The correlation between ion beam/material interactions and practical FIB specimen preparation.

The focused ion beam (FIB) tool has been successfully used as both a stand alone analytical instrument and a means to prepare specimens for subsequent analysis by SEM, TEM, SIMS, XPS, and AUGER. In this work, special emphasis is given to TEM specimen preparation by the FIB lift-out technique. The fundamental ion/solid interactions that govern the FIB milling process are examined and discussed with respect to the preparation of electron transparent membranes. TRIM, a Monte Carlo simulation code, is used to physically model variables that influence FIB sputtering behavior. The results of such computer generated models are compared with empirical observations in a number of materials processed with an FEI 611 FIB workstation. The roles of incident ion attack angle, beam current, trench geometry, raster pattern, and target-material-dependent removal rates are considered. These interrelationships are used to explain observed phenomena and predict expected milling behaviors, thus increasing the potential for the FIB to be used more efficiently with reproducible results.     

NMR Studies of H2O: N-Phenyl (N-Phenyl-β-D-Glucopyranosylamine) Urokamide Interactions in Dimethyl Sulfoxide at two Fields

Abstract

During the course of NMR structural investigations of the title compound (N-phenyl uronamide) we noticed the presence of a strong H₂O activity-dependent NOE between the small amount of H₂O associated with the carbohydrate's hydroxyl protons in solutions of DMSO-d₆ . The -OH/H₂O off-diagonal t₁ slices displayed a NOESY τ_m-dependence similar to molecules (τ_c = 0.1–5 ns) experiencing slow exchange (1–10 s^?1). From T₁ data at two fields a τ_c for the title compound was calculated to be ca. 0.54 ns at 313 K. The -OH/H₂O exchange rate constant, K, increased from 0.32 to 11.14 s^?1 as the molar ratio of [H₂O]:[N-phenyl uronamide] increased from ca. 4.5 to 5.2. The latter finding indicated that the -OH/H₂O proton exchange process, which is strongly affected by the translational diffusion of H₂O, diminished as [H₂O] approached that which was inherently a complex in the crystalline structure (e.g., C₁₈H₂₀O₅N₂·4H₂O) and was, presumably, tightly hydrogen-bound to the -OH/NH funtional groups. To test this, the title compound was recrystallized from ethanol/2, 2-dimethoxypropane whereupon the bound H₂O was eliminated; the lack of H₂O induced a significant upfield shift in the resonance frequencies of all the exchangable (-OH Δδ=86.33Hz; -NH Δδ=67.84Hz) functional groups relative to the methine protons (CH Δδ=0.25Hz).     

MISTRAL: a transmission soft X‐ray microscopy beamline for cryo nano‐tomography of biological samples and magnetic domains imaging

The performance of MISTRAL is reported, the soft X‐ray transmission microscopy beamline at the ALBA light source (Barcelona, Spain) which is primarily dedicated to cryo soft X‐ray tomography (cryo‐SXT) for three‐dimensional visualization of whole unstained cells at spatial resolutions down to 30 nm (half pitch). Short acquisition times allowing for high‐throughput and correlative microscopy studies have promoted cryo‐SXT as an emerging cellular imaging tool for structural cell biologists bridging the gap between optical and electron microscopy. In addition, the beamline offers the possibility of imaging magnetic domains in thin magnetic films that are illustrated here with an example.     

Preconditioning of deep snowpack for off-road vehicle mobility

This paper addresses several preconditioning techniques for strengthening a deep snowpack in order to support vehicular loadings. The criteria imposed on preconditioning a deep snowpack were: (1) only light commercially-available vehicles or equipment could be used, (2) preconditioning would only be applied to the snow surface and (3) any additives to be used should be easily acquired in remote areas. Viable preconditioning techniques were first evaluated in the laboratory using artificial snow. The techniques explored were surface loading (surcharging), heating and mixing with additives (sand and straw) followed by surcharging. The properties of the laboratory-preconditioned snow were evaluated primarily in terms of footing penetration resistance and Rammsonde hardness. Based on the laboratory results, preconditioning of a deep natural snowpack was carried out. Surcharging the snowpack was achieved by a BV206 Carrier. The preconditioning techniques studied were surcharging, heating and mixing with additives (salt and straw). Various ageing periods were imposed. The load-carrying capacity of the preconditioned snowpack was evaluated by multipasses of two wheeled vehicles (Iltis and 5/4 ton truck). The results indicated that a soft deep snowpack can be preconditioned to the extent that it can support multipasses of wheeled vehicles.     

Predicting substrates by docking high-energy intermediates to enzyme structures

With the emergence of sequences and even structures for proteins of unknown function, structure-based prediction of enzyme activity has become a pragmatic as well as an interesting question. Here we investigate a method to predict substrates for enzymes of known structure by docking high-energy intermediate forms of the potential substrates. A database of such high-energy transition-state analogues was created from the KEGG metabolites. To reduce the number of possible reactions to consider, we restricted ourselves to enzymes of the amidohydrolase superfamily. We docked each metabolite into seven different amidohydrolases in both the ground-state and the high-energy intermediate forms. Docking the high-energy intermediates improved the discrimination between decoys and substrates significantly over the corresponding standard ground-state database, both by enrichment of the true substrates and by geometric fidelity. To test this method prospectively, we attempted to predict the enantioselectivity of a set of chiral substrates for phosphotriesterase, for both wild-type and mutant forms of this enzyme. The stereoselectivity ratios of the six enzymes considered for those four substrate enantiomer pairs differed over a range of 10- to 10,000-fold and underwent 20 switches in stereoselectivities for favored enantiomers, compared to the wild type. The docking of the high-energy intermediates correctly predicted the stereoselectivities for 18 of the 20 substrate/enzyme combinations when compared to subsequent experimental synthesis and testing. The possible applications of this approach to other enzymes are considered.