Towards Efficient Execution of MPI Applications on the Grid: Porting and Optimization Issues

The message passing interface (MPI) is a standard used by many parallel scientific applications. It offers the advantage of a smoother migration path for porting applications from high performance computing systems to the Grid. In this paper Grid-enabled tools and libraries for developing MPI applications are presented. The first is MARMOT, a tool that checks the adherence of an application to the MPI standard. The second is PACX-MPI, an implementation of the MPI standard optimized for Grid environments. Besides the efficient development of the program, an optimal execution is of paramount importance for most scientific applications. We therefore discuss not only performance on the level of the MPI library, but also several application specific optimizations, e.g., for a sparse, parallel equation solver and an RNA folding code, like latency hiding, prefetching, caching and topology-aware algorithms.     

Probabilistic proximity search: Fighting the curse of dimensionality in metric spaces

Proximity searches become very difficult on “high dimensional” metric spaces, that is, those whose histogram of distances has a large mean and/or a small variance. This so-called “curse of dimensionality”, well known in vector spaces, is also observed in metric spaces. The search complexity grows sharply with the dimension and with the search radius. We present a general probabilistic framework applicable to any search algorithm and whose net effect is to reduce the search radius. The higher the dimension, the more effective the technique. We illustrate empirically its practical performance on a particular class of algorithms, where large improvements in the search time are obtained at the cost of a very small error probability.     

Decentralized adaptive recurrent neural control structure

This paper presents a novel decentralized variable structure neural control approach for large-scale uncertain systems, which is developed using recurrent high-order neural networks (RHONN). It is assumed that each subsystem belongs to a class of block-controllable nonlinear systems whose vector fields includes interconnection terms, which are bounded by nonlinear functions. A decentralized RHONN structure and the respective learning law are proposed in order to approximate online the dynamical behavior of each nonlinear subsystem. The control law, which is able to regulate and to track the desired reference signals, is designed using the well-known variable structure theory. The stability of the whole system is analyzed via the Lyapunov methodology. The applicability of the proposed decentralized identification and control algorithm is illustrated via simulations as applied to an interconnected double inverted pendulum.     

A Time-Domain Digital-Intensive Built-In Tester for Analog Circuits

To solve test challenges in nanometer CMOS technologies, a time-domain digital-intensive built-in tester for analog circuits is proposed. The compact tester allows characterizations of AC response and DC gain for various analog circuits which have a low-pass frequency characteristic. By applying ramp signals to stimulate the circuit under test and measuring slopes and time delays of its responses, the testing can be simple and robust over process-voltage-temperature variations. Also, it is well suited for nanometer technologies because of its digital-intensive implementation. The tester was fabricated in 65 nm standard CMOS process and occupies 0.026 mm².     

Binary ant colony optimization applied to variable screening in the Mahalanobis–Taguchi System

This work presents the application of the Mahalanobis–Taguchi System (MTS) to a dimensional problem in the automotive industry. The combinatorial optimization problem of variable selection is solved by the application of a recent version of binary ant colony optimization algorithm. Moreover, a comparison with respect to binary particle swarm optimization algorithm is also presented and a discussion regarding the numerical results is given.     

Public reaction to wind development in California

Substantial controversy has been produced from the location of over 4000 wind turbines in San Gorgonio Pass, California. The principal point of controversy is the conflicting land use which results from developing wind power in a populated area. A public opinion survey was conducted which demonstrated that the vocal opposition to the wind turbines so commonly expressed is not borne out in fact. While there is indeed some opposition to the development of wind power at this site, particularly in terms of aesthetic degradation, the majority of respondents favoured the development. This level of approval will be of interest to those developing large wind projects elsewhere.     

Theophylline: Old Drug in a New Light,Application in COVID-19 through Computational Studies

Theophylline (3-methyxanthine) is a historically prominent drug used to treat respiratory diseases, alone or in combination with other drugs. The rapid onset of the COVID-19 pandemic urged the development of effective pharmacological treatments to directly attack the development of new variants of the SARS-CoV-2 virus and possess a therapeutical battery of compounds that could improve the current management of the disease worldwide. In this context, theophylline, through bronchodilatory, immunomodulatory, and potentially antiviral mechanisms, is an interesting proposal as an adjuvant in the treatment of COVID-19 patients. Nevertheless, it is essential to understand how this compound could behave against such a disease, not only at a pharmacodynamic but also at a pharmacokinetic level. In this sense, the quickest approach in drug discovery is through different computational methods, either from network pharmacology or from quantitative systems pharmacology approaches. In the present review, we explore the possibility of using theophylline in the treatment of COVID-19 patients since it seems to be a relevant candidate by aiming at several immunological targets involved in the pathophysiology of the disease. Theophylline down-regulates the inflammatory processes activated by SARS-CoV-2 through various mechanisms, and herein, they are discussed by reviewing computational simulation studies and their different applications and effects.     

Inactivation of Shigella boydii 18 IDPH and Listeria monocytogenes Scott A with power ultrasound at different acoustic energy densities and temperatures

ABSTRACT:  The effect of acoustic energy density (AED) on inactivation of Shigella boydii 18 IDPH and Listeria monocytogenes Scott A in a cell suspension was studied at sublethal temperatures and at AEDs of 0.49, 0.85, and 1.43 W/mL. The effect of temperature on ultrasonic inactivation of L. monocytogenes Scott A at 35, 50, and 65 °C was examined at an AED of 1.43 W/mL. Increasing AED increased the rate of inactivation for both S. boydii and L. monocytogenes . The destruction of S. boydii and L. monocytogenes followed 1st order kinetics in a 20-min treatment, except for S. boydii inactivation at 1.43 W/mL where a tailing effect was observed after 15 min. At sublethal temperatures, the D-values of S. boydii were 8.8, 4.3, and 2.5 min for AEDs of 0.49, 0.85, and 1.43 W/mL, whereas those for L. monocytogenes at the 3 AED levels were 31.5, 13.5, and 7.3 min, respectively. Ultrasonic treatment of L. monocytogenes at 35 and 50 °C enhanced inactivation. However, at 65 °C, application of ultrasound did not result in additional inactivation compared to thermal treatment alone at the same temperature. With the experimental conditions and the ultrasound system used in this study, an upper temperature limit for thermosonication was evident above which no added killing due to ultrasound was observed.     

Characterization of palladium supported on sulfated zirconia catalysts by DRIFTS, XAS and n-butane isomerization reaction in the presence of hydrogen

Palladium supported on sulfated zirconia (PdSZ) has been characterized by the n-butane isomerization reaction in the presence of hydrogen, X-ray absorption spectroscopy (XAS) and diffuse reflectance Fourier transform infrared spectroscopy (DRIFTS) of adsorbed carbon monoxide. Catalyst calcination at 873 K followed by hydrogen reduction at 513 K results in the formation of 30–40 Å Pd metal clusters, but the surface can only weakly adsorb CO, though stronger than Pd-free, sulfated zirconia catalysts. In the presence of hydrogen, PdSZ has a lower n-butane isomerization activity than SZ, and the Pd function cannot stabilize the reaction at low H₂/n-butane ratios.     

Verfahrenstechnische und wirtschaftliche Vorteile der Kochextrusion im Vergleich zu herkömmlichen Verfahren der Lebensmittel-Industrie

Economic and process engineering advantages of extrusion cooking in comparison with conventional processes in the food industry . Extrusion cooking is introduced as a modern high-temperature short-time process. Possible process steps in extruder machine systems, such as continuous conveying, mixing, homogenizing and reactions, mechanical and thermal energy dissipation for plasticizing and modifying biopolymers, are explained. This process creates new products with completely new textures, for example in the snack and breakfast cereal sector, while on the other hand the extrusion process competes with long-standing conventional processes. The latter work slowly with low pressures, low temperatures and energy dissipation with high water contents in large batch-operated machines. The quality of extruder-cooked products depends on the extrusion system. The self-cleaning corotating twin-screw extruder with its narrow residence time spectrum is the optimum system. However, the counter-rotating intermeshing machine has certain advantages for products of low viscosity. The cooking time at high temperature is a matter of seconds, which serves to maintain the properties of the ingredients and active substances, while ensuring fast destruction of microorganisms. The end-products have a long shelf-life on account of their low process moisture content. Continuous extrusion cooking has economic advantages mainly because it replaces many batch processes and because extrusion is carried out entirely or almost entirely with the final moisture content, thus avoiding the necessity to evaporate huge quantities of water.