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129 results for “Flow simulation”
Faster‐haplodiploid evolution under divergence‐with‐gene‐flow: Simulations and empirical data from pine‐feeding hymenopterans
<p>Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of <em>Neodiprion lecontei </em>and <em>N. pinetum</em>, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of <em>N. lecontei </em>and <em>N. pinetum</em>, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.</p>
Demonstration of Simulation Tools for Electricity Markets considering Power Flow Analysis
<p>Two novel publicly available web services for electricity market (EM) simulation and study and power flow evaluation and validation are proposed, namely the Electricity Market Service (EMS) and Power Flow Service (PFS). EMS enables the simulation of two auction-based algorithms and the execution of three wholesale EMs. PFS provides the creation and evaluation of electrical grids from the transmission to distribution grids. Combining both services one can simulate EMs from wholesale to local markets and test if the results are compatible with a specific electrical grid. This dataset publishes the input and output data of a case study simulation scenario.</p>
Synthetic velocity profiles for simulations of blood flow in the aorta
<p>Synthetic dataset of aortic velocity profiles, suitable to be used for numerical simulations of blood flow.</p> <p>Please refer to the profile number ID when using it.</p>
Energetic Particle Injection during Short Isolated Bubble as seen in RCM Simulation and Spacecraft Observations in the Flow Braking Region
<p>The names of the RCM simulation output files specify the simulation time in a format of "hhmmss". The stored quantities are, "I","J","COLAT","ALOCT","MLT","BNDLOC","XMIN","YMIN","FTV","BMIN","V", "BIRK_fromV(NH)","P(RCM),nPa", "PV_gamma","Vtotx", "Vtoty","Vx_exb","Vy_exb","vel_x","vel_y","Ey","PEDLAM", "PEDPSI", "HALL", "RCM_T_p","RCM_T_e","RCM_N_e","EFLUX","EAVG","f_i_50-75","f_i_75-125","f_i_125-200","f_i_200-300","f_e_50-75","f_e_75-125","f_e_125-200","f_e_200-300","Vm","dbxdz","dbydz","dbrdz","dbzdx","dbzdy".<br> For the first hour of substorm-growth-phase-like quasi-steady convection, we uploaded the RCM simulation output files at 1-minute intervals. Then, the RCM output files were uploaded at 20-second intervals for the next 7 minutes of bubble injection, and at 1-minute intervals for the rest of the simulation.</p>
A Benchmark Analytical Solution for Variable Viscosity Flow in Fractured Media: Development and Comparative Analysis with Numerical Simulations
<p>This data is associated with <strong>(a) Figure 3.</strong> Comparison between the velocities obtained through analytical calculations and those estimated numerically, and <strong>(b) Figure 4.</strong> Comparison of the BTCs obtained through analytical calculations and those estimated numerically.</p>
Faster‐haplodiploid evolution under divergence‐with‐gene‐flow: Simulations and empirical data from pine‐feeding hymenopterans
Open the record for dataset details and reuse information.
LES-DPM simulation dataset for oscillatory flow over a mobile, rippled bed
Open the record for dataset details and reuse information.
Dataset for Lattice Boltzmann simulation of water flow through rough nanopores
<p>All the datasets used to produce the figures in our paper "<strong>Lattice Boltzmann simulation of water flow through rough nanopores</strong>".</p>
Experimental and Simulation Results of "3D Printed Biomodels for Flow Visualization in Stenotic Vessels: An Experimental and Numerical Study" - version 2
<p>This repository contains the experimental and simulation results of the article "3D Printed Biomodels for Flow Visualization in Stenotic Vessels: An Experimental and Numerical Study" by Carvalho, V., Rodrigues, N., Ribeiro, R., Costa, P., Lima, R., Teixeira, S., published in <em>Micromachines</em> <strong>11, 6</strong> (2020). https://doi.org/10.3390/mi11060549</p>
Simulation data and scripts for CFD-DEM simulation of granular flows in ambient fluid
<ul> <li>Data sets - contains the raw data required to replicate and validate all plots in the main article. Contains folders in containing measurements of basic flow properties, e.g. velocities, shear rates, etc., of monodisperse and bidisperse granular flows in different flow regimes. Each folder contains a ReadMe.txt briefly explaining the content and lay out of each data set.</li> <li>Sample case - a .zip file which includes codes which are needed to simulate a CFD-DEM case of a steady granular flow in water with cyclic boundaries in the stream wise direction. Also enclosed is a ReadMe.txt file detailing the implementation instructions for both Esys particle and OpenFOAM codes. Download links for Esys particle and OpenFOAM are also included.</li> <li>Geo file generator - a .zip file which includes Esys particle codes that can be used to generate a .geo file specifying the initial position of the particles used in the test simulations. A ReadMe.txt file is enclosed with more detailed implementation instructions.</li> </ul>
Reduction of blob-filament radial propagation by parallel variation of flows: analysis of a gyrokinetic simulation
<p>The accompanying files contain digital data for figures in the article "Reduction of blob-filament radial propagation by parallel variation of flows: analysis of a gyrokinetic simulation" by J. R. Myra, S. Ku, D.A. Russell, J. Cheng, I. Keramidas Charidakos, S. E. Parker, R.M. Churchill, and C.S. Chang, submitted to the journal Physics of Plasmas.</p> <p> </p> <p><strong>Abstract</strong></p> <p>Data from the XGC1 gyrokinetic simulation is analyzed to understand the three-dimensional spatial structure and the radial propagation of blob-filaments generated by quasi-steady turbulence in the tokamak edge pedestal and scrape-off layer plasma. Spontaneous toroidal flows vary in the poloidal direction and shear the filaments within a flux surface resulting in a structure that varies in the parallel direction. This parallel structure allows the curvature and grad-B induced polarization charge density to be shorted out via parallel electron motion. As a result, it is found that the blob-filament radial velocity is significantly reduced from estimates which neglect parallel electron kinetics, broadly consistent with experimental observations. Conditions for when this charge shorting effect tends to dominate blob dynamics are derived and compared with the simulation.</p>
Soil water retention and water flow simulation data
<p>The data is for the manuscript of a paper entitled "<strong>Simulation of water flow and calculation of </strong><strong>the related physical quality indices as influenced by soil water retention curve fitting methods".</strong></p> <p>Accurate fitting of soil water retention curve (SWRC) parameters is crucial in the modeling of soil water flow and the assessment of soil quality. The un-weighted least squares regression (ULS) is the most common approach applied for fitting the SWRC functions to the observed data-points in order to optimize their parameters. However, the variance of SWRC data varies in different water contents; therefore, unlike the wet-end of the SWRC, the ULS method may not be sufficiently effective in estimating its dry-end. This study examined the differences between parameter approximations achieved by the ULS and the weighted least-squares (WLS) in the SWRC. Then, an analysis of both approaches in the simulation of water redistribution and the related soil physical quality indicators (SPQIs) was done. Accordingly</p>
Data from: The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data.
Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.
Water depth time series derived by FLOW-R2D model simulating the Tous dam break
<p>In this dataset, the water depth time series in 21 gauges of Sumacarcel town are derived by the FLOW-R2D model,<br> assuming 240 different combinations of three input paramaters:</p> <p>a) input flow to the computatioal domain (upstream boundaries) (Q)<br> b) the Manning coefficient of the computational domain (n)<br> c) effective slope (required at the upstream boundaries) (S)</p> <p>The sampling for the three parameters is made by Latin Hypercube technique, assuming for each parameter the following interval:</p> <p>a) 10000-20000 m^3/s<br> b) 0.03-0.21 s/m^(1/3)<br> c) 0.0001 - 0.02</p> <p>The dataset consists of the following:<br> <br> 1) input_data.csv file, in which the 240 combinations of the three input parameters is provided (Scenario 100 - 399)<br> 2) runs_tous folder, in which files 100.cv-399.csv. Water depth time series are recorded in 21 gauges.<br> The first column is time (in seconds), and the water dpeths are in meters.<br> <br> Papers relative to this dataset:</p> <p>1) Description of the case study:<br> Alcrudo F and Mulet J (2007). Description of the Tous Dam break case study (Spain).<br> Journal of Hydraulic Research, 45, 45-57.</p> <p>2) Simulation of tous dam break with FLOW-R2D:<br> Bellos V and Tsakiris G (2015). 2D flood modelling: the case of Tous dam break.<br> Proceedings of 36th World Congress of IAHR, the Hague, the Netherlands. (e-proceedings).</p> <p>3) Calibration of the case study of the FLOW-R2D paramteters:<br> Christelis V, Bellos, V, Tsakiris, G (2016). Employing surrogate modelling for the calibration of a 2D flood simulation model.<br> Proceedings of 4th European Congress of IAHR, “Sustainable Hydraulics in the era of global change”,<br> edited by S. Erpicum, B. Dewals, P. Archambeau, M. Pirotton, Liege, Belgium: 727-732.</p> <p>4) Presentation of the FLOW-R2D model:<br> Tsakiris G and Bellos, V (2014) A numerical model for two-dimensional flood routing in complex terrains.<br> Water Resources Management 28(5):1277-1291</p>
Simulations Supporting 'Representing Intra-Hillslope Lateral Subsurface Flow in the Community Land Model', JAMES, 2019
<p>CLM5 Simulations used for the paper "Representing Intra-Hillslope Lateral Subsurface Flow in the Community Land Model". Files are in NetCDF format.</p> <p>Filenames beginning with 'RME_' contain single point simulations for the Reynolds Mountain East catchment. Filenames beginning with 'Global_' contains global simulations used in the sensitivity study. Filenames beginning with 'surfdata_' contain input surface data files used in CLM5 Hillslope simulations.</p>
Performance of high-order Godunov-type methods in simulations of astrophysical low Mach number flows
<p>Supplementary materials for the paper "Performance of high-order Godunov-type methods in simulations of astrophysical low Mach number flows". The supplementary materials are split into two .zip archives (KH2D-plots.zip and 3D-TURBULENCE-WAVES-plots.zip) containing figures not shown in the paper.</p>
Global environmental flow requirement estimates based on multimodel simulations
<p><a href="../api/files/5d8d266f-99bd-4351-8c7a-684f0bc0df90/global_natural_discharge_multimodel_medians.nc4">global_natural_discharge_multimodel_medians.nc4</a>: multimodel medians of simulations of monthly naturalized streamflow during 1971-2010 provided by six global hydrological models (DBH, H08, LPJmL, MATSIRO, PCR-GLOBWB, and WaterGAP), derived from the ISIMIP2a dataset (https://doi.org/10.5880/PIK.2017.010).</p> <p>Global environmental flow requirement estimated with different methods: Qxx (Q90, Q50), Smakhtin (Smakhtin et al. 2004), Tennant (Tennant 1976), Tessmann (Tessmann 1980), VMF (variable monthly flow, Pastor et al. 2014). The unit for the EFR data is m3 s-1.</p> <p>Related reference<br>Liu, X., Liu, W., Liu, L., Tang, Q., Liu, J., & Yang, H. (2021). Environmental flow requirements largely reshape global surface water scarcity assessment. Environmental Research Letters, 16(10), 104029.</p>
Simulation data from "Mass Flows in Expanding Coronal Loops"
<p>24 HYDRAD hydrodynamic simulations from the paper "Mass Flows in Expanding Coronal Loops" by Reep, Scott, Chhabra, Unverferth & Knizhnik, accepted for publication in the Astrophysical Journal, 2024 (https://arxiv.org/abs/2403.12358). Each of Figures 1, 2, 3, and 9 have six simulations with varying cross-sectional area expansion factors. These simulations were used to generate the plots in the paper.</p> <p>The output of the simulation data can be found in the ./Results/ folder of each simulation's directory. The source code was modified to hard code the expansion factors in ./HYDRAD/source/eqns.cpp, under the functions double CEquations::CalculateMagneticField and double CEquations::CalculateCrossSection, rather than using polynomial fits as is standard in HYDRAD. </p> <p> </p>
Large Eddy Simulation data of flow in a rectangular diffuser
<p>This dataset contains the results of large-eddy simulations of the flow in a rectangular asymmetric diffuser. Here only the D2 diffuser's data are provided because experimental and DNS data are avilable for D1. .</p>
Data, plotting scripts, and figures for "Accelerating Reactive-Flow Simulations using Vectorized Chemistry Integration"
<p>Data, plotting scripts, and figures for the article "Accelerating Reactive-Flow Simulations using Vectorized Chemistry Integration".</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.