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10,561 results for “mechanics”
Artifacts for Keyword Extraction From Specification Documents for Planning Security Mechanisms
<p>This dataset contains the data used for evaluating VDocScan - a keyword extraction based security vulnerability prediction method. The repository includes an extensive list of Products and Vulnerability reports from CVE, a custom created dataset mapping vulnerability reports to product documentations, as well as, intermediate results from the study such as decision trees rendered for each vulnerability, correlation matrix of vulnerabilities etc. </p>
Dataset for Charge collection efficiency, underlying recombination mechanisms, and the role of electrode distance of vented ionization chambers under ultra-high dose-per-pulse conditions
<p>Dataset for paper: Kranzer et al., <a href="https://www.sciencedirect.com/journal/physica-medica">Physica Medica</a> <a href="https://www.sciencedirect.com/journal/physica-medica/vol/104/suppl/C">Volume 104</a>, December 2022, Pages 10-17</p> <p><a href="https://doi.org/10.1016/j.ejmp.2022.10.021">https://doi.org/10.1016/j.ejmp.2022.10.021</a></p>
Supplementary Data for "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase"
<p>This dataset contains atomic coordinates of the molecular dynamics simulations described in "Substrate-Assisted Mechanism for the Degradation of N-glycans by a Gut Bacterial Mannoside Phosphorylase" by M. Alfonso-Prieto, I. Cuxart, G. Potocki-Véronèse, I. André and C. Rovira, published in ACS Catalysis (https://doi.org/10.1021/acscatal.3c00451). Further details on the setup of the simulations can be found in the Supplementary Information of the article. </p> <p>If you use this dataset, please cite this zenodo upload (https://doi.org/10.5281/zenodo.7704778), as well as the the original journal article (https://doi.org/10.1021/acscatal.3c00451). </p> <p>This dataset is organized in the following folders:</p> <p><strong>Snapshots_Figures_Main_Text.zip</strong>, that contains a README.txt file and:</p> <p><strong>- Figure_3</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP in complex with 3 different disaccharide molecules, Man-b-(1,4)-GlcNAc, Man-b-(1,4)-Glc and Man-b-(1,4)-Man.</p> <p><strong>- Figure_4</strong> contains representative structures (atomic coordinates) of the hexameric form of UhgbMP at the three minima observed along the reaction coordinate corresponding to phosphorolysis of the disaccharide Man-b-(1,4)-GlcNAc: Michaelis complex (MC), transition state (TS) and product (P) complex.</p> <p>Files in this dataset are in PDB format. For all structures, the solvation box (water and ions) has been stripped to reduce file size. See README.txt inside <a href="https://zenodo.org/api/files/f3836540-b7b6-4820-87b3-7fa5dff7840c/Snapshots_Figures_Main_Text.zip">Snapshots_Figures_Main_Text.zip </a>for more information.</p>
Binding site plasticity regulation of the FimH catch-bond mechanism: Molecular Dynamics dataset
<p>Dataset of Molecular Dynamics simulations and analysis scripts used in the article "Binding site plasticity regulation of the FimH catch-bond mechanism" [<a href="https://doi.org/10.1016/j.bpj.2023.05.029">paper</a>][<a href="https://doi.org/10.1101/2022.11.15.516604">bioRxiv</a>].</p> <p>Contains:</p> <ul> <li>Replica Exchange with Solute Scaling (REST2) simulations of the FimH protein lectin domain in its two main allosteric states (Associated and Separated), in presence and absence of its synthetic ligand heptyl α-ᴅ-mannose (input files and trajectories of the unscaled replicas)</li> <li>Replica Exchange Umbrella Sampling (REUS) simulations of the liganted systems along a collective variable (CV) describing binding site opening (input files and trajectories)</li> <li>REUS simulations in presence of a pulling force on the protein-ligand complex.</li> </ul> <p>See the article for more details.</p>
HyUSPRe Report & Data on 'New experimental data on reactions between H2 and well cement and effects on fluid flow and mechanical properties of well cement
<p>In this study, new experimental data is presented of the effects of H<sub>2</sub> exposure and cyclic loading on mechanical properties of oil well (class G) cement, relevant for underground hydrogen storage operations. Changes in mechanical properties (Young’s modulus, Poisson’s ratio and ultimate strength) have been analyzed using unconfined compressive strength (UCS) tests and confined cyclic loading tests on class G cement samples that were unreacted (cured for 3 days at 80°C) and exposed to lime-saturated brine and N<sub>2</sub> or H<sub>2</sub> for 1 and 2 months. Changes in cement mineralogy were analyzed by XRD analysis of the unreacted and exposed samples. The mechanical properties of elastic modulus and Poisson’s ratio are within the expected range of an oil well cement. Differences in Young’s modulus, Poisson’s ratio and ultimate strength are limited between unreacted, N<sub>2</sub>-exposed and H<sub>2</sub>-exposed samples, when comparing UCS tests or confined cyclic loading tests. Repeated UCS tests seem to indicate that the variation in Young’s modulus and ultimate strength increases after N<sub>2</sub> and H<sub>2</sub> exposure, but this observation needs to be confirmed in additional tests. During cyclic axial loading of confined cement samples, irreversible (plastic) deformation (compaction) occurs that affect static Young’s modulus. Also, effects of exceeding yield and failure strength on Young’s modulus are observed. Dynamic Young’s moduli and Poisson’s ratios derived from acoustic velocity measurements during confined cyclic tests show limited variation, in particular if static and dynamic Young’s modulus are compared. The mineralogical changes as identified using XRD analysis suggest minor changes between unexposed and H<sub>2</sub>- and N<sub>2</sub>-exposed samples, although XRD patterns indicate some minerals that could not be identified. The main conclusion is that effects of H<sub>2</sub> exposure and cyclic loading on mechanical properties and mineralogical changes of class G cement is limited compared to unreacted or N<sub>2</sub> exposed samples for the investigated conditions. There is no indication that changes in mechanical properties of cement are such that cement integrity of wells used for underground hydrogen storage will be significantly affected. It should be emphasized that this conclusion is based on experiments on one type of cement (class G) and a limited set of conditions. In particular, additional tests to assess the reproducibility of current results and tests on samples that were exposed longer to H<sub>2</sub> and N<sub>2</sub> are of interest. Detailed effects of changing properties for the durability and integrity of wells can be derived by performing a parameter sensitivity analysis with well integrity modelling for the range in mechanical properties measured in this study.</p>
An integrated approach including docking, MD simulations, and network analysis highlights the action mechanism of the cardiac hERG activator RPR260243
<p>500 ns MD trajectories of the hERG bound states (protein and ligand) used for the analyses discussed in the paper. There are three replica for each system. The trajectories can be visualized using molecular visualization programs such as Pymol or VMD uploading the PDB and the DCD file.</p> <p>The PDB and the topology files of the hERG bound state (protein, membrane, ions and ligand) are also included.</p> <p>An example of input file used for the production step of the dynamics has been provided (production_1.conf). </p>
Supplementary codes and datasets for "Wang tiles enable combinatorial design and robot-assisted manufacturing of modular mechanical metamaterials"
<p>This repository provides data and codes for manuscript “Wang tiles enable combinatorial design and robot-assisted manufacturing of modular mechanical metamaterials” by M. Doškář, M. Somr, R. Hlůžek, J. Havelka, J. Novák, and J. Zeman, published first as a preprint <a href="https://arxiv.org/abs/2305.09280">arXiv:2305.09280</a> at arXiv.org; see the actual description of the Zenodo entry for the latest reference.</p> <p>This repository contains:</p> <ol> <li>MATLAB and C++ source codes for combinatorial design and numerical analyses (folder <code>./numerics/</code>),</li> <li>experimental data (folder <code>./experiments/</code>),</li> <li>3D models of parts used in robotic-assembly (folder <code>./models/</code>),</li> <li>a control script for robotic assembly (folder <code>./robotics/</code>).</li> </ol> <p><strong>Numerics</strong></p> <p>All simulations were performed with an in-house MATLAB code, which extends the finite element toolbox for finite strain calculations accompanying the work of <a href="https://doi.org/10.1016/j.cma.2020.113333">van Bree, S. E. H. M., Rokoš, O., Peerlings, R. H. J., Doškář, M., & Geers, M. G. D. (2020). A Newton solver for micromorphic computational homogenization enabling multiscale buckling analysis of pattern-transforming metamaterials. Computer Methods in Applied Mechanics and Engineering, 372, 113333</a>. In particular, this snapshot corresponds to a cleaned-up version (excluding files unrelated to the publications) of commit <code>21cfc2e9</code>.</p> <p>The MATLAB codebase contains MEX files written in C++ to accelerate selected procedures. In order to run any code, these MEX files must be compiled first. We use CMake build automation, with the main <code>CMakeLists.txt</code> located in <code>./numerics/mex</code>.</p> <p>Combinatorial search was performed by the <code>RUN_modular_exploration.m</code> script; see definition of problems with the script. The results of the enumerations, stored in <code>./dat/exploration</code>, were analysed with <code>POST_modular_S_v3.m</code>, identifying layouts leading to the extreme (min/max) tilt angles.</p> <p>Comparison against experimental measurements was facilitated by a series of scripts <code>POST_DIC_{...}.m</code>. First, run <code>POST_DIC_step1_extract_points_in_mesh.m</code> to identify locations.mat. Next, post-process extensometer data with <code>POST_DIC_step2_merge_extensometer_data.m</code>, and use <code>POST_DIC_step3_impose_extracted_BC.m</code> to parse DIC results in a format suitable for imposing BC later in this script. Finally, comparison between experimental and computed displacements is provided by <code>POST_DIC_step4_modular_comparison_experiments.m</code>. (Note that the particular files need to be manually provided in the “Compute deformation process” part of <code>POST_DIC_step4_modular_comparison_experiments.m</code>.)</p> <p><strong>Experimental data</strong></p> <p>This folder contains data from (i) an unixaial tension test of a dogbone specimen (both from a MTS loading machine and DIC data) and (ii) two measurement sessions extracting the L-shape domain responses using DIC (<code>20_11_30 - Hluzek_Elka_newassemblyplan</code> and <code>21_04_12 - Hluzek_ Elka_quarters</code> with lower loading threshold). For post-processing, see the above-mentioned <code>POST_DIC_{...}.m</code> scripts. <code>*.mat</code> files present directly in <code>./experiments/</code> folder were obtained and are need by those scripts.</p> <p><strong>3D models</strong></p> <p>The folder contains geometrical models for individual parts needed for robot-assisted assembly of module molds for casting. This includes:</p> <ol> <li>a silo extension to store more tiles (file <code>silo_extension.stl</code>),</li> <li>formwork modules around the main structure for the purpose of casting silicone (file <code>tile_formwork.stl</code>),</li> <li>all types of tiles for the inside structure (file <code>tile_inside_types.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_1.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_2.stl</code>),</li> <li>a spacer shaped for YuMi base to ensure correct distance of the silo and build plate (file <code>yumi_base_3.stl</code>),</li> <li>connection for spacers (file <code>yumi_base_4.stl</code>),</li> <li>spacer holding a silo and the build plate (file <code>yumi_base_5.stl</code>),</li> <li>YuMi grippers with extensions to hold the tiles (file <code>grippers_extend.st</code>).</li> </ol> <p><strong>Robotics</strong></p> <p>The folder contains a single file with a script created in RobotStudio (RobotWare Version: 6.08.01.00, SmartGripper Version: 3.55.0000.00) to assemble the plan with YuMi IRB 14000-0.5/0.5 left hand.</p> <p><strong>Acknowledgement</strong></p> <p>The related research, experiments, and code development were supported by the <a href="https://gacr.cz/en/">Czech Science Foundation</a>, project No. 19-26143X.</p>
Friction extrusion processing of aluminum powders: microstructure homogeneity and mechanical properties
<p>This dataset contains the data from the publication</p> <p><strong>"Friction extrusion processing of aluminum powders: microstructure homogeneity and mechanical properties"</strong></p> <p> </p> <p> </p>
Catalytic Rules and Validation Results for "EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions"
<p>Dataset containing the "Rules of Enzyme Catalysis" as created during the development of EzMechanism and the validation results of the software. For more information see https://www.biorxiv.org/content/10.1101/2022.09.05.506575v1, and the M-CSA website in https://www.ebi.ac.uk/thornton-srv/m-csa/</p>
Model output from CAABA/MECCA study "Development of a multiphase chemical mechanism to improve secondary organic aerosol formation in CAABA/MECCA (version 4.7.0)"
<p>This dataset includes the main data obtained during the study "Development of a multiphase chemical mechanism to improve secondary organic aerosol formation in CAABA/MECCA (version 4.7.0)" (DOI:10.5194/gmd-2023-102). The updated model code can be found at zenodo.org (DOI:10.5281/zenodo.7944174). The data can be used to replicate the results shown in the manuscript. Contained are results produced by the updated CAABA/MECCA (version 4.7.0) and reference data from CAABA/MECCA version 4.5.5. In version 4.7.0, new biogenic and anthropogenic species are introduced to the model (limonene and long-chained alkanes) with refined multiphase chemistry, while new reaction pathways are added for existing compounds (isoprene, benzene and IEPOX). The output is generated to evaluate model results in terms of temperature- and NOx-dependency.</p>
Photoinduced Mechanical Cloaking of Diarylethene-Crosslinked Microgels
<p>Original data of the manuscript and supporting information sorted after Figures and respective panels.</p>
Dataset for Nanoscale Growth Mechanisms of Gypsum: Implications for Environmental Control of Crystal Habits
<p>This dataset collected here has been used in the paper "Nanoscale Growth Mechanisms of Gypsum: Implications for Environmental Control of Crystal Habits".</p> <p>The files are in .dat format and each one corresponds to the images indicated in the file name.</p>
Mechanism-Based Redesign of GAP to Activate Oncogenic Ras
<p>Additional material for Berta et al. <em>J. Am. Chem. Soc.</em> 2023, 145, 37, 20302–20310</p> <ul> <li>Paths: minimised structures corresponding to the the GTP hydrolysis mechanism.</li> <li>MD setup: equilibriated inputs for classical MD simulations for WT and mutant systems in CHARMM/NAMD format, set up for the charmm36m FF.</li> <li>NBO: outputs for Natrual Bonding Orbitals analysis carried out for TS and RS structures.</li> <li>GAP mutants: optimised TS and RS structures of the most promising designed GAP mutants.</li> </ul>
Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations"
<p>Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations", containing the most relevant simulation output trajectories ran with GROMACS 2021:</p> <p>1) apo simulations, including wildtype, Y28F, and H228A;<br> 2) holo simulations, including the two tested protonation states for the antibiotic;<br> 3) mutant simulations, including Y18F, H228A, E268Q, and E284Q.</p> <p>All folders contain the topology file (.top), restraint files (.itp), the initial coordinates file (.gro), and the coordinates after the first minimization (em1.gro). The output trajectories of all replicas (per system) have been concatenated in a single compressed file (.xtc).</p>
Scripts, models, and data for manuscript "On the Role of Stern- and Diffuse-Layer Polarization Mechanisms in Porous Media"
<p>This repository contains Matlab scripts, Comsol Multiphysics models, and numerical simulation data used to generate the plots in the manuscript</p> <p>Bücker, M., Flores Orozco, A., Undorf, S., and Kemna, A., 2019, <em>On the Role of Stern- and Diffuse-Layer Polarization Mechanisms in Porous Media</em>, submitted to JGR: Solid Earth.</p> <p>If you find this data useful in your own research, please cite this manuscript.</p>
Mechanisms influencing physically sequestered soil carbon in temperate restored grasslands in South Africa and North America
This dataset contains a measurement of physically protected carbon (microaggregate-within-macroaggregate C) and potential drivers of physically protected C accumulation during grassland restoration. The data were collected from three independent grassland restorations from agriculture in North America and South Africa. Northeast Kansas, USA data were collected in May 2013. Northeast Free State, RSA data were collected in September–November 2005. Southeast Nebraska, USA data were collected in October 2008–May 2008. Aggregate fractionations were performed by hierarchical wet sieving (Six et al 2000). Carbon and N quantification were done by flash combustion-gas chromatography. Microbial biomass C quantification was performed with chloroform fumigation-incubation (chloroform fumigation-extraction in the case of northeast Kansas). Phospholipid fatty acid biomass analysis was conducted using the methods of Bligh and Dyer (1959).
Probing the mechanisms by which sub-canopy evergreen shrubs inhibit tree seedling recruitment at the Coweeta Hydrologic Laboratory from 1999 to 2003
Two hundred 2x2 meter plots along transects and traversing 3 understory conditions; rhododendron, kalmia, open. Light conditions will be assessed for each plot and the extreme 50% will be used for experimentation. All plots will be planted to a combination of northern red oak, chestnut oak, red maple, and pitch pine. Inoculated (with mychorrizae) and non-inoculated seedlings will be planted in the plots. Relationships between performance and mychorrizal infection will be determined.
Machine Demonstration: mechanical weed control in soybeans
<p>This video was provided by the EU funded project Legumes Translated, which supports the production and use of grain legumes in Europe. On the project website <a href="https://www.youtube.com/redirect?v=Bm_5JluTpc0&event=video_description&redir_token=Sf_vP1RmyENuQtEbJbo_0YXcxpN8MTU3ODQxNTk2OUAxNTc4MzI5NTY5&q=https%3A%2F%2Fwww.legumestranslated.eu">https://www.legumestranslated.eu</a> you will find more information and practical guidelines on the production and use of grain legumes. More Info: «Mechanical weed control in organic soy cultivation - how and when to use which machine?» <a href="https://www.youtube.com/redirect?v=Bm_5JluTpc0&event=video_description&redir_token=Sf_vP1RmyENuQtEbJbo_0YXcxpN8MTU3ODQxNTk2OUAxNTc4MzI5NTY5&q=https%3A%2F%2Fwww.bioattualita.ch%2Fcoltura%2Fa">https://www.bioattualita.ch/coltura/a</a>... Weed control is one of the main factors of economic success in organic soybean production. This video presents the following machines for mechanical weed control: 1. Weeding between and in the rows MATER Macc Unica-F Einböck Chopstar Garford Robocrop Schmotzer 2. Machines working row-independent Treffler TS 620/3M Einböck Aerostar-Rotation Carre Rotanet</p>
Proteomic analysis reveals different molecular mechanisms to face water deficit in mycorrhizal and nonmycorrhizal sorghum plants
<p>Differential accumulated proteins in response to water deficit in mycorrhizal and nonmycorrhizal sorghum plants were recovered from 2D gels and identified by HPLC-MSMS. MS analysis was performed by a Nano acquity nanoflow LC system (Waters, Milford, MA, USA) coupled to a linear ion trap (LTQ) velos mass spectrometer (Thermo Fisher Scientific, Bremen, Germany) equipped with a nanoelectrospray ion source.</p>
Supplementary data: Computational analysis of mechanical stress in colonic diverticulosis
<p>The data set contains code, source data, and derivatives data for the results presented in our research paper titled "Computational analysis of mechanical stress in colonic diverticulosis".</p> <p>The "code" contains Abaqus (SIMULIA, Providence, RI) files for the simulations presented in the paper (tested with Abaqus version 6.13) and jupyter notebooks developed to analyze simulation results.</p> <p>The "sourcedata" folder contains Excel files with parameters used for the simulations as well as data directly extracted from the simulation results.</p> <p>The "derivatives" folder contains secondary data calculated based on the files from "sourcedata".</p> <p>The README document included in the dataset contains a more detailed description of the files and folders.</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.