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31 results for “numerical effects”
NIMROD growth rates (1/s) by finite element poly_degree (columns) and case from "The Impact of Collisionality, FLR and Parallel Closure Effects on Instabilities in the Tomakak Pedestal: Numerical Studies with the NIMROD code”
<p>NIMROD growth rates (1/s) by finite element poly_degree (columns) and case from "The Impact of Collisionality, FLR and Parallel Closure Effects on Instabilities in the Tomakak Pedestal: Numerical Studies with the NIMROD code” as submitted to Physics of Plasmas</p>
Numerical simulation of the equatorial plasma bubble: the effect of seeding by the vertical winds and random background noise perturbations.
<p>A wide variety of small-amplitude waves widely exist in the ionosphere and have significant effects on the evolution of equatorial plasma bubbles. In this paper, we simulated equatorial plasma bubbles (EPB) seeded by vertical neutral wind perturbations with wavelengths of 125 km and 250 km, and compared the morphology characteristics of plasma bubble structures with those under random noise perturbations in the background density. The numerical results showed that both vertical winds and random background noise perturbations can contribute to the growth of plasma bubbles, and the perturbations under additional random background noise can promote the growth of the plasma bubble structures faster. Additionally, several processes of the nonlinear behavior of bifurcated EPB structures, including bifurcation, pinching, and small-scale turbulent structures, were successfully obtained. Our simulation captured supersonic flows within the low-density plasma structures characterized by vertical velocities of about 1.5 km/s, which is consistent with experimental studies found in the literature.</p>
The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility [complement to Supplementary Material 3]
<p>Raw data, and RStudio project, R markdown scripts and HTML outputs of the statistical procedures.</p> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
Files for the numerical results shown in "Far-from-equilibrium travelling pulses in sloped semi-arid environments driven by autotoxicity effects" by Gabriele Grifò, Annalisa Iuorio, and Frits Veerman
<p>This folder contains the code used to produce Fig. 1 and Fig. 8-10 in the paper: "Far-from-equilibrium travelling pulses in sloped semi-arid environments driven by autotoxicity effects" by Gabriele Grifò, Annalisa Iuorio, and Frits Veerman. The preprint version of this paper is available at <a href="https://arxiv.org/abs/2405.1560">https://arxiv.org/abs/2405.1560</a>.</p> <p>In the subfolder "Direct_simulations", the code (to obtain Fig. 1) is based on a MATLAB routine which uses finite differences for spatial discretization with periodic boundary conditions together with MATLAB’s ode15s routine for time integration.</p> <p>The continuation procedure (to obtain Fig. 8-10) is shown in the subfolder "Continuation" based on the software AUTO to analyse the dependence of the constructed travelling pulse solutions of Eq. (3.2) with respect to three system parameters, i.e. A, D, and H. Correspondingly, in each folder 'Continuation_X' where X=A, D, H, the results can be obtained by running the file 'AUTO_script_cont_X', based on the two files 'parab_X.f90' and 'c.parab_X'.</p> <p>Selected solutions for each continuation are stored in the corresponding subfolders 'solutions_X', whereas the tables resulting from the continuation procedure in the scripts are shown in the files 'bifdiag_X.dat'. In each script file further details are provided in order to clarify how to extract the solutions used for the plots.</p>
Experimental and numerical study of the effect of model geometric distortion on laboratory modelling of urban flooding
<p>The supporting datasets includes: </p> <p>(1) All the figures in the manuscript in .fig format (in case possible)</p> <p>- Figures in main text</p> <p>- Figure in Support Information</p> <p>(2) Datasets for generating the main outcomes of the manuscript</p> <p>- two files that explain detailed data content in three structure</p> <p>- 3 sub-repositories which contains the results for the three models</p> <p>- one repository contains the data for Figure 8</p> <p> </p>
Data from: Numerical data for systemic effects of photoactivated 5,10,15,20-tetrakis(N-methylpyridinium-3-yl) porphyrin on healthy Drosophila melanogaster
<p>Porphyrins are commonly used as photosensitizing agents (PA) in photodynamic therapy (PDT), a non-invasive method predominantly used for the treatment of subcutaneous tumors. Development of novel PA with increased tissue selectivity and effectiveness is important for the wider use of PDT in the treatment of various types of cancers. We used <em>Drosophila melanogaster</em> as a model organism to study the systemic effects of 5,10,15,20-tetrakis(<em>N</em>-methylpyridinium-3-yl)-porphyrin (TMPyP3). First, we defined the optimal feeding protocol and showed that TMPyP3 was absorbed and retained longer in the neuronal than the non-neuronal extracts. Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) concentration increased 24 hours after the photoactivation of orally delivered TMPyP3 but only in the head extracts. After 7 days, regardless of the photoactivation, TMPyP3 led to lower concentration of H<sub>2</sub>O<sub>2</sub>, which correlated with the decreased climbing ability measured as negative geotaxis. The results suggest that systemic treatment with TMPyP3 may interfere with redox regulation and thus impair cellular signaling and behavioral output. Further studies are needed to establish the disruptive effect that porphyrins have on redox homeostasis, how long it persists, and mechanistic differences of retention between different tissues.</p>
Dataset for "Quantifying the effects of bed roughness on transit time distributions via direct numerical simulations of turbulent hyporheic exchange"
<p>This dataset contains the sediment models, DNS flow field data, subsurface path data, and calculated transit time distributions for both the regular- and random-interface cases used in the paper: "Quantifying the effects of bed roughness on transit time distributions via direct numerical simulations of turbulent hyporheic exchange" by Guangchen Shen, Junlin Yuan, and Mantha S. Phanikumar (Submitted to Water Resources Research). <br> Detailed introduction of each data file is as follows.</p> <p>1. DNS flow field data</p> <p>Flowfield_Reg.h5 and Flowfield_Ran.h5 contains the following fields for the regular and random cases, respectively. 'ni', 'nj', 'nk' are the numbers of grid points along x, y, and z directions. 'xc', 'yc', 'zc' are the cell center locations. 'u3d','v3d','w3d' are the three-dimensional time-averaged velocities at each grid point. 'vof' is the volume-of-fluid field used by the immersed-boundary method to prescribe the fluid-solid interface (vof=1 in fluid and 0 in solid), at each grid point. 'vof' contains the information of sediment grain distribution and bed roughness geometry. Only the subsurface data (those below the sediment crest) are shared due to dataset size limit.</p> <p>2. Particle-tracked subsurface flow paths and corresponding transit time distributions</p> <p>The mat files “xxx_pathline” store the (x,y,z) location of each point (saved as 'StrX', 'StrY, 'StrZ') along the subsurface paths, discretized by uniform steps of travel time (with time intervals of 0.1 for 'A' and 0.01 for 'MD' cases, normalized by channel height and friction velocity). The files “xxx_TT” store the array of transit times corresponding to the tracked paths, where the 1d array T is the transit time. 'A' denotes calculations based on time-mean advection only, while 'MD' denotes calculations accounting for additional molecular diffusion. 'Interface' and '3DiameterBelow' indicate that the particles were released at the interface and -3 D below the interface, respectively.</p>
Code for APJAS publication - Numerical errors in ice microphysics parameterizations and their effects on simulated regional climate
<p>In this repository, we include the source codes for WRF microphysics parameterization used in the APJAS publication "Numerical errors in ice microphysics parameterizations and their effects on simulated regional climate"</p> <p>There are three WDM6 codes for simulations. The original WDM6 code (ORG) using parameter defined by Hong et al (2004), the revised WDM6 code (NEW) those revised by removing the numerical errors, and the additional WDM6 code (SEN) for sensitivity experiment adopting the column-shaped parameters.</p> <p>In supplement, several cloud-ice characteristics presented in the paper were induced in detail and compared with Hong et al (2004) and this study.</p>
Data from: A shared numerical magnitude representation evidenced by the distance effect in frequency-tagging EEG
<p>Humans can effortlessly abstract numerical information from various codes and contexts. However, whether the access to the underlying magnitude information relies on common or distinct brain representations remains highly debated. Here, we recorded electrophysiological responses to periodic variation of numerosity (every five items) occurring in rapid streams of numbers presented at 6Hz in randomly varying codes – Arabic digits, number words, canonical dot patterns and finger configurations. Results demonstrated that numerical information was abstracted and generalized over the different representation codes by revealing clear discrimination responses (at 1.2 Hz) of the deviant numerosity from the base numerosity, recorded over parieto-occipital electrodes. Crucially, and supporting the claim that discrimination responses reflected magnitude processing, the presentation of a deviant numerosity distant from the base (e.g., base "2" and deviant "8") elicited larger right-hemispheric responses than the presentation of a close deviant numerosity (e.g., base "2" and deviant "3"). This finding nicely represents the neural signature of the distance effect, an interpretation further reinforced by the clear correlation with individuals' behavioral performance in an independent numerical comparison task. Our results, therefore, provide for the first time unambiguously a reliable and specific neural marker of a magnitude representation that is shared among several numerical codes.</p>
The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility [complement to Supplementary Material 2]
<p>3D micro surface data processed in ConfoMap v7.4.8633 (a derivative of MountainsMap Imaging Topography developed by Digital Surf, Besançon, France).</p> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
The effect of numerical aperture on quantitative use-wear studies and its implication on reproducibility [complement to Supplementary Material 4]
<p>Python script and results of the Bayesian Multi-factor ANOVA.</p> <p>Instructions to download all files at once are given here: <a href="https://doi.org/10.5281/zenodo.4011952">https://doi.org/10.5281/zenodo.4011952</a></p>
Data from: Numerical top-down effects on red deer (Cervus elaphus) are mainly shaped by humans rather than large carnivores across Europe
<p>Terrestrial ecosystems are shaped by interacting top-down and bottom-up processes, with the magnitude of top-down control by large carnivores largely depending on environmental productivity. While carnivore-induced numerical effects on ungulate prey populations have been demonstrated in large, relatively undisturbed ecosystems, whether large carnivores can play a similar role in more human-dominated systems is a clear knowledge gap. As humans influence both predator and prey in a variety of ways, the ecological impacts of large carnivores can be largely modified. We quantified the interactive effects of human activities and large carnivore presence on red deer (<em>Cervus elaphus</em>) population density and how their impacts interacted and varied with environmental productivity</p> <p>Data on red deer density were collected based on a literature survey encompassing 492 study sites across 28 European countries. Variation in density across study sites was analysed using a generalised additive model in which productivity, carnivore presence (grey wolf, European lynx, Brown bear), human activities (hunting, intensity of human land-use activity), site protection status and climatic variables served as predictors. </p> <p>The results showed that a reduction in deer density only occurred when wolf, lynx and bear co-occurred within the same site. In the absence of large carnivores, red deer density varied along a productivity gradient without a clear pattern. Although a linear relationship with productivity in the presence of all three large carnivore species was found, this was not statistically significant. Moreover, hunting by humans had a stronger effect than the presence of all large carnivores in reducing red deer density and red deer density increased with increasing intensity of human land-use, with stronger large carnivore effects (all three carnivore species present) at sites with low human land-use activities. </p> <p><em>Synthesis and applications</em>: This study provides evidence for the dominant role played by humans (i.e. hunting, land-use activities) relative to large carnivores in reducing red deer density across European human-dominated landscapes. These findings suggest that when we would like large carnivores to exert numeric effects, we should focus on minimizing human impacts to allow the ecological impacts of large carnivores on ecosystem functioning.</p>
Effect of egocentric and allocentric reference frames on spatial numerical associations
<p>From an embodied view of cognition, sensorimotor mechanisms are strongly involved in abstract processing, such as Arabic number meanings. For example, spatial cognition can influence number processing. These spatial-numerical associations (SNAs) have been deeply explored since the seminal spatial-numerical associations of response code (SNARC) effect (i.e., faster left/right sided responses to small/large magnitude numbers, respectively). While these SNAs along the transverse plane (left-to-right axis) have been extensively studied in cognitive sciences, no systematic assessment of other planes of the tridimensional space has been afforded. Moreover, there is no evidence of how SNAs organize themselves throughout the changes in spatial body-reference frames (egocentric and allocentric). Hence, this study aimed to explore how SNAs organize themselves along the transverse and sagittal planes when egocentric and allocentric changes are processed during body displacements in the environment. In the first experiment, the results revealed that when the participants used an egocentric reference, SNAs were observed only along the sagittal plane. In a second experiment that used an allocentric reference, the reversed pattern of results was observed: SNAs were present only along the transverse plane of the body. Overall, these findings suggest that depending on the spatial reference frames of the body, SNAs are strongly flexible.</p>
Data from: Numerical top-down effects on red deer (Cervus elaphus) are mainly shaped by humans rather than large carnivores across Europe
Open the record for dataset details and reuse information.
Data from: A shared numerical magnitude representation evidenced by the distance effect in frequency-tagging EEG
Open the record for dataset details and reuse information.
Numerical data for systemic effects of photoactivated 5,10,15,20-tetrakis(N-methylpyridinium-3-yl) porphyrin on healthy Drosophila melanogaster
Open the record for dataset details and reuse information.
Supporting dataset for "Numerical insights into the effects of model geometric distortion in laboratory experiments of urban flooding"
<p>The supporting datasets includes:</p> <p>(1) All the Figures in the manuscript in .fig format </p> <p> - Figures in main text</p> <p> - Figures in SI</p> <p>(2) Original matrice data for the results of each run</p> <p> - A file that explains detailed data content in tree structure;</p> <p> - 4 sub-repositories which contain data for models in different scales</p>
Data for paper "Effects of inflow conditions on plunge points and vertical profiles of turbidity currents on sloping flume based on 3D numerical simulation"
<p>This set of xlsx files, metadata of model results and Matlab code accompanies the manuscript "Effects of inflow conditions on plunge points and vertical profiles of turbidity currents on sloping flume based on 3D numerical simulation" by Ruoyin Zhang, Baosheng Wu, and Bangwen Zhang. This is the first release of the data.</p>
Model codes, data, and plot scripts for the paper "A numerical modeling study on the Earth's surface brightening effect of cirrus thinning"
<p>The model codes, data, and plot scripts used in the paper "A numerical modeling study on the Earth's surface brightening effect of cirrus thinning".</p><ul><li>Mods: the modified CAM model code used in these three experiments.</li><li>Results: post-processing NCL scripts and the results used for making plots.</li><li>figs: the NCL scripts and figures used in the paper.</li><li>Parcel: parcel model that represents the ice nucleation process.</li></ul><p> </p>
Experimental and numerical study of a PCM solar air heat exchanger and its ventilation preheating effectiveness
<p>Dataset including experimental data and data for numerical validation. The corresponding figures can be found in the paper Experimental and numerical study of a PCM solar air heat exchanger and its ventilation preheating effectiveness.</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.
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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.