SUPRENUM: System essentials and grid applications

The SUPRENUM idea, the project, and the system has generally been described and presented in several papers. There is also a great deal of more detailed technical papers describing SUPRENUM as a whole or certain elements of it.

Here we want to give only a very general and rough survey on the essentials of the SUPRENUM system in order to enable the reader to categorize and understand the more specific SUPRENUM papers in this special issue.

Most of the supercomputer applications today are based on grid or grid-like data structures. Grid applications play also an essential role in the SUPRENUM development: in the top-down design of the architecture, in the programming environment, in the parallelization concept of algorithms, and, of course, in the application software development itself. We therefore place some emphasis on this grid orientation in our presentation.     

Comparison of Different Mass Spectrometry Workflows for the Proteomic Analysis of Tear Fluid

The tear film is a multi-layer fluid that covers the corneal and conjunctival epithelia of the eye and provides lubrication, nutrients, and protection from the outside environment. Tear fluid contains a high concentration of proteins and has thus been recognized as a potential source of biomarkers for ocular disorders due to its proximity to disease sites on the ocular surface and the non-invasive nature of its collection. This is particularly true in the case of dry eye disease, which directly impacts the tear film and its components. Proteomic analysis of tear fluid is challenging mainly due to the wide dynamic range of proteins and the small sample volumes. However, recent advancements in mass spectrometry have revolutionized the field of proteomics enabling unprecedented depth, speed, and accuracy, even with small sample volumes. In this study using the Orbitrap Fusion Tribrid mass spectrometer, we compared four different mass spectrometry workflows for the proteomic analysis of tear fluid collected via Schirmer strips. We were able to establish a method of in-strip protein digestion that identified >3000 proteins in human tear samples from 11 healthy subjects. Our method offers a significant improvement in the number of proteins identified compared to previously reported methods without pooling samples.     

Heterogeneous Enantioselective Hydrogenation of Activated Ketones Catalyzed by Modified Pt‐Catalysts: A Systematic Structure‐Selectivity Study

A systematic structure‐selectivity study was carried out for the enantioselective hydrogenation of activated ketones with chirally modified Pt/Al₂O₃ catalysts. For this, 18 modifiers containing an extended aromatic system able to form a strong adsorption complex with the Pt surface, and a suitable chiral group with an amino function capable to interact with the keto group of the substrate ( HCd, Qd, HCn, Qn , and semi‐synthetic derivatives, as well as synthetic analogues) were prepared and tested on 8 different activated ketones in AcOH and toluene under standard conditions. It was found that relatively small structural changes of the substrate and/or modifier structures strongly affected the enantioselectivity, and that no “best” modifier exists for all substrates. The highest ees for all substrates were obtained with quinuclidine‐derived modifiers in combination with naphthalene or quinoline rings, either in AcOH (substrates 1 – 5 and 8 , all carrying an sp³ carbon next to the keto group) or toluene ( 6 and 7 , with an sp² carbon next to the ketone). The presence and nature of the substituent R' at the quinuclidine significantly affected the ee (positive and negative effects). Certain combinations of an aromatic system and an amino function were preferred: For the quinuclidine moiety, quinoline and to a somewhat lesser extent naphthalene were a better match, while for the pyrrolidinylmethyl group anthracene was better suited. Methylation of the OH group often had a positive effect for hydrogenations in AcOH but not in toluene. With the exception of 8 , higher ees were obtained for the Cd / Qn series [leading to (R)‐products] than for the Cn / Qd series [leading to (S)‐products]. In several cases, opposite structure‐selectivity trends were detected when comparing reactions in toluene and AcOH, indicating a significant influence of the solvent.     

Easily made and handled carbon nanocones for scanning tunneling microscopy and electroanalysis

Well-formed carbon nanocones at the ends of micrometer-diameter carbon fibers (CFs) were fashioned into functional tips for scanning tunneling microscopy (STM) and miniaturized voltammetric sensors. Sharpening of single graphite filaments was achieved by simple DC electrochemical etching in 0.1 N NaOH. Operated as STM tips, pointed CFs resolved in air the contour and surface morphology of a nanoscopic Au line pattern and imaged in vacuum a Si (1 1 1) surface with clear atomic resolution. Subjecting already etched CFs to tip-sparing insulation with electrodeposited paint produced conical carbon ultramicroelectrodes (UMEs) with effective radii down to about 900 nm. Comparative cyclic voltammetry trials in alkaline, neutral and acidic solutions showed that the conical carbon UME’s had a wider practical potential window for electroanalytic applications than, for instance, Pt disk UMEs. The CF-based conical sensors described here are exceptionally easy to make with simple laboratory equipment and perform well in STM topography imaging and voltammetry. The inherent simplicity of sensor production widens the field of potential users, and offers clear advantages over existing types of UMEs, in particular those based on carbon nanotubes, which are especially hard to handle in an optical microscope setting.     

Nitrate Radicals in Tropospheric Chemistry

Nitrate radicals are being recognized as key intermediates in a growing list of important chemical processes in the atmosphere. Here, the role of nitrate radicals (NO₃) in tropospheric chemistry is discussed, with special emphasis on results from field measurements, most of which have been made by differential optical absorption spectroscopy (DOAS), with matrix-isolation electron spin resonance being an alternative technique. Nitrate radicals were observed in the atmosphere at peak mixing ratios of 350 ppt. Long-term observation of NO₃ shows that 24-h averages in rural air masses are closer to a few ppt. Nevertheless, the NO₃ radical plays an important role in the non-photochemical conversion of NO_x to HNO₃. Also, NO₃ is a strong oxidizing agent and initiates the night-time removal of atmospheric trace species such as olefins, aromatic hydrocarbons, and organic sulfur compounds. Finally, night-time peroxy radical production and release of reactive halogen species from sea salt aerosol might be initiated by NO₃ reactions.     

Monoclinic Zirconia Bodies by Thermoplastic Ceramic Extrusion

Two ultrafine, undoped ZrO₂ powders with median primary particle sizes of 9 and 25 nm were used to prepare ceramic suspensions for thermoplastic extrusion. The organic vehicle consisted of an industrial-grade poly(ethylene- co -vinyl acetate) (EVA) or polyethylene (PE-HD) and decanoic acid as a dispersing agent. The powder volume loadings achieved were 44% and 52% by volume for the two powders, respectively. The amount of dispersant needed was calculated from a new model based on available chemisorption sites on the powder surface. Mixing and extrusion were conducted using a conventional modular plastic processing unit. Green bodies were dewaxed up to 450°C in an inert atmosphere and sintered to full density in air at 1060° and 1100°C, respectively. Analysis of the ceramic phase content and the microstructure of the bodies is presented.     

The Estimation of the Molecular Weight of Polytetrafluoroethylene Based on the Heat of Crystallisation. A Comment on Suwa's Equation

Summary: The influence of number‐average molecular weight ranging from 1.4 · 10⁴ to 1.2 · 10⁶ g/mol on the thermal behaviour of polytetrafluoroethylene (PTFE) has been studied. Samples have been prepared by radiation‐induced degradation of commercial PTFE. The molecular weight has been calculated using end‐group concentration determined by infrared (IR) spectroscopy and ¹⁹F solid‐state nuclear magnetic resonance (NMR) spectroscopy. Melting and crystallisation heats were investigated by differential scanning calorimetry (DSC). The results have been discussed with respect to quantitative relationships between number‐average molecular weight and heat of crystallisation of PTFE described in the literature. The molecular weight calculated from Suwa's equation, which is often used in the literature, has been found to be too low.

Concentration of end‐groups and the molecular weight of PTFE versus the irradiation dose.     

Facile preparation of water-soluble fluorescent gold nanoclusters for cellular imaging applications

We report a facile strategy to synthesize water-soluble, fluorescent gold nanoclusters (AuNCs) in one step by using a mild reductant, tetrakis(hydroxymethyl)phosphonium chloride (THPC). A zwitterionic functional ligand, D-penicillamine (DPA), as a capping agent endowed the AuNCs with excellent stability in aqueous solvent over the physiologically relevant pH range. The DPA-capped AuNCs displayed excitation and emission bands at 400 and 610 nm, respectively; the fluorescence quantum yield was 1.3%. The effect of borohydride reduction on the optical spectra and X-ray photoelectron spectroscopy (XPS) results indicated that the AuNC luminescence is closely related to the presence of Au(I) on their surfaces. In a first optical imaging application, we studied internalization of the AuNCs by live HeLa cells using confocal microscopy with two-photon excitation. A cell viability assay revealed good biocompatibility of these AuNCs. Our studies demonstrate a great potential of DPA-stabilized AuNCs as fluorescent nanoprobes in bioimaging and related applications.     

Magnetite core-shell nano-composites with chlorine functionality: preparation by miniemulsion polymerization and characterization

Magnetic composite particles with a magnetic core consisting of superparamagnetic iron oxide and a cover layer of hydrophobic polyvinylbenzylchloride are described. The magnetite was prepared by precipitation starting with mixed iron II and iron III salts and coating of the solid with oleic acid. The coating is conducted via the liquid–liquid phase transfer. Thereby oleic acid adsorbed on the magnetite surface. In a second step the oleic acid treated magnetite was coated with polyvinylbenzylchloride in a miniemulsion polymerization to get a protective layer. The obtained magnetite core-shell nano-composites with chlorine functionality were characterized by different methods: particle size measurement, acid treatment, iron content, morphology and elemental profiles across the composite particles diameter. The test result reveals the binding of the iron oxide inside the composites which can be also recognize in TEM pictures.