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19 results for “Normal modes”
Centre frequencies and uncertainties for "Evidence for a kilometre-scale seismically slow layer atop the core-mantle boundary from normal modes"
<p>A table containing the centre frequencies and uncertainties used for the study presented in "Evidence for a kilometre-scale seismically slow layer atop the core-mantle boundary from normal modes". This table is the same as is contained in the supplementary materials of that paper.</p> <p>Russell, S., Irving, J. C. E., Jagt, L., & Cottaar, S. (2023). Evidence for a kilometer-scale seismically slow layer atop the core-mantle boundary from normal modes. Geophysical Research Letters, 50, e2023GL105684. <a href="https://doi.org/10.1029/2023GL105684">https://doi.org/10.1029/2023GL105684</a></p>
Data for the article "Computational micromagnetics based on normal modes: Bridging the gap between macrospin and full spatial discretization"
<p>Data for the article "Computational micromagnetics based on normal modes: Bridging the gap between macrospin and full spatial discretization".</p> <p>Link to publisher: https://www.sciencedirect.com/science/article/abs/pii/S0304885321009197</p> <p>Link to Arxiv preprint: https://arxiv.org/abs/2105.08829</p>
Normal mode splitting function predictions for mantle anisotropy
<p>Predictions for normal mode splitting functions for 6 models of mantle anisotropy, accompanying the paper published in Geophysical Journal International by Restelli, Koelemeijer & Ferreira (2023). This is version 2 related to the revised manuscript. </p> <p>More details can be found in the README. </p>
Supplementary data frames, AlphaFold models, Normal Mode Analysis (NMA) Data, and NMA of Corresponding NMR Ensembles in the S2RCI, MD, and S2 Datasets for "Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics"
<h1><strong>Changes applied to V2</strong></h1> <p>In addition to the supplementary dataframes and AlphaFold models from each dataset in V1, V2 includes the additional data outlined below.</p> <p>The <strong>S2RCI</strong> and <strong>MD</strong> datasets include comprehensive analyses of AlphaFold2 models (both before and after truncation). These datasets feature: </p> <ul> <li><strong>AlphaFold2 Models</strong>: Both original and truncated structures. </li> <li><strong>WEBnma Modes</strong>: `modes.txt` files generated from WEBnma analysis, available for both non-truncated and truncated AF2 models. </li> <li><strong>Root-Mean-Square-Fluctuations (RMSF)</strong>: Profiles calculated before and after truncation of AF2 models. </li> <li><strong>NMR Data: Normal Mode Analysis (NMA)</strong>: Performed on corresponding NMR ensembles (see below). </li> </ul> <p> </p> <p>The <strong>NMR Data</strong> of NMA in these datasets includes: </p> <ul> <li>NMR ensembles </li> <li>Individual NMR models extracted from each ensemble </li> <li>STRIDE secondary structure calculations per-individual NMR models</li> <li>RMSF profiles per-individual NMR models</li> </ul> <p>For detailed information, please refer to the `Readme.txt` file within each corresponding folder. </p> <p>The <strong>S2 dataset</strong> includes all the features listed above, except for the NMR analysis.</p>
Buoyancy Waves in Earth's Nightside Magnetosphere: Normal-Mode Oscillations of Thin Filaments
<ul> <li>A theory has been developed for small oscillations of a thin filament in the magnetosphere.</li> <li>For the lowest-frequency even modes, the eigenfunctions are essentially buoyancy waves in the plasma sheet, but they are more like slow modes in the inner magnetosphere.</li> <li>For the lowest-frequency even modes, the eigenfrequencies (radians/s) have peak values of approximately 0.07 s<sup>-1</sup> between the inner plasma sheet and plasmapause, for an average magnetospheric field. </li> <li>This includes software and model data used in this paper.</li> <li>Submitted to JGR for review</li> </ul>
The dataset for the submitted paper " Time Series Analysis of Normal Mode Energetics for Rossby Wave Breaking and Saturation using a Simple Barotropic Model".
<p>These files are the data of the result in the submitted paper, titled "Time Series Analysis of Normal Mode Energetics for Rossby Wave Breaking and Saturation using a Simple Barotropic Model".</p> <ul> <li>File Description</li> </ul> <p>pv13.data : Exp. 1<br> pv17.data : Exp. 2</p> <p>The raw potential vorticity (PV) data for the Exp.1 and Exp.2, respectively, used in drawing the Fig.1, 2, and the supplemental movie 1 and 2.<br> These are the grid point value files, 72 levels for the zonal direction, 30 levels for meridional direction. More details are described in the next ctl files.</p> <p> </p> <p>pv13.ctl<br> pv17.ctl</p> <p>Description files for pv13.data and pv17.data. This will be called from grads_pv13.gs and grads_pv17.data, respectively.</p> <p>grads_pv13.gs<br> grads_pv17.gs</p> <p>GrADS script for mapping the PV.</p> <p> </p> <p>energy17.txt : Exp.2</p> <p>The time series table of energy values for exp.2.<br> One raw is identified by combination of the TIME in the experiment and zonal wave number N.</p>
Experimentally Measuring an Isolated Branch of Nonlinear Normal Modes
<p>Dataset for "Experimentally Measuring an Isolated Branch of Nonlinear Normal Modes", Journal of Sound and Vibration.</p> <p>See "readme.txt" for details</p>
Internal Normal Mode Analysis applied to RNA flexibility and conformational changes
<p>We investigated the capability of internal normal modes to reproduce RNA dynamics and predict observed RNA conformational changes, and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified rep- resentation of RNA structure and its potential energy. In this study, we considered three main data sets to investigate different aspects : i) one based on single-stranded RNA molecules for which all-atom MD simulations were computed; ii) one based on the available structures belonged to a specific Rfam family; iii) one based on the transition from unbound to bound RNA.</p> <p><strong>In each folder</strong></p> <p><em>modes.dat</em>: results obtained by iNMA (frequency and normal modes)</p> <p><em>das1.dat</em>: conversion from internal to cartesian normal modes</p> <p>Each file <em>name_enm.pdb</em> refers to a PDB structure with a CG representation (RNA three-bead model).</p> <p><strong>Dataset 1</strong>: d1.zip</p> <p>For the first dataset, we provide MD simulations converted into CG representation (RNA three-bead model), PCA analysis, the results obtained by iNMA for different values of distance cut-off <em>R</em><sub><em>c</em> </sub> and some scripts.</p> <p>Matlab and python scripts: </p> <p><em>analysis_pca.py</em>: to extract the different principal components</p> <p><em>analysis_PCA.m</em>: to compute overlap and cumative overlap in each folder</p> <p><em>analysis_complete_new.m</em>: to summarize the results</p> <p><strong>Dataset 2</strong>: d2.zip</p> <p>For this dataset, we provide the structure ensemble for Rfam family and the results obtained by iNMA for different values of distance cut-off <em>R</em><sub><em>c</em> </sub>and some scripts.</p> <p>PDB files:</p> <p><em>allensemble.pdb</em>: ensemble of PDB structures for a given Rfam family</p> <p><em>allensemble_enm.pdb</em>: ensemble of PDB structures for a given Rfam family converted to CG representation (RNA three-bead model)</p> <p><em>allensemble_enm_new.pdb</em>: ensemble of PDB structures for a given Rfam family with the same number of atoms for each model converted to CG representation (RNA three-bead model)</p> <p><em>model.pdb</em>: reference PDB structure</p> <p><em>model_enm.pdb</em>: reference PDB structure converted to CG representation (RNA three-bead model)</p> <p>Matlab script: </p> <p><em>pca_xray_anal.m</em>: PCA analysis, overlap, cumulative overlap, rmsip and plots</p> <p><strong>Dataset 3</strong>: d3.zip</p> <p>PDB structure:</p> <p><em>bound.pdb</em>: bound structure</p> <p><em>unbound.pdb</em>: unbound structure</p> <p><em>diff.dat</em>: difference between bound and unbound structure after superimposition </p> <p>RMSD<em>n </em>with n a number: the first column represents <span class="math-tex">\(\sqrt{\beta/2}\)</span></p> <p>Matlab script:</p> <p><em>rmsd_anal.m</em>: analysis best mode based on RMSD</p> <p><strong>Application to the CrPV-IRES</strong>: IRES.zip</p> <p>PDB structures:</p> <p> <em>IRES_cg.pdb</em>: Coarse-grain structure based on the PDB ID 5IT9</p> <p><em>b_end001_01_70.pdb</em>, <em>b_end001_01_80.pdb, b_end001_01_90.pdb</em>: Example of modified structures using the first lowest modes and different amplitudes <span class="math-tex">\(\beta\)</span></p> <p><em>b_end002_03_50.pdb</em>, <em>b_end002_03_60.pdb, b_end002_03_70.pdb</em>: Example of modified structures using the third lowest modes and different amplitudes <span class="math-tex">\(\beta\)</span></p>
Research data supporting: "Extended sampling of macromolecular conformations from uniformly distributed points on multidimensional normal mode hyperspheres"
<p>This repository contains protein structures generated by the approach "distributed points Molecular Dynamics using Normal Modes" (dpMDNM). dpMDNM is an enhanced-sampling approach that allows large protein conformational sampling based on normal mode (NM) vector combinations.</p> <p>Input parameter and equilibrated files for Lysozyme and CYP3A4 are provided, including their respective ensemble of structures after conformational exploration combining from 2 to 8 NMs.</p> <p>For more information, please visit the <a href="https://github.com/antonielgomes/dpMDNM">dpMDNM GitHub repository</a>.</p>
Dataset and Software for An anisotropic shear velocity model of the Earth's mantle using normal modes, body waves, surface waves and long-period waveforms
<p><strong>What is the nature of flow in the mantle?</strong><br> <strong>How fast do waves travel anywhere on Earth?</strong><br> <strong>Where can radial anisotropy be robustly detected?</strong><br> <strong>Can we reconcile a broad spectrum of seismic data? What are the benefits?</strong></p> <p>We use normal-mode splitting functions in addition to surface-wave phase anomalies, body-wave travel times and long-period waveforms to construct a three-dimensional model of anisotropic shear-wave velocity in the Earth's mantle. This is the <strong>first tomographic study</strong> to exploit the sensitivity of mode-splitting data to constrain radial anisotropy in the Earth's mantle jointly with several other types of data. Our modeling approach inverts for mantle velocity and anisotropy as well as transition-zone discontinuity topographies, and incorporates new crustal corrections for the splitting functions that are consistent with the nonlinear corrections we employ for the waveforms. Our preferred anisotropic model, S362ANI+M, is an update to the earlier model S362ANI, which did not include normal-mode splitting functions in its derivation.</p> <p><strong>Feedback/Questions?</strong> Please contact Raj Moulik (<a href="https://rajmoulik.com">rajmoulik.com</a>) at <a href="mailto:moulik@caa.columbia.edu?subject=Query%20from%20Zenodo">moulik@caa.columbia.edu</a> </p> <p><strong>Reference:</strong></p> <p><em>Please cite the following work if you use this data or software.</em></p> <ul> <li>Moulik, P. & Ekström, G., 2014. An anisotropic shear velocity model of the Earth's mantle using normal modes, body waves, surface waves and long-period waveforms, <em>Geophys. J. Int.</em>, <strong>199</strong>(3), 1713-1738, doi: <a href="http://dx.doi.org/10.1093/gji/ggu356">10.1093/gji/ggu356</a>. <em><a href="https://rajmoulik.com/Publications/MoulikEkstrom_GJI2014.pdf">pdf</a></em></li> </ul> <p><em>You can also cite the dataset and software from this Zenodo page (Optional).</em></p> <ul> <li> <p>Moulik, P. & Ekström, G., 2014. Dataset and Software for An anisotropic shear velocity model of the Earth's mantle using normal modes, body waves, surface waves and long-period waveforms. In Geophys. J. Int. (v1.0, Vol. 199, pp. 1713–1738). Zenodo. doi: <a href="https://doi.org/10.5281/zenodo.8357379">10.5281/zenodo.8357379</a></p> </li> </ul> <p><strong>Data Products:</strong></p> <ul> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/S362ANIplusM_Figures.tar.gz"><strong>S362ANIplusM_Figures.tar.gz</strong></a> - contains all figures from the paper in .png format</li> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/S362ANI%2BM_MapViewsCrossSections.pdf"><strong>S362ANI+M_MapViewsCrossSections.pdf</strong></a> - Some cross sections and map views at various depths in the mantle</li> <li><strong><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/S362ANI%2BM">S362ANI+M</a> - </strong>Coefficients of the spline basis functions for each parameter. Refer c<sub>ij</sub> in equation 11. This is our preferred global model of shear-wave velocity. In this model, radial anisotropy is confined to the uppermost mantle (that is, since the anisotropy is parameterized with only the four uppermost splines, it becomes very small below a depth of 250 km, and vanishes at 410 km). This is an updated version of S362ANI (Kustowski et al., 2008) which did not include normal modes in its derivation. Please note the stronger isotropic shear velocity anomalies in the transition zone.</li> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/STW105"><strong>STW105</strong></a> - reference model used in S362ANI+M. Described in Kustowski et al. (2008)</li> <li><strong><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/setup.cfg">setup.cfg</a> - </strong>Some configuration metadata relevant to this model for reproducibility.</li> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/epix.tar.gz"><strong>epix.tar.gz</strong></a> - Perturbations in horizontally (vsh) and vertically polarized shear velocity (vsv), Voigt-average isotropic velocity (vs), ansotropy (as) and topography of the internal boundaries. This is calculated from the spline coefficients at every 1 by 1 degree cell-centered pixel and at every ~25 km depth region from Moho to the core-mantle boundary and stored in extended pixel format (.epix) ASCII files. </li> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/S362ANI%2BM.BOX25km_PIX1X1.avni.nc4"><strong>S362ANI+M.BOX25km_PIX1X1.avni.nc4</strong></a> - The perturbations in a standard AVNI format that utilizes the NETCDF4 container format. This file can be read in Python using either xarray or AVNI libraries. For example, to plot vs perturbations at 24.4-50 km depth range <ul> <li><em>import xarray as xr</em></li> <li><em>ds = xr.open_dataset('S362ANI+M.BOX25km_PIX1X1.avni.nc4')</em></li> <li><em>ds.vs[0].plot()</em></li> </ul> </li> <li><strong>Fortran Code</strong> <ul> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/readme"><strong>readme</strong></a> - contains a description of all files in the folder below</li> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/PROGRAMS.tar.gz"><strong>PROGRAMS.tar.gz</strong></a> - tools for obtaining model values at specific locations and some GMT plotting tools</li> </ul> </li> <li><a href="https://zenodo.org/api/files/a15ed123-5262-4c4b-9806-1b50e7f8ee82/GRD.tar.gz"><strong>GRD.tar.gz</strong></a> - longitude-latitide-velocity files with vsh, vsv, and Voigt average in km/s evaluated on a grid of points at many depths in the mantle</li> </ul>
Model data for normal modes of poloidal field line oscillations
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Exploration of the electron density and bare nuclear potential along the selected normal modes of the selected water clusters - W6 - changedHexamers
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Exploration of the electron density and bare nuclear potential along the selected normal modes of the selected water clusters - W6
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Results and evaluation of ModeNet in extracting normal mode signals
<p>These are the datasets of the main figures in our manuscript, which include the evaluation of the training process, the predictions of ModeNet and the performance evaluation of ModeNet on the test set.</p>
A novel RAF kinase inhibitor with DFG-out binding mode: high efficacy in BRAF-mutant tumor xenograft models in the absence of normal tissue hyperproliferation
GEO Series GSE74729. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Heart structure as visualized with high-resolution normal multiscan mode CECT in 3D (left) and on 2D orthoslice (right)
<p>Ao = aorta, RV = right ventricle, LV = left ventricle, RA = right atrium, LA = left atrium, RAA = right atrial appendage, LAA = left atrial appendage, PV = pulmonary valve, TV = tricuspid valve, AV = aortic valve, MV = mitral valve, PM = papillary muscle.</p>
STEREO-B In-Situ Measurements of Particles and CME Transients (IMPACT) Fluxgate Magnetometer (MAG) Burst Mode, Magnetic Field Vector, Radial-Tangential-Normal (RTN) Coordinates, Level 1 (L1), 31 ms Data
This data product contains Level 1 0.03125-s or 32 Hz burst-mode values of solar wind magnetic field data measured by the IMPACT Magnetometer on STEREO-B in Radial-Tangential-Normal, RTN, coordinates.
STEREO-A In-Situ Measurements of Particles and CME Transients (IMPACT) Fluxgate Magnetometer (MAG) Burst Mode, Magnetic Field Vector, Radial-Tangential-Normal (RTN) Coordinates, Level 1 (L1), 31 ms Data
This data product contains Level 1 0.03125-s or 32 Hz burst-mode values of solar wind magnetic field data measured by the IMPACT Magnetometer on STEREO-A in Radial-Tangential-Normal, RTN, coordinates.
Kerr Quasi-Normal Mode Mathematica Data l=2--16, n=0--32
<p>This tar.gz file contains the original Mathematica data files for the gravitational quasi-normal modes of the Kerr geometry. For n=0--15, all m values for the l=2--16 modes are present. For n=16--32, all m values for the l=2--4 modes are present. These data sets were constructed using the methods outlines in Cook & Zalutskiy, <em>Phys. Rev. D</em> <strong>90</strong> (2014) pp. 124021 (DOI: https://doi.org/10.1103/PhysRevD.90.124021).</p>
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