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1,028 results for “simulation model”
Simple Biosphere model version 4.2 (SiB4) simulations for the present day atmosphere with 500 ppt OCS and the two OCS geoengineering scenarios with 4.8 ppb and 35.5 ppb OCS.
<p>This dataset was prepared for a publication by von Hobe et al. (2023):</p> <p><strong>Comment on “An approach to sulfate geoengineering with surface emissions of carbonyl sulfide” by Quaglia et al. (2022)</strong></p> <p>In that publication, the data are displayed in Figures 1 and 2.</p> <p>Simple Biosphere model version 4.2 (SiB4, Haynes et al., 2019; Sellers et al., 1986) was used to calculate (i) the average increase in evapotranspiration anticipated under an elevated OCS scenario for the years 2000-2021 on a 0.5 ° latitude x 0.5 ° longitude grid and (ii) OCS uptake by plants and soils, per month, at baseline (500 ppt) and elevated (4.8 and 35.5 ppb) OCS levels averaged over the years 2000-2021.</p> <p>- - - - - - - - - - -</p> <p><em>File 1: vonHobe_et_al_2023_CarbonylSulfideGeoengineeringScenarios_DeltaEvapotranspiration_GloballyGridded_SiB4.nc</em></p> <p>File Format:</p> <p> netCDF</p> <p>Index Variables:</p> <p> latitude</p> <p> longitude</p> <p>Parameters:</p> <p> percent_diff_et: relative increase in % of evapotranspiration in a scenario where 20% of terrestrial plants exhibit a 50% increase in stomatal conductance under high OCS</p> <p>- - - - - -</p> <p><em>File 2: vonHobe_et_al_2023_CarbonylSulfideGeoengineeringScenarios_BiosphereUptake_MonthlyIntegrated_SiB4.csv</em></p> <p>File Format:</p> <p> comma delimited text file (.csv)</p> <p>Index Variable:</p> <p> time: monthly, format m/dd/yy</p> <p>Parameters:</p> <p> ocs_veg_base: simulated monthly OCS uptake by terrestrial vegetation at an atmospheric OCS mole fraction of 500 ppt</p> <p> ocs_soil_base: simulated monthly OCS uptake by soils at an atmospheric OCS mole fraction of 500 ppt</p> <p> ocs_veg_4.8ppb: simulated monthly OCS uptake by terrestrial vegetation at an atmospheric OCS mole fraction of 4.8 ppb</p> <p> ocs_soil_4.8ppb: simulated monthly OCS uptake by soils at an atmospheric OCS mole fraction of 4.8 ppb</p> <p> ocs_veg_35.5ppb: simulated monthly OCS uptake by terrestrial vegetation at an atmospheric OCS mole fraction of 35.5 ppb</p> <p> ocs_soil_35.5ppb: simulated monthly OCS uptake by soils at an atmospheric OCS mole fraction of 35.5 ppb</p> <p>- - - - - - - - - - -</p> <p><strong>References:</strong></p> <p>Haynes, K. D., Baker, I. T., Denning, A. S., Stöckli, R., Schaefer, K., Lokupitiya, E. Y., and Haynes, J. M.: Representing<br> Grasslands Using Dynamic Prognostic Phenology Based on Biological Growth Stages: 1. Implementation in the Simple<br> Biosphere Model (SiB4), Journal of Advances in Modeling Earth Systems, 11, 4423-4439, 10.1029/2018ms001540, 2019.</p> <p>Quaglia, I., Visioni, D., Pitari, G., and Kravitz, B.: An approach to sulfate geoengineering with surface emissions of carbonyl sulfide, Atmos. Chem. Phys., 22, 5757-5773, 10.5194/acp-22-5757-2022, 2022.</p> <p>Sellers, P. J., Mintz, Y., Sud, Y. C., and Salcher, A.: A Simple Biosphere Model (SiB) for Use within General Circulation Models, Journal of the Atmospheric Sciences, 43, 505-531, 1986.</p> <p>von Hobe, M., Brühl, C., Lennartz, S. T., Whelan, M. E., and Kaushik, A.: Comment on “An approach to sulfate geoengineering with surface emissions of carbonyl sulfide” by Quaglia et al. (2022) ,</p>
Code and initial metapopulation data for model construction and simulation analyses for: Genetic rescue from protected areas is modulated by migration, hunting rate and timing of harvest
<p>Migrants from protected areas may buffer the risk of harvest-induced evolutionary changes in exploited populations that face strong selective harvest pressures in both terrestrial and marine ecosystems. Understanding the mechanisms favouring genetic rescue through migration could help ensure sustainable harvest outside protected areas and conserve genetic diversity inside those areas. We developed a stochastic individual-based metapopulation model to evaluate the potential for migration from protected areas to mitigate the evolutionary consequences of selective harvest. We parameterized the model with detailed data from individual monitoring of two populations of bighorn sheep subjected to trophy hunting. We tracked horn length through time in a metapopulation including large protected and trophy-hunted populations connected through male breeding migrations. We quantified and compared declines in horn length and rescue potential under various combinations of migration rate, hunting rate in hunted areas and temporal overlap in timing of harvest and migrations, which affects the migrants' survival and chances to breed within exploited areas. Our simulations suggest that the effects of size-selective harvest on male horn length in hunted populations can be dampened or avoided if harvest pressure is low, migration rate is substantial, and migrants have a low risk of being shot. Intense size-selective harvest impacts the phenotypic and genetic diversity in horn length, and population structure through changes in proportions of large-horned males, sex ratio and age structure. When hunting pressure is high and overlaps with male migrations, effects of selective removal also emerge in the protected population, so that instead of a genetic rescue of hunted populations, our model predicts undesirable effects inside protected areas. Our results stress the importance of a metapopulational approach to management, to promote genetic rescue from protected areas and limit ecological and evolutionary impacts of harvest on both harvested and protected populations.</p>
Ultrasound Stochastic Tomography simulation data for In-silico 2D Breast Phantom model with tumour
<p>An anatomically realistic numerical breast phantom model (with realistic acoustic properties of speed of sound, density, and attenuation coefficient of tissues) derived from [1] is presented with details of a ultrasound tomography experiment in simulation. Details of source wavelets, geometry of transducer set, observed data at each transducer for each shots are provided with phantom model.</p> <p>References</p> <p>[1] <a href="https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/">https://anastasio.bioengineering.illinois.edu/downloadable-content/oa-breast-database/</a></p>
Supplementary material for: PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow
<p>We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages, or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example.</p> <p>We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at <a href="https://github.com/cecileane/PhyloCoalSimulations.jl">https://github.com/cecileane/PhyloCoalSimulations.jl</a>.</p>
model results from NHWAVE simulations of lobe-and-cleft instabilities at a river plume front
<p>The dataset contains the results from NHWAVE simulations of the lobe-and-cleft instabilities at a river plume front. The data format is .mat. The postprocessing scripts are included. </p>
CT Simulations of MITA Low Contrast Detectability Phantom for Model Observer Assessments
<p>Dataset of CT Simulations of MITA Low Contrast Detectability Phantom for Model Observer Assessments. </p>
Data set used in "Effect of turbulence and viscosity models on wall shear stress derived biomarkers for aorta simulations"
<p>Data set used in "Effect of turbulence and viscosity models on wall shear stress derived biomarkers for aorta simulations"</p> <p>Includes the data for 20 heartbeats. Divided into external and internal walls regions. </p>
In silico design, docking simulation, and ANN-QSAR model for predicting the anticoagulant activity of thiourea isosteviol compounds as FXa inhibitors
<p>The present work combined molecular modeling and docking approach for searching and designing novel thiourea isosteviol-based compounds as potential FXa inhibitors. Elaborated regression model establishes the relationships between experimentally determined anticoagulant activity and molecular descriptors and enables the prediction of FXa inhibitory activity for novel compounds. The obtained results proved that the Artificial Neural Network algorithm facilitates the search for the most promising isosteviol derivatives incorporating thiourea fragments as FXa inhibitors. Moreover, docking simulation confirms the prominent binding of the newly in silico designed molecules with the active sites of the protein, which may be the lead molecules and can be further optimized for the efficient pharmacodynamic and pharmacokinetic profiles. The enclosed files are representations of molecular structures of thiourea isosteviol compounds with experimentally tested FXa inhibitory activity (i20-i39) geometrically optimized in hyperchem, newly in silico designed thiourea isosteviol compounds geometrically optimized in hyperchem (e1-e11), one file contains molecular descriptors for optimized structures calculated in Dragon and there is also a code for ANN QSAR model for predicting activity of novel thiourea isosteviol compounds. </p>
Input and Output simulation data of the THOR GCM for the paper Dynamical and radiative effects resulting from the deep non-hydrostatic vs deep quasi-hydrostatic equations in the global circulation model THOR with an added non-grey radiative transfer scheme
<p>The input and ouput simulation data of the THOR GCM for Dynamical and radiative effects resulting from the deep non-hydrostatic vs deep quasi-hydrostatic equations in the global circulation model THOR with an added non-grey radiative transfer scheme</p> <p>Global circulation models (GCMs) play an important role in contemporary investigations of exoplanet atmospheres. Different GCMs evolve various sets of dynamical equations which can result in obtaining different atmospheric properties between models. In this study, we investigate the effect of different dynamical equation sets on the atmospheres of hot Jupiter exoplanets. We compare GCM simulations using the quasi-primitive dynamical equations (QHD) and the deep Navier-Stokes equations (NHD) in the GCM THOR. We utilise a two-stream non-grey "picket-fence" scheme to increase the realism of the radiative transfer scheme. We perform GCM simulations covering a wide parameter range grid of system parameters in the population of exoplanets. Our results show significant differences between simulations with the NHD and QHD equation sets at lower gravity, higher rotation rates or at higher irradiation temperatures. The parameter exploration shows the relevance of choosing dynamical equation sets dependent on system and planetary properties.Climate states of hot Jupiters seemed to be more diverse than previously thought. There are exceptions to prograde superrotation. Overall, our study shows the evolution of different climate states which arise just due to different selection of Navier-Stokes equations and approximations. We show the shortcomings of approximations in GCMs made for Earth, but used for non Earth-like planets.</p>
Validation of an Idealized Aorta Model Analysed through Fluid-Structure Interaction Simulation with Robin-Neumann Partitioned Approach
<p>The aorta is multiphysics system where hemodynamics and wall structural mechanic are mutually influenced. A fluid-structure interaction approach is appropriate to describe the mechanical alterations suffered by the aortic wall in response to altered hemodynamic patterns. This work demonstrates the validation of the simulated idealized aorta model with a fluid-structure interaction (FSI) model through modified PIMPLE solver to use Robin-Neumann partitioned approach for the strongly-coupled algorithm using solids4foam v2. The validation involves the comparison of streamlines, pressure, and displacements with in vivo measurements. The geometry is reconstructed from the healthy aorta presented in 10.5281/zenodo.5801938. Our analysis shows that the streamlines and pressure pattern are comparable with the literature data acquired using rich medical imaging data. The maximum diameter deformation at the level of abdominal aorta is comparable with measured data and the diameter deformation profile along the cardiac cycle correctly follow the velocity profile. According to this results, our work shows a high-performance simulation suitable for several future works.</p>
Holocene climate change in southern Oman deciphered by speleothem records and climate model simulations
<p>8 ka BP (thousand year, before present, 8K) and pre-industrial period (PI) paleoclimate equilibrium experiment, including precipitation (pr), near-surface relative humidity (hurs), evaporation (evspsbl) and 850hPa wind (u850 & v850).</p>
Simulated Well Production Data using a Transient Well Model and a Developed Simulator
<p>This is a simulated dataset of transient well production data. This dataset was used in my Masters thesis at King Abullah University of Science and Technology (KAUST), and it is shared for academic use and research work.</p> <p>The dataset has 100 wells simulated at time steps of 0.2 hours for an entire year. This gives 43,800 observations per well, and grand total of 4,380,000 observations in the entire dataset. The resulting production data is then perturbed with systemic and random gauge errors to better simulate real-world gauge readings.</p> <p>The simulator code used to generate this dataset can be found at: <a href="https://github.com/ykh-1992/TransientNodalAnalysis.jl">https://github.com/ykh-1992/TransientNodalAnalysis.jl</a></p> <p>The data consists of three files:<br> - "wells.csv": This file details the input parameters for each simulated well.<br> - "data.zip": This file houses an 850 MB "data.csv" that includes the simulated well production data.<br> - "auxiliary.csv": This file includes information related to the simulation run.</p>
Model simulation data used in "The global impact of the transport sectors on the atmospheric aerosol and the resulting climate effects under the Shared Socioeconomic Pathways (SSPs)" (Righi et al., Earth Syst. Dynam., 2023)
<p>This dataset contains the output of the EMAC global model simulations analysed and discussed in Righi et al. (<i>Earth Syst. Dynam.</i>, 2023). For details see the README.md file.</p>
PALM Model System v 6.0 input and configuration files for coupled large eddy simulations of land surface heterogeneity effects and diurnal evolution of late summer and early autumn atmospheric boundary layers during the CHEESEHEAD19 field campaign
<p>Namelist, configuration and forcing files for the PALM Model System 6.0 revision number 21.10-rc.2 used for the numerical simulations Coupled Large Eddy Simulations of land surface heterogeneity induced atmospheric boundary layer response during the CHEESEHEAD19 field campaign.</p>
Data presented in "Fitting cumulus cloud size distributions from idealized cloud resolving model simulations"
<p>Updated repository containing the data produced and analzed in the manuscript entitled "Fitting cumulus cloud size distributions from idealized cloud resolving model simulations" by J. Savre and G. Craig, submitted to the Journal of Advances in Modeling Earth Systems.</p> <p>New uploads: time series file (T_S), vertical profiles (profiles_tot.nc) and horizontal slices at 2km (slice_z_2000_bis.nc). Uploaded files concern the LBA case only.</p>
Model_Input_Files_and_Simulation_Output
<p>This provides the BioRT-HBV model input and output for the paper submission "As above, so below: the growing importance of water and carbon processes beneath soils in a warmer and drier climate".<br><br>Coal_Creek_Original: Input and Output files associated with the model calibrated to average DOC years; used for making Figures 3, 4, 5, 6, 7, and 8.<br><br>Coal_Creek_High: Input and Output files associated with the model calibrated to high DOC years; used for making Figure 4.</p> <p>Rxn_Implementation_Results: Output files associated with the model simulations that have Resp-SZ only, and Resp-SZ & Resp-DZ; used for making Figure 5.<br><br>Input files and output for the various numerical experiments, used in figure 9: Coal_Creek_DryandWet, Coal_Creek_DryYears, Num_Exp_HBVResults_and_precipchem_files, Num_Exp_output<br><br>HBV-BioRT-new_ver(1).zip : files for the BioRT-HBV model</p>
Input and output data from simulations of 2D valves and 3D inflow-outflow model using particle methods
<p>Input and output data of open-source softwares for computational fluid dynamics simulation involving fluid-structure interaction.</p> <p> </p> <p><strong>Data from two studies</strong></p> <ol> <li>Verifications of the weakly-compressible smoothed particle hydrodynamics (WCSPH) method, open-source code <a href="https://www.sphinxsys.org">SPHinXsys</a>, when applied to the flow of idealized 2D valve models.</li> <li>Validations of inflow-outflow model in moving particle semi-implicit (MPS) method, open-source code <a href="https://github.com/rubensamarojr/polymps/tree/inOutflow">PolyMPS</a>.</li> </ol> <p> </p> <p><strong>Folders and Files</strong></p> <p><strong>valve-2D.zip </strong>is the folder with data from the idealized models of vertical and curved 2D valves:</p> <ul> <li>Vertical valves with parameters provided in <a href="https://doi.org/10.1016/j.jcp.2010.08.005">Gil et al., 2010</a></li> <li>Curved valves with parameters provided in <a href="http://doi.org/10.1007/s00466-013-0890-3">Wick, 2014</a></li> <li>source files (.cpp): input data (physical and numerical parameters) for SPHinXsys</li> <li>text files: SPHinXsys (.dat) and Reference (.tsv) results</li> <li>python files (.py): Generates the graphics</li> </ul> <p> </p> <p><strong>inflow-outflow-3D.zip </strong>is the folder with data from the inflow-outflow model in MPS:</p> <ul> <li>Fluid physical properties of water <ul> <li><span>\(\rho=1000kg/m^3 , \,\, \nu=10^{-6}m/s^{-2}\)</span></li> </ul> </li> <li>Pipes of length <span>\(L=0.15m\)</span>: <ul> <li>circular section of diameter <span>\(D=0.1m\)</span>.</li> <li>square section of sides <span>\(S=0.1m\)</span>.</li> </ul> </li> <li>Constante pressure variation (<span>\(\Delta P = 30 \,\, or \,\, 50 \,\, Pa\)</span>) between inflow and outflow: <ul> <li><span>\(\frac{\partial p}{\partial x} = - \frac{\Delta P}{L}, \\ \Delta P = P_{outflow} - P_{inflow}\)</span></li> </ul> </li> </ul> <ul> <li>Sinusoidal pressure variation (<span>\(\Delta P =700Pa \,\, , \,\, T = 2.0s\)</span>) between inflow and outflow <ul> <li><span>\(\frac{\partial p}{\partial x} = - \frac{\Delta P}{L} \sin \omega t \, \\ \omega = \frac{2\pi}{T} \\ Delta P = P_{outflow} - P_{inflow}\)</span></li> </ul> </li> <li>input data (.json, .grid, .stl): physical properties, numerical parameters and geometries for PolyMPS can be found at <a href="https://github.com/rubensamarojr/polymps/tree/inOutflow/input">https://github.com/rubensamarojr/polymps/tree/inOutflow/input</a></li> <li>text files (.txt): PolyMPS and OpenFOAM results</li> <li>python files (.py): Generates the graphics</li> </ul> <p> </p> <p><strong>References</strong></p> <p><a href="https://doi.org/10.1016/j.jcp.2010.08.005">A. J. Gil. The Immersed Structural Potential Method for haemodynamic applications. J. Comput. Phys., 229 (2010), pp. 8613-8641</a></p> <p><a href="https://doi.org/10.1007/s00466-013-0890-3">T. Wick. Flapping and contact FSI computations with the fluid–solid interface-tracking/interface-capturing technique and mesh adaptivity. Comput Mech 53, 29–43 (2014)</a></p> <p><a href="https://doi.org/10.1016/j.cma.2014.10.040">D. Kamensky, et al. An immersogeometric variational framework for fluid–structure interaction: Application to bioprosthetic heart valves Comput. Methods Appl. Mech. Engrg., 284 (2015), pp. 1005-1053</a></p> <p><a href="https://doi.org/10.1016/j.cma.2015.12.023">C. Kadapa et al. A fictitious domain/distributed Lagrange multiplier based fluid–structure interaction scheme with hierarchical B-Spline grids. Comput. Methods Appl. Mech. Engrg., 301 (2016), pp. 1-27</a></p> <p><a href="https://doi.org/10.1016/j.jcp.2015.10.015">Jie Liu. A second-order changing-connectivity ALE scheme and its application to FSI with large convection of fluids and near contact of structures. J. Comput. Phys., 304 (2016), pp. 308-423</a></p>
SWAN wave model simulations of the Terra Nova Bay Polynya
<p>Results of SWAN model simulations of the Terra Nova Bay Polynya, described in Herman and Bradtke 2023 "Fetch-limited, strongly forced wind waves in waters with frazil and grease ice — spectral modelling and satellite observations in an Antarctic coastal polynya".</p> <p>The zip file contains two folders:</p> <ol> <li>"swan", with subfolders:</li> </ol> <ul> <li>"input" (input grids, wind, and ice concentration for the ten polynya events)</li> <li>"S0" (SWAN input files and results for mode version S0)</li> <li>"S2_f5" (SWAN input files and results for mode version S2_f5)</li> </ul> <ol> <li>"Tp_from_satellite_swangrid" (peak wave periods and peak wave directions derived from satellite data, interpolated onto the grid of the SWAN model)</li> </ol> <p>Input files for other model versions discussed in the paper can be easily obtained by manipulating coefficients in *.swn files.</p> <p>The input files work with SWAN version 41.45</p>
Automatic message sequence chart creation from simulation run of the Chandy-Lamport algorithm modeled by colored Petri net
<p>Videos of two message sequence chart creation from simulation runs of the Chandy-Lamport algorithm modeled by colored Petri net using the CPN tool.</p> <p><strong>Message Sequence Chart Of Model With Automatic Simulation Run_SuppInfo.mp4</strong>: This video shows the automatic generation of a message sequence chart of a proposed colored Petri net model of the Chandy-Lamport distributed global snapshot algorithm using the CPN tool version 4.0.1. The video has been generated by the authors' updated extension server of the CPN tool. The automatic simulation run of the model has been used to create this video. The CPN tool randomly selects the enabled transition in an automatic simulation run.</p> <p><strong>Message Sequence Chart Of Model With Step-By-Step Simulation Run_SuppInfo.mp4:</strong> This video shows the automatic generation of a message sequence chart of the proposed colored Petri net model of the Chandy-Lamport algorithm in a step-by-step simulation run with our updated extension server of the CPN tools version 4.0.1. We fired our selected enabled transition of the model to create this video.</p>
Clear-sky Outgoing Longwave Radiation Fluxes from Offline RTE-RRTMGP for AMIP Simulation of CMIP6 Models
<p>This study utilizes RTE-RRTMGP (<a href="https://doi.org/10.1029/2019MS001621">https://doi.org/10.1029/2019MS001621</a>) to compute clear-sky, aerosol-free outgoing longwave radiation (OLR) fluxes for AMIP simulation of CMIP6 models, using 36-year average of monthly-mean temperature and humidity profiles at 19 pressure level as an input. This dataset is used to investigate the cause of inter-model spread in OLR when the same set of radiative transfer schemes is used.</p>
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.