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1,670 results for “FORCE”
OPEPv7 Force Field: Parameters of Non-Bonded Interaction Potentials
<p>Parameters defining interaction potentials between amino-acid beads in the OPEPv7 force field.</p> <p>CA stands for the C<span class="math-tex">\(\alpha\)</span> bead of any residue except for glycine, which has a dedicated bead type, labeled as CAG. The side-chain beads are each named after the corresponding residue.</p> <p>“12-6” represents the Lennard-Jones potential, in which case the <span class="math-tex">\(C_{12}\)</span> and <span class="math-tex">\(C_{6}\)</span> parameters are given in the table. “OPEP” denotes the OPEP side-chain potential with an attractive term while “OPEM” stands for the purely repulsive variant (see <a href="https://doi.org/10.1039/C4CS00048J">Chem. Soc. Rev., 2014,43, 4871-4893</a>). In both cases, the <span class="math-tex">\(r^{0}_{ij}\)</span> and <span class="math-tex">\(\varepsilon_{ij}\)</span> parameters are given.</p> <p>The parameters of the default OPEPv7 force field are listed in the <strong>OPEPv7.dat file</strong>. The <strong>OPEPv7_LJ_fit.dat</strong> file provides a simplified version of the force field where the “OPEP” potentials are replaced by Lennard-Jones fits.</p>
Inputs (forcing and observations) ready for use by 'MuSA: The Multiscale Snow Data Assimilation System (v1.0)'
<p>MuSA is a snow data assimilation system that can fuse observations with snowpack simulations generated by the Flexible Snow Model (FSM2). This repository contains meteorological forcing developed with the Micromet model and 5 m resolution snow depth observations in the Izas basin (central Spanish Pyrenees) generated with drones, ready to be used in MuSA.</p>
Figure 3. Strict consensus trees from the constrained analyses. First constrained analysis forcing a in Taxonomic, palaeobiological and evolutionary implications of a phylogenetic hypothesis for Ornithischia (Archosauria: Dinosauria)
Figure 3. Strict consensus trees from the constrained analyses. First constrained analysis forcing a monophyletic Silesauridae apart from the 'traditional ornithischians'. Abbreviations: Aphan, Aphanosauria; Herrer, Herrerasauridae. Silhouettes are based on artwork by Márcio L. Castro, Gabriel Lio, Rodrigo T. Müller, Maurício S. Garcia, John Sibbick and Douglas M. Heman.
Figure 4. Second constrained analysis forcing a in Taxonomic, palaeobiological and evolutionary implications of a phylogenetic hypothesis for Ornithischia (Archosauria: Dinosauria)
Figure 4. Second constrained analysis forcing a monophyletic Ornithoscelida. Abbreviations: Aphan, Aphanosauria; Herrer, Herrerasauridae. Silhouettes are based on artwork by Márcio L. Castro, Gabriel Lio, Rodrigo T. Müller, Maurício S. Garcia, John Sibbick and Douglas M. Heman.
Piezo1 as a force-through-membrane sensor in red blood cells
<p>Piezo1 is the stretch-activated Ca<sup>2+</sup> channel in red blood cells that mediates homeostatic volume control. Here we study the organization of Piezo1 in red blood cells using a combination of super-resolution microscopy techniques and electron microscopy. Piezo1 adopts a nonuniform distribution on the red blood cell surface, with a bias towards the biconcave "dimple". Trajectories of diffusing Piezo1 molecules, which exhibit confined Brownian diffusion on short timescales and hopping on long timescales, also reflect a bias towards the dimple. This bias can be explained by "curvature coupling" between the intrinsic curvature of the Piezo dome and the curvature of the red blood cell membrane. Piezo1 does not form clusters with itself, nor does it co-localize with F-actin, Spectrin or the Gardos channel. Thus, Piezo1 exhibits the properties of a force-through-membrane sensor of curvature and lateral tension in the red blood cell.</p>
The dataset for "Force-free current sheets in the Jovian magnetodisk: a key role of electron field-aligned anisotropy"
<p>The dataset for "Force-free current sheets in the Jovian magnetodisk: a key role of electron field-aligned anisotropy" submitted to J. Geophys. Res. This dataset contains information about 18 current sheet in the Jovian magnetodisk. PDF file includes the table and eighteen figures with current sheets. The table lists corresponding dates/times of the current sheet crossings by Juno spacecraft. Archive includes ASCII flies with data plotted on these figures.</p>
Blowing in the wind: Experimental assessment of clinging performance and behavior in Anolis lizards during hurricane-force winds
<p>1. Extreme weather events, such as hurricanes, can be ecologically devastating and cause widespread mortality. Recent studies in <em>Anolis</em> lizards report hurricane-induced phenotypic shifts and selection favoring morphological variation related to clinging performance. Although it is difficult to observe organismal responses during extreme events in nature, we can experimentally simulate the high-speed winds associated with hurricanes to evaluate the putative mechanism underlying observed patterns of natural selection.</p> <p>2. In this study, we used two laboratory experiments to better understand the clinging performance and behavior of <em>Anolis</em> lizards when experiencing hurricane-force winds. We assessed the physical ability of lizards when using the combined function of their claws, limbs, toepads, and other traits to resist forces pulling them off a perch. We also evaluated the combination of this physical clinging ability of lizards and their behavioral responses to avoid being blown off a perch during high winds. We assessed behavior that could decrease exposure of lizards to wind and increase their clinging ability.</p> <p>3. Clinging force measurements revealed variation in performance among species and substrates not reflected in clinging times for lizards experiencing hurricane-force winds, revealing the importance of behavior when experiencing high winds. The most arboreal species (<em>A</em>. <em>carolinensis</em>) had substantially longer clinging times on rough substrates compared to the other species, presumably due to its larger toepads for increased clinging as well as its shorter limbs that reduced drag.</p> <p>4. Under high-speed winds, lizards commonly shifted to the more protected leeward side of dowels, especially on broad and rough substrates, presumably to reduce exposure. This reveals how behavior can mediate factors influencing clinging ability during hurricanes and, in conjunction with ecologically relevant variation in morphology and substrate properties, contribute to clinging performance.</p> <p>5. Our experiments reveal that behavior strongly influences clinging performance during high winds beyond that predicted by physical traits alone. Thus, microhabitat selection of perches and the position of a lizard on its perch during a hurricane will likely have important consequences for clinging performance. This may alter how selection acts on morphological traits and influence the susceptibility of different species to these extreme weather events.</p>
Data for CSJin et al., 2023, PNAS, " Tectonic and orbital forcing of the South Asian monsoon in central Tibet during the late Oligocene"
<p>This zip file contains data presented in the PNAS paper “Tectonic and orbital forcing of the South Asian monsoon in central Tibet during the late Oligocene” by Jin et al., 2023. There are 7 Excel files for Figure 2, 3, 4, S4, S11, S13 and S14 of the paper, respectively.</p>
Last glacial cycle simulations forced by PMIP3 climate with a matrix and index method using a 3D thermodynamical ice-sheet model IMAU-ICE
<p>IMAU-ICE 2.0 model output of the ice evolution during the last glacial cycle at a 10 ka temporal resolution, as described in Scherrenberg at al., 2023.</p>
Sensitivity of glaciers in the European Alps to anthropogenic atmospheric forcings: case study of the Argentière glacier
<p>This Zenodo repository contains all datasets (IPSL CMIP6 data, glaciological data, SAFRAN data), ElmerIce codes and Python Jupyter Notebook used in the study reported in the article <strong><em>"Sensitivity of glaciers in the European Alps to anthropogenic atmospheric forcings: case study of the Argentière glacier"</em></strong></p>
Data to reproduce figures for the paper "The Effect of Tropical Pacific Air-sea Coupling on the Rainfall Response to Abrupt Greenhouse Gas Forcing"
<p>Data to reproduce figures for the paper "The Effect of Air-sea Coupling over the Tropical Pacific on the Response in Rainfall to Abrupt Greenhouse Gas Forcing".</p>
Craniodental divergence associated with bite force between hybridizing pine squirrels (Tamiasciurus)
<p>Bite force can be a limiting factor in foraging and can significantly affect the competitive ability and lifetime fitness of mammals. <em>Tamiasciurus</em> squirrels feed primarily on conifer seeds and have a strong bite force to mechanically extract seeds from conifer cones with their mouths. In the North Cascades region, Douglas squirrels (<em>Tamiasciurus</em> <em>douglasii</em>) and red squirrels (<em>T</em>. <em>hudsonicus</em>) occupy ecologically different forests with different hardnesses in conifer cones. The ranges of these species overlap in a narrow hybrid zone where these forests meet near the crest of the North Cascades. We examined interspecific divergence in dietary ecomorphology in allopatry, in sympatry within the hybrid zone, and between hybrids and each parental species. We focused on three craniodental traits, including the incisor-strength index as a proxy measure for maximal bite force, cranial-suture complexity, and mandible shape. We find that these sister squirrel species differ in bite force and suture complexity in allopatry and sympatry and that mandible shape changes with the expected hardness of accessed food items, but is not significantly different between species. Furthermore, we find that hybrids display morphologies that overlap with hybrid zone red squirrels but not with hybrid zone Douglas squirrels. This work shows how important ecological processes at shallow evolutionary timescales can impact the divergence of morphological traits in taxa with extreme conservation of craniomandibular shape.</p>
Distributive plural/singular cross-linguistic data – Likert-scale and forced-choice data
<p>Forced-choice: Our survey contains 15 pairs of sentences to be compared (languages: English, Czech, German, Polish). The sentences are indicated in the initial row (full case in A2, short notation in next columns). In each pair of sentences, we asked the participant to indicate the variant that seemed "better" or "more natural" to them. The following rows contain the choices made by each of the 30 participants. Rarely have both variants been chosen by a single participant.</p> <p>Likert scale: 50 participants were asked to rate the sentences given in column 2. The participants were explicitly asked to not evaluate the content or reliability of the sentences. Answers of the participants are given in the following rows. The answers mean: 1 (very unnatural/unacceptable); 2 (somewhat unnatural/weird); 3 (hard to say); 4 (quite natural/acceptable); 5 (fully natural/acceptable). The columns marked purple contain the test sentences, whereas the sentences in blue columns contain filler sentences. </p>
Pure POPC bilayer MD simulations with CHARMM36 force field with GROMACS_v2019
<p>500 ns MD simulation of POPC bilayer with CHARMM36 force field at 300 K generated with GROMACS 2019 simulation engine. The system contains 100 POPC lipids per leaflet (200 in total) and 2000 TIP3P water molecules. No, NaCl in the system. This data set contains 500 ns data with 50000 frames (saving frequency is every 10 ps). </p>
The heterogeneous driving forces behind carbon emissions change in 30 selective emerging economies
<p>The CO<sub>2</sub> emission inventories included 30 emerging economies, spanning from 2010 to 2018. We matched 17 sectors based on indicators such as energy consumption and economic statistics.</p>
OpenMM simulations of POPE using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872447</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
OpenMM simulations of POPC using the CHARMM Drude2023 force field in xtc format
<p>PSF, single CRD file, and XTC format trajectories for the final 200 ns of triplicate POPC simulations, from the publication</p> <p><strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*</p> <p> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in<span> 10.5281/zenodo.7871949 have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</span></p>
The linear baroclinic model ouput forced by Indian summer monsoonal diabatic heating.
<p>The linear baroclinic model (Watanabe and Kimoto 2000, 2001) ouput forced by Indian summer monsoonal diabatic heating. The LBM source code can be requested via https://ccsr.aori.u-tokyo.ac.jp/~lbm/sub/lbm.html.</p> <p>Forcing file: ISM_forcing.nc<br> Simulation output files: LBM_T42_xxx.nc; each file denotes different monthly mean atmohpsheric basic state is used from May to September.</p> <p>The data are generated and analyzed in the following study:</p> <p>Li, S., Sato, T., Nakamura, T. <em>et al.</em> East Asian summer rainfall stimulated by subseasonal Indian monsoonal heating. <em>Nat Commun</em> <strong>14</strong>, 5932 (2023). https://doi.org/10.1038/s41467-023-41644-5</p>
OpenMM simulations of DMPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872767</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
OpenMM simulations of DLPC using the CHARMM Drude2023 force field in xtc format
<p>The dataset contains a PSF, a formatted coordinate file (CRD), and XTC files with the final 200 ns from<br> each of 3 replicate simulations from the paper</p> <p><br> <strong>Drude Polarizable Lipid Force Field with Explicit Treatment of LongRange Dispersion:<br> Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids</strong><br> Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor,*<br> Benoît Roux,* Alexander D. MacKerell, Jr.,* and Jeffery B. Klauda*<br> https://doi.org/10.1021/acs.jctc.3c00203</p> <p>XTC file names indicate the lipid and the replica number; each file has frames spaced at 10 ps over a 200 ns interval.</p> <p>The DCD sub-files in <span>10.5281/zenodo.7872783</span> have been concatenated into a single 200 ns long trajectory in xtc format by Batuhan Kav using MDAnalysis.</p>
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