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50 results for “computational mechanics”
Computational Data Archive in Support of the Ping-Pong Mechanism for Peptide Bond Formation and Hydrolysis
<p>In search for the goldilocks zone in the chemical space for amino acid oligomerization that is relevant to the emergence of protein-based metabolism, we identified a significant gap in our understanding about how peptide bond is formed and hydrolyzed under ambient aqueous conditions. We identified a six-step mechanism that reproduces the experimentally known experimental barriers. By careful evaluation of a comprehensive set of levels of theory, modelling of solvation effect, and calculation of thermochemical parameters, we established a robust computational model to expand the bulk water focus to interfacial phenomena of atmospheric/hydrospheric and litospheric/hydrospheric boundaries. </p> <p>While we cannot travel back in time billions of years to witness the "birth" of the first macromolecule with pre-biotic relevance, we present the dataset and the corresponding publication in RSC Organic and Biomolecular Chemistry (July 26, 2023 issue) our attempt to establish an unbiased computational platform where we can evaluate experiments and generate experimentally testable ideas.</p>
Internal defect database of mechanically deformed ferritic steel via X-ray computed tomography
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Hydrate spatial distribution influence on the mechanical behavior hydrate-bearing sediment using computed tomography
<p>This supporting information includes two Movie S1-2, illustrating the deformation evolution of the specimen # O-1 and specimen # O-2.</p> <p>Movie S1 is uploaded with file name Movie S1.gif. Detailed information includes the deformation evolution of the specimen # O-1.</p> <p>Movie S2 is uploaded with file name Movie S2. gif. Detailed information includes the deformation evolution of the specimen # O-2.</p>
Noise study data for: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation
<p>This dataset contains noise study data used in the paper: Mechanisms of root-reinforcement in soils: an experimental methodology using four-dimensional X-ray computed tomography and digital volume correlation. These include raw CT scans and processed digital volume correlation data.</p> <p>This dataset is part of another dataset which covers other aspects of the paper DOI: <a href="http://www.doi.org/10.5281/zenodo.3352268">10.5281/zenodo.3352268</a></p> <p>The structure of the dataset is as follows:</p> <ul> <li>Noise study CT raw volumes are contained in a zip file. There are four raw files corresponding to the four noise study steps. These files are 8-bit unsigned, dimensions are 1800 x 1800 x 1400 pixels. A txt file giving more details to the data is included. <ul> <li><strong>CT_Raw_data_Noise_Scans.zip</strong></li> </ul> </li> <li>Metadata files generated for each scan given details of scan parameters are found in the zip file: <ul> <li><strong>CT_Scan_Metadata.zip</strong></li> </ul> </li> <li>Tabulated digital volume data for the noise study scans are contained in the zip file. Tabulated data for each subset size is included in subfolders. A .txt file explains the structure of the tab separated .dat files, i.e. what each column of data represents, and what CT scan each of the four .dat files relate to. <ul> <li><strong>DVC_Noise_Study_Data.zip</strong></li> </ul> </li> </ul> <p> </p> <p> </p>
input and TS ensemble for "Converging experimental and computational views of the knotting mechanism of the smallest knotted protein"
<p>PLUMED input and TS ensemble for "Converging experimental and computational views of the knotting mechanism of the smallest knotted protein"</p>
Pore-Opening and Ion-Conduction Mechanism in Channelrhodopsins C1C2, ChR2, and iChloC by Computational Electrophysiology and Constant-pH Simulations
<p>The simulation run input files, comprising the starting configuration and all necessary parameters for performing the<br>MD simulations.</p>
The input data of the multi-patch geometries used in: M. Kapl, A. Kosmač, V. Vitrih, Isogeometric collocation for solving the biharmonic equation over planar multi-patch domains, Computer Methods in Applied Mechanics and Engineering 424 (2024) 116882; DOI: 10.1016/j.cma.2024.116882
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Molecular dynamic trajectory for the article "The Binding Mechanism between Inositol Phosphate (InsP) and the Jasmonate Receptor Complex: A Computational Study"
<p>Molecular dynamic trajectory preparation file of Jasmonate receptor complex. We set up six systems. </p> <p>Each system contains PSF file and PDB file.</p>
Microscale Investigation of the Mechanical and Seepage Characteristics of Hydrate-bearing Sands by Computed Tomography
<p>This supporting information includes four movies S1-S4, providing animations of hydrate decomposition process and shear deformations in the main article.</p> <p> </p> <p>Movie S1 is uploaded with file name Movie S1. gif. Detailed information includes vertical-sectional view of a specimen during the decomposition process.</p> <p>Movie S2 is uploaded with file name Movie S2. gif. Detailed information includes longitudinal cross-sectional X-ray CT images of #T-1 specimen during shear deformation.</p> <p>Movie S3 is uploaded with file name Movie S3. gif. Detailed information includes longitudinal cross-sectional X-ray CT images of #T-2 specimen during shear deformation.</p> <p>Movie S4 is uploaded with file name Movie S5. gif. Detailed information includes longitudinal cross-sectional X-ray CT images of #T-3specimen during shear deformation.</p>
Input data for "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses"
<p>Topologies, coordinates, input and analysis scripts for Amber20 simulations performed in "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses", Structure, 2023</p>
Exploring the Mechanism of Plaque Rupture in Acute Coronary Syndrome Using Coronary CT Angiography and Computational Fluid Dynamics II (EMERALD II) Study
ClinicalTrials.gov study NCT03591328. IPD Sharing: UNDECIDED. Countries: 1. Publications: 21.
Exploring the MEchanism of Plaque Rupture in Acute Coronary Syndrome Using Coronary CT Angiography and computationaL Fluid Dynamic
ClinicalTrials.gov study NCT02374775. IPD Sharing: YES. Countries: 1. Publications: 1.
Weaning Children From Mechanical Ventilation:Computer-driven System Versus Usual Care
ClinicalTrials.gov study NCT00678912. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Integrated Computational modelIng of Right Heart Mechanics and Blood Flow Dynamics in Congenital Heart Disease
ClinicalTrials.gov study NCT03217240. IPD Sharing: UNDECIDED. Countries: 1. Publications: 15.
Data from: Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: an approximate Bayesian computation approach
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Supporting data for Formation of Highly Oxidized Molecules from NO3 Radical Oxidation of Δ-3-Carene: A Computational Mechanism
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Raw data on computational analysis the relationships of energy and mechanical properties with sensitivity for 1, 1-diamino-2, 2-dinitroethene based polymer bonded explosives
<p>The dataset provides raw data on key properties in the text as well as raw data on the temperature and energy balances of the P, P1, P2, P3 and P4 systems at room temperature. These data allow the results obtained in the article to be reproduced, while the reader can obtain the raw data for the plots not labeled with data in the article and thus quantify the exact magnitude of the changes shown in the plots. The main work of the article is: Molecular dynamics (MD) simulations have been applied to investigate 1, 1-diamino-2, 2-dinitroethene (FOX-7) crystal and FOX-7(011)-based polymer-bonded explosives (PBXs) with four typical polymers, polyethylene glycol (PEG), fluorine-polymer (F<sub>2603</sub>), ethylene-vinyl acetate copolymer (EVA) and ester urethane (ESTANE5703) under COMPASS force field. Binding energy (E<sub>bind</sub>), cohesive energy density (CED), initiation bond length distribution, radial distribution function, and isotropic mechanical properties of FOX-7 and its PBXs at different temperatures were reported for the first time, and the relationship between them and sensitivity. Using quantum chemistry, FOX-7 was optimized with the four polymers at the B3LYP/6-311++G(d,p) level, and the structure and RDG of the optimized composite system were analyzed.</p>
Screening and mechanism of novel angiotensin-I-converting enzyme inhibitory peptides in X. sorbifolium seed meal: A computer-assisted experimental study method
<p>本文档是补充材料</p>
Supporting Data for Manuscript "Unraveling Thermally Regulated Gating Mechanisms in TPT Pore-Partitioned MOF-74: A Computational Endeavor"
<p>This dataset contains the supplementary computational data associated with the research article titled "Unraveling Thermally Regulated Gating Mechanisms in TPT Pore-Partitioned MOF-74: A Computational Endeavor" (currnetly under review). It encompasses trajectory files and calculated properties of TPT-X ligands in various modeling scenarios, providing insights into their dynamic behavior within the MOF-74 framework under different conditions.</p>
Clinical Trial of a Computer-driven Weaning System for Patients Requiring Mechanical Ventilation
ClinicalTrials.gov study NCT00606554. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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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.