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Climate change is causing arctic regions to warm disproportionally faster than those at lower latitudes, leading to alterations in carbon and nitrogen cycling, and potentially higher greenhouse gas emissions. It is thus increasingly important to better characterize the microorganisms driving arctic biogeochemical processes and their potential responses to changing conditions. Here, we describe a novel thaumarchaeon enriched from an arctic soil, Candidatus Nitrosocosmicus arcticus strain Kfb, which has been maintained for seven years in stable laboratory enrichment cultures as an aerobic ammonia oxidizer, with ammonium or urea as substrates. Genomic analyses show that this organism harbors all genes involved in ammonia oxidation and in carbon fixation via the 3-hydroxypropionate/4-hydroxybutyrate cycle, characteristic of all AOA, as well as the capability for urea utilization and potentially also for heterotrophic metabolism, similar to other AOA. Ca. N. arcticus oxidizes ammonia optimally between 20 and 28°C, well above average temperatures in its native high arctic environment (-13-4°C). Ammonia oxidation rates were nevertheless much lower than those of most cultivated mesophilic AOA (20-45°C). Intriguingly, we repeatedly observed apparent faster growth rates (based on marker gene counts) at lower temperatures (4-8°C) but without detectable nitrite production. Together with potential metabolisms predicted from its genome content, these observations indicate that Ca. N. arcticus is not a strict chemolithotrophic ammonia oxidizer and add to cumulating evidence for a greater metabolic and physiological versatility of AOA. The physiology of Ca. N. arcticus suggests that increasing temperatures might drastically affect nitrification in arctic soils by stimulating archaeal ammonia oxidation.

A characteristic‐based Off‐Lattice Boltzmann Method (OLBM) and a stochastic One‐Dimensional Turbulence (ODT) model is utilized for numerical simulation of turbulent thermal convection. Standalone ODT results for low‐order statistics are compared with those from various eddy‐viscosity‐based subgrid‐scale models utilized in Large‐Eddy Simulations (LES) with OLBM. The predictive capabilities of both approaches are discussed by comparison with available reference Direct Numerical Simulation (DNS) results. All turbulence models are able to predicted the mean temperature, but fail to fully capture fluctuations. While the OLBM aims to represent large‐scale structures, it misses some constitutional small‐scale fluctuations. By contrast, the reduced‐order ODT model captures small‐scale fluctuations in the vicinity of the wall, but cannot resolve the organized bulk flow. Here, the modeling capabilities of both OLBM and ODT as standalone tools are discussed. On this basis, a strategy for the incorporation of ODT as wall model in OLBM is suggested. [ABSTRACT FROM AUTHOR]

Turbulent mixing is an omnipresent phenomenon that constantly affects our everyday life and plays an important role in a variety of industrial applications. The simulation of turbulent mixing poses great challenges, since the full resolution of all relevant length and time scales is associated with an immense computational effort. This limitation can be overcome by only resolving the large‐scale effects and completely model the sub‐grid scales. The development of an accurate sub‐grid mixing model is therefore a key challenge to capture all interactions in the sub‐grid scales. At this place, the hierarchical parcel‐swapping (HiPS) model formulated by A.R. Kerstein [J. Stat. Phys. 153, 142–161 (2013)] represents a computationally efficient and scale‐resolving turbulent mixing model. HiPS mimics the effects of turbulence on time‐evolving, diffusive scalar fields. In HiPS, the diffusive scalar fields or a state space is interpreted as a binary tree structure, which is an alternative approach compared to the most common mixing models. Every level of the tree represents a specific length and time scale, which is based on turbulence inertial range scaling. The state variables are only located at the base of the tree and are treated as fluid parcels. The effects of turbulent advection are represented by stochastic swaps of sub‐trees at rates determined by turbulent time scales associated with the sub‐trees. The mixing only takes places between adjacent fluid parcels and at rates consistent with the prevailing diffusion time scales. In this work, the HiPS model formulation for the simulation of passive scalar mixing is detailed first. Preliminary results for the mean square displacement, passive scalar probability density function (PDF) and scalar dissipation rate are given and reveal the strengths of the HiPS model considering the reduced order and computational efficiency. These model investigations are an important step of further HiPS advancements. The integrated auxiliary binary tree structure allows HiPS to satisfy a large number of criteria for a good mixing model. From this point of view, HiPS is an attractive candidate for modeling the mixing in transported PDF methods. [ABSTRACT FROM AUTHOR]

The present study numerically investigates turbulent momentum transfer in concentric coaxial (annular) pipe flow with small radius ratios (η=Ri/Ro=0.1,0.04,0.02)$(\eta ={R}_{i}/{R}_{o}=0.1,0.04,0.02)$. To model the flow, a stochastic one‐dimensional turbulence (ODT) model formulated for cylindrical geometry is used that provides full‐scale resolution along a representative radial coordinate. The present investigation extends the model validation by Tsai et al. (PAMM, 22:e202200272, 2023), to radius ratios smaller than 0.1 and addresses boundary layers with strong spanwise curvature effects. The focus is on the assessment and analysis of statistical flow features in the vicinity of the inner cylinder wall, particularly in cases with small radius ratios. Following Boersma & Breugem (Flow Turbul. Combust., 86:113–127, 2011), classical boundary‐layer and mixing‐length theory is utilized to analyze the model predictions. The results demonstrate that the ODT model captures leading‐order curvature and mixing‐length effects by its physics‐compatible construction. Utilizing the model for extrapolation to high Reynolds numbers inaccessible to conventional high‐fidelity numerical approaches shows that curvature effects persist and nonlocally affect the entire boundary layer. The model results provide support for a spanwise‐curvature‐modified wall function. [ABSTRACT FROM AUTHOR]

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This work presents a novel framework for the evaluation of far‐field sound radiation, specializing to a low Mach number jet flow. The framework comprises an analytical and a numerical part. In the analytical part, a low Mach number asymptotic analysis is presented to obtain the spectral sources of sound radiation starting from a pressure wave equation that is directly obtained from the Navier–Stokes equations. The derivation procedure is based on the fundamental premise of Lighthill's acoustic analogy. In the numerical part, a reduced‐order model for turbulent flow, the one‐dimensional turbulence model, is used to simulate the velocity field of a low Mach number turbulent round jet, assumed fully developed and statistically steady, hence homogeneous in the azimuthal direction and for a cross‐sectional slab assumed locally homogeneous in axial direction, too. The generated velocity field is used for the calculation of the spectral pressure sources, and consequently, to estimate the far‐field sound pressure level (SPL) of the jet. The results of the analysis are compared against available experimental SPL measurements from a subsonic jet. A reasonable agreement is obtained for the SPL. Furthermore, the analysis sheds light into the different contributions of the subsonic flow to sound radiation. The framework is readily extendable for any kind of low Mach number flow, including variable density flows and jet flames. [ABSTRACT FROM AUTHOR]

Reynolds‐averaged Navier–Stokes simulation (RaNS) is state‐of‐the‐art for numerical analysis of complex flows at high Reynolds number. Standalone RaNS may yield a reasonable estimate of the wall‐shear stress and turbulent drag if a proper wall‐function is prescribed, but detailed turbulence statistics cannot be obtained, especially at the wall. This lack in modeling is addressed here by a stochastic deconvolution strategy based on a stochastic one‐dimensional turbulence (ODT) model. Here, a one‐way coupling strategy is proposed in which a forcing term is computed from the balanced RaNS solution that is in turn utilized in the ODT model. The temporally developing ODT solution exhibits turbulent perturbations but relaxes toward the local RaNS solution due to resolved molecular‐diffusive processes. It is demonstrated that the approach is able to recover the distribution of positive wall‐shear stress fluctuations in turbulent channel flow. When formulated as post‐processing tool, it is suggested that RaNS can be enhanced by ODT providing economical means for local high‐fidelity numerical modeling based on a low‐fidelity flow solution. [ABSTRACT FROM AUTHOR]

Turbulent mixed convection in an air‐water system is evaluated with a novel numerical solver implementing the stochastic One‐Dimensional Turbulence (ODT) model in a turbulent air flow surrounded by a laminar cocurrent water falling film in a cylindrical geometry. The ODT model is used as a reduced order surrogate model for the effects of turbulent advection, turbulent heat flux, and turbulent mass‐flux within a one‐dimensional domain. An ad‐hoc temporal‐to‐spatial transformation relying on the bulk flow gas velocity is used to obtain streamwise‐dependent statistics of the flow. The ODT simulation results are compared to simulations obtained with the assumption of a quasi‐laminar one‐dimensional gas flow, and to Reynolds‐Averaged Navier‐Stokes (RANS) reference data for a cocurrent water falling film evaporator [1]. The results show that the turbulent transport plays a decisive role in the estimation of interface gradients of temperature and vapor mass fraction. Although ODT predicts global quantities such as the interface temperature in a reasonable way, the model falls short of successfully predicting streamwise‐dependent radial profiles. Despite the shortcomings, the framework presented here is the first stepping stone towards the evaluation of complex multiphase momentum, mass, and heat transfer couplings with full scale resolution on potential evaporative devices. The model, thus, provides valuable information with minimal empiricism on the dynamics of the small scales for pioneering engineering applications. [ABSTRACT FROM AUTHOR]

One-dimensional turbulence (ODT) is a simulation methodology that represents the essential physics of three-dimensional turbulence through stochastic resolution of the full range of length and time scales on a one-dimensional domain. In the present study, full compressible modifications are incorporated into ODT methodology, based on an Eulerian framework and a conservative form of the governing equations. In the deterministic part of this approach, a shock capturing scheme is introduced for the first time. In the stochastic part, one-dimensional eddy events are modeled and sampled according to standard methods for compressible flow simulation. Time advancement adjustments are made to balance comparable time steps between the deterministic and stochastic parts in compressible flows. Canonical shock–turbulence interaction cases involving Richtmyer–Meshkov instability at Mach numbers 1.24, 1.5, and 1.98 are simulated to validate the extended model. The ODT results are compared with available reference data from large eddy simulations and laboratory experiments. The introduction of a shock capturing scheme significantly improves the performance of the ODT method, and the results for turbulent kinetic energy are qualitatively improved compared with those of a previous compressible Lagrangian ODT method [Jozefik et al., "Simulation of shock–turbulence interaction in non-reactive flow and in turbulent deflagration and detonation regimes using one-dimensional turbulence," Combust. Flame 164, 53 (2016)]. For the time evolution of profiles of the turbulent mixing zone width, ensemble-averaged density, and specific heat ratio, the new model also yields good to reasonable results. Furthermore, it is found that the viscous penalty parameter Z of the ODT model is insensitive to compressibility effects in turbulent flows without wall effects. A small value of Z is appropriate for turbulent flows with weak wall effects, and the parameter Z serves to suppress extremely small eddy events that would be dissipated instantly by viscosity. [ABSTRACT FROM AUTHOR]

Accurate but economical modeling of supersonic turbulent boundary layers is a standing challenge due to the intricate entanglement of temperature, density, and velocity fluctuations on top of the mean-field variation. Application of the van Driest transformation may describe well the mean state but cannot provide detailed flow information. This lack-in modeling coarse and fine-scale variability is addressed by the present study using a stochastic one-dimensional turbulence (ODT) model. ODT is a simulation methodology that represents the evolution of turbulent flow in a low-dimensional stochastic way. In this study, ODT is extended to fully compressible flows. An Eulerian framework and a conservative form of the governing equations serve as the basis of the compressible ODT model. Computational methods for statistical properties based on ODT realizations are also extended to compressible flows, and a comprehensive way of turbulent kinetic energy budget calculation based on compressible ODT is put forward for the first time. Two canonical direct numerical simulation cases of supersonic isothermal-wall channel flow at Mach numbers 1.5 and 3.0 with bulk Reynolds numbers 3000 and 4880, respectively, are used to validate the extended model. A rigorous numerical validation is presented, including the first-order mean statistics, the second-order root mean square statistics, and higher-order turbulent fluctuation statistics. In ODT results, both mean and root mean square profiles are accurately captured in the near-wall region. Near-wall temperature spectra reveal that temperature fluctuations are amplified at all turbulent scales as the effects of compressibility increase. This phenomenon is caused by intensified viscous heating at a higher Mach number, which is indicated by the steeper profiles of viscous turbulent kinetic energy budget terms in the very near-wall region. The low computational cost and predictive capabilities of ODT suggest that it is a promising approach for detailed modeling of highly turbulent compressible boundary layers. Furthermore, it is found that the ODT model requires a Mach-number-dependent increase in a viscous penalty parameter Z in wall-bounded turbulent flows to enable accurate capture of the buffer layer. [ABSTRACT FROM AUTHOR]

Turbulent mixing plays an important role in a variety of applications ranging from astrophysics to combustion and even pollutant dispersion. The Direct Numerical Simulation (DNS) that resolves all scales is not feasible for most engineering applications since the flow has a wide range of length and time scales, which yields extremely high resolution requirements. Large Eddy Simulations (LES) overcome this limitation by modeling the sub‐grid scale effects. In transported Probability Density Function (PDF) methods, the key challenge is to develop an accurate mixing model. At this point, the Hierarchical Parcel‐Swapping (HiPS) model, introduced by A.R. Kerstein [J. Stat. Phys. 153, 142‐161 (2013)], is an attractive candidate. It is characterized by a computationally efficient representation of the effects of turbulence on a time‐evolving structure of diffusive scalar fields. The interpretation of the diffusive scalar fields or a state space as a binary tree structure is an alternative approach compared to the most common mixing models. The characteristic feature of HiPS is that every level of the tree corresponds to a specific length and time scale, which is based on turbulence inertial range scaling. The state variables only reside at the base of the tree and are understood as fluid parcels. The effects of turbulent advection are represented by stochastic swaps of sub‐trees at rates determined by prevailing turbulent time scales associated with the sub‐trees. The mixing of adjacent fluid parcels is done either instantaneously or at rates consistent with the corresponding diffusion time scales. In this work, HiPS is detailed for the simulation of passive scalar mixing first. Preliminary results for the scalar power spectra, mean square displacement and scalar dissipation rate are shown and reveal a reasonable agreement with experimental findings. Furthermore, the integrated binary tree structure allows to satisfy a large number of criteria for a good mixing model. Considering the reduced order and computational efficiency, HiPS is an attractive candidate for modeling the mixing in transported PDF methods. [ABSTRACT FROM AUTHOR]

Simultaneous momentum and passive scalar transfer in weakly heated pressure‐driven turbulent concentric annular pipe flow is numerically investigated using the cylindrical formulation of the stochastic one‐dimensional turbulence (ODT) model, which is utilized here as standalone tool. In the present study, we focus on the model calibration for heated annular pipes based on recent reference direct numerical simulations (DNS) from Bagheri and Wang (Int. J. Heat Fluid Flow 86, 108725, 2020; Phys. Fluids 33, 055131, 2021). It is shown that the model is able to individually capture scalar and momentum transfer, but not both equally well at the same time. We attribute this to less dissimilar scalar and momentum transport in the model at the low Reynolds number investigated. It is argued that the model prefers a fully developed turbulent state due to its construction. Nevertheless, it is demonstrated that ODT is able to reasonably capture the radial inner‐outer asymmetry of the scalar and momentum boundary layers which yields better predictive capabilities than wall‐function‐based approaches. [ABSTRACT FROM AUTHOR]

Atmospheric boundary layers (ABLs) exhibit transient processes on various time scales that range from a few days down to seconds, with a scale separation of the large-scale forcing and the small-scale turbulent response. One of the standing challenges in modeling and simulation of ABLs is a physically based representation of complex multiscale boundary layer dynamics. In this study, an idealized time-dependent ABL, the so-called Ekman–Stokes boundary layer (ESBL), is considered as a simple model for the near-surface flow in the mid latitudes and polar regions. The ESBL is driven by a prescribed temporal modulation of the bulk–surface velocity difference. A stochastic one-dimensional turbulence (ODT) model is applied to the ESBL as standalone tool that aims to resolve all relevant scales of the flow along a representative vertical coordinate. It is demonstrated by comparison with reference data that ODT is able to capture relevant features of the time-dependent boundary layer flow. The model predicts a parametric enhancement of the bulk–surface coupling in the event of a boundary layer resonance when the flow is forced with the local Coriolis frequency. The latter reproduces leading order effects of the critical latitudes. The model results suggest that the bulk flow decouples from the surface for high forcing frequencies due to a relative increase in detached residual turbulence. [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 (1). 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 (2,3), 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., An animal body plan can be described by using the axes of a Cartesian coordinate system (1,4). Bilaterian animals, for example, exhibit one major body axis, passing from anterior to [...]

An accurate prediction of the turbulent jet noise is usually only possible with direct numerical simulation (DNS) or high-resolution large-eddy simulation (LES) of the turbulent sources in the acoustic near field. The required level of fidelity comes at the price of high numerical resolution requirements, a severe restriction of the accessible parameter space, and high computational costs in general. These limitations can be partially mitigated by reduced-order models. In the present work, the stochastic one-dimensional turbulence (ODT) model is utilized as a stand-alone tool in order to study turbulent fluctuations in the far downstream region of turbulent round jets with finite co-flow velocity. ODT is a dimensionally reduced turbulence model that aims to resolve flow-field over a broad range of scales and, thus, the turbulent noise sources at all relevant scales, but only for a single, radially oriented, physical coordinate that is advected downstream with the flow during a simulation run. Here, unheated round jets with nozzle diameter D, nominal Mach number Ma = 0.9 but Reynolds number R e D ∈ { 9 × 10 4 , 2 × 10 5 , 4 × 10 5 } are studied as a canonical problem. An ensemble of ODT realizations is used to obtain flow statistics from a detailed representation of fluctuations that may be used to estimate turbulent noise by small-scale resolved sources in the near future. As the first step in this direction, we analyze the model representation of the flow field and the participating flow scales in detail. This is done even far downstream of the nozzle, which is not possible with high-resolution LES or DNS. The present ODT results agree well with the available reference data. The model accurately reproduces the asymptotic mean and fluctuating velocity behavior, and radial turbulence spectra of the jet that approximately obey large-scale jet similarity but are modified by axially decreasing the turbulence intensity. Based on these results, an outlook on the model application for turbulent jet noise prediction is given. [ABSTRACT FROM AUTHOR]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2010.08.007 Byline: Kyle A. Gurley, Sarah A. Elliott, Oleg Simakov, Heiko A. Schmidt, Thomas W. Holstein, Alejandro Sanchez Alvarado Keywords: Stem cells; Regeneration; Tissue remodeling; Wnt signaling pathway; Planarians Abstract: Regeneration is widespread throughout the animal kingdom, but our molecular understanding of this process in adult animals remains poorly understood. Wnt/[beta]-catenin signaling plays crucial roles throughout animal life from early development to adulthood. In intact and regenerating planarians, the regulation of Wnt/[beta]-catenin signaling functions to maintain and specify anterior/posterior (A/P) identity. Here, we explore the expression kinetics and RNAi phenotypes for secreted members of the Wnt signaling pathway in the planarian Schmidtea mediterranea. Smed-wnt and sFRP expression during regeneration is surprisingly dynamic and reveals fundamental aspects of planarian biology that have been previously unappreciated. We show that after amputation, a wounding response precedes rapid re-organization of the A/P axis. Furthermore, cells throughout the body plan can mount this response and reassess their new A/P location in the complete absence of stem cells. While initial stages of the amputation response are stem cell independent, tissue remodeling and the integration of a new A/P address with anatomy are stem cell dependent. We also show that WNT5 functions in a reciprocal manner with SLIT to pattern the planarian mediolateral axis, while WNT11-2 patterns the posterior midline. Moreover, we perform an extensive phylogenetic analysis on the Smed-wnt genes using a method that combines and integrates both sequence and structural alignments, enabling us to place all nine genes into Wnt subfamilies for the first time. Article History: Received 11 June 2010; Revised 1 August 2010; Accepted 3 August 2010

Author(s): Arne Kusserow [1]; Kevin Pang [2]; Carsten Sturm [1]; Martina Hrouda [3]; Jan Lentfer [1]; Heiko A. Schmidt [4]; Ulrich Technau [1, 7]; Arndt von Haeseler [4, 5]; Bert [...]

Small-scale processes in atmospheric boundary layers are typically not resolved due to cost constraints but modeled based on physical relations with the resolved scales, neglecting expensive backscatter. This lack in modeling is addressed in the present study with the aid of the one-dimensional turbulence (ODT) model. ODT is applied as stand-alone column model to numerically investigate stratification effects in long-lived transient Ekman flows as canonical example of polar boundary layers by resolving turbulent winds and fluctuating temperature profiles on all relevant scales of the flow. We first calibrate the adjustable model parameters for neutral cases based on the surface drag law which yields slightly different optimal model set-ups for finite low and moderate Reynolds numbers. For the stably stratified cases, previously calibrated parameters are kept fixed and the model predictions are compared with various reference numerical simulations and also observations by an exploitation of boundary layer similarity. ODT reasonably captures the temporally developing flow for various prescribed stratification profiles, but fails to fully capture the near-surface laminarization by remaining longer in a fully developed turbulent state, which suggests preferential applicability to high-Reynolds-number flow regimes. Nevertheless, the model suggests that large near-surface turbulence scales are primarily affected by the developing stratification due to scale-selective buoyancy damping which agrees with the literature. The variability of the wind-turning angle represented by the ensemble of stratified cases simulated covers a wider range than reference reanalysis data. The present study suggests that the vertical-column ODT formulation that is highly resolved in space and time can help to accurately represent multi-physics boundary-layer and subgrid-scale processes, offering new opportunities for analysis of very stable polar boundary layer and atmospheric chemistry applications. [ABSTRACT FROM AUTHOR]

Abstract Background The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches. Results We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information. Conclusions For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict.

Abstract Background Anomalous gene trees (AGTs) are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs. Results Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny. Conclusion Evidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.

Maximum likelihood and maximum parsimony are two key methods for phylogenetic tree reconstruction. Under certain conditions, each of these two methods can perform more or less efficiently, resulting in unresolved or disputed phylogenies. We show that a neural network can distinguish between four-taxon alignments that were evolved under conditions susceptible to either long-branch attraction or long-branch repulsion. When likelihood and parsimony methods are discordant, the neural network can provide insight as to which tree reconstruction method is best suited to the alignment. When applied to the contentious case of Strepsiptera evolution, our method shows robust support for the current scientific view, that is, it places Strepsiptera with beetles, distant from flies. [ABSTRACT FROM AUTHOR]

The One‐Dimensional Turbulence (ODT) model framework for the simulation of particle‐laden wire‐tube electrostatic precipitators is detailed in this work by specifying initial conditions, governing equations, and the mechanism for two‐way coupling between the electrostatic fields and the hydrodynamic flow. Unlike in a previous investigation [1], a two‐way coupling is required due to the low electrical mobility of aerosol particles, making flow motion responsible for the appearance of electrical convective currents. The ultimate goal of this framework is to develop a method which is able to investigate the precipitation phenomenon in wire‐tube precipitators, e.g., the collection efficiency, while relying on highly resolved physics. [ABSTRACT FROM AUTHOR]

Turbulent electroconvection denotes a fluctuating multiphysical flow in which hydrodynamics and electrokinetics interact on multiple scales. The dynamical processes at work are entangled down to the molecular‐diffusive scales that are determined by the Schmidt (Sc) and Reynolds (Re) number. Turbulence properties are generally nonuniversal which leads to high numerical resolution requirements. We address the numerical challenges associated with accuracy and feasibility by utilizing a stochastic one‐dimensional turbulence (ODT) model. Here, ODT is applied to turbulent Couette flow of dilute electrolytes as canonical problem for turbulent electroconvection. For Sc ⩾ O(10), ODT predicts an increase of the skin friction drag due to electrohydrodynamically (EHD) enhanced small‐scale eddy production once the flow is sufficiently turbulent. [ABSTRACT FROM AUTHOR]

This preliminary numerical study investigates a lifted methane/air jet flame in a vitiated coflow by means of the One‐Dimensional Turbulence (ODT) model. In the considered Cabra Burner configuration [Combust. Flame 143 491‐506 (2005)], a jet flame issues from a central nozzle into a vitiated coflow of hot combustion products from lean premixed hydrogen/air flames. ODT is a map‐based model for turbulent flow simulations which uses a stochastic formulation for the turbulent advection. The diffusion and reaction effects along the one‐dimensional domain are considered by temporally advancing deterministic evolution equations. ODT simulations are performed with a representation of the methane/air chemistry by a reduced 19‐species mechanism with 15 reactions and a detailed 53‐species mechanism with 325 reactions. In this work, we present centerline profile of temperature and species concentrations obtained from ODT simulations using a cylindrical ODT‐formulation. Additionally, two‐dimensional renderings of the temperature distribution are shown. Although the simulation of reactive jet configurations by means of ODT is not novel, the complex stabilization region depending on the flow conditions represents a challenge for the model. Considering the reduced order of the model, ODT is able to predict the flow characteristics and reasonably matches the existing experimental data. [ABSTRACT FROM AUTHOR]

Neutral and stably‐stratified Ekman boundary layers (EBLs) are numerically investigated with a stochastic one‐dimensional turbulence (ODT) model. EBLs achieve the bulk‐surface coupling in Earth's atmosphere. They are numerically challenging due to transient and non‐universal turbulence properties even at small scales. ODT addresses this problem by distinguishing turbulent‐advective from molecular‐diffusive transport processes for a vertical column along which all relevant scales of the flow are resolved. We demonstrate the model's capabilities for economical, accurate, and stratification regime independent simulation of EBLs for the wind‐turning angle. ODT reproduces and extrapolates reference direct numerical simulation results consistent with observations. We conclude that ODT may be useful for modeling of atmospheric surface layers. [ABSTRACT FROM AUTHOR]

The recent discovery and structure determination of a novel ubiquitin‐like dimerization domain in protein kinase D (PKD) has significant implications for its activation. PKD is a serine/threonine kinase activated by the lipid second messenger diacylglycerol (DAG). It is an essential and highly conserved protein that is implicated in plasma membrane directed trafficking processes from the trans‐Golgi network. However, many open questions surround its mechanism of activation, its localization, and its role in the biogenesis of cargo transport carriers. In reviewing this field, the focus is primarily on the mechanisms that control the activation of PKD at precise locations in the cell. In light of the new structural findings, the understanding of the mechanisms underlying PKD activation is critically evaluated, with particular emphasis on the role of dimerization in PKD autophosphorylation, and the provenance and recognition of the DAG that activates PKD. [ABSTRACT FROM AUTHOR]