Extensible Component Based Architecture for FLASH, A Massively Parallel, Multiphysics Simulation Code

FLASH is a publicly available high performance application code which has evolved into a modular, extensible software system from a collection of unconnected legacy codes. FLASH has been successful because its capabilities have been driven by the needs of scientific applications, without compromising maintainability, performance, and usability. In its newest incarnation, FLASH3 consists of inter-operable modules that can be combined to generate different applications. The FLASH architecture allows arbitrarily many alternative implementations of its components to co-exist and interchange with each other, resulting in greater flexibility. Further, a simple and elegant mechanism exists for customization of code functionality without the need to modify the core implementation of the source. A built-in unit test framework providing verifiability, combined with a rigorous software maintenance process, allow the code to operate simultaneously in the dual mode of production and development. In this paper we describe the FLASH3 architecture, with emphasis on solutions to the more challenging conflicts arising from solver complexity, portable performance requirements, and legacy codes. We also include results from user surveys conducted in 2005 and 2007, which highlight the success of the code.Comment: 33 pages, 7 figures; revised paper submitted to Parallel Computin

Hydrothermal, catalyst-free production of a cyclic dipeptide from lysine

The formation of cyclic dipeptides, 2,5-diketopiperazines (DKP), from lysine in aqueous solution was investigated at hydrothermal conditions (250 to 350 °C) without the addition of catalyst. The products obtained were analyzed by GC–MS combined with extensive $^{1}$H,$^{13}$C NMR analysis, after purification via preparative chromatography. The main product of the conversion of lysine, octahydrodipyrido[1,2-a:1\u27,2\u27-d]pyrazine-6,12(2H,6aH)-dione, was successfully isolated and identified. The purification/separation protocol is rapid, environmentally friendly, and highly efficient with excellent selectivity (81 wt%) in the oils obtained from the conversion of lysine at 300 °C. Performing the conversion step at higher temperatures or lysine concentrations led to the formation of complicated side products. Based on the evolution of key compounds during hydrothermal conversion of lysine, we propose a tentative mechanism for the formation of diketopiperazine. The technique presented in this work provides a novel catalyst-free pathway for the synthesis of DKP

ОБОБЩЕНИЕ РЕЗУЛЬТАТОВ ИССЛЕДОВАНИЙ МАГНИТНОЙ ВОСПРИИМЧИВОСТИ СОСТАВЛЯЮЩИХ БАЗАЛЬТОВОГО СЫРЬЯ

Объектом исследований являлись базальты Волыни, поскольку здесь ве-дется их интенсивная карьерная разработка. Внимание исследователей привле-кает уникальный состав базальтов и возможность их более рационального ис-пользования. В настоящее время базальт используется в основном как строи-тельный материал в виде щебня, в небольших количествах – для производства теплоизоляционной ваты. Однако исследования, выполненные геологами, уче-ными различных организаций, показали [1-4], что базальт является ценным ми-неральным сырьем и требует комплексной переработки для извлечения полез-ных компонентов, содержащихся в количествах, представляющих промышлен-ный интерес, и технологическую возможность их извлечения. Наличие приме-сей в массиве базальта в виде лавобрекчий и туфов не снижает актуальности и ценности идеи комплексной переработки, поскольку эти ингредиенты в своем составе содержат те же полезные компоненты, что и базальт. Основными из них являются самородная медь, железо и титан [4]. Более глубокие исследования показали, что в них содержатся окислы меди, редкие и ценные металлы, извле-чение которых требует более тонких технологий

ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA

The cytosolic antiviral innate immune sensor RIG-I distinguishes 5' tri- or diphosphate containing viral double-stranded (ds) RNA from self-RNA by an incompletely understood mechanism that involves ATP hydrolysis by RIG-I's RNA translocase domain. Recently discovered mutations in ATPase motifs can lead to the multi-system disorder Singleton-Merten Syndrome (SMS) and increased interferon levels, suggesting misregulated signaling by RIG-I. Here we report that SMS mutations phenocopy a mutation that allows ATP binding but prevents hydrolysis. ATPase deficient RIG-I constitutively signals through endogenous RNA and co-purifies with self-RNA even from virus infected cells. Biochemical studies and cryo-electron microscopy identify a 60S ribosomal expansion segment as a dominant self-RNA that is stably bound by ATPase deficient RIG-I. ATP hydrolysis displaces wild-type RIG-I from this self-RNA but not from 5' triphosphate dsRNA. Our results indicate that ATP-hydrolysis prevents recognition of self-RNA and suggest that SMS mutations lead to unintentional signaling through prolonged RNA binding

ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA

The cytosolic antiviral innate immune sensor RIG-I distinguishes 5' tri- or diphosphate containing viral double-stranded (ds) RNA from self-RNA by an incompletely understood mechanism that involves ATP hydrolysis by RIG-I's RNA translocase domain. Recently discovered mutations in ATPase motifs can lead to the multi-system disorder Singleton-Merten Syndrome (SMS) and increased interferon levels, suggesting misregulated signaling by RIG-I. Here we report that SMS mutations phenocopy a mutation that allows ATP binding but prevents hydrolysis. ATPase deficient RIG-I constitutively signals through endogenous RNA and co-purifies with self-RNA even from virus infected cells. Biochemical studies and cryo-electron microscopy identify a 60S ribosomal expansion segment as a dominant self-RNA that is stably bound by ATPase deficient RIG-I. ATP hydrolysis displaces wild-type RIG-I from this self-RNA but not from 5' triphosphate dsRNA. Our results indicate that ATP-hydrolysis prevents recognition of self-RNA and suggest that SMS mutations lead to unintentional signaling through prolonged RNA binding

COSIMA-Rosetta calibration for in-situ characterization of 67P/Churyumov-Gerasimenko cometary inorganic compounds

20 pages, 3 figures, 5 tablesInternational audienceCOSIMA (COmetary Secondary Ion Mass Analyser) is a time-of-flight secondary ion mass spectrometer (TOF-SIMS) on board the Rosetta space mission. COSIMA has been designed to measure the composition of cometary dust grains. It has a mass resolution m/{\Delta}m of 1400 at mass 100 u, thus enabling the discrimination of inorganic mass peaks from organic ones in the mass spectra. We have evaluated the identification capabilities of the reference model of COSIMA for inorganic compounds using a suite of terrestrial minerals that are relevant for cometary science. Ground calibration demonstrated that the performances of the flight model were similar to that of the reference model. The list of minerals used in this study was chosen based on the mineralogy of meteorites, interplanetary dust particles and Stardust samples. It contains anhydrous and hydrous ferromagnesian silicates, refractory silicates and oxides (present in meteoritic Ca-Al-rich inclusions), carbonates, and Fe-Ni sulfides. From the analyses of these minerals, we have calculated relative sensitivity factors for a suite of major and minor elements in order to provide a basis for element quantification for the possible identification of major mineral classes present in the cometary grains

Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters

Antigene RNAs (agRNAs) are small RNA duplexes that target non-coding transcripts rather than mRNA and specifically suppress or activate gene expression in a sequence-dependent manner. For many applications in vivo, it is likely that agRNAs will require chemical modification. We have synthesized agRNAs that contain different classes of chemical modification and have tested their ability to modulate expression of the human progesterone receptor gene. We find that both silencing and activating agRNAs can retain activity after modification. Both guide and passenger strands can be modified and functional agRNAs can contain 2′F-RNA, 2′OMe-RNA, and locked nucleic acid substitutions, or combinations of multiple modifications. The mechanism of agRNA activity appears to be maintained after chemical modification: both native and modified agRNAs modulate recruitment of RNA polymerase II, have the same effect on promoter-derived antisense transcripts, and must be double-stranded. These data demonstrate that agRNA activity is compatible with a wide range of chemical modifications and may facilitate in vivo applications

Carbon-rich dust in comet 67P/Churyumov-Gerasimenko measured by COSIMA/Rosetta

Cometary ices are rich in CO2, CO and organic volatile compounds, but the carbon content of cometary dust was only measured for the Oort Cloud comet 1P/Halley, during its flyby in 1986. The COmetary Secondary Ion Mass Analyzer (COSIMA)/Rosetta mass spectrometer analysed dust particles with sizes ranging from 50 to 1000 μm, collected over 2 yr, from 67P/Churyumov-Gerasimenko (67P), a Jupiter family comet. Here, we report 67P dust composition focusing on the elements C and O. It has a high carbon content (atomic |${\rm{C}}/{\rm{Si}} = 5.5{\rm{\ }}_{ - 1.2}^{ + 1.4}\ \ {\rm{on\ average}}$ |⁠) close to the solar value and comparable to the 1P/Halley data. From COSIMA measurements, we conclude that 67P particles are made of nearly 50 per cent organic matter in mass, mixed with mineral phases that are mostly anhydrous. The whole composition, rich in carbon and non-hydrated minerals, points to a primitive matter that likely preserved its initial characteristics since the comet accretion in the outer regions of the protoplanetary disc.</p