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700 results for “Dynamical model”
NAIADES Dynamical Treatments Suggestion Tool Modelling Dataset
<p>This data was generated within the European NAIADES project (grant agreement No 820985) for the development of the Dynamical Treatments Suggestion (DTS) Service. The DTS purpose is the estimation of the most efficient treatments (dosage of coagulant and chlorine) for drinking Water Treatment Plants (dWTPs) whose configuration is: coagulation/sedimentation, filtration and chlorination. The inlet water quality (pH, conductivity and turbidity) of the dWTP is used as input of the service. Then, it suggests the most efficient treatments that guarantee good drinking water quality at the outlet of the dWTP, based on WHO recommendations (turbidity below 5 NTU and chlorine concentration between 0.5 and 1 mg/L).</p> <p>The dataset includes data generated with Stimela, an open source water treatments processes simulation SW; and data collected in a scaled down replica of a real dWTP.</p>
Datasets for "Dynamics and deposits of pyroclastic density currents in magmatic and phreatomagmatic eruptions revealed by a two-layer depth-averaged model"
<p>Dataset for the manuscript entitled "Dynamics and Deposits of Pyroclastic Density Currents in Magmatic and Phreatomagmatic Eruptions Revealed by a Two-Layer Depth-Averaged Model" by H. A. Shimizu, T. Koyaguchi, and Y. J. Suzuki for submission in Geophysical Research Letter. This contains datasets for each run.</p>
Dataset with the node discretisations employed for training advection models in "Multi-scale rotation-equivariant graph neural networks for unsteady Eulerian fluid dynamics"
<p>Dataset with the node discretisations employed for training advection models in "Multi-scale rotation-equivariant graph neural networks for unsteady Eulerian fluid dynamics" (https://doi.org/10.1063/5.0097679).</p> <p>The training code is available at https://github.com/mario-linov/graphs4cfd.</p>
Data and Code for Blaszczak et al. 2023, Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience
<p>Data and code for analyses in Blaszczak et al. 2023, Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience.</p> <p>See publication and ReadMe file for analysis description and further details. </p> <p>bioRxiv pre-print: Blaszczak, J.R., Yackulic, C., Shriver, R., & R.O. Hall, Jr. 2023. Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience. https://doi.org/10.1101/2023.04.11.535773</p>
Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase.
<p>The data deposited here accompany the manuscript "Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase" and include the molecular dynamics trajectories and the AMBER topology (parm) files. Detailed file contents are summarized in the README file.</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>
Data from: Evaluating the importance of individual heterogeneity in reproduction to Weddell seal population dynamics using integral projection models
<ol> <li>Identifying and accounting for unobserved individual heterogeneity in vital rates in demographic models is important for estimating population-level vital rates and identifying diverse life-history strategies, but much less is known about how this individual heterogeneity influences population dynamics.</li> <li>We aimed to understand how the distribution of individual heterogeneity in reproductive and survival rates influenced population dynamics using vital rates from a Weddell seal population by altering the distribution of individual heterogeneity in reproduction, which also altered the distribution of individual survival rates through the incorporation of our estimate of the correlation between the two rates and assessing resulting changes in population growth.</li> <li>We constructed an integral projection model (IPM) structured by age and reproductive state using estimates of vital rates for a long-lived mammal that has recently been shown to exhibit large individual heterogeneity in reproduction. Using output from the IPM, we evaluated how population dynamics changed with different underlying distributions of unobserved individual heterogeneity in reproduction.</li> <li>Results indicate that the changes to the underlying distribution of individual heterogeneity in reproduction cause very small changes in the population growth rate and other population metrics. The largest difference in the estimated population growth rate resulting from changes to the underlying distribution of individual heterogeneity was less than 1%.</li> <li>Our work highlights the differing importance of individual heterogeneity at the population level compared to the individual level. Although individual heterogeneity in reproduction may result in large differences in the lifetime fitness of individuals, changing the proportion of above- or below-average breeders in the population results in much smaller differences in annual population growth rate. For a long-lived mammal with stable and high adult-survival that gives birth to a single offspring, individual heterogeneity in reproduction has a limited effect on population dynamics. We posit that the limited effect of individual heterogeneity on population dynamics may be due to canalization of life-history traits.</li> </ol>
Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management
<p><span>Extensive applications of fishery stock enhancement worldwide bring up broad concerns about its negative effects, creating a pivotal need for science-based assessment and planning of enhancement strategies. However, the lack of mechanistic understanding of enhanced population dynamics, particularly the density-dependent processes, leads to compromise in model development and limits the capacity in predicting enhancement effects. Here, we developed an individual-based model based on dynamic energy budget theory and full life history processes, to understand the mechanism of density dependence in population dynamics that emerge from individual-level processes. We demonstrated the utility of the model framework by applying it </span><span>to an extensively enhanced species, Chinese prawn (<em>Fenneropenaeus chinensis</em></span><span>, Penaeidae</span><span>). The model could yield projections reflecting the observed trajectory of population biomass and yields. The model also delineated the key effects of density dependence on the vital rates of growth, fecundity, and starvation mortality. Regarding the manifold effects of stock enhancement, we demonstrated a dampened shape in population biomass and yields with increasing magnitude of enhancement, and trade-offs between the ecological and economic objectives, i.e., pursuing high benefit might compromise the wild population without proper management. Furthermore, we illustrated the possibility of combining stock enhancement and harvest regulation in promoting population recovery while maintaining fisheries yields. We highlight the potential of the proposed model for understanding density dependence in enhancement program, and for designing integrated management strategies. The approach developed herein may serve as a general approach to assess the population dynamics in stock enhancement and inform enhancement management.</span><span> </span></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>
Data and code for: A quantitative model for spatio-temporal dynamics of root gravitropism
<p>This repository contains the experimental data presented in "A quantitative model for spatio-temporal dynamics of root gravitropism" and Python scripts for the presented root model.</p>
Extending a generic and fast coarse-grained molecular dynamics model to examine the mechanical behavior of grafted polymer nanocomposites: data set
<p>Abstract:<br> from [1]</p> <blockquote> <p>Polymer nanocomposites are an important class of materials for engineering applications due to their high versatility and good mechanical properties combined with low density. By directly attaching the polymer chains to the nanofillers, the so-called grafting, a better load transfer between matrix and filler is achieved, and, in addition, a better dispersion of the fillers is obtained. Both result in enhanced mechanical properties. Since experimental investigations on the nanoscale are extremely challenging, complementary numerical studies are needed to unravel the mechanical behavior of polymer nanocomposites. To this end, molecular dynamics is ideally suited since it captures the microstructure, but is also numerically expensive. Therefore, this contribution presents a fast coarse-grained molecular dynamics model for the investigation of the mechanical behavior of grafted polymer nanocomposites. For this purpose, we extend an existing model by grafting bonds, which allows us to compare the effect of untreated and grafted fillers directly. In particular, we investigate the influence of filler content, grafting degree, and filler size on the stiffness and strength of the polymer (grafted) nanocomposites. We conclude that the grafting bonds have little effect on the stiffness, while the strength is significantly improved compared to the untreated fillers, which is in agreement with the literature. The presented molecular dynamics model for polymer grafted nanocomposites provides the basis for further investigations, particularly of the crucial matrix-filler interphase. In addition, this contribution translates molecular dynamics insights into mechanical properties, which bridges the gap to the engineering scale and thus represents a step towards exploiting the full potential of polymer (grafted) nanocomposites.</p> </blockquote> <p> </p> <p><strong>Contact:</strong></p> <p>Maximilian Ries<br> Institute of Applied Mechanics<br> Friedrich-Alexander-Universität Erlangen-Nürnberg<br> Egerlandstr. 5<br> 91058 Erlangen</p> <p><strong>Software:</strong></p> <p>All MD simulations were performed with LAMMPS [2,3], version: 29 Oct 2020 / 20201029</p> <p>Compiled with<br> Compiler: GNU C++ 4.8.5 20150623 (Red Hat 4.8.5-39) with OpenMP not enabled<br> C++ standard: C++11</p> <p>Active compile time flags:<br> -DLAMMPS_GZIP<br> -DLAMMPS_SMALLBIG</p> <p>Installed packages:<br> CLASS2, KSPACE, MANYBODY, MC, MOLECULE, MPIIO, OPT, VORONOI, USER-INTEL, USER-MISC, USER-MOLFILE, USER-NETCD</p> <p>Polymer and polymer composite samples generated with self-avoiding random-walk algorithm [4]</p> <p>Post-processing Matlab R2019b</p> <p><strong>License:</strong></p> <p>Creative Commons Attribution 4.0 International</p> <p><strong>Context:</strong></p> <p>Data set supplementing journal paper:</p> <p>[1] M. Ries, S. Reber, P. Steinmann, & S. Pfaller, “Extending a generic and fast coarse-grained molecular dynamics model to examine the mechanical behavior of grafted polymer nanocomposites,” <em>Forces in Mechanics</em>, vol. 12, p. 100 207, <strong>2023</strong>.</p> <p><strong>Content:</strong></p> <p>structure of data set:</p> <ul> <li>04_Equilibration<br> folders containing the sample equilibration used in the presented parameter study <ul> <li>01_filler_content<br> variation of filler content</li> <li>02_grafting_density<br> variation of grafting density</li> <li>03_grafting_potential<br> variation of grafting potential</li> <li>04_filler_size<br> variation of filler size</li> <li>05_reference<br> reference samples without grafting</li> </ul> </li> <li>05_UT<br> folders containing the uniaxial tension simulations used in the presented parameter study <ul> <li>01_filler_content<br> variation of filler content</li> <li>02_grafting_density<br> variation of grafting density</li> <li>03_grafting_potential<br> variation of grafting potential</li> <li>04_filler_size<br> variation of filler size</li> <li>05_reference<br> reference samples without grafting</li> </ul> </li> </ul> <p>Each simulation directory contains:</p> <ul> <li> <p>lammps input file (*.in) of the specific simulation</p> </li> <li> <p>data file (*.data) containing the initial sample configuration</p> </li> <li> <p>input.prm: input parameters of the specific simulation (read by the input file)</p> </li> <li> <p>meta.info: meta data of the specific simulation run</p> </li> <li> <p>LAMMPS_out:<br> simulation results (lammps thermo_out) in tabulated form, an overview of columns is given below</p> <ul> <li> <p>thermo_out.Dat: raw output </p> </li> <li> <p>thermo_out_SG.Dat: smoothed output (Savitzky-Golay filter)</p> </li> <li> <p>thermo_out_STD.Dat: standard deviation of raw output</p> </li> </ul> </li> </ul> <p>Output quantities (columns of *.Dat files):<br> Please note that the normalized Lennard-Jones unit set is used, so all quantities are normalized to fundamental mass, length, energy, time and the Boltzmann constant. Thus all entries are unitless [1].</p> <ul> <li> <p>Step: time step </p> </li> <li> <p>Time: time </p> </li> <li> <p>TotEng: total energy </p> </li> <li> <p>PotEng: potential energy</p> </li> <li> <p>KinEng: kinetic energy </p> </li> <li> <p>E_pair: pair energy </p> </li> <li> <p>E_bond: bond energy </p> </li> <li> <p>E_angle: angle energy </p> </li> <li> <p>E_dihed: dihedral energy </p> </li> <li> <p>Temp: temperature</p> </li> <li> <p>Press: hydrostatic pressure</p> </li> <li> <p>Pxx: xx component of pressure tensor </p> </li> <li> <p>Pyy: yy component of pressure tensor </p> </li> <li> <p>Pzz: zz component of pressure tensor </p> </li> <li> <p>Pxy: xy component of pressure tensor</p> </li> <li> <p>Pxz: xz component of pressure tensor</p> </li> <li> <p>Pyz: yz component of pressure tensor</p> </li> <li> <p>Volume: volume of simulation box </p> </li> <li> <p>Lx: box length in x direction </p> </li> <li> <p>Ly: box length in y direction </p> </li> <li> <p>Lz: box length in z direction </p> </li> <li> <p>Density: density </p> </li> <li> <p>c_RG: radius of gyration scalar </p> </li> <li> <p>c_RG[1]: squared radius of gyration tensor (xx component) </p> </li> <li> <p>c_RG[2]: squared radius of gyration tensor (yy component) </p> </li> <li> <p>c_RG[3]: squared radius of gyration tensor (zz component) </p> </li> <li> <p>c_RG[4]: squared radius of gyration tensor (xy component) </p> </li> <li> <p>c_RG[5]: squared radius of gyration tensor (xz component) </p> </li> <li> <p>c_RG[6]: squared radius of gyration tensor (yz component) </p> </li> <li> <p>c_bondave[1]: bond energy averaged over all atoms </p> </li> <li> <p>c_bondave[2]: bond distance averaged over all atoms </p> </li> <li> <p>c_bondave[3]: squared bond distance averaged over all atoms </p> </li> <li> <p>c_angleave[1]: angle energy averaged over all atoms </p> </li> <li> <p>c_angleave[2]: angle averaged over all atoms degree</p> </li> <li> <p>c_angleave[3]: cosine of angle </p> </li> <li> <p>c_angleave[4]: squared cosine of angle </p> </li> <li> <p>c_MSD[1]: mean squared displacement x-direction </p> </li> <li> <p>c_MSD[2]: mean squared displacement y-direction </p> </li> <li> <p>c_MSD[3]: mean squared displacement z-direction </p> </li> <li> <p>c_MSD[4]: total mean squared displacement </p> </li> <li> <p>c_COM[1]: x coordinate of center of mass </p> </li> <li> <p>c_COM[2]: y coordinate of center of mass </p> </li> <li> <p>c_COM[3]: z coordinate of center of mass </p> </li> <li> <p>v_strain_xx: xx component of engineering strain tensor </p> </li> <li> <p>v_strain_yy: yy component of engineering strain tensor </p> </li> <li> <p>v_strain_zz: zz component of engineering strain tensor </p> </li> <li> <p>v_vMisesequivstress: von Mises equivalent stress </p> </li> <li> <p>v_Cauchy_xx: xx component of stress tensor </p> </li> <li> <p>v_Cauchy_yy: yy component of stress tensor</p> </li> <li> <p>v_Cauchy_zz: zz component of stress tensor</p> </li> <li> <p>v_Cauchy_xy: xy component of stress tensor </p> </li> <li> <p>v_Cauchy_xz: xz component of stress tensor </p> </li> <li> <p>v_Cauchy_yz: yz component of stress tensor </p> </li> <li> <p>v_strain_xy: xy component of engineering strain tensor </p> </li> <li> <p>v_strain_xz: xz component of engineering strain tensor </p> </li> <li> <p>v_strain_yz: yz component of engineering strain tensor </p> </li> </ul> <p><strong>References</strong>:</p> <p>[1] M. Ries et al., “Extending a generic and fast coarse-grained molecular dynamics model to examine the mechanical behavior of grafted polymer nanocomposites,” <em>Forces in Mechanics</em>, vol. 12, p. 100 207, <strong>2023</strong>.</p> <p>[2] S. Plimpton, “Fast parallel algorithms for short-range molecular dynamics,” <em>Journal of computational physics</em>, <strong>1995</strong>, 117, 1-19.</p> <p>[3] A. P. Thompson et al., “LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales,” <em>Computer Physics Communications</em>, vol. 271, p. 108171, <strong>2022</strong>.</p> <p>[4] M. Ries, V. Dötschel, J. Seibert, S. Pfaller. “A self-avoiding random walk algorithm (SARW) for generic thermoplastic polymers and nanocomposites”, <em>Zenodo</em>, 2022. <a href="https://doi.org/10.5281/zenodo.6245699">https://doi.org/10.5281/zenodo.6245699</a></p>
Statistical and Dynamic Model of Surface Morphology Evolution during Polishing in Additive Manufacturing
<p>This repository maintains data and code associated with our accepted paper in IISE Transactions titled "Statistical and Dynamical model of Surface Morphology Evolution during Polishing in Additive Manufacturing". To briefly summarize,</p> <p><strong>1. Polishing_stagewise_data.zip</strong> - Contains height values measured at 32 different locations on the 3D printed sample using an optical profilometer prior to polishing (Stage 0) and post every stage of polishing (Stages 1 to 6). Please refer to the following paper for experimentation details and process parameters: "<em>Jin, S., A. Iquebal, S. Bukkapatnam, A. Gaynor, and Y. Ding (2019, 10). A gaussian process model-guided surface polishing process in additive manufacturing. Journal of Manufacturing Science and Engineering 142, 1–17.</em>"</p> <p><strong>2. Initial_surface_generation.m</strong> - Script containing the Initial surface generation algorithm using the random circle packing algorithm. This file generates the surface asperity distribution and their graph connectivity of a 3D printed sample prior to polishing (Figure 4(b) in paper). One such realization is stored and compared with experimental data (Refer #3).</p> <p><strong>3. Stage0_fitted_data.mat</strong> - .mat file containing data pertaining to height measures of the 3D printed sample prior to polishing and generated initial surface (simulation) which is statistically similar to the actual data.</p> <p><strong>4. Parameter_fitting_Polishing.m</strong> - Script containing the model capturing polishing dynamics with network formation, evaluated at each stage of polishing. This file generates the Bearing Area Curves of the initial surface simulated after each stage of polishing and compares with experimental data (Figures 3, 5, 6, 7 and 8 in paper). (The script makes use of other functions defined in #5).</p> <p><strong>5. surface_roughness.m, graph_evolution.m, solve_for_d.m, KLDiv.m</strong> and <strong>Gen_hurst.m</strong> - Matlab scripts containing functions that are called within the main script (Parameter_fitting_Polishing.m)</p> <p><strong>6. Simulated_Annealing.zip</strong> - Zip file containing files related to Simulated Annealing Algorithm. Please read the <strong>README_Simulated_Annealing.txt</strong> for instructions to reproduce the optimized parameter solutions.</p> <p><strong>7. pub_fig.m</strong> - Script containing the formatting options for plots and figures.</p>
A dynamic von Mises-based model to evaluate the impact of urbanization and climate change on flood timing in Yangtze and Huaihe River Basins, China
<p>The daily streamflow data extracted from 8 selected stations from the Huaihe and Yangtze River Basins, China.</p>
Investigating cooccurrence patterns and dynamics for many imperfectly detected species, using a log-linear modelling parameterisation
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Modeling single-cell heterogeneity in signaling dynamics of macrophages reveals principles of information transmission
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A dynamic in vitro model of Down Syndrome neurogenesis with Trisomy 21 gene dosage correction
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'CellTrajectory' for cellular automata modelling of leukaemic stem cell dynamics in acute myeloid leukaemia: insights into predictive outcomes and targeted therapies
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Modelling seasonal dynamics of secondary growth in R
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Effects of temporal abiotic drivers on the dynamics of an allometric trophic network model
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Data for: Coupling dynamic energy budget and population dynamic models to inform stock enhancement in fisheries management
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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.