Understanding mixing processes in stars using hydrodynamic simulations

Waves that propagate in stellar interiors are essential to stellar physics for two reasons. First, the interiors of stars are studied by detection of global modes of oscillations resulting from wave interference. Secondly, waves are involved in various transport phenomena. In stars, there are two main types of waves: acoustic and gravity. This duality of waves as observational tools and physical processes impacting stellar structure makes them a crucial field of study in astrophysics. In this thesis, we focus on internal gravity waves (IGWs), which are well known for transporting angular momentum, energy and chemical elements in stably stratified media. Despite observations of very high precision, detection of IGWs is still challenging and their properties in stellar interiors remain poorly understood and/or constrained. This is mostly because IGWs are inherently 3D, non-linear and anisotropic phenomena. Consequently, multidimensional modelling is a great tool to study these waves. However, stellar hydrodynamics faces important challenges such as numerical stability and thermal relaxation. To face them, an artificial increase of the stellar luminosity and of the thermal diffusivity by several orders of magnitudes is a commonly used tactic. Using two-dimensional simulations of a solar-like model, we quantify the impact of such a technique on IGWs. Our results suggest that this technique affect the excitation of IGWs, because of an impact on convective motions and overshooting, but also their damping. Main-sequence intermediate-mass stars, with M ≳ 2M⊙, possess a convective core and a radiative envelope. It remains unclear if waves generated at the edge of the convective core should be able to propagate up to the stellar surface. In this context, we have carried out an analysis of IGWs in simulations of 5 M⊙ star model. Our results show that low frequency waves excited by core convection are strongly impacted by radiative effects as they propagate. In the upper layers of the simulation domain, we observe an increase of the temperature, likely due to heat added in these layers by IGWs damped by radiative diffusion. We show that nonlinear effects linked to large amplitude IGWs may be relevant just above the convective core. Both these effects are intensified by the artificial enhancement of the luminosity and radiative diffusivity. Our results also highlight that direct comparison between numerical simulations with enhanced luminosity and observations must be made with caution

Characterization of Multiple Groups of Data

In this paper we propose a new approach for computing characterizations of sets of data by means of partially defined Boolean functions. The main objective is to provide minimal sets of characters that allows the user to discriminate groups of Boolean data representing individuals described by means of presence or absence of characters. Compared to previous approaches, our algorithms are more efficient and are able to compute complete sets of solutions, which may be useful according to our underlying application domain in plant biology

ABCC6 is a basolateral plasma membrane protein

RATIONALE:: ABCC6 plays a crucial role in ectopic calcification; mutations of the gene cause pseudoxanthoma elasticum and general arterial calcification of infancy. To elucidate the role of ABCC6 in cellular physiology and disease, it is crucial to establish the exact subcellular localization of the native ABCC6 protein. OBJECTIVE:: In a recent article in Circulation Research, ABCC6 was reported to localize to the mitochondria-associated membrane and not the plasma membrane. As the suggested mitochondrial localization is inconsistent with published data and the presumed role of ABCC6, we performed experiments to determine the cellular localization of ABCC6 in its physiological environment. METHODS AND RESULTS:: We performed immunofluorescent labeling of frozen mouse and human liver sections, as well as primary hepatocytes. We used several different antibodies recognizing human and mouse ABCC6. Our results unequivocally show that ABCC6 is in the basolateral membrane of hepatocytes and is not associated with the mitochondria, mitochondria-associated membrane, or the endoplasmic reticulum. CONCLUSIONS:: Our findings support the model that ABCC6 is in the basolateral membrane, mediating the sinusoidal efflux of a metabolite from the hepatocytes to systemic circulation. © 2013 American Heart Association, Inc

Photochemical Organocatalytic Functionalization of Pyridines via Pyridinyl Radicals

We report a photochemical method for the functionalization of pyridines with radicals derived from allylic C–H bonds. Overall, two substrates undergo C–H functionalization to form a new C(sp2)–C(sp3) bond. The chemistry harnesses the unique reactivity of pyridinyl radicals, generated upon single-electron reduction of pyridinium ions, which undergo effective coupling with allylic radicals. This novel mechanism enables distinct positional selectivity for pyridine functionalization that diverges from classical Minisci chemistry. Crucial was the identification of a dithiophosphoric acid that masters three catalytic tasks, sequentially acting as a Brønsted acid for pyridine protonation, a single electron transfer (SET) reductant for pyridinium ion reduction, and a hydrogen atom abstractor for the activation of allylic C(sp3)–H bonds. The resulting pyridinyl and allylic radicals then couple with high regioselectivit

Two-dimensional simulations of internal gravity waves in a 5 M⊙M_{\odot} Zero-Age-Main-Sequence model

Main-sequence intermediate-mass stars present a radiative envelope that supports internal gravity waves (IGWs). Excited at the boundary with the convective core, IGWs propagate towards the stellar surface and are suspected to impact physical processes such as rotation and chemical mixing. Using the fully compressible time-implicit code MUSIC, we study IGWs in two-dimensional simulations of a zero-age-main-sequence 5 solar mass star model up to 91\% of the stellar radius with different luminosity and radiative diffusivity enhancements. Our results show that low frequency waves excited by core convection are strongly impacted by radiative effects as they propagate. This impact depends on the radial profile of radiative diffusivity which increases by almost 5 orders of magnitude between the centre of the star and the top of the simulation domain. In the upper layers of the simulation domain, we observe an increase of the temperature. Our study suggests that this is due to heat added in these layers by IGWs damped by radiative diffusion. We show that non-linear effects linked to large amplitude IGWs may be relevant just above the convective core. Both these effects are intensified by the artificial enhancement of the luminosity and radiative diffusivity, with enhancement factors up to $10^4$ times the realistic values. Our results also highlight that direct comparison between numerical simulations with enhanced luminosity and observations must be made with caution. Finally, our work suggests that thermal effects linked to the damping of IGWs could have a non-negligible impact on stellar structure.Comment: 15 pages, 10 figures, accepted for publication in MNRA

ProRule: a new database containing functional and structural information on PROSITE profiles

Motivation: Increase the discriminatory power of PROSITE profiles to facilitate function determination and provide biologically relevant information about domains detected by profiles for the annotation of proteins. Summary: We have created a new database, ProRule, which contains additional information about PROSITE profiles. ProRule contains notably the position of structurally and/or functionally critical amino acids, as well as the condition they must fulfill to play their biological role. These supplementary data should help function determination and annotation of the UniProt Swiss-Prot knowledgebase. ProRule also contains information about the domain detected by the profile in the Swiss-Prot line format. Hence, ProRule can be used to make Swiss-Prot annotation more homogeneous and consistent. The format of ProRule can be extended to provide information about combination of domains. Availability: ProRule can be accessed through ScanProsite at http://www.expasy.org/tools/scanprosite. A file containing the rules will be made available under the PROSITE copyright conditions on our ftp site (ftp://www.expasy.org/databases/prosite/) by the next PROSITE release. Contact: [email protected]