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83 results for “Kinetic modeling”
Lattice kinetic Monte Carlo model to simulate RNA polymerase II clusters during stem cell differentiation
<p>This data set includes Python scripts (numerical simulation and analysis) and already generated simulation data for RNA polymerase II clusters during stem cell differentiation. It includes the whole data to recreate panels.</p>
Dataset of paper "Removal of diclofenac by UV-B and UV-C light-emitting diodes (LEDs) driven advanced oxidation processes (AOPs): Wavelength dependence, kinetic modelling and energy consumption"
<p>Dataset of paper "Removal of diclofenac by UV-B and UV-C light-emitting diodes (LEDs) driven advanced oxidation processes (AOPs): Wavelength dependence, kinetic modelling and energy consumption"</p> <ul> <li>Molar absorption coefficient of the DCF (pH 7.2), FC (pH 8.5), and H<sub>2</sub>O<sub>2</sub> (pH 6.5) in the wavelength range of 200-400 nm. </li> <li>Time-based and UV fluence-based kinetic constant and synergy factor for the DCF degradation.</li> <li>Diclofenac degradation fitted by the proposed models (UV/H<sub>2</sub>O<sub>2</sub> and UV/FC).</li> <li>Oxidant degradation fitted by the proposed models (UV/H<sub>2</sub>O<sub>2</sub> and UV/FC).</li> </ul>
Dataset of paper "Evaluation of new photochemical systems for water disinfection by the integration of particle tracking into kinetic models for microbial inactivation"
<p>Dataset of paper "Evaluation of new photochemical systems for water disinfection by the integration of particle tracking into kinetic models for microbial inactivation":</p> <ul> <li>Results for the CFD model of the residence time distribution in the tubular reactor and E(t) curve for an ideal laminar.</li> <li>UV dosage histograms at the outlet surface for the tubular reactor illuminated with the four different LED configurations.</li> <li>Microbial inactivation histograms at the outlet surface for the tubular reactor illuminated with the four different LED configurations.</li> <li>Results for the CFD model of the residence time distribution in the annular reactor for different flow rates.</li> <li>UV dosage histograms at the outlet surface for the annular reactor for different flow rates.</li> <li>Microbial inactivation histograms at the outlet surface in the annular reactor for different flow rates.</li> </ul>
Kinetic Model Data: Effect of Calcium on the Bioavailability of Dissolved Uranium (VI) in Plant Roots under Circumneutral pH
We integrated field measurements, hydroponic experiments, microscopy, and spectroscopy to investigate the effect of Ca(II) on dissolved U(VI) uptake by plants in 1 mM HCO3 − solutions at circumneutral pH. The accumulation of U in plants (3.1−21.3 mg kg−1) from the stream bank of the Rio Paguate, Jackpile Mine, New Mexico served as a motivation for this study. Brassica juncea was the model plant used for the laboratory experiments conducted over a range of U (30−700 μg L−1) and Ca (0−240 mg L−1) concentrations. The initial U uptake followed pseudo-second-order kinetics. The initial U uptake rate (V0) ranged from 4.4 to 62 μg g−1 h−1 in experiments with no added Ca and from 0.73 to 2.07 μg g−1 h−1 in experiments with 12 mg L−1 Ca. No measurable U uptake over time was detected for experiments with 240 mg L−1 Ca. Ternary Ca−U−CO3 complexes may affect the decrease in U bioavailability observed in this study. Elemental X-ray mapping using scanning transmission electron microscopy−energy dispersive spectrometry detected U−P-bearing precipitates within root cell walls in water free of Ca. These results suggest that root interactions with Ca and carbonate in solution affect the bioavailability of U in plants. This study contributes relevant information to applications related to U transport and remediation of contaminated sites.
Open source physiological data and physiological-based kinetic model code for the chicken (Gallus gallus domesticus)
<p>This excel file and mode code (DOI:10.5281/zenodo.3603114) provides:</p> <p>1. Physiological parameters and associated inter-individual variability (sample size, mean, coefficient of variation,) for chicken (<em>Gallus gallus domesticus</em>). These physiological parameters were estimated based on the results of extensive literature searches and specific experimental data described in Lautz et al., (2020).</p> <p>2. An R code for the generic chicken physiologically based model as well as the “soboljansen” code to carry out sensitivity analysis using sobol plots. The code for the generic model allows to run:</p> <p>a. A deterministic PBK model which represents only a single animal.</p> <p>b. A probabilistic PBK model to simulate individual differences in physiological parameters within a population. Sensitivity analyses can be performed to identify which parameters have the most impact on the model’s outputs. Predictions can be compared with experimental data. The model can be used to assess the influence of physiological parameters on the kinetics of chemicals. For PBK modelling purposes, species and chemical specific kinetics (e.g clearance, absorption rate, etc…) should be provided by the user.</p> <p>The full data collection and implementation of the models using case studies are described in (Lautz et al., 2020).</p> <p><strong>The dataset providing the physiological parameters is available in Excel.<br> The R code is presented as meta data to be implemented in R.</strong></p>
Dataset - Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
<p>Models developed for the manuscript “Large-scale kinetic metabolic models of<em> Pseudomonas putida</em> for consistent design of metabolic engineering strategies" by M. Tokic, V. Hatzimanikatis, and L. Miskovic.</p> <ul> <li>Thermodynamically curated and gap-filled genome-scale model of <em>P. putida</em> iJN1411, iJN1411cur. <ul> <li>CuratediJN1411GEM.mat</li> </ul> </li> <li>Three systematically reduced stoichiometric models of <em>P. putida</em>: <ul> <li>D1 model, RedModelD1SminP2.mat</li> <li>D2 model, RedModelD2SminP2.mat - used for the studies performed in the manuscript</li> <li>D3 model, RedModelD3SminP2.mat</li> </ul> </li> </ul> <p> </p>
Data access - Operando characterization and theoretical modelling of metal|electrolyte interphase growth kinetics in solid-state-batteries - part I: experiments
<p>The zip file contains XPS and EIS data used in parts 1 and 2 of the publication entitled: "New insights into the kinetics of metal|electrolyte interphase growth in solid-state-batteries via an <em>operando</em> XPS analysis"</p> <p>Folders description: </p> <p>- "XPS" contains three subfolders with the XPS data and fitting models (in .vms format, CasaXPS) corresponding to the reference Na metal sample, the Na|NZSPas interface and Na|NZSPpolished interface</p> <p>- "EIS" contains two subfolders with the EIS data from the Na|NZSPas and Na|NZSPpolished symmetrical cells. The raw data is stored as .mpr files (EC-lab), and the fitted data is stored as .eis3 files (RelaxIS)</p>
Model data for " Topography Influence on Changes in Spatial Distribution of Eddy Kinetic Energy in the Southern Ocean"
<p>This dataset is for the paper " Topography influence on Changes in Spatial Distribution of Eddy Kinetic Energy in the Southern Ocean"</p>
Ammonia and ammonia/hydrogen combustion: Comprehensive quantitative assessment of kinetic models and examination of critical parameters
<p>This repository contains data on laminar burning velocity, ignition delay time, and species concentration measured in fundamental combustion experiments involving ammonia and ammonia/hydrogen mixtures. The data, compiled from literature sources, is used in the publication titled 'Ammonia and ammonia/hydrogen combustion: Comprehensive quantitative assessment of kinetic models and examination of critical parameters' in Combustion and Flame.</p>
Fig. 3 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments
Fig. 3. Deprotonated forms of CA under the physiological aqueous environment. The proton affinity (PA) values are in kcal/mol.
Fig. 6 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments
Fig. 6. Optimized structures of the TSs of CA + HOO• reaction in physiological environments (W = water and PE = pentyl ethanoate). Distances are in Aand angles in ◦.
Fig. 2 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments
Fig. 2. The stable conformation, HOMO, LUMO, and ESP of CA calculated at M06–2X/6–311++ G(d,p) level.
Fig. 4 in Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments
Fig. 4. Computed BDE values in kcal/mol of CA in the gas phase (G) and pentyl ethanoate (PE) as well as of CA– in water (W).
Key Factors Determining the Formation of Sulfate Aerosols through Multiphase Chemistry – A Kinetic Modeling Study based on Beijing Conditions
<p>We developed a kinetic model that reveals the key factors, including aerosol oxidants and atmospheric variables, that determine the multiphase formation of sulfate aerosols in the atmosphere. This dataset includes the output results discussed in an unpublished paper. </p>
Data for: The kinetic Ising model encapsulates essential dynamics of land pattern change
<p>A land pattern change represents a globally significant trend with implications for the environment, climate, and societal well-being. While various methods have been developed to predict land change, our understanding of the underlying change processes remains inadequate. To address this issue, we investigate the suitability of the 2D kinetic Ising model (IM), an idealized model from statistical mechanics, for simulating land change dynamics. We test the IM on a variety of patterns, each with different focus land type. Specifically, we investigate four sites characterized by distinct patterns, presumably driven by different physical processes. Each site is observed on eight occasions between 2001 and 2019. Given the observed pattern at the time $t_i$ we find two parameters of the IM such that the model-evolved land pattern at $t_{i+1}$ resembles the observed land pattern at that time. The data supports simulating seven such transitions per site.</p> <p>Our findings indicate that the IM produces approximate matches to the observed patterns in terms of layout, composition, texture, and patch size distributions. Notably, the IM simulations even achieve a high degree of cell-scale pattern accuracy in two of the sites. Nevertheless, the IM has certain limitations, including its inability to model linear features, account for the formation of new large patches, and handle pattern shifts.</p>
Vitamin A Kinetics and Mathematical Modeling in American Women
ClinicalTrials.gov study NCT03248700. IPD Sharing: NO. Countries: 1. Publications: 1.
Study to Develop a Kinetic Model for FDG and Me4FDG in Kidneys of Type 2 Diabetic Patients
ClinicalTrials.gov study NCT03557138. IPD Sharing: UNDECIDED. Countries: 1. Publications: 4.
Data for: The kinetic Ising model encapsulates essential dynamics of land pattern change
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Dataset of Paper "Kinetic modeling of the synergistic thermal and spectral actions on the inactivation of Cryptosporidium parvum in water by sunlight"
<p>Dataset of Paper "Kinetic modeling of the synergistic thermal and spectral actions on the inactivation of Cryptosporidium parvum in water by sunlight"</p> <p>- Data of the experimental disinfection profiles for the viable <em>C. parvum</em> oocysts.</p>
Dataset of Paper: "Kinetic modeling of the synergistic thermal and spectral actions on the inactivation of viruses in water by sunlight" (DOI:
<p>Dataset of Paper: "Kinetic modeling of the synergistic thermal and spectral actions on the inactivation of viruses in water by sunlight"</p> <p>- Data of the experimental disinfection of the MS2 virus.</p> <p>- Data of the kinetic constant value of the MS2 virus inactivation for experimental data and predicted data using action spectra models with different quantum yield values.</p> <p>- Observed and predicted kinetic constants for the MS2 inactivation by SODIS for all the scenarios and conditions studied. The predicted kinetic constants were obtained from the complete kinetic model described 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.