Aix-Marseille University

About: Aix-Marseille University is a education organization based out in Marseille, France. It is known for research contribution in the topics: Population & Galaxy. The organization has 24326 authors who have published 54240 publications receiving 1455416 citations. The organization is also known as: University Aix-Marseille & université d'Aix-Marseille.

Recent Advances and Perspectives on Nonadiabatic Mixed Quantum-Classical Dynamics.

Abstract: Nonadiabatic mixed quantum–classical (NA-MQC) dynamics methods form a class of computational theoretical approaches in quantum chemistry tailored to investigate the time evolution of nonadiabatic phenomena in molecules and supramolecular assemblies. NA-MQC is characterized by a partition of the molecular system into two subsystems: one to be treated quantum mechanically (usually but not restricted to electrons) and another to be dealt with classically (nuclei). The two subsystems are connected through nonadiabatic couplings terms to enforce self-consistency. A local approximation underlies the classical subsystem, implying that direct dynamics can be simulated, without needing precomputed potential energy surfaces. The NA-MQC split allows reducing computational costs, enabling the treatment of realistic molecular systems in diverse fields. Starting from the three most well-established methods—mean-field Ehrenfest, trajectory surface hopping, and multiple spawning—this review focuses on the NA-MQC dynamics...

Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

Abstract: Background The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5.

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

Abstract: The rapid evolution of 454 GS-FLX sequencing technology has not been accompanied by a reassessment of the quality and accuracy of the sequences obtained. Current strategies for decision-making and error-correction are based on an initial analysis by Huse et al. in 2007, for the older GS20 system based on experimental sequences. We analyze here the quality of 454 sequencing data and identify factors playing a role in sequencing error, through the use of an extensive dataset for Roche control DNA fragments. We obtained a mean error rate for 454 sequences of 1.07%. More importantly, the error rate is not randomly distributed; it occasionally rose to more than 50% in certain positions, and its distribution was linked to several experimental variables. The main factors related to error are the presence of homopolymers, position in the sequence, size of the sequence and spatial localization in PT plates for insertion and deletion errors. These factors can be described by considering seven variables. No single variable can account for the error rate distribution, but most of the variation is explained by the combination of all seven variables. The pattern identified here calls for the use of internal controls and error-correcting base callers, to correct for errors, when available (e.g. when sequencing amplicons). For shotgun libraries, the use of both sequencing primers and deep coverage, combined with the use of random sequencing primer sites should partly compensate for even high error rates, although it may prove more difficult than previous thought to distinguish between low-frequency alleles and errors.

How cholesterol interacts with membrane proteins: an exploration of cholesterol-binding sites including CRAC, CARC, and tilted domains

Abstract: The plasma membrane of eukaryotic cells contains several types of lipids displaying high biochemical variability in both their apolar moiety (e.g. the acyl chain of glycerolipids) and their polar head (e.g. the sugar structure of glycosphingolipids). Among these lipids, cholesterol is unique because its biochemical variability is almost exclusively restricted to the oxidation of its polar -OH group. Although generally considered the most rigid membrane lipid, cholesterol can adopt a broad range of conformations due to the flexibility of its isooctyl chain linked to the polycyclic sterane backbone. Moreover, cholesterol is an asymmetric molecule displaying a planar face and a rough  face. Overall, these structural features open up a number of possible interactions between cholesterol and membrane lipids and proteins, consistent with the prominent regulatory functions that this unique lipid exerts on membrane components. The aim of this review is to describe how cholesterol interacts with membrane lipids and proteins at the molecular/atomic scale, with special emphasis on transmembrane domains of proteins containing either the consensus cholesterol-binding motifs CRAC and CARC or a tilted peptide. Despite their broad structural diversity, all these domains bind cholesterol through common molecular mechanisms, leading to the identification of a subset of amino acid residues that are overrepresented in both linear and three-dimensional membrane cholesterol-binding sites.

B→Vℓ+ℓ− in the Standard Model from Light-Cone Sum Rules

Abstract: We present B q → ρ, B q → ω, B q → K ∗, B s → K ∗ and B s → ϕ form factors from light-cone sum rules (LCSR) at $$ \mathcal{O}\left({\alpha}_s\right) $$ for twist-2 and 3 and $$ \mathcal{O}\left({\alpha}_s^0\right) $$ for twist-4 with updated hadronic input parameters. Three asymptotic light-cone distribution amplitudes of twist-4 (and 5) are determined, necessary for the form factors to obey the equations of motion. It is argued that the latter constrain the uncertainty of tensor-to-vector form factor ratios thereby improving the prediction of zeros of helicity amplitudes of major importance for B → K ∗ll angular observables. We provide easy-to-use fits to the LCSR results, including the full error correlation matrix, in all modes at low q 2 as well as combined fits to LCSR and lattice results covering the entire kinematic range for B q → K ∗, B s → K ∗ and B s → ϕ. The error correlation matrix avoids the problem of overestimating the uncertainty in phenomenological applications. Using the new form factors and recent computations of non-factorisable contributions we provide Standard Model predictions for B → K ∗γ as well as B → K ∗l+l− and B s → ϕμ + μ − at low dilepton invariant mass. Employing our B → (ρ,ω) form factor results we extract the CKM element |V ub| from the semileptonic decays B → (ρ, ω)lν and find good agreement with other exclusive determinations.