Extending snBench to Support a Graphical Programming Interface for a Sensor Network Tasking Language (STEP)

The purpose of this project is the creation of a graphical "programming" interface for a sensor network tasking language called STEP. The graphical interface allows the user to specify a program execution graphically from an extensible pallet of functionalities and save the results as a properly formatted STEP file. Moreover, the software is able to load a file in STEP format and convert it into the corresponding graphical representation. During both phases a type-checker is running on the background to ensure that both the graphical representation and the STEP file are syntactically correct. This project has been motivated by the Sensorium project at Boston University. In this technical report we present the basic features of the software, the process that has been followed during the design and implementation. Finally, we describe the approach used to test and validate our software.

Atomic layer deposition of interface control layers for the fabrication of III/V MOS devices

The continued advancement of metal oxide semiconductor field effect transistor (MOSFET) technology has shifted the focus from Si/SiO2 transistors towards high-κ/III-V transistors for high performance, faster devices. This has been necessary due to the limitations associated with the scaling of the SiO2 thickness below ~1 nm and the associated increased leakage current due to direct electron tunnelling through the gate oxide. The use of these materials exhibiting lower effective charge carrier mass in conjunction with the use of a high-κ gate oxide allows for the continuation of device scaling and increases in the associated MOSFET device performance. The high-κ/III-V interface is a critical challenge to the integration of high-κ dielectrics on III-V channels. The interfacial chemistry of the high-κ/III-V system is more complex than Si, due to the nature of the multitude of potential native oxide chemistries at the surface with the resultant interfacial layer showing poor electrical insulating properties when high-κ dielectrics are deposited directly on these oxides. It is necessary to ensure that a good quality interface is formed in order to reduce leakage and interface state defect density to maximise channel mobility and reduce variability and power dissipation. In this work, the ALD growth of aluminium oxide (Al2O3) and hafnium oxide (HfO2) after various surface pre-treatments was carried out, with the aim of improving the high-κ/III-V interface by reducing the Dit – the density of interface defects caused by imperfections such as dangling bonds, dimers and other unsatisfied bonds at the interfaces of materials. A brief investigation was performed into the structural and electrical properties of Al2O3 films deposited on In0.53Ga0.47As at 200 and 300oC via a novel amidinate precursor. Samples were determined to experience a severe nucleation delay when deposited directly on native oxides, leading to diminished functionality as a gate insulator due to largely reduced growth per cycle. Aluminium oxide MOS capacitors were prepared by ALD and the electrical characteristics of GaAs, In0.53Ga0.47As and InP capacitors which had been exposed to pre-pulse treatments from triethyl gallium and trimethyl indium were examined, to determine if self-cleaning reactions similar to those of trimethyl aluminium occur for other alkyl precursors. An improved C-V characteristic was observed for GaAs devices indicating an improved interface possibly indicating an improvement of the surface upon pre-pulsing with TEG, conversely degraded electrical characteristics observed for In0.53Ga0.47As and InP MOS devices after pre-treatment with triethyl gallium and trimethyl indium respectively. The electrical characteristics of Al2O3/In0.53Ga0.47As MOS capacitors after in-situ H2/Ar plasma treatment or in-situ ammonium sulphide passivation were investigated and estimates of interface Dit calculated. The use of plasma reduced the amount of interface defects as evidenced in the improved C-V characteristics. Samples treated with ammonium sulphide in the ALD chamber were found to display no significant improvement of the high-κ/III-V interface. HfO2 MOS capacitors were fabricated using two different precursors comparing the industry standard hafnium chloride process with deposition from amide precursors incorporating a ~1nm interface control layer of aluminium oxide and the structural and electrical properties investigated. Capacitors furnished from the chloride process exhibited lower hysteresis and improved C-V characteristics as compared to that of hafnium dioxide grown from an amide precursor, an indication that no etching of the film takes place using the chloride precursor in conjunction with a 1nm interlayer. Optimisation of the amide process was carried out and scaled samples electrically characterised in order to determine if reduced bilayer structures display improved electrical characteristics. Samples were determined to exhibit good electrical characteristics with a low midgap Dit indicative of an unpinned Fermi level

Probing the Electrochemical Interface by In Situ Infrared Spectroscopy

info:eu-repo/semantics/published

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae).

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.

Electronic Techtonics: Thinking at the Interface

This volume originated in HASTAC’s first international conference, “Electronic Techtonics: Thinking at the Interface,” held at Duke University during April 19-21, 2007. “Electronic Techtonics” was the site of truly unforgettable conversations and encounters that traversed domains, disciplines, and media – conversations that explored the fluidity of technology both as interface as well as at the interface. This hardcopy version of the conference proceedings is published in conjunction with its electronic counterpart (found at www.hastac.org). Both versions exist as records of the range and depth of conversations that took place at the conference. Some of the papers in this volume are almost exact records of talks given at the conference, while others are versions that were revised and reworked some time after the conference. These papers are drawn from a variety of fields and we have not made an effort to homogenize them in any way, but have instead retained the individual format and style of each author.

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.

Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of 'fitness for use' for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC's standard checklists for genomics and metagenomics and (b) TDWG's Darwin Core standard, used primarily in taxonomy and systematic biology.

Suppression of conformational heterogeneity at a protein-protein interface.

Staphylococcal protein A (SpA) is an important virulence factor from Staphylococcus aureus responsible for the bacterium's evasion of the host immune system. SpA includes five small three-helix-bundle domains that can each bind with high affinity to many host proteins such as antibodies. The interaction between a SpA domain and the Fc fragment of IgG was partially elucidated previously in the crystal structure 1FC2. Although informative, the previous structure was not properly folded and left many substantial questions unanswered, such as a detailed description of the tertiary structure of SpA domains in complex with Fc and the structural changes that take place upon binding. Here we report the 2.3-Å structure of a fully folded SpA domain in complex with Fc. Our structure indicates that there are extensive structural rearrangements necessary for binding Fc, including a general reduction in SpA conformational heterogeneity, freezing out of polyrotameric interfacial residues, and displacement of a SpA side chain by an Fc side chain in a molecular-recognition pocket. Such a loss of conformational heterogeneity upon formation of the protein-protein interface may occur when SpA binds its multiple binding partners. Suppression of conformational heterogeneity may be an important structural paradigm in functionally plastic proteins.

VizMaps: A Bayesian Topic Modeling Based PubMed Search Interface

A common challenge that users of academic databases face is making sense of their query outputs for knowledge discovery. This is exacerbated by the size and growth of modern databases. PubMed, a central index of biomedical literature, contains over 25 million citations, and can output search results containing hundreds of thousands of citations. Under these conditions, efficient knowledge discovery requires a different data structure than a chronological list of articles. It requires a method of conveying what the important ideas are, where they are located, and how they are connected; a method of allowing users to see the underlying topical structure of their search. This paper presents VizMaps, a PubMed search interface that addresses some of these problems. Given search terms, our main backend pipeline extracts relevant words from the title and abstract, and clusters them into discovered topics using Bayesian topic models, in particular the Latent Dirichlet Allocation (LDA). It then outputs a visual, navigable map of the query results.

An application of quasi-Newton methods for the numerical solution of interface problems

Quasi-Newton methods are applied to solve interface problems which arise from domain decomposition methods. These interface problems are usually sparse systems of linear or nonlinear equations. We are interested in applying these methods to systems of linear equations where we are not able or willing to calculate the Jacobian matrices as well as to systems of nonlinear equations resulting from nonlinear elliptic problems in the context of domain decomposition. Suitability for parallel implementation of these algorithms on coarse-grained parallel computers is discussed.

Investigating the representation of merging behavior at the floor–stair interface in computer simulations of multi-floor building evacuations

In this article, the representation of the merging process at the floor— stair interface is examined within a comprehensive evacuation model and trends found in experimental data are compared with model predictions. The analysis suggests that the representation of floor—stair merging within the comprehensive model appears to be consistent with trends observed within several published experiments of the merging process. In particular: (a) The floor flow rate onto the stairs decreases as the stair population density increases. (b) For a given stair population density, the floor population's flow rate onto the stairs can be maximized by connecting the floor to the landing adjacent to the incoming stair. (c) In situations where the floor is connected adjacent to the incoming stair, the merging process appears to be biased in favor of the floor population. It is further conjectured that when the floor is connected opposite the incoming stair, the merging process between the stair and floor streams is almost in balance for high stair population densities, with a slight bias in favor of the floor stream at low population densities. A key practical finding of this analysis is that the speed at which a floor can be emptied onto a stair can be enhanced simply by connecting the floor to the landing at a location adjacent to the incoming stair rather than opposite the stair. Configuring the stair in this way, while reducing the floor emptying time, results in a corresponding decrease in the descent flow rate of those already on the stairs. While this is expected to have a negligible impact on the overall time to evacuate the building, the evacuation time for those higher up in the building is extended while those on the lower flows is reduced. It is thus suggested that in high-rise buildings, floors should be connected to the landing on the opposite side to the incoming stair. Information of this type will allow engineers to better design stair—floor interfaces to meet specific design objectives.

Time-dependent modelling and experimental validation of the metal/flux interface in a continuous casting mould

A finite volume computer model of the continuous casting process for steel flat products has been developed. In this first stage, the model concentrates on the hydrodynamic aspects of the process and in particular the dynamic behavior of the metal/slag interface. The model was validated against experimental measurements obtained in a water model apparatus.

Singular stresses at the tip of a crack terminating at frictional interface of fibre reinforced composites

The stress singularities at the tip of a crack that terminates at a frictional interface between two layers in anisotropic composites are investigated. The order of stress singularities is determined by solving the characteristic equations obtained from the boundary conditions and the frictional interface conditions for the cases concerned. The interface is assumed to be governed by Coulomb's law of friction. Numerical results are presented for the cases with a crack terminating at a frictional interface of a fibre reinforced composite, and it is shown that there is a big difference of stress singularities between cases with and without considering friction along the interface.