The supragenic organization of glycoside hydrolase encoding genes reveals distinct strategies for carbohydrate utilization in bacteria

Glycoside hydrolases (GHs) are carbohydrate-active enzymes essential for many environmental (e.g., carbon cycling) and biotechnological (e.g., biofuels) processes. The complete processing of carbohydrates by bacteria requires many enzymes acting synergistically. Here, I investigated the clustered or scattered distribution of 406,337 GH-genes and their association with transporter genes identified in 15,640 completely sequenced bacterial genomes. Different bacterial lineages displayed conserved levels of clustered or scattered GH-genes, but overall, the GH-genes clustering was generally higher than in randomized genomes. In lineages with highly clustered GH-genes (e.g., Bacteroides, Paenibacillus), clustered genes shared the same orientation. These codirectional gene clusters potentially facilitate the genes' co-expression by allowing transcriptional read-through and, at least in some cases, forming operons. In several taxa, the GH-genes clustered with distinct types of transporter genes. The type of transporter genes and the distribution of the so-called GH:TR-genes clusters were conserved in selected lineages. Globally, the phylogenetically conserved clustering of the GH-genes with transporter genes highlights the central function of carbohydrate processing across bacterial lineages. In addition, in bacteria with the most identified GH-genes, the genomic adaptations for carbohydrate processing also mirrored the broad environmental origin of the sequenced strains (e.g., soil and mammal gut) suggesting that a combination of evolutionary history and the environment selects for the specific supragenic organization of the GH-genes supporting the carbohydrate processing in bacterial genomes

Le langage silencieux dans les postures d’autorité

Le langage silencieux constitue la face cachée de la communication humaine en apparence dominée par le verbe. Campé au cœur de l’expérience professionnelle le non-verbal interpelle fortement le chercheur en communication. Mais comment rendre compte de cette terra incognita, de ce soubassement discret voire hyper-implicite de la culture sans tomber dans le délire d’interprétation ? Pourtant il importe de mieux connaître le non-verbal tant il structure notre vie quotidienne et professionnelle. ..

Hybrid treatment of small droplets in atomized jet

International audienceL'atomisation de combustible a un impact direct sur l'émission de polluants dans l'atmosphère. Face au besoin de caractériser l'atomisation primaire, l'étude numérique de l'intéraction liquide-gaz croît dans le but de maîtriser la création de particules polluantes et de la réduire. Elle est effectuée sur l'ensemble du spray, de son injection dans la chambre de combustion jusqu'à l'évaporation des gouttes créées suite au secondary breakup. Notre but est d'augmenter la précision du transport des gouttes au sein des jets atomisés, typiquement, une goutte est 100 fois plus petite que le diamètre d'injection. Cette différence d'échelle rend la définition de l'interface liquide-gaz complexe et crééer des zones sous résolues. Pour résoudre ce probleme d'échelle, un coupling entre un suivi Eulérien et un suivi Lagrangian a été proposé, voir Hermann, [1]. Cette communication se concentre sur les critères de transformation d'une goutte eulérienne en particule lagrangienne et les modifications physiques et numériques entourant cette transformation. Cette communication se concentre sur l'implémentation d'une méthode de suivi de particule polydisperse basée sur des critères géometriques. Ils sont finalement appliqués sur l'étude d'un jet atomisé. Abstract : Atomization of liquid fuel has a direct impact on the production of pollutant emission in engineering propulsion devices. Due to the multiple challenges in experimental investigations, motivation for numerical study is increasing on liquid/gas interaction from injection till dispersed spray zone. Our purpose is to increase the accuracy of the treatment of droplets in atomized jet, which are typically 100 times smaller than the injection size. As the size of the droplets reduces with the primary breakup of liquid fuel, it is increasingly challenging to track the interface of the droplets accurately. To solve this multis-cale issue, a coupled tracking Eulerian-Lagrangian Method is proposed, see Hermann, [1]. This communication focuses on the criteria of transformation of this coupling from interface captured droplets to Lagrangian particles and numerical/physical reconstruction during this process. From the literature, interaction criteria of transformation are all geometric, implementation of physical parameter is made in this communication. Those criteria are finally applied on a liquid jet atomization

From droplets to particles: Transformation criteria

International audienceAtomization of liquid fuel has a direct impact on the production of pollutant emission in engineering propulsion devices. Due to the multiple challenges in experimental investigations, motivation for numerical study is increasing on liquid-gas interaction from injection till dispersed spray zone. Our purpose is to increase the accuracy of the treatment of droplets in atomized jet, which are typically 100 times smaller than the characteristic injection length size. As the characteristic length reduces downstream to the jet, it is increasingly challenging to track the interface of the droplets accurately. To solve this multiscale issue, a coupled tracking Eulerian-Lagrangian Method exists [1]. It consists in transforming the small droplets to Lagrangian droplets that are transported with drag models. In addition to the size transformation criteria, one can consider geometric parameters to determine if a droplet has to be transformed. Indeed, the geometric criteria are there for two reasons. The first one is the case where the droplets can break if there are not spherical. The second one is about the drag models that are based on the assumption that the droplet is spherical. In this paper we make a review of the geometric criteria used in the literature. New geometric criteria are also proposed. Those criteria are validated and then discussed in academic cases and a 3D airblast atomizer simulation. Following the analysis of the results the authors advise the use of the deformation combined with surface criteria as the geometric transformation criteria. Introduction Atomization is a phenomenon encountered in many applications such as sprays in cosmetic engineering or aerospace engineering for jet propulsion [2]. In the combustion chamber, the total surface of the interface separating the two phases is a key parameter. Primary and secondary breakup have been extensively investigated in the literature. However, in order to fully describe the complete process, one has to capture droplets in dispersed zone 100 times smaller than jet diameter. Atomization is then a multiphase and a multiscale flow phenomenon which is still far from being understood. Due to this wide range of scale, the Direct Numerical Simulation (DNS) of such process requires robust and efficient codes. DNS is an important tool to analyse the experimental results and go further into the atomization understanding. In the past few years, numerical schemes of Interface Capturing Method (ICM) have been improved but faced numerical limitation. For instance, the treatment of the small droplets is the most challenging part when the entire process is treated in DNS. When dealing with unresolved structures we face different problems such as the dilution or the creation of numerical instabilities. To avoir them, a strategy is to remove small structures during the simulation, see Shinjo et al. [3]. But, those methods do not collect information on smallest droplets in atomization application. Introduction of Adaptive Mesh Refinement (AMR) in DNS is a first answer to this issue, it consists in refining unresolved area under numerical concept and focus on the interface between two phases instead of refining the entire domain. In dense spray, AMR tends to refine the entire zone and becomes as expensive as a full domain refinement. A solution is to transform the smallest droplets into point particles and remove AMR in this area. This strategy is called Eulerian-Lagrangian coupling [1], it assumes that small droplets will no longer break during the simulation and that the Lagrangian models reproduce correctly the droplet transport. These physical assumptions are implemented to answer numerical issue and improve the computational cost. This Eulerian-Lagrangian coupling is based on transformation criteria that defines when an ICM structure has to be transformed into Lagrangian particle and when a Lagrangian particle has to be transformed back into ICM. The main purpose of the present communication is to provide a detailed analysis of the ICM to Lagrangian transformation criteria. The geometri

Coupled Level set moment of fluid method for simulating multiphase flows

International audienceA coupled level set moment of fluid (CLSMOF) method for numerical simulation of multiphase flows is presented in this paper. This numerical method of liquid/gas interface capture is a hybrid of classical moment of fluid (MOF) method and coupled level set volume of fluid (CLSVOF) method. In this CLSMOF method, MOF interface reconstruction is used only for the under-resolved liquid structures while the level set function is used for the interface reconstruction for the resolved structures. This method combines the advantages of accurate capture of under-resolved liquid strucutres from MOF method and sharp interface representation by the level set function. The results presented in this paper demonstrates the ability and accuracy of the CLSMOF method to be as high as that of the MOF method while incurring relatively less computational expense. Finally, the application of CLSMOF method to simulation of turbulent diesel jet yeilded a very satisfactory volume conservation

A 3D Moment of Fluid method for simulating complex turbulent multiphase flows

International audienceThis paper presents the moment of fluid method as a liquid/gas interface reconstruction method coupled with a mass momentum conservative approach within the context of numerical simulations of incompressible two-phase flows. This method tracks both liquid volume fraction and phase centroid for reconstructing the interface. The interface reconstruction is performed in a volume (and mass) conservative manner and accuracy of orientation of interface is ensured by minimizing the centroid distance between original and reconstructed interface. With two-phase flows, moment of fluid method is able to reconstruct interface without needing phase volume data from neighboring cells. The performance of this method is analyzed through various transport and deformation tests, and through simple two-phase flows tests that encounter changes in the interface topologies. Exhaustive mesh convergence study for the reconstruction error has been performed through various transport and deformation tests involving simple two-phase flows. It is then applied to simulate atomization of turbulent liquid diesel jet injected into a quiescent environment. The volume conservation error for the moment of fluid method remains small for this complex turbulent case

A comparative study of DNS of airblast atomization using CLSMOF and CLSVOF methods

International audienceThe results from direct numerical simulations (DNS) of planar pre-filming airblast atomization are presented in this paper. The configuration of the airblast atomization is inspired from a published experimental configuration of Gepperth et al (2012, "Ligament and Droplet Characteristics in Prefilming Airblast Atomization", ICLASS 2012). The simulations have been performed using our in-house Navier-Stokes solver ARCHER. Two DNS have been performed each respectively using coupled level moment of fluid (CLSMOF) and coupled level set volume of fluid (CLSVOF) methods for liquid/gas interface reconstruction. The operating point investigated in the simulations correspond to aircraft altitude relight conditions. The DNS data are post-processed consistent to that of the experimental data to extract droplet and ligament statistics. The droplet diameter distribution from the simulations is found to be having satisfactory agreement with the experimental data. Two breakup mechanisms of atomization are observed: sheet breakup producing small droplets and ligament breakup producing medium and bulgy droplets. The CLSMOF method is observed to produce more medium and bulgy droplets owing to dominant ligament breakup while CLSVOF method produced more number of small droplets owing to predominant sheet breakup mechanism. A good agreement was found between simulations and experiments for Sauter Mean Diameter (SMD) of the droplets. The droplet diameter distribution from the simulations are found to under-predict the peak of the distribution but displays similar profile as that of the experiments. The droplet velocity distribution from the simulations is found to agree well with that of the experiments. The liquid ligaments formed at the trailing edge of the pre-filmer plate are characterized by their lengths. The breakup length of the ligaments, defined as arithmetic mean of the ligament lengths, computed from the simulations agree satisfactorily with the value computed from the experimental data

An investigation of characteristics of airblast atomization using 3D DNS for altitude relight conditions

International audienceThis paper presents results from direct numerical simulations (DNS) of planar pre-filming airblast atomization. The liquid/gas interface has been captured using coupled level set moment of fluid method. This method is a hybrid between moment of fluid and coupled level set volume of fluid methods. The numerical method has been applied to airblast atomization analyzed experimentally by Gepperth et al. (2012, "Ligament and Droplet Characteristics in Prefilming Air-blast Atomization", ICLASS 2012). The operating point investigated in this work correspond to aircraft altitude relight condition. The post-processing of the DNS data is performed consistently with that for the experimental data. The main mode of breakup observed is torn sheet breakup. A good agreement was found between simulations and experiments for Sauter Mean Diameter and droplet streamwise velocity distribution while satisfactory agreement has been found for the droplet diameter distribution and ligament breakup length