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226 results for “symmetry”
Dataset for the manuscript "Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2" in Science Advances Vol. 10, No. 5
<p>Dataset for publication "Observation of time-reversal symmetry breaking in the band structure of altermagnetic RuO2" in Science Advances Vol. 10, No. 5, https://doi.org/10.1126/sciadv.adj4883.</p> <p>The details corresponding to the dataset of the figures are given in a readme file in the corresponding folders.</p>
Pair Wavefunction Symmetry in UTe2 from Zero-Energy Surface State Visualization
<p>This dataset contains all the data in "Pair Wavefunction Symmetry in UTe2 from Zero-Energy Surface State Visualization"</p>
Dataset for "selection rules in symmetry-broken systems by symmetries in synthetic dimensions"
<p>Data for the article "Selection rules in symmetry-broken systems by symmetries in synthetic dimensions" by Matan Even Tzur, Ofer Neufeld, Eliyahu Bordo, Avner Fleischer, and Oren Cohen.</p>
ATITPhysics 2021 - Conformal Symmetry in Field Theories
<p>These lecture series are given in ATITPhysics 2021 Summer School, and are tailored for entry-level graduate students who have not taken any quantum field theory course.</p>
Dataset for: Pressure-driven symmetry transitions in dense H2O ice
<p>This dataset comprises of all of the XRD patterns for ice and gold used for the equation of state in "Pressure-driven symmetry transitions in dense H<sub>2</sub>O ice." Also included is a key for correlating ice and gold as well as the calibration files and CeO<sub>2</sub> diffraction patterns for obtaining the calibration</p>
Global distribution and evolutionary transitions of floral symmetry in angiosperms
<p><span>Floral symmetry plays a crucial role in plant-pollinator interactions and has remarkable impacts on angiosperm evolution. However, the spatiotemporal patterns in floral symmetry and drivers of these patterns </span><span>remain poorly known</span><span>. Here, using global distributions and </span><span>floral symmetry data </span><span>of 280,140 angiosperm species, we presented the global geographic and evolutionary patterns of floral symmetry </span><span>composition and demonstrated the climatic drivers of these patterns</span><span>. We found that the frequency of actinomorphic (radial) species increased with latitude, while that of </span><span>zygomorphic</span><span> (</span><span>bilateral</span><span>) species decreased</span><span>.</span><span> Solar radiation, present-day temperature and Quaternary temperature change explained the geographic variation in floral symmetry. Evolutionary transitions from actinomorphy to</span><span> zygomorphy dominated floral symmetry evolution, although the rate of this transition decreased through the Cenozoic associated with decreasing </span><span>paleo-temperature</span><span>. </span><span>Our study </span><span>provides novel insights into the ecology and evolution of angiosperm floral symmetry and suggests that climate change may influence species distributions via its effect on floral symmetry.</span></p>
Complex morphologies of biogenic crystals emerge from anisotropic growth of symmetry-related facets
<p>Directing crystal growth into complex morphologies is challenging, as crystals tend to adopt thermodynamically stable morphologies. Yet, many organisms form crystals with intricate morphologies, as exemplified by coccoliths, microscopic calcite crystal-arrays produced by unicellular algae. The complex morphologies of the coccolith crystals were hypothesized to materialize from numerous crystallographic facets, stabilized by fine-tuned interactions between organic molecules and the growing crystals. Using state-of-the-art electron tomography, we examined multiple stages of coccolith development in 3D. We found that the crystals are expressing only one set of symmetry-related crystallographic facets, which grow differentially to yield highly anisotropic shapes. Morphological chirality arises from positioning the crystals along specific edges of these same facets. Our findings show that manipulations of growth kinetics can yield complex crystalline morphologies.</p>
Symmetry as a grouping cue for numerosity perception
<p>For the numerosity experiments: each file contains a matrix called “a”. Each row of the matrix “a” is a trial. </p> <p>The columns contain the following information:</p> <ul> <li>1st: Numerosity of test stimulus</li> <li>2nd: Log10 of numerosity of test stimulus divided by the standard numerosity</li> <li>3rd: Participant response (0 = standard stimulus; 1 = test stimulus)</li> <li>4th: 200</li> <li>5th: Standard numerosity </li> <li>6th: Dots size in pixels</li> <li>7th: 10</li> <li>8th: Condition (0= symmetry condition; 1= random condition)</li> <li>9th: Standard-Test order (1 = standard first; 2 = standard second)</li> <li>10th: Response time</li> </ul> <p>For the control experiment: each file contains a matrix called “a”. Each row of the matrix “a” is a trial. </p> <p>The columns contain the following information:</p> <ul> <li>1st: Numerosity of test stimulus</li> <li>2nd: Log10 of numerosity of test stimulus divided by the standard numerosity</li> <li>3rd: Participant response (0 = standard stimulus; 1 = test stimulus)</li> <li>4th: 200</li> <li>5th: Standard numerosity </li> <li>6th: Dots size in pixels</li> <li>7th: 10</li> <li>8th: 0= standard stimulus symmetric and test stimulus random</li> <li>9th: Standard-Test order (1 = standard first; 2 = standard second)</li> <li>10th: Response time</li> </ul>
Ground-state structural disorder and excited-state symmetry breaking in a quadrupolar molecule
<p>The files contains all the data that are shown in the figures of the article:</p> <p>Soederberg, M.; Dereka, B.; Marrocchi, A.; Carlotti, B.; Vauthey, E. Ground-state Structural Disorder and Excited-state Symmetry Breaking in a Quadrupolar Molecule. J. Phys. Chem. Lett. 10 (2019), 10.1021/acs.jpclett.9b01024</p> <p> </p>
Cross-correlations and symmetries in genetic sequences
<p>Data sets and supporting material used in the manuscript</p> <p>"The common origin of symmetry and structure in genetic sequences" by<br> G. Cristadoro , M. Degli Esposti , E. G. Altmann<br> https://arxiv.org/abs/1710.02348</p> <p>Output of calculations can be seen in the file:<br> Notebook.html</p> <p>In order to repeat calculations or explore different choices:</p> <ol> <li>Download all files to the same directory</li> <li>Uncompress the "data.tar.gz" file (e.g., using tar -xzvf data.tar.gz)</li> <li>Open the Notebook using Python 3.0 in Jupyter (www.jupyter.org)</li> </ol> <p> </p>
Data for "Tetramine Aspect Ratio and Flexibility Determine Framework Symmetry for Zn8L6 Self-Assembled Structures"
<p>In the following subdirectories are the input and outputs of cage and face analysis for:</p> <p>Published DOI: <a href="https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202217987">10.1002/anie.202217987 </a></p> <p>Code: <a href="https://github.com/andrewtarzia/sca_cage_assembler/tree/cubism-production">sca_cage_assembler</a></p> <p>Previously uploaded in 10.5281/zenodo.8432296 and <a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer">https://github.com/andrewtarzia/citable_data</a></p> <p>NOTES:</p> <ul> <li>the naming convention differs from manuscript:</li> </ul> <table> <tbody> <tr> <th>manuscript tetra-aniline</th> <th>computational label</th> <th>xtal-label</th> </tr> <tr> <td>A</td> <td>5</td> <td>370</td> </tr> <tr> <td>B</td> <td>16</td> <td>326</td> </tr> <tr> <td>C</td> <td>12</td> <td>235</td> </tr> <tr> <td>D</td> <td>3</td> <td>301</td> </tr> <tr> <td>E</td> <td>8</td> <td>257</td> </tr> <tr> <td>F</td> <td>2</td> <td>354</td> </tr> </tbody> </table> <ul> <li>computational labels are often preceded by `quad2_` or `cl1_quad2_`</li> <li>much of the analysis was not used in the manuscript but remains part of the accumulated data</li> </ul> <p> </p> <p>cage_library directory:</p> <ul> <li>_CS.json: information on all cages in the set of diastereomers - properties and whether they optimized successfully.</li> <li>_ligand_measures.json: information on the ligand associated with a set of cage diastereomers.</li> <li>_measures.json: represenets a cleaned up collation of all measures the diastereomers made from a given ligand</li> <li>C_NAME_optc.mol: optimized (at xTB level) structure of each cage.</li> <li>set_dft_run directory contains the input and output of the CP2K optimisations of one set of diastereomers</li> </ul> <p>complex_library directory:</p> <ul> <li>contains the optimised structures of both complexes</li> </ul> <p>ligand_library directory:</p> <ul> <li>contains `_opt.mol` input ligand structures for cage construction</li> <li>for cap, the input was provided manually in `manual/` directory</li> <li>in `face_analysis` directory: <ul> <li>contains manual_complex directory, with necessary input for face construction</li> <li>_long_properties.json files contains the measurements for the named face (in file name)</li> <li>_long_lopt.mol files contain the optimised structure of the named face, on which analysis was performed</li> <li>`long` corresponds to the longer restricted optimization discussed in the SI.</li> </ul> </li> </ul> <p>xray_structures directory:</p> <ul> <li>analysis directory: <ul> <li>contains input .pdb files for xray structure (as single molecules) used in analysis</li> <li>contains `all_xray_csv_data.csv`, which has all data needed on xray structures.</li> </ul> </li> </ul>
Data for "High-Throughput Computational Evaluation of Low Symmetry Pd2L4 Cages to Aid in System Design"
<p>In the following subdirectories are the input and output of Gaussian calculations + structures from screening for this publication:</p> <p>chemrxiv: <a href="https://chemrxiv.org/engage/chemrxiv/article-details/60c758e0ee301c7eadc7b7df">10.26434/chemrxiv.14604294</a></p> <p>Published: <a href="https://onlinelibrary.wiley.com/doi/10.1002/anie.202106721">10.1002/anie.202106721</a></p> <p>Previously uploaded in 10.5281/zenodo.8432296 and <a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer">https://github.com/andrewtarzia/citable_data</a></p> <p>Software repository: <a href="https://github.com/andrewtarzia/unsymm_match">github.com/andrewtarzia/unsymm_match</a></p> <p>screening_structures directory:</p> <ul> <li>contains the structures from xTB optimisation that were used in ranking in structures.tar.gz as `.mol` files</li> <li>all_cage_results.txt contains their properties for ranking</li> </ul> <p>single_point_dft directory:</p> <ul> <li>contains the structures and output of single point DFT calculations</li> <li>during the revision process, we confirmed (based on reviewer suggestions) our DFT validation results using ORCA 4.2.1 with PBE0 and B97-3c in the gas phase. These results were consistent with our previous ones, so were not added to the manuscript. But are useful for future work! <ul> <li>These results are in the s_orca directory.</li> </ul> </li> </ul> <p>free_energy_calculations directory:</p> <ul> <li>during the revision process, it was suggested to calculate the free energies using the xTB method (low-cost) and compare that to the total energies we use.</li> <li>the script `run_gfn2_free_energy.py` in the unsymm_match code repository does this for top candidate ligands using the stko.XTB class. <ul> <li>for each structure, the free energy is output to a .fey file.</li> </ul> </li> </ul>
DNA sequences for: Synthetic control of actin polymerization and symmetry breaking in active protocells
<p>Non-linear biomolecular interactions on membranes drive membrane remodeling crucial for biological processes including chemotaxis, cytokinesis, and endocytosis. The complexity of biomolecular interactions, their redundancy, and the importance of spatiotemporal context in membrane organization impede understanding of the physical principles governing membrane mechanics. Developing a minimal in vitro system that mimics molecular signaling and mem- brane remodeling while maintaining physiological fidelity poses a significant challenge. Inspired by chemotaxis, we reconstructed chemically regulated actin polymerization inside vesicles, guiding membrane self-organization. An external, undirected chemical input induced directed actin polymerization and membrane deformation uncorrelated with upstream biochemical cues, suggesting symmetry breaking. A biophysical model incorporating actin dynamics and membrane mechanics proposes that uneven actin distributions cause non-linear membrane deformations, consistent with experimental findings. This protocellular system illuminates the interplay between actin dynamics and membrane shape during symmetry breaking, offering insights into chemotaxis and other cell biological processes.</p>
Data for "Diastereoselective Self-Assembly of Low-Symmetry PdnL2n Nanocages through Coordination-Sphere Engineering"
<p>In the following subdirectories are the input and outputs of cage and face analysis for:</p> <p>Published DOI: 10.1002/anie.202315451</p> <p>Previously uploaded in <span>10.5281/zenodo.8432296 and </span><a href="https://github.com/andrewtarzia/citable_data" rel="noopener noreferrer"><span>https://github.com/andrewtarzia/citable_data</span></a></p> <p>Note that all scripts are self-contained. There is some duplicate code between them.</p> scripts: <ul> <li> build_cages.py: <ul> <li>Builds the Pd2L4 cage models.</li> <li>Some manual optimisation is assumed.</li> <li>Paths for xTB and GULP are set to my machine.</li> <li>All outputs are relative to working directory.</li> </ul> </li> <li> build_dwall_triangles.py: <ul> <li>Builds the Pd3L6 cage models.</li> <li>Some manual optimisation is assumed.</li> <li>Paths for xTB and GULP are set to my machine.</li> <li>All outputs are relative to working directory.</li> </ul> </li> </ul>
Experimental data and benchmarks used in the paper "Theoretical Foundations for Structural Symmetries of Lifted PDDL Tasks"
<p>This dataset contains both benchmarks and data used in the paper.</p> <p>PDDL benchmark files can be found in the files benchmarks.tar.gz and<br> bagged-benchmarks.tar.gz. The former contains all domains from all IPCs from the<br> repository https://bitbucket.org/aibasel/downward-benchmarks, without duplicate<br> domains that have been used in multiple IPCs. The latter contains the subset of<br> these tasks for which the reformulation in the "bagged representation" from the<br> following paper succeeded:</p> <p>Riddle, P.; Douglas, J.; Barley, M.; and Franco, S. 2016. Improving<br> performance by reformulating PDDL into a bagged representation.<br> In ICAPS 2016 Workshop on Heuristics and Search for Domain-<br> independent Planning, 28–36.</p> <p>We obtained the implementation of the baggy reformluation from the authors.</p> <p>All other files in this dataset contain raw and processed data of all<br> experiments, which were generated using Downward-Lab (see<br> https://doi.org/10.5281/zenodo.399255). The scripts used to run the experiments<br> can be found in the software bundle for this paper (see<br> https://doi.org/10.5281/zenodo.2621897).</p> <p>Directories without the "-eval" ending contain raw data, distributed over a<br> subdirectory for each experiment. Each of these contain a subdirectory tree<br> structure "runs-*" where each planner run has its own directory. For each run,<br> there are symbolic links to the input PDDL files domain.pddl and problem.pddl<br> (can be resolved by putting the benchmarks directory to the right place), the<br> run log file "run.log" (stdout), possibly also a run error file "run.err"<br> (stderr), the run script "run" used to start the experiment, and a "properties"<br> file that contains data parsed from the log file(s). Some directories (not for<br> the ground experiments, where these files got too large) also contain a file<br> generators.py that contain all symmetry group generators in permutation<br> notation.</p> <p>Directories with the "-eval" ending contain a "properties" file, which contains<br> a JSON directory with combined data of all runs of the corresponding<br> experiment. In essence, the properties file is the union over all properties<br> files generated for each individual planner run.</p>
False-match symmetry: Data files and simulation code
<p>This record provides data from random-dot stereograms to use in solving the binocular correspondence problem through false-match symmetry. It also provides an implementation of the algorithm used in the article ‘Solving the stereo correspondence problem with false matches’ [Ng CJ, Farell B (2019) Solving the stereo correspondence problem with false matches. PLoSONE 14(7): e0219052. https://doi.org/10.1371/journal.pone.0219052].</p> <p>The record consists of two parts, Data and Algorithm Demo. The Data component consists of pre-computed Keplerian arrays of all possible matches between filtered random-dot image pairs containing stereoscopically defined surfaces. The Algorithm Demo allows data files to be computed afresh from supplied pairs of images of various surface configurations. Plotting of data is possible in both cases. An interactive demo can also be used to explore the target image selection process.</p>
Towards Symmetry Driven and Nature Inspired UVA Filter Design
<p>In plants, sinapate esters offer crucial protection from the deleterious effects of ultraviolet radiation exposure. These esters are a promising foundation for designing UV filters, particularly for the UVA region (400 – 315 nm), where adequate photoprotection is currently lacking. Whilst sinapate esters are highly photostable due to a cis-trans (and vice versa) photoisomerization, the cis-isomer can display increased genotoxicity; an alarming concern for current cinnamate ester-based human sunscreens. To eliminate this potentiality, here we synthesize a sinapate ester with equivalent cis- and trans-isomers. We investigate its photostability through innovative ultrafast spectroscopy on a skin mimic, thus modelling the as close to true environment of sunscreen formulas. These studies are complemented by assessing endocrine disruption activity and antioxidant potential. We contest, from our results, that symmetrically functionalized sinapate esters may show exceptional promise as nature-inspired UV filters in next generation sunscreen formulations.</p>
Data for "Entanglement Dynamics in Monitored Kitaev Circuits: Loop Models, Symmetry Classification, and Quantum Lifshitz Scaling"
<p>We provide the data and scripts used to produce the figures shown in our publication "Entanglement Dynamics in Monitored Kitaev Circuits:<br>Loop Models, Symmetry Classification, and Quantum Lifshitz Scaling".</p>
MEFI Theory: The Grand Symmetry of the Universe
<div> </div> <div>Title:</div> <div>MEFI Theory: The Grand Symmetry of the Universe</div> <div> </div> <div>Abstract:</div> <div>This paper introduces the MEFI Theory (Modified Einstein Field Interaction), a revolutionary framework that unveils the Grand Symmetry of the Universe. MEFI theory builds upon Einstein’s field equations, proposing a universal model in which the forces governing quantum interactions and cosmic dynamics are fundamentally linked by a single unifying principle.</div> <div> </div> <div>Through a series of meticulously crafted simulations, MEFI theory demonstrates how self-similar patterns, waveforms, and energy propagations manifest uniformly across all scales, from the subatomic to the cosmic. The study explores:</div> <div> </div> <div>• Quantum-to-Cosmic Energy Propagation: Showcasing how energy inputs at the quantum scale propagate seamlessly through to large cosmic structures.</div> <div>• Fractal Emergence: Revealing fractal patterns under dark field compression, illustrating the natural symmetry from quantum interactions to galaxy formations.</div> <div>• Oscillatory and Waveform Scaling: Demonstrating the consistency of oscillations and waveforms across scales, from particle interactions to cosmic waveforms.</div> <div>• Cosmic Feedback Loops: Simulating the feedback between quantum-level interactions and large-scale cosmic systems, highlighting the interconnectedness of all systems.</div> <div>• Holographic Principle: Modeling how quantum systems encode information that projects onto larger cosmic structures, supporting the idea of a unified field.</div> <div>• Universal Resonance Frequencies: Identifying the resonance frequencies that are constant across all scales, reinforcing the concept of a deeply connected universe.</div> <div> </div> <div>These simulations provide compelling visual evidence that MEFI theory explains the scale-invariant nature of the forces shaping the universe. By modifying Einstein’s field interactions, this theory proposes that the same governing principles apply consistently at all levels of reality—from the smallest particles to the largest cosmic structures. The Grand Symmetry of the Universe is not merely a theoretical insight but a law of nature that binds the cosmos together, ensuring harmony and coherence across all scales.</div> <div> </div> <div>Keywords:</div> <div>MEFI theory, Modified Einstein Field Interaction, grand symmetry, dark field compression, quantum interactions, cosmic dynamics, fractal patterns, holographic principle, universal resonance, scale-invariance, unified forces.</div> <p> </p> <p> </p> <p>Sincerely,</p> <p>Steven Greenmyer</p>
ResNet and Asymmetric ResNet Weights, for "The Empirical Impact of Neural Parameter Symmetries, or Lack Thereof"
<p>Trained checkpoints of tens of thousands of neural networks, for use in our paper "The Empirical Impact of Neural Parameter Symmetries, or Lack Thereof" (https://arxiv.org/abs/2405.20231).</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.