This dissertation describes the development andimplementation of a visible/near infrared pump/mid-infrared probeapparatus. Chapter 1 describes the background and motivation ofinvestigating optically induced structural dynamics, paying specificattention to solvation and the excitation selection rules of highlysymmetric molecules such as carotenoids. Chapter 2 describes thedevelopment and construction of the experimental apparatus usedthroughout the remainder of this dissertation. Chapter 3 will discuss theinvestigation of DCM, a laser dye with a fluorescence signal resultingfrom a charge transfer state. By studying the dynamics of DCM and of itsmethyl deuterated isotopomer (an otherwise identical molecule), we areable to investigate the origins of the charge transfer state and provideevidence that it is of the controversial twisted intramolecular (TICT)type. Chapter 4 introduces the use of two-photon excitation to the S1state, combined with one-photon excitation to the S2 state of thecarotenoid beta-apo-8'-carotenal. These 2 investigations show evidencefor the formation of solitons, previously unobserved in molecular systemsand found only in conducting polymers Chapter 5 presents an investigationof the excited state dynamics of peridinin, the carotenoid responsiblefor the light harvesting of dinoflagellates. This investigation allowsfor a more detailed understanding of the importance of structuraldynamics of carotenoids in light harvesting.

Run IIa of the D0 experiment at the Tevatron took place between Spring 2002 and Spring 2006, collecting approximately 1.2 fb{sup -1} of data. A fundamental principal of the D0 computing model is the utilization of globally distributed computing resources as part of a grid. In particular use is made of the 'SAMGrid'. The first part of this thesis describes the work undertaken at Imperial College on several D0 distributed computing projects. These included the deployment and development of parts of the SAMGrid software suite, and participation in the Winter 2003/2004 data reprocessing effort. One of the major goals of the D0 experiment is the observation of mixing in the B{sub s}{sup 0}-meson system. The measurement of the mixing frequency is important as it can be used to constrain the CKM matrix, which describes CP violation in the Standard Model. The second part of this thesis describes the development of an opposite side flavour tagging algorithm and its calibration using B{sup +} and B{sub d}{sup 0} meson decays. The application of this algorithm to an analysis of the B{sub s}{sup 0} meson system is then described, which lead to the world's first two-sided limit on the B{sub s}{sup 0} meson …

W{sup {+-}} + b{bar b} events contain the associated production of a W{sup {+-}} boson, a pair of bottom quarks (b{bar b}), and any number of additional partons. This process is of much importance at hadron collider experiments due to its role as a background source in searches for Standard Model Higgs boson and single top-quark production. In this thesis the results are presented for a measurement of the b-jet cross-section in W{sup {+-}} + b{bar b} events containing 1 or 2 jets in 695 pb{sup -1} of {radical}s =1.96 TeV p{bar p} collisions at the CDF experiment. This is the first measurement of the cross-section of W{sup {+-}} b{bar b} performed in any experiment. The cross-section is defined to be proportional to the number of b-jets from W{sup {+-}} b{bar b} events with one or two jets, and a leptonically decaying W{sup {+-}} with decay products passing kinematics cuts (p{sub T}({ell}{sup {+-}}) {ge} 20.0 GeV, |{eta}({ell}{sup {+-}})| {le} 1.1, p{sub T}({nu}) {ge} 25.0 GeV). The invariant mass distribution of jets identified as containing a long-lived hadron is fit with components for bottom, charm, and light-flavor to find the fraction due to true b-decays. Background b-jet sources are subtracted to …

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In this thesis, we report the study on one such particle called the B{sub s}{sup 0} meson made up of a bottom and a strange quark. B{sub s}{sup 0} mesons are currently produced in a great numbers only at the Tevatron and we report a study done to measure the mixing parameter {Delta}m{sub s} between the B{sub s}{sup 0} meson and its anti-particle {bar B}{sub s}{sup 0}. Mixing is the ability of a very few neutral mesons to change from their particle to their antiparticle and vice versa. Until recently there existed only a lower limit on this measurement, here we report an upper bound and a most probable value for the mixing parameter. In the following chapter, we discuss the theoretical motivation behind this study. The measurement technique and the different factors that effect the measurement are also given. In Chapter 3, we provide an overview of the experimental setup needed to perform the study. In Chapter 4, we present a new initial state flavor tagging algorithm using electrons and measurement of the B{sub d}{sup 0} mixing parameter {Delta}m{sub d} with the new technique. Details of the combined initial state tagging used in the B{sub s}{sup 0} mixing study …

The authors observed a new neutral kaon decay mode, K{sub L} {yields} {pi}{sup {+-}}e{sup {-+}}{bar {nu}}e{sup +}e{sup -} for the first time. Based on the 20225 events including 1018 {+-} 25 background events, they determined the branching ratio, B(K{sub L} {yields} {pi}{sup {+-}}e{sup {-+}}{bar {nu}}e{sup +}e{sup -}; M{sub e{sup +}e{sup -}} > 5 MeV/c{sup 2}, E*{sub e{sup +}e{sup -}} > 30 MeV) = (1.281 {+-} 0.041) x 10{sup -5}. This branching ratio agrees with a theoretical prediction based on the chiral perturbation theory ({chi}PT) calculation at {Omicron}(p{sup 4}). Most of the kinematical distributions agree with the {chi}PT {Omicron}(p{sup 4}) calculation. They also measured one of the low energy coupling constants for the {chi}PT {Omicron}(p{sup 4}), L{sub 9}{sup r} = (8.0 {+-} 1.6) x 10{sup -3}. The M{sub e{sup +}e{sup -}} distribution below 100 MeV showed a 3 {sigma} deviation from the {chi}PT {Omicron}(p{sup 4}) calculation. This requires further studies in theory and experiments.

The advance of High Energy Physics research using circulating accelerators strongly depends on increasing the magnetic bending field which accelerator magnets provide. To achieve high fields, the most powerful present-day accelerator magnets employ NbTi superconducting technology; however, with the start up of Large Hadron Collider (LHC) in 2007, NbTi magnets will have reached the maximum field allowed by the intrinsic properties of this superconductor. A further increase of the field strength necessarily requires a change in superconductor material; the best candidate is Nb{sub 3}Sn. Several laboratories in the US and Europe are currently working on developing Nb{sub 3}Sn accelerator magnets, and although these magnets have great potential, it is suspected that their performance may be fundamentally limited by conductor thermo-magnetic instabilities: an idea first proposed by the Fermilab High Field Magnet group early in 2003. This thesis presents a study of thermo-magnetic instability in high field Nb{sub 3}Sn accelerator magnets. In this chapter the following topics are described: the role of superconducting magnets in High Energy Physics; the main characteristics of superconductors for accelerator magnets; typical measurements of current capability in superconducting strands; the properties of Nb{sub 3}Sn; a description of the manufacturing process of Nb{sub 3}Sn strands; superconducting cables; …

One of the biggest challenges in the study of the nucleon structure is the understanding of the transition from partonic degrees of freedom to hadronic degrees of freedom. In 1970, Bloom and Gilman noticed that structure function data taken at SLAC in the resonance region average to the scaling curve of deep inelastic scattering (DIS). Early theoretical interpretations suggested that these two very different regimes can be linked under the condition that the quark-gluon and quark-quark interactions are suppressed. Substantial efforts are ongoing to investigate this phenomenon both experimentally and theoretically. Quark-hadron duality has been confirmed for the unpolarized structure function F{sub 2} of the proton and the deuteron using data from the experimental Hall C at Jefferson Lab (JLab). Indications of duality have been seen for the proton polarized structure function g{sub 1} and the virtual photon asymmetry A{sub 1} at JLab Hall B and HERMES. Because of the different resonance behavior, it is expected that the onset of duality for the neutron will happen at lower momentum transfer than for the proton. Now that precise spin structure data in the DIS region are available at large x, data in the resonance region are greatly needed in order to …

Direct imaging of extrasolar planets is an important, but challenging, next step in planetary science. Most planets identified to date have been detected indirectly--not by emitted or reflected light but through the effect of the planet on the parent star. For example, radial velocity techniques measure the doppler shift in the spectrum of the star produced by the presence of a planet. Indirect techniques only probe about 15% of the orbital parameter space of our solar system. Direct methods would probe new parameter space, and the detected light can be analyzed spectroscopically, providing new information about detected planets. High contrast adaptive optics systems, also known as Extreme Adaptive Optics (ExAO), will require contrasts of between 10{sup -6} and 10{sup -7} at angles of 4-24 {lambda}/D on an 8-m class telescope to image young Jupiter-like planets still warm with the heat of formation. Contrast is defined as the intensity ratio of the dark wings of the image, where a planet might be, to the bright core of the star. Such instruments will be technically challenging, requiring high order adaptive optics with > 2000 actuators and improved diffraction suppression. Contrast is ultimately limited by residual static wavefront errors, so an extrasolar planet …

Laser vibrometry is a technique used to detect vibrations on objects using the interference of coherent light with itself. Most vibrometry systems process only one target location at a time, but processing multiple locations simultaneously provides improved detection capabilities. Traditional laser vibrometry systems employ oversampling to sample the incoming modulated-light signal, however as the number of channels increases in these systems, certain issues arise such a higher computational cost, excessive heat, increased power requirements, and increased component cost. This thesis describes a novel approach to laser vibrometry that utilizes undersampling to control the undesirable issues associated with over-sampled systems. Undersampling allows for significantly less samples to represent the modulated-light signals, which offers several advantages in the overall system design. These advantages include an improvement in thermal efficiency, lower processing requirements, and a higher immunity to the relative intensity noise inherent in laser vibrometry applications. A unique feature of this implementation is the use of a parallel architecture to increase the overall system throughput. This parallelism is realized using a hierarchical multi-channel architecture based on off-the-shelf programmable logic devices (PLDs).

The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by …

In an effort to mimic the growth of natural bone, self-assembling, micelle and gel-forming copolymers were used as a template for calcium phosphate precipitation. Because of the cationic characteristics imparted by PDEAEM end group additions to commercially available Pluronic{reg_sign} Fl27, a direct ionic attraction mechanism was utilized and a polymer-brushite nanocomposite spheres were produced. Brushite coated spherical micelles with diameters of {approx}40 nm, and agglomerates of these particles (on the order of 0.5 {mu}m) were obtained. Thickness and durability of the calcium phosphate coating, and the extent of agglomeration were studied. The coating has been shown to be robust enough to retain its integrity even below polymer critical micelle concentration and/or temperature. Calcium phosphate-polymer gel nanocomposites were also prepared. Gel samples appeared as a single phase network of agglomerated spherical micelles, and had a final calcium phosphate concentration of up to 15 wt%. Analysis with x-ray diffraction and NMR indicated a disordered brushite phase with the phosphate groups linking inorganic phase to the polymer.

Fluidized beds (FB) reactors are widely used in the polymerization industry due to their superior heat- and mass-transfer characteristics. Nevertheless, problems associated with local overheating of polymer particles and excessive agglomeration leading to FB reactors defluidization still persist and limit the range of operating temperatures that can be safely achieved in plant-scale reactors. Many people have been worked on the modeling of FB polymerization reactors, and quite a few models are available in the open literature, such as the well-mixed model developed by McAuley, Talbot, and Harris (1994), the constant bubble size model (Choi and Ray, 1985) and the heterogeneous three phase model (Fernandes and Lona, 2002). Most these research works focus on the kinetic aspects, but from industrial viewpoint, the behavior of FB reactors should be modeled by considering the particle and fluid dynamics in the reactor. Computational fluid dynamics (CFD) is a powerful tool for understanding the effect of fluid dynamics on chemical reactor performance. For single-phase flows, CFD models for turbulent reacting flows are now well understood and routinely applied to investigate complex flows with detailed chemistry. For multiphase flows, the state-of-the-art in CFD models is changing rapidly and it is now possible to predict reasonably well …

Magnetic materials exhibiting magnetic phase transitions simultaneously with structural rearrangements of their crystal lattices hold a promise for numerous applications including magnetic refrigeration, magnetomechanical devices and sensors. We undertook a detailed study of a single crystal of dysprosium metal, which is a classical example of a system where magnetic and crystallographic sublattices can be either coupled or decoupled from one another. Magnetocaloric effect, magnetization, ac magnetic susceptibility, and heat capacity of high purity single crystals of dysprosium have been investigated over broad temperature and magnetic field intervals with the magnetic field vector parallel to either the a- or c-axes of the crystal. Notable differences in the behavior of the physical properties when compared to Dy samples studied in the past have been observed between 110 K and 125 K, and between 178 K and {approx}210 K. A plausible mechanism based on the formation of antiferromagnetic clusters in the impure Dy has been suggested in order to explain the reduction of the magnetocaloric effect in the vicinity of the Neel point. Experimental and theoretical investigations of the influence of commensurability effects on the magnetic phase diagram and the value of the magnetocaloric effect have been conducted. The presence of newly found …

In this thesis our main interest has been to investigate metallic photonic crystal and its applications. We explained how to solve a periodic photonic structure with transfer matrix method and when and how to use modal expansion method. Two different coating methods were introduced, modifying a photonic structure's intrinsic optical properties and rigorous calculation results are presented. Two applications of metallic photonic structures are introduced. For thermal emitter, we showed how to design and find optimal structure. For conversion efficiency increasing filter, we calculated its efficiency and the way to design it. We presented the relation between emitting light spectrum and absorption and showed the material and structural dependency of the absorption spectrum. By choosing a proper base material and structural parameters, we can design a selective emitter at a certain region we are interested in. We have developed a theoretical model to analyze a blackbody filament enclosed by a metallic mesh which can increase the efficiency of converting a blackbody radiation to visible light. With this model we found that a square lattice metallic mesh enclosing a filament might increase the efficiency of incandescent lighting sources. Filling fraction and thickness dependency were examined and presented. Combining these two parameters …

The inductively coupled plasma (ICP) is an atmospheric pressure ionization source. Traditionally, the plasma is sampled via a sampler cone. A supersonic jet develops behind the sampler, and this region is pumped down to a pressure of approximately one Torr. A skimmer cone is located inside this zone of silence to transmit ions into the mass spectrometer. The position of the sampler and skimmer cones relative to the initial radiation and normal analytical zones of the plasma is key to optimizing the useful analytical signal [1]. The ICP both atomizes and ionizes the sample. Polyatomic ions form through ion-molecule interactions either in the ICP or during ion extraction [l]. Common polyatomic ions that inhibit analysis include metal oxides (MO{sup +}), adducts with argon, the gas most commonly used to make up the plasma, and hydride species. While high resolution devices can separate many analytes from common interferences, this is done at great cost in ion transmission efficiency--a loss of 99% when using high versus low resolution on the same instrument [2]. Simple quadrupole devices, which make up the bulk of ICP-MS instruments in existence, do not present this option. Therefore, if the source of polyatomic interferences can be determined and …

This research describes Fountain, a suite of programs used to monitor the resources of a cluster. A cluster is a collection of individual computers that are connected via a high speed communication network. They are traditionally used by users who desire more resources, such as processing power and memory, than any single computer can provide. A common drawback to effectively utilizing such a large-scale system is the management infrastructure, which often does not often scale well as the system grows. Large-scale parallel systems provide new research challenges in the area of systems software, the programs or tools that manage the system from boot-up to running a parallel job. The approach presented in this thesis utilizes a collection of separate components that communicate with each other to achieve a common goal. While systems software comprises a broad array of components, this thesis focuses on the design choices for a node monitoring component. We will describe Fountain, an implementation of the Scalable Systems Software (SSS) node monitor specification. It is targeted at aggregate node monitoring for clusters, focusing on both scalability and fault tolerance as its design goals. It leverages widely used technologies such as XML and HTTP to present an interface …

We have calculated the equilibrium thermodynamic properties of Heisenberg spin systems using a quantum Monte Carlo (QMC) method. We have used some of these systems as models to describe recently synthesized magnetic molecules, and-upon comparing the results of these calculations with experimental data-have obtained accurate estimates for the basic parameters of these models. We have also performed calculations for other systems that are of more general interest, being relevant both for existing experimental data and for future experiments. Utilizing the concept of importance sampling, these calculations can be carried out in an arbitrarily large quantum Hilbert space, while still avoiding any approximations that would introduce systematic errors. The only errors are statistical in nature, and as such, their magnitudes are accurately estimated during the course of a simulation. Frustrated spin systems present a major challenge to the QMC method, nevertheless, in many instances progress can be made. In this chapter, the field of magnetic molecules is introduced, paying particular attention to the characteristics that distinguish magnetic molecules from other systems that are studied in condensed matter physics. We briefly outline the typical path by which we learn about magnetic molecules, which requires a close relationship between experiments and theoretical calculations. …

This dissertation is organized in an alternate format. Several manuscripts which have already been published or are to be submitted for publication have been included as separate chapters. Chapter 1 is a general introduction which describes the dissertation organization and introduces the human bone and ceramic materials as bone substitute. Chapter 2 is the background and literature review on dissolution behavior of calcium phosphate, and discussion of motivation for this research. Chapter 3 is a manuscript entitled ''Si,Zn-modified tricalcium phosphate: a phase composition and crystal structure study'', which was published in ''Key Engineering Materials'' [1]. Chapter 4 gives more crystal structure details by neutron powder diffraction, which identifies the position for Si and Zn substitution and explains the stabilization mechanism of the structure. A manuscript entitled ''Crystal structure analysis of Si, Zn-modified Tricalcium phosphate by Neutron Powder Diffraction'' will be submitted to Biomaterials [2]. Chapter 5 is a manuscript, entitled ''Dissolution behavior and cytotoxicity test of Si, Zn-modified tricalcium phosphate'', which is to be submitted to Biomaterials [3]. This paper discusses the additives effect on the dissolution behavior of TCP, and cytotoxicity test result is also included. Chapter 6 is the study of hydrolysis process of {alpha}-tricalcium phosphate in the …

This dissertation describes several projects to realize low-cost and high-quality three-dimensional (3D) microfabrication using non-photolithographic techniques for layer-by-layer photonic crystals. Low-cost, efficient 3D microfabrication is a demanding technique not only for 3D photonic crystals but also for all other scientific areas, since it may create new functionalities beyond the limit of planar structures. However, a novel 3D microfabrication technique for photonic crystals implies the development of a complete set of sub-techniques for basic layer-by-layer stacking, inter-layer alignment, and material conversion. One of the conventional soft lithographic techniques, called microtransfer molding ({mu}TM), was developed by the Whitesides group in 1996. Although {mu}TM technique potentially has a number of advantages to overcome the limit of conventional photolithographic techniques in building up 3D microstructures, it has not been studied intensively after its demonstration. This is mainly because of technical challenges in the nature of layer-by-layer fabrication, such as the demand of very high yield in fabrication. After two years of study on conventional {mu}TM, We have developed an advanced microtransfer molding technique, called two-polymer microtransfer molding (2P-{mu}TM) that shows an extremely high yield in layer-by-layer microfabrication sufficient to produce highly layered microstructures. The use of two different photo-curable prepolymers, a filler and an …

Multianalyte bio(chemical) sensors are extensively researched for monitoring analytes in complex systems, such as blood serum. As a step towards developing such multianalyte sensors, we studied a novel, structurally integrated, organic light emitting device (OLED)-based sensing platform for detection of lactate. Lactate biosensors have attracted numerous research efforts, due to their wide applications in clinical diagnosis, athletic training and food industry. The OLED-based sensor is based on monitoring the oxidation reaction of lactate, which is catalyzed by the lactate oxidase (LOX) enzyme. The sensing component is based on an oxygen-sensitive dye, Platinum octaethyl porphyrin (PtOEP), whose photoluminescence (PL) lifetime {tau} decreases as the oxygen level increases. The PtOEP dye was embedded in a thin film polystyrene (PS) matrix; the LOX was dissolved in solution or immobilized in a sol-gel matrix. {tau} was measured as a function of the lactate concentration; as the lactate concentration increases, {tau} increases due to increased oxygen consumption. The sensors performance is discussed in terms of the detection sensitivity, dynamic range, and response time. A response time of {approx}32 sec was achieved when the LOX was dissolved in solution and kept in a closed cell. Steps towards development of a multianalyte sensor array using an array …

Immunoassays have been utilized for the detection of biological analytes for several decades. Many formats and detection strategies have been explored, each having unique advantages and disadvantages. More recently, surface-enhanced Raman scattering (SERS) has been introduced as a readout method for immunoassays, and has shown great potential to meet many key analytical figures of merit. This technology is in its infancy and this dissertation explores the diversity of this method as well as the mechanism responsible for surface enhancement. Approaches to reduce assay times are also investigated. Implementing the knowledge gained from these studies will lead to a more sensitive immunoassay requiring less time than its predecessors. This dissertation is organized into six sections. The first section includes a literature review of the previous work that led to this dissertation. A general overview of the different approaches to immunoassays is given, outlining the strengths and weaknesses of each. Included is a detailed review of binding kinetics, which is central for decreasing assay times. Next, the theoretical underpinnings of SERS is reviewed at its current level of understanding. Past work has argued that surface plasmon resonance (SPR) of the enhancing substrate influences the SERS signal; therefore, the SPR of the extrinsic …

Eddy current nondestructive evaluation (NDE) is usually carried out by exciting a time harmonic field using an inductive probe. However, a viable alternative is to use transient eddy current NDE in which a current pulse in a driver coil produces a transient .eld in a conductor that decays at a rate dependent on the conductivity and the permeability of the material and the coil configuration. By using transient eddy current, it is possible to estimate the properties of the conductive medium and to locate and size potential .aws from the measured probe response. The fundamental study described in this dissertation seeks to establish a theoretical understanding of the transient eddy current NDE. Compared with the Fourier transform method, the derived analytical formulations are more convenient when the transient eddy current response within a narrow time range is evaluated. The theoretical analysis provides a valuable tool to study the effect of layer thickness, location of defect, crack opening as well as the optimization of probe design. Analytical expressions have been developed to evaluate the transient response due to eddy currents in a conductive plate based on two asymptotic series. One series converges rapidly for a short time regime and the other …

This study establishes a set of magnetics-based tools that have been integrated with microfluidic systems. The overall impact of the work begins to enable the rapid and efficient manipulation and detection of magnetic entities such as particles, picoliter-sized droplets, or bacterial cells. Details of design, fabrication, and theoretical and experimental assessments are presented. The manipulation strategy has been demonstrated in the format of a particle diverter, whereby micron-sized particles are actively directed into desired flow channels at a split-flow junction by means of integrated microelectromagnets. Magnetic detection has been realized by deploying Giant Magnetoresistance (GMR) sensors--microfabricated structures originally developed for use as readout elements in computer hard-drives. We successfully transferred the GMR technology to the lab-on-a-chip arena, and demonstrated the versatility of the concept in several important areas: real-time, integrated monitoring of the properties of multiphase droplet flows; rapid quantitative determination of the concentration of magnetic nanoparticles in droplets of ferrofluids; and high-speed detection of individual magnetic microparticles and magnetotactic bacteria. The study also includes novel schemes for hydrodynamic flow focusing that work in conjunction with GMR-based detection to ensure precise navigation of the sample stream through the GMR detection volume, therefore effectively establishing a novel concept of a microfabricated …