An implicit version of the Smooth Particle Hydrodynamic (SPH) code SPHINX has been written and is working. In conjunction with the SPHINX code the new implicit code models fluids and solids under a wide range of conditions. SPH codes are Lagrangian, meshless and use particles to model the fluids and solids. The implicit code makes use of the Krylov iterative techniques for solving large linear-systems and a Newton-Raphson method for non-linear corrections. It uses numerical derivatives to construct the Jacobian matrix. It uses sparse techniques to save on memory storage and to reduce the amount of computation. It is believed that this is the first implicit SPH code to use Newton-Krylov techniques, and is also the first implicit SPH code to model solids. A description of SPH and the techniques used in the implicit code are presented. Then, the results of a number of tests cases are discussed, which include a shock tube problem, a Rayleigh-Taylor problem, a breaking dam problem, and a single jet of gas problem. The results are shown to be in very good agreement with analytic solutions, experimental results, and the explicit SPHINX code. In the case of the single jet of gas case it has …

A new type of thermodynamic device combining a thermodynamic cycle with the externally applied steady flow of an open thermodynamic process is discussed and experimentally demonstrated. The gas flowing through this device can be heated or cooled in a series of semi-open cyclic steps. The combination of open and cyclic flows makes possible the elimination of some or all of the heat exchangers (with their associated irreversibility). Heat is directly exchanged with the process fluid as it flows through the device when operating as a refrigerator, producing a staging effect that tends to increase First Law thermodynamic efficiency. An open-flow thermoacoustic refrigerator was built to demonstrate this concept. Several approaches are presented that describe the physical characteristics of this device. Tests have been conducted on this refrigerator with good agreement with a proposed theory.

Reliable group ordered delivery of multicast messages in a distributed system is a useful service that simplifies the programming of distributed applications. Such a service helps to maintain the consistency of replicated information and to coordinate the activities of the various processes. With the increasing popularity of the Internet, there is an increasing interest in scaling the protocols that provide this service to the environment of the Internet. The InterGroup protocol suite, described in this dissertation, provides such a service, and is intended for the environment of the Internet with scalability to large numbers of nodes and high latency links. The InterGroup protocols approach the scalability problem from various directions. They redefine the meaning of group membership, allow voluntary membership changes, add a receiver-oriented selection of delivery guarantees that permits heterogeneity of the receiver set, and provide a scalable reliability service. The InterGroup system comprises several components, executing at various sites within the system. Each component provides part of the services necessary to implement a group communication system for the wide-area. The components can be categorized as: (1) control hierarchy, (2) reliable multicast, (3) message distribution and delivery, and (4) process group membership. We have implemented a prototype of the …

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 …

This dissertation has involved the exploration of a new effect in photoelectron emission, multi-atom resonant photoemission (MARPE), as well as the development of new software, data analysis techniques, and detectors of general use in such research. We present experimental and theoretical results related to MARPE, in which the photoelectron intensity from a core level on one atom is influenced by a core-level absorption resonance on another. We point out that some of our and others prior experimental data has been strongly influenced by detector non-linearity and that the effects seen in new corrected data are smaller and of different form. Corrected data for the MnO(001) system with resonance between the O 1s and Mn 2p energy levels are found to be well described by an extension of well-known intraatomic resonant photoemission theory to the interatomic case, provided that interactions beyond the usual second-order Kramers-Heisenberg treatment are included. This theory is also found to simplify under certain conditions so as to yield results equivalent to a classical x-ray optical approach, with the latter providing an accurate and alternative, although less detailed and general, physical picture of these effects. Possible future applications of MARPE as a new probe of near-neighbor identities and …

The ability to model wave propagation in circular cylindrical bars of finite length numerically or analytically has many applications. In this thesis the capability of an explicit finite element method to model longitudinal waves in cylindrical rods with circular cross-sections is explored. Dispersion curves for the first four modes are compared to the analytical solution to determine the accuracy of various element sizes and time steps. Values for the time step and element size are determined that retain accuracy while minimizing computational time. The modeling parameters are validated by calculating a signal propagated with a broadband input force. Limitations on the applicability are considered along with modeling parameters that should be applicable to more general geometries.

The author performs image reconstruction for a novel Positron Emission Tomography camera that is optimized for breast cancer imaging. This work addresses for the first time, the problem of fully-3D, tomographic reconstruction using a septa-less, stationary, (i.e. no rotation or linear motion), and rectangular camera whose Field of View (FOV) encompasses the entire volume enclosed by detector modules capable of measuring Depth of Interaction (DOI) information. The camera is rectangular in shape in order to accommodate breasts of varying sizes while allowing for soft compression of the breast during the scan. This non-standard geometry of the camera exacerbates two problems: (a) radial elongation due to crystal penetration and (b) reconstructing images from irregularly sampled data. Packing considerations also give rise to regions in projection space that are not sampled which lead to missing information. The author presents new Fourier Methods based image reconstruction algorithms that incorporate DOI information and accommodate the irregular sampling of the camera in a consistent manner by defining lines of responses (LORs) between the measured interaction points instead of rebinning the events into predefined crystal face LORs which is the only other method to handle DOI information proposed thus far. The new procedures maximize the use …

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S{sub 3} {r_arrow} [S{sub 4}] {r_arrow} S{sub 0} transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn K{beta} X-ray emission spectroscopy (Kb XES) to this problem for the first time. The K{beta} XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electron paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S{sub 2} {r_arrow} S{sub 3} transition, in contrast to the S{sub 0} {r_arrow} S{sub 1} and S{sub 1} {r_arrow} S{sub 2} transitions, does not involve a Mn-centered oxidation. This is rationalized by manganese {mu}-oxo bridge radical formation during the S{sub 2} {r_arrow} S{sub 3} transition. Using extended X-ray absorption fine structure (EXAFS) spectroscopy, the local environment of the Mn atoms in the S{sub 0} state has been structurally characterized. These results show that the Mn-Mn distance in one of the di-{mu}-oxo-bridged Mn-Mn moieties increases from 2.7 …

An accelerator-based experiment was performed using the CEBAF accelerator of the Thomas Jefferson National Accelerator Facility to investigate a predicted sensitivity of the beam polarization to the vertical betatron orbit in the recirculation arcs. This is the first measurement of any such effect at CEBAF, and provides information about the polarized beam delivery performance of the accelerator. A brief description of the accelerator is given, followed by the experimental methods used and the relevant issues involved in measuring a small ({approximately} 10{sup {minus}2}) change in the beam polarization. Results of measurements of the polarization sensitivity parameters and the machine energy by polarization transport techniques are presented. The parameters were obtained by measurement of the strength of the effect as a function of orbit amplitude and spin orientation, to confirm the predicted coupling between the spin orientation and the quadrupole fields in the beam transport system. This experiment included characterizing the injector spin manipulation system and 5 MeV Mott polarimeter, modeling of the polarization transport of the accelerator, installation of magnets to create a modulated orbit perturbation in a single recirculation arc, and detailed studies of the Hall C Moeller polarimeter.

The surface structures of NaCl(100), LiF(100) and alpha-MgCl2(0001) adsorbed on various metal single crystals have been determined by low energy electron diffraction (LEED). Thin films of these salts were grown on metal substrates by exposing the heated metal surface to a molecular flux of salt emitted from a Knudsen cell. This method of investigating thin films of insulators (ionic salts) on a conducting substrate (metal) circumvents surface charging problems that plagued bulk studies, thereby allowing the use of electron-based techniques to characterize the surface.

Semiconductor nanocrystals are a system which has been the focus of interest due to their size dependent properties and their possible use in technological applications. Many chemical and physical properties vary systematically with the size of the nanocrystal and thus their study enables the investigation of scaling laws. Due to the increasing surface to volume ratio as size is decreased, the surfaces of nanocrystals are expected to have a large influence on their electronic, thermodynamic, and chemical behavior. In spite of their importance, nanocrystal surfaces are still relatively uncharacterized in terms of their structure, electronic properties, bonding, and reactivity. Investigation of nanocrystal surfaces is currently limited by what techniques to use, and which methods are suitable for nanocrystals is still being determined. This work presents experiments using x-ray and electronic spectroscopies to explore the structure, reactivity, and electronic properties of semiconductor (CdSe, InAs) nanocrystals and how they vary with size. Specifically, x-ray absorption near edge spectroscopy (XANES) in conjunction with multiple scattering simulations affords information about the structural disorder present at the surface of the nanocrystal. X-ray photoelectron spectroscopy (XPS) and ultra-violet photoelectron spectroscopy (UPS) probe the electronic structure in terms of hole screening, and also give information about band …

Functionally Graded Materials (FGMs) have a spatial variation in physical properties that can be tailored to meet the needs of a specific application and/or to minimize internal stresses arising from thermal and elastic mismatch. Modeling these materials as inhomogeneous continua allows assessment of the role of the gradient without requiring detailed knowledge of the microstructure. Motivated by the relative difficulty of obtaining analytical solutions to boundary value problems for FGMs, an accurate finite-element code is developed for obtaining numerical planar and axisymmetric linear thermoelastic solutions. In addition an approximate analytical technique for mapping homogeneous-modulus solutions to those for FGMs is assessed and classes of problems to which it applies accurately are identified. The fracture mechanics analysis of FGMs can be characterized by the classic stress intensities, KI and KII, but there has been scarce progress in understanding the role of the modulus gradient in determining fracture initiation and propagation. To address this question, a statistical fracture model is used to correlate near-tip stresses with brittle fracture initiation behavior. This describes the behavior of a material experiencing fracture initiation away from the crack tip. Widely dispersed zones of fracture initiation sites are expected. Finite-length kinks are analyzed to describe the crack …

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Relationships between intrinsic mechanical hardness and atomic-scale properties are reviewed, Hardness scales closely and linearly with shear modulus for a given class of material (covalent, ionic or metallic). A two-parameter fit and a Peierls-stress model produce a more universal scaling relationship, but no model can explain differences in hardness between the transition metal carbides and nitrides. Calculations of ''ideal strength'' (defined by the limit of elastic stability of a perfect crystal) are proposed. The ideal shear strengths of fcc aluminum and copper are calculated using ab initio techniques and allowing for structural relaxation of all five strain components other than the imposed strain. The strengths of Al and Cu are similar (8-9% of the shear modulus), but the geometry of the relaxations in Al and Cu is very different. The relaxations are consistent with experimentally measured third-order elastic constants. The general thermodynamic conditions of elastic stability that set the upper limits of mechanical strength are derived. The conditions of stability are shown for cubic (hydrostatic), tetragonal (tensile) and monoclinic (shear) distortions of a cubic crystal. The implications of this stability analysis to first-principles calculations of ideal strength are discussed, and a method to detect instabilities orthogonal to the direction of …

The fundamental motivation for the research presented in this dissertation was the need to development a more accurate prediction method for characterization of mixed radiation fields around medical electron accelerators (MEAs). Specifically, a model is developed for simulation of neutron and other particle production from photonuclear reactions and incorporated in the Monte Carlo N-Particle (MCNP) radiation transport code. This extension of the capability within the MCNP code provides for the more accurate assessment of the mixed radiation fields. The Nuclear Theory and Applications group of the Los Alamos National Laboratory has recently provided first-of-a-kind evaluated photonuclear data for a select group of isotopes. These data provide the reaction probabilities as functions of incident photon energy with angular and energy distribution information for all reaction products. The availability of these data is the cornerstone of the new methodology for state-of-the-art mutually coupled photon-neutron transport simulations. The dissertation includes details of the model development and implementation necessary to use the new photonuclear data within MCNP simulations. A new data format has been developed to include tabular photonuclear data. Data are processed from the Evaluated Nuclear Data Format (ENDF) to the new class ''u'' A Compact ENDF (ACE) format using a standalone processing …

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In this work, we develop a new spatial discretization scheme that may be used to numerically solve the neutron transport equation. This new discretization extends the family of corner balance spatial discretizations to include spatial grids of arbitrary polyhedra. This scheme enforces balance on subcell volumes called corners. It produces a lower triangular matrix for sweeping, is algebraically linear, is non-negative in a source-free absorber, and produces a robust and accurate solution in thick diffusive regions. Using an asymptotic analysis, we design the scheme so that in thick diffusive regions it will attain the same solution as an accurate polyhedral diffusion discretization. We then refine the approximations in the scheme to reduce numerical diffusion in vacuums, and we attempt to capture a second order truncation error. After we develop this Upstream Corner Balance Linear (UCBL) discretization we analyze its characteristics in several limits. We complete a full diffusion limit analysis showing that we capture the desired diffusion discretization in optically thick and highly scattering media. We review the upstream and linear properties of our discretization and then demonstrate that our scheme captures strictly non-negative solutions in source-free purely absorbing media. We then demonstrate the minimization of numerical diffusion of a …

This experiment was one of the first photoproduction experiments performed at Jefferson Lab using the CLAS and the Photon Tagger. The event reconstruction and the photon flux determination procedures have been developed and were proven to work well as we can see from the cross section measurement of the {gamma}p {yields} {pi}{sup +}n reaction. The preliminary results at CLAS for this reaction agree very well with previous world data. The analysis procedure has been developed to analyze the double-pion photoproduction. The differential cross sections for the {gamma}p {yields} P{pi}{sup +}{pi}{sup 0}n reaction have been measured with incident photon energies between 1 and 2 GeV. The Chew-Low extrapolation technique was used to extract the associated {gamma}{pi} {yields} {pi}{pi} cross sections from the differential cross sections. The extrapolation procedure of extracting the pole cross section has been explored. F{sup 3{pi}} was obtained from the {gamma}{pi} {yields} {pi}{pi} cross sections. The results show a momentum dependence of the F{sup 3{pi}} amplitude in which they agree with Holstein's calculation. These measurements test fundamental predictions of low energies QCD. Future work on this analysis will help reduce the uncertainty in F{sup 3{pi}}, and extend the measurements to the lower and higher s regions.

The spin dependent cross sections, {sigma}{sup T}{sub 1/2} and {sigma}{sup T}{sub 3/2}, and asymmetries, A{sub {parallel}} and A{sub {perp}}, for {sup 3}He have been measured at the Jefferson Lab's Hall A facility. The inclusive scattering process {sup 3}{vec He}({vec e},e)X was performed for initial beam energies ranging from 0.86 to 5.1 GeV, at a scattering angle of 15.5°. Data includes measurements from the quasielastic peak, resonance region, and the deep inelastic regime. An approximation for the extended Gcrasimov-Drell-Hcarn integral is presented at a 4-momentum transfer Q{sup 2} of 0.2-1.0 GeV{sup 2} . Also presented are results on the performance of the polarized {sup 3}He target. Polarization of {sup 3}He vvas achieved by the process of spin-exchange collisions with optically pumped rubidium vapor. The {sup 3}He polarization was monitored using the NMR technique of adiabatic fast passage (AFP). The average target polarization was approximately 35% and was determined to have a systematic uncertainty of roughly ±4% relative.

Magnetic resonance is the most powerful analytical tool used by chemists today. Its applications range from determining structures of large biomolecules to imaging of human brains. Nevertheless, magnetic resonance remains a relatively young field, in which many techniques are currently being developed that have broad applications. In this dissertation, two new techniques are presented, one that enables the determination of torsion angles in solid-state peptides and proteins, and another that involves imaging of heterogenous materials at ultra-low magnetic fields. In addition, structural studies of the prion protein via solid-state NMR are described. More specifically, work is presented in which the dependence of chemical shifts on local molecular structure is used to predict chemical shift tensors in solid-state peptides with theoretical ab initio surfaces. These predictions are then used to determine the backbone dihedral angles in peptides. This method utilizes the theoretical chemicalshift tensors and experimentally determined chemical-shift anisotropies (CSAs) to predict the backbone and side chain torsion angles in alanine, leucine, and valine residues. Additionally, structural studies of prion protein fragments are described in which conformationally-dependent chemical-shift measurements were made to gain insight into the structural differences between the various conformational states of the prion protein. These studies are of …

Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone ({phi}/{psi}) dihedral angles by comparing experimentally determined {sup 13}C{sub a}, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized …

Lasershot peening is an emerging modern process that impresses a compressive stress into the surfaces of metals, improving their operational lifetime. Almost everyone is familiar with taking a strip of metal or a wire and bending it multiple times until it breaks. In this situation, when the metal is bent, the surface of outer radius is stretched into a tensile state. Under tension, any flaw or micro-crack will grow in size with each bending of the metal until the crack grows through the entire strip, breaking it into two pieces. Flexure of metal components occurs in most applications. The teeth of a transmission gear flex as they deliver torque in a vehicle. Springs and valves flex every time they transfer loads. If fatigue failure from flexing occurs in the tooth of a transmission gear of light or heavy vehicles, in a fan blade of a diesel engine, in shock-absorbers or safety-related supporting structures, significant loss of assets and potentially loss of human life occurs. Lasershot peening, better than any other technique, has the potential to extend the fatigue lifetime of metal components. In the process, the laser generates a high intensity shock wave at the surface of the metal, straining …

We focus on two known NP-hard problems that have applications in sparse matrix computations: the envelope/wavefront reduction problem and the fill reduction problem. Envelope/wavefront reducing orderings have a wide range of applications including profile and frontal solvers, incomplete factorization preconditioning, graph reordering for cache performance, gene sequencing, and spatial databases. Fill reducing orderings are generally limited to--but an inextricable part of--sparse matrix factorization. Our major contribution to this field is the design of new and improved heuristics for these NP-hard problems and their efficient implementation in a robust, cross-platform, object-oriented software package. In this body of research, we (1) examine current ordering algorithms, analyze their asymptotic complexity, and characterize their behavior in model problems, (2) introduce new and improved algorithms that address deficiencies found in previous heuristics, (3) implement an object-oriented library of these algorithms in a robust, modular fashion without significant loss of efficiency, and (4) extend our algorithms and software to address both generalized and constrained problems. We stress that the major contribution is the algorithms and the implementation; the whole being greater than the sum of its parts. The initial motivation for implementing our algorithms in object-oriented software was to manage the inherent complexity. During our research …