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695 results for “topologies”
Observing the quantum topology of light
<p>Includes all experimental data and simulation data in the manuscript "Observing the quantum topology of light"</p>
Observing the quantum topology of light
<p>Includes all experimental data and simulation data in the manuscript "Observing the quantum topology of light"</p>
Data For Topological supermodes in Photonic Crystal Fibre
<p>Experimental Data and corresponding simulation data for main text of manuscript.</p>
A Putative New Role of Tv-PSP1 Recognizes IRE and ERE Hairpin Structures from Trichomonas vaginalis. Figure S1. Tv-PSP1 crystal packing. Figure S2. Tv-PSP1 secondary structure and general topology.
<p>Figure S1. Tv-PSP1 crystal packing. Crystal packing of the hexagonal space group P63 with cell dimensions<br> a=81.9 Å, b=81.9 Å, c=129.3 Å, and γ=120°. A) Trimer A in Grey surface is around the threefold axis symbol. B)<br> Trimer D in blue steel color, this trimer is under Trimer A on the same threefold axis. The trimer D on the final<br> structure is not visible in a large part of the structure, only are visible the fragments in contact with monomer A,<br> here was built a complete Trimer from previous refinement process to illustrate the position on the crystal.<br> C)Trimer B in green color is around the threefold axis symbol in the symmetric object of the twofold screw axis<br> of the cell. D)Trimer C in orange color is around the sixfold axis symbol. Figure was made in VMD program [39]. ID PDB: 7KGC.</p> <p> </p> <p>Figure S2. Tv-PSP1 secondary structure and general topology. A) Tv-PSP1 secondary structure of the<br> asymmetric unit monomers obtained with VMD program [39]. Marginal differences are observed on the L1 and<br> L7. B) General topology of the monomer A structure. Beta strands in yellow color, 3-10 helixes in blue color, alfa<br> helixes in magenta color, turns and coil in green color.</p>
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files
<p>The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.</p> <p>ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.</p> <p>eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.</p> <p>standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.</p> <p>metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.</p> <p>metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.</p> <p>ions.tar.gz: Data used for Figure.3 in the manuscript</p> <p>si_data.tar.gz: All data used for SI figures.</p>
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S in Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods
Figure 2. Maximum likelihood phylogenetic tree topology derived from the combined 16S rRNA + COI sequence data, demonstrating the evolutionary relationships within the P. sidneyi s.l. species complex. Statistical support for nodes is provided as posterior probability values above nodes (> 0.95 PP) and bootstrap values below nodes (> 75%). An * or # denotes nodal relationships that were not supported (<0.95 PP/ <75%). Potamonautes sidneyi s.s. (clade 3) localities are marked with a dark blue triangle, while P. danielsi (clade 5) localities are marked by an orange square. The two new species, P. karooensis, (clade 2) and P. Ʋalles (clade 4), are marked by a light-blue circle and a green diamond, respectively. Specimens of P. barbarai are confined to clade 1.
Probing the topologically trivial nature of end states in antiferromagnetic atomic chains on superconductors
<p>This .zip file includes the Mathematica Notebook used to create all figures of the main text as well as the relevant raw data needed to reproduce the results of the paper.</p>
FIGURE 4. Seven topologically parsimonious constrained trees retrieved from cladistic analysis using a in On the first Baryonychinae (Theropoda, Spinosauridae) teeth from South America
FIGURE 4. Seven topologically parsimonious constrained trees retrieved from cladistic analysis using a dentition-based data matrix (tree length = 1318; CI = 0.198; RI = 0.466), Bremer support is displayed below each node; LPUFS specimens (bold) are recovered within the Spinosauridae clade. Theropod silhouette from phylopic.org, see acknowledgements.
Topological packing statistics of living and non-living matter
<p>This repository contains the data and code needed to recreate figures in the main and supplementary text of the paper "Topological packing statistics of living and non-living matter" by the same authors. Instructions for running the code are provided in the README.md file.</p> <p>For those looking to apply the computational framework to their own data, a GitHub repository of the core Julia package is maintained at <a href="https://github.com/Dom-Skinner/LocalCellularStructure">https://github.com/Dom-Skinner/LocalCellularStructure</a></p>
Simulation Topologies and Structures
<p>Inclosed in this .zip file are some of the files used to produce the results shown in "Controlling Swelling in Mixed Transport Polymers Through Alkyl Side Chain Physical Cross-linking" published in PNAS. Files include:</p> <p> </p> <p> - topology files</p> <p> - the forcefield used for the simulation</p> <p> - a README file to navigate what is in the different folders</p> <p> - final structures for each of the simulations </p> <p> - checkpoint files so the simulations can be continued by other users. </p> <p>For any more data or for the trajectories of the simulations please contact the authors. </p>
Supporting Information for "Broadening the scope of binding free energy calculations using a Separated Topologies approach"
<p>Supporting Information for the publication "Broadening the scope of binding free energy calculations using a Separated Topologies approach" including input files for the datasets used in that study.</p>
Data and code for "Migration and division in cell monolayers on substrates with topological defects"
<p>Raw data for experiment (experiment.zip) and basic simulation code (simulation.zip) for the paper "Migration and division in cell monolayers on substrates with topological defects"</p>
Structures and data for minimalistic models of cage-like molecules in "Systematic exploration of accessible topologies of cage molecules via minimalistic models"
<p>Archives of .csv files containing data of lowest energy conformers for all cage configurations tested and associated .mol files. </p><p> </p><p>For paper: Systematic exploration of accessible topologies of cage molecules via minimalistic models with DOI: <a href="https://doi.org/10.1039/D3SC03991A">10.1039/D3SC03991A</a> </p>
Topological data analysis of vortices in the magnetically-induced current density in LiH molecule
<p>This is the accompanying data for the paper titled "Topological data analysis of vortices in the magnetically-induced current density in LiH molecule" by Malgorzata Olejniczak and Julien Tierny</p>
Data and code for ""Smoking gun" signatures of topological milestones in trivial materials by measurement fine-tuning and data postselection"
<p><strong>Brief description</strong></p> <p>This repository contains data, code, and other materials for ""Smoking gun" signatures of topological milestones in trivial materials by measurement fine-tuning and data postselection". Files are zipped by project.</p> <p><strong>Data formats</strong></p> <ul> <li>MTX: A simple 2D/3D matrix format developed for <a href="https://nsweb.tn.tudelft.nl/~gsteele/spyview/">Spyview</a>.</li> <li>DAT: Plain-text tabular data.<br> DAT and MTX files can be plotted with Spyview, qtplot (a portable version for Windows can be downloaded <a href="https://github.com/cover-me/qtplot/releases/download/2020.09.21/qt_plot.2020.09.21.7z">here</a>), Jupyter notebooks in ZIP files or <a href="https://github.com/cover-me/qtview">here</a>.</li> <li>SET: Instrument settings.</li> <li>PY: Measurement scripts.</li> <li>IPYNB or HTML: Jupyter notebooks with code and figures. IPYNB can be previewed on this <a href="https://kokes.github.io/nbviewer.js/viewer.html">page</a>.</li> </ul> <p><strong>Additional repositories</strong></p> <p>MATLAB codes for theoretical simulations in Ref 63: https://github.com/frolovgroup/</p> <p>Full data and code from the Shapiro step project: [https://zenodo.org/record/6416083](Data and code for "smash junction" papers)</p>
Information Trapping by Topologically Protected Edge States: Scrambling and the Butterfly Velocity
<p>Data files, in the form of Mathematica mx files, for "Information Trapping by Topologically Protected Edge States: Scrambling and the Butterfly Velocity". Included are data for the OTOCs for two models. Parameters and models are given in the file names. For the Kitaev model the form is {System size, location of perturbation, {J_0, Delta_0, mu_}, {J_1, Delta_1, mu_1}, Invariant, Invariant} (The invariant is written twice at the end due to bookkeeping). For the SSH model 'pert' refers to the location of the unitary perturbation, 'edge' refers to OTOCs only calculated at teh system boundary, and 'longt' are data for longer times. See the paper for further details.</p> <p><a href="https://doi.org/10.1103/PhysRevB.108.184303">https://doi.org/10.1103/PhysRevB.108.184303</a></p> <p><a href="https://doi.org/10.48550/arXiv.2306.00527">https://doi.org/10.48550/arXiv.2306.00527</a></p>
Topological structure and dynamics of three-dimensional active nematics
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Data from: Sex-specific graphs: Relating group-specific topology to demographic and landscape data
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Data from: Rethinking refugia: tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day
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Supporting information for: The frequency and topology of pseudoorthologs
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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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.