EDEN EDEN EDEN

An overnight audiovisual composition for 13 musicians and film projections. The ensemble continuously constructs and deconstructs a 26-part chord, a 13-part natural harmonic series that always beats in near-unison with itself. A projector shows three superimposed films prepared as continuously extending loops. Members of the audience, who are invited to sleep during the performance, shift between waking and dreaming states. Concept and composition by Gascia Ouzounian. Film by Chloe Griffin.

Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the x-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the x-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA- M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.

Small-scale Hα jets in the solar chromosphere

Aims. High temporal and spatial resolution observations from the Rapid Oscillations in the Solar Atmosphere (ROSA) multiwavelength imager on the Dunn Solar Telescope are used to study the velocities of small-scale Hα jets in an emerging solar active region.
Methods. The dataset comprises simultaneous imaging in the Hα core, Ca ii K, and G band, together with photospheric line-of-sight magnetograms. Time-distance techniques are employed to determine projected plane-of-sky velocities.
Results. The Hα images are highly dynamic in nature, with estimated jet velocities as high as 45 km s-1. These jets are one-directional, with their origin seemingly linked to underlying Ca ii K brightenings and G-band magnetic bright points.
Conclusions. It is suggested that the siphon flow model of cool coronal loops is suitable for interpreting our observations. The jets are associated with small-scale explosive events, and may provide a mass outflow from the photosphere to the corona.

Optimization of heat transfer characteristics, flow distribution, and reaction processing for a microstructured reactor/heat-exchanger for optimal performance in platinum catalyzed ammonia oxidation

The present work is focused on the demonstration of the advantages of miniaturized reactor systems which are essential for processes where potential for considerable heat transfer intensification exists as well as for kinetic studies of highly exothermic reactions at near-isothermal conditions. The heat transfer characteristics of four different cross-flow designs of a microstructured reactor/heat-exchanger (MRHE) were studied by CFD simulation using ammonia oxidation on a platinum catalyst as a model reaction. An appropriate distribution of the nitrogen flow used as a coolant can decrease drastically the axial temperature gradient in the reaction channels. In case of a microreactor made of a highly conductive material, the temperature non-uniformity in the reactor is strongly dependent on the distance between the reaction and cooling channels. Appropriate design of a single periodic reactor/heat-exchanger unit, combined with a non-uniform inlet coolant distribution, reduces the temperature gradients in the complete reactor to less than 4degreesC, even at conditions corresponding to an adiabatic temperature rise of about 1400degreesC, which are generally not accessible in conventional reactors because of the danger of runaway reactions. To obtain the required coolant flow distribution, an optimization study was performed to acquire the particular geometry of the inlet and outlet chambers in the microreactor/heat-exchanger. The predicted temperature profiles are in good agreement with experimental data from temperature sensors located along the reactant and coolant flows. The results demonstrate the clear potential of microstructured devices as reliable instruments for kinetic research as well as for proper heat management in the case of highly exothermic reactions. (C) 2002 Elsevier Science B.V. All rights reserved.

The Paralax Infrastructure: Automatic Parallelization With a Helping Hand

Speeding up sequential programs on multicores is a challenging problem that is in urgent need of a solution. Automatic parallelization of irregular pointer-intensive codes, exempli?ed by the SPECint codes, is a very hard problem. This paper shows that, with a helping hand, such auto-parallelization is possible and fruitful. This paper makes the following contributions: (i) A compiler framework for extracting pipeline-like parallelism from outer program loops is presented. (ii) Using a light-weight programming model based on annotations, the programmer helps the compiler to ?nd thread-level parallelism. Each of the annotations speci?es only a small piece of semantic information that compiler analysis misses, e.g. stating that a variable is dead at a certain program point. The annotations are designed such that correctness is easily veri?ed. Furthermore, we present a tool for suggesting annotations to the programmer. (iii) The methodology is applied to autoparallelize several SPECint benchmarks. For the benchmark with most parallelism (hmmer), we obtain a scalable 7-fold speedup on an AMD quad-core dual processor. The annotations constitute a parallel programming model that relies extensively on a sequential program representation. Hereby, the complexity of debugging is not increased and it does not obscure the source code. These properties could prove valuable to increase the ef?ciency of parallel programming.

A profile-based tool for finding pipeline parallelism in sequential programs

Traditional static analysis fails to auto-parallelize programs with a complex control and data flow. Furthermore, thread-level parallelism in such programs is often restricted to pipeline parallelism, which can be hard to discover by a programmer. In this paper we propose a tool that, based on profiling information, helps the programmer to discover parallelism. The programmer hand-picks the code transformations from among the proposed candidates which are then applied by automatic code transformation techniques.

This paper contributes to the literature by presenting a profiling tool for discovering thread-level parallelism. We track dependencies at the whole-data structure level rather than at the element level or byte level in order to limit the profiling overhead. We perform a thorough analysis of the needs and costs of this technique. Furthermore, we present and validate the belief that programs with complex control and data flow contain significant amounts of exploitable coarse-grain pipeline parallelism in the program’s outer loops. This observation validates our approach to whole-data structure dependencies. As state-of-the-art compilers focus on loops iterating over data structure members, this observation also explains why our approach finds coarse-grain pipeline parallelism in cases that have remained out of reach for state-of-the-art compilers. In cases where traditional compilation techniques do find parallelism, our approach allows to discover higher degrees of parallelism, allowing a 40% speedup over traditional compilation techniques. Moreover, we demonstrate real speedups on multiple hardware platforms.

Molecular Dynamics of HIV1-Integrase in Complex with 93del - A Structural Perspective on the Mechanism of Inhibition

HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.

Interface mediated resistive switching in epitaxial NiO nanostructures

We report on the non-volatile resistive switching properties of epitaxial nickel oxide (NiO) nanostructures, 10-100 nm wide and up to 30 nm high grown on (001)-Nb:SrTiO3 substrates. Conducting-atomic force microscopy on individual nano-islands confirms prominent bipolar switching with a maximum ON/OFF ratio of similar to 10(3) at a read voltage of similar to+0.4V. This ratio is found to decrease with increasing height of the nanostructure. Linear fittings of I-V loops reveal that low and high resistance states follow Ohmic-conduction and Schottky-emission mechanism, respectively. The switching behavior (dependence on height) is attributed to the modulation of the carrier density at the nanostructure-substrate interface due to the applied electric field.

Epitaxial strain stabilization of ferroelectric phase in PbZrO3 thin films

PbZrO3/SrRuO3/SrTiO3 (100) epitaxial heterostructures with different thickness of the PbZrO3 (PZO) layer (d(PZO) similar to 5-160 nm) were fabricated by pulsed laser deposition. The ultrathin PZO films (d(PZO) <= 10 nm) were found to possess a rhombohedral structure. On increasing the PZO film thickness, a bulk like orthorhombic phase started forming in the film with d(PZO) similar to 22 nm and became abundant in the thicker films. Nanobeam electron diffraction and room-temperature micro-Raman measurements revealed that the stabilization of the rhombohedral phase of PZO could be attributed to the epitaxial strain accommodated by the heterostructures. Room-temperature polarization vs electric field measurements performed on different samples showed characteristic double hysteresis loops of antiferroelectric materials accompanied by a small remnant polarization for the thick PZO films (dPZO >= 50 nm). The remnant polarization increased by reducing the PZO layer thickness, and a ferroelectric like hysteresis loop was observed for the sample with d(PZO) similar to 22 nm. Local ferroelectric properties measured by piezoresponse force microscopy also exhibited a similar thickness-dependent antiferroelectric-ferroelectric transition. Room-temperature electrical properties observed in the PZO thin films in correlation to their structural characteristics suggested that a ferroelectric rhombohedral phase could be stabilized in thin epitaxial PZO films experiencing large interfacial compressive stress.

Membrane Topology and Identification of Critical Amino Acid Residues in the Wzx O-Antigen Translocase from Escherichia coli O157:H4

Wzx belongs to a family of membrane proteins involved in the translocation of isoprenoid lipid-linked glycans, which is loosely related to members of the major facilitator superfamily. Despite Wzx homologs performing a conserved function, it has been difficult to pinpoint specific motifs of functional significance in their amino acid sequences. Here, we elucidate the topology of the Escherichia coli O157 Wzx (Wzx(EcO157)) by a combination of bioinformatics and substituted cysteine scanning mutagenesis, as well as targeted deletion-fusions to green fluorescent protein and alkaline phosphatase. We conclude that Wzx(EcO157) consists of 12 transmembrane (TM) helices and six periplasmic and five cytosolic loops, with N and C termini facing the cytoplasm. Four TM helices (II, IV, X, and XI) contain polar residues (aspartic acid or lysine), and they may form part of a relatively hydrophilic core. Thirty-five amino acid replacements to alanine or serine were targeted to five native cysteines and most of the aspartic acid, arginine, and lysine residues. From these, only replacements of aspartic acid-85, aspartic acid-326, arginine-298, and lysine-419 resulted in a protein unable to support O-antigen production. Aspartic acid-85 and lysine-419 are located in TM helices II and XI, while arginine-298 and aspartic acid-326 are located in periplasmic and cytosolic loops 4, respectively. Further analysis revealed that the charge at these positions is required for Wzx function since conservative substitutions maintaining the same charge polarity resulted in a functional protein, whereas those reversing or eliminating polarity abolished function. We propose that the functional requirement of charged residues at both sides of the membrane and in two TM helices could be important to allow the passage of the Und-PP-linked saccharide substrate across the membrane.

Functional analysis of the large periplasmic loop of the Escherichia coli K-12 WaaL O-antigen ligase

WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. We determined the periplasmic location of a large (EL5) and small (EL4) adjacent loops in the Escherichia coli K-12 WaaL. Structural models of the EL5 from the K-12, R1 and R4 E. coli ligases were generated by molecular dynamics. Despite the poor amino acid sequence conservation among these proteins, the models afforded similar folds consisting of two pairs of almost perpendicular alpha-helices. One alpha-helix in each pair contributes a histidine and an arginine facing each other, which are highly conserved in WaaL homologues. Mutations in either residue rendered WaaL non-functional, since mutant proteins were unable to restore O antigen surface expression. Replacements of residues located away from the putative catalytic centre and non-conserved residues within the centre itself did not affect ligation. Furthermore, replacing a highly conserved arginine in EL4 with various amino acids inactivates WaaL function, but functionality reappears when the positive charge is restored by a replacement with lysine. These results lead us to propose that the conserved amino acids in the two adjacent periplasmic loops could interact with Und-PP, which is the common component in all WaaL substrates.

Functional characterization and membrane topology of Escherichia coli WecA, a sugar-phosphate transferase initiating the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide

WecA is an integral membrane protein that initiates the biosynthesis of enterobacterial common antigen and O-antigen lipopolysaccharide (LPS) by catalyzing the transfer of N-acetylglucosamine (GlcNAc)-1-phosphate onto undecaprenyl phosphate (Und-P) to form Und-P-P-GlcNAc. WecA belongs to a large family of eukaryotic and prokaryotic prenyl sugar transferases. Conserved aspartic acids in putative cytoplasmic loops 2 (Asp90 and Asp91) and 3 (Asp156 and Asp159) were targeted for replacement mutagenesis with either glutamic acid or asparagine. We examined the ability of each mutant protein to complement O-antigen LPS synthesis in a wecA-deficient strain and also determined the steady-state kinetic parameters of the mutant proteins in an in vitro transfer assay. Apparent K(m) and V(max) values for UDP-GlcNAc, Mg(2+), and Mn(2+) suggest that Asp156 is required for catalysis, while Asp91 appears to interact preferentially with Mg(2+), possibly playing a role in orienting the substrates. Topological analysis using the substituted cysteine accessibility method demonstrated the cytosolic location of Asp90, Asp91, and Asp156 and provided a more refined overall topological map of WecA. Also, we show that cells expressing a WecA derivative C terminally fused with the green fluorescent protein exhibited a punctate distribution of fluorescence on the bacterial surface, suggesting that WecA localizes to discrete regions in the bacterial plasma membrane.

Conserved aspartic acids are essential for the enzymic activity of the WecA protein initiating the biosynthesis of O-specific lipopolysaccharide and enterobacterial common antigen in Escherichia coli

The integral membrane protein WecA mediates the transfer of N-acetylglucosamine (GlcNAc) 1-phosphate to undecaprenyl phosphate (Und-P) with the formation of a phosphodiester bond. Bacteria employ this reaction during the biosynthesis of enterobacterial common antigen as well as of many O-specific lipopolysaccharides (LPSs). Alignment of a number of prokaryotic and eukaryotic WecA-homologous sequences identified a number of conserved aspartic acid (D) residues in putative cytoplasmic loops II and III of the inner-membrane protein. Site-directed mutagenesis was used to study the role of the conserved residues D90, D91 (loop II), D156 and D159 (loop III). As controls, D35, D94 and D276 were also mutagenized. The resulting WecA derivatives were assessed for function by complementation analysis of O-antigen biosynthesis, by the ability to incorporate radiolabelled precursor to a biosynthetic intermediate, by detection of the terminal GlcNAc residue in LPS and by a tunicamycin competition assay. It was concluded from these analyses that the conserved aspartic acid residues are functionally important, but also that they participate differently in the transfer reaction. Based on these results it is proposed that D90 and D91 are important in forwarding the reaction product to the next biosynthetic step, while D156 and D159 are a part of the catalytic site of the enzyme.

Conformational Dynamics of the Human Propeller Telomeric DNA Quadruplex on a Microsecond Time Scale

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. While G-quartet stems have been well characterised, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 µs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.

Pipelined two-port adaptor for wave digital filtering

The application of fine-grain pipelining techniques in the design of high-performance wave digital filters (WDFs) is described. The problems of latency in feedback loops can be significantly reduced if computations are organized most significant, as opposed to least significant, bit first and if the results are fed back as soon as they are formed. The result is that chips can be designed which offer significantly higher sampling rates than otherwise can be obtained using conventional methods. How these concepts can be extended to the more challenging problem of WDFs is discussed. It is shown that significant increases in the sampling rate of bit-parallel circuits can be achieved using most significant bit first arithmetic.