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1,026 results for “kinetics”
Correlation of the kinetics of viral antigen and genomic RNA with restoration of normal cell homeostasis
<p>The main objective of the studies within COCID Work Package 6 is to understand basic mechanisms by which viral replication machineries are removed from cells after pharmacological interruption of viral replication using functional as well as imaging techniques, including soft X-ray tomography.</p> <p>In this document, we highlight the progress in establishing the HCV replication models (replicons), the antiviral treatment chosen to eliminate viral structures from the host cells and the correlation between elimination of the viral replication machinery and restoration of a normal host cell homeostasis, using markers of HCV-induced stress. These data are essential to frame the experimental setup chosen for the imaging process required in subsequent stps of the project.</p>
Supplementary Material for Automated Kinetic Models to Predict the Flame Speeds of Halocarbons
<p>Supplementary material to accompany the paper "Automated Kinetic Models to Predict the Flame Speeds of Halocarbons" by Nora Khalil, Sevy Harris, Richard H. West, submitted to the 13th U. S. National Combustion Meeting, Organized by the Central States Section of the Combustion Institute, March 19–22, 2023, College Station, Texas.</p> <p>RMG input files.</p> <p> </p>
Topological kinetic crossover in a nanomagnet array
<p>Common explanations of equilibrium thermodynamics depend critically on ergodicity, i.e., the ability to explore all available states, but ergodic kinetics can be constrained by a system's topology. We report an experimental study of a model nanomagnetic array, in which such constraints visibly affect the behavior. In this system, magnetic excitations are connected in thermally active one-dimensional strings whose motion can be imaged in real-time. At high temperatures, the kinetics include the merging, breaking, and reconnecting of strings, resulting in the system transitioning between topologically distinct configurations. Below a crossover temperature, however, the string motion is dominated by simple changes in length and shape. In this low-temperature regime, the system is energetically stable because of the inability to explore the full set of possible topological configurations. This kinetic crossover suggests a generalizable conception of topologically broken ergodicity and limited equilibration.</p>
Calculation data for "Scattering of Radiation Belt Electrons by Fast Magnetosonic Waves: Considering the Kinetic Effects"
<p>Here are the calculation data for "Scattering of Radiation Belt Electrons by Fast Magnetosonic Waves: Considering the Kinetic Effects", using the format of ".mat". </p> <p>Term of "cold_plasma_dispersion_relation.mat" is the numerical results of cold plasma dispersion relation for MS waves;</p> <p>Term of "kinetic_dispersion_relation.mat" is the numerical results of kinetic dispersion relation for MS waves, using the WHAMP code by K. Rönnmark;</p> <p>Term of "Diffusion_coefficients_cold.mat" is the diffusion rates calculated based on the cold plasma dispersion relation;</p> <p>Term of "Diffusion_coefficients_kinetic.mat" is the diffusion rates calculated based on the kinetic dispersion relation;</p> <p>To be noted, the "D_{\alpha\alpha}_Bw2" in term "Diffusion_coefficients_kinetic.mat" is derived from the inferred wave magnetic field power spectral density.</p>
QM and COSMO-RS calculation results and experimental data for: Computing kinetic solvent effects and liquid phase rate constants using quantum chemistry and COSMO-RS methods
<p>This dataset contains the calculation results and the experimental data compiled from literature for the manuscript "Computing kinetic solvent effects and liquid phase rate constants using quantum chemistry and COSMO-RS methods". Citations should refer directly to the manuscript (Chung, Y.; Green, W. H. Computing kinetic solvent effects and liquid phase rate constants using quantum chemistry and COSMO-RS methods. <em>J. Phys. Chem. A</em> <strong>2023</strong>, 127, 27, 5637–5651. doi: <a href="https://doi.org/10.1021/acs.jpca.3c01825">10.1021/acs.jpca.3c01825</a>).This includes:</p> <ul> <li>expt_data_collected.xlsx: Experimental rate constants of various liquid phase reactions collected from various sources</li> <li>For each levels of theory used for gas-phase quantum chemical calculations and COSMO-RS calculations: <ul> <li>Gas-phase quantum chemical calculation results (output log files) and computed gas phase rate constants</li> <li>COSMO-RS calculation results and computed solvation free energies</li> <li>Predicted liquid phase rate constants and relative rate constants </li> </ul> </li> </ul> <p> </p>
Kinetic in support of "Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC"
<p>These are KinTek Explorer mechanism files containing the data and analysis described in the manuscript "Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC" (bioRxiv 2022.10.04.510889; doi: https://doi.org/10.1101/2022.10.04.510889). </p>
Spatiotemporally resolved transcriptomics reveals subcellular RNA kinetic landscape
<p>Spatiotemporal regulation of the cellular transcriptome is crucial for proper protein expression and cellular function. However, the intricate subcellular dynamics of RNA synthesis, decay, export, and translocation remain obscured due to the limitations of existing transcriptomics methods Here, we report a spatiotemporally resolved RNA mapping method (TEMPOmap) to uncover subcellular RNA profiles across time and space at the single-cell level in heterogeneous cell populations. TEMPOmap integrates pulse-chase metabolic labeling of the transcriptome with highly multiplexed three-dimensional (3D) in situ sequencing to simultaneously profile the age and location of individual RNA molecules. Using TEMPOmap, we constructed the subcellular RNA kinetic landscape of 991 genes in human HeLa cells from upstream transcription to downstream subcellular translocation. Clustering analysis of critical RNA kinetic parameters across single cells revealed kinetic gene clusters whose expression patterns were shaped by multistep kinetic sculpting. Importantly, these kinetic gene clusters are functionally segregated, suggesting that subcellular RNA kinetics are differentially regulated to serve molecular and cellular functions in a cell-cycle-dependent manner. We further demonstrated that functionally segregated RNA kinetics could be seen in heterogeneous human primary cell cultures, revealing cell-type-dependent RNA dynamic regulation. Together, these single-cell spatiotemporally resolved transcriptomics measurements provide us the gateway to uncovering new gene regulation principles and understanding how kinetic strategies enable precise RNA expression in time and space.</p> <p>Please use the most recent version of the dataset.</p>
Discrete and continuum simulations of bedload transport with kinetic theory of granular flow
<p>This depository contains the simulation results used in the publication Chassagne, R., Chauchat J. & Cyrille B. (2023). A frictional-collisional model for bedload transport based on kinetic theory of granular flows: discrete and continuum approaches.</p> <p>It contains DEM results as well as the results of the continuum model. The results are written in text files containing headers with name and units of the variables.</p>
Data for Coupling Covariance Matrix Adaptation with Continuum Modeling for Determination of Kinetic Parameters Associated with Electrochemical CO2 Reduction
<p>This data set contains digitized and tagged polarization and partial current density data for 18 datasets of CO<sub>2</sub> reduction to H<sub>2</sub> and CO over Ag catalysts, as well as 8 datasets of CO<sub>2</sub> reduction to HCOO<sup>-</sup>, CO, and H<sub>2</sub> over Sn catalysts. We analyze this data using a coupled continuum modeling and covariance matrix adaptation approach for which the codebase is provided in DOI: 10.5281/zenodo.7866195.</p>
Figure data for stochastic kinetics calculations of water autoionization in nanoscopic pools
<p>CSV files of data arrays used to construct figures shown in a submitted manuscript. V2 of the data set adds one new CSV. No other changes have been made.</p>
Dataset and fitting methods for Kinetic Proofreading can Enhance Single Nucleotide Discrimination in a Non-enzymatic DNA Strand Displacement Network
<p>This upload contains raw experimental data and the fitting methods used for the article "Kinetic Proofreading can Enhance Single Nucleotide Discrimination in a Non-enzymatic DNA Strand Displacement Network".</p>
Datasets for ``Electromagnetic conversion into kinetic and thermal energies''
<pre>This directory contains an index.html file with links to the run directories and idl plotting routines with secondary data for the other figures for the paper "Electromagnetic conversion into kinetic and thermal energies" by A. Brandenburg and N. Protiti. If anything turns out to be incomplete, please email brandenb@nordita.org. </pre>
Scripts and datas for "Global Estimation of the Eddy Kinetic Energy Dissipation from a Diagnostic Energy Balance"
<p>Input and output datasets used for a global reconstruction of the eddy kinetic energy (EKE) dissipation rate in relation to a submitted work :</p> <p><strong>R. Torres, R. Waldman, J. Mak and R. Séférian </strong>: <em>Global Estimation of the Eddy Kinetic Energy Dissipation from a Diagnostic Energy Balance</em>.</p> <p>Inputs datas include a merge of 2 datasets from the World Ocean Atlas 2018 (WOA18, Garcia et al., 2019) and cover the 1995-2017 (95B7) period. Folder structure for the surface altimetry L4 datasets from the EU-Copernicus Marine Services (2021) is kept empty in order to limit the archive size. Datas can be download <a href="https://data.marine.copernicus.eu/product/SEALEVEL_GLO_PHY_L4_MY_008_047/services">here</a>.</p> <p>Optional datasets include CMEMS MDT product (<em>CMEMS/SEALEVEL_GLO_PHY_MDT_008_063/P20Y</em>) downloaded <a href="https://data.marine.copernicus.eu/product/SEALEVEL_GLO_PHY_MDT_008_063/">here</a> and ocean masks (<em>misc/basins/doi_10.5281</em>) from Martinez-Moreno et al. (2021).</p> <p>In addition, simulation outputs from the NEMO-OMIP2 model runned with the GEOMETRIC parameterization are processed (mainly time-averaged) and stored in <em>CNRM/runs/omip2_LR.Geom_Emin0-alpha01_1cyc-trd/post</em>. These files are used in the uncertainties and errors quantification.</p> <p>Outputs and published results are stored in each individual product post-processing folder while final EKE dissipation computation are located in the <em>EKE_dissipation_rate</em> folder since it results from a combination of multiple products.</p> <p>IPython notebooks for computing and plotting global maps are also provided :</p> <ul> <li><em>1-post_process_climato.ipynb</em> : compute from the climatology (e.g. WOA18 datas) the EKE dissipation timescales (units in days) and the surface modes with rough topography (LaCasce and Groeskamp, 2020).</li> <li><em>2-post_process_altimetry.ipynb</em> : compute from altimetry (CMEMS) datasets the EKE at surface and eventually coarsen the grid from 0.25 to 1 degree in order to match the climatology grid.</li> <li><em>3-compute_global_eke_dissipation.ipynb</em> : combine both outputs from the two above scripts to compute the global EKE dissipation. The script also plots new maps.</li> <li><em>0-plot_global_maps.ipynb</em> : plot the global maps for climatology and altimetry products.</li> <li><em>0-plot_lbekedis_ogcm.ipynb</em> : plot and analyse EKE timescale errors from the NEMO-OMIP2 simulation outputs.</li> </ul> <p>Note however that these scripts use the author python library XOCE availbale on GitHub: https://github.com/torresr-cnrm/xoce. All the scripts have been runned using the version 0.2 of XOCE. Feel free to contact (romain.torres@meteo.fr) for any help in installing and using this library.</p>
Data for Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates
<p>Data and scripts for the preprint "Automatic Mechanism Generation Involving Kinetics of Surface Reactions with Bidentate Adsorbates".</p>
Mechanistic Drivers of Acute PAPE Responsiveness: Muscle Architecture, Contractile Kinetics, and Excitability in a Randomized Controlled Trial
ClinicalTrials.gov study NCT06982937. IPD Sharing: NO. Countries: 1. Publications: 1.
Organ kinetics measurements
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Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters
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Data from: Can IR images of the water surface be used to quantify the energy spectrum and the turbulent kinetic energy dissipation rate?
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Kinetic modules in biochemical networks/ Upstream Algorithm
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Catch bond kinetics are instrumental to cohesion of fire ant rafts under load
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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)
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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.