Materials integrity in microsystems: a framework for a petascale predictive-science-based multiscale modeling and simulation system

Microsystems have become an integral part of our lives and can be found in homeland security, medical science, aerospace applications and beyond. Many critical microsystem applications are in harsh environments, in which long-term reliability needs to be guaranteed and repair is not feasible. For example, gyroscope microsystems on satellites need to function for over 20 years under severe radiation, thermal cycling, and shock loading. Hence a predictive-science-based, verified and validated computational models and algorithms to predict the performance and materials integrity of microsystems in these situations is needed. Confidence in these predictions is improved by quantifying uncertainties and approximation errors. With no full system testing and limited sub-system testings, petascale computing is certainly necessary to span both time and space scales and to reduce the uncertainty in the prediction of long-term reliability. This paper presents the necessary steps to develop predictive-science-based multiscale modeling and simulation system. The development of this system will be focused on the prediction of the long-term performance of a gyroscope microsystem. The environmental effects to be considered include radiation, thermo-mechanical cycling and shock. Since there will be many material performance issues, attention is restricted to creep resulting from thermal aging and radiation-enhanced mass diffusion, material instability due to radiation and thermo-mechanical cycling and damage and fracture due to shock. To meet these challenges, we aim to develop an integrated multiscale software analysis system that spans the length scales from the atomistic scale to the scale of the device. The proposed software system will include molecular mechanics, phase field evolution, micromechanics and continuum mechanics software, and the state-of-the-art model identification strategies where atomistic properties are calibrated by quantum calculations. We aim to predict the long-term (in excess of 20 years) integrity of the resonator, electrode base, multilayer metallic bonding pads, and vacuum seals in a prescribed mission. Although multiscale simulations are efficient in the sense that they focus the most computationally intensive models and methods on only the portions of the space–time domain needed, the execution of the multiscale simulations associated with evaluating materials and device integrity for aerospace microsystems will require the application of petascale computing. A component-based software strategy will be used in the development of our massively parallel multiscale simulation system. This approach will allow us to take full advantage of existing single scale modeling components. An extensive, pervasive thrust in the software system development is verification, validation, and uncertainty quantification (UQ). Each component and the integrated software system need to be carefully verified. An UQ methodology that determines the quality of predictive information available from experimental measurements and packages the information in a form suitable for UQ at various scales needs to be developed. Experiments to validate the model at the nanoscale, microscale, and macroscale are proposed. The development of a petascale predictive-science-based multiscale modeling and simulation system will advance the field of predictive multiscale science so that it can be used to reliably analyze problems of unprecedented complexity, where limited testing resources can be adequately replaced by petascale computational power, advanced verification, validation, and UQ methodologies.     

Modulation of the Rev-RRE interaction by aromatic heterocyclic compounds

The HIV-1 Rev protein regulates the nucleocytoplasmic distribution of viral precursor RNAs that encode HIV-1 structural proteins. Rev-mediated viral RNA expression requires a sequence-specific interaction between Rev and a viral RNA sequence, the Rev responsive element (RRE). Because the Rev-RRE interaction is essential for HIV-1 replication, anti-viral agents that selectively block this interaction may be effective anti-HIV-1 therapeutics. Here, we show that certain aromatic heterocyclic compounds, in particular, a tetracationic diphenylfuran, AK.A, can block binding of Rev to its high-affinity viral RNA binding site. AK.A abolishes Rev-RRE interactions at concentrations as low as 0.1 microM. Inhibition appears to be selective and results from competitive binding of the drug to a discrete region within the Rev binding site. Interestingly, the molecular basis for the AK.A-RNA interaction, as well as the mode of RNA binding differs from previously described aminoglycoside Rev inhibitors. Analysis of a variety of aromatic heterocyclic compounds and their derivatives reveals stereo-specific features required for the inhibition. Our results further demonstrate the feasibility of identifying and designing small molecules that selectively block viral RNA-protein interactions.     

Myxovirescin A biosynthesis is directed by hybrid polyketide synthases/nonribosomal peptide synthetase, 3-hydroxy-3-methylglutaryl-CoA synthases, and trans-acting acyltransferases

Myxococcus xanthus DK1622 is shown to be a producer of myxovirescin (antibiotic TA) antibiotics. The myxovirescin biosynthetic gene cluster spans at least 21 open reading frames (ORFs) and covers a chromosomal region of approximately 83 kb. In silico analysis of myxovirescin ORFs in conjunction with genetic studies suggests the involvement of four type I polyketide synthases (PKSs; TaI, TaL, TaO, and TaP), one major hybrid PKS/NRPS (Ta-1), and a number of monofunctional enzymes similar to the ones involved in type II fatty-acid biosynthesis (FAB). Whereas deletion of either taI or taL causes a dramatic drop in myxovirescin production, deletion of both genes (DeltataIL) leads to the complete loss of myxovirescin production. These results suggest that both TaI and TaL PKSs might act in conjunction with a methyltransferase, reductases, and a monooxygenase to produce the 2-hydroxyvaleryl-S-ACP starter that is proposed to act as the biosynthetic primer in the initial condensation reaction with glycine. Polymerization of the remaining 11 acetates required for lactone formation is directed by 12 modules of Ta-1, TaO, and TaP megasynthetases. All modules, except for the first module of TaL, lack cognate acyltransferase (AT) domains. Furthermore, deletion of a discrete tandem AT-encoded by taV-blocks myxovirescin production; this suggests an "in trans" mode of action. To embellish the macrocycle with methyl and ethyl moieties, assembly of the myxovirescin scaffold is proposed to switch twice from PKS to 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA)-like biochemistry during biosynthesis. Disruption of the S-adenosylmethionine (SAM)-dependent methyltransferase, TaQ, shifts production toward two novel myxovirescin analogues, designated myxovirescin Q(a) and myxovirescin Q(c). NMR analysis of purified myxovirescin Q(a) revealed the loss of the methoxy carbon atom. This novel analogue lacks bioactivity against E. coli.     

The effect of food dry matter intake on endogenous ileal amino acid excretion determined under peptide alimentation in the 50 kg liveweight pig

The daily ileal excretion of amino acids was measured at different food dry matter intakes for the 50 kg liveweight pig under conditions of peptide alimentation. The experiment comprised two cross-over design trials each involving four pairs of entire male pigs fitted with simple T-cannulae at the terminal ileum and fed a hydrolysed casein semi-synthetic diet. Each pair of pigs received one of four sequences of food dry matter intake arranged in a Latin square design, namely 0.06, 0.08, 0.10 and 0.12 (Trial 1) and 0.05, 0.07, 0.09 and 0.11 (Trial 2) of metabolic body weight (W^0.75) day^?1. Each pig received the diet at its described level of intake for 8 days, with continuous 24 h collection of ileal digesta on the fifth and eighth days. Chromic oxide was included in the diet to permit correction of ileal flows to complete digesta collection. Pooled digesta from each pig at each level of dry matter intake were centrifuged and ultrafiltered and the high-molecular-weight fraction was analysed for amino acid and nitrogen contents. There were significant (P < 0.05) linear relationships between endogenous ileal amino acid, nitrogen and dry matter excretion (mg day^?1) and food dry matter intake (g day^?1) except for lysine, glutamic acid and phenylalanine which increased in a curvilinear manner (P < 0.05). The results indicate that dietary dry matter intake influences endogenous excretion from the ileum. The relationships, determined under physiological conditions, provide preliminary data on the magnitude of small intestinal amino acid loss in the young growing pig.     

Powernet — das neue EIB-Medium

Powernet EIB is a powerline-based information transmission system using the powerline medium to exchange information for communication purposes. The first implementation of the EIB makes use of the twisted pair transmission medium only. Introducing Powernet EIB, the new transmission medium powerline opens new application fields for the EIB. Powerline is a very hostile medium for carrier based data transmission. Powernet EIB presents a reliable data transmission with considerable speed. Half duplex transceiver technology enables two-way communication in Powernet EIB. The transmission method is based on spread frequency shift keying (SFSK).     

Nanoparticles made of fluorescence-labelled Poly(L-lactide-co-glycolide): preparation, stability, and biocompatibility

Nanoparticles have recently been demonstrated in a rat model to be a promising tool for targeting inflamed areas of the intestinal mucosa in inflammatory bowel diseases whilst concentrating anti-inflammatory drugs at their site of action. Still, however, this novel concept has to be proven in vivo in humans. As a first step biodegradable and biocompatible fluorescent nanoparticles were prepared and characterized to serve as markers for successful inflammation targeting in future clinical trials. To achieve stable fluorescence labelling, fluoresceinamine was covalently bound to poly(L-lactide-co-glycolide) (PLGA) as described by Horisawa et al. The modification rate of carboxyl-end groups of the PLGA chains determined by 1H NMR was 65%. From this modified polymer, nanoparticles (FA-PLGA nanoparticles) of approximately 270 nm size were prepared via nanoprecipitation. Apart from an initial burst effect, most of the label (> 88%) appeared to be strongly bound and was leaked only slowly from the particles. In contrast, we found an immediate leakage of encapsulated sodium fluorescein with nanoparticles prepared by a double emulsion method. In degradation experiments we studied and visualized the changes in morphology and elastic properties of the FA-PLGA nanoparticles within 15 weeks using atomic force microscopy. When FA-PLGA nanoparticles were applied on an in vitro model of the intestinal mucosa (Caco-2 cell culture), only minor amounts of their fluorescent degradation products (approximately 0.02% after 6 h) were transported. In a cytotoxicity study with Caco-2 cells, FA-PLGA nanoparticles yielded an IC50 value as for plain PLGA nanoparticles. In conclusion, the polymer modification method allows to prepare fluorescently labelled nanoparticles from a well-known biodegradable pharmaceutical polymer with sufficient stability to be monitored over a period of several days. Some initial leakage of fluorescence label appears to be unavoidable but negligible with respect to potential absorption and cytotoxicity when applied in vivo.