Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns

We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model, as well as the BIBEE approximation to BEM. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. The applications demonstrated include the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of lysozyme molecules. The parallel scalability of the software was studied in a cluster at the Nagasaki Advanced Computing Center, using 128 nodes, each with 4 GPUs. Delicate tuning has resulted in strong scaling with parallel efficiency of 0.8 for 256 and 0.5 for 512 GPUs. The largest application run, with over 20 million atoms and one billion unknowns, required only one minute on 512 GPUs. We are currently adapting our BEM software to solve the linearized Poisson-Boltzmann equation for dilute ionic solutions, and it is also designed to be flexible enough to be extended for a variety of integral equation problems, ranging from Poisson problems to Helmholtz problems in electromagnetics and acoustics to high Reynolds number flow

Inhomogeneous molecular ring around the B[e] supergiant LHA 120-S 73

We aim to improve our knowledge on the structure and dynamics of the circumstellar disk of the LMC B[e] supergiant LHA 120-S 73. High-resolution optical and near-IR spectroscopic data were obtained over a period of 16 and 7 years, respectively. The spectra cover the diagnostic emission lines from [CaII] and [OI], as well as the CO bands. These features trace the disk at different distances from the star. We analyzed the kinematics of the individual emission regions by modeling their emission profiles. A low-resolution mid-infrared spectrum was obtained as well, which provides information on the composition of the dusty disk. All diagnostic emission features display double-peaked line profiles, which we interpret as due to Keplerian rotation. We find that LHA 120-S 73 is surrounded by at least four individual rings of material with alternating densities (or by a disk with strongly non-monotonic radial density distribution). Moreover, we find that the molecular ring must have gaps or at least strong density inhomogeneities, or in other words, a clumpy structure. The mid-infrared spectrum displays features of oxygen- and carbon-rich grain species, which indicates a long-lived, stable dusty disk. We cannot confirm the previously reported high value for the stellar rotation velocity. The line profile of HeI 5876 A is strongly variable in both width and shape and resembles of those seen in non-radially pulsating stars. A proper determination of the real underlying stellar rotation velocity is hence not possible. The existence of multiple stable and clumpy rings of alternating density recalls ring structures around planets. Although there is currently insufficient observational evidence, it is tempting to propose a scenario with one (or more) minor bodies or planets revolving around LHA 120-S 73 and stabilizing the ring system, in analogy to the shepherd moons in planetary systems.Comment: 14 pages, 13 figure, accepted for pulication in A&

Usual energy and macronutrient intakes in 2-9-year-old European children

OBJECTIVE: Valid estimates of population intakes are essential for monitoring trends as well as for nutritional interventions, but such data are rare in young children. In particular, the problem of misreporting in dietary data is usually not accounted for. Therefore, this study aims to provide accurate estimates of intake distributions in European children. DESIGN: Cross-sectional setting-based multi-centre study. SUBJECTS: A total of 9560 children aged 2-9 years from eight European countries with at least one 24-h dietary recall (24-HDR). METHODS: The 24-HDRs were classified in three reporting groups based on age- and sex-specific Goldberg cutoffs (underreports, plausible reports, overreports). Only plausible reports were considered in the final analysis (N=8611 children). The National Cancer Institute (NCI)-Method was applied to estimate population distributions of usual intakes correcting for the variance inflation in short-term dietary data. RESULTS: The prevalence of underreporting (9.5%) was higher compared with overreporting (3.4%). Exclusion of misreports resulted in a shift of the energy and absolute macronutrient intake distributions to the right, and further led to the exclusion of extreme values, that is, mean values and lower percentiles increased, whereas upper percentiles decreased. The distributions of relative macronutrient intakes (% energy intake from fat/carbohydrates/proteins) remained almost unchanged when excluding misreports. Application of the NCI-Method resulted in markedly narrower intake distributions compared with estimates based on single 24-HDRs. Mean percentages of usual energy intake from fat, carbohydrates and proteins were 32.2, 52.1 and 15.7%, respectively, suggesting the majority of European children are complying with common macronutrient intake recommendations. In contrast, total water intake (mean: 1216.7 ml per day) lay below the recommended value for >90% of the children. CONCLUSION: This study provides recent estimates of intake distributions of European children correcting for misreporting as well as for the daily variation in dietary data. These data may help to assess the adequacy of young children's diets in Europe

Facies generadoras de carbón en el Westfaliense superior de la Cuenca Carbonífera Central Asturiana

La Cuenca Carbonífera Central Asturiana constituye una cuenca de antepais individualizada en la Zona Cantábrica durante el Carbonifero Superior coincidiendo con la máxima actividad de la orogenia Hercinica. Durante el Westfaliense, se acumularon en ella importantes volúmenes de material clástico procedentes de los relieves en elevación situados al W. Los abanicos aluviales costeros constituyeron unos sistemas deposicionales muy eficientes en la dispersión de estos materiales, generaron extensas cuñas clásticas en relación con las cuales se originaron capas de carbón explotables. En este trabajo se estudian varios litosomas de edad Westfaliense Superior que representan episodios progradantes de estos sistemas sobre ambientes marinos someros v de transición. El análisis e interpretación de sus facies y geometrías permite la reconstrucción de las condiciones ambientales en que se generaron las capas de carbón asociadas a cada una de las unidades estudiadas. Estas se desarrollaron: 1) en zonas marginales a los lóbulos progradantes y zonas interlóbulos y 2) sobre los mismos una vez que éstos fueron abandonados y previamente a su enterramiento

Contribution to phaneroptical study in andalusian hound dog breed

We have studied the type of hair and the coat colour of the Andalusian Hound breed with a view to characterise and typify the nine varieties recognised in the racial pattern. We have concluded the existence of highly significant differences between sizes for the variables type of hair and coat colour, what it is confirming the present reproductive separation and isolation of each variety in the management of the breed book. At the same time we have developed a study of the variable related to the mouth form obtaining the majority of the animal presenting correct mouth caught, but the defect prognatism appear in all the varieties, while the enogmatism only appear in the medium size varieties.Se estudia el tipo de pelo y la coloración de la capa dentro de la raza Podenco Andaluz con vistas a conseguir la caracterización y tipificación de las nueve variedades reconocidas en su patrón racial. Se concluye la existencia de diferencias altamente significativas entre la variable talla y las variables tipo de pelo y color de la capa lo que confirma el actual tratamiento en la separación y aislamiento reproductivo en cada una de las variedades dentro de la gestión de los registros genealógicos de la raza. Asimismo se realiza un estudio de las variables fanerópticas de la boca obteniendo una mayoría de animales que presentan un tipo de mordidas correctas si bien el defecto de mordida prognata está presente en todas las variedades mientras que el enogmatismo sólo aparece en las correspondientes a la talla media