Find research datasets worth reusing

opencc-by-4.0May 2023View details →

Extreme dynamics in a biomolecular condensate

Simulation inputs, subsampled trajectory, and outputs of lifetime calculation from paper "Extreme dynamics in a biomolecular condensate". Lifetime outputs are provided because these cannot be correctly calculated from the subsampled trajectory made available here.

opencc-zeroMay 2023View details →

Density dependence of seed dispersal and fecundity profoundly alters the spread dynamics of plant populations

<ol> <li>Plant population spread has fundamental ecological and evolutionary importance. Both determinants of plant population spread, fecundity and dispersal, can be density-dependent, which should cause feedback between population densities and spread dynamics. Yet it is poorly understood how density-dependence affects key characteristics of spread: spread rate at which the location of the furthest forward individual moves, edge depth (the geographical area over which individuals contribute to spread) and population continuity (occupancy of the spreading population).</li> <li>We present a general modelling framework for analysing the effects of density-dependent fecundity and dispersal on population spread and parameterize this framework with experimental data from a common-garden experiment using five wind-dispersed plant species grown at different densities. </li> <li>Our model shows that density-dependent fecundity and dispersal strongly affect all three population spread characteristics for both exponential and lognormal dispersal kernels. Spread rate and edge depth are strongly correlated but show weaker correlations with population continuity. Positive density-dependence of fecundity increases all three spread characteristics. Increasingly positive density-dependence of dispersal increases spread rate and edge depth but generally decreases population continuity. Density-dependent fecundity and dispersal are largely additive in their effect on spread characteristics. For population continuity, the joint effects of density-dependent fecundity and dispersal are somewhat contingent on the dispersal kernel.</li> <li>The common-garden experiment and the experimentally parameterized mechanistic dispersal model revealed density-dependent fecundity and dispersal across study species. All study species exhibited negative density-dependent fecundity, but they differed qualitatively in the density-dependence of dispersal distance and probability of long-distance dispersal. The negative density-dependence of fecundity and dispersal found for three species reinforced each other in reducing spread rate and edge depth. The positively density-dependent dispersal found for two species markedly increased spread rate and edge depth. Population continuity was hardly affected by population density in all study species except Crepis sancta in which it was strongly reduced by negatively density-dependent fecundity.</li> <li> Synthesis. Density-dependent fecundity and seed dispersal profoundly alter population spread. In particular, positively density-dependent dispersal should promote the spread and genetic diversity of plant populations migrating under climate change but also complicate the control of invasive species.</li> </ol>

opencc-by-4.0May 2023View details →

Dataset - Fast mechanical and biochemical cell wall dynamics underlie plant nutation

Dataset and codes (Python and Matlab) used to produce the figures in the article "Fast mechanical and biochemical cell wall dynamics underlie plant nutation".

opencc-by-4.0Dec 2022View details →

A dynamic modelling approach to quantify pollution contributions from critical source areas within watersheds at fine temporal resolutions

The support data for A dynamic modelling approach to quantify pollution contributions from critical source areas within watersheds at fine temporal resolutions

opencc-zeroJun 2023View details →

Mechanical transmission of Dengue Virus by Aedes aegypti may influence disease transmission dynamics during outbreaks data

Summary Background: Dengue virus outbreaks are increasing in number and severity worldwide. Viral transmission is assumed to require a minimum time period of viral replication within the mosquito midgut. It is unknown if alternative transmission periods not requiring replication are possible. Methods: We used a mouse model of dengue virus transmission to investigate the potential of mechanical transmission of dengue virus. We investigated minimal viral titres necessary for development of symptoms in bitten mice and used resulting parameters to inform a new model of dengue virus transmission within a susceptible population. Findings: Naïve mice bitten by mosquitoes immediately after they took partial blood meals from dengue infected mice showed symptoms of dengue virus, followed by mortality. Incorporation of mechanical transmission into mathematical models of dengue virus transmission suggests that this supplemental transmission route could result in larger outbreaks which peak sooner. Interpretation: The potential of dengue transmission routes independent of midgut viral replication has implications for vector control strategies that target mosquito lifespan and suggest the possibility of similar mechanical transmission routes in other disease-carrying mosquitoes.

Molecular Dynamics Trajectory of CsPbI3 produced using ACE MLFF

Molecular dynamics trajectories of CsPbI3, with 2 fs timestep between computed frames, frames are recorded every 200 fs. Under each folder, there are three npz files (each contains 100 ps of trajectory) and one initial configuration LAMMPS data file. The npz files can be read with 'numpy.load'. There are three entries for each npz object, 'positions' for the atomic positions, 'cells' for the lattice dimensions, and 'numbers' for the atomic number of the species.

Molecular Dynamics Trajectory of CH3NH3PbBr3 produced using VASP MLFF

Molecular dynamics trajectories of CH3NH3PbBr3, with 1 fs timestep between computed frames, frames are recorded every 50 fs.

opencc-by-4.0May 2023View details →

Common Observations/Measurements Between Incoherent Scatter Radars (ISR) and Atmosphere Explorers (AE) -C, -D, -E, Dynamic Explorer 2

Common observations/measurements between Incoherent Scatter Radars (ISR) and each satellite of Atmosphere Explorer mission (AE-C, -D, -E), plus common observations from ISRs and Dynamic Explorer 2.

Sample data for "Urban Dynamics Through the Lens of Human Mobility"

Sample data in Boston for paper "Urban Dynamics Through the Lens of Human Mobility".

opencc-by-4.0Apr 2023View details →

Infrared action spectroscopy as tool for probing gas-phase dynamics: Protonated Dimethyl Ether ((CH3)2OH+) formed by the reaction of CH3OH2+ with CH3OH

The series of folder contain the .log files from Gaussian(R) 16 of the different species and at different level of theories, as specified in the subfolders and filenames. The data refer to calculations that have been submitted for publication as an original research paper: Title: "Infrared action spectroscopy as tool for probing gas-phase dynamics: Protonated Dimethyl Ether, (CH3)2OH+, formed by the reaction of CH3OH2+ with CH3OH Journal: Molecular Physics Authors: V. Richardson, D.B. Rap, S. Brünken and D. Ascenzi

opencc-zeroJun 2023View details →

A Great Escape: resource availability and density-dependence shape population dynamics along trailing range edges

Populations along geographical range limits are often exposed to unsuitable climate and low resource availability relative to core populations. As such, there has been a renewed focus on understanding the factors that determine range limits to better predict how species will respond to global change. Using recent theory on range limits and classical understanding of density dependence, we evaluated the influence of resource availability on the snowshoe hare Lepus americanus along its trailing range edge. We estimated variation in population density, habitat use, survival, and parasite loads to test the Great Escape Hypothesis (GEH), i.e. that density dependence determines, in part, a species' persistence along trailing edges. We found that variability in resource availability affected density and population fluctuations and led to trade-offs in survival for snowshoe hare populations in the northeastern USA. Hares living in resource-limited environments had lower and less variable population density, yet higher survival and lower parasitism compared to populations living in resource-rich environments. We suggest that density-dependent dynamics, elicited by resource availability, provide hares a unique survival advantage and partly explain persistence along their trailing edge. We hypothesize that this low-density escape from predation and parasitism occurs for other prey species along trailing edges, but the extent to which it occurs is likely conditional on the quality of matrix habitat. Our work indicates that biotic factors play an important role in shaping species' trailing edges and more detailed examination of non-climatic factors is warranted to better inform conservation and management decisions.

opencc-byDec 2020View details →

Data supporting Mixed-anion mixed-cation perovskite (FAPbI3)0.875(MAPbBr3)0.125: an ab initio molecular dynamics study

Data of a molecular dynamics simulation of the mixed cation and mixed halide perovskite (FAPbI3)0.875(MAPbBr3)0.125 , as well as the end compounds FAPbI3 and MAPbBr3. Related article:  J. Mater. Chem. A, 2022,10, 9592-9603, <a href="https://doi.org/10.1039/D1TA10860C">https://doi.org/10.1039/D1TA10860C</a> arXiv:2112.09795 [cond-mat.mtrl-sci] arXiv: 2112.09795 <a href="https://doi.org/10.48550/arXiv.2112.09795">https://doi.org/10.48550/arXiv.2112.09795</a>

Viscoelasticity modeling of clay minerals by dynamic viscoelasticity measurement and its implications for earthquake faulting

We conducted dynamic viscoelastic measurements on three clay minerals, kaolinite, illite and smectite with water. These concentrated (dense) suspension systems of clay minerals were investigated using a high-temperature and high-fluid-pressure rheometer to determine their viscoelastic properties, which help further the understanding of tectonic and non-tectonic phenomena in the shallow unconsolidated portion of the lithosphere. Our results suggested that the rheological properties resulting from the network structure of the clay mineral were temperature, pressure and peak shear strain rate dependent. In addition, it was observed during this study that the amount of change in the phase angle varied systematically with the type of clay mineral. This suggests that the viscoelastic behaviour of unconsolidated systems saturated with fluid varies with the type of clay minerals that compose it. (Abstract)

opencc-zeroJun 2023View details →

Data from: Dynamics of reproductive isolation in stick insects at the transition between populations and species

Speciation is often viewed as a continuum along which populations diverge until they become reproductively-isolated species. However, such divergence may be heterogeneous, proceeding in `fits and bursts', rather than being uniform and gradual. We show in Timema stick insects that one form of reproductive isolation indeed evolves non-uniformly across this continuum, whereas another does not. Specifically, we use thousands of host-preference and mating trials to study habitat and sexual isolation among 42 pairs of taxa spanning a range of genomic differentiation and divergence time. We find that the evolution of habitat isolation is uncoupled from genomic differentiation within species, but accumulates linearly with it between species. In contrast, sexual isolation accumulates linearly across the speciation continuum. The results show different evolutionary dynamics for different components of reproductive isolation, indicate sudden transitions between phases of speciation, and highlight a special relevance for species status in the evolution of reproductive isolation.

opencc-by-4.0Dec 2022View details →

Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery

Molecular dynamics simulation input files: Histone Tail Electrostatics Modulate E2-E3 Enzyme Dynamics: A Gateway to Regulate Ubiquitination Machinery (<a href="https://zenodo.org/record/7423328">https://zenodo.org/record/7423328</a>)

Supporting dataset for "Surface energy dynamics and canopy structural properties in intact and disturbed forests in the Southern Amazon"

Supporting dataset for the manuscript “Surface energy dynamics and canopy structural properties in intact and disturbed forests in the Southern Amazon", currently under review in the Journal of Geophysical Research: Biogeosciences.

opencc-by-4.0Nov 2015View details →

Figure 5 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)

Figure 5. Adult worm (♂). Scale: 1 mm.

opencc-by-4.0Nov 2015View details →

Figure 6 in The population dynamics and reproduction of Streblospio gynobranchiata (Annelida, Spionidae), an alien polychaete worm, in the Sevastopol Bay (the Black Sea)

Figure 6. Average abundance of S. gynobranchiata in Sevastopol Bay in May and in October 2013.

Molecular dynamics simulations of CD59 and CD59-inhibited Membrane Attack Complex

Coarse-grain (CG) trajectories of CD59-C5b8 (last 1,500 ns): <ul> <li>cd59-c5b8_1500ns_rep1.xtc</li> <li>cd59-c5b8_1500ns_rep2.xtc</li> <li>cd59-c5b8_1500ns_rep3.xtc</li> </ul> PyLipID analysis results from CG CD59-C5b8 simulations: <ul> <li>Interactions_CHOL.csv</li> <li>Interactions_DOPC.csv</li> </ul> Atomistic CD59 simulations in DOPC membrane: <ul> <li>cd59_at_rep1_light.trr</li> <li>cd59_at_rep2_light.trr</li> <li>cd59_at_rep3_light.trr</li> </ul> CD59 Euler angles relative to the membrane:  <ul> <li>rep1.csv</li> <li>rep2.csv</li> <li>rep3.csv</li> </ul> All xtc and trr files were down-sampled (frames removed) to decrease file size.

Nighttime geomagnetic response to jumps of solar wind dynamic pressure: A possible cause of Québec blackout in March 1989

This contains the original simulation data used by the paper 'Nighttime geomagnetic response to jumps of solar wind dynamic pressure:  A possible cause of Québec blackout in March 1989', which will appear in Space Weather. The data were obtained by the global MHD simulation (REPPU). Each sav file (IDL saveset format) contains the physical variables in the ionosphere at each grid point (mlt*mlat: 321*221, starting at 0 MLT and -90 MLAT) for Run 02n, 30n, 30s, 33n, and 33s, including <ul> <li>MHD time series ('time' in minutes),</li> <li>field-aligned current ('fac1' in A/m2),</li> <li>electric potential ('pot' in V),</li> <li>ionospheric conductivities ('ss11', 'ss12', and 'ss22' in S).</li> </ul> The sav file can be opened by IDL. By typing, for example, IDL> restore,'run02n.sav' you can load the file to the memory of IDL. Type 'help' to confirm the variables that are loaded.