Accelerating Scientific Discovery Through Computation and Visualization III. Tight-Binding Wave Functions for Quantum Dots

This is the third in a series of articles that describe, through examples, how the Scientific Applications and Visualization Group (SAVG) at NIST has utilized high performance parallel computing, visualization, and machine learning to accelerate scientific discovery. In this article we focus on the use of high performance computing and visualization for simulations of nanotechnology.     

Water Content and Water Evolution from Reaction-Bonded Aluminum Oxide (RBAO) Powder Precursors

Water evolution behavior from reaction-bonded aluminum oxide (RBAO) powder precursor was studied by the Carl-Fischer titration method. RBAO mixtures were milled for 4 and 8 h in absolute ethanol and water–ethanol mixtures containing 5 and 10 vol% water. The water content was then determined under dynamic heating conditions from 20°C to 250°C and static heating at 250°C. When the aluminum content is increased from 30 to 60 vol%, the water content of the milled powder precursor mixtures also increased. The higher water contents observed in powders milled in absolute ethanol are discussed in terms of the possible interaction of the ethanol with the surface of the aluminum particles.     

Modelling and simulation of the nonlinear behaviour of paper: A cellular materials approach

Paper is a stochastic network of fibres, water and additives, and in that sense it may be envisaged as a composite material. Since fibres are much longer than the thickness of the paper sheet, the network is planar and almost two-dimensional. The two-dimensional structure governs many paper properties but the three-dimensional porous structure is also important. Insight into the structural changes that take place when paper is compressed in the paper machine may be gained by modelling and simulation of its viscoelastoplastic behaviour. The present work describes a mathematical model based on the cellular solids theory, characterising the nonlinear rheologic behaviour of the material. This approach results in an unsteady state problem and the resulting set of ODEs is solved by means of the DLSODES subroutine, which uses an integrator based in the Gear method. Experiments were conducted on a laboratory-scale dynamic press in order to validate the mechanical model.     

Reactivity between La(Sr)FeO3 cathode,doped CeO2 interlayer and yttria-stabilized zirconia electrolyte for solid oxide fuel cell applications

Detailed X-ray diffraction (XRD) analysis of two different Sr-doped LaFeO₃ cathodes, YSZ electrolyte and two Sm/Gd-doped CeO₂ interlayer and their mixtures were used to evaluate the formation of undesired secondary reaction compounds. The analysis of room temperature X-ray diffraction data of the mixtures indicates the crystallization of strontium and/or lanthanum zirconates between the cathode and the electrolyte materials and no detected reaction between the cathode and the interlayer materials.     

An Adaptive Programming Model for Fault-Tolerant Distributed Computing

The capability of dynamically adapting to distinct runtime conditions is an important issue when designing distributed systems where negotiated quality of service (QoS) cannot always be delivered between processes. Providing fault tolerance for such dynamic environments is a challenging task. Considering such a context, this paper proposes an adaptive programming model for fault-tolerant distributed computing, which provides upper-layer applications with process state information according to the current system synchrony (or QoS). The underlying system model is hybrid, composed by a synchronous part (where there are time bounds on processing speed and message delay) and an asynchronous part (where there is no time bound). However, such a composition can vary over time, and, in particular, the system may become totally asynchronous (e.g., when the underlying system QoS degrade) or totally synchronous. Moreover, processes are not required to share the same view of the system synchrony at a given time. To illustrate what can be done in this programming model and how to use it, the consensus problem is taken as a benchmark problem. This paper also presents an implementation of the model that relies on a negotiated quality of service (QoS) for communication channels     

Emergent societies: advanced IT support of crisis relief missions

A novel distributed control ideology and technology is described for the management of advanced crisis relief missions. The approach is based on the installation of a universal “social” module in massively wearable electronic devices, such as laptops and mobile phones, which can collectively interpret a spatial scenario language, exchange high-level program code (waves) and data, and control other modules in parallel. This can dynamically integrate any scattered post-disaster human and technical resources into an operable distributed system capable of solving autonomously complex survivability, relief, and reconstruction problems. This work was presented in part at the 11th International Symposium on Artificial Life and Robotics, Oita, Japan, January 23–25, 2006     

Effect of salt content on the rheological properties of salad dressing-type emulsions stabilized by emulsifier blends

The effects that salt content and composition of emulsifier blends exert on the rheological properties of salad dressing-type emulsions were studied. Binary blends of egg yolk and different types of amphiphilic molecules (Tween 20, sucrose laurate and pea protein), in several proportions, were used to stabilize emulsions. Salt concentration was ranged from 0 to 2.3% w/w. Steady-state flow tests and small-amplitude oscillatory shear measurements within the linear viscoelastic region were carried out. Rheological tests were complemented with droplet size distribution measurements. Rheological properties and physical stability of the emulsions studied were significantly influenced by salt content and the nature of binary emulsifier blends. In general, the values of rheological parameters studied increased with salt content. However, salt affects in much higher extent the properties of emulsions stabilized by high proportions of egg yolk or pea protein in the emulsifier blend, rather than those mainly stabilized by non-ionic low-molecular-weight surfactants, which are less sensitive to changes in the ionic strength. In this sense, the increase observed in the values of viscosity and linear viscoelastic functions of emulsions is more important when a protein is predominant in the emulsifier blend. This effect was explained on the basis of a more apparent increasing interdroplet interactions and viscosity of the continuous medium, both of them induced by salt addition, which lead to the consecution of an extensively flocculated state and improved creaming stability. On the contrary, different blends of pea protein and egg yolk showed a quite similar evolution of the rheological parameters with salt concentration.     

Nutritional composition and safety of Patagonotothenramsayi, a discard species from Patagonian Shelf

Patagonotothen ramsayi, a nototheniid discard species from the southwest Atlantic, was studied to evaluate its composition, quality and suitability for human consumption. The chemical composition of the flesh revealed that P. ramsayi is a valuable food with protein and fat contents ranging between 16–19% and 0.78–1.34%, respectively. It has a high amount of unsaturated fatty acids, especially docosahexaenoic acid (30–42%) and eicosapentaenoic acid (12–18%). It is also a potential source of minerals, with important amounts of magnesium, potassium and phosphorous. The microbial quality of P. ramsayi was good and the detection of toxic metals such as Pb, Cd and Hg revealed that there is no intrinsic risk associated with its consumption. Additionally, no parasites with potential public health implications were found in the flesh. Finally, its flesh is white, with a shellfish odour, and has a firm and elastic texture. The present study shows that P. ramsayi is a nutritious species of high value for human consumption.     

Identification of a cysteine proteinase from Jumbo squid (Dosidicus gigas) hepatopancreas as cathepsin L

A cysteine proteinase from Jumbo squid (Dosidicus gigas) hepatopancreas was partially purified by a two step procedure involving ammonium sulfate precipitation and gel filtration chromatography and further by SDS–PAGE. The molecular weight of the proteinase was 24 kDa determined by SDS–PAGE and 23.7 kDa with mass spectrometry. The activity had an optimum pH of 4.5 and optimum temperature of 55 °C under the assay for cathepsin L specific synthetic substrate Z-PAAFC. The cathepsin B and H specific synthetic substrates Z-AAAFC and H-AMC did not show any hydrolysis with the partially purified enzyme. Peptide mapping of trypsin digests of the 24 kDa band from SDS–PAGE showed the squid cysteine proteinase was homologous to cathepsin L from different animal sources. The activity of the partially purified fraction with the cathepsin L specific substrate Z-PAAFC was inhibited 75–89% by enzyme inhibitors specific for cysteine proteinases but was also significantly inhibited by serine and aspartate proteinase inhibitors.     

Linking Late Endosomal Cholesterol with Cancer Progression and Anticancer Drug Resistance

Cancer cells undergo drastic metabolic adaptions to cover increased bioenergetic needs, contributing to resistance to therapies. This includes a higher demand for cholesterol, which often coincides with elevated cholesterol uptake from low-density lipoproteins (LDL) and overexpression of the LDL receptor in many cancers. This implies the need for cancer cells to accommodate an increased delivery of LDL along the endocytic pathway to late endosomes/lysosomes (LE/Lys), providing a rapid and effective distribution of LDL-derived cholesterol from LE/Lys to other organelles for cholesterol to foster cancer growth and spread. LDL-cholesterol exported from LE/Lys is facilitated by Niemann–Pick Type C1/2 (NPC1/2) proteins, members of the steroidogenic acute regulatory-related lipid transfer domain (StARD) and oxysterol-binding protein (OSBP) families. In addition, lysosomal membrane proteins, small Rab GTPases as well as scaffolding proteins, including annexin A6 (AnxA6), contribute to regulating cholesterol egress from LE/Lys. Here, we summarize current knowledge that links upregulated activity and expression of cholesterol transporters and related proteins in LE/Lys with cancer growth, progression and treatment outcomes. Several mechanisms on how cellular distribution of LDL-derived cholesterol from LE/Lys influences cancer cell behavior are reviewed, some of those providing opportunities for treatment strategies to reduce cancer progression and anticancer drug resistance.