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11,506 results for “Dynamics”
Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa
Open the record for dataset details and reuse information.
Data for "Observation of Generalized t-J Spin Dynamics with Tunable Dipolar Interactions"
<p>Calculated dipole parameters, experimental and theoretical data and code needed to reproduce all plots of the paper, and separate csv files with data points of main figures. </p> <p> </p>
Molcular Dynamics Trajectories for Delta Opioid Receptor bound with C6-Quino
<p>Molecular Dynamics Data for publication at Nature Communications, doi.org/10.1038/s41467-025-57734-5.</p> <p>Balazs R. Varga1#, Sarah M. Bernhard1#, Amal El Daibani1#, Saheem Zaidi2#, Jordy H. Lam2, Jhoan Aguilar1, Kevin Appourchaux1, Antonina Nazarova2, Alexa Kouvelis1, Ryosuke Shinouchi3, Haylee R. Hammond3, Shainnel O. Eans3, Violetta Weinreb4, Elyssa B. Margolis5, Jonathan F. Fay6, Xi-Ping Huang4, Amynah Pradhan1, Vsevolod Katritch2*, Jay P. McLaughlin3*, Susruta Majumdar1* and Tao Che1*</p> <p>Structure-guided design of partial agonists at an opioid receptor</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.5 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Molcular Dynamics Trajectories for Delta Opioid Receptor bound with C5-Quino
<p>Molecular Dynamics Data for publication at Nature Communications, doi.org/10.1038/s41467-025-57734-5.</p> <p>Balazs R. Varga1#, Sarah M. Bernhard1#, Amal El Daibani1#, Saheem Zaidi2#, Jordy H. Lam2, Jhoan Aguilar1, Kevin Appourchaux1, Antonina Nazarova2, Alexa Kouvelis1, Ryosuke Shinouchi3, Haylee R. Hammond3, Shainnel O. Eans3, Violetta Weinreb4, Elyssa B. Margolis5, Jonathan F. Fay6, Xi-Ping Huang4, Amynah Pradhan1, Vsevolod Katritch2*, Jay P. McLaughlin3*, Susruta Majumdar1* and Tao Che1*</p> <p>Structure-guided design of partial agonists at an opioid receptor</p> <p>This folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.5 ns per frame. Periodic boundary condition (pbc) can be restored using VMD's standard pbc commands.</p> <p>Please cite us if you find this data useful!</p>
Water table depth dynamics and surface soil moisture content from three Scottish peatland areas (2021-2022)
<p>This compilation of datasets from three monitoring sites on peatland in Scotland includes water table depth dynamics and surface soil moisture content and covers the period 2021-2022. Further data will be added on an annual basis. This is version 2 of the dataset, which corrects a small number of data QC issues (see README).</p>
Data presented in Stress regimes and dynamic implications of the southeastern margin of the Tibetan Plateau: Insights from a refined focal mechanism catalog
<p>The dataset includes thewaveform data required for source mechanism inversion presented in the paper Stress regimes and dynamic implications of the southeastern margin of the Tibetan Plateau: Insights from a refined focal mechanism catalog</p>
Data from: The mutualism-antagonism continuum in Neotropical palm-frugivore interactions: from interaction outcomes to ecosystem dynamics
<p>Frugivory, i.e. feeding on fruits, pulp or seeds by animals, is usually considered a mutualism when interactions involve seed dispersal, and an antagonism when it results in the predation and destruction of seeds. Nevertheless, most frugivory interactions involve both benefits and disadvantages for plants, and the net interaction outcomes thus tend to vary along a continuum from mutualism to antagonism. Quantifying outcome variation is challenging and the ecological contribution of frugivorous animals to plant demography thus remains little explored. This is particularly true for interactions in which animals do not ingest entire fruits, i.e. in seed-eating and pulp-eating. Here, we provide a comprehensive review of Neotropical palm–frugivore interactions, with a focus on how frugivore consumption behaviour (i.e. digestive processing, caching behaviour and fruit-handling ability) and feeding types (fruit-eating, pulp-eating and seed-eating) influence interaction outcomes at different demographic stages of palms. We compiled a total of 1043 species-level palm–frugivore interaction records that explicitly captured information on which parts of palm fruits are eaten by animals. These records showed consumption of fruits of 106 Neotropical palm species by 273 vertebrate species, especially birds (50%) and mammals (45%), but also fish (3%) and reptiles (2%). Fruit-eating involved all four taxonomic vertebrate classes whereas seed-eating and pulp-eating were only observed among birds and mammals. Most fruit-eating interactions (77%) resulted in positive interaction outcomes for plants (e.g. gut-passed seeds are viable or seeds are successfully dispersed), regardless of the digestive processing type of vertebrate consumers (seed defecation versus regurgitation). The majority of pulp-eating interactions (91%) also resulted in positive interaction outcomes, for instance via pulp removal that promoted seed germination or via dispersal of intact palm seeds by external transport, especially if animals have a good fruit-handling ability (e.g. primates, and some parrots). By contrast, seed-eating interactions mostly resulted in dual outcomes (60%), where interactions had both negative effects on seed survival and positive outcomes through seed caching and external (non-digestive) seed dispersal. A detailed synthesis of available field studies with qualitative and quantitative information provided evidence that 12 families and 27 species of mammals and birds are predominantly on the mutualistic side of the continuum whereas five mammalian families, six mammal and one reptile species are on the antagonistic side. The synthesis also revealed that most species can act as partial mutualists, even if they are typically considered antagonists. Our review demonstrates how different consumption behaviours and feeding types of vertebrate fruit consumers can influence seed dispersal and regeneration of palms, and thus ultimately affect the structure and functioning of tropical ecosystems. Variation in feeding types of animal consumers will influence ecosystem dynamics via effects on plant population dynamics and differences in long-distance seed dispersal, and may subsequently affect ecosystem functions such as carbon storage. The quantification of intra- and inter-specific variation in outcomes of plant–frugivore interactions – and their positive and negative effects on the seed-to-seedling transition of animal-dispersed plants – should be a key research focus to understand better the mutualism–antagonism continuum and its importance for ecosystem dynamics.</p>
Data from: The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection
<p>Emerging epidemics and local infection clusters are initially prone to stochastic effects that can substantially impact the epidemic trajectory. While numerous studies are devoted to the deterministic regime of an established epidemic, mathematical descriptions of the initial phase of epidemic growth are comparatively rarer. Here, we review existing mathematical results on the epidemic size over time, and derive new results to elucidate the early dynamics of an infection cluster started by a single infected individual. We show that the initial growth of epidemics that eventually take off is accelerated by stochasticity. These results are critical to improve early cluster detection and control. As an application, we compute the distribution of the first detection time of an infected individual in an infection cluster depending on the testing effort, and estimate that the SARS-CoV-2 variant of concern Alpha detected in September 2020 first appeared in the United Kingdom early August 2020. We also compute a minimal testing frequency to detect clusters before they exceed a given threshold size. These results improve our theoretical understanding of early epidemics and will be useful for the study and control of local infectious disease clusters.</p>
Data from: Family dynamics reveal that female house mice preferentially breed in their maternal community
<p>Whether females breed in their natal group is an important factor in the evolution of extended families in animal sociality. Breeding in natal groups comes with costs and benefits, depending on group size and presence of older relatives, including mothers. Studying the consequences of breeding in the natal versus another group provides insight into the decisions and trade-offs governing the formation and structure of family groups. We investigated the family dynamics of a population of free-ranging commensal house mice. Using dynamic community detection on long term datasets, we determined which females first bred in their natal group. We then looked at how this influenced breeding success. We found most females (77%) exhibited strong philopatry, breeding in their natal groups. Breeding elsewhere was only somewhat predictable at very large and very small group sizes. Despite their philopatric preference, breeding elsewhere made no difference in how quickly and successfully a female bred. However, presence of their mother did lead females to breed sooner when born during high breeding activity, when competition over reproduction is high. Based on these results, potential loss of reproductive success from leaving the natal group does not seem to be the main driver of philopatry in female house mice. The effect of the presence of mothers suggests that benefiting from established social connections promotes breeding in the natal group. Mothers providing benefits also implies a lack of conflict between generations, which will be important for the development of stable social groups.</p>
3D dataset of root soil bacteria dynamics obtained using large field of view light sheet microscope
<p>A tailor made dual-illumination light-sheet system acquired photons scattered from the plant whilst fluorescence emissions were simultaneously captured from transparent soil particles and labelled microorganisms, allowing the generation of quantitative data on samples approximately 3600 mm<sup>3</sup> in size with as good as 5 µm resolution at a rate of up to one scan every 30 minutes. The dataset shows the dynamics of Bacillus subtilis populations in the rhizosphere of lettuce plants in real time.</p> <p> </p> <p> </p>
Data from: Host-parasite dynamics shaped by temperature and genotype: quantifying the role of underlying vital rates
<p>1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea <i>Daphnia magna</i>.</p> <p>2. We carried out a common garden experiment monitoring the dynamics of <i>Daphnia</i> populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite <i>Amoebidium parasiticum</i>, enabling us to study interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and <i>Daphnia</i> clones originating from two latitudes.</p> <p>3. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones, mainly due to higher survival. Infected <i>Daphnia</i> populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modeling results.</p> <p>4. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming.</p>
Live-cell fluorescence microscopy data for: Structural Dynamics of the Functional Nonameric Type III Translocase Export Gate
<p><strong>yuan_t3ss_raw_data.zip:</strong></p> <p>Microscopy data types:<br> <strong>- </strong>Brightfield images<br> - Fluorescence images (514 nm excitation)</p> <p>Microscope:<br> Olympus IX-83 with 1.49NA oil-immersion objective (Olympus UAPON 100x)<br> ET442/514/561 Laser triple band set filtercube (69904, Chroma)</p> <p>Camera:<br> Hamamatsu C9100-13 EM-CCD Camera<br> 80 nm pixel size</p> <p><strong>yuan_t3ss_cell_objects.zip:</strong></p> <p>EPEC and C41 ColiCoords cell objects derived from the raw data. The set contains a total of 24979 individual cells (brightfield, binary, fluorescence and localization datasets for each cell) with corresponding coordinate systems.</p> <p>Code to generate these cell objects from the raw data: https://github.com/Jhsmit/T3SS-paper</p> <p>The data format is .hdf5 and can be read with any HDF5 reader or directly with ColiCoords: https://github.com/Jhsmit/ColiCoords</p> <p><strong>Contact:</strong><br> Jochem Smit</p>
Dataset and simulation files on Quantifying Wetting Dynamics with Triboelectrification
<p>The uploaded data contains software and results about the simulation of Triboelectrification and Wetting Dynamics of Multiscale Polymer Surfaces.</p> <p>Folders structure:<br> A) Folder name: NanopillarTextureDropletSim<br> 1) Wolfram Mathematica Notebook file "laplace.solvers.random.nb";<br> Code for the simulation of droplet wetting on a nanopillar forest (nanopillar surface imported from input file). It consists of three sections: one for FEM simulation on deterministic forest arrangement (section fem), one for analytical modelling of droplet wetting on random forest (section fem random measured - analytical), and the final section with the FEM simulation on the random forest (fem random generated - FEM). The different sections return embedded results (graphs or numerical) and results saved to file.<br> 2) Input file of (single realization of) nanopillar forest "pillars.random.xls";<br> Single realization of nanopillar forest, xls file. Measured from optical acquisition. Needed as input for the "laplace.solvers.random.nb".<br> B) Folder name: MicrocubeTextureDropletSim<br> 1) Wolfram Mathematica Notebook file "MicroTextureGenerator.nb";<br> Code for generation of the random microcubes texture. The different sections return embedded results (graphs or numerical) and results saved to file, such as the file "functionpython.py" used as input surface for FEniCS wetting mchanics simulation.<br> 2) FEniCS input file "contact.angle.3D_mesh.refinement.v3.2018.py";<br> Python code to run simulation of wetting dynamics with FEniCS FEM solver. The code consists of a main computation loop and several subroutines, each dedicated to perform specific computation step (such as adaptive mesh refinement nearby triple lines). The most important numerical parameters are N (e.g. with assignment N = 128) controlling the initial side discretization number of the computation square, and max_number_of_refinements (e.g with assignment max_number_of_refinements = 4) which controls the number of consecutive refinements of the solution near the triple lines. The code will save several *.pvd files containing the deformed droplet surface (top surface) and corresponding bottom surface. The code will also save the file "wet_area.dat", which contains (in each line) the (dimensionless) applied squeezing pressure, the normalized wetting area and the droplet free-surface normalized area.<br> 3) Wolfram Mathematica Notebook file "contact.angle.micro.one.plate.nb";<br> The file is used to simulate the whole droplet contact on single plate, under constant droplet volume. The different sections return embedded results (graphs or numerical) and results saved to file. As input, among the other physical parameters, the effective contact angle is needed.<br> 4) Wolfram Mathematica Notebook file "contact.angle.micro.nb";<br> The code consists of two sections, the first for droplet on single plate and the second for the droplet among two plates. In particular, the second section allows to determine the penetration vs squeezing load for the two-plates case. As input, among the other physical parameters, the effective contact angles are needed.<br> C) Folder name: Sloshing<br> 1) Wolfram Mathematica Notebook file "cylinder.sloshing.nb";<br> It contains code for the simulation of sloshing dynamics in a partially-filled tank, as well as extra analysis on the sloshing dynamics.<br> D) Folder name: Example.FEniCS.results<br> It contains a full set of FEniCS simulation results (at three simulated squeezing pressures) for the input python code "temp.contact.angle.3D_mesh.refinement.v3.2018.py".</p>
Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests
<p><span><span><span><span><span><span><span><span><span><span><span>Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical datasets are required to account for taxon- and context-dependency but relevant research in understudied areas is often compromised by the taxonomic impediment<span><span>. </span></span>We here employed haplotype-level community DNA metabarcoding, enabled by stringent filtering of Amplicon Sequence Variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, Operational Taxonomic Unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented <i>Quercus alnifolia</i> habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterising metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.</span></span></span></span></span></span></span></span></span></span></span></p>
Dynamic combinatorial optimization of in vitro and in vivo heparin antidotes
<p>This folder contains selected molecular dynamics simulations movies for the paper " Dynamic combinatorial optimization of <em>in vitro</em> and <em>in vivo</em> heparin antidotes"</p>
Dynamic targeting enables domain-general inhibitory control over action and thought by the prefrontal cortex (data & code)
<p><strong>Data and code for:</strong></p> <p>Apšvalka, D., Ferreira, C. S., Schmitz, T. W., Rowe, J. B., & Anderson, M. C. (2022). Dynamic targeting enables domain-general inhibitory control over action and thought by the prefrontal cortex. <em>Nature Communications, </em> <strong>13, </strong>274<em>.</em> <a href="https://doi.org/10.1038/s41467-021-27926-w"> https://doi.org/10.1038/s41467-021-27926-w</a></p> <blockquote> <p>Over the last two decades, inhibitory control has featured prominently in accounts of how humans and other organisms regulate their behaviour and thought. Previous work on how the brain stops actions and thoughts, however, has emphasised distinct prefrontal regions supporting these functions, suggesting domain-specific mechanisms. Here we show that stopping actions and thoughts recruits common regions in the right dorsolateral and ventrolateral prefrontal cortex to suppress diverse content, via dynamic targeting. Within each region, classifiers trained to distinguish action-stopping from action-execution also identify when people are suppressing their thoughts (and vice versa). Effective connectivity analysis reveals that both prefrontal regions contribute to action and thought stopping by targeting the motor cortex or the hippocampus, depending on the goal, to suppress their task-specific activity. These findings support the existence of a domain-general system that underlies inhibitory control and establish Dynamic Targeting as a mechanism enabling this ability.</p> </blockquote>
Fig. 2 in Dynamics of fish assemblages on a continuous rocky reef and adjacent unconsolidated habitats at Fernando de Noronha Archipelago, tropical western Atlantic
Fig. 2. Mean values (±SE) of temporal fluctuation and temporal stability.
Molecular dynamics of solids at constant pressure and stress using anisotropic stochastic cell rescaling - dataset
<p>Supporting data related to manuscript "Molecular dynamics at constant pressure and stress using anisotropic stochastic cell rescaling"</p>
Research Data Supporting "Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures"
<p>This repository contains the set of data shown in the paper "<strong>Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures</strong>", published on <strong>Nature Chemistry </strong>(DOI: 10.1038/s41557-021-00752-9).</p> <p>The files in the folders are organized as follow:</p> <p><strong>AA_models/ : </strong>contains all the files needed to run the Atomistic simulations discussed in the paper (including the topologies and starting configurations).</p> <p><strong>CG_models/ : </strong>contains all the files needed to run the Coarse Grained simulations discussed in the paper (including the topologies and starting configurations).</p> <p><strong>citrate_analysis/ : </strong>contains all the files needed to reproduce the analysis of the CV and SOAP+PCA+PAMM (including input files and python scripts).</p> <p>Additional details are available in the methods section and in the Supporting Information of the main paper.</p>
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility
<p>This zip contains all input structures for paper the: Alchemical Free<br> Energy Estimators and Molecular Dynamics<br> Engines: Accuracy, Precision and Reproducibility</p> <p>Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney</p> <p>The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files</p> <p>The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q)</p> <p>There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop</p> <p>complex.pdb is structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file</p> <p>For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column.</p> <p>These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engiens that take AMBER input.</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.