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Text-fig. 15. Aeduellidae. Scale bars 5 mm. a: isolated left maxilla in lateral view, locality Otovice "Chmelnice", P 64678; b: the skull in lateral view, locality Otovice "Stěnava", G 58; c, d: drawing and photograph of the skull roof in dorsal view, locality Otovice, NM-M 4910. Abbreviations: Dpt – dermopterotic, Dsph – dermosphenotic, Ext – extrascapular, Fr – frontal, Io – infraorbital, ioc – infraorbital canal, Md – mandible, mp – medial pit line, Mx – maxilla, Na – nasal, Op – operculum, Pa – parietal, pp – posterior pit line, soc – supraorbital canal, stc – supratemporal canal. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 15. Aeduellidae. Scale bars 5 mm. a: isolated left maxilla in lateral view, locality Otovice "Chmelnice", P 64678; b: the skull in lateral view, locality Otovice "Stěnava", G 58; c, d: drawing and photograph of the skull roof in dorsal view, locality Otovice, NM-M 4910. Abbreviations: Dpt – dermopterotic, Dsph – dermosphenotic, Ext – extrascapular, Fr – frontal, Io – infraorbital, ioc – infraorbital canal, Md – mandible, mp – medial pit line, Mx – maxilla, Na – nasal, Op – operculum, Pa – parietal, pp – posterior pit line, soc – supraorbital canal, stc – supratemporal canal.
Text-fig. 9. Progyrolepis heyleri POPLIN, 1999. a: right dentalosplenial of adult specimen in lateral view, GMC 1, scale bar 5 mm; b: left dentalospelenial and suboperculum in medial view, GMC 1, scale bar 5 mm; c: set of bones of the right side of the cheek displaying maxilla, preoperculum, hyomandibula, left and right ceratohyal, epibranchial and neural spine from the axial skeleton, G 123, scale bar 5 mm; d: drawing of the right frontal in dorsal view, GMC 81, scale bar 5 mm; e: right operculum in lateral view, GMC 10, scale bar 5 mm. Abbreviations: Cbr – ceratobranchial, Cer – ceratohyal, Ds – dorsal spine, Hy – hyomandibula, Md – mandible, Mx – maxilla, Op – operculum, Pop – preoperculum. in New Actinopterygians From The Permian Of The Brive Basin, And The Ichthyofaunas Of The French Massif Central
Text-fig. 9. Progyrolepis heyleri POPLIN, 1999. a: right dentalosplenial of adult specimen in lateral view, GMC 1, scale bar 5 mm; b: left dentalospelenial and suboperculum in medial view, GMC 1, scale bar 5 mm; c: set of bones of the right side of the cheek displaying maxilla, preoperculum, hyomandibula, left and right ceratohyal, epibranchial and neural spine from the axial skeleton, G 123, scale bar 5 mm; d: drawing of the right frontal in dorsal view, GMC 81, scale bar 5 mm; e: right operculum in lateral view, GMC 10, scale bar 5 mm. Abbreviations: Cbr – ceratobranchial, Cer – ceratohyal, Ds – dorsal spine, Hy – hyomandibula, Md – mandible, Mx – maxilla, Op – operculum, Pop – preoperculum.
Results of MD simulations of collision cascades in hcp Zr at 600 K.
<p>This is a database consisting of pre- and post-processing scripts, input files and results from molecular dynamics (MD) simulations of collision cascades in LAMMPS. The database is associated with the paper: <a href="https://arxiv.org/abs/2405.03332">Molecular dynamics simulations of neutron induced collision cascades in Zr</a>. The material studied was hcp Zr at the temperature of 600 K. A detailed description of the record can be found in the <code>pdf</code> file, as well as in Emacs <code>org</code> and Jupyter notebooks (<code>ipynb</code>). Files also include Python code describing how to access and process the data.</p>
Revealing the percolation–agglomeration transition in polymer nanocomposites via MD-informed continuum RVEs with elastoplastic interphases - dataset
<p><strong>Abstract</strong>:<br>from [1]</p> <p>This contribution builds the concluding step of a multiscale approach to effectively capture the mechanical <br>behavior of polymer nanocomposites (PNCs), in this case, silica-modified polystyrene. By introducing <br>continuum-based representative volume elements (RVEs) that employ previously identified elastoplastic property <br>gradients for the interphases surrounding the fillers, the effects of particle size, particle volume fraction, <br>and agglomeration on the mechanical performance are investigated. Uniaxial tension tests are simulated with <br>the respective finite-element RVEs, and stress–strain curves are derived. The elastic and plastic material <br>properties of the RVE can then be extracted and analyzed quantitatively by fitting the stress–strain curves <br>with a Voce-type elastoplasticity formulation. <br>At small degrees of agglomeration, i.e., good particle dispersion, in combination with sufficiently large <br>particle volume fraction, percolation bands form, leading to improved elastic and plastic properties. Higher <br>degrees of agglomeration or particle clusters behave like large single particles, which has an adverse effect, i.e., <br>the nanoscale size effect is thereby neutralized. Therefore, the precise MD-informed elastoplastic interphase <br>representation of our RVEs enables the investigation of the transition from beneficial percolation to unfavorable <br>agglomeration. Ultimately, this contribution establishes a link between the effects of particle size, particle <br>volume fraction, agglomeration, and percolation, which have so far only been discussed separately in the <br>literature. <br>Our methodology offers new insights into the structure–property relations of PNCs and their resulting <br>mechanical behavior. The underlying multiscale approach with a systematic transition from molecular to <br>microscopic scales is required to complement experimental observations and exploit the full potential of PNCs. </p> <p><br><strong>Contact</strong>:</p> <p>Maximilian Ries<br>Institute of Applied Mechanics<br>Friedrich-Alexander-Universität Erlangen-Nürnberg<br>Egerlandstr. 5<br>91058 Erlangen</p> <p><strong>Software</strong>:</p> <p>All finite element simulations were performed with Simulia Abaqus/CAE2018 </p> <p><strong>License</strong>:</p> <p>Creative Commons Attribution Non Commercial 4.0 International</p> <p><strong>Context</strong>:</p> <p>Data set supplementing journal paper:</p> <p>[1] E.-M. Richter, G. Possart, P. Steinmann, S. Pfaller, & M. Ries, “Revealing the percolation–agglomeration transition in polymer nanocomposites via MD-informed continuum RVEs with elastoplastic interphases,” Composites Part B: Engineering, vol. 281, p. 111477, 2024.</p> <p><strong>Content</strong>:</p> <p>- excel sheet summarizing all RVE simulations in combination with the elastoplastic constitutive model calibration: elastoplastic_constitutive_model_calibration.xlsx<br>- input data for each RVE FE simulation in *.inp format following the naming convention:<br> agg_<degree of agglomeration>-fillercont_<filler content>Percent-fillerrad_<filler radius>nm<br> - degree of agglomeration is defined in [1]<br> - filler content is given in volume percent<br> - filler radius is given in nanometer </p> <p> </p>
Dataset: Kindly MD, Inc. (KDLYW) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Dataset: Kindly MD, Inc. (KDLY) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain
Gelatinous zooplankton abundances in the Rhode River Estuary, MD, USA, 2004-2005 and 2013-2018
<p>Field sampling of ctenophore (<em>Mnemiopsis </em>and <em>Beroe</em>) and scyphomedusae (<em>Chrysaora</em>) abundances in the Rhode River and adjacent Chesapeake Bay (MD, USA). Samples were taken using 0.5 m and 1.0 m diameter nets in 2004-2005 and 2013-2018.</p>
A structural model of the human serotonin transporter in an outward-occluded state: MD simulation data
<p>The uploads contain relevant data to supplement the study https://www.biorxiv.org/content/10.1101/637009v1, where the details of the methods are described.</p> <p>charmm_energy_minimization.inp is the input file that was used to run an energy minimization on structural models</p> <p>The two archives contain relevant MD simulation data in coordinate, parameter and trajectory files:</p> <p>hSERT_Ce.tar.gz outward-open X-ray structure PDB 5I71</p> <p>hSERT_Ceo.tar.gz outward-occluded structural model</p>
MD SIMULATION DATA for cytochromeP450 with SCC and AFB1.
<p>MD simulation data submission.</p>
MD simulations of bOG:DMPC in CHARMM36 force field
<p>CHARMM-GUI based series of simulations of beta-octyl-D-glucopyranoside (b-OG) mixed with DMPC at different dilutions. bOG:DMPC mol ratios are 1:1, 1:2, and 2:3. The only change in the force field was changing atom names from 2H2 to H2 in BOG residue to allow **gmx grompp** to recognize protons as protons when setting up constraints for bonds with hydrogens.</p> <p>Simulations are performed in highly hydrated state. I can name it "more than 50 water per two acyl chains"; "water per lipid" measure doesn't work here because bOG has just a single hydrocarbon tail.</p> <p>Trajectory length: 500 ns (20 ps step). T = 303 K. </p> <p>In this version we add *znd files where atom names are unique (changed in a new version of BOG.itp).</p>
Limma-voom differential expression results for GTEx CVD and MD analyses
<p>Supplementary File 5 for the paper entitled "Exploring the Impact of Cerebrovascular Disease and Major Depression on Non-diseased Human Tissue Transcriptomes" (doi: 10.3389/fgene.2021.696836).</p>
Molecular trajectories and general MD files: Molecular insights on confined water in the nanochannels of self-assembled ionic liquid crystal
<p>This repository includes the MD simulation dataset of self-assembled ionic liquid crystal reported in the article of <a href="https://doi.org/10.1126/sciadv.abf0669"><em>Sci. Adv.</em> <strong>7</strong>, eabf0669 (2021) [DOI: 10.1126/sciadv.abf0669]</a>. The chemical structure of ionic liquid crystal is described in <a href="https://advances.sciencemag.org/content/advances/7/31/eabf0669/F1.large.jpg">Fig. 1A</a>. The cation involves an ionic moiety of <em>N</em>-methyl-<em>N</em>,<em>N</em>,<em>N</em>-triethylammonium group, and the terminals of the two alkyl chains are conjugated dienes. The anion is tetrafluoroborate BF<sub>4</sub>. The molecular and atomic-group charges of cation and anion are shown in the topology files named "ilc-oplsdft.itp" and "bf4-oplsdft.itp", respectively. The TIP3P and TIP4P/2005 models are employed for water molecules. After the careful equilibration process, the production MD was performed for 50 ns under the <em>NPT</em> condition at each composition. This dataset provides the configuration, topology, and general MD input files of Gromacs for all the states and models of bicontinuous and columnar structures obtained in the article. The 3D view of bicontinuous and columnar structures can be available in <a href="https://advances.sciencemag.org/content/advances/7/31/eabf0669/F2.large.jpg">Fig. 2</a>. The attached edr and log files are energy and general outputs of the MD simulation generated in our environment, and the xtc file is a trajectory output generated with a time interval of 20 ps.</p>
MD trajectories for "Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases"
<p>This dataset contains Amber MD trajectories for the MD simulations described in the manuscript "Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases" by Christopher D. Fage, Simone Kosol, Matthew Jenner, Carl Öster, Angelo Gallo, Milda Kaniusaite, Roman Steinbach, Michael Staniforth, Vasilios G. Stavros, Mohamed A. Marahiel, Max J. Cryle, and Józef R. Lewandowski published in ACS Catalysis (<a href="https://doi.org/10.1021/acscatal.1c02113">https://doi.org/10.1021/acscatal.1c02113</a>). If you use these data please cite the original manuscript (follow the manuscript DOI for the final citation, which was not available at the time of publishing this data set). </p> <p>To reduce their size the trajectories were stripped of water and ions. Only frames every 1 ns or 5 ns were saved. Please see the Supporting Information of the source manuscript for the conditions for the simulations. </p>
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1- MD simulations
<p>Topology, parameter and coordinates files of the Molecular dynamics (MD) simulations of OR5K1 3D models from AlphaFold 2 (AF2) and Homology Modeling (HM). We used ACEMD3 (v3.5.1) as a molecular engine, CHARMM36 as force field. Three replicas of 100 ns (dcd files) for both systems are reported. Water molecules, ions, and membrane atoms (POPC: phosphatidylcholine) atoms were removed from the original trajectories before the upload.</p>
The 400 ns molecular dynamic (MD) trajectories for the wild type and mutant forms of the S. tuberosum eIF4E1 and eIF4E2
<p>Truncated from the N termini models of the wild type and mutant forms of the S. tuberosum eIF4E1 and eIF4E2. <br> The molecular dynamic (MD) trajectories with 400-ns length for each wild type and mutant forms of the eIF4E in the water environment according to the standard MD procedure.</p>
Data Set For Revels-MD tutorials
<p>This small data set contains the trajectory files necessary to run the tutorials for the revelsmd (<a href="https://github.com/user200000/revelsmd">https://github.com/user200000/revelsmd</a>) the trajectories were generated using lammps (<a href="https://www.lammps.org/#gsc.tab=0">https://www.lammps.org/#gsc.tab=0</a>) and gromacs (<a href="https://www.gromacs.org/">https://www.gromacs.org/</a>). </p> <ul> <li>Lennard jones sphere radial distribution functions (as in <a href="https://doi.org/10.1063/5.0053737">https://doi.org/10.1063/5.0053737</a>) (number 1)</li> <li>Solvation of an immobilised Lennard jones sphere in a solvent of identicle Lennard Jones spheres.(number 2)</li> <li>Solvation of a static water molecule (as in <a href="https://aip.scitation.org/doi/abs/10.1063/1.5111697">https://aip.scitation.org/doi/abs/10.1063/1.5111697</a>) (number 4)</li> </ul> <p><br> A fourth tutorial is in development</p>
MD-RA-USWEST_data
<p>Data and analysis pipelines from the paper "Meteorological Drivers of Resource Adequacy Failures in Current and High Renewable Western U.S. Power Systems"</p>
Input files for the MD simulations and free energy calculations for the article "Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions"
<p>Article:<em> </em><a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.1c04818">J. Phys. Chem. B. 125, 9357–9371 (2021) [DOI: 10.1021/acs.jpcb.1c04818]</a></p> <p>The structures of the homopolymers and copolymers simulated are shown in Figures 1 and S1 and Tables 2 and 3. All-atom MD simulation was carried out using GROMACS, and this repository provides the input files with the GAFF/RESP force and initial coordinate files. The free energy of water dissolution was obtained with <a href="https://sourceforge.net/projects/ermod/">ERmod</a>, and the input files for the free-energy calculations are also contained. See the README files for details.</p>
MD simulation of sphingomyelin (d18:1/18:0) bilayer in water
<p>MD simulations of sphingomyelin (d18:1/18:0) bilayer in water, NPT, 328 K. 128 SM + 5120 TIP3P water molecules, CHARMM36 force field.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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