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9,153 results for “behavior”
Data for "Exemplifying parametric timed specifications over signals with bounded behavior"
<p>Data for "<strong>Exemplifying parametric timed specifications over signals with bounded behavior</strong>" by Étienne André, Masaki Waga, Natuski Urabe, and Ichiro Hasuo, published in the proceedings of the 14th NASA Formal Methods Symposium (NFM 2022)</p> <p>See README.md in the zipped file for explanations and instructions for reproductibility.</p>
Longitudinal structural MRI, MRS, and behavioral data for mice prenatally exposed to maternal immune activation at gestational day 9
<p>Previous evidence from our lab (https://cobralab.ca/) and others suggest that prenatal exposure to maternal immune activation (MIA) can impact trajectories of neurodevelopment as measured through brain anatomy and behavior in mice. Yet, there are still open questions regarding the alterations to developmental trajectories, as well as the impact on brain chemistry, that this data set seeks to explore. The dataset presented here includes magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) data from two timepoints, adolescence (postnatal day [PND 35]) and young adulthood (PND 60) in C57BL/6J mice prenatally exposed either to poly I:C (POL) inducing maternal immune activation (MIA) or saline (SAL) at gestational day (GD) 9. The dataset also includes three behaviors acquired after each scanning session with 2 days of rest between the scans and each behavior: open field test, social novel object preference test, and prepule inhibition. Finally, the data also include cytokine assays acquired from a separate sample of pregnant mice and a test-retest of MRS acquired from a voxel in the anterior cingulate area. </p> <p>The data here published were collected and analyzed for a paper under review, available as a preprint where more details can be found here: https://www.preprints.org/manuscript/202203.0136/v1. In brief, using whole-brain, voxelwise analysis techniques (deformation-based morphometry) we found MIA subtly altered developmental trajectories, reducing volume relative to SAL offspring in the hippocampus and the anterior, right caudate putamen, and increasing volume in the posterior, left caudate putamen and cerebellum. Additionally, there was a trending decrease of myo-inositol and GABA in MIA offspring at PND 60 compared to SAL controls. Finally, there was a trending decrease in ratio of distance travelled in the anxiogenic center zone of an open field compared to the outer areas at PND 35 for MIA offspring. </p> <p>In this dataset you will find a total of <strong>80 preprocessed structural MRIs</strong> in minc format acquired at postnatal day ~35 and ~60 in mice exposed to 5mg/kg poly I:C or vehicle control (0.9% sterile saline) at GD9. The images are included in CUPO_MIA_mncs.zip. These are T1-weighted structural images with two averages; repetition time (TR)/echo time (TE) = 21.55 ms/5.13 ms, matrix size = 260 x 158 x 210, voxel dimensions =&thinsp;70 µm isotropic, flip angle =&thinsp;20°, 23 min total using 5% isoflurane for induction, 1.5% for maintenance of anesthesia during the scan on a cryogenically-cooled surface coil. T1-weighted scans were preprocessed by stripping native coordinates, flipping left-right to maintain fidelity, denoising, correcting inhomogeneities in the bias field using the N4 algorithm, and registering in LSQ6 alignment (i.e. 6 degrees of freedom are allowed for imagine alignment: translations and rotations along x, y, and z dimensions). The demographics information for each animal is included in the <strong>demographics.csv</strong> file. </p> <p>Behavioural tests were performed following the postnatal day 35 and 60 scans in all animals with a 2 day rest period. These include: open field test, three chambered social approach, and prepulse inhibition. The data for all of these tests is presented in individual .csv spreadsheet and includes data for both the timepoints evaluated. Additionally, cytokine panels were collected from an independent cohort of 7 dams. <strong>MRS </strong>data are included in two formats: 1) preprocessed quantifications from LCModel software in csvs, and 2) raw data with press and press_w (respectively water supressed and unsupressed acquisitions) for analysis. The raw data were released in upload version 1.1.0. MRS was acquired from a 1.2 x 2.6 x 2.5 mm3 voxel in the ACA with a Point Resolved Spectroscopy sequence (PRESS; TR/TE=3000/8.5 ms, 256 averages). Within the raw_data.zip,</p> <p>Included in this data set are the structural MRIs in MINC format, the behavioural .csv data, the MRS data (csvs and raw files), and a <strong>README</strong> file providing further detail on the data structure and content, and on how to interpret the data column titles. DICOMS are also available for the structural MRI data, as are the raw (not-preprocessed) MINC files, available upon request to the authors. </p>
Caregivers and MDR-TB patients: Dataset for the importance of knowledge and behavior on drug resistance tuberculosis
<p>Multidrug-resistant Tuberculosis (MDR-TB) is a type of Tuberculosis (TB) that is resistant to at least one or more of the main anti-TB drugs, namely Rifampin or Isoniazid, so this infection is more difficult to eliminate. Good knowledge and behavior of caregivers and patients can affect the success of treatment because they tend not to be late in taking treatment. In this data note we provide the details of a research database of 228 MDR-TB caregivers and patients underwent treatment from January 2020 to December 2021 in preferred hospital in West Java, Indonesia. The purposes of this publication are to describe the dataset for external researchers who may be interested in making use of it, and to detail the methods used to obtain the dataset to determine the level of knowledge and behavior of MDR-TB caregivers and patients regarding the disease through a validated questionnaire consisted of the knowledge and behavior distributed to respondents via online and offline.</p>
Prosthetic Sockets: Tensile Behavior of Vacuum Infiltrated Fused Deposition Modeling Sandwich Structure Composites
<p>The development of novel materials will enable a new generation of prosthetic devices to be built with additive manufacturing (AM). Vacuum infiltrated sandwich structure composites are a promising approach for building prosthetic sockets via AM. In this dataset, we test the tensile properties of 18 different composite material configurations using ASTM D638. These composites were manufactured using a custom vacuum infiltration method and had varying filament materials, infiltrated matrix materials, and print directions. Several material-matrix-print composites showed higher ultimate tensile strengths and reduced anisotropy compared to full-infill control samples. However, the mechanical properties of these composites were limited by a large degree of porosity due to the manufacturing method. Still, the results were promising enough to create a proof of concept prosthetic socket via the vacuum infiltration method. Future research should focus on reducing porosity defects and investigating additional material-matrix-print combinations.</p>
Pathogen prevalence modulates medication behavior in ant Formica fusca
<p><span>Ants face unique challenges regarding pathogens, as the sociality which has allowed them to form large and complex colonies also raises the potential for transmission of disease within these colonies. To cope with the threat of pathogens, ants have developed a variety of behavioral and physiological strategies. One of these strategies is self-medication, in which animals use biologically active compounds to combat pathogens in a way which would be harmful in the absence of them. <em>Formica fusca</em> ants are to date the only species of ants proven to successfully self-medicate against an active infection caused by a fungal pathogen by supplementing their diet with food containing hydrogen peroxide. Here, we build on that research by investigating how the prevalence of disease in colonies of <em>F. fusca</em> affects the strength of the self-medication response. We exposed either half of the workers of each colony or all of them to a fungal pathogen and offered them different combinations of diets. We see that workers of <em>F. fusca</em> engage in self-medication behavior even if exposed to a low lethal dose of a pathogen, and that the strength of that response is affected by the prevalence of the disease in the colonies. We also saw that the infection status of the individual foragers did not significantly affect their decision to forage on either control food or medicinal food as uninfected workers were also foraging on hydrogen peroxide food, which opens up the possibility of kin medication in partially infected colonies. Our results further affirm the ability of ants to self-medicate against fungal pathogens, shed new light on plasticity of self-medication and raise new questions to be investigated on the role self-medication has in social immunity.</span></p>
Data set of Reversing anterior insular cortex neuronal hypoexcitability attenuates compulsive behavior in juvenile rats
<p>Development of self-regulatory competencies during adolescence is partially dependent on normative brain maturation. Here we report that adolescent rats as compared to adults exhibit impulsive and compulsive-like behavioral traits, the latter being associated with lower expression of mRNA levels of the immediate early gene zif268 in the anterior insula cortex (AIC). This suggests that underdeveloped AIC function in adolescent rats could contribute to an immature pattern of interoceptive cue integration in decision-making and a compulsive phenotype. In support of this, we report that layer 5 pyramidal neurons in the adolescent rat AIC are hypoexcitable and receive fewer glutamatergic synaptic inputs compared to adults. Chemogenetic activation of the AIC attenuated compulsive traits in adolescent rats supporting the idea that in early stages of AIC maturity there exists a suboptimal integration of sensory and cognitive information that contributes to inflexible behaviors in specific conditions of reward availability.</p>
Stimulation of medial amygdala GABA neurons with kinetically different channelrhodopsins yields opposite behavioral outcomes
<p>This dataset represents the raw data that gave rise to the study by Baleisyte et al., Cell Reports 2022 (DOI: 10.1016/j.celrep.2022.110850), previously published as a preprint at bioRxiv (DOI: 10.1101/2021.06.30.450543). Please refer to the original publication regarding experimental design and methodological details of data acquisition and analysis. Below we supply information on the provided metadata files which, in turn, refer to individual raw data files.</p> <p><strong>General repository structure:</strong></p> <ul> <li>the raw data is organized in 11 datasets related to the Figures 1, S1, 2, S2, 3A-H, 3I-K, 3L-N, S3A-I, S3J-P, 4A;C-G;H_top;I-J;S4, 4B;C-G;H_bottom;I-J;S4;</li> <li>the metadata listing individual data filenames from the individual dataset are stored in separate “.csv” files, one per dataset. Field separator: comma;</li> <li>the custom script for the reconstruction of the optic fiber placement is described in a separate metadata file “script_metadata.csv”. Field separator: comma;</li> <li>all individual metadata files are summarized in a master metadata file “metadata_master.csv”. Field separator: comma.</li> <li>the data files related to Figures 2, S2, S3A-I are continued in a separate linked repository accessible by the following doi: 10.5281/zenodo.6489354</li> </ul> <p> </p> <p><strong>Description of the data formats:</strong></p> <ul> <li>video recordings of resident-intruder test experiments (Figures 1, 3, S1) are provided as unmodified “.mpg” files created by the acquisition software EthoVision (Noldus Information Technology). The files were, however, renamed for convenience. Video stream parameters: MPEG-4 (DIVX) codec, color space yuv420p, 1280x512 pixels, 30 fps. Along with each video file, there is an associated text file (“.txt”) containing the metadata of video recording and the timestamps of hardware state changes. In these files, unmodified after creation by the EthoVision software, the status of hardware TTL inputs was logged whenever a change of state of these inputs was detected. Typically, “input 2” was sampling the gating signal from the Master-8 pulse generator, with the "high" signal level indicating the application of train of light pulses. This hardware state, signaling the presence of the light train, is noted in the individual metadata files; </li> <li>widefield fluorescent images of single coronal sections containing the MeApd (Figures 2, S2) were converted from the proprietary format of Olympus slide scanning microscope into composite TIFF format, readable by FIJI/ImageJ (<a href="https://fiji.sc/">https://fiji.sc/</a> or <a href="https://imagej.net/Fiji/Downloads">https://imagej.net/Fiji/Downloads</a>). The information on pixel resolution and inter-section distance is embedded in the individual image files as TIFF metadata. Attribution of fluorescent probes to the color channels is given in the corresponding metadata files.</li> <li>confocal fluorescent image stacks acquired from single coronal sections containing MeApd (Figure S3) are provided in composite TIFF format after stitching the tiles (originally stored as “lsm” format; Carl Zeiss) using a stitching plugin (Preibisch et al., Bioinformatics 2009) in FIJI. The information on pixel resolution is embedded inside the individual image files as TIFF metadata. Attribution of fluorescent probes to the color channels is given in the corresponding metadata file. For each stack, a region of interest (ROI) highlighting the borders of the MeApd is provided as a separate file in a “.roi“ format (FIJI).</li> <li>patch clamp recordings (Figures 4, S4) are provided as “.dat” files, unmodified from the original version created by the acquisition software PatchMaster (HEKA Elektronik, Germany). Besides by the original PatchMaster software, these files can be imported using one of the following methods: I) via Igor Pro extension bpc_ReadHeka.xop (for 32-bit Igor Pro versions 5.xx - 6.37) by Holger Taschenberger (<a href="https://www.wavemetrics.com/project/bpc_ReadHeka">https://www.wavemetrics.com/project/bpc_ReadHeka</a>); II) via Python script by Luke Campagnola (<a href="https://github.com/campagnola/heka_reader">https://github.com/campagnola/heka_reader</a>); III) via Matlab script HEKA PatchMaster Importer by Christian Keine (<a href="https://github.com/ChristianKeine/HEKA_Patchmaster_Importer">https://github.com/ChristianKeine/HEKA_Patchmaster_Importer</a>).</li> </ul>
Mechanical behavior of textile reinforced alkali-activated mortar based on fly ash, metakaolin and ladle furnace slag
<p>Data corresponding to all figures and tables presented in the publication</p>
Data and code of "Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats"
<p>This dataset contains behavioral and transcriptomic data, and the original code related to the following article:</p> <p>Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats. Fanny Demars, Ralitsa Todorova, Gabriel Makdah, Antonin Forestier, Marie-Odile Krebs, Bill P Godsil, Thérèse M Jay, Sidney I Wiener, & Marco N Pompili (2022) Current Biology <em>32. https://doi.org/10.1016/j.cub.2022.05.050</em></p>
raw behavioral data, raw questionnaire data, and raw neuroimaging data for a genuine-and-pretended disgust task
<p>Raw behavioral data, raw questionnaire data, and raw neuroimaging data for a genuine-and-pretended disgust task. Particularly, a document indicating all parameters used in the datasets and file names is attached as well.</p>
Data from: Evolved differences in thermal plasticity of mosquitofish mating behavior are unrelated to source temperature
<p>Phenotypic plasticity in response to temperature is expected to play a key role in how organisms cope with climate change. Evolved differences in plastic responses are often linked to historical differences in average temperatures, yet we know little about how behavioral plasticity is affected by prevailing thermal environments. In this study, we used a common-garden design to test whether historical differences in average temperatures caused evolutionary divergence in the plasticity of mating behavior of Western mosquitofish (<em>Gambusia affinis</em>) inhabiting geothermal springs with average source temperatures spanning from 18.8 to 33.3 C. We found population differences in the thermal plasticity of courtship displays, copulation attempts, copulations, and mating efficiency, but these differences could not be explained by average source temperatures. We also tested for differences in thermal optima and maximum performance in mating behavior among populations. We found that only the maximum number of displays differed among populations, although these differences were also unrelated to source temperature. While temperature may have predictable evolutionary consequences for some thermally sensitive traits, our findings are inconsistent with theoretical predictions of evolutionary responses to divergent average temperatures, highlighting the need for greater synergy between empirical and theoretical work to understand thermal adaptation.</p>
Prosocial behavior in adult mice is sex-dependent
<p>The data from three behavioral test performed on adult male and female C57BL/6 mice.</p> <p><strong>1_Misiolek_et_al_2022_Prosocial.csv</strong></p> <p>Two-choice food motivated prosocial behavior task.</p> <p><strong>2_Misiolek_et_al_2022_SCPP.csv</strong></p> <p>Social conditioned place preference test.</p> <p><strong>3_Misiolek_et_al_2022_Affective_State_Discriminatiion.csv</strong></p> <p>Affective State Discrimination test.</p>
Behavioral "bycatch" from camera trap surveys yields insights on prey responses to human-mediated predation risk
<p>Human disturbance directly affects animal populations but indirect effects of disturbance on species behaviors are less well understood. Camera traps provide an opportunity to investigate variation in animal behaviors across gradients of disturbance. We used camera trap data to test predictions about predator-sensitive behavior in three ungulate species (caribou Rangifer tarandus; white-tailed deer, Odocoileus virginianus; moose, Alces alces) across two boreal forest landscapes varying in disturbance. We quantified behavior as the number of camera trap photos per detection event and tested its relationship to predation risk between a landscape with greater industrial disturbance and predator abundance (Algar) and a "control" landscape with lower human and predator activity (Richardson). We also assessed the influence of predation risk and habitat on behavior across camera sites within the disturbed Algar landscape. We predicted that animals in areas with greater predation risk (more wolf activity, less cover) would travel faster and generate fewer photos per event, while animals in areas with less predation risk would linger (rest, forage), generating more photos per event. Consistent with predictions, caribou and moose had more photos per event in the landscape where predation risk was reduced. Within the disturbed landscape, no prey species showed a significant behavioral response to wolf activity, but the number of photos per event decreased for white-tailed deer with increasing line of sight (m) along seismic lines (i.e. decreasing visual cover), consistent with a predator-sensitive response. The presence of juveniles was associated with shorter behavioral events for caribou and moose, suggesting greater predator sensitivity for females with calves. Only moose demonstrated a positive association with vegetation productivity (NDVI), suggesting that for other species influences of forage availability were generally weaker than those from predation risk. Behavioral insights can be gleaned from camera trap surveys and provide information about animal responses to predation risk and the indirect impacts of human disturbances.</p>
Evolution of a mosquito's hatching behavior to match its human-provided habitat
<p>A subspecies of the yellow fever mosquito, <em>Aedes aegypti</em>, has recently evolved to specialize in biting and living alongside humans. It prefers human odor and breeds in human-provided artificial containers rather than the forest tree holes of its ancestors. Here, we report one way this human specialist has adapted to the distinct ecology of human environments. While eggs of the ancestral subspecies rarely hatch in pure water, those of the derived human-specialist do so readily. We trace this novel behavior to a shift in how eggs respond to dissolved oxygen, low levels of which may signal food abundance. Moreover, we show that while tree holes are consistently low in dissolved oxygen, artificial containers often have much higher levels. There is thus a concordance between the hatching behavior of each subspecies and the aquatic habitat it uses in the wild. We find this behavioral variation is heritable, with both maternal and zygotic effects. The zygotic effect depends on dissolved oxygen concentration (i.e., GxE), pointing to potential changes in oxygen-sensitive circuits. Together, our results suggest that a shift in hatching response contributed to the pernicious success of this human-specialist mosquito and illustrate how animals may rapidly adapt to human-driven changes in the environment.</p>
An experimental data set for analysis of the thermophysical behavior of a single-story mechanically ventilated double-skin façade (DSF) in fixed boundary conditions corresponding to winter/mid-season and summer cases
<p>Double-skin facades (DSFs) are dynamic and flexible building envelopes that employ a ventilated cavity to either prevent or reduce the solar-induced cooling load or exploit solar energy for passive solar heating. The mechanical ventilation of the cavity offers higher flexibility and control than natural ventilation, as the latter largely depends on stochastic and unpredictable external conditions. Furthermore, when mechanical ventilation rates are combined with the operation of a shading device, the possibilities for controlling the accumulated heat in the cavity of the DSF increase further. Therefore, this experimental campaign systematically investigates how these two important features interact in controlling the cavity's thermal load and airflow conditions. The measurement collected during the experiments constitutes a dataset that contains the results of a series of experimental runs where the different configurations of DSF, in terms of mechanical ventilation rate and venetian blinds, have been subjected to two representative boundary conditions through a climate simulator facility equipped with a solar simulator device. The full-scale DSF mock-up, which includes venetian blinds installed in a 200 mm ventilated cavity, is operated in this experiment in two modes: outdoor air curtain (OAC) and supply air (SA) mode. Tests were carried out under a steady-state regime with different boundary conditions. For the analysis of the utilization of the excess heat accumulated in the cavity and prevention of DSF overheating, boundary conditions corresponding to g-value calculations were selected. For the analysis of air preheating in the DSF cavity, the boundary conditions corresponding to late winter/mid-season weather (cold outdoor air and low-to-moderate solar irradiance) were chosen. The entire set of experimental data collected during the tests is made publicly available to enable the scientific community to access experimental data to further analyze this problem or for model validation purposes. The data set supplements the open-access paper entitled "<strong>Control of heat transfer in single-story mechanically ventilated facades</strong>" (<a href="https://doi.org/10.1016/j.enbuild.2022.112304">https://doi.org/10.1016/j.enbuild.2022.112304</a>), where additional information about the aims of the experiments, the detailed methods, and other data processing procedures can be found. The database is supported by a guide ("Guide.pdf"), where further explanations about how to read data and schematic drawings of the sensor layout are provided. The collection of experimental tests is divided into two files, according to two considered cases:</p> <ul> <li><strong>DSF operating in outdoor air curtain mode </strong>(24 steady-state measurements). The following factors were changed: mechanical ventilation rate (0, 10, 15, 20, 30, 40, 50, and 100 % of maximum fan power) and venetian blind configuration (closed θ=0 º, semi-open θ=45 º, and raised blinds). The outdoor and indoor temperatures, 30 ℃ and 25 ℃, and solar irradiance of 500 Wm<sup>-2</sup> were replicated. [file name: "Summer.csv"],</li> <li><strong>DSF operating in supply air mode</strong> (27 steady-state measurements). The following factors were changed: mechanical ventilation rate (0, 10, 15, 20, 30, 40, 50, 75, and 100 % of maximum fan power) and venetian blind configuration (closed θ=0 º, semi-open θ=45 º, and raised blinds). The outdoor and indoor temperatures, 10 ℃ and 25 ℃, and solar irradiance of 300 Wm<sup>-2</sup> were replicated. [file name: " Winter_MidSeason.csv"]</li> </ul> <p>Any inquiries about the experimental data can be sent to: <a href="mailto:aleksandar.jankovic@ntnu.no">aleksandar.jankovic@ntnu.no</a></p> <p>The activities presented in this paper were carried out within the research project "REsponsive, INtegrated, VENTilated - REINVENT – windows," supported by the Research Council of Norway through the research grant 262198, and the partners SINTEF, Hydro Extruded Solutions, Politecnico di Torino and Aalto University.</p>
Anthropogenic noise and light alter temporal but not spatial breeding behavior in a wild frog
<p><span>Increasing urbanization has led to large scale land-use changes, exposing persistent populations to drastically altered environments. Sensory pollutants, including low-frequency anthropogenic noise and artificial light at night (ALAN), are typically associated with urban environments and known to impact animal populations in a variety of ways. Both ALAN and anthropogenic noise can alter behavioral and physiological processes important for survival and reproduction, including communication and circadian rhythms. Although noise and light pollution typically co-occur in urbanized areas, few studies have addressed their combined impact on species' behavior. Here we assessed how anthropogenic noise and ALAN can influence spatial and temporal variation in breeding activity of a wild frog population. By exposing artificial breeding sites inside a tropical rainforest to multiple sensory environments, we found that both anthropogenic noise and ALAN impact breeding behavior of túngara frogs (<em>Engystomops pustulosus</em>), albeit in different ways. Males arrived later in the night at their breeding sites in response to anthropogenic noise. ALAN, on the other hand, led to an increase in calling effort. We found no evidence that noise or light pollution either attracted frogs to or repelled frogs from</span> <span>breeding sites. Thus, anthropogenic noise may negatively affect calling males by shifting the timing of sexual signaling. Conversely, ALAN may increase the attractiveness of calling males. These changes in breeding behavior highlight the complex ways that urban multisensory pollution can influence behavior and suggest that such changes may have important ecological implications for the wildlife that are becoming increasingly exposed to urban multisensory pollution.</span></p>
Behavior preferences between medium-large mammals in Atlantic Forest and Cerrado inside a public university of Southeastern Brazil
<p>We studied large and medium-sized mammals in a modified landscape between the Atlantic Forest and a Cerrado transitional zone (Brazil). We used eight camera traps between August 2016 and August 2017, totaling 75840 camera hours or 3,160 camera trap days. The sampling effort was evaluated from a rarefaction curve based on the daily sampling. We conducted comparative univariate and multivariate ordination statistical analyses. We recorded 19 species in 13 families. The most recorded species were S. scrofa and Cerdocyon thous , while the least recorded were Cuniculus paca, Didelphis albiventris and Tamandua tetradactyla. Richness and total records do not differ among day period, month, season, vegetation type, and moon phase. Individually, species abundance nevertheless sometimes showed trends for these factors. S. scrofa dominated all landscapes and periods of the year because it is an opportunist species that rapidly reproduces and lacks natural efficient predators. The presence of this species reduces the dissimilarity of the community, but when it is removed, the dissimilarity of native species increases. The modified landscape studied here is an important area for mammalian fauna owing to high richness; some species in the area are threatened with extinction. The wide temporal sampling effort contributed to a high number of mammal species records, although without spatial variation.</p>
Characterization of the material behavior and identification of effective elastic moduli based on molecular dynamics simulations of coarse-grained silica: dataset
<p><strong>Abstract</strong>:<br> (from [1])</p> <blockquote> <p>The addition of fillers can significantly improve the mechanical behavior of polymers. The responsible mechanisms at the molecular level can be well assessed<br> by particle-based simulation techniques, such as molecular dynamics. However, the high computational cost of these simulations prevents the study of macroscopic<br> samples. Continuum-based approaches, particularly micromechanics, offer a more efficient alternative but require precise constitutive models for all<br> constituents, which are usually unavailable at these small length scales. In this contribution, we derive a molecular-dynamics-informed constitutive law by<br> employing a characterization strategy introduced in a previous publication. We choose silicon dioxide (silica) as an exemplary filler material used in polymer<br> composites and perform uniaxial and shear deformation tests with molecular dynamics. The material exhibits elastoplastic behavior with a pronounced anisotropy.<br> Based on the pseudo-experimental data, we calibrate an anisotropic elastic constitutive law and reproduce the material response for small strains accurately. <br> The study validates the characterization strategy that facilitates the calibration of constitutive laws from molecular dynamics simulations. Furthermore, the<br> obtained material model for coarse-grained silica forms the basis for future continuum-based investigations of polymer nanocomposites. In general, the presented<br> transition from a fine-scale particle model to a coarse and computationally efficient continuum description adds to the body of knowledge of molecular science<br> as well as the engineering community.<br> </p> </blockquote> <p><br> <strong>Contact</strong>:<br> Maximilian Ries<br> Institute of Applied Mechanics<br> Friedrich-Alexander-Universität Erlangen-Nürnberg<br> Egerlandstr. 5<br> 91058 Erlangen</p> <p><br> <strong>Software</strong>:<br> All simulations were performed with LAMMPS [3], version: 29 Oct 2020 / 20201029<br> 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<br> Active compile time flags:<br> -DLAMMPS_GZIP<br> -DLAMMPS_SMALLBIG</p> <p><strong>Installed packages:</strong><br> CLASS2, KSPACE, MANYBODY, MC, MOLECULE, MPIIO, OPT, VORONOI, USER-INTEL, USER-MISC, USER-MOLFILE, USER-NETCD</p> <p><br> <strong>License:</strong><br> Creative Commons Attribution 4.0 International<br> <br> <strong>Context</strong>:<br> Data set supplementing journal paper:<br> [1] Ries, M.; Bauer, C.; Weber, F.; Steinmann, P. & Pfaller, S., "Characterization of the material behavior and identification of effective elastic moduli based on molecular dynamics simulations of coarse-grained silica", Mathematics and Mechanics of Solids, 2022, 108128652211080.</p> <p><br> This dataset contains the results presented in [1] and the necessary data to obtain those.</p> <p><br> <strong>Content</strong>:<br> The files to reproduce our simulations and their results are structured as follows:</p> <ul> <li>01_potentials<br> tabulated potentials calibrated via iterative Boltzmann inversion in [2] kindly provided by the Müller-Plathe group at Technische Universität Darmstadt <ul> <li>Angle_table<br> angular interactions</li> <li>Bond_table<br> bond interactions</li> <li>Nonbond_table<br> pair interactions</li> </ul> </li> <li>02_sample<br> Lammps data file (molecular style) of the investigated silica sample</li> <li>03_simulations<br> The condensed simulation directories with the naming convention given below are organized in the following subfolders: <ul> <li>01_time-proportional<br> time-proportional simulation data</li> <li>02_time-periodic<br> time-periodic simulation data</li> </ul> </li> </ul> <p>Each simulation directory contains:</p> <ul> <li>lammps input file (*.in) of the specific simulation</li> <li>input.prm: input parameters of the specific simulation (read by the input file)</li> <li>meta.info: meta data of the specific simulation run</li> <li>LAMMPS_out:<br> simulation results (lammps thermo_out) in tabulated form, an overview of columns is given below <ul> <li>thermo_out.Dat: raw output</li> <li>thermo_out_SG.Dat: smoothed output (Savitzky-Golay filter)</li> <li>thermo_out_STD.Dat: standard deviation of raw output</li> </ul> </li> </ul> <p><br> <strong>Naming convention</strong>:<br> Silica-[deformation]-[direction]_[deformation function]-[deformation magnitude]_[deformation rate]<br> ● [deformation]: uniaxial tension (UT), simple shear (SS)<br> ● [direction]: deformation carried out in X/Y/Z (UT) or XY/XZ/YZ (SS)<br> ● [deformation function]: time-proportional (strain), time-periodic (strain_ampl)<br> ● [deformation magnitude]: maximum strain (time-proportional), strain amplitude (time-periodic); unitless<br> ● [deformation rate]: rate-[strain rate] (only time-proportional): 0.001/ns-0.1/ns</p> <p><br> <strong>Output quantities</strong> (columns of *.Dat files):<br> ● Step: time step<br> ● Time: time in fs<br> ● TotEng: total energy in kcal/mol<br> ● PotEng: potential energy in kcal/mol<br> ● KinEng: kinetic energy in kcal/mol<br> ● E_pair: pair energy in kcal/mol<br> ● E_bond: bond energy in kcal/mol<br> ● E_angle: angle energy in kcal/mol<br> ● E_dihed: dihedral energy in kcal/mol<br> ● Temp: temperature in K<br> ● Press: hydrostatic pressure in atm<br> ● Pxx: xx component of pressure tensor in atm<br> ● Pyy: yy component of pressure tensor in atm<br> ● Pzz: zz component of pressure tensor in atm<br> ● Pxy: xy component of pressure tensor in atm<br> ● Pxz: xz component of pressure tensor in atm<br> ● Pyz: yz component of pressure tensor in atm<br> ● Volume: volume of simulation box in (Angstroms)^3<br> ● Lx: box length in x direction in Angstroms<br> ● Ly: box length in y direction in Angstroms<br> ● Lz: box length in z direction in Angstroms<br> ● Density: density in g/(cm^3)<br> ● c_RG: radius of gyration in Angstroms<br> ● c_RG[1]: squared radius of gyration tensor (xx component) in (Angstroms)^2<br> ● c_RG[2]: squared radius of gyration tensor (yy component) in (Angstroms)^2<br> ● c_RG[3]: squared radius of gyration tensor (zz component) in (Angstroms)^2<br> ● c_RG[4]: squared radius of gyration tensor (xy component) in (Angstroms)^2<br> ● c_RG[5]: squared radius of gyration tensor (xz component) in (Angstroms)^2<br> ● c_RG[6]: squared radius of gyration tensor (yz component) in (Angstroms)^2<br> ● c_bondave[1]: bond energy averaged over all atoms in kcal/mol<br> ● c_bondave[2]: bond distance averaged over all atoms in Angstroms<br> ● c_bondave[3]: squared bond distance averaged over all atoms in (Angstroms)^2<br> ● c_angleave[1]: angle energy averaged over all atoms in kcal/mol<br> ● c_angleave[2]: angle averaged over all atoms degree<br> ● c_angleave[3]: cosine of angle (unitless)<br> ● c_angleave[4]: squared cosine of angle (unitless)<br> ● c_MSD[1]: mean squared displacement x-direction in (Angstroms)^2<br> ● c_MSD[2]: mean squared displacement y-direction in (Angstroms)^2<br> ● c_MSD[3]: mean squared displacement z-direction in (Angstroms)^2<br> ● c_MSD[4]: total mean squared displacement in (Angstroms)^2<br> ● c_COM[1]: x coordinate of center of mass in Angstroms<br> ● c_COM[2]: y coordinate of center of mass in Angstroms<br> ● c_COM[3]: z coordinate of center of mass in Angstroms<br> ● v_strain_xx: xx component of engineering strain tensor (unitless) <br> ● v_strain_yy: yy component of engineering strain tensor (unitless) <br> ● v_strain_zz: zz component of engineering strain tensor (unitless) <br> ● v_vMisesequivstress: von Mises equivalent stress in MPa<br> ● v_Cauchy_xx: xx component of stress tensor in MPa <br> ● v_Cauchy_yy: yy component of stress tensor in MPa<br> ● v_Cauchy_zz: zz component of stress tensor in MPa<br> ● v_Cauchy_xy: xy component of stress tensor in MPa<br> ● v_Cauchy_xz: xz component of stress tensor in MPa<br> ● v_Cauchy_yz: yz component of stress tensor in MPa<br> ● v_strain_xy: xy component of engineering strain tensor (unitless) <br> ● v_strain_xz: xz component of engineering strain tensor (unitless) <br> ● v_strain_yz: yz component of engineering strain tensor (unitless) </p> <p><strong>References</strong>:<br> [1] Ries, M.; Bauer, C.; Weber, F.; Steinmann, P. & Pfaller, S., "Characterization of the material behavior and identification of effective elastic moduli based on molecular dynamics simulations of coarse-grained silica", Mathematics and Mechanics of Solids, 2022, 108128652211080.<br> [2] Ghanbari, A.; Ndoro, T. V. M.; Leroy, F.; Rahimi, M.; Böhm, M. C. & Müller-Plathe, F., “Interphase Structure in Silica-Polystyrene<br> Nanocomposites: A Coarse-Grained Molecular Dynamics Study”, Macromolecules, 2012, 45, 572-584.<br> [3] Plimpton, S., “Fast parallel algorithms for short-range molecular dynamics,” Journal of computational physics, 1995, 117, 1-19.</p> <p> </p>
Data to reproduce: Cultural diffusion dynamics depend on behavioral production rules
<p>This repository contains data to reproduce the manuscript titled "Cultural diffusion dynamics depend on behavioural production rules". These RDAs contain simulation data, as well as inference data from NBDA and EWA analyses. They are intended to be used with the analysis code found at <a href="http://www.github.com/michaelchimento/acquisition_production_abm" rel="noopener">www.github.com/michaelchimento/acquisition_production_abm</a>.</p>
Insight into the Mechanical Coupling Behavior of Loose Sediment and Embedded Fiber-optic Cable using Discrete Element Method
<p>The dataset contains the simulation codes and generated data in the manuscript titled "Insight into the mechanical coupling behavior of loose sediment and embedded fiber-optic cable using discrete element method". The codes (M files) were written in MatDEM, version 3.0 (free access at <strong>www.matdem.com</strong>), and the data is stored in MAT files.</p> <ul> <li>Test2D_2L1.m - codes for initial compacted elements</li> <li>Test2D_2L1.mat - generated data for initial compacted elements</li> <li>Test2D_2L2.m - codes for compacted elements with embedded fiber-optic cable</li> <li>Test2D_2L2.mat - generated data for compacted elements with embedded fiber-optic cable</li> <li>Test2D_2L3.m – codes for confining pressure setting</li> <li>Test2D_2L-0MPa3.mat ~ Test2D_2L-1.0MPa3.mat - generated data for confining pressure setting</li> <li>Test2D_2L4.m – codes for fiber-optic cable pullout tests under various confining pressures</li> <li>Test2D_2L-05-26-20mm-0MPa-un-No1-4.mat ~ Test2D_2L-07-21-20mm-1MPa-un-No1-4.mat - generated data for fiber-optic cable pullout tests under various confining pressures</li> </ul>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.