The Data Vortex, an All Optical Path Multicomputer Interconnection Network

All optical path interconnection networks employing dense wavelength division multiplexing can provide vast improvements in supercomputer performance. However, the lack of efficient optical buffering requires investigation of new topologies and routing techniques. This paper introduces and evaluates the data vortex optical switching architecture which uses cylindrical routing paths as a packet buffering alternative. In addition, the impact of the number of angles on the overall network performance is studied through simulation. Using optimal topology configurations, the data vortex is compared to two existing switching architectures-butterfly and omega networks. The three networks are compared in terms of throughput, accepted traffic ratio, and average packet latency. The data vortex is shown to exhibit comparable latency and a higher acceptance rate (2times at 50 percent load) than the butterfly and omega topologies     

Drinking Water Treatment Plant Design Incorporating Variability and Uncertainty

Both inherent natural variability and model parameter uncertainty must be considered in the development of robust and reliable designs for drinking water treatment. This study presents an optimization framework for investigating the effects of five variable influent parameters and three uncertain model parameters on the least-cost treatment plant configuration (contact, direct, or nonsweep conventional filtration) that reliably satisfies an effluent particulate matter concentration constraint. Incorporating variability and uncertainty within the decision-making framework generates information for investigating: (1) impacts on total cost and treatment reliability; (2) shifts on the least-cost treatment configuration for providing reliable treatment; and (3) the importance of the individual variable and uncertain parameter distributions for reliably satisfying an effluent water quality constraint. Increasing the magnitude of influent variability and model parameter uncertainty results in a greater expected design cost due, generally, to increases in process sizing required to reliably satisfy the effluent concentration constraint. The inclusion of variability and uncertainty can also produce a shift in the locations of the least-cost configuration regions, which are dependent on the expected influent water quality and the magnitude of variability and uncertainty. The additional information provided by incorporating the variable and uncertain parameters illustrates that parameter distributions related to the primary removal mechanism are critical, and that contact and direct filtration are more sensitive to variability and uncertainty than conventional filtration.     

Prototype Fabrication and Preliminary In Vitro Testing of a Shape Memory Endovascular Thrombectomy Device

An electromechanical microactuator comprised of shape memory polymer (SMP) and shape memory nickel-titanium alloy (nitinol) was developed and used in an endovascular thrombectomy device prototype. The microactuator maintains a straight rod shape until an applied current induces electro-resistive (Joule) heating, causing the microactuator to transform into a corkscrew shape. The straight-to-corkscrew transformation geometry was chosen to permit endovascular delivery through (straight form) and retrieval of (corkscrew form) a stroke-causing thrombus (blood clot) in the brain. Thermal imaging of the microactuator during actuation in air indicated that the steady-state temperature rise caused by Joule heating varied quadratically with applied current and that actuation occurred near the glass transition temperature of the SMP (86degC). To demonstrate clinical application, the device was used to retrieve a blood clot in a water-filled silicone neurovascular model. Numerical modeling of the heat transfer to the surrounding blood and associated thermal effects on the adjacent artery potentially encountered during clinical use suggested that any thermal damage would likely be confined to localized areas where the microactuator was touching the artery wall. This shape memory mechanical thrombectomy device is a promising tool for treating ischemic stroke without the need for infusion of clot-dissolving drugs.     

Protocol Customization for Improving MPI Performance on RDMA-Enabled Clusters

Optimizing Message Passing Interface (MPI) point-to-point communication for large messages is of paramount importance since most communications in MPI applications are performed by such operations. Remote Direct Memory Access (RDMA) allows one-sided data transfer and provides great flexibility in the design of efficient communication protocols for large messages. However, achieving high point-to-point communication performance on RDMA-enabled clusters is challenging due to both the complexity in communication protocols and the impact of the protocol invocation scenario on the performance of a given protocol. In this work, we analyze existing protocols and show that they are not ideal in many situations, and propose to use protocol customization, that is, different protocols for different situations to improve MPI performance. More specifically, by leveraging the RDMA capability, we develop a set of protocols that can provide high performance for all protocol invocation scenarios. Armed with this set of protocols that can collectively achieve high performance in all situations, we demonstrate the potential of protocol customization by developing a trace-driven toolkit that allows the appropriate protocol to be selected for each communication in an MPI application to maximize performance. We evaluate the performance of the proposed techniques using micro-benchmarks and application benchmarks. The results indicate that protocol customization can out-perform traditional communication schemes by a large degree in many situations.     

Interpretation of the 685nm peak in water-leaving radiance spectra in terms of fluorescence,absorption and scattering,and its observation by MERIS

One of the major design goals of the Medium Resolution Imaging Spectrometer (MERIS) was the capability to use the signal from chlorophyll fluorescence stimulated by ambient sunlight to detect and map phytoplankton. This is considered tobe especially useful in coastal waters, where the determination of chlorophyll from water-leaving radiance spectra using the conventional blue/green ratio method is often complicated by high concentrations of gelbstoff and suspended matter. Based on a variety of studies, three spectral channels centred at 665, 681.25 and 705nm were included in the design of MERIS for retrieving the fluorescence signal. This paper presents observations with highresolution spectrometers which demonstrate the main factors affecting the observed signal in the red part of the spectrum. These factors are absorption by pure water, scattering by suspended particles, absorption and fluorescence of chlorophyll and the influence of submerged macrophyta. The influence of exceptional blooms such as 'red tides' on radiance spectra is also discussed. The paper shows how the combination of these effects can be understood using simple and easy-to-use radiative transfer models, and can be exploited by MERIS for improved mapping of phytoplankton, red tides and coastal, submerged and tidal flat vegetation.     

Striped nanowires and nanorods from mixed SAMS

We investigate the use of mixed self-assembled monolayers (SAMs) for creating nanoscale striped patterns on nanowires and nanorods. Our simulations predict that SAMs comprised of an equal composition of length-mismatched, thermodynamically incompatible surfactants adsorbed on nanowire surfaces self-organize into equilibrium stripes of alternating composition always perpendicular, rather than parallel, to the nanowire axis. We support the simulation results with preliminary experimental investigations of gold nanorods coated with binary mixtures of ligand molecules, which show stripes roughly perpendicular to the rod axis in all cases.     

Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation

DNA repair proteins participate in extensive protein−protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent “RPA−Spy−UNG2” complex could identify and excise uracil bases in duplex areas next to ssDNA−dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA−Spy−UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA−dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.     

A bacteriophage reagent for Salmonella: molecular studies on Felix 01

Felix 01 (F01) is a bacteriophage originally isolated by Felix and Callow which lyses almost all Salmonella strains and has been widely used as a diagnostic test for this genus. Molecular information about this phage is entirely lacking. In the present study, the DNA of the phage was found to be a double-stranded linear molecule of about 80 kb. 11.5 kb has been sequenced and in this region A + T content is 60%. There are relatively few restriction endonuclease cleavage sites in the native genome and clones show this is due to their absence rather than modification. A restriction map of the genome has been constructed. The ends of the molecule cannot be ligated although they contain 5' phosphates. At least 60% of the genome must encode proteins. In the sequenced portion, many open reading frames exist and these are tightly packed together. These have been examined for homology to published proteins but only 1 to 17 shows similarity to known proteins. F01 is therefore the prototype of a new phage family. On the basis of restriction sites, codon usage and the distribution of nonsense codons in the unused reading frames, a strong case can be made for natural selection that reacts to mRNA structure and function.