Metacomputing in practice: a distributed compute server for pharmaceutical industry

We describe a distributed high-performance compute server that has been implemented for running compute-intensive applications on a mixture of HPC systems interconnected by Inter-and Intranet. With a practical industrial background, our work focusses on high availability, efficient job load balancing, security, and the easy integration of HPC computing into the daily work-flow at pharmaceutical companies.

The work was done in the course of the ESPRIT project P A Distributed Pharmaceutical Application Server The client software is implemented in Java. All results are displayed in a web browser and can be forwarded to the next stage of applications used in the drug design cycle. The server software handles the job load balancing between the participating HPC nodes and is capable of managing multi-site applications.

Our environment currently supports four key applications that are used in rational drug design and drug target identification. They range from the automatic functional annotation of protein sequences to three-dimensional protein structure prediction tools and protein comparison applications.     

Note on the interpretation of electroluminescence images using their spectral information

We show how to use the reciprocity between electroluminescence and solar cell quantum efficiency for the simulation and interpretation of electroluminescence images. The analysis of the spectral properties of the electroluminescence images obtained by using different short- and long-pass filters yields information about surface recombination velocity, bulk diffusion length and reflection of the back side in flat and textured solar cells.     

Potent Inhibition of Acid Sphingomyelinase by Phosphoinositide Analogues

The different mammalian sphingomyelinases are involved in cell regulation, apoptosis and inflammatory events. Recent reports suggest pharmacological potential especially for inhibitors of the acid sphingomyelinase. Phosphatidyl inositol‐3,5bisphosphate (PtdIns3,5P₂) is the most potent selective acid sphingomyelinase inhibitor known to date. In the present study, we synthesized analogues of PtdIns3,5P₂ for initial structure–activity‐relationship (SAR) studies. We identified an inhibitor that is easy to synthesize, that has superior chemical and biophysical properties when compared to PtdIns3,5P₂ and that should be stable against virtually all phospholipases. Last but not least, the new inhibitor partially protected cells from dexamethasone‐induced cell death.     

Imaging-sonar observations of salmonid interactions with a vertical axis instream turbine

Anthropogenic activities and their influences on aquatic systems is an important topic, especially considering the growing interest in using the earth's resources in a sustainable way. One of those anthropogenic activities is the introduction of renewable technologies into the aquatic environment such as instream turbines. Environmental studies around those technologies are often still ongoing due to their novelty. During the spring of 2018, juvenile individuals of two salmonid species, Atlantic salmon and brown trout were released upstream a vertical axis instream turbine in the river Dal (Dalälven) in eastern Sweden. The aim of this study was to investigate the swimming behavior of the salmonids around a small-scale prototype vertical axis instream turbine. The swimming pattern and the possible response of avoiding the vertical axis instream turbine were documented with a multi beam sonar. A control area, next to the turbine, was used as reference. No consistent results were shown for trout as they were passing the control area with a statistically high variation, and specimens were rarely observed in proximity of the turbine, neither if the turbine was operating nor at stand still. Salmon clearly avoided the operating turbine, but did not avoid the turbine when it was at stand still, and was often observed swimming straight through the turbine area. These findings indicate that operating this type of instream turbine in a river affects the swimming behavior of Atlantic salmon but is unlikely to affect its migration paths. For brown trout, the statistical results are inconclusive, although data indicate a response of avoiding the turbine. The species are in little risk to suffer physical harm as no fish entered the rotating turbine, despite very turbid water conditions.     

WDX-Analysis of the New Superconductors RO1−x F x FeAs and Its Consequences on the Electronic Phase Diagram

Polycrystalline samples of RO_1−x F _x FeAs (0≤x≤0.25) (R=La, Sm, Gd) were investigated by wavelength-dispersive X-ray spectroscopy (WDX) in the electron microscope to determine the composition of the samples, in particular the fluorine content. It was found that the measured fluorine content can deviate considerably from the initial weight. In the lanthanum compound LaO_1−x F _x FeAs, we found good agreement mainly for x≥0.05, but for x<0.05 the fluorine hardly goes into the sample. For the samarium compound we measured less than half the fluorine in the sample as initially weighed at all fluorine concentrations. These measured values are taken into account when drawing the electronic phase diagrams of LaO_1−x F _x FeAs and SmO_1−x F _x FeAs. This leads to a more consistent picture of both of the diagrams in comparison to the plot of the initial weight.     

Effects of Zwitterionic buffers on sorption of ferrous iron at goethite and its oxidation by CCl4

A major factor which controls sorption and oxidation of Fe(II) at the mineral-water interface is pH, hence buffers are commonly used to control pH in experimental studies. Here, we examined the effects of widely used organic buffers (3-morpholinopropane-1-sulfonic acid (MOPS) and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES)) on Fe(II) uptake and oxidation by CCl(4) in aqueous suspensions of goethite. Significant sorption of these zwitterionic buffers occurred only at Fe(II)-loaded goethite but not at native goethite. The addition of MOPS and HEPES caused substantial release of Fe(II) from goethite, retarded the oxidation of surface-bound Fe(II) by CCl(4) and changed the reaction pathway as indicated by lower yields of CHCl(3). To explore electrostatic and steric contributions of MOPS and HEPES to the observed phenomena we studied sorption and competitive effects of model sorbates (Ca(2+), sulfonates) which suggest the formation of a complex between surface-bound Fe(II) and MOPS or HEPES. Our study shows for the first time that these frequently used zwitterionic organic buffers may interfere significantly with the surface chemistry and thus with redox reactions of Fe(II) at goethite. Hence, kinetic or mechanistic information obtained in such systems requires careful interpretation.     

Hydrodynamische Einlauflänge und Widerstandsgesetz von reibungsmindernden kationschen Tensidlösungen

Zusammenfassung Durch Zugabe geeigneter Tensidsysteme in Wasser kann der Str?mungsdruckverlust in geraden Rohren erheblich gesenkt werden. Die diesem Effekt zugrunde liegenden Mechanismen wurden in früheren Arbeiten eingehend diskutiert. In dieser Arbeit werden neue Ergebnisse vorgestellt, die sowohl die Bestimmung der hydrodynamischen Einlaufl?nge als auch die Ermittlung der Widerstandsbeiwerte im ausgebildeten Str?mungszustand erm?glichen. Für den Bereich der ausgebildeten Rohrstr?mung wird eine neue Berechnungsgleichung vorgeschlagen. Durch Erweiterung der bisherigen Modellvorstellungen ergibt sich ein Widerstandsgesetz für den gesamten Wirkungsbereich des Tensids. Die Ergebnisse stützen sich auf Untersuchungen mit zwei verschiedenen Additivsystemen, bei denen die Parameter Str?mungsgeschwindigkeit, Temperatur und Einsatzkonzentration variiert wurden.