Search

Point Group (PG) symmetries play a fundamental role in many aspects of theoretical chemistry and computational materials science. With the objective to automatize the search of PG symmetry operations of generic atomic clusters, we present a new algorithm called Symmetry Operation FInder (SOFI). SOFI addresses the problem of identifying PG symmetry by framing it as a degenerate shape-matching problem, where the multiple solutions correspond to distinct symmetry operations. The developed algorithm is compared against three other algorithms dedicated to PG identification on a large set of atomic clusters. The results, along with some illustrative use cases, showcase the effectiveness of SOFI. The SOFI algorithm is released as part of the iterative rotations and assignments library, accessible at https://github.com/mammasmias/IterativeRotationsAssignments. [ABSTRACT FROM AUTHOR]

Saddle points on high-dimensional potential energy surfaces (PES) play a determining role in the activated dynamics of molecules and materials. Building on approaches dating back more than 50 years, many open-ended transition-state search methods have been developed to follow the direction of negative curvature from a local minimum to an adjacent first-order saddle point. Despite the mathematical justification, these methods can display a high failure rate: using small deformation steps, up to 80% of the explorations can end up in a convex region of the PES, where all directions of negative curvature vanish, while if the deformation is aggressive, a similar fraction of attempts lead to saddle points that are not directly connected to the initial minimum. In high-dimension PES, these reproducible failures were thought to only increase the overall computational cost, without having any effect on the methods' capacity to find all saddle points surrounding a minimum. Using activation-relaxation technique nouveau (ARTn), we characterize the nature of the PES around minima, considerably expanding on previous knowledge. We show that convex regions can lie on activation pathways and that not exploring beyond them can introduce significant bias in the saddle-point search. We introduce an efficient approach for traversing the convex regions, almost eliminating exploration failures, while multiplying by almost 10 the number of identified unique and connected saddle points as compared to the standard ARTn, thus underlining the importance of correctly handling convex regions for completeness of saddle point explorations. [ABSTRACT FROM AUTHOR]

The reaction of oxygen molecules on an oxidized silicon model-substrate is investigated using an efficient potential energy hypersurface exploration that provides a rich picture of the associated energy landscape, energy barriers, and insertion mechanisms. Oxygen molecules are brought in, one by one, onto an oxidized silicon substrate, and accurate pathways for sublayer oxidation are identified through the coupling of density functional theory to the activation relaxation technique nouveau, an open-ended unbiased reaction pathway searching method, allowing full exploration of potential energy surface. We show that strain energy increases with O coverage, driving the kinetics of diffusion at the Si/SiO2 interface in the interfacial layer and deeper into the bulk: at low coverage, interface reconstruction dominates while at high coverage, oxygen diffusion at the interface or even deeper into the bottom layers is favored. A changing trend in energetics is observed that favors atomic diffusions to occur at high coverage while they appear to be unlikely at low coverage. Upon increasing coverage, strain is accumulated at the interface, allowing the oxygen atom to diffuse as the strain becomes large enough. The observed atomic diffusion at the interface releases the accumulated strain, which is consistent with a layer-by-layer oxidation growth. [ABSTRACT FROM AUTHOR]

In Brazil, the circulation of hepatitis E virus (HEV) has been demonstrated in distinct groups of individuals and some animals, but its prevalence among individuals with human immunodeficiency virus (HIV) infection is unknown. This study aimed to assess the frequency of serological and molecular HEV markers in individuals infected with HIV from São Paulo, Brazil. Serum and plasma samples of 354 HIV-infected patients collected between 2007 and 2013 were included. All samples were tested for anti-HEV IgG and IgM antibodies and HEV RNA. Anti-HEV IgG and IgM antibodies were detected in 10.7% (38/354) and 1.4% (5/354) of the samples, respectively. Both antibodies were detected simultaneously in only two samples. HEV RNA was not detected in any sample. There was no significant correlation of anti-HEV serological status (positivity to anti-HEV IgG and/or IgM) with sex, age, CD4 T cell count, HIV viral load, antiretroviral therapy, liver enzyme levels, or coinfection with hepatitis B virus and/or hepatitis C virus. Our study provides serological evidence of past and recent HEV infections in HIV-infected patients from São Paulo, Brazil. However, the occurrence of ongoing HEV infection appears be a rare event in this population. [ABSTRACT FROM AUTHOR]

onvolution quadrature (CQ) methods have enjoyed tremendous interest in recent years as an efficient tool for solving time-domain wave problems in unbounded domains via bound-ary integral equation techniques. In this paper we consider CQ type formulations for the parallel space-time evaluation of multistep or stiffly accurate Runge-Kutta rules for the wave equation. In particular, we decouple the number of Laplace domain solves from the number of time steps. This allows us to overresolve in the Laplace domain by computing more Laplace domain solutions than there are time steps. We use techniques from complex approximation theory to analyze the error of the CQ approximation of the underlying time-stepping rule when overresolving in the Laplace do-main and show that the performance is intimately linked to the location of the poles of the solution operator. Several examples using boundary integral equation formulations in the Laplace domain are presented to illustrate the main results. [ABSTRACT FROM AUTHOR]

A tight-binding variable-charge model aimed at performing large-scale realistic simulations of bulk, surfaces and interfaces of aluminum oxides have been developed. This model is based on the charge equilibration (QEq) method and explicitly takes into account the mixed iono–covalent character of the metal–oxygen bond by means of a tight-binding analytical approach in the second-moment approximation of the electronic structure. The parameters of the model were optimized to reproduce structural and energetic properties of the α-Al 2 O 3 corundum structure at room temperature and pressure. The model exhibits a good transferability between five alumina polymorphs: corundum, Rh 2 O 3 (II)-type, perovskite (Pbnm), CaIrO 3 -type and U 2 S 3 -type structures. In this paper, we present results obtained by molecular dynamics for pressure ranging from 0 to 500 GPa. First, static relaxations reproduce satisfactorily experimental and ab initio results concerning the stability domains and transitions from corundum to Rh 2 O 3 (II) and then to CaIrO 3 -type structure when pressure increases. At higher pressure, the transition from CaIrO 3 to U 2 S 3 structure is also observed at a pressure significantly lower than that given ab initio . Molecular dynamics confirm these results and also predict a phase transition at about 400 GPa from corundum to a triclinic structure. [ABSTRACT FROM AUTHOR]

Résumé: Parmi les différents thèmes priorisés dans le programme régional de télémédecine, le soin en établissements d’hébergement pour personnes âgées dépendantes (EHPAD) a été choisi pour cette expérimentation. Le projet cible le parcours de la personne âgée, de plus de 75 ans, posant le problème d’une plaie chronique dans un contexte de dépendance et de polypathologie. Objectif: L’objectif de cette expérimentation est d’améliorer à la fois l’accès aux soins des personnes âgées et la continuité des soins ville/hôpital et de favoriser la formation des soignants. Méthodes: Cette expérimentation (septembre 2012 à septembre 2013) est basée sur la téléconsultation lors de laquelle l’équipe d’experts (gériatre, infirmière, ergothérapeute, diététicienne et secrétaire) intervient deux demi-journées par semaine au sein du pôle de gérontologie clinique (CHU Bordeaux, France). Après avoir obtenu le consentement du patient, le médecin traitant et l’équipe de l’EHPAD se connectent dans une salle virtuelle avec l’équipe du centre expert. Pour la structure demandeuse, cette connexion s’établit soit dans la chambre du patient à l’aide d’un chariot de télémédecine (EHPAD avec Wifi), soit depuis une salle dédiée (EHPAD sans Wifi). Suite à la téléconsultation, un compte rendu est écrit puis envoyé via une messagerie sécurisée à la structure demandeuse. Résultats: Au total, six EHPAD (en Gironde et Dordogne) ont été inclus dans ce projet. Les résultats préliminaires rapportent un total de 51 téléconsultations avec la prise en soins et le suivi d’escarres (57,9 %), d’ulcères trophiques vasculaires (26,3 %) et de plaies d’origine traumatique (15,8 %). Ces premiers résultats montrent que la télémédecine améliore de manière significative la cicatrisation des plaies et diminue les dépenses en pansements en réduisant le rythme des changements de pansements (p =0,005). Sans ces téléconsultations, les médecins généralistes auraient adressé leurs patients en consultation spécialisée dans 31,6 % des cas et en hospitalisation de jour dans 47,4 % des cas. Conclusion: Les enjeux de la télémédecine sont importants en gériatrie, notamment dans le suivi des personnes âgées avec des pathologies chroniques nécessitant des allers et retours répétés à l’hôpital. Une des perspectives est d’élargir les téléconsultations à tous les syndromes gériatriques (chutes, confusion, dénutrition, etc.) et d’assurer la formation continue aux professionnels de santé. L’outil peut également permettre le suivi des patients âgés par d’autres spécialistes afin d’assurer au mieux la continuité des soins. [Copyright &y& Elsevier]

The tight-binding variable-charge model SMTB-Q was used to study the properties of the (001) surfaces and ultra-thin films of the SrTiO3 perovskite. First, the bulk properties of SrTiO3 were successfully reproduced from a set of parameters independently determined for bulk SrO and TiO2. The formation energies, atomic relaxations and charge transfer for SrO- and TiO2-terminated SrTiO3 (001) surfaces were then derived from 0 to 1200K. The TiO2-terminated surface is more stable than the SrO-terminated surface by about 0.15jm‐2 under 500K. This difference decreases by a factor 3 at higher temperature. At 0K, the surface energies (ETiO2 =1.10jm‐2 and ESrO =1.20jm‐2) are in accordance with the mean value yielded by ab initio calculations. A strong Sr displacement towards the SrO-terminated surface (0.33Å) was observed in agreement with both experimental data and DFT calculations. In contrast, the other atomic relaxations included the Ti displacement towards the TiO2-terminated surface (0.13Å), are in good agreement with ab initio results but strongly differ from experimental data (≈0.00Å). The displacements of surface oxygen planes being small, one observes a splitting of the SrO and TiO2 surface planes by 0.30 and 0.13Å respectively. Moreover, the distance between the Sr and Ti planes is reduced by 19%. The charge transfers at the TiO2-terminated surface are comparable to those at the pure TiO2 surfaces (−0.18 and +0.14, for titanium and oxygen atoms respectively) leading to the increase of the Ti‐O bond covalency near the surface. At the SrO-terminated surface, we found negligible charge transfers as at the pure SrO(100) surface. Moreover, we studied the effect of a 1.66% compressive strain (corresponding to the STO/Si(001) lattice mismatch) on the relaxation of thin films from 2 to 40nm at 273K. The atomic surface relaxations are not significantly modified apart from the Sr‐Ti (resp. Ti‐Sr) distances which relaxed by 25%. The ratio between out-of-plane and in-plane lattice parameters is in good agreement with the elasticity theory for a thickness up to 5nm. Beyond 20nm thick the film is almost fully relaxed. [ABSTRACT FROM AUTHOR]

Abstract: Purposes: Helicobacter pylori (H. pylori) infection is a chronic gastric Gram-negative infection that increases with age. Acquired in childhood, H. pylori infection may induce a whole cascade of events leading to gastric pathologies such as peptic ulcer diseases, gastric precancerous lesions, and gastric lymphomas (MALT). The characteristics of the diagnosis and the treatment of this infection in geriatrics are thus particularly important to take into account. Main points: 1) The incidence of gastric and duodenal ulcers and their bleeding complications is increasing in old-aged populations. Clinical signs such as anorexia and malnutrition are proven to be excellent indications for endoscopic explorations in the elderly. NSAID-use and H. pylori infection were shown to be independent and unrelated risk factors for peptic ulcer and gastroduodenal bleeding in elderly subjects; 2) H. pylori infection diagnosis is difficult to realize in the very old population, and the urea breath test is the test which obtain the best performances in this population. Perspectives: Recent work showed the part played by H. pylori chronic infection in gastric aging and in appetite regulation in the elderly. Research tasks should be continued in this field in order to better understand the part played by this chronic infection in gastric aging and in other pathologies (i.e. neurological or cardiovascular diseases) in this population. [Copyright &y& Elsevier]