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No description available.

The mechanism of the non-enzymatic breakdown of the tetrahedral intermediate of MurA (a carboxyvinyl transferase) was determined in order to better understand the corresponding enzyme catalyzed reaction. The breakdown was general acid-catalyzed, with simultaneous C-O bond cleavage and protonation at the bridging oxygen of the phosphate leaving group. The carboxyl was shown to play an important role in the breakdown, with its pKₐ of 3.2 appearing in the rate 𝘷𝘦𝘳𝘴𝘶𝘴 pH profile. The product distribution varied with pH. At pH 1, the products were predominantly UDP-GIcNAc, pyruvate and phosphate. Increasing proportions of MurA ketal arising from intramolecular attack of the 4'-0H, and EP-UDP-GicNAc resulting from elimination were observed with higher pHs. The MurA ketal was structurally characterized, and shown to be analogous to the ketal formed by AroA, a related enzyme. pKₐs corresponding to those expected of phosphate monoesters (1.6 and 6.2) were found in the product distribution 𝘷𝘦𝘳𝘴𝘶𝘴 pH profile. Observation of these pKₐs supported the initial product of phosphate departure being an oxocarbenium ion-phosphate tight ion pair complex. A corresponding oxocarbenium ion intermediate in the enzymatic reaction could not be demonstrated. / Thesis / Master of Science (MSc)

Thesis (Ph. D.)--Florida State University, 2004. / Advisor: Dr. Samuel L. Tabor and Dr. Ingo L. Wiedenhoever, Florida State University, College of Arts and Sciences, Dept. of Physics. Title and description from dissertation home page (viewed June 6, 2005). Document formatted into pages; contains xv, 143 pages. Includes bibliographical references (p. 138-142).

The implementation of a general-purpose tetrahedral mesh phantom geometry library for the Monte Carlo radiation transport code EGSnrc is described. Recently, tetrahedral mesh geometries have been proposed as standard reference phantoms to advance the state of the art over rectilinear voxel phantoms. Prior to this work, EGSnrc already supported voxelized geometries, but not tetrahedral meshes. Other major radiation transport codes such as MCNP6, Geant4, and PHITS, are also capable of simulating the interaction of ionizing radiation with tetrahedral mesh phantoms. Tetrahedral mesh phantoms have a number of advantages over voxel phantoms including improved modelling fidelity and locally varying element resolution. In addition, CAD geometries can be converted into meshes, which can then be directly used in simulations. In this work, an EGSnrc tetrahedral mesh geometry library called EGS_Mesh is implemented. The implementation uses fast computational geometry algorithms from the literature and is accelerated using an octree spatial partitioning scheme. For a preliminary verification, results obtained using EGS_Mesh are compared to classical EGSnrc geometries and theoretical results (including a Fano test) and found to match within 0.1%. To demonstrate the capability of EGS_Mesh to simulate transport in complex mesh phantoms from the literature, results using the ICRP 145 reference human phantoms are compared to published results obtained using Geant4. The comparison has found agreement mostly within 5% of the Geant4 results, but with some differences up to 10%.

Nuclei near N=90 and Z=64 have recently been suggested to be `tetrahedral-magic'. One of the main signatures for tetrahedral symmetry is a vanishing quadrupole moment in low-lying negative-parity bands, resulting in very weak or even vanishing E2 matrix elements. With N=90 and Z=62, the transitional nucleus 152Sm is a potential candidate for relatively stable tetrahedral symmetry. Its structure was investigated using deuteron inelastic scattering with a 22 MeV polarized beam at the MP tandem Van de Graaff accelerator of the TU/LMU Munich. The scattered deuterons were momentum analyzed using the Q3D spectrometer. The experimental spectra obtained have allowed the extraction of high-quality differential cross-sections and analyzing powers for levels up to 1.8 MeV. The low-lying negative-parity bands are observed to be strongly populated and the angular distributions associated to their levels exhibit several structural features. The overall agreement is relatively good when considering strong intra-band E2 transitions, but further calculations must be performed to allow precise matrix element extraction. In particular, a simple population pathway test on the 1- state has demonstrated that calculations with vanishing E2 transitions in the negative-parity band are also capable of reproducing its experimental angular distributions. Therefore, the presence of tetrahedral symmetry signature in 152Sm is not excluded. / This work has been supported in part by the Natural Sciences and Engineering Research Council of Canada.

Dans le cadre du projet européen ENVISION (2010-2014) et en collaboration avec l'équipe CAS-PHABIO de l'IPNL, cette thèse constitue une contribution méthodologique et technique dans le domaine de la dosimétrie et de l'imagerie de contrôle par émission des positons (TEP) pour les organes en mouvement. Les méthodes actuelles utilisent le recalage déformable d'images CT pour estimer le mouvement des organes internes. Le recalage déformable permet d'estimer le déplacement de chaque voxel d'une image à une autre. La dose radio-thérapeutique ainsi que l'activité TEP sont accumulées sur des voxels. Ces approches ont des difficultés quand il s'agit de prendre en compte la variation de densité à l'intérieur des organes et l'aspect non-répétitif du mouvement respiratoire. Les travaux antérieurs de l'équipe ont permis de développer un premier modèle biomécanique complet du système respiratoire qui, corrélé avec des signaux externes, pourrait prendre en compte la variabilité du mouvement respiratoire. Cette thèse présente une approche qui permet d'intégrer un tel modèle biomécanique dans un système de planification de traitement pour l'hadronthérapie. Dans cette thèse, nous avons choisi d'investiguer de près l'utilisation des maillages tétraédriques déformables dans la dosimétrie et la reconstruction d'images TEP afin d'estimer les avantages et inconvénients de ce type de géométrie. En conclusion, notre approche peut être utilisée avec n'importe quel modèle de déformation basé sur une géométrie tétraédrique et dont le mouvement est décrit par le déplacement des nœuds des maillages et donc contrairement aux méthodes basés images, notre approche n'est pas nécessairement dépendante de l'existence des images internes à tout moment. Dans le futur, les méthodes développées dans cette thèse pourraient être utilisées avec un modèle biomécanique complet du système respiratoire afin de quantifier, par exemple, les effets de la variabilité de la respiration sur le dépôt de dose / Respiratory-induced organ motion is a technical challenge to nuclear imaging and to charged particle therapy dose calculations for lung cancer treatment in particular. Internal organ tissue displacements and deformations induced by breathing need to be taken into account when calculating Monte Carlo dose distributions as well as when performing tomographic reconstructions for PET imaging. Current techniques based on Deformable Image Registration (DIR) cannot fully take into account the density variations of the tissues nor the fact that respiratory motion is not reproducible. As part of the ENVISION (2010-2014) European project, in collaboration with the CAS-PHABIO team from IPNL (the Nuclear Physics Institute from Lyon), this PhD project presents a methodological contribution to physical dose calculations and PET-based treatment verification for hadron therapy in the case of moving tumours. Contrary to DIR-based methods where motion is described by relative voxel displacement, each organ is represented as a deformable grid of tetrahedra where internal motion is described by mesh vertex transformations calculated using continuum mechanics. First, this PhD project proposes a new method to calculate four dimensional dose distribution over tetrahedral meshes, which are deformed using biomechanical modeling based on Finite Element Analysis (FEA). The second part of the PhD is focused on motion compensation for PET image reconstruction using deformable tetrahedral meshes

A three-dimensional unstructured incompressible RANS code has been developed using artificial compressibility and Spalart-Allmaras eddy viscosity model. A node-based finite volume method is used in which all flow variables are defined at the vertices of tetrahedrons in an unstructured grid. The inviscid fluxes are computed by using the Roe's flux difference splitting method, and higher order accuracy is attained by data reconstruction based on Taylor series expansion. Gauss theorem is used to formulate necessary gradients. For time integration, an implicit scheme based on linearized Euler backward method is used. A tetrahedral unstructured grid generation code has been also developed and applied to the tip clearance flow in a highly staggered cascade. Surface grids are first generated in the flow passage and blade tip by using several triangulation methods including Delaunay triangulation, advancing front method and advancing layer method. Then the whole computational domain including tip gap region is filled with prisms using the surface grids. Each prism is divided into three tetrahedrons. To accomplish this division in a consistent manner, connectivity pattern is assigned to each triangle in the surface grids. A new algorithm is devised to assign the connectivity pattern without reference to the particular method of triangulation. This technique offers great flexibility in surface grid generation. The code has been validated by comparisons with available computational and experimental results for several test cases: invisicd flow around NACA section, laminar and turbulent flow over a flat plate, turbulent flow through double-circular arc cascade and laminar flow through a square duct with 90° bend. For the laminar flat plate case, the velocity profile and skin friction coefficient are in excellent agreement with Blasius solution. For the turbulent flat plate case, velocity profiles are in full agreement with the law of the wall up to Reynolds number of 1.0E8, however, the skin friction coefficient is under-predicted by about 10% in comparison with empirical formula. Blade loading for the two-dimensional circular arc cascade is also compared with experiments. The results obtained with the experimental inflow angle (51.5° ) show some discrepancies at the trailing edge and severely under-predict the suction peak at the leading edge. These discrepancies are completely remedied if the inflow angle is increased to 53.5° . The code is also capable of predicting the secondary flow in the square duct with 90° bend, and the velocity profiles are in good agreement with measurements and published Navier-Stokes computations. Finally the code is applied to a linear cascade that has GE rotor B section with tip clearance and a high stagger angle of 56.9° . The overall structure of the tip clearance flow is well predicted. Loss of loading due to tip leakage flow and reloading due to tip leakage vortex are presented. On the end wall, separation line of the tip leakage vortex and reattachment line of passage vortex are identified. The location of the tip leakage vortex in the passage agrees very well with oil flow visualization. Separation bubble on the blade tip is also predicted. Mean streamwise velocity contours and cross sectional velocity vectors are compared with experimental results in the near wake, and good agreements are observed. It is concluded that Spalart-Allmaras turbulence model is adequate for this type of flow field except at locations where the tip leakage vortex of one blade interacts with the wake of a following blade. This situation may prevail for blades with longer span and/or in the far wake. Prediction of such an interaction presents a challenge to RANS computations. The effects of blade span on the flow structure have been also investigated. Two cascades with blades of aspect ratios of 0.5 and 1.0 are considered. By comparing pressure distributions on the blade, it is shown that the aspect ratio has strong effects on loading distribution on the blade although the tip gap height is very small (0.016 chord). Grid convergence study has been carried out with three different grids for pressure distributions and limiting streamlines on the end wall. / Ph. D.

Mesh generation is a fundamental precursor to finite element implementations for solution of partial differential equations in engineering and science. This dissertation advances the field in three distinct but coupled areas. A robust and fast three dimensional mesh generator for arbitrarily shaped geometries was developed. It deploys nodes throughout the domain based upon user-specified mesh density requirements. The system is integer and pixel based which eliminates round off errors, substantial memory requirements and cpu intensive calculations. Linked, but fully detachable, to the mesh generation system is a physical boundary recovery routine. Frequently, the original boundary topology is required for specific boundary condition applications or multiple material constraints. Historically, this boundary preservation was not available. An algorithm was developed, refined and optimized that recovers the original boundaries, internal and external, with fidelity. Finally, a node repositioning algorithm was developed that maximizes the minimum solid angle of tetrahedral meshes. The highly coveted 2D Delaunay property that maximizes the minimum interior angle of a triangle mesh does not extend to its 3D counterpart, to maximize the minimum solid angle of a tetrahedron mesh. As a consequence, 3D Delaunay created meshes have unacceptable sliver tetrahedral elements albeit composed of 4 high quality triangle sides. These compromised elements are virtually unavoidable and can foil an otherwise intact mesh. The numerical optimization routine developed takes any preexisting tetrahedral mesh and repositions the nodes without changing the mesh topology so that the minimum solid angle of the tetrahedrons is maximized. The overall quality enhancement of the volume mesh might be small, depending upon the initial mesh. However, highly distorted elements that create ill-conditioned global matrices and foil a finite element solver are enhanced significantly.

The development and numerical implementation of a three-dimensional Particle-In-Cell (PIC) methodology on unstructured Voronoi-Delauney tetrahedral grids is presented. Charge assignment and field interpolation weighting schemes of zero- and first-order are formulated based on the theory of long-range constraints for three-dimensional unstructured grids. The algorithms for particle motion, particle tracing, particle injection, and loading are discussed. Solution to Poisson's equation is based on a finite-volume formulation that takes advantage of the Voronoi-Delauney dual. The PIC methodology and code are validated by application to the problem of current collection by cylindrical Langmuir probes in stationary and moving collisionless plasmas. Numerical results are compared favorably with previous numerical and analytical solutions for a wide range of probe radius to Debye length ratios, probe potentials, and electron to ion temperature ratios. A methodology for evaluation of the heating, slowing-down and deflection times in 3D PIC simulations is presented. An extensive parametric evaluation is performed and the effects of the number of computational particles per cell, the ratio of cell-edge to Debye length, and timestep are investigated. The unstructured PIC code is applied to the simulation of Field Emission Array (FEA) cathodes. Electron injection conditions are obtained from a Field Emission microtip model and the simulation domain includes the FEA cathode and anode. Currents collected by the electrodes are compared to theoretical values. Simulations show the formation of the virtual cathode and three-dimensional effects under certain injection conditions. The unstructured PIC code is also applied to the simulation of a micro-Retarding Potential Analyzer. For simple cases the current at the collector plate is compared favorably with theoretical predictions. The simulations show the complex structure of the potential inside the segmented microchannel, the phase space of plasma species and the space-charge effects not captured by the theory.