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1,670 results for “FORCE”
POPC with 40 and 50 mol-% of cholesterol at 310 K. Charmm36 force field.
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 40% (134 molecules) and 50 % (200 molecules) of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</p>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Charmm36 force field.
<p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 0% (0 molecules), 10 % (22 molecules), 20 % (50 molecules), or 30 % (86 molecules) of cholesterol. The Charmm36 model [1] is employed for lipids and the Charmm-compatible variant of the tip3p model for water.</p> <p>The Charmm36 force field parameters were obtained from CHARMM-GUI [2] at http://www.charmm-gui.org</p> <p>*** IMPORTANT ***</p> <p>This is a correction to an earlier dataset simulated with some missing dihedrals, see: DOI: 10.5281/zenodo.61649</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the initial structure (.gro), topology (.top), index file (.ndx), simulation paremeter file (.mdp), binary run input file for GROMACS v. 5.0–> (.tpr) and the energy output file (.edr) are provided. </p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types</p> <p>Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, Jr., and Richard W. Pastor</p> <p>The Journal of Physical Chemistry B 2010 114 (23), 7830-7843</p> <p>DOI: 10.1021/jp101759q</p> <p> </p> <p>[2] CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field</p> <p>Jumin Lee, Xi Cheng, Jason M. Swails, Min Sun Yeom, Peter K. Eastman, Justin A. Lemkul, Shuai Wei, Joshua Buckner, Jong Cheol Jeong, Yifei Qi, Sunhwan Jo, Vijay S. Pande, David A. Case, Charles L. Brooks, III, Alexander D. MacKerell, Jr., Jeffery B. Klauda, and Wonpil Im</p> <p>Journal of Chemical Theory and Computation 2016 12 (1), 405-413</p> <p>DOI: 10.1021/acs.jctc.5b00935</p>
POPC with 40 and 50 mol-% of cholesterol at 310 K. Slipids force field.
<p>Simulations of a POPC bilayer with varying amounts of cholesterol. This data is employed for the NMRlipids project, see <em>http://nmrlipids.blogspot.fi</em> for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) is simulated in the presence of 40% (134 molecules) or 50 % (200 molecules) of cholesterol. The Slipids model [1–3] is employed for lipids, and the tip3p model for water.</p> <p>The Slipids force field parameters were downloaded from http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is 100 ns long with data saved every 100 ps. Additionally, the final structure (.gro), topology (.top), index file (.ndx), binary run input file for GROMACS v. 4.6–> (.tpr) and the energy output file (.edr) are provided together with the run parameter file (.mdp) employed to run all the simulations.</p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
POPC with 0, 10, 20, and 30 mol-% of cholesterol at 310 K. Slipids force field.
<p>Simulations of a POPC bilayer with varying amounts<br> of cholesterol. This data is employed for the NMRlipids<br> project, see <em>http://nmrlipids.blogspot.fi</em> for more information.</p> <p>A POPC bilayer consisting of 200 lipids (100 per leaflet) <br> is simulated in the presence of 0% (0 molecules), 10 %<br> (22 molecules), 20 % (50 molecules), or 30 % (86 molecules)<br> of cholesterol. The Slipids model [1–3] is employed for lipids,<br> and the tip3p model for water.</p> <p>The Slipids force field parameters were downloaded from<br> http://mmkluster.fos.su.se/slipids/</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>The files are in GROMACS format. Trajectory (.xtc) is <br> 100 ns long with data saved every 100 ps. Additionally,<br> the initial structure (.gro), topology (.top), index file (.ndx),<br> binary run input file for GROMACS v. 4.6–> (.tpr) and the<br> energy output file (.edr) are provided together with the run<br> parameter file (.mdp) employed to run all the simulations.</p> <p>UPDATE: Longer 500 ns trajectories are updated together with the checkpoint files.</p> <p>––––––––––––––––––––––––––––––––––––––––––––––––––––––</p> <p>[1] Derivation and Systematic Validation of a Refined <br> All-Atom Force Field for Phosphatidylcholine Lipids<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> The Journal of Physical Chemistry B 2012 116 (10), 3164-3179<br> DOI: 10.1021/jp212503e</p> <p>[2] An Extension and Further Validation of an All-Atomistic <br> Force Field for Biological Membranes<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2012 8 (8), 2938-2948<br> DOI: 10.1021/ct300342n</p> <p>[3] Another Piece of the Membrane Puzzle: Extending Slipids Further<br> Joakim P. M. Jämbeck and Alexander P. Lyubartsev<br> Journal of Chemical Theory and Computation 2013 9 (1), 774-784<br> DOI: 10.1021/ct300777p</p>
Supplemental material to 'Evaluation of force-based and displacement-based out-of-plane seismic assessment methods for unreinforced masonry walls through refined model simulations'
<p>This repository contains the results of discrete element simulations used to study the response of vertically-spanning unreinforced masonry walls under different wall configurations. The simulations are run using the software package UDEC 6.0 (<a href="https://www.itascacg.com/">Itasca</a>). The dataset has served as basis for the study conducted in the following paper:</p> <blockquote> <p>Godio M, Beyer K. Evaluation of force-based and displacement-based out-of-plane seismic assessmentmethods for unreinforced masonrywalls through refined model simulations. Earthquake Engng Struct Dyn. 2019;48:454-475. <a href="http://doi.org/10.1002/eqe.3144">DOI:10.1002/eqe.3144</a></p> </blockquote> <p>Version history:<br> V1: datasets '01_UDEC_VALIDATION' and '02_UDEC_RESULTS are added<br> V2: minor modifications to the datasets: deletion of unwanted temporary files from the datasets<br> V3: '00_CONTENT' PDF-file is added </p>
Molecular dynamics simulations of lipid bilayers containing POPC and POPS (5:1) with ECC-lipids force field, and Na+ (K+) counterions at various additional concentrations of NaCl and KCl
<p>Classical molecular dynamics simulations of various mixtures of POPC:POPS lipid bilayers in water solution with Na+ counterions (or with K+ counterions when noted with "_KCl" suffix) and an additional concentration of NaCl or KCl.</p> <p>The numbers in the file names denote the number of additional cations.</p> <p>ECC-lipids force field parameters used for lipids, SPC/E water model and ECC-ions, all parameters are included in this repository in GROMACS format and are also available at <a href="https://github.com/jmelcr/ecc_lipids">https://github.com/jmelcr/ecc_lipids</a></p> <p>simulations performed with Gromacs 2018.0 (*.xtc files)</p> <p>simulation length 1000 ns = 1 microsecond</p> <p>temperature 298 K</p> <p>Simulations without additional salts are at a <a href="https://doi.org/10.5281/zenodo.1488094">separate deposit: 10.5281/zenodo.1488094</a>.</p>
Simulations of POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field
<p>Classical molecular dynamics simulations of a POPC lipid bilayer in water solution at various NaCl, KCl and CaCl2 concentrations using ECC-POPC force field parameters, SPC/E water model and ECC-ions.</p> <p>file names report molar fraction of cations (i.e. not bulk concentrations)</p> <p>simulations performed with Gromacs 5.1.4 (*.xtc files) and openMM 7 (*.dcd files)</p> <p>simulation length 300 ns</p> <p>temperature 313 K (otherwise noted)</p> <p>Gromacs simulation setting is in the file npt_lipid_bilayer.mdp</p>
Dataset: Forced subduction at passive margin
<p>This dataset contains simulation results used for visualizing Figures in <br> “Forced subduction initiation at passive continental margins: velocity-driven versus stress-driven”</p>
Thermodynamics of small-molecule insertion across membrane mixtures: Insight from the potential of mean force
<p>This repository contains input data referenced in supporting information of the paper titled "Thermodynamics of small-molecule insertion across membrane mixtures: Insight from the potential of mean force" by Alessia Centi, Arghya Dutta, Sapun H. Parekh, and Tristan Bereau.</p>
Traction Force Microscopy Dataset
<p>Traction Force Microscopy dataset composed of fibrosarcoma cell line.</p>
The source code for a new capillary and adsorption‒force model predicting hydraulic conductivity of soil during freeze‒thaw processes
<p>The source code is related to "A New Capillary and Adsorption‒Force Model Predicting Hydraulic Conductivity of Soil during Freeze‒thaw Processes" (Shufeng Qiao, Rui Ma, Yunquan Wang, Ziyong Sun, Helen Kristine French, Yanxin Wang)</p>
FIGURES 45‑56 in Female monopolization and paternity assurance in South American crickets (Orthoptera, Grylloidea): mating plugs, extra claspers and forced copulation
FIGURES 45‑56: Terminalia of several species of Aracamby. 45, 46, male of undescribed species "A", lateral and ventral respectively; 47, female of same, lateral; 48, 49, 50, male of undescribed species "B" dorsal, ventral and lateral respectively; 51, 52, 53, male of undescribed species "C", lateral, dorsal and ventral respectively; 54, 55, 56, male of Aracamby balneatorius Mello, 1992, dorsal, lateral and ventral respectively. Conventions: IB = inferior bristle of paraproct; SB = superior bristle of paraproct; PC = paraproctal clasper. Figures not to scale.
FIGURES 26‑38 in Female monopolization and paternity assurance in South American crickets (Orthoptera, Grylloidea): mating plugs, extra claspers and forced copulation
FIGURES 26‑38: Dorsal, ventral and lateral views, respectively, of the phallic complex and copulatory papilla of Izecksohniella aimore and Cacruzia bahiana. 26, 27, 28, phallic complex of I. aimore; 29, 30, 31, copulatory papilla of I. aimore; 32, 33, 34, phallic complex of C. bahiana; 35, dorso-distal portion of pseudepiphallus of another specimen showing completely swollen pseudepiphallic parameres (compare with Fig. 32); 36, 37, 38, copulatory papilla of C. bahiana. Conventions: PG = phallic gland; O = outer opening of phallic. Figures not to scale.
FIGURES 39‑44 in Female monopolization and paternity assurance in South American crickets (Orthoptera, Grylloidea): mating plugs, extra claspers and forced copulation
FIGURES 39‑44: 39, 40, spermatophore of Eidmanacris sp. in dorsal and ventral views, showing the specialized neck which functions as a mating plug; 41, detailed side view of spermatophore neck; 42, 43, 44, dorsal, lateral and ventral views of copulatory papilla of same species showing the mating plug inserted in its orifice. Figures not to scale.
FIGURES 14‑25 in Female monopolization and paternity assurance in South American crickets (Orthoptera, Grylloidea): mating plugs, extra claspers and forced copulation
FIGURES 14‑25: Dorsal, ventral and lateral views, respectively, of the phallic complex and copulatory papilla of Vanzoliniella sambophila and of a species belonging to an undescribed genus. 14, 15, 16, phallic complex of V. sambophila; 17, 18, 19, copulatory papilla of V. sambophila; 20, 21, 22, phallic complex of "undescribed genus and species"; 23, 24, 25, copulatory papilla of same. Conventions: PG = phallic gland; O = outer opening of phalic gland. Figures not to scale.
FIGURES 5‑13 in Female monopolization and paternity assurance in South American crickets (Orthoptera, Grylloidea): mating plugs, extra claspers and forced copulation
FIGURES 5‑13: Phallic complex and copulatory papilla of Aracamby sp (undescribed species). 5, 6, 7, phallic complex in dorsal, ventral and lateral views, respectively; 8, tubular pseudepiphallic arms in rear view; 9, idem in dorsal view; 10, 11, copulatory papilla of virgin female in dorsal and lateral views, respectively; 12, 13, copulatory papilla of a female seven days after copulation. Conventions: PsA = pseudepiphallic arm; PsP = pseudepiphallic paramere; PG = phallic gland; PM = "petrified" membrane; O = outer opening of pseudepiphallic gland; FM = flexible membrane". Figures not to scale.
FIGURES 1‑4 in Female monopolization and paternity assurance in South American crickets (Orthoptera, Grylloidea): mating plugs, extra claspers and forced copulation
FIGURES 1‑4: Phallic complex and female terminalia of Adenophallusia naiguatana. 1, 2, 3, phallic complex in dorsal, ventral and lateral views, respectively; 4, female distal abdominal sternites. Conventions: PG = phallic gland; Ct = cement; O = outer opening of phallic gland; SgP = dashed line indicating the position of the subgenital plate prior to its removal; OVIP = basal portion of ovipositor. Figures not to scale.
Datasets for "Global Assessment of Atmospheric Forcing Uncertainties in The Common Land Model 2024 Simulations"
<p>This repository provides the datasets for the publication "Global Assessment of Atmospheric Forcing Uncertainties in The Common Land Model 2024 Simulations".</p>
FIGURE 4. Magnolia montebelloensis. A. Flower after male phase. B. Flower manually forced open with stamens removed. C. Flower bud with densely hirsute spathaceous bract and early vegetative buds. D in Magnolia montebelloensis, a new species in section Magnolia from Lagunas de Montebello National Park, Chiapas, México, with a key to Magnoliaceae of Chiapas
FIGURE 4. Magnolia montebelloensis. A. Flower after male phase. B. Flower manually forced open with stamens removed. C. Flower bud with densely hirsute spathaceous bract and early vegetative buds. D. Leaf stipule in late vegetative bud. E. Gynoecium with early axillary leaf buds and terminal internode; sepals, petals and stamens removed. F. Developing fruit. G–H. Fruits during dehiscence. Illustration by Esaú Vázquez-Verdejo. A–C & E from the holotype. D, F–G from Vázquez-García et al. 10107; H from Vázquez-García et al. 10108.
Influence of Orbital Forcing on the Snowball Earth Deglaciation
<p>CAM3&CLM3 simulation results that support the findings of this study are archived here.</p>
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.