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67 results for “Martini”
input files for " Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data".
<p>input files for " Martini bead form factors for nucleic-acids and their application in the refinement of protein/nucleic-acid complexes against SAXS data", cf plumed-nest</p>
Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations"
<p>Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations".</p> <p>See <a href="https://aip.scitation.org/doi/10.1063/5.0095523">https://aip.scitation.org/doi/10.1063/5.0095523</a> for details.</p> <p>NOTE: some combinations of settings result in simulations that crash!<br> </p>
CG molecular dynamics simulations. Supporting data for "Improving Martini 3 for Disordered and Multidomain Proteins".
<pre>Coarse-grained molecular dynamics simulations with Martini 3 with varying rescaling of protein-water interactions. Supporting data for "Improving Martini 3 for Disordered and Multidomain Proteins".</pre>
FIGURES 1–6. Stenchaetothrips martini. Female 1–6 in A new species of Stenchaetothrips (Thysanoptera, Thripidae) from Bamboo, based on morphological and molecular data
FIGURES 1–6. Stenchaetothrips martini. Female 1–6: (1) antenna; (2) head & pronotum; (3) Meso & metanotum and tergite I; (4) tergites II–III; (5) hind coxae and sternites I–II; (6) thoracic sternites and mesofurca.
Supplementary material 2 from: van Nieukerken EJ, Lees DC, Doorenweerd C, Koster S(JC), Bryner R, Schreurs A, Timmermans MJTN, Sattler K (2018) Two European Cornus L. feeding leafmining moths, Antispila petryi Martini, 1899, sp. rev. and A. treitschkiella (Fischer von Röslerstamm, 1843) (Lepidoptera, Heliozelidae): an unjustified synonymy and overlooked range expansion. Nota Lepidopterologica 41(1): 39-86. https://doi.org/10.3897/nl.41.22264
Figure S1. Cornus species, details of leaf underside. a C. sanguinea subsp. sanguinea, fresh leaf, Netherlands, Leiden, 26.ix.2017. b C. sanguinea subsp. australis, dried leaf, Greece, RMNH.INS.41827. c C. mas, fresh leaf, Netherlands, Leiden, 26.ix.2017. d C. sericea, dried leaf, Netherlands, RMNH.INS.41493. e C. officinalis, dried leaf, UK, Wisley 1996, Wisley herbarium. Figure S2. NJ tree of barcodes, from BOLD. : Explanation note: Tree topology for the phylogenetic hypothesis adopted, to be used as input in applications reading nexus (requires some slight previous edition).
FIGURE 5 in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 5. Types of Spiraea martini var. pubescens and S. martini var. tomentosa. A, B, C. C. W. Wang 88321 (holotype of Spiraea martini var. pubescens); D, E, F. H. T. Tsai 53033 (isolectotype of S. martini var. tomentosa).
FIGURE 4 in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 4. Variation of the leaf size of Spiraea martini. The triangles indicate leaves in the holotype of Spiraea martini (Em. Bodinier 89), the diamonds show the leaves in the holotype of Spiraea cavalariei (J. Cavalerie 2602), the dots mean leaves in the additional
FIGURE 3 in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 3. Leaf variation of Spiraea martini. A. Kunming Botanical Garden, Kunming City, Yunnan; B. West Mountain, Kunming City, Yunnan.
FIGURE 1 in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 1. Type specimens of Spiraea martini and S. cavaleriei. A, B, C. Em. Bodinier 89 (holotype of Spiraea martini); D, E, F. J. Cavalerie 2602 (holotype of S. cavaleriei)
FIGURE 2 in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 2. Variation of Spiraea martini. A. no leaf rosette, B. variation of flowers' number, C. variation of peduncle, D. variation of pedicel.
FIGURE 6. Spriaea martini. A in Taxonomic notes on Spiraea martini Léveillé (Rosaceae)
FIGURE 6. Spriaea martini. A. shrub habit in spring flowering, B. shrub habit in summer, C. flowers, D. inflorescences, E. leaf blades, F. infrutescences with undeveloped follicles follicles.
FIGURES 1–6 in Description of immatures of Galeacius martini Schouteden (Hemiptera: Heteroptera: Scutelleridae)
FIGURES 1–6. Egg and first instar of Galeacius martini, in scanning electron microscopy: 1—lateral wall of chorion, 2— superior pole bearing aero-micropylar process (arrows), 3—lateral margin of abdominal segments III to X, 4—stridulitrum and rows of spinose projections on middle of urosternites, 5—urosternite V, 6—lateral margin of abdominal segments VII to X. Abbreviations: III–X–abdominal segments, sp—spiracle, st—stridulitrum, tr—trichobothrium.
FIGURES 20–24. Galeacius martini Schouteden, nymphs respectively 1 in Description of immatures of Galeacius martini Schouteden (Hemiptera: Heteroptera: Scutelleridae)
FIGURES 20–24. Galeacius martini Schouteden, nymphs respectively 1st to 5th instars, lateral, legs and antennae not shown. Scale bars = 1mm.
FIGURES 13–14 in Description of immatures of Galeacius martini Schouteden (Hemiptera: Heteroptera: Scutelleridae)
FIGURES 13–14. Fifth instar of Galeacius martini, in scanning electron microscopy: 13—abdomen bearing stridulitrum, 14— microsculpture of stridulitrum.
FIGURES 15–19. Galeacius martini Schouteden, nymphs respectively 1 in Description of immatures of Galeacius martini Schouteden (Hemiptera: Heteroptera: Scutelleridae)
FIGURES 15–19. Galeacius martini Schouteden, nymphs respectively 1st to 5th instars, dorsal. Scale bars = 1mm.
FIGURES 7–12 in Description of immatures of Galeacius martini Schouteden (Hemiptera: Heteroptera: Scutelleridae)
FIGURES 7–12. Fifth instar of Galeacius martini, in scanning electron microscopy: 7—tibiae bearing plectrum, 8—magnification of plectrum, 9—second median plate bearing ostiole, evaporatorium, auricular peritreme, and periostiolar depression, 10—third median plate bearing ostiole, evaporatorium, discal peritreme, and periostiolar depression, 11—mycoid surface of mesial portion of evaporatorium, bearing alveole, bridges interconnecting mushroom bodies and trabeculae on bottom of alveole, 12—mycoid surface of lateral portion of evaporatorium, bearing bridges interconnecting mushroom bodies and trabeculae on bottom of alveole. Abbreviations: al—alveole, ap—auricular peritreme, b—bridges interconnecting mushroom bodies,dp— discal peritreme, ev—evaporatorium, osII, osIII—respectively, 2nd and 3rd paired ostioles, pd—periostiolar depression, t— trabeculae on bottom of alveole.
Supporting data for "Recalibration of protein interactions in Martini 3"
<p>Coarse-grained molecular dynamics simulations from "Recalibration of protein interactions in Martini 3". Simulations were run with the Martini 3.0 force field, as well as several modified versions of Martini 3.0 in which the well-depth, ε, in the Lennard-Jones potential between all protein and water beads was rescaled by a factor <em>λ</em><sub>PW</sub>, ε in the Lennard-Jones potential between all protein beads was rescaled by a factor <em>λ</em><sub>PP</sub>, or ε in the Lennard-Jones potential between all protein backbone and water beads was rescaled by a factor <em>λ</em><sub>PW-BB</sub>. The simulation files are organized into one tar file for each rescaling approach. The simulation files are in xtc format, and are accompanied by a structure in gro format that can be used for system topology. There is also a tar file containing the atomistic starting structures used to set up the simulations (in pdb format).</p>
Figures 24-29 from: Vitecek S, Martini J, Zittra C, Kuhlmann H, Vieira A, Waringer J (2020) The larva of Drusus dudor Oláh, 2017, including an updated key to larval Drusinae Banks, 1916 (Insecta, Trichoptera, Limnephilidae). ZooKeys 908: 137-155. https://doi.org/10.3897/zookeys.908.47032
Figures 24-29 24–25 Heads and pronota of 5th instar larvae, right lateral views. 24Ecclisopteryx dalecarlica Kolenati, 1848 25Drusus botosaneanui Kumanski, 1968 26Drusus serbicus Marinkovic-Gospodnetic, 1971, 5th instar larva, head, right lateral view (dotted oval: spinule area). 27–29 Heads and pronota of 5th instar larvae, frontal views. 27Drusus nigrescens Meyer-Duer, 1875 (arrows: long dark setae reaching dorsal midline; sro: serrated outline of pronotal ridge; numbers refer to setal positions) 28Drusus mixtus (Pictet, 1834) (arrows: long dark setae not reaching dorsal midline; numbers refer to setal positions) 29Drusus aprutiensis Moretti, 1981 (arrows: long dark setae not reaching dorsal midline; numbers refer to setal positions). Scale bars: 0.5 mm.
Figures 18-23 from: Vitecek S, Martini J, Zittra C, Kuhlmann H, Vieira A, Waringer J (2020) The larva of Drusus dudor Oláh, 2017, including an updated key to larval Drusinae Banks, 1916 (Insecta, Trichoptera, Limnephilidae). ZooKeys 908: 137-155. https://doi.org/10.3897/zookeys.908.47032
Figures 18-23 18–21.Drusus alpinus Meyer-Duer, 1875, 5th instar larva. 18 Head and prothorax, right lateral view (arrow: mandibles with terminal teeth) 19 Head, thorax and abdominal segment I, ventral view 20 Detail of mesosternum, ventral view (vs: ventral setae) 21 Tip of abdomen, dorsal view (arrows: long posterodorsal setae). 22–23.Drusus franzi Schmid, 1955, 5th instar larva. 22 Detail of mesosternum, ventral view (vs: ventral seta) 23 Tip of abdomen, dorsal view (arrows: long posterodorsal setae). Scale bars: 0.5 mm.
Figures 58-63 from: Vitecek S, Martini J, Zittra C, Kuhlmann H, Vieira A, Waringer J (2020) The larva of Drusus dudor Oláh, 2017, including an updated key to larval Drusinae Banks, 1916 (Insecta, Trichoptera, Limnephilidae). ZooKeys 908: 137-155. https://doi.org/10.3897/zookeys.908.47032
Figures 58-63 Drusus dudor Oláh, 2017, male genitalia. 58 Tip of abdomen, left lateral view 59 Tip of abdomen, posterior view 60 Tip of abdomen, dorsal view 61 Tip of abdomen, ventral view 62 Apex of aedeagus and parameres (arrow: dorsal tooth of parameres) 63 Detail of paraproct, dorsal view (dotted ovals: basolateral bulges). Scale bars: 0.5 mm (except Fig. 63: 0.1 mm).
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