Large-eddy simulations of co-annular turbulent jet using a Voronoi-based mesh generation framework

Large eddy simulations are performed for a cold ideally-expanded dual-stream jet issued from cylindrical co-axial nozzles, with supersonic primary stream (Mach number M_1 = 1.55) and subsonic secondary stream (M_2 = 0.9). The geometry includes the internal screw holes used to fasten the two nozzles together and to the plenum chamber. These slanted cylindrical holes over which the secondary stream flows were not covered in the experiment and were seamlessly captured in the computational mesh thanks to a novel grid generation paradigm based on the computation of Voronoi diagrams. A simulation with the screw holes covered is also performed and the preliminary results tends to indicate that these features have minimal impact on the flow and acoustic fields for the present operating conditions. As expected, the present dual-stream configuration with subsonic annular stream surrounding the primary supersonic stream features a reduced shear-layer growth, a longer potential core and a lack of strong Mach wave radiation. A long LES database is currently being collected for analysis and modeling of wavepackets and noise sources in such complex turbulent jets

Sparse-Lagrangian PDF Modelling of Silica Synthesis from Silane Jets in Vitiated Co-flows with Varying Inflow Conditions

This paper presents a comparison of experimental and numerical results for a series of turbulent reacting jets where silica nanoparticles are formed and grow due to surface growth and agglomeration. We use large-eddy simulation coupled with a multiple mapping conditioning approach for the solution of the transport equation for the joint probability density function of scalar composition and particulate size distribution. The model considers inception based on finite-rate chemistry, volumetric surface growth and agglomeration. The sub-models adopted for these particulate processes are the standard ones used by the community. Validation follows the “paradigm shift” approach where elastic light scattering signals (that depend on particulate number and size), OH- and SiO-LIF signals are computed from the simulation results and compared with “raw signals” from laser diagnostics. The sensitivity towards variable boundary conditions such as co-flow temperature, Reynolds number and precursor doping of the jet is investigated. Agreement between simulation and experiments is very good for a reference case which is used to calibrate the signals. While keeping the model parameters constant, the sensitivity of the particulate size distribution on co-flow temperature is predicted satisfactorily upstream although quantitative differences with the data exist downstream for the lowest coflow temperature case that is considered. When the precursor concentration is varied, the model predicts the correct direction of the change in signal but notable qualitative and quantitative differences with the data are observed. In particular, the measured signals show a highly non-linear variation while the predictions exhibit a square dependence on precursor doping at best. So, while the results for the reference case appear to be very good, shortcomings in the standard submodels are revealed through variation of the boundary conditions. This demonstrates the importance of testing complex nanoparticle synthesis models on a flame series to ensure that the physical trends are correctly accounted for

Chemical tools selectively target components of the PKA system

<p>Abstract</p> <p>Background</p> <p>In the eukaryotic cell the cAMP-dependent protein kinase (PKA) is a key enzyme in signal transduction and represents the main target of the second messenger cAMP. Here we describe the design, synthesis and characterisation of specifically tailored cAMP analogs which can be utilised as a tool for affinity enrichment and purification as well as for proteomics based analyses of cAMP binding proteins.</p> <p>Results</p> <p>Two sets of chemical binders were developed based on the phosphorothioate derivatives of cAMP, Sp-cAMPS and Rp-cAMPS acting as cAMP-agonists and -antagonists, respectively. These compounds were tested via direct surface plasmon resonance (SPR) analyses for their binding properties to PKA R-subunits and holoenzyme. Furthermore, these analogs were used in an affinity purification approach to analyse their binding and elution properties for the enrichment and improvement of cAMP binding proteins exemplified by the PKA R-subunits. As determined by SPR, all tested Sp-analogs provide valuable tools for affinity chromatography. However, Sp-8-AEA-cAMPS displayed (i) superior enrichment properties while maintaining low unspecific binding to other proteins in crude cell lysates, (ii) allowing mild elution conditions and (iii) providing the capability to efficiently purify all four isoforms of active PKA R-subunit in milligram quantities within 8 h. In a chemical proteomics approach both sets of binders, Rp- and Sp-cAMPS derivatives, can be employed. Whereas Sp-8-AEA-cAMPS preferentially binds free R-subunit, Rp-AHDAA-cAMPS, displaying antagonist properties, not only binds to the free PKA R-subunits but also to the intact PKA holoenzyme both from recombinant and endogenous sources.</p> <p>Conclusion</p> <p>In summary, all tested cAMP analogs were useful for their respective application as an affinity reagent which can enhance purification of cAMP binding proteins. Sp-8-AEA-cAMPS was considered the most efficient analog since Sp-8-AHA-cAMPS and Sp-2-AHA-cAMPS, demonstrated incomplete elution from the matrix, as well as retaining notable amounts of bound protein contaminants. Furthermore it could be demonstrated that an affinity resin based on Rp-8-AHDAA-cAMPS provides a valuable tool for chemical proteomics approaches.</p

Expression of Streptococcus pneumoniae Bacteriocins Is Induced by Antibiotics via Regulatory Interplay with the Competence System

Pneumococcal bacteriocins (pneumocins) are antibacterial toxins that mediate intra-species competition within the human host. However, the triggers of pneumocin expression are poorly understood. Using RNA-sequencing, we mapped the regulon of the pneumocin cluster (blp) of Streptococcus pneumoniae D39. Furthermore, by analogy with pneumococcal competence, we show that several antibiotics activate the blp-genes. Using real-time gene expression measurements we show that while the promoter driving expression of the two-component regulatory system blpR/H is constitutive, the remaining blp-promoters that control pneumocin expression, immunity and the inducer peptide BlpC, are pH-dependent and induced in the late exponential phase. Intriguingly, competence for genetic transformation, mediated by the paralogous ComD/E two-component quorum system, is induced by the same environmental cues. To test for interplay between these regulatory systems, we quantified the regulatory response to the addition of synthetic BlpC and competence-stimulating peptide (CSP). Supporting the idea of such interplay, we found that immediately upon addition of CSP, the blp-promoters were activated in a comD/E-dependent manner. After a delay, blp-expression was highly induced and was strictly dependent on blpRH and blpC. This raised the question of the mechanism of BlpC export, since bioinformatic analysis showed that the genes encoding the putative exporter for BlpC, blpAB, are not intact in strain D39 and most other strains. By contrast, all sequenced pneumococcal strains contain intact comAB genes, encoding the transport system for CSP. Consistent with the idea that comAB mediate BlpC export, we finally show that high-level expression of the blp-genes requires comAB. Together, our results demonstrate that regulation of pneumocin expression is intertwined with competence, explaining why certain antibiotics induce blp-expression. Antibiotic-induced pneumocin expression might therefore have unpredictable consequences on pneumococcal colonization dynamics by activating genes that mediate intra-specific interference competition

Size dependent exciton dynamics in one-dimensional perylene bisimide aggregates

The size dependent exciton dynamics of one-dimensional aggregates of substituted perylene bisimides are studied by ultrafast transient absorption spectroscopy and kinetic Monte-Carlo simulations in dependence on the temperature and the excitation density. For low temperatures the aggregates can be treated as infinite chains and the dynamics is dominated by diffusion driven exciton-exciton annihilation. With increasing temperature the aggregates decompose into small fragments consisting of very few monomers. This scenario is also supported by the time dependent anisotropy deduced from polarization dependent experiments

Are your covariates under control? How normalization can re-introduce covariate effects

Many statistical tests rely on the assumption that the residuals of a model are normally distributed. Rank-based inverse normal transformation (INT) of the dependent variable is one of the most popular approaches to satisfy the normality assumption. Studies regularly adjust for covariates and then normalize the residuals. This study investigated the effect of regressing covariates against the dependent variable and then applying rank-based INT to the residuals. The correlation between the dependent variable and covariates at each stage of processing was assessed. An alternative approach was tested of applying rank-based INT to the dependent variable before regressing covariates was tested. Analyses based on both simulated and real data examples demonstrated that applying rank-based INT to the dependent variable residuals after regressing out covariates re-introduces a linear correlation between the dependent variable and covariates in almost all situations. This will increase type-1 errors and reduce power. Our proposed alternative approach, where rank-based INT was applied prior to controlling for covariate effects, gave residuals that were normally distributed and linearly uncorrelated with covariates. This approach is therefore recommended

Biology, Ecology, and Management of Nonnative Ambrosia Beetles (Coleoptera: Curculionidae: Scolytinae) in Ornamental Plant Nurseries

Xylosandrus germanus (Blandford) and Xylosandrus crassiusculus (Motschulsky) (Coleoptera: Curculionidae: Scolytinae) are two of the most damaging nonnative ambrosia beetle pests in ornamental plant nurseries. Adult females tunnel into the stems and branches of host plants to create galleries with brood chambers. Hosts are infected with symbiotic Ambrosiella spp. fungi that serve as food for the larvae and adults. Plants can also become infected with secondary opportunistic pathogens, including Fusarium spp. Both X. germanus and X. crassiusculus have broad host ranges, and infestations can result in “toothpicks” of extruded chewed wood and sap flow associated with gallery entrances, canopy dieback, stem and trunk cankers, and plant death. Beetles efficiently locate and preferentially attack living, weakened plants, especially those physiologically stressed by flooding, inadequate drainage, frost injury, or winter injury and low temperature. Maintaining plant health is the foundation of a management plan. Vulnerable hosts can be partially protected with preventive pyrethroid applications in the spring before peak flight and attack, which are monitored using ethanol-based trapping tactics