasegawa, Petr Havlík, Florian Humpenöder, Lara Aleluia Da Silva, Steve Smith, Elke Stehfest, Valentina Bosetti, Jiyong Eom, David Gernaat, Toshihiko Masui, Joeri Rogelj, Jessica Strefler, Laurent Drouet, Volker Krey, Gunnar Luderer, Mathijs Harmsen, Kiyoshi Takahashi, Lavinia Baumstark, Jonathan C. Doelman, Mikiko Kainuma, Zbigniew Klimont, Giacomo Marangoni, Hermann Lotze-Campen, Michael Obersteiner, Andrzej Tabeau, Massimo Tavoni.<br>The Shared Socioeconomic Pathways and their energy, land use, and greenhouse gas emissions implications: An overview, Global Environmental Change, Volume 42, Pages 153-168, 2017,<br>DOI:110.1016/j.gloenvcha.2016.05.009</p> <p>Rogelj, J., Popp, A., Calvin, K.V., Luderer, G., Emmerling, J., Gernaat, D., Fujimori, S., Strefler, J., Hasegawa, T., Marangoni, G., Krey, V., Kriegler, E., Riahi, K., van Vuuren, D.P., Doelman, J., Drouet, L., Edmonds, J., Fricko, O., Harmsen, M., Havlik, P., Humpenöder, F., Stehfest, E., Tavoni, M., Scenarios towards limiting global mean temperature increase below 1.5 °C. Nature Climate Change 8, 2018, 325-332.<br>DOI:10.1038/s41558-018-0091-3</p>
Membrane lipid metabolism, heat shock response, and energy costs mediate the interaction between acclimatization and heat hardening response
<p>Thermal plasticity on different timescales, including acclimation/acclimatization and heat hardening response – a rapid adjustment for thermal tolerance after a nonlethal thermal stress, can interact on organisms to improve the resilience to thermal stress. However, little is known about the physiological mechanisms mediating this interaction. To investigate underpinnings of heat hardening responses after acclimatization in warm season, we measured thermal tolerance plasticity, compared transcriptomic and metabolomic changes after heat hardening at 33 or 37<sup>o</sup>C followed by recovery of 3 h or 24 h in an intertidal bivalve <i>Sinonovacula constricta</i>. The clams showed explicit heat hardening responses after acclimatization in warm season. The higher inducing temperature (37<sup>o</sup>C) caused a less effective heat hardening effect than the inducing temperature that was closer to seasonal maximum temperature (33<sup>o</sup>C). Metabolomic analysis highlighted the elevated contents of membrane glyceropholipids in all heat hardened clams, which may help to maintain structure and function of membrane. Heat shock proteins (HSPs) tended to be up-regulated after heat hardening at 37<sup>o</sup>C but not at 33<sup>o</sup>C, indicating that there was no complete dependency of heat hardening effects on up-regulated HSPs. Enhanced energy metabolism and decreased energy reserves were observed after heat hardening at 37<sup>o</sup>C, suggesting more energy costs during exposure to higher inducing temperature which may restrict heat hardening effects. These results highlighted the mediating role of membrane lipid metabolism, heat shock responses and energy costs in the interaction of heat hardening response and seasonal acclimatization, and benefit the mechanistic understanding of evolutionary change and thermal plasticity during global climate change.</p>
Structure Databases: Analysis and Augmentation of Guest-Host Interaction Energy Models as CHA and AEI Zeolite Crystallization Phase Predictors
<p>Structures and energies associated with the paper: Analysis and Augmentation of Guest-Host Interaction Energy Models as CHA and AEI Zeolite Crystallization Phase Predictors</p>
Data for the study: "Variational principle to regularize machine-learned density functionals: the non-interacting kinetic-energy functional"
<p>This set of files contains the raw data generated by the study titled:</p> <p>"Variational principle to regularize machine-learned density functionals: the non-interacting kinetic-energy functional"</p> <p>Contains:</p> <p>- A set of Jupyter Notebooks to analyzed the data and produce the figures presented in the paper.</p> <p>- runs: Contains the training and validation scripts for each of the systems studied in this work. Also holds the model weights and validation data.</p> <p>Three folders are found: Hchain, noninteracting and Atoms.</p> <p>- datasets: Holds all the datasets generated and employed in this work.</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.