The purpose of this research was to expand the chemiluminescence microscopy applications in live bacterial/mammalian cell imaging and to improve the detection sensitivity for ATP leaking or release events. We first demonstrated that chemiluminescence (CL) imaging can be used to interrogate single bacterial cells. While using a luminometer allows detecting ATP from cell lysate extracted from at least 10 bacterial cells, all previous cell CL detection never reached this sensitivity of single bacteria level. We approached this goal with a different strategy from before: instead of breaking bacterial cell membrane and trying to capture the transiently diluted ATP with the firefly luciferase CL assay, we introduced the firefly luciferase enzyme into bacteria using the modern genetic techniques and placed the CL reaction substrate D-luciferin outside the cells. By damaging the cell membrane with various antibacterial drugs including antibiotics such as Penicillins and bacteriophages, the D-luciferin molecules diffused inside the cell and initiated the reaction that produces CL light. As firefly luciferases are large protein molecules which are retained within the cells before the total rupture and intracellular ATP concentration is high at the millmolar level, the CL reaction of firefly luciferase, ATP and D-luciferin can be kept for a relatively …

Groundwater irrigation is critical to food production and, in turn, to humankind's relationship with its environment. The development of groundwater in Santa Clara Valley, California during the early twentieth century is instructive because (1) responses to unsustainable resource use were largely successful; (2) the proposals for the physical management of the water, although not entirely novel, incorporated new approaches which reveal an evolving relationship between humans and the hydrologic cycle; and (3) the valley serves as a natural laboratory where natural (groundwater basin, surface watershed) and human (county, water district) boundaries generally coincide. Here, I investigate how water resources development and management in Santa Clara Valley was influenced by, and reflective of, a broad understanding of water as a natural resource, including scientific and technological innovations, new management approaches, and changing perceptions of the hydrologic cycle. Market demands and technological advances engendered reliance on groundwater. This, coupled with a series of dry years and laissez faire government policies, led to overdraft. Faith in centralized management and objective engineering offered a solution to concerns over resource depletion, and a group dominated by orchardists soon organized, fought for a water conservation district, and funded an investigation to halt the decline of well …

Millions of people suffering from diseases such as retinitis pigmentosa and macular degeneration are legally blind due to the loss of photoreceptor function. Fortunately a large percentage of the neural cells connected to the photoreceptors remain viable, and electrical stimulation of these cells has been shown to result in visual perception. These findings have generated worldwide efforts to develop a retinal prosthesis device, with the hope of restoring vision. Advances in microfabrication, integrated circuits, and wireless technologies provide the means to reach this challenging goal. This dissertation describes the development of innovative silicone-based microfabrication techniques for producing an implantable microelectrode array. The microelectrode array is a component of an epiretinal prosthesis being developed by a multi-laboratory consortium. This array will serve as the interface between an electronic imaging system and the human eye, directly stimulating retinal neurons via thin film conducting traces. Because the array is intended as a long-term implant, vital biological and physical design requirements must be met. A retinal implant poses difficult engineering challenges due to the size of the intraocular cavity and the delicate retina. Not only does it have to be biocompatible in terms of cytotoxicity and degradation, but it also has to be structurally …

The detection and positive identification of the short-lived, low cross section isotopes used in the chemical studies of the heaviest elements are usually accomplished by measuring their alpha-decay, thus the nuclear properties of the heaviest elements must be examined simultaneously with their chemical properties. The isotopes 224 Pa and 266,267 Bh have been studied extensively as an integral part of the investigation of the heaviest members of the groups five and seven of the periodic table. The half-life of 224 Pa was determined to be 855 plus/minus19 ms by measuring its alpha-decay using our rotating wheel, solid state detector system at the Lawrence Berkeley National Laboratory 88-Inch Cyclotron. Protactinium was produced by bombardment of a bismuth target. New neutron rich isotopes, 267 Bh and 266 Bh, were produced in bombardments of a 249 Bk target and their decay was observed using the rotating wheel system. The 266 Bh that was produced decays with a half-life of approximately 1 s by emission of alpha particles with an average energy of 9.25 plus/minus 0.03 MeV. 267 Bh was observed to decay with a 17 s half-life by emission of alpha-particles with an average energy of 8.83 plus/minus 0.03 MeV. The chemical behavior …

Information technology (IT) is becoming increasingly pervasive throughout society as more data is digitally processed, stored, and transferred. The infrastructure that supports IT activity is growing accordingly, and data center energy demands haveincreased by nearly a factor of four over the past decade. Data centers house IT equipment and require significantly more energy to operate per unit floor area thanconventional buildings. The economic and environmental ramifications of continued data center growth motivate the need to explore energy-efficient methods to operate these buildings. A substantial portion of data center energy use is dedicated to removing the heat that is generated by the IT equipment. Using economizers to introduce large airflow rates of outside air during favorable weather could substantially reduce the energy consumption of data center cooling. Cooling buildings with economizers is an established energy saving measure, but in data centers this strategy is not widely used, partly owing to concerns that the large airflow rates would lead to increased indoor levels of airborne particles, which could damage IT equipment. The environmental conditions typical of data centers and the associated potential for equipment failure, however, are not well characterized. This barrier to economizer implementation illustrates the general relationship between energy use …

Air quality planning in Central California is complicated and controversial despite millions of dollars invested to improve scientific understanding. This research describes and critiques the use of photochemical air quality simulation modeling studies in planning to attain standards for ground-level ozone in the San Francisco Bay Area and the San Joaquin Valley during the 1990's. Data are gathered through documents and interviews with planners, modelers, and policy-makers at public agencies and with representatives from the regulated and environmental communities. Interactions amongst organizations are diagramed to identify significant nodes of interaction. Dominant policy coalitions are described through narratives distinguished by their uses of and responses to uncertainty, their exposures to risks, and their responses to the principles of conservatism, civil duty, and caution. Policy narratives are delineated using aggregated respondent statements to describe and understand advocacy coalitions. I found that models impacted the planning process significantly, but were used not purely for their scientific capabilities. Modeling results provided justification for decisions based on other constraints and political considerations. Uncertainties were utilized opportunistically by stakeholders instead of managed explicitly. Ultimately, the process supported the partisan views of those in control of the modeling. Based on these findings, as well as a review …

A digital network of 24 seismograph stations was operated from September 15, 1987 to September 30, 1988, by Lawrence Livermore National Laboratory and Unocal as part of the Salton Sea Scientific Drilling Project to study seismicity related to tectonics and geothermal activity near the drilling site. More than 2001 microearthquakes were relocated in this study in order to image any pervasive structures that may exist within the Salton Sea geothermal field. First, detailed velocity models were obtained through standard 1-D inversion techniques. These velocity models were then used to relocate events using both single event methods and Double-Differencing, a joint hypocenter location method. An anisotropic velocity model was built from anisotropy estimates obtained from well logs within the study area. During the study period, the Superstition wills sequence occurred with two moderate earthquakes of MS 6.2 and MS 6.6. These moderate earthquakes caused a rotation of the stress field as observed from the inversion of first motion data from microearthquakes at the Salton Sea geothermal field. Coulomb failure analysis also indicates that microearthquakes occurring after the Superstition Hills sequence are located within a region of stress increase suggesting stress triggering caused by the moderate earthquakes.

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 …

The computing infrastructures of the modern high energy physics experiments need to address an unprecedented set of requirements. The collaborations consist of hundreds of members from dozens of institutions around the world and the computing power necessary to analyze the data produced surpasses already the capabilities of any single computing center. A software infrastructure capable of seamlessly integrating dozens of computing centers around the world, enabling computing for a large and dynamical group of users, is of fundamental importance for the production of scientific results. Such a computing infrastructure is called a computational grid. The SAM-Grid offers a solution to these problems for CDF and DZero, two of the largest high energy physics experiments in the world, running at Fermilab. The SAM-Grid integrates standard grid middleware, such as Condor-G and the Globus Toolkit, with software developed at Fermilab, organizing the system in three major components: data handling, job handling, and information management. This dissertation presents the challenges and the solutions provided in such a computing infrastructure.

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.

Single Particle Aerosol Mass Spectrometry (SPAMS) was evaluated as a real-time detection technique for single particles of high explosives. Dual-polarity time-of-flight mass spectra were obtained for samples of 2,4,6-trinitrotoluene (TNT), 1,3,5-trinitro-1,3,5-triazinane (RDX), and pentaerythritol tetranitrate (PETN); peaks indicative of each compound were identified. Composite explosives, Comp B, Semtex 1A, and Semtex 1H were also analyzed, and peaks due to the explosive components of each sample were present in each spectrum. Mass spectral variability with laser fluence is discussed. The ability of the SPAMS system to identify explosive components in a single complex explosive particle ({approx}1 pg) without the need for consumables is demonstrated. SPAMS was also applied to the detection of Chemical Warfare Agent (CWA) simulants in the liquid and vapor phases. Liquid simulants for sarin, cyclosarin, tabun, and VX were analyzed; peaks indicative of each simulant were identified. Vapor phase CWA simulants were adsorbed onto alumina, silica, Zeolite, activated carbon, and metal powders which were directly analyzed using SPAMS. The use of metal powders as adsorbent materials was especially useful in the analysis of triethyl phosphate (TEP), a VX stimulant, which was undetectable using SPAMS in the liquid phase. The capability of SPAMS to detect high explosives and CWA …

Colloidal processing is an effective and reliable approach in the fabrication of the advanced ceramic products. Successful colloidal processing of fine ceramic powders requires accurate control of the rheological properties. The accurate control relies on the understanding the influences of various colloidal parameters on the rheological properties. Almost all research done on the rheology paid less attention to the interactions of particle and solvent. However, the interactions of the particles are usually built up through the media in which the particles are suspended. Therefore, interactions of the particle with the media, the adsorbed layers on the particle surface, and chemical and physical properties of media themselves must influence the rheology of the suspension, especially for the dense suspensions containing nanosized particles. Relatively little research work has been reported in this area. This thesis addresses the rheological properties of nanometric alumina aqueous suspensions, and paying more attention to the interactions between particle and solvent, which in turn influence the particle-particle interactions. Dense nanometric alumina aqueous suspensions with low viscosity were achieved by environmentally-benign fructose additives. The rheology of nanometric alumina aqueous suspensions and its variation with the particle volume fraction and concentration of fructose were explored by rheometry. The adsorptions of …

The risk of accidental detonation is present whenever any type of high explosives processing activity is performed. These activities are typically carried out indoors to protect processing equipment from the weather and to hide possibly secret processes from view. Often, highly strengthened reinforced concrete buildings are employed to house these activities. These buildings may incorporate several design features, including the use of lightweight frangible blowout panels, to help mitigate blast effects. These panels are used to construct walls that are durable enough to withstand the weather, but are of minimal weight to provide overpressure relief by quickly moving outwards and creating a vent area during an accidental explosion. In this study the behavior of blowout panels under various blast loading conditions was examined. External loadings from explosions occurring in nearby rooms were of primary interest. Several reinforcement systems were designed to help blowout panels resist failure from external blast loads while still allowing them to function as vents when subjected to internal explosions. The reinforcements were studied using two analytical techniques, yield-line analysis and modal analysis, and the hydrocode AUTODYN. A blowout panel reinforcement design was created that could prevent panels from being blown inward by external explosions. This design …

Abstract: The risk of accidental detonation is present whenever any type of high explosives processing activity is performed. These activities are typically carried out indoors to protect processing equipment from the weather and to hide possibly secret processes from view. Often, highly strengthened reinforced concrete buildings are employed to house these activities. These buildings may incorporate several design features, including the use of lightweight frangible blowout panels, to help mitigate blast effects. These panels are used to construct walls that are durable enough to withstand the weather, but are of minimal weight to provide overpressure relief by quickly moving outwards and creating a vent area during an accidental explosion. In this study the behavior of blowout panels under various blast loading conditions was examined. External loadings from explosions occurring in nearby rooms were of primary interest. Several reinforcement systems were designed to help blowout panels resist failure from external blast loads while still allowing them to function as vents when subjected to internal explosions. The reinforcements were studied using two analytical techniques, yield-line analysis and modal analysis, and the hydrocode AUTODYN. A blowout panel reinforcement design was created that could prevent panels from being blown inward by external explosions. This …

Capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) are widely used analytical separation techniques with many applications in chemical, biochemical, and biomedical sciences. Conventional analyte identification in these techniques is based on retention/migration times of standards; requiring a high degree of reproducibility, availability of reliable standards, and absence of coelution. From this, several new information-rich detection methods (also known as hyphenated techniques) are being explored that would be capable of providing unambiguous on-line identification of separating analytes in CE and HPLC. As further discussed, a number of such on-line detection methods have shown considerable success, including Raman, nuclear magnetic resonance (NMR), mass spectrometry (MS), and fluorescence line-narrowing spectroscopy (FLNS). In this thesis, the feasibility and potential of combining the highly sensitive and selective laser-based detection method of FLNS with analytical separation techniques are discussed and presented. A summary of previously demonstrated FLNS detection interfaced with chromatography and electrophoresis is given, and recent results from on-line FLNS detection in CE (CE-FLNS), and the new combination of HPLC-FLNS, are shown.

Collagen is a key structural protein in the body; several pathological conditions lead to changes in collagen. Among imaging modalities that can be used in vivo, second harmonic generation (SHG) microscopy has a key advantage: it provides {approx}1 {micro}m resolution information about collagen structure as a function of depth. A new technique--polarization-modulated SHG--is presented: it permits simultaneous measurement of collagen orientation, of a lower bound on the magnitude of the second order nonlinear susceptibility tensor, and of the ratio of the two independent elements in this tensor. It is applied to characterizing SHG in collagen and to determining effects of biologically relevant changes in collagen structure. The magnitude of the second harmonic signal in two dimensional images varies with position even in structurally homogeneous tissue; this phenomenon is due to interference between second harmonic light generated by neighboring fibrils, which are randomly oriented parallel or anti-parallel to each other. Studies in which focal spot size was varied indicated that regions where fibrils are co-oriented are less than {approx}1.5 {micro}m in diameter. A quartz reference was used to determine the spot size as well as a lower limit (d{sub xxx} > 0.3 pm/V) for the magnitude of the second order nonlinear …

An analysis of completed decommissioning projects is used to construct predictive estimates for worker exposure to radioactivity during decommissioning activities. The preferred organizational method for the completed decommissioning project data is to divide the data by type of facility, whether decommissioning was performed on part of the facility or the complete facility, and the level of radiation within the facility prior to decommissioning (low, medium, or high). Additional data analysis shows that there is not a downward trend in worker exposure data over time. Also, the use of a standard estimate for worker exposure to radioactivity may be a best estimate for low complete storage, high partial storage, and medium reactor facilities; a conservative estimate for some low level of facility radiation facilities (reactor complete, research complete, pits/ponds, other), medium partial process facilities, and high complete research facilities; and an underestimate for the remaining facilities. Limited data are available to compare different decommissioning alternatives, so the available data are reported and no conclusions can been drawn. It is recommended that all DOE sites and the NRC use a similar method to document worker hours, worker exposure to radiation (person-rem), and standard industrial accidents, injuries, and deaths for all completed decommissioning …

Hard, wear-resistant coatings of thin film borides based on AlMgB{sub 14} have the potential to be applied industrially to improve the tool life of cutting tools and pump vanes and may account for several million dollars in savings as a result of reduced wear on these parts. Past work with this material has shown that it can have a hardness of up to 45GPa and be fabricated into thin films with a similar hardness using pulsed laser deposition. These films have already been shown to be promising for industrial applications. Cutting tools coated with AlMgB{sub 14} used to mill titanium alloys have been shown to substantially reduce the wear on the cutting tool and extend its cutting life. However, little research into the thin film fabrication process using pulsed laser deposition to make AlMgB{sub 14} has been conducted. In this work, research was conducted into methods to optimize the deposition parameters for the AlMgB{sub 14} films. Processing methods to eliminate large particles on the surface of the AlMgB{sub 14} films, produce films that were at least 1m thick, reduce the surface roughness of the films, and improve the adhesion of the thin films were investigated. Use of a femtosecond laser …

This thesis concerns the development and characterization of a prototype Silicon micro-strip detector that can be used in the forward (high rapidity) region of a hadron collider. These detectors must operate in a high radiation environment without any important degradation of their performance. The innovative feature of these detectors is the readout electronics, which, being completely data-driven, allows for the direct use of the detector information at the lowest level of the trigger. All the particle hits on the detector can be readout in real-time without any external trigger and any particular limitation due to dead-time. In this way, all the detector information is available to elaborate a very selective trigger decision based on a fast reconstruction of tracks and vertex topology. These detectors, together with the new approach to the trigger, have been developed in the context of the BTeV R&D program; our aim was to define the features and the design parameters of an optimal experiment for heavy flavour physics at hadron colliders. Application of these detectors goes well beyond the BTeV project and, in particular, involves the future upgrades of experiments at hadron colliders, such as Atlas, CMS and LHCb. These experiments, indeed, are already considering for …

The phenomenon of flavour oscillations of neutrinos created in the atmosphere was first reported by the Super-Kamiokande collaboration in 1998 and since then has been confirmed by Soudan 2 and MACRO. The MINOS Far Detector is the first magnetized neutrino detector able to study atmospheric neutrino oscillations. Although it was designed to detect neutrinos from the NuMI beam, it provides a unique opportunity to measure the oscillation parameters for neutrinos and anti-neutrinos independently. The MINOS Far Detector was completed in August 2003 and since then has collected 2.52 kton-years of atmospheric data. Atmospheric neutrino interactions contained within the volume of the detector are separated from the dominant background from cosmic ray muons. Thirty seven events are selected with an estimated background contamination of less than 10%. Using the detector's magnetic field, 17 neutrino events and 6 anti-neutrino events are identified, 14 events have ambiguous charge. The neutrino oscillation parameters for {nu}{sub {mu}} and {bar {nu}}{sub {mu}} are studied using a maximum likelihood analysis. The measurement does not place constraining limits on the neutrino oscillation parameters due to the limited statistics of the data set analysed. However, this thesis represents the first observation of charge separated atmospheric neutrino interactions. It also …

The MINOS experiment uses a long baseline neutrino beam, measured 1 km downstream from its origin in the Near Detector at Fermilab, and 734 km later in the large underground Far Detector in the Soudan mine. By comparing these two measurements, MINOS can probe the atmospheric domain of the neutrino oscillation phenomenology with unprecedented precision. Besides the ability to perform a world leading determination of the {Delta}m{sub 23}{sup 2} and {theta}{sub 23} parameters, via {nu}{sub {mu}} flux disappearance, MINOS has the potential to make a leading measurement of {nu}{sub {mu}} {yields} {nu}{sub e} oscillations in the atmospheric sector by looking for {nu}{sub e} appearance at the Far Detector. The observation of {nu}{sub e} appearance, tantamount to establishing a non-zero value of the {theta}{sub 13} mixing angle, opens the way to studies of CP violation in the leptonic sector, the neutrino spectral mass pattern ordering and neutrino oscillations in matter, the driving motivations of the next generation of neutrino experiments. In this thesis, we study the MINOS potential for measuring {theta}{sub 13} in the context of the MINOS Mock Data Challenge using a multivariate discriminant analysis method. We show the method's validity in the application to {nu}{sub e} event classification and …

The main aim of physics research is to obtain a consistent description of nature leading to a detailed understanding of the phenomena observed in experiments. The field of particle physics focuses on the discovery and understanding of the fundamental particles and the forces by which they interact with each other. Using methods from group theory, the present knowledge can be mathematically described by the so-called ''Standard Model'', which interprets the fundamental particles (quarks and leptons) as quantum-mechanical fields interacting via the electromagnetic, weak and strong force. These interactions are mediated via gauge particles such as the photon (for the electromagnetic force), W{sup {+-}} and Z{sup 0} (for the weak force) and gluons (for the strong force). Gravitation is not yet included in this description as it presently cannot be formulated in a way to be incorporated in the Standard Model. However, the gravitational force is negligibly small on microscopic levels. The validity of this mathematical approach is tested experimentally by accelerating particles such as electrons and protons, as well as their antiparticles, to high energies and observing the reactions as these particles collide using sophisticated detectors. Due to the high energy of the particles involved, these detectors need to be …

Recent clinical evaluations of scintimammography (radionuclide breast imaging) are promising and suggest that this modality may prove a valuable complement to X-ray mammography and traditional breast cancer detection and diagnosis techniques. Scintimammography, however, typically has difficulty revealing tumors that are less than 1 cm in diameter, are located in the medial part of the breast, or are located in the axillary nodes. These shortcomings may in part be due to the use of large, conventional Anger cameras not optimized for breast imaging. In this thesis I present compact single photon camera technology designed specifically for scintimammography which strives to alleviate some of these limitations by allowing better and closer access to sites of possible breast tumors. Specific applications are outlined. The design is modular, thus a camera of the desired size and geometry can be constructed from an array (or arrays) of individual modules and a parallel hole lead collimator for directional information. Each module consists of: (1) an array of 64 discrete, optically-isolated CsI(Tl) scintillator crystals 3 x 3 x 5 mm{sup 3} in size, (2) an array of 64 low-noise Si PIN photodiodes matched 1-to-1 to the scintillator crystals, (3) an application-specific integrated circuit (ASIC) that amplifies the …

The penetration of ambient air pollutants into the indoor environment is of concern owing to several factors: (1) epidemiological studies have shown a strong association between ambient fine particulate pollution and elevated risk of human mortality; (2) people spend most of their time in indoor environments; and (3) most information about air pollutant concentration is only available from ambient routine monitoring networks. A good understanding of ambient air pollutant transport from source to receptor requires knowledge about pollutant penetration across building envelopes. Therefore, it is essential to gain insight into particle penetration in infiltrating air and the factors that affect it in order to assess human exposure more accurately, and to further prevent adverse human health effects from ambient particulate pollution. In this dissertation, the understanding of air pollutant infiltration across leaks in the building envelope was advanced by performing modeling predictions as well as experimental investigations. The modeling analyses quantified the extent of airborne particle and reactive gas (e.g., ozone) penetration through building cracks and wall cavities using engineering analysis that incorporates existing information on building leakage characteristics, knowledge of pollutant transport processes, as well as pollutant-surface interactions. Particle penetration is primarily governed by particle diameter and by the …