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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

Constant volume premixed lean n-Heptane/air autoignition at high pressure is investigated using the One-Dimensional Turbulence (ODT) model. The configuration consists of a 1D fixed volume domain with a prescribed velocity spectrum and temperature fluctuations superimposed on an initial uniformly elevated scalar field. The sensitivity of the heat release rate and pressure evolution to the initial temperature distribution is studied by imposing different initial temperature fields while holding the mean, RMS and integral length scale of the field constant. Three detailed chemical mechanisms are employed for the prediction of autoignition and heat release rate. To mitigate the high computational cost associated with the calculation of the chemical source terms in the stiff complex mechanisms, an approach based on the Strang-Splitting method is presented. Finally, a study of the ODT model uncertainty is carried out. For validation, ODT results are compared to 2D DNS data from Yoo et al. (2011) for the temporal evolution of heat release rate, pressure and density-weighted displacement speed. Ensemble averaged ODT results show good agreement with the DNS data. ODT results generated from varying the initial temperature fields show that the ignition delay time is highly sensitive to the initial temperature field. The ODT model uncertainty study shows that dispersion due to the stochastic nature of the model is considerably smaller than the dispersion resulting from varying the initial temperature field. Overall, this study demonstrates that ODT accurately captures the evolution of complex chemistry reactive flows in constant volume autoignition simulations and that once validated, ODT is an efficient tool that can be used to carry out parametric studies not feasible by DNS. [ABSTRACT FROM AUTHOR]

[Display omitted] • Lower-order modeling of transient boundary-layer dynamics in turbulent channel flows. • All relevant time and length scales of the flow are resolved by the model. • State-space statistics of surface scalar and momentum fluxes are captured. • Surface layer obeys inner scaling independent of the scalar forcing used. • Regime-independent prediction of Sc, Pe, and Re dependence of the scalar transfer. Accurate and economical modeling of near-surface transport processes is a standing challenge for various engineering and atmospheric boundary-layer flows. In this paper, we address this challenge by utilizing an economical stochastic one-dimensional turbulence (ODT) model. ODT aims to resolve all relevant scales of a turbulent flow for a one-dimensional domain. Here ODT is applied to turbulent channel flow as stand-alone tool. The ODT domain is a wall-normal line that is aligned with the mean shear. The free model parameters are calibrated once for the turbulent velocity boundary layer at a fixed Reynolds number. After that, we use ODT to investigate the Schmidt (Sc), Reynolds (Re), and Peclet (Pe) number dependence of the scalar boundary-layer structure, turbulent fluctuations, transient surface fluxes, mixing, and transfer to a wall. We demonstrate that the model is able to resolve relevant wall-normal transport processes across the turbulent boundary layer and that it captures state-space statistics of the surface scalar-flux fluctuations. In addition, we show that the predicted mean scalar transfer, which is quantified by the Sherwood (Sh) number, self-consistently reproduces established scaling regimes and asymptotic relations with respect to Sc , Re , and Pe. For high asymptotic Sc and Re , ODT results fall between the Dittus–Boelter, Sh ∼ Re 4 / 5 Sc 2 / 5 , and Colburn, Sh ∼ Re 4 / 5 Sc 1 / 3 , scalings but they are closer to the former. For finite Sc and Re , the model prediction reproduces the relation proposed by Schwertfirm and Manhart (Int. J. Heat Fluid Flow , 28 , 1204–1214, 2007) that is based on boundary-layer theory and yields a locally steeper effective scaling than any of the established asymptotic relations. The model extrapolates the scalar transfer to small asymptotic Sc ≪ Re τ - 1 (diffusive limit) with a functional form that has not been previously described. [ABSTRACT FROM AUTHOR]

A map-based stochastic approach, One-Dimensional Turbulence (ODT), is applied to analyze the incompressible spatially developing turbulent boundary layer (SBL). In the present study, the SBL is formed by a plane moving wall and a free stream at rest. The flow variables are resolved on all scales along a 1-D domain. A deterministic process represents the molecular diffusion and a stochastic process is modeling the effect of turbulent advection and pressure fluctuations. Due to the reduced dimensions in the model, it achieves major cost reductions as compared to the full 3-D simulations and is, thus, able to explore large parameter regimes. The simulations are presented for momentum thickness Reynolds numbers, Re θ , varied in the range Re θ ≈ 1968 - 8000. We have investigated various features related to the SBL, such as mean, root mean square, Reynolds shear stress, skewness, flatness and pre-multiplied velocity profiles and skin friction coefficient and shape factor, all for two bulk velocities using ODT and compared our results to the available reference Direct Numerical Simulations (DNS) and large-eddy simulations (LES) results. We have further compared the results for spatial and temporal ODT formulations used to investigate the turbulent boundary layer with the reference data at matched Re θ . The comparison presented suggests that ODT is a reasonably accurate approach for the simulations of the spatially developing turbulent boundary layers which can be further improved to yield accurate statistics at high Reynolds number by implementing Fourier transformation of the kernels which in the present formulation of the model is not implemented. [ABSTRACT FROM AUTHOR]

• Species distribution models (SDM) were built with the MaxEnt algorithm for two species of river fish. • Two spatial modelling scales (river reach and subcatchments) were compared and differences measured for the first time. • Models showed heterogeneous predictions in medium suitable rivers but yielded similar results in unsuitable rivers. • Restricting the model extent led to a shift in environmental predictor contributions,emphasizing small-scale river structures. • Information given by both model types are complimentary and beneficial for management. Species Distribution Models (SDM) are frequently used in ecological research, but the effects of model extent and granularity on model outcomes are rarely addressed. In freshwater SDMs, two different approaches are commonly used to define the granularity of the models, i.e. to subdivide entire river systems into appropriate spatial modelling units: river reaches on the actual river network or subcatchments. We built maximum entropy (MaxEnt) SDMs for barbel (Barbus barbus) and grayling (Thymallus thymallus) in the River Ruhr catchment in Germany with identical environmental predictor data and analysed the difference between these two approaches. All models performed well (AUC > 0.9) and geographic predictors (e.g. distance to the river source) dominated over hydromorphological predictors in explaining species distributions. There was high agreement between the two model setups in river parts of low and high habitat suitability but considerably lower agreement in river parts of medium habitat suitability. In these medium suitable river parts, model results were spatially very heterogeneous and alternated at fine spatial scales especially in models based on river reaches. Increasing model regularization, a setting to control overfitting, had a smoothing effect on the environmental variables in the river reach models similar to the coarser subcatchment granularity. A restriction of the spatial extent led to a shift in predictor contributions to the model and an increase of the importance of hydromorphologic predictors by ca. 45 %. Restricting the model extend to the natural core distributional area of a given fish species might therefore be considered beneficial for the application of SDMs in a management context. By decreasing the weight of fixed geographic predictors in the model, predictors relating to hydromorphological river structures (i.e. which are accessible for restoration projects) gain importance. We conclude that SDM setups based on river reaches and subcatchments can both give valuable complementary information about the distribution of species. The high-resolution model based on river reaches might better discover individual local habitat features, whereas the subcatchment model might better account for the minimum spatial requirements of a fish population. [ABSTRACT FROM AUTHOR]

The one-dimensional turbulence (ODT) methodology is extended to include an efficient compressible implementation and a model for capturing shock-induced turbulence is presented. Lignell et al. recently introduced a Lagrangian ODT implementation using an adaptive mesh. As the code operates in the incompressible regime (apart from constant-pressure dilatation) it cannot handle compressibility effects and their interactions with turbulence and chemistry. The necessary algorithmic changes to include compressibility effects are highlighted and our model for capturing shock–turbulence interaction is presented. To validate our compressible solver, we compare results for the Sod shock tube problem against a finite volume Riemann solver. To validate our model for shock–turbulence interaction, we present comparisons for a non-reactive and a reactive case. First, results of a shock traveling from light (air) to heavy (SF 6 ) with reshock have been simulated to match mixing width growth data of experiments and turbulent kinetic energy results from LES. Then, for one-step chemistry calibrated to represent an acetylene/air mixture we simulate the interaction of a shock wave with an expanding flame front, and compare results with 2D simulation (2D-sim) data for flame brush formation and ensuing deflagration-to-detonation transitions (DDT). Results for the Sod shock tube comparison show that the shock speed and profile are captured accurately. Results for the non-reactive shock–reshock problem show that interface growth at all simulated Mach numbers is captured accurately and that the turbulent kinetic energy agrees in order of magnitude with LES data. The reactive shock tube results show that the flame brush thickness compares well to 2D-sim data and that the approximate location and timing of the DDT can be captured. The known sensitivity of DDT characteristics to details of individual flow realizations, seen also in ODT, implies that model agreement can be quantified only by comparing flow ensembles, which are presently unavailable other than in an ODT run-to-run sensitivity study that is reported herein. [ABSTRACT FROM AUTHOR]

Friction factor enhancements in pipe-flows subject to fixed electric fields are evaluated using the stochastic One-Dimensional Turbulence (ODT) model. To that extent, low Mach asymptotics are used to derive the leading order effects of the governing equations in electrohydrodynamic (EHD) flows considering low mobility ratios. Temporal and spatial ODT formulations are then carried out for three different Reynolds numbers (Re = 3000 , Re = 4000 and Re = 5000) at a set of electrohydrodynamic numbers in the range 0 ≤ N EHD ≤ 600. The ODT simulation results are compared to published experimental data on Darcy friction factor enhancements of Nelson et al. (1990). The results signalize the importance of the developing flow for the EHD-enhanced drag. On one hand, the ratio N EHD 2/Re2 characterizes the enhancement. On the other hand, the developing flow and the laminar-to-turbulent transition also have an important contribution to the friction factor. The ODT results presented here show that reduced order models can deliver relevant insights in otherwise numerically challenging flow simulations, therefore aiding the quantitative analysis of experimental observations in EHD flows. [ABSTRACT FROM AUTHOR]

The one-dimensional turbulence (ODT) model is applied to a reactant-to-product counterflow configuration and results are compared with DNS data. The model employed herein solves conservation equations for momentum, energy, and species on a one dimensional (1D) domain corresponding to the line spanning the domain between nozzle orifice centers. The effects of turbulent mixing are modeled via a stochastic process, while the Kolmogorov and reactive length and time scales are explicitly resolved and a detailed chemical kinetic mechanism is used. Comparisons between model and DNS results for spatial mean and root-mean-square (RMS) velocity, temperature, and major and minor species profiles are shown. The ODT approach shows qualitatively and quantitatively reasonable agreement with the DNS data. Scatter plots and statistics conditioned on temperature are also compared for heat release rate and all species. ODT is able to capture the range of results depicted by DNS. However, conditional statistics show signs of underignition. [ABSTRACT FROM AUTHOR]

• We introduce an extension of the spatial ODT formulation (S-ODT), in order to study a variable density internal air flow. • S-ODT results are compared to the results of a traditional temporal ODT formulation (T-ODT) and to reference DNS data. • For bulk quantities, both the T-ODT and S-ODT formulations have a similar performance in comparison to DNSs. • For the evaluation of radial distributions, the S-ODT formulation clearly outperforms the T-ODT formulation. A novel spatial formulation of the One-Dimensional Turbulence (ODT) model is applied to a vertical pipe-flow with heat transfer, analogous to the Direct Numerical Simulation (DNS) performed by Bae et al. [Phys. Fluids 18, (075102) (2006)]. The framework presented here is an extension for radially confined domains of the cylindrical ODT spatial formulation for low Mach number flows with variable density. The variable density simulations for air (Prandtl number P r = 0.71) are performed at an initial bulk Reynolds number R e b , 0 , D N S = 6000 and Grashof number G r 0 , D N S = 6.78 × 10 6. ODT results are presented for both the spatial formulation introduced in this work and the standard temporal formulation for cylindrical flows introduced by Lignell et al. [Theor. Comput. Fluid Dyn. 32, 4 (2018), pp. 495–20]. Streamwise bulk profiles and radial profiles at specific streamwise positions for the temporal and spatial formulations are in good agreement with the DNS results from Bae et al. For the present application, the spatial formulation yields physically better results in comparison to the temporal formulation. Overall, the findings in the original work of Bae et al. were corroborated with ODT. Although the framework proposed in this work is not a compressible framework and has some clear limitations regarding conservation properties, we suggest its use for future studies in the low Mach number variable density regime. [ABSTRACT FROM AUTHOR]

Modeling turbulent mixing is a standing challenge for nonpremixed chemically reacting flows. Key complications arise from the requirement to capture all relevant scales of the flow and the necessity to distinguish between turbulent advective transport and molecular diffusive transport processes. In addition, anisotropic mean shear, variable advection time scales, and the coexistence of turbulent and nonturbulent regions need to be represented. The fundamental issues at stake are addressed by investigating multi-scalar mixing in a three-stream coaxial jet with a map-based stochastic one-dimensional turbulence model. ODT provides full-scale resolution at affordable costs by a radical reduction of complexity compared to high-fidelity Navier–Stokes solvers. The approach is partly justified by an application of the boundary-layer approximation, but neglects fluctuating axial pressure gradients. It is demonstrated that low-order scalar statistics are reasonably but not fully captured. Despite this shortcoming, it is shown that the model is able to reproduce experimental state-space statistics of multi-stream multi-scalar mixing. The model therefore offers physics-compatible improvements in multi-stream mixing modeling despite some fundamental limitations that remain from unjustified assumptions. [Display omitted] • Map-based stochastic modeling of multi-stream mixing with full-scale resolution. • Comprehensive assessment of spatial sensitivities of scalar joint probabilities. • State-space statistics of scalar mixing in shear turbulence are reproduced. • Scalar statistics are obtained diagnostically without closure assumptions. • Local advection velocities and turbulent/nonturbulent regions are represented. [ABSTRACT FROM AUTHOR]

Abstract: Recent measurements of the direct response of premixed hydrocarbon flames to acoustic pressure fluctuations have shed doubt on the validity of analytical models that use irreversible one-step chemistry (Wangher et al., 2008) , and suggest that more realistic chemical kinetic models are needed to fully describe the unsteady dynamics of premixed flames. In this paper we present experimental results and numerical simulations for planar hydrogen flames which have simpler chemical kinetics than hydrocarbon flames. The simulations employ detailed chemical kinetics, including OH∗ chemiluminescence chemistry, so that the validity of using the emission from the excited OH∗ radical as a marker of the reaction rate can be assessed. By comparing our numerical results with measurements on hydrogen, and with previous measurements on methane, we show that OH∗ chemiluminescence does not always provide a reliable measure of heat release rate in the presence of a pressure driven interaction. Finally, our results are compared to the predictions of an analytical model for two-step chemistry with a chain-branching and a chain-breaking reaction (Clavin and Searby, 2008) . We conclude that multi-step chemistry must be taken into account when evaluating the unsteady response of flames to pressure waves. [Copyright &y& Elsevier]