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Tools, rules and incentives are buckling under the flood of coronavirus genome sequences — to help control the pandemic, researchers need new approaches. [ABSTRACT FROM AUTHOR]

The one-dimensional turbulence (ODT) model resolves a full range of time and length scales and is computationally efficient. ODT has been applied to a wide range of complex multi-scale flows, such as turbulent combustion. Previous ODT comparisons to experimental data have focused mainly on planar flows. Applications to cylindrical flows, such as round jets, have been based on rough analogies, e.g., by exploiting the fortuitous consistency of the similarity scalings of temporally developing planar jets and spatially developing round jets. To obtain a more systematic treatment, a new formulation of the ODT model in cylindrical and spherical coordinates is presented here. The model is written in terms of a geometric factor so that planar, cylindrical, and spherical configurations are represented in the same way. Temporal and spatial versions of the model are presented. A Lagrangian finite-volume implementation is used with a dynamically adaptive mesh. The adaptive mesh facilitates the implementation of cylindrical and spherical versions of the triplet map, which is used to model turbulent advection (eddy events) in the one-dimensional flow coordinate. In cylindrical and spherical coordinates, geometric stretching of the three triplet map images occurs due to the radial dependence of volume, with the stretching being strongest near the centerline. Two triplet map variants, TMA and TMB, are presented. In TMA, the three map images have the same volume, but different radial segment lengths. In TMB, the three map images have the same radial segment lengths, but different segment volumes. Cylindrical results are presented for temporal pipe flow, a spatial nonreacting jet, and a spatial nonreacting jet flame. These results compare very well to direct numerical simulation for the pipe flow, and to experimental data for the jets. The nonreacting jet treatment overpredicts velocity fluctuations near the centerline, due to the geometric stretching of the triplet maps and its effect on the eddy event rate distribution. TMB performs better than TMA. A hybrid planar-TMB (PTMB) approach is also presented, which further improves the results. TMA, TMB, and PTMB are nearly identical in the pipe flow where the key dynamics occur near the wall away from the centerline. The jet flame illustrates effects of variable density and viscosity, including dilatational effects. [ABSTRACT FROM AUTHOR]

In bilaterians, three orthogonal body axes define the animal form, with distinct anterior-posterior, dorsal-ventral and left-right asymmetries. The key signalling factors are Wnt family proteins for the anterior-posterior axis, Bmp family proteins for the dorsal-ventral axis and Nodal for the left-right axis. Cnidarians, the sister group to bilaterians, are characterized by one oral-aboral body axis, which exhibits a distinct biradiality of unknown molecular nature. Here we analysed the biradial growth pattern in the radially symmetrical cnidarian polyp Hydra, and we report evidence of Nodal in a pre-bilaterian clade. We identified a Nodal-related gene (Ndr) in Hydra magnipapillata, and this gene is essential for setting up an axial asymmetry along the main body axis. This asymmetry defines a lateral signalling centre, inducing a new body axis of a budding polyp orthogonal to the mother polyp's axis. Ndr is expressed exclusively in the lateral bud anlage and induces Pitx, which encodes an evolutionarily conserved transcription factor that functions downstream of Nodal. Reminiscent of its function in vertebrates, Nodal acts downstream of β-Catenin signalling. Our data support an evolutionary scenario in which a 'core-signalling cassette' consisting of β-Catenin, Nodal and Pitx pre-dated the cnidarian-bilaterian split. We presume that this cassette was co-opted for various modes of axial patterning: for example, for lateral branching in cnidarians and left-right patterning in bilaterians. [ABSTRACT FROM AUTHOR]

Numerical simulations using the one-dimensional-turbulence (ODT) model are compared to water-tank measurements emulating convection and entrainment in stratiform clouds driven by cloud-top cooling. Measured dependences of the entrainment rate on Richardson number were numerically reproduced for water trials in which the initial stratification is due to temperature differences. For an additional set of trials where the initial stratification is obtained by adding dextrose to the lower layer of the tank, measured dependences of the entrainment rate on Richardson number were partially reproduced, and importantly, the model also captures the measured sensitivity of entrainment to molecular transport. Additional parameter variations suggest other dependences of the entrainment rate. Analysis suggests possible qualitative differences between laboratory and cloud entrainment behaviors that might be testable using ODT. [ABSTRACT FROM AUTHOR]

Large-eddy simulation (LES) has been extensively used as a tool to understand how various processes contribute to the dynamics of the stratocumulus layer. These studies are complicated by the fact that many processes are tied to the dynamics of the stably stratified interface that caps the stratocumulus layer, and which is inadequately resolved by LES. Recent direct numerical simulations (DNS) of isobaric mixing due to buoyancy reversal in a cloud-top mixing layer show that molecular effects are in some instances important in setting the cloud-top entrainment rate, which in turn influences the global development of the layer. This suggests that traditional LES are fundamentally incapable of representing cloud-top processes that depend on buoyancy reversal and that numerical artefacts can affect significantly the results. In this study, we investigate a central aspect of this issue by developing a test case that embodies important features of the buoyancy-reversing cloud-top layer. So doing facilitates a one-to-one comparison of the numerical algorithms typical of LES and DNS codes in a well-established case. We focus on the numerical effects only by switching off the subgrid-scale model in the LES code and using instead a molecular viscosity. We systematically refine the numerical grid and quantify numerical errors, validate convergence and assess computational efficiency of the low-order LES code compared to the high-order DNS. We show that the high-order scheme solves the cloud-top problem computationally more efficiently. On that basis, we suggest that the use of higher-order schemes might be more attractive than further increasing resolution to improve the representation of stratocumulus in LES. [ABSTRACT FROM AUTHOR]

mixture fraction formulation to perform direct numerical simulations of a disperse and dilute two-phase system consisting of water liquid and vapor in air in local thermodynamic equilibrium using a two-fluid model is derived and discussed. The goal is to understand the assumptions intrinsic to this simplified but commonly employed approach for the study of two-layer buoyancy reversing systems like the cloud-top mixing layer. Emphasis is placed on molecular transport phenomena. In particular, a formulation is proposed that recovers the actual nondiffusive liquid-phase continuum as a limiting case of differential diffusion. High-order numerical schemes suitable for direct numerical simulations in the compressible and Boussinesq limits are described, and simulations are presented to validate the incompressible approach. As expected, the Boussinesq approximation provides an accurate and efficient description of the flow on the scales (of the order of meters) that are considered. [ABSTRACT FROM AUTHOR]

The Wnt gene family encodes secreted signalling molecules that control cell fate in animal development and human diseases. Despite its significance, the evolution of this metazoan-specific protein family is unclear. In vertebrates, twelve Wnt subfamilies were defined, of which only six have counterparts in Ecdysozoa (for example, Drosophila and Caenorhabditis). Here, we report the isolation of twelve Wnt genes from the sea anemone Nematostella vectensis, a species representing the basal group within cnidarians. Cnidarians are diploblastic animals and the sister-group to bilaterian metazoans. Phylogenetic analyses of N. vectensis Wnt genes reveal a thus far unpredicted ancestral diversity within the Wnt family. Cnidarians and bilaterians have at least eleven of the twelve known Wnt gene subfamilies in common; five subfamilies appear to be lost in the protostome lineage. Expression patterns of Wnt genes during N. vectensis embryogenesis indicate distinct roles of Wnts in gastrulation, resulting in serial overlapping expression domains along the primary axis of the planula larva. This unexpectedly complex inventory of Wnt family signalling factors evolved in early multi-cellular animals about 650?million years (Myr) ago, predating the Cambrian explosion by at least 100?Myr (refs 5, 8). It emphasizes the crucial function of Wnt genes in the diversification of eumetazoan body plans. [ABSTRACT FROM AUTHOR]