A linear stability analysis of compressible hybrid lattice Boltzmann methods

An original spectral study of the compressible hybrid lattice Boltzmann method (HLBM) on standard lattice is proposed. In this framework, the mass and momentum equations are addressed using the lattice Boltzmann method (LBM), while finite difference (FD) schemes solve an energy equation. Both systems are coupled with each other thanks to an ideal gas equation of state. This work aims at answering some questions regarding the numerical stability of such models, which strongly depends on the choice of numerical parameters. To this extent, several one- and two-dimensional HLBM classes based on different energy variables, formulation (primitive or conservative), collision terms and numerical schemes are scrutinized. Once appropriate corrective terms introduced, it is shown that all continuous HLBM classes recover the Navier-Stokes Fourier behavior in the linear approximation. However, striking differences arise between HLBM classes when their discrete counterparts are analysed. Multiple instability mechanisms arising at relatively high Mach number are pointed out and two exhaustive stabilization strategies are introduced: (1) decreasing the time step by changing the reference temperature $T_{ref}$ and (2) introducing a controllable numerical dissipation $\sigma$ via the collision operator. A complete parametric study reveals that only HLBM classes based on the primitive and conservative entropy equations are found usable for compressible applications. Finally, an innovative study of the macroscopic modal composition of the entropy classes is conducted. Through this study, two original phenomena, referred to as shear-to-entropy and entropy-to-shear transfers, are highlighted and confirmed on standard two-dimensional test cases.Comment: 49 pages, 23 figure

Dynamic evolution of porosity in lower-crustal faults during the earthquake cycle

Earthquake-induced fracturing of the dry and strong lower crust can transiently increase permeability for fluids to flow and trigger metamorphic and rheological transformations. However, little is known about the porosity that facilitates these transformations. We analyzed microstructures that have recorded the mechanisms generating porosity in the lower crust from a pristine pseudotachylyte (solidified earthquake-derived frictional melt) and a mylonitized pseudotachylyte from Lofoten, Norway to understand the evolution of fluid pathways from the coseismic to the post- and interseismic stages of the earthquake cycle. Porosity is dispersed and poorly interconnected within the pseudotachylyte vein (0.14 vol%), with a noticeably increased amount along garnet grain boundaries (0.25–0.41 vol%). This porosity formed due to a net negative volume change at the grain boundary when garnet overgrows the pseudotachylyte matrix. Efficient healing of the damage zone by fluid-assisted growth of feldspar neoblasts resulted in the preservation of only a few but relatively large interconnected pores along coseismic fractures (0.03 vol% porosity). In contrast, porosity in the mylonitized pseudotachylyte is dramatically reduced (0.02 vol% overall), because of the efficient precipitation of phases (amphibole, biotite and feldspars) into transient pores during grain-size sensitive creep. Porosity reduction on the order of >85% may be a contributing factor in shear zone hardening, potentially leading to the development of new pseudotachylytes overprinting the mylonites. Our results show that earthquake-induced rheological weakening of the lower crust is intermittent and occurs when a fluid can infiltrate a transiently permeable shear zone, thereby facilitating diffusive mass transfer and creep

Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data

Improving the surveillance of tuberculosis (TB) is one of the eight core activities identified by the World Health Organization (WHO) and the European Respiratory Society to achieve TB elimination, defined as less than one incident case per million [1]. Monitoring transmission is especially important for multidrug-resistant (MDR) Mycobacterium tuberculosis isolates – defined as being resistant to rifampicin and isoniazid – and for extensively drug-resistant (XDR) M. tuberculosis isolates – defined as MDR isolates with additional resistance to at least one of the fluoroquinolones and at least one of the second-line injectable drugs. In 2017, the WHO estimated that worldwide more than 450,000 people fell ill with MDR-TB and among these, more than 38,000 fell ill with XDR-TB [2]. The rapid advance in molecular typing technology – especially the availability of whole genome sequencing (WGS) to identify and characterise pathogens – gives us the chance to integrate this information into disease surveillance. For TB surveillance, it is possible to combine the results of molecular typing of isolates from the M. tuberculosis complex with traditional epidemiological information to infer or to exclude TB transmission [3,4]. This is of particular relevance if transmission occurs among multiple countries, where epidemiological data such as social contacts are more difficult to get and where data exchange is more difficult to organise. The European Centre for Disease Prevention and Control (ECDC) reported 44 events of international transmission (international clusters) of MDR-TB in different European countries between 2012 and 2015 [5]. In that report, the authors inferred TB transmission using the mycobacterial interspersed repetitive units variable number of tandem repeats (MIRU-VNTR) typing method. However, this method has limitations such as low correlation with epidemiological information in outbreak settings and low discriminatory power [3,6]. In comparison, WGS analysis offers a much higher discriminatory power and allows inferring (or excluding) TB transmission at a higher resolution [4]. In a recent systematic review, van der Werf et al. identified three studies that used WGS to investigate the international transmission of TB [7]. In recent years, the amount of available WGS data is increasing, especially because sequencing has become cheaper [8]. In addition, more and more authors deposit the raw data of their projects in open access public repositories such as the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) [9]. These publicly available raw WGS data for thousands of isolates enable the re-use and the additional analyses at a large and global scale [10]. For example, it is possible to compare genomic data among different studies or countries since the data are available in a single place. Moreover, new software tools can be tested using the same raw WGS data [11]. However, standards in bioinformatics analysis and interpretation of these WGS data for surveillance purposes are not yet fully established [12]. We aimed to assess the usefulness of raw WGS data of global MDR/XDR M. tuberculosis isolates available in public repositories to improve TB surveillance. Specifically, we wanted to identify potential international events of TB transmission and to compare the international isolates with a collection of M. tuberculosis isolates collected in Germany in 2012 and 2013.Peer Reviewe

Dynamic Evolution of Porosity in Lower-Crustal Faults During the Earthquake Cycle

Earthquake-induced fracturing of the dry and strong lower crust can transiently increase permeability for fluids to flow and trigger metamorphic and rheological transformations. However, little is known about the porosity that facilitates these transformations. We analyzed microstructures that have recorded the mechanisms generating porosity in the lower crust from a pristine pseudotachylyte (solidified earthquake-derived frictional melt) and a mylonitized pseudotachylyte from Lofoten, Norway to understand the evolution of fluid pathways from the coseismic to the post- and interseismic stages of the earthquake cycle. Porosity is dispersed and poorly interconnected within the pseudotachylyte vein (0.14 vol%), with a noticeably increased amount along garnet grain boundaries (0.25–0.41 vol%). This porosity formed due to a net negative volume change at the grain boundary when garnet overgrows the pseudotachylyte matrix. Efficient healing of the damage zone by fluid-assisted growth of feldspar neoblasts resulted in the preservation of only a few but relatively large interconnected pores along coseismic fractures (0.03 vol% porosity). In contrast, porosity in the mylonitized pseudotachylyte is dramatically reduced (0.02 vol% overall), because of the efficient precipitation of phases (amphibole, biotite and feldspars) into transient pores during grain-size sensitive creep. Porosity reduction on the order of >85% may be a contributing factor in shear zone hardening, potentially leading to the development of new pseudotachylytes overprinting the mylonites. Our results show that earthquake-induced rheological weakening of the lower crust is intermittent and occurs when a fluid can infiltrate a transiently permeable shear zone, thereby facilitating diffusive mass transfer and creep

Mistral 7B

We introduce Mistral 7B v0.1, a 7-billion-parameter language model engineered for superior performance and efficiency. Mistral 7B outperforms Llama 2 13B across all evaluated benchmarks, and Llama 1 34B in reasoning, mathematics, and code generation. Our model leverages grouped-query attention (GQA) for faster inference, coupled with sliding window attention (SWA) to effectively handle sequences of arbitrary length with a reduced inference cost. We also provide a model fine-tuned to follow instructions, Mistral 7B -- Instruct, that surpasses the Llama 2 13B -- Chat model both on human and automated benchmarks. Our models are released under the Apache 2.0 license.Comment: Models and code are available at https://mistral.ai/news/announcing-mistral-7b

Challenges of operational river forecasting

Skillful and timely streamflow forecasts are critically important to water managers and emergency protection services. To provide these forecasts, hydrologists must predict the behavior of complex coupled human–natural systems using incomplete and uncertain information and imperfect models. Moreover, operational predictions often integrate anecdotal information and unmodeled factors. Forecasting agencies face four key challenges: 1) making the most of available data, 2) making accurate predictions using models, 3) turning hydrometeorological forecasts into effective warnings, and 4) administering an operational service. Each challenge presents a variety of research opportunities, including the development of automated quality-control algorithms for the myriad of data used in operational streamflow forecasts, data assimilation, and ensemble forecasting techniques that allow for forecaster input, methods for using human-generated weather forecasts quantitatively, and quantification of human interference in the hydrologic cycle. Furthermore, much can be done to improve the communication of probabilistic forecasts and to design a forecasting paradigm that effectively combines increasingly sophisticated forecasting technology with subjective forecaster expertise. These areas are described in detail to share a real-world perspective and focus for ongoing research endeavors

HERA Collider Physics

HERA, the first electron-proton collider, has been delivering luminosity since 1992. It is the natural extension of an impressive series of fixed-target lepton-nucleon scattering experiments. The increase of a factor ten in center-of-mass energy over that available for fixed-target experiments has allowed the discovery of several important results, such as the large number of slow partons in the proton, and the sizeable diffractive cross section at large $Q^2$. Recent data point to a possible deviation from Standard Model expectations at very high $Q^2$, highlighting the physics potential of HERA for new effects. The HERA program is currently in a transition period. The first six years of data taking have primarily elucidated the structure of the proton, allowed detailed QCD studies and had a strong impact on the understanding of QCD dynamics. The coming years will bring the era of electroweak studies and high $Q^2$ measurements. This is therefore an appropriate juncture at which to review HERA results.Comment: 351 pages, 154 figures, submitted to Reviews of Modern Physic

Méthode de Boltzmann sur réseau hybride pour les écoulements compressibles

Ces dernières années, les méthodes de simulations numériques appliquées à la mécanique des fluides sont devenues des outils indispensables pour l'industrie aéronautique. Ces méthodes sont utilisées de concert avec les approches expérimentales. Elles permettent, par exemple, d'avoir une compréhension précise d'un écoulement pour développer et dimensionner un composant d'avion. Ainsi, ces méthodes sont sans cesse améliorées pour restituer plus fidèlement la physique des écoulements simulés. Grâce à son coup de calcul réduit, sa facilité d'implémentation et d'utilisation, la méthode de Boltzmann sur réseau (LBM) s'est peu à peu imposée comme une solution alternative aux méthodes numériques traditionnelles. De plus, cette méthode possède les avantages d'être intrinsèquement instationnaire et est parfaitement adaptée aux géométries complexes. Malheureusement, sous sa forme standard, elle reste limitée à la simulation d'écoulements isothermes et faiblement compressibles, ce qui écarte de nombreuses applications aéronautiques. Néanmoins, des variantes compressibles existent. Parmi les plus prometteuses, on peut trouver la méthode hybride (HLBM) qui utilise la LBM pour calculer les équations de la masse et de la quantité de mouvement et un schéma aux différences finies pour calculer l'équation d'énergie. Cette thèse se consacre au développement et à l'étude de méthodes hybrides pour la simulation d'écoulements compressiblesIn recent years, computational fluid dynamic (CFD) methods have become essential for the aeronautics industry. These methods are used in conjunction with experimental approaches. They allow, for example, to have a precise understanding of a flow in order to help the design of aircraft components. Thus, these methods are constantly being improved to accurately reproduce the physics of simulated flows. Thanks to its reduced computational cost, its ease of implementation and use, the lattice Boltzmann method (LBM) has gradually emerged as an alternative approach to traditional numerical methods. In addition to its efficiency, this method has the advantages of being inherently unsteady and is perfectly adapted to complex geometries. Unfortunately, in its standard form, it remains limited to the simulation of isothermal and weakly compressible flows, which excludes many aeronautical applications. Nevertheless, compressible versions of this method do exist. Among the most promising ones, one can find the Hybrid method (HLBM) which uses the LBM to compute the mass and momentum equations and a finite difference scheme to computed the energy equation. This thesis focuses on the development and study of hybrid methods for the simulation of compressible flow

First enzymatic hydrolysis/thio-Michael addition cascade route to synthesis of AChE inhibitors.

International audienceThe irreversible Michael addition of thiols to acrylamides is reported as a new tool for the kinetic target-guided synthesis. In an unprecedented enzymatic hydrolysis/thio-Michael addition procedure, potent and selective acetylcholinesterase inhibitors are assembled by the enzyme using both its esterasic and templating ability