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13 results for “gap dynamics”
Data from paper: "Large-scale variations in the dynamics of Amazon forest canopy gaps from airborne lidar data and opportunities for tree mortality estimates"
<p>Data from the paper:</p> <p>Dalagnol, R. <em>et al.</em> Large-scale variations in the dynamics of Amazon forest canopy gaps from airborne lidar data and opportunities for tree mortality estimates. <em>Sci Rep</em> <strong>11, </strong>1388 (2021). https://doi.org/10.1038/s41598-020-80809-w</p> <p>Link: https://www.nature.com/articles/s41598-020-80809-w</p> <p> </p> <p>This repository contains:</p> <p>1) Data frame with data from static and dynamic gaps used in Figure 2 (Dalagnol_2020_Data_Multitemporal_gaps.csv). Each row is the aggregated measurement at 5-km resolution. The site component referes to the five site studied with multitemporal data. Site order from 1 to 5 is DUC, TAP, FN1, BON and TAL.</p> <p>2) Data frame with data from static gaps and environmental factors used in Table 1, Figure 3, 4, 5 (Dalagnol_2020_Data_Singledate_gaps_Modeling.csv). Each row is the aggregated measurement of one site observed by airborne lidar data.</p> <p>3) Raster file at 5-km resolution with dynamic gap fraction estimates presented in Figure 5 (dynamic_gap_fraction_amazon.tif).</p> <p> </p> <p>If you need anything else, please contact the corresponding author: Ricardo Dalagnol (ricds@hotmail.com).</p>
Connexin 46 and connexin 50 gap junction channel properties are shaped by structural and dynamic features of their N-terminal domains
<p>Provided are reduced trajectories (.dcd) of the MD simulations -- each trajectory has 100 ps/frame with only protein and ion atoms remaining. Each set of trajectories are accompanied by a protein structure file (.psf) which is required to visualize the trajectories in VMD. Additionally, the z-trajectories of each intracellular ion (2 ps/frame) are provided in zipped files.<br> <br> To re-create the potentials of mean force (PMF) in Yue & Haddad et al., use the scripts provided with the paper (https://github.com/reichow-lab/Yue-Haddad_et-al.JPhysiol2021):<br> <br> </p> <pre><code class="language-bash">python3 GapJ_Analysis.py "Cx46_Ace_Produc-1_POT_*"</code></pre> <ul> <li>Choose a bin size in Å (3)</li> <li>Choose an output name (Cx46_Ace)</li> <li>Choose option (M)</li> <li>Choose time (ps) / frame (2)</li> <li>Choose column from file (1)</li> <li>Choose bin<sub>min</sub>/bin<sub>max </sub>(auto)</li> </ul>
Molecular dynamics simulation data 1: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 gap junction channel</p>
Vortex input files -- Ashe et al., "Minding the data-gap trap: predicting the dynamics of abundant dolphin species under uncertainty"
<p>Vortex input file used for analyses presented in:<br> "Minding the data-gap trap: predicting the dynamics of abundant dolphin species under uncertainty", <br> by Erin Ashe, Rob Williams, Christopher Clark, Christine Erbe, Leah Gerber, Ailsa Hall, Philip Hammond, Robert C. Lacy, Randall Reeves, & Nicole Vollmer<br> </p>
Forest gap dynamics with repeat lidar in Berchtesgaden National Park - Data and analysis scripts
<p>This repository holds data and code for the paper: Krüger, K., Senf, C., Jucker, T., Pflugmacher, D., Seidl, R. (2024). Gap expansion is the dominant driver of canopy openings in a temperate mountain forest landscape. Journal of Ecology. <span><a href="http://doi.org/10.1111/1365-2745.14320">http://doi.org/10.1111/1365-2745.14320</a> </span></p> <p><strong>NOTE:</strong> This is a static repository, but the project might evolve. See the connected GitHub repository for latest updates!</p> <p>All data to reproduce the results are available, all other layers can be generated with the code provided in this repository. The Canopy Height Models underlying the analysis and respective processing scripts for the lidar data, are available from the corresponding author upon reasonable request. Gap layers derived from the Canopy Height Models are available in this repository.</p> <p>Empty folders are set up to follow the directory structure of the scripts. </p>
Molecular dynamics simulation data 3: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes: Production run gromacs trajectories for the Cx43 gap junction channel (500 mV)</p>
Molecular dynamics simulation data 2: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 hemichannel</p>
Selective dynamic band gap tuning in metamaterials using graded photoresponsive resonator arrays
<p>Raw Data for figures:</p> <p>Fig. 2: Dispersion diagrams for non-illuminated (off) and illuminated (on) pillars of different heights (hp). hp1 = 7 mm, hp2 = 9 mm, hp3 = 11 mm, hp4 = 13 mm; p = 0 (1) for purely in- (out-of-plane) behavior</p> <p>Fig. 4: Computed transmission spectrum of a finite structure. a) Numerically simulated transmission spectrum for the considered 8-pillar specimen, both without ("Laser off") and with laser illumination ("Laser on 7th pillar").</p> <p>Fig. 5: Transmission spectrum of the finite structure considered experimentally. a) Measured spectra before (blue) and after (red) illumination of pillar 1. Band gaps are highlighted in light blue and numbered from I to IV; b) Corresponding colour map representing transmission vs. frequency and time (vertical axis) when switching laser illumination on (t = 700 s) and off (t = 2300 s); c) same as a), with illumination of pillar 6; d) same as b), with illumination on pillar 6.</p> <p>Fig. 6: Dynamic modulation of signal frequencies (f1 = 21.5 kHz, f2 = 71.5 kHz) in a graded pillar structure. The different temporal intervals depict tunable suppression and enhancement of specific frequencies through selective pillar illumination.</p>
Nanoporous carbon structures of different densities generated through GAP molecular dynamics
<p>These nanoporous (NP) carbon atomic structures, in extendend XYZ format, have been generated using a melt-graphitization-quench molecular dynamics (MD) protocol using a Gaussian interatomic potential (GAP) for amorphous carbon [1]. Simulation details and characterization of structural and mechanical properties will follow shortly in a scientific paper.</p> <p><strong>References</strong></p> <p>[1] M.A. Caro. GAP interatomic potential for amorphous carbon (2.0) [Data set]. Zenodo, 10.5281/zenodo.5243184 (2021).</p>
Data from: Carbon flux and forest dynamics: increased deadwood decomposition in tropical rainforest tree-fall gaps
<p>This study was carried out within an area of lowland, old growth dipterocarp rainforest in the Maliau Basin Conservation Area, Sabah, Malaysia (4° 44' 35" to 55" N and 116° 58' 10" to 30" E; mean annual rainfall 2838 mm ± 93 mm). On the 20<sup>th</sup> of July 2017, there was a storm at the study site, which generated winds speeds of 8.4 m/s (Fig. S1). These were among the strongest winds normally experienced in inland forests of the region, which placed extreme sheer stress on trees. Consequently, a large number of trees fell within the same 24-hour period in the study location. Ten tree-fall gaps (mean length: 32 m ± 2.8, mean width: 24.5 m ± 3; see table S1 for gap characteristics) created during this event were selected for use in this investigation, along with ten adjacent closed canopy sites, located 20 m from the edge of each gap. We took 10 hemispherical photos in each gap and closed canopy sites to quantity canopy openness at each location.</p>
Selection in space and time: individual tree growth is adapted to tropical forest gap dynamics
<p>In the present study, we assessed genotypic diversity within closely-related sympatric tree species belonging to the widespread tropical tree species complex <em>Symphonia globulifera</em>. We addressed the fine-scale spatial and temporal genetic adaptations of individuals through differential growth strategies in response to forest gap dynamics. We finally compared the breadth of successional niches encountered by <em>Symphonia</em> species to other locally abundant species. Combining tree diameter censuses, indirect measures of light environment of the recent past and present, and single nucleotide polymorphisms (SNPs), we used population genomics, environmental association analyses, genome wide association and growth modelling to address the following questions:</p> <ul> <li>Are individual genotypes structured by the mosaic of light and competition environments resulting from forest gap dynamics?</li> <li>Is the growth of individuals determined by genotypes?</li> <li>Is there an association between genotypic adaptations to gap dynamics and to growth?</li> <li>How are genotypic adaptations to gap dynamics and to growth structured in time, i.e., across life stages?</li> <li>Are breadths of successional niches for <em>Symphonia</em> species wider than those of other locally abundant species?</li> </ul> <p>Find the analyses here : https://sylvainschmitt.github.io/GOING/introduction.html</p>
Data from: Carbon flux and forest dynamics: increased deadwood decomposition in tropical rainforest tree-fall gaps
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Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling
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