SPACE: A lightweight collaborative caching for clusters

In this paper, we introduce Systematic P2P Aided Cache Enhancement or SPACE, a new collaboration scheme among clients in a computer cluster of a high performance computing facility to share their caches with each other. The collaboration is achieved in a distributed manner, and is designed based on peer-to-peer computing model. The objective is to provide (1) a decentralized solution, and (2) a near optimal performance with reasonably low overhead. Simulation results are given to demonstrate the performance of the proposed scheme. In addition, the results show that SPACE evenly distributes work loads among participators, and entirely eliminates any requirement of a central cache manager.     

Flow simulations in arbitrarily complex cardiovascular anatomies – An unstructured Cartesian grid approach

Image guided computational fluid dynamics is attracting increasing attention as a tool for refining in vivo flow measurements or predicting the outcome of different surgical scenarios. Sharp interface Cartesian/Immersed-Boundary methods constitute an attractive option for handling complex in vivo geometries but their capability to carry out fine-mesh simulations in the branching, multi-vessel configurations typically encountered in cardiovascular anatomies or pulmonary airways has yet to be demonstrated. A major computational challenge stems from the fact that when such a complex geometry is immersed in a rectangular Cartesian box the excessively large number of grid nodes in the exterior of the flow domain imposes an unnecessary burden on both memory and computational overhead of the Cartesian solver without enhancing the numerical resolution in the region of interest. For many anatomies, this added burden could be large enough to render comprehensive mesh refinement studies impossible. To remedy this situation, we recast the original structured Cartesian formulation of Gilmanov and Sotiropoulos [Gilmanov A, Sotiropoulos F. A hybrid Cartesian/immersed boundary method for simulating flows with 3D, geometrically complex, moving bodies. J Comput Phys 2005;207(2):457–92] into an unstructured Cartesian grid layout. This simple yet powerful approach retains the simplicity and computational efficiency of a Cartesian grid solver, while drastically reducing its memory footprint. The method is applied to carry out systematic mesh refinement studies for several internal flow problems ranging in complexity from flow in a 90° pipe bend to flow in an actual, patient-specific anatomy reconstructed from magnetic resonance images. Finally, we tackle the challenging clinical scenario of a single-ventricle patient with severe arterio-venous malformations, seeking to provide a fluid dynamics prospective on a clinical problem and suggestions for procedure improvements. Results from these simulations demonstrate very complex cardiovascular flow dynamics and underscore the need for high-resolution simulations prior to drawing any clinical recommendations.     

A waveform concatenation technique for text-to-speech synthesis

Designing text-to-speech systems capable of producing natural sounding speech segments in different Indian languages is a challenging and ongoing problem. Due to the large number of possible pronunciations in different Indian languages, a number of speech segments are needed to be stored in the speech database while a concatenative speech synthesis technique is used to achieve highly natural speech segments. However, the large speech database size makes it unusable for small hand held devices or human computer interactive systems with limited storage resources. In this paper, we proposed a fraction-based waveform concatenation technique to produce intelligible speech segments from a small footprint speech database. The results of all the experiments performed shows the effectiveness of the proposed technique in producing intelligible speech segments in different Indian languages even with very less storage and computation overhead compared to the existing syllable-based technique.     

Effect of engine-based thermal aging on surface morphology and performance of Lean NOx Traps

A small single-cylinder diesel engine is used to thermally age model (Pt + Rh/Ba/γ-Al₂O₃) lean NO_x traps (LNTs) under lean/rich cycling at target temperatures of 600 °C, 700 °C, and 800 °C. During an aging cycle, fuel is injected into the exhaust to achieve reproducible exotherms under lean and rich conditions with the average temperature approximating the target temperature. Aging is performed until the cycle-average NO_x conversion measured at 400 °C is approximately constant. Engine-based NO_x conversion decreased by 42% after 60 cycles at 600 °C, 36% after 76 cycles at 700 °C and 57% after 46 cycles at 800 °C. The catalyst samples were removed and characterized by XRD and using a microreactor that allowed controlled measurements of surface area, precious metal size, NO_x storage, and reaction rates. Three aging mechanisms responsible for the deactivation of LNTs have been identified: (i) loss of dispersion of the precious metals, (ii) phase transitions in the washcoat materials, and (iii) loss of surface area of the storage component and support. These three mechanisms are accelerated when the aging temperature exceeds 850 °C—the γ to δ transition temperature of Al₂O₃. Normalization of rates of NO reacted at 400 °C to total surface area demonstrates the biggest impact on performance stems from surface area losses rather than from precious metal sintering.     

Plasma lipids are affected similarly by dietary lauric or palmitic acid in gerbils and monkeys

To compare the relative impact of dietary lauric acid (12∶0) and palmitic acid (16∶0) on plasma lipids, two fat-sensitive species, Mongolian gerbils and cebus monkeys, were fed cholesterol-free, purified diets enriched with either 12∶0-rich or 16∶0-rich fats, while all other fatty acids were held constant by selective blending of up to five natural fats or oils. The two gerbil diets (40 en% from fat) allowed for an 8 en% exchange between 12∶0 and 16∶0, and the monkey diets (31 en% from fat) allowed for 6 en% exchange beteen these two fatty acids. Eight gerbils received the diets for eight weeks, and 12 cebus monkeys were fed each diet in a cross-over design for up to 22 wk. Both diets resulted in similar plasma cholesterol, triglyceride, and high density lipoprotein cholesterol concentrations within each species. Additionally, separation of cebus lipoproteins by discontinuous density-gradient ultracentrifugation failed to show any dietary differences in concentration or composition of the three major lipoprotein classes (d<1.019, 1.019–1.055, and 1.055–1.168 g/mL). Thus, in two species sensitive to manipulations in dietary fat while consuming cholesterol-free diets, 16∶0 was not hypercholesterolemic relative to 12∶0. Based on a paper presented at the PORIM International Palm Oil Congress (PIPOC) held in Kuala Lumpur, Malaysia, September 1993.     

A comparative dielectric relaxation study of PMN–PT and PMN–PZ ceramics using impedance spectroscopy

AC-impedance spectroscopic studies in the temperature range of 30–400 °C are carried out on solid solutions of lead magnesium niobate (PMN) with lead titanate (PT) and lead zirconate (PZ), both of them in the 65/35 atomic ratio. For PMN–PT this corresponds to the morphotropic phase boundary composition (with normal ferroelectric behaviour), and for PMN–PZ it is near the phase boundary between normal ferroelectric and relaxor ferroelectric compositions. The variation of dielectric permittivity with temperature at different frequencies shows normal ferroelectric and relaxor-like dependence for PMN–PT and PMN–PZ, respectively. Temperature-dependent spectroscopic modulus plots reveal a much broader peak for PMN–PZ compared to that for PMN–PT, which is consistent with the dielectric behaviour. PMN–PT shows nearly ideal Debye behaviour below T_m (the temperature of the permittivity maximum) and the behaviour departs from ideality above T_m, whereas non-ideal Debye behaviour is seen both below and above T_m for PMN–PZ. Complex modulus plots fit well with two depressed semicircles and three depressed semicircles, respectively, for PMN–PT and PMN–PZ. The relaxation observed in the spectroscopic plots around 1 MHz for PMN–PT has been assigned to polarisation relaxation expected for normal-sized domains. No such relaxation could be observed for PMN–PZ around 1 MHz because of the mesoscopic domain sizes.     

Feedback based simultaneous correction of imaging artifacts due to geometrical and mechanical cross-talk and tip-sample stick in atomic force microscopy

This paper presents a feedback scheme that simultaneously corrects, in real time, for the imaging artifacts caused by cantilever and photosensor misalignments as well as misinterpretations in relative lateral position of the tip with respect to the sample due to the tip-sample stick in atomic force microscopy (AFM). The optical beam bounce method, typically used in AFM for imaging, is sensitive to inaccuracies of cantilever geometry and the relative misalignment of the laser source, cantilever, and the laser sensitive diode from the intended design. These inaccuracies, which contribute to the geometrical cross-talk between the normal and the lateral signals, become prominent at the atomic and subnanometer scales, and thereby impede high resolution imaging studies. The feedback scheme accounts for these artifacts and makes imaging insensitive to, in fact, practically independent of these inaccuracies. This scheme counteracts the lateral twisting dynamics of the cantilever, and as a result, it avoids the misinterpretation problem of the relative lateral position of the cantilever tip from the sample and thereby avoids the corresponding imaging artifacts that are typically prominent in contact mode friction force microscopy (FFM). The feedback scheme consists of simultaneously regulating the normal as well as the lateral cantilever deflection signal at their respective set points. This not only removes the imaging artifacts due to geometrical misalignments, mechanical cross-talk, and irregular sliding but also the corresponding compensatory control signal gives a more accurate real time measure of the lateral interaction force between the sample and the cantilever as compared to the lateral deflection signal used in FFM. Experimental results show significant improvement, and in some cases, practical elimination of the artifacts. The design and implementation of a split piezoassembly needed for the lateral actuation for the feedback scheme are also presented.     

Engineering the acyltransferase substrate specificity of assembly line polyketide synthases

Polyketide natural products act as a broad range of therapeutics, including antibiotics, immunosuppressants and anti-cancer agents. This therapeutic diversity stems from the structural diversity of these small molecules, many of which are produced in an assembly line manner by modular polyketide synthases. The acyltransferase (AT) domains of these megasynthases are responsible for selection and incorporation of simple monomeric building blocks, and are thus responsible for a large amount of the resulting polyketide structural diversity. The substrate specificity of these domains is often targeted for engineering in the generation of novel, therapeutically active natural products. This review outlines recent developments that can be used in the successful engineering of these domains, including AT sequence and structural data, mechanistic insights and the production of a diverse pool of extender units. It also provides an overview of previous AT domain engineering attempts, and concludes with proposed engineering approaches that take advantage of current knowledge. These approaches may lead to successful production of biologically active ‘unnatural’ natural products.     

From Active Sites to Machines: A Challenge for Enzyme Chemists

As researchers who study enzyme chemistry embrace increasingly complex systems, especially biological machines, our attention is also shifting from steps involving covalent bond formation or cleavage to those that exclusively involve changes in non‐covalent bonding. Assembly line polyketide synthases are an example of this growing challenge. By now, the chemical reactions underpinning polyketide biosynthesis can be unequivocally mapped to well‐defined active sites and are, for the most part, readily explicable in the language of physical organic chemistry. Yet, all of these insights merely serve as a backdrop to the real problem of explaining how the catalytic functions of dozens of active sites are synchronized in order to allow these remarkable machines to turn over with remarkable specificity. Notwithstanding the fact that the time‐honored language of physical organic chemistry can teach us a lot, it is often insufficient to describe many of these events, and must therefore evolve.