Partially Cooled Shocks: Detectable Precursors in the Warm/hot Intergalactic Medium

I present computations of the integrated column densities produced in the post-shock cooling layers and in the radiative precursors of partially cooled fast shocks as a function of the shock age. The results are applicable to the shock-heated warm/hot intergalactic medium which is expected to be a major baryonic reservoir and contain a large fraction of the so-called missing baryons. My computations indicate that readily observable amounts of intermediate and high ions, such as C IV, N V, and O VI, are created in the precursors of young shocks, for which the shocked gas remains hot and difficult to observe. I suggest that such precursors may provide a way to identify and estimate the "missing" baryonic mass associated with the shocks. The absorption-line signatures predicted here may be used to construct ion-ratio diagrams, which will serve as diagnostics for the photoionized gas in the precursors. In my numerical models, the time evolution of the shock structure, self-radiation, and associated metal-ion column densities are computed by a series of quasi-static models, each appropriate for a different shock age. The shock code used in this work calculates the non-equilibrium ionization and cooling, follows the radiative transfer of the shock self-radiation through the post-shock cooling layers, takes into account the resulting photoionization and heating rates, follows the dynamics of the cooling gas, and self-consistently computes the photoionization states in the precursor gas. I present a complete set of the age-dependent post-shock and precursor columns for all ionization states of the elements H, He, C, N, O, Ne, Mg, Si, S, and Fe as functions of the shock velocity, gas metallicity, and magnetic field. I present my numerical results in convenient online tables

The GNAT method for nonlinear model reduction: effective implementation and application to computational fluid dynamics and turbulent flows

The Gauss--Newton with approximated tensors (GNAT) method is a nonlinear model reduction method that operates on fully discretized computational models. It achieves dimension reduction by a Petrov--Galerkin projection associated with residual minimization; it delivers computational efficency by a hyper-reduction procedure based on the `gappy POD' technique. Originally presented in Ref. [1], where it was applied to implicit nonlinear structural-dynamics models, this method is further developed here and applied to the solution of a benchmark turbulent viscous flow problem. To begin, this paper develops global state-space error bounds that justify the method's design and highlight its advantages in terms of minimizing components of these error bounds. Next, the paper introduces a `sample mesh' concept that enables a distributed, computationally efficient implementation of the GNAT method in finite-volume-based computational-fluid-dynamics (CFD) codes. The suitability of GNAT for parameterized problems is highlighted with the solution of an academic problem featuring moving discontinuities. Finally, the capability of this method to reduce by orders of magnitude the core-hours required for large-scale CFD computations, while preserving accuracy, is demonstrated with the simulation of turbulent flow over the Ahmed body. For an instance of this benchmark problem with over 17 million degrees of freedom, GNAT outperforms several other nonlinear model-reduction methods, reduces the required computational resources by more than two orders of magnitude, and delivers a solution that differs by less than 1% from its high-dimensional counterpart

Ion-by-ion Cooling efficiencies

We present ion-by-ion cooling efficiencies for low-density gas. We use Cloudy (ver. 08.00) to estimate the cooling efficiencies for each ion of the first 30 elements (H-Zn) individually. We present results for gas temperatures between 1e4 and 1e8K, assuming low densities and optically thin conditions. When nonequilibrium ionization plays a significant role the ionization states deviate from those that obtain in collisional ionization equilibrium (CIE), and the local cooling efficiency at any given temperature depends on specific non-equilibrium ion fractions. The results presented here allow for an efficient estimate of the total cooling efficiency for any ionic composition. We also list the elemental cooling efficiencies assuming CIE conditions. These can be used to construct CIE cooling efficiencies for non-solar abundance ratios, or to estimate the cooling due to elements not explicitly included in any nonequilibrium computation. All the computational results are listed in convenient online tables.Comment: Submitted to ApJS. Electronic data available at http://wise-obs.tau.ac.il/~orlyg/ion_by_ion

Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis.

Natural product biosynthetic pathways are replete with enzymes repurposed for new catalytic functions. In some modular polyketide synthase (PKS) pathways, a GCN5-related N-acetyltransferase (GNAT)-like enzyme with an additional decarboxylation function initiates biosynthesis. Here, we probe two PKS GNAT-like domains for the dual activities of S-acyl transfer from coenzyme A (CoA) to an acyl carrier protein (ACP) and decarboxylation. The GphF and CurA GNAT-like domains selectively decarboxylate substrates that yield the anticipated pathway starter units. The GphF enzyme lacks detectable acyl transfer activity, and a crystal structure with an isobutyryl-CoA product analog reveals a partially occluded acyltransfer acceptor site. Further analysis indicates that the CurA GNAT-like domain also catalyzes only decarboxylation, and the initial acyl transfer is catalyzed by an unidentified enzyme. Thus, PKS GNAT-like domains are re-classified as GNAT-like decarboxylases. Two other decarboxylases, malonyl-CoA decarboxylase and EryM, reside on distant nodes of the superfamily, illustrating the adaptability of the GNAT fold

Gastric normal adjacent mucosa versus healthy and cancer tissues: Distinctive transcriptomic profiles and biological features

Gastric cancer (GC) is a leading cause of cancer-related deaths in the world. Molecular heterogeneity is a major determinant for the clinical outcomes and an exhaustive tumor classification is currently missing. Histologically normal tissue adjacent to the tumor (NAT) is commonly used as a control in cancer studies, nevertheless a recently published paper described the unique characteristics of the NAT in several tumor types. Little is known about the global gene expression profile of gastric NAT (gNAT) which could be an effective tool for a more realistic definition of GC molecular signature. Here, we integrated data of 512 samples from the Genotype- Tissue Expression project (GETx) and The Cancer Genome Atlas (TCGA) to analyze the transcriptome of healthy gastric tissues, gNAT, and GC samples. We validated TCGA-GETx data mining through inHouse gNAT and GC expression dataset. Differential gene expression together with pathway enrichment analyses, indeed, led to different results when using the gNAT or the healthy tissue as control. Based on our analyses, gNAT showed a peculiar gene signature and biological features, like the estrogen receptor pathways activation, suggesting a molecular behavior partially different from both healthy and GC tissues. Therefore, using gNAT as healthy control tissue in the characterization of tumor associated biological processes and pathways could lead to suboptimal results

Wendekreisel Golden Gnat WK16-10

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