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676 results for “Manis”
Data Set "Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions"
<p>This data set accompanies the publication "Protein-Ligand Interaction Energies from Quantum-Chemical Fragmentation Methods: Upgrading the MFCC-Scheme with Many-Body Contributions" by Johannes Vornweg and Christoph R. Jacob (TU Braunschweig, Germany) </p> <p>It contains the following files:</p> <p><br>Directory 1_structures:</p> <p> PDB files of all structures used for the test calculations. <br> The PDB files correspond to the protonated structures obtained <br> as described in the main text.</p> <p><br>Directory 02_figure_scripts:</p> <p> Jupyter Notebook for generating all plots included in the manuscript, <br> including raw numerical data.</p> <p><br>Directory 03_input_scripts:</p> <p> - min_congrad.mdp: input file for partial optimization of protonated <br> protein--ligand complexes with Gromacs</p> <p> PyADF input scripts:</p> <p> - sp_single.pyadf: single-point calculations of separate protein and ligand<br> - sp_complex.pyadf: single-point calculation of protein-ligand complex<br> - mfccmbe3.pyadf: MFCC and MFCC-MBE(2) calculations of P-L interaction energy</p> <p> These scripts can be used with PyADF v1.5 (DOI: 10.5281/zenodo.13236550)</p>
Figure 3 in New species of many-plumed moths (Lepidoptera: Alucitidae) from the Republic of South Africa
Figure 3. Biotope: Mpumalanga, Lows Creek Lodge. Photo by Pavel Udovichenko.
Figure 1 in New species of many-plumed moths (Lepidoptera: Alucitidae) from the Republic of South Africa
Figure 1. Alucita udovichenkoi Kovtunovich & Ustjuzhanin sp. nov. adult, male (Holotype, ZISP).
Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery
<p>Dataset of transition metal complex structures in .xyz file format, computed and predicted energies in comma delimited format, model information in JSON format, and the Mathematica script for uncertainty analysis for associated manuscript.</p>
Assessing many-body methods on the potential energy surface of the H2_2 hydrogen dimer
<p>Density functional theory, RPA, and quantum Monte Carlo datasets produced for the "Assessing many-body methods on the potential energy surface of the H2_2 hydrogen dimer" paper submitted to the Journal of Chemical Physics and to the arXiv (https://arxiv.org).</p>
Data for: Many-body thermodynamics on quantum computers via partition function zeros
<p>Partition functions are ubiquitous in physics: they are important in determining the thermodynamic properties of many-body systems, and in understanding their phase transitions. As shown by Lee and Yang, analytically continuing the partition function to the complex plane allows us to obtain its zeros and thus the entire function. Moreover, the scaling and nature of these zeros can elucidate phase transitions. Here we show how to find partition function zeros on noisy intermediate-scale trapped ion quantum computers in a scalable manner, using the XXZ spin chain model as a prototype, and observe their transition from XY-like behavior to Ising-like behavior as a function of the anisotropy. While quantum computers cannot yet scale to the thermodynamic limit, our work provides a pathway to do so as hardware improves, allowing the future calculation of critical phenomena for systems beyond classical computing limits.</p>
Many roads to success: Different combinations of life-history traits provide accurate germination timing in seasonally dry environments
Germination timing is determined by several plant life-history traits. Seed dormancy regulates the time and place of early plant development and spreads recruitment risks over time. Dispersal phenology and syndrome can influence germination timing and buffer spatial heterogeneity. The ecological requirements for germination (the germination niche) can also influence when and where germination takes place. To date, the relative importance of each of these four traits to ensure the phenological adaptation of individual species in diverse communities remains unexplored. Here, we investigated the functional interactions among them and their relevance in heterogenous, seasonally dry environments. We collected seed dispersal phenology and syndrome for 82 species of the Brazilian savanna (cerrado) and evaluated the dormancy and germination behavior of the seeds of every taxon. Based on these data, we developed two new ecological indexes to estimate the likelihood of a non-dormant seed to germinate upon dispersal (∆G) and the overall variability of germination through time (σT). We then evaluated the influence of each trait on germination timing within a phylogenetically controlled framework. Our results show that even though germination is concentrated at the beginning of the rainy season, seed dispersal takes place year-round. Non-dormant seeds released during the dry season were characterized by high ∆G values that delayed their germination until the onset of the favorable season. Simultaneously, seed dormancy and spatial dispersal (i.e., the two risk-reduction mechanisms) were negatively correlated as dormancy and high σT values were only prevalent in seeds with reduced spatial dispersal ability. We conclude that the timing of seed germination is ultimately the net outcome of adaptive interactions among life-history traits, which can result in multiple functionally equivalent phenotypes. It is possible that this might contribute to community diversity by providing opportunities for the coexistence of different species.
Dataset for: Estimating heating times in periodically driven quantum many-body systems via avoided crossing spectroscopy
<p>The dataset includes data and Python scripts for all figures in the corresponding article.</p> <p>The data is organized into self-contained folders for each individual figure (possibly consisting of multiple subplots) and should be accessible using standard libraries for scientific Python. The included scripts can serve as a guide for accessing and plotting the data.</p>
Many-body machine learning models for water, acetonitrile, and methanol
<p><a href="https://keithgroup.github.io/mbGDML/">GDML</a>, <a href="https://libatoms.github.io/GAP/">GAP</a>, and <a href="https://schnetpack.readthedocs.io/en/stable/">SchNet</a> models trained on 1-, 2-, and 3-body energies and forces of water, acetonitrile, and methanol. Size-transferable <a href="https://github.com/mir-group/nequip">NequIPs</a> are trained on trimer data. Energies and forces were computed at the MP2/def2-TZVP level of theory in ORCA v4.2.0. Data sets, training scripts, and analyses of these potentials are available <a href="https://github.com/keithgroup/mbgdml-h2o-meoh-mecn">here</a>. Applications of these models on molecular dynamics simulations are found <a href="https://doi.org/10.5281/zenodo.7112198">here</a>.</p> <p><strong>Changelog</strong></p> <p>The format is based on <a href="https://keepachangelog.com/en/1.0.0/">Keep a Changelog</a>, and this project adheres to <a href="https://semver.org/spec/v2.0.0.html">Semantic Versioning.</a></p> <p>[0.0.2] - 2022-12-20</p> <p>Added</p> <ul> <li><a href="https://github.com/mir-group/nequip">NequIPs</a> trained for all solvents using 1000 trimers.</li> </ul> <p>[0.0.1] - 2022-09-25</p> <ul> <li>Initial release!</li> </ul> <p> </p>
Supplementary Material to "An improved grand-potential phase-field model of solid-state sintering for many particles"
<p>Supplementary Material to the publication "An improved grand-potential phase-field model of solid-state sintering for many particles" by Seiz, Hierl and Nestler. This contains the pre-study for determining the effective stiffness for the rigid-body velocity calculation and video files showing the 3D evolution of the green body in more detail than possible in the paper itself.</p> <p> </p> <p>slicethru_{start,end}.webm: Moving slices through the 400^3 nm green body at t=0.045ms and t=1.8ms representing the start and end of the simulation respectively. White/transparency indicates the surrounding vapor, with the colourmap showing different grains. Any interfaces are shown as black lines.</p> <p> </p> <p>greenbody_400.webm : Time evolution of the 400^3 nm green body based on the solid-vapor interface. White/transparent indicates the surrounding vapor, with the brownish material indicating the grains.</p> <p> </p> <p>prestudy.zip: Contains the notebook and data used for the pre-study for determining the effective stiffness. A binder is available at</p> <pre>https://mybinder.org/v2/git/https%3A%2F%2Fgit.scc.kit.edu%2Fxt5201%2Fsupplementary-material-for-improved-pf-sintering-model/master?labpath=eval-kvar.ipynb</pre> <p> </p> <p> </p>
Many ways to build an angler: diversity of feeding morphologies in a deep-sea evolutionary radiation
<p>Almost nothing is known about the diets of bathypelagic fishes, but functional morphology can provide useful tools to infer ecological processes. Here we quantify variation in jaw and tooth morphologies across anglerfishes (Lophiiformes), a clade spanning shallow and deep-sea habitats. Deep-sea ceratioid anglerfishes are believed to be dietary generalists due to the presumed necessity of opportunistic feeding in the food-limited bathypelagic zone. However, we found unexpected diversity in the trophic morphologies of ceratioid anglerfishes. Ceratioid jaws span a functional continuum ranging from species with numerous stout teeth, a relatively slow but forceful bite, and high jaw protrusibility at one extreme (characteristics shared with benthic anglerfishes), to species with large fang-like teeth, a fast but weak bite, and low jaw protrusibility at the other (including a unique "wolftrap" phenotype). Our finding of high morphological diversity seems to be at odds with ecological generality, reminiscent of Liem's paradox (morphological specialization allows organisms to have broader niches). Another possible explanation is that diverse ceratioid morphologies may yield similar trophic success (many-to-one mapping of morphology to diet), allowing diversity to arise through neutral evolutionary processes. Our results highlight that there are many ways to be a successful predator in the deep sea.</p>
Data of "Dissipative quantum many-body dynamics in (1+1)D quantum cellular automata and quantum neural networks"
<p>The uploaded files contain the data of the simulations presented in the figures in <a href="https://doi.org/10.48550/arXiv.2304.11209">https://doi.org/10.48550/arXiv.2304.11209</a>.</p>
Efficient Algorithms for the Group Steiner Tree Problem with Many Groups
<p>The datasets for our paper 'Efficient Algorithms for the Group Steiner Tree Problem with Many Groups'. It concludes two datasets: <code>PCSG_dataset</code> and <code>KeywordSearch_dataset</code>.</p> <p><code>PCSG_dataset</code> is in <code>PCSG_dataset.zip</code>.</p> <p>The <code>KeywordSearch_dataset</code> is compressed into several volumes in the following files: <code>KeywordSearch_dataset.zip</code>, <code>KeywordSearch_dataset.z01</code>, <code>KeywordSearch_dataset.z02</code>, <code>KeywordSearch_dataset.z03</code>, <code>KeywordSearch_dataset.z04</code>, <code>KeywordSearch_dataset.z05</code>. We recommend using <code>Bandizip</code> to unzip them.</p>
Data repository accompanying "Many-Body Majorana Braiding without an Exponential Hilbert space"
<p>This repository includes the data and notebooks to generate the figures published in "Many-body Majorana braiding without an exponential Hilbert space".</p>
Evaluation of Many Men, Many Voices, An STD/HIV Prevention Intervention for Black MSM
ClinicalTrials.gov study NCT00137631. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Cancer Health Assessments Reaching Many
ClinicalTrials.gov study NCT03426878. IPD Sharing: YES. Countries: 1. Publications: 3.
Mucilage-binding to ground protects seeds of many plants from harvester ants: a functional investigation
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Data from: How many characters are needed to reconstruct a phylogeny?
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Data from: Uncovering new lineages in the Sunda Pangolin (<em>Manis javanica</em>) with museum mitogenomics
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Many roads to reservoirs? How susceptibility and shedding shape host competence in amphibians
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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)
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.