Conventional implementations of collective communications are based on point-to-point communications, and their optimizations have been focused on efficiency of those communication algorithms. However, point-to-point communications are not the optimal choice for modern computing clusters of SMPs due to their two-level communication structure. In recent years, a few research efforts have investigated efficient collective communications for SMP clusters. This dissertation is focused on platform-independent algorithms and implementations in this area. There are two main approaches to implementing efficient collective communications for clusters of SMPs: using shared memory operations for intra-node communications, and overlapping inter-node/intra-node communications. The former fully utilizes the hardware based shared memory of an SMP, and the latter takes advantage of the inherent hierarchy of the communications within a cluster of SMPs. Previous studies focused on clusters of SMP from certain vendors. However, the previously proposed methods are not portable to other systems. Because the performance optimization issue is very complicated and the developing process is very time consuming, it is highly desired to have self-tuning, platform-independent implementations. As proven in this dissertation, such an implementation can significantly out-perform the other point-to-point based portable implementations and some platform-specific implementations. The dissertation describes in detail the architecture of the platform-independent …

The combination of giant magnetoresistive sensors, magnetic labeling strategies, and biomolecule detection is just beginning to be explored. New readout methods and assay formats are necessary for biomolecules detection to flourish. The work presented in this dissertation describes steps toward the creation of a novel detection method for bioassays utilizing giant magnetoresistive sensors as the readout method. The introduction section contains a brief review of some of the current methods of bioassay readout. The theoretical underpinnings of the giant magnetoresistive effect are also discussed. Finally, the more prominent types of giant magnetoresistive sensors are described, as well as their complicated fabrication. Four data chapters follow the introduction; each chapter is presented as a separate manuscript, either already published or soon to be submitted. Chapter 1 presents research efforts toward the production of a bioassay on the surface of a gold-modified GMR sensor. The testing of this methodology involved the capture of goat a-mouse-coated magnetic nanoparticles on the mouse IgG-modified gold surface. The second, third and fourth chapters describe the utilization of a self-referenced sample stick for scanning across the GMR sensor. The sample stick consisted of alternating magnetic reference and bioactive gold addresses. Chapter 2 is concerned with the characterization …

In this study, we applied the Nested Partitions method to a U-line balancing problem and conducted experiments to evaluate the application. From the results, it is quite evident that the Nested Partitions method provided near optimal solutions (optimal in some cases). Besides, the execution time is quite short as compared to the Branch and Bound algorithm. However, for larger data sets, the algorithm took significantly longer times for execution. One of the reasons could be the way in which the random samples are generated. In the present study, a random sample is a solution in itself which requires assignment of tasks to various stations. The time taken to assign tasks to stations is directly proportional to the number of tasks. Thus, if the number of tasks increases, the time taken to generate random samples for the different regions also increases. The performance index for the Nested Partitions method in the present study was the number of stations in the random solutions (samples) generated. The total idle time for the samples can be used as another performance index. ULINO method is known to have used a combination of bounds to come up with good solutions. This approach of combining different performance …

The purposes of our research were: (1) To characterize subunits of highly fluorescent protein R-Phycoerythrin (R-PE) and check their suitability for single-molecule detection (SMD) and cell imaging, (2) To extend the use of R-PE subunits through design of similar proteins that will be used as probes for microscopy and spectral imaging in a single cell, and (3) To demonstrate a high-throughput spectral imaging method that will rival spectral flow cytometry in the analysis of individual cells. We first demonstrated that R-PE subunits have spectroscopic and structural characteristics that make them suitable for SMD. Subunits were isolated from R-PE by high-performance liquid chromatography (HPLC) and detected as single molecules by total internal reflection fluorescence microscopy (TIRFM). In addition, R-PE subunits and their enzymatic digests were characterized by several separation and detection methods including HPLC, capillary electrophoresis, sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE) and HPLC-electrospray ionization mass spectrometry (ESI-MS). Favorable absorption and fluorescence of the R-PE subunits and digest peptides originate from phycoerythrobilin (PEB) and phycourobilin (PUB) chromophores that are covalently attached to cysteine residues. High absorption coefficients and strong fluorescence (even under denaturing conditions), broad excitation and emission fluorescence spectra in the visible region of electromagnetic spectrum, and relatively low molecular …

This work is presented in the following order: A review of the relevant physics and discussion of theoretical predictions for a two gap superconducting compound is given in chapter 2. Chapter 3 provides a review of the basic properties of MgB{sub 2}. Details of sample synthesis and characterization are given in chapter 4. Chapter 5 presents normal state and superconducting properties of Mg(B{sub 1-x}C{sub x}){sub 2} wires. Attempts to increase critical current densities in filaments via titanium additions are discussed in chapter 6. In chapters 7 and 8 alternative methods for synthesizing doped MgB{sub 2} powders are explored. In chapter 7 we synthesize Mg(B{sub 1-x}C{sub x}){sub 2} up to x=0.069 using a mixture of Mg, B, and the binary compound B{sub 4}C. Chapter 8 explores an alternative method, plasma spray synthesis, to produce nanometer sized doped boron powders for powder-in-tube applications. The effects of neutron irradiation on pure MgB{sub 2} wires is discussed in chapter 9. This is followed by a study of the effects of neutron irradiation on Mg(B{sub .962}C{sub .038}){sub 2} wires, presented in chapter 10. I will summarize the results of all of these studies in chapter 11 and discuss future directions for research in understanding the …

Quantification in liquid chromatography (LC) is becoming very important as more researchers are using LC, not as an analytical tool itself, but as a sample introduction system for other analytical instruments. The ability of LC instrumentation to quickly separate a wide variety of compounds makes it ideal for analysis of complex mixtures. For elemental speciation, LC is joined with inductively coupled plasma mass spectrometry (ICP-MS) to separate and detect metal-containing, organic compounds in complex mixtures, such as biological samples. Often, the solvent gradients required to perform complex separations will cause matrix effects within the plasma. This limits the sensitivity of the ICP-MS and the quantification methods available for use in such analyses. Traditionally, isotope dilution has been the method of choice for LC-ICP-MS quantification. The use of naturally abundant isotopes of a single element in quantification corrects for most of the effects that LC solvent gradients produce within the plasma. However, not all elements of interest in speciation studies have multiple naturally occurring isotopes; and polyatomic interferences for a given isotope can develop within the plasma, depending on the solvent matrix. This is the case for reverse phase LC separations, where increasing amounts of organic solvent are required. For such …

Atomic clusters are unique objects, which occupy an intermediate position between atoms and condensed matter systems. For a long time it was thought that physical and chemical properties of atomic dusters monotonically change with increasing size of the cluster from a single atom to a condensed matter system. However, recently it has become clear that many properties of atomic clusters can change drastically with the size of the clusters. Because physical and chemical properties of clusters can be adjusted simply by changing the cluster's size, different applications of atomic clusters were proposed. One example is the catalytic activity of clusters of specific sizes in different chemical reactions. Another example is a potential application of atomic clusters in microelectronics, where their band gaps can be adjusted by simply changing cluster sizes. In recent years significant advances in experimental techniques allow one to synthesize and study atomic clusters of specified sizes. However, the interpretation of the results is often difficult. The theoretical methods are frequently used to help in interpretation of complex experimental data. Most of the theoretical approaches have been based on empirical or semiempirical methods. These methods allow one to study large and small dusters using the same approximations. However, …

Many of the current methods for pathogenic bacterial detection require long sample-preparation and analysis time, as well as complex instrumentation. This dissertation explores simple analytical approaches (e.g., flow cytometry and diffuse reflectance spectroscopy) that may be applied towards ideal requirements of a microbial detection system, through method and instrumentation development, and by the creation and characterization of immunosensing platforms. This dissertation is organized into six sections. In the general Introduction section a literature review on several of the key aspects of this work is presented. First, different approaches for detection of pathogenic bacteria will be reviewed, with a comparison of the relative strengths and weaknesses of each approach, A general overview regarding diffuse reflectance spectroscopy is then presented. Next, the structure and function of self-assembled monolayers (SAMs) formed from organosulfur molecules at gold and micrometer and sub-micrometer patterning of biomolecules using SAMs will be discussed. This section is followed by four research chapters, presented as separate manuscripts. Chapter 1 describes the efforts and challenges towards the creation of imunosensing platforms that exploit the flexibility and structural stability of SAMs of thiols at gold. 1H, 1H, 2H, 2H-perfluorodecyl-1-thiol SAM (PFDT) and dithio-bis(succinimidyl propionate)-(DSP)-derived SAMs were used to construct the platform. Chapter …

Metal on semiconductor surfaces has been the topic of intense studies due to its technological applications. As nano-devices shrink in size, the conventional understanding of electronic devices are no longer applicable as quantum effects start to play an important role in the behavior of the devices. At the same time, when structures are approaching atomic scale, the precise fabrication by lithographic techniques, for example, are not even applicable. Very often, the fabrication of regular structures rely on self-assembly which is susceptible to fluctuations. Therefore, a deeper understanding to exploit the quantum behavior of nano-devices and precise control of building nano-structures are highly desired. Si(100) and Si(111) surfaces are the most studied system because they are the Si surfaces with the lowest surface energy. Pb on Si(100) and Si(111) is often chosen as the prototype system for the study of metal/semiconductor interfaces because Pb is not reactive with Si thus forming a clean well-defined hetero-interface. A prominent problem for studying the physics of metal/semiconductor interfaces is that the interface structures are usually not known. While various experimental techniques can be employed to provide clues to the atomic geometries, definite conclusions usually cannot be drawn due to the intrinsic limitations of the …

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Funeral program for Mrs. Thelma Redd, born July 14, 1921 and died December 9, 2005. The funeral was held Saturday, December 17, 2005 at Calvary Baptist Church, officiated by Rev. Kevin Nelson. Funeral arrangements were made through Lewis Funeral Home and she was buried in Southern Memorial Park in San Antonio, Texas.

Encyclopedia article in the 'International Encyclopedia of Economic Sociology' discussing health care, globalization and health, and the effect of the economy on the structure of the health care system.

Video recording from The Black Academy of Arts and Letters recorded during their Annual Christmas Kwanzaa Concert event in 2005. This video features various holiday performances by youth and adults to celebrate Christmas and Kwanzaa live on the Naomi Bruton Main Stage. The video shows a reception after the performances. This video is Part 2 of 2 of the event.

Video recording from The Black Academy of Arts and Letters recorded during their Annual Christmas Kwanzaa Concert event in 2005. This video features various holiday performances by youth and adults to celebrate Christmas and Kwanzaa live on the Naomi Bruton Main Stage. The video shows a reception after the performances. This video is Part 1 of 2 of the event.

This work explores the development and application of chip-scale bioassays based on surface-enhanced Raman scattering (SERS) for high throughput and high sensitivity analysis of biomolecules. The size effect of gold nanoparticles on the intensity of SERS is first presented. A sandwich immunoassay was performed using Raman-labeled immunogold nanoparticles with various sizes. The SERS responses were correlated to particle densities, which were obtained by atomic force microscopy (AFM). The response of individual particles was also investigated using Raman-microscope and an array of gold islands on a silicon substrate. The location and the size of individual particles were mapped using AFM. The next study describes a low-level detection of Escherichia coli 0157:H7 and simulants of biological warfare agents in a sandwich immunoassay format using SERS labels, which have been termed Extrinsic Raman labels (ERLs). A new ERL scheme based on a mixed monolayer is also introduced. The mixed monolayer ERLs were created by covering the gold nanoparticles with a mixture of two thiolates, one thiolate for covalently binding antibody to the particle and the other thiolate for producing a strong Raman signal. An assay platform based on mixed self-assembled monolayers (SAMs) on gold is then presented. The mixed SAMs were prepared from …

The central theme of this thesis work is to develop new block copolymer materials for biomedical applications. While there are many reports of stimuli-responsive amphiphilic [19-21] and crosslinked hydrogel materials [22], the development of an in situ gel forming, pH responsive pentablock copolymer is a novel contribution to the field, Figure 1.1 is a sketch of an ABCBA pentablock copolymer. The A blocks are cationic tertiary amine methacrylates blocked to a central Pluronic F127 triblock copolymer. In addition to the prerequisite synthetic and macromolecular characterization of these new materials, the self-assembled supramolecular structures formed by the pentablock were experimentally evaluated. This synthesis and characterization process serves to elucidate the important structure property relationships of these novel materials, The pH and temperature responsive behavior of the pentablock copolymer were explored especially with consideration towards injectable drug delivery applications. Future synthesis work will focus on enhancing and tuning the cell specific targeting of DNA/pentablock copolymer polyplexes. The specific goals of this research are: (1) Develop a synthetic route for gel forming pentablock block copolymers with pH and temperature sensitive properties. Synthesis of these novel copolymers is accomplished with ATRP, yielding low polydispersity and control of the block copolymer architecture. Well defined macromolecular …

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Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

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