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Data supplement for "Bifurcations of front motion in passive and active Allen-Cahn-type equations"
<p>This dataset contains the data and source files for figures 5 and 7-10 in the following publication: </p> <p>F. Stegemerten, S.V. Gurevich, U. Thiele</p> <p><em>'Bifurcations of front motion in passive and active Allen–Cahn-type equations' </em></p> <p>published in 2020 in CHAOS.</p> <p>Please follow the instructions given in 'Readme.txt'.</p>
Morphodynamic stability of river and tidal bifurcations around bars tested in the Fast Flow Facility
<p>Multithread rivers such as the Jamuna and Mekong have networks of channels and bars that change with every flood. Tidal systems such as the Scheldt, Humber and Columbia estuaries and short tidal basins in the Wadden Sea and in Florida, have perpetually changing and interacting channels and shoals formed by ebb and flood currents. Current models fail to forecast these natural dynamics, yet main channels are economically important shipping fairways, whilst shoal areas that emerge and submerge daily are ecologically valuable habitats. Human interference, changing river discharge and sealevel rise threaten all functions. Furthermore, there are strong indications that fairway deepening leads to reduced urban safety due to enhanced flow resistance by groynes in rivers and enhanced tidal range in estuaries (e.g. Bolla Pittaluga et al. 2015 in AWR, Seminara et al., in EH 2011). This enhances dike failure risk during low water level and flooding during high water level. We urgently need dynamic forecasting models to optimise management strategies for these multiple functions (Wang et al. 2012 in Ocean Coastal Manage., Coco et al. 2013 in Mar. Geol.).</p> <p>Here we target firstly river bifurcations and secondly the mutually evasive ebb- or flood-dominated channels that form around bars and are found in all sandy tidal systems in the world (van Veen 1950/2002 in J. R. Dutch Geograph. Soc.). The cause for the mutual evasion is still incompletely understood despite the fact that they also appear in our numerical model results and experiments (Canestrelli et al., in JGR 2010; Kleinhans et al. 2015 in JGR). The nodes where ebb and flood channels connect can be seen as asymmetric bifurcations where one channel is preferred during ebb and the other during flood. Such bifurcations are critical elements that partition flow and sediment through the channel network, govern bar merging and splitting and are locations where bed steps form in shipping lanes, as in river bifurcations. Stability and equilibrium configurations are mostly unknown for tidal bifurcations except for one recent theory (Wang et al in prep.). In particular, we have a fair understanding of the tidal dynamics, but this is incomplete for the morphodynamics, especially related to understanding the sediment division at the bifurcation.</p> <p>We take advantage of the better but yet incomplete understanding of river bifurcations. The stability of river bifurcations has been studied for two decades in fieldwork, experimentation, linear stability theory and numerical modelling (e.g. Wang et al. 1995, JHR, see review in Kleinhans et al. 2013, ESPL) and our recent theory (Bolla Pittaluga et al. 2015 in GRL) synthesises many of the earlier results as follows: In bedload-dominated rivers, symmetrical bifurcations are unstable and develop towards a highly asymmetrical division of discharge and sediment. The same is the case for suspended sediment-dominated rivers, but the theory predicts stable bifurcations for intermediate sediment mobility. However, there is very little data for conditions intermediate between low and high mobility rivers. Moreover, we have no idea whether bifurcations in reversing tidal flow are unstable for similar configurations and conditions as in rivers. Here we mean configurations that are entirely free of topographic forcings on the flow: straight channels split into two channels over some length and depth.</p> <p>Our objective was therefore to experimentally investigate bifurcation stability in a range of sediment mobilities in unidirectional flow and reversing tidal flow ceteris paribus.</p>
Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families
<p>Analyses of evolutionary dynamics can be profoundly affected by age calibrations of phylogenetic nodes under different models of lineage branching. Most time-calibrated molecular phylogenies of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. Lineages can also split via budding, in which a parent lineage persists following the origin of a daughter lineage, and nodes are calibrated using the age of the lineage with the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale empirical test of how the choice of branching model affects macroevolutionary analyses. We time-calibrated 91% of nodes in a phylogeny of 97 extant bivalve families using 86 calibration points ranging in age from 2.59 to 485 Ma. Allowing budding-based calibrations minimizes conflict between the tree topology and timing of evolutionary events in the fossil record, reducing the summed duration of inferred "ghost lineages," from 6.76 billion yrs (Gyr; bifurcating model) to 1.00 Gyr (budding model). Adding 31 extinct paraphyletic families – many major groups contain such extinct taxa – shifts deep splits further back in time and raises ghost-lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but more accurately reflects the time since separation of lineages. Lineage-through-time plots from phylogenetic data scaled under a bifurcating model of evolution push more inferred bivalve diversification into the Paleozoic, conflicting with other palaeontological evidence on the magnitude of the end-Paleozoic extinction and subsequent recovery, and strongly reduce the magnitude of the Cenozoic diversification of the group. Consideration of the hypothesized branching model within a given clade is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, an evolutionary model that allows budding and does not force bifurcations is the most appropriate one, and likely common for many other clades as well.</p>
Text-fig. 17. Aeduellidae. Scale bars 5 mm. a: the scales of oblong shape on the lateral side of the body, locality Otovice "Stěnava", DP 4307, whitened; b: drawing of the scales with fine denticles on their posterior edge, locality Otovice "Stěnava", DP 4307; c, d: drawing and photograph (whitened) of the scales of lateral side of the body, two times large scales occur in the rows 14, 16, 17, 19 (they are marked with arrows), locality Otovice "Černý potok", NM-M 4912; e: lepidotrichia of the anal fin with sigmoidal sutures between the segments (marked by arrows), locality Otovice, NM-M 4931, whitened; f: anterior edge of the dorsal fin and lepidotrichia with sigmoidal sutures between the segments, locality Otovice "Stěnava", DP 4307, whitened; g: anterior edge of the ventral lobe of the caudal fin, locality Otovice, NM-M 4931, whitened; h: the caudal peduncle with begin of bifurcation of the dorsal and ventral lobes of the caudal fin, locality Otovice, NM-M 4931. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)
Text-fig. 17. Aeduellidae. Scale bars 5 mm. a: the scales of oblong shape on the lateral side of the body, locality Otovice "Stěnava", DP 4307, whitened; b: drawing of the scales with fine denticles on their posterior edge, locality Otovice "Stěnava", DP 4307; c, d: drawing and photograph (whitened) of the scales of lateral side of the body, two times large scales occur in the rows 14, 16, 17, 19 (they are marked with arrows), locality Otovice "Černý potok", NM-M 4912; e: lepidotrichia of the anal fin with sigmoidal sutures between the segments (marked by arrows), locality Otovice, NM-M 4931, whitened; f: anterior edge of the dorsal fin and lepidotrichia with sigmoidal sutures between the segments, locality Otovice "Stěnava", DP 4307, whitened; g: anterior edge of the ventral lobe of the caudal fin, locality Otovice, NM-M 4931, whitened; h: the caudal peduncle with begin of bifurcation of the dorsal and ventral lobes of the caudal fin, locality Otovice, NM-M 4931.
Exploring Bifurcations in Bose-Einstein Condensates via Phase Field Crystal Models
<p>Supplementary data for the following paper: Alina Barbara Steinberg, Fabian Maucher, Svetlana Gurevich, Uwe Thiele, "Exploring Bifurcations in Bose-Einstein Condensates via Phase Field Crystal Models"</p>
Human SET domain bifurcated 1 (SETDB1), Tudor domain; A Target Enabling Package
<p>SETDB1 is a H3K9 methyltransferase involved in transcriptional silencing with a catalytic SET domain and a triple Tudor domain containing a methyl-lysine binding site. SGC Toronto previously solved the apo structure of the Tudor domain (PDB code 3DLM). Amplification of SETDB1 in over 15% lung adenocarcinoma correlates with high mRNA and protein levels and its depletion in SETDB1-amplified cells reduces cancer growth in cell culture and nude mice models, whereas its overexpression increases tumour invasiveness (Rodriguez-Paredes et al. Oncogene 2014, Shah et al. Epigenetic Chromatin 2014). Several histone methyltransferases are known to have non-catalytic functions that might be alternative targeting strategies. For instance, recognition of H3K9 methylation by the ankyrin repeat of the methyltransferase GLP is required for efficient establishment of H3K9 methylation (Liu et al. Genes Dev. 2015). No catalytic domain inhibitor of SETDB1 has been reported to date. The goal of this TEP is to enable the discovery of potent, selective compounds targeting the Tudor domain of SETDB1.</p>
Figures 15‒27 in New data on Neotropical Carpenter-Moths of Subfamily Hypoptinae Neumoegen & Dyar, 1894 (Lepidoptera: Cossidae). I. New taxa with bifurcated uncus
Figures 15‒27. Male genitalia of Hypoptinae: 15. Uretiana vicunensis ♂ Chile, Elqui, El Bosque - Hurtado, 17 September 1996 (GenPr-Heterocera MWM 37.007); 16. U. vicunensis, ♂ Brasil, Parana Curitiba, Serra Do Mar, Estrada De Castelhanos, March 1998, ca. 500m, leg H. Thöny (GenPr-Heterocera MWM 37.006); 17. U. tucumana, holotype: ♂ Argentina, prov. Tucuman (PREP. GEN. MLP №6 F.C. Penco); 18. U. infans, holotype: ♂ S Bernardino, Paraguay, K. Fiebrig collector, Nov., Type №41717 U.S.N.M. (Genitalia slide by P. Gentili, USNM 85.243); 19. Dogniniya sterila holotype: ♂ Saint-Laurent-du-Maroni, Guyane française, Dognin Collection, Type №29892 U.S.N.M. (Genitalia slide by P. Gentili, USNM 85.275); 20. D. beatrix, holotype: ♂ Quirigua, Guatemala, Schaus and Barnos coll., April, Type №23431 U.S.N.M. (Genitalia slide by P. Gentili, USNM 85.213); 21. D. lemoulti, holotype: ♂ Uypiranga, Bresil, E. Le Moult 1933 (MNHN, Genitalia slide by A.E. Naydenov, №6); 22. D. huanuco, holotype: ♂ Peru, prov. Huánuco, Yayapichis, ACP Panguana, 9°36″S / 74°56″W, September 2013, 220 m., leg. Hubert Thöny (GenPr-Heterocera MWM 37.004); 23. Qhichwaruna pennata, holotype: ♂ Argentinien, Cafayate, Prov. Catamarca, 16-11-98, Leg. A. Ugarte P. (GenPr-Heterocera MWM 26.730); 24. Wiraqucha huberti, holotype: ♂ Brasilien, Minas Gerais Poté, ca. 500m., 30.03.1996, Leg. Hubert Thöny (GenPr-Heterocera MWM 28.539); 25. W. equadorica, holotype: ♂ Ecuador oriente Napo Rte Cosanga-Tena PK 18 2.000 m., 4-VIII/90, J. Haxaire D. Herbin, (EC HAX 90 020), (MNHN, Genitalia slide by A.E. Naydenov №9); 26. Thonyocossus brasiliensis holotype: ♂ Brasilien, Minas Gerais Poté, ca. 500m., 01.03.1996, Leg. Hubert Thöny (GenPr-Heterocera MWM 28.538); 27. Hastam gracilis, holotype: ♂ Brasilien, Esp. Santo, Santa Leopoldina, Boquerao, ca. 600m, 15.09.1997, leg. H. Thöny (GenPrHeterocera MWM 28.537).
Figsures 1‒14 in New data on Neotropical Carpenter-Moths of Subfamily Hypoptinae Neumoegen & Dyar, 1894 (Lepidoptera: Cossidae). I. New taxa with bifurcated uncus
Figsures 1‒14. Adult specimens of Hypoptinae, males: 1 ‒ Uretiana vicunensis, holotype: ♂ Chile, Vicuña, 606 m., Prov. de Coquimbo, 15-II-1936, E. Ureta coll. (Col. M. N. n. 2105); 2. U. vicunensis, ♂, Chile, Elqui, El Bosque - Hurtado, 17 September 1996 (GenPr-Heterocera MWM 37.007); 3. U. vicunensis, ♂ Brasil, Parana Curitiba, Serra Do Mar, Estrada De Castelhanos, March 1998, ca. 500m, leg H. Thöny; 4. U. tucumana, holotype: ♂ Argentina, prov. Tucuman (MLP); 5. U. infans, holotype: ♂ S Bernardino, Paraguay, K. Fiebrig collector, Nov., Type №41717 U.S.N.M. (USNM); 6. Dogniniya sterila holotype: ♂ Saint-Laurent-du-Maroni, Guyane française, Dognin Collection, Type №29892 U.S.N.M. (USNM); 7. D. beatrix, holotype: ♂ Quirigua, Guatemala, Schaus and Barnos coll., April, Type №23431 U.S.N.M. (USNM); 8. D. lemoulti, holotype: ♂ Uypiranga, Bresil, E. Le Moult 1933 (MNHN); 9. D. huanuco, holotype: ♂ Peru, prov. Huánuco, Yayapichis, ACP Panguana, 9°36″S / 74°56″W, September 2013, 220 m., leg. Hubert Thöny (MWM); 10. Qhichwaruna pennata, holotype: ♂ Argentinien, Cafayate, Prov. Catamarca, 16-11-98, Leg. A. Ugarte P. (MWM); 11. Wiraqucha huberti, holotype: ♂ Brasilien, Minas Gerais Poté, ca. 500m., 30.03.1996, Leg. Hubert Thöny (MWM); 12. W. equadorica, holotype: ♂ Ecuador oriente Napo Rte Cosanga-Tena PK 18 2.000 m., 4-VIII/90, J. Haxaire D. Herbin, (EC HAX 90 020), (MNHN); 13. Thonyocossus brasiliensis, holotype: ♂ Brasilien, Minas Gerais Poté, ca. 500m., 01.03.1996, Leg. Hubert Thöny (MWM); 14. Hastam gracilis, holotype: ♂ Brasilien, Esp. Santo, Santa Leopoldina, Boquerao, ca. 600m, 15.09.1997, leg. H. Thöny (MWM).
Armature formula of P1–P4 as follows: P5 (Fig. 2B). With outer seta of BENP arising from long setophore. Endopodal lobe triangular, reaching middle of exopod; with small spinules along outer margin and at base of inner setae; with five elements – one outer subdistal, one apical and one inner subdistal normal seta, and two inner bifurcate elements. Exopod elongate, 2.8 times as long as wide; with spinules along inner margin and with few proximal outer spinules; with six elements – three outer slender, short setae, two apical elements, of which outermost one shorter, and one inner seta. in Proposal of new genera and species of the subfamily Diosaccinae (Copepoda: Harpacticoida: Miraciidae)
Armature formula of P1–P4 as follows: P5 (Fig. 2B). With outer seta of BENP arising from long setophore. Endopodal lobe triangular, reaching middle of exopod; with small spinules along outer margin and at base of inner setae; with five elements – one outer subdistal, one apical and one inner subdistal normal seta, and two inner bifurcate elements. Exopod elongate, 2.8 times as long as wide; with spinules along inner margin and with few proximal outer spinules; with six elements – three outer slender, short setae, two apical elements, of which outermost one shorter, and one inner seta.
Airglow Imaging Observations of Plasma Blobs: Merging and Bifurcation During Solar Minimum over Tropical Region
<p>This is the dataset for the plasma blobs merging (26/10/2019) and bifurcations (01/03/2019) used in our research. It is the OI 630nm wavelength.</p>
Experimental data of a channel bifurcation with mobile-bed without and with vane-fields
<p>Experimental data of laboratory experiments of a channel bifurcation: a main and a lateral diversion channel, both with mobile bed, rectangular cross-section, performing a 90º angle between them.<br> Experiments run until the equilibrium bed was reached.</p> <p>4 experiments:<br> (i) no vanes - NV;<br> (ii) with a vane-field - VF;<br> (iii) with a second vane-field configuration with the alignment of the vanes (angle beta) = 30º - VF30;<br> (iv) with the same vane-field configuration as (iii) but with angle beta = 10º - VF10.</p> <p>Water depth at the downstream end of the main channel is equal to 0.10 m.<br> Width of the main channel = 0.68 m in (i)-(ii), and 0.67 in (iii)-(iv).<br> Width of the diversion channel = 0.26 m in (i)-(ii), and 0.25 in (iii)-(iv).<br> Discharge at the entrance of the main channel = 29 l/s.<br> Discharge ratio per unit width of the channels: 0.5 in (i)-(ii), and 0.2 in (iii)-(iv).<br> Height of the vanes = 0.03 m above the average bed level of the approach flow.</p> <p>Data measured provided for each experiment: <br> (i) profiles along direction x of the water surface levels and the bed topography;<br> (ii) average values and fluctuations of the 3 components of velocities at a dense grid of points (see figures with the plan views of the measured grid). In the vertical direction z, the points are spaced in 0.5 cm or 1 cm.<br> All the data was measured for the equilibrium bed.</p> <p>The velocities were measured with a side-looking Vectrino. Data was despiked (see Goring and Nikora, 2002 DOI 10.1061/(ASCE)0733-9429(2002)128:1(117) ), and points with correlation < 70% or SNR < 15 db were discarded.</p> <p>For further information see:</p> <p>Baltazar, J.; Alves, E.; Bombar, G.; Cardoso, A.H. Effect of a Submerged Vane-Field on the Flow Pattern of a Movable Bed Channel with a 90º Lateral Diversion. Water 2021, 13, 828. https://doi.org/10.3390/w13060828</p> <p>PhD thesis "Sediment control at lateral water intakes through submerged vane-fields", by Joana Baltazar (Instituto Superior Técnico, Lisbon, Portugal)<br> </p>
Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families
Open the record for dataset details and reuse information.
Why do equatorial plasma bubbles bifurcate?
<p>For whom it may concern:<br> The files are the numerical results obtained by Carrasco et al. 2020.<br> Any use of the files must be cited the original authors. <br> Commercial use prohibited.</p>
Bifurcation diagram dataset for the paper "A minimal hyperbolic system for unstable shock waves"
<p>This dataset belongs to the paper "A minimal hyperbolic system for unstable shock waves" (doi:<a href="https://doi.org/10.1016/j.cnsns.2018.10.022">10.1016/j.cnsns.2018.10.022</a></p> <p><strong>Format.</strong> Dataset is in the npz file, which is NumPy Zip binary file format, which can be read with function `np.load(filename)`.</p> <p><strong>Reason for uploading.</strong> It was a part of the Git repository <a href="http://github.com/dmitry-kabanov/fickettmodel-reproducibility">https://github.com/dmitry-kabanov/fickettmodel-reproducibility</a> before, but it was noticed that Git LFS objects require special treatment, hence, for simplicity, it is uploaded here and the corresponding Makefile takes care of downloading it.</p>
Figure 4. - Brightfield image showing the posterior mesosoma and anterior metasoma of Pteroceraphronmirabilipennis Dessart 1981. Arrows point to bifurcated anteromedian process of the propodeum-metanotum complex.
Figure 4. - Brightfield image showing the posterior mesosoma and anterior metasoma of Pteroceraphronmirabilipennis Dessart 1981. Arrows point to bifurcated anteromedian process of the propodeum-metanotum complex.
Bifurcation points for tropical cyclone genesis in sheared and dry environments - simulation data
<p>Key information to reproduce the idealized WRF ensemble simulations used for tropical cyclone genesis </p>
Effect of freshwater discharge from estuary dam on residual circulation in bifurcated channel
<p>Zip-files contain matlab m-files and raw data of transects data in Yeoungsan Rver estuary. The code was designed to analysis the changes from the raw data.</p> <p>During freshwater discharge.zip file contains data set with a freshwater impact from a estuary dam,</p> <p>Whereas during non-freshwater discharge.zip file contains data set without a freshwater impacts period.</p> <p> </p> <p> </p>
Figure 28 in New data on Neotropical Carpenter-Moths of Subfamily Hypoptinae Neumoegen & Dyar, 1894 (Lepidoptera: Cossidae). I. New taxa with bifurcated uncus
Figure 28. Map of distribution species of Hypoptinae.
Early-Stage Bifurcation of Crystallization in a Sphere
<p>This is the raw data for the manuscript:</p> <p>Early-Stage Bifurcation of Crystallization in a Sphere</p> <p>All data are sorted in folders according to their appearance in the figures of the main manuscript.</p> <p>Data types:<br> * Particle position files (text format): .pos<br> * Data files (text format): .dat, .txt, .rdf<br> * Tables: .xlsx<br> * Images/Graphics: .tif, .tiff, .png, .eps, .pdf<br> * Gnuplot scripts: .gnu, .plot<br> * Shell scripts: .sh</p>
Simulation Data for Electron Scattering due to Asymmetric Drift-Orbit Bifurcation: Geometric Jumps of Adiabatic Invariant
<p>Simulation dataset for the paper “Electron Scattering due to Asymmetric Drift-Orbit Bifurcation: Geometric Jumps of Adiabatic Invariant.” The archive “artemis_solar_dataset.zip” contains the solar wind magnetic field data used to plot Figure 1. The three “…_jump.txt” files are tracing data used to plot Figures 6a, 6b, and 6c, while “test_particle.txt” is the tracing data for Figure 5. The file “t04_L_shells__Pd_4.00_B_5.00_theta_225.txt” provides magnetic field B(s, MLT) profiles at different L-shells (used to plot Figure 7); each line corresponds to a specific MLT sector at one specific L-shell.</p>
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