Final Report for grant DE-FG02-06ER54888, "Simulation of Beam-Electron Cloud Interactions in Circular Accelerators Using Plasma Models" Viktor K. Decyk, University of California, Los Angeles Los Angeles, CA 90095-1547 The primary goal of this collaborative proposal was to modify the code QuickPIC and apply it to study the long-time stability of beam propagation in low density electron clouds present in circular accelerators. The UCLA contribution to this collaborative proposal was in supporting the development of the pipelining scheme for the QuickPIC code, which extended the parallel scaling of this code by two orders of magnitude. The USC work was as described here the PhD research for Ms. Bing Feng, lead author in reference 2 below, who performed the research at USC under the guidance of the PI Tom Katsouleas and the collaboration of Dr. Decyk The QuickPIC code [1] is a multi-scale Particle-in-Cell (PIC) code. The outer 3D code contains a beam which propagates through a long region of plasma and evolves slowly. The plasma response to this beam is modeled by slices of a 2D plasma code. This plasma response then is fed back to the beam code, and the process repeats. The pipelining is based on the observation that …

This report is the final update on ARM research conducted at DRI through May of 2006. A relatively minor amount of work was done after May, and last month (November), two journal papers partially funded by this project were published. The other investigator on this project, Dr. Bob d'Entremont, will be submitting his report in February 2007 when his no-cost extension expires. The main developments for this period, which concludes most of the DRI research on this project, are as follows: (1) Further development of a retrieval method for cirrus cloud ice particle effective diameter (De) and ice water path (IWP) using terrestrial radiances measured from satellites; (2) Revision and publication of the journal article 'Testing and Comparing the Modified Anomalous Diffraction Approximation'; and (3) Revision and publication of our radar retrieval method for IWC and snowfall rate.

The overall objective of this collaborative project is to integrate an existing general equilibrium energy-economic growth model with a biogeochemical cycles and biophysical models in order to more fully explore the potential contribution of land use-related activities to future emissions scenarios. Land cover and land use change activities, including deforestation, afforestation, and agriculture management, are important source of not only CO2, but also non-CO2 GHGs. Therefore, contribution of land-use emissions to total emissions of GHGs is important, and consequently their future trends are relevant to the estimation of climate change and its mitigation. This final report covers the full project period of the award, beginning May 2006, which includes a sub-contract to Brown University later transferred to the National Center for Atmospheric Research (NCAR) when Co-PI Brian O'Neill changed institutional affiliations.

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An extended structure zone diagram is proposed that includes energetic deposition, characterized by a large flux of ions typical for deposition by filtered cathodic arcs and high power impulse magnetron sputtering. The axes are comprised of a generalized homologous temperature, the normalized kinetic energy flux, and the net film thickness, which can be negative due to ion etching. It is stressed that the number of primary physical parameters affecting growth by far exceeds the number of available axes in such a diagram and therefore it can only provide an approximate and simplified illustration of the growth condition?structure relationships.

We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.

This report documents the results of a project undertaken to develop an ultra-high-accuracy measurement capability, which is necessary to address a rising trend toward miniaturized mechanical products exhibiting dramatically reduced product tolerances. A significant improvement in measurement capability is therefore required to insure that a 4:1 ratio can be maintained between product tolerances and measurement uncertainty.

Chromosomal mosaicism in human preimplantation embryos is a common cause ofspontaneous abortions, however, our knowledge of its etiology is limited. We used multicolor fluorescence in situ hybridization (FISH) painting to investigate whether paternally-transmitted chromosomal aberrations result in mosaicism in mouse 2-cell embryos. Paternal exposure to acrylamide, an important industrial chemical also found in tobacco smoke and generated during the cooking process of starchy foods, produced significant increases in chromosomally defective 2-cell embryos, however, the effects were transient primarily affecting the postmeiotic stages of spermatogenesis. Comparisons with our previous study of zygotes demonstrated similar frequencies of chromosomally abnormal zygotes and 2-cell embryos suggesting that there was no apparent selection against numerical or structural chromosomal aberrations. However, the majority of affected 2-cell embryos were mosaics showing different chromosomal abnormalities in the two blastomeric metaphases. Analyses of chromosomal aberrations in zygotes and 2-cell embryos showed a tendency for loss of acentric fragments during the first mitotic division ofembryogenesis, while both dicentrics and translocations apparently underwent propersegregation. These results suggest that embryonic development can proceed up to the end of the second cell cycle of development in the presence of abnormal paternal chromosomes and that even dicentrics can persist through cell division. The high …

We have started upgrading the control room programs for the injector at the Advanced Light Source (ALS). We chose to program in C* exclusively on the .NET Framework to create EPICS client programs on Windows Vista PCs. This paper reports the status of this upgrade project.

We report the demonstration of a reflection microscope that operates at 13.2-nm wavelength with a spatial resolution of 55 {+-} 3 nm. The microscope uses illumination from a table-top EUV laser to acquire aerial images of photolithography masks with a 20 second exposure time. The modulation transfer function of the optical system was characterized.

That tumor cells for all practical purposes are unstable and plastic could be expected. However, the astonishing ability of the nuclei from cells of normal adult tissues to be reprogrammed - given the right embryonic context - found its final truth even for mammals in the experiments that allowed engineering Dolly (1). The landmark experiments showed that nuclei originating from cells of frozen mammary tissues were capable of being reprogrammed by the embryonic cytoplasm and its microenvironment to produce a normal sheep. The rest is history. However, whether microenvironments other than those of the embryos can also reprogram adult cells of different tissue origins still containing their cytoplasm is of obvious interest. In this issue of PNAS, the laboratory of Gilbert Smith (2) reports on how the mammary gland microenvironment can reprogram both embryonic and adult stem neuronal cells. The work is a follow-up to their previous report on testis stem cells that were reprogrammed by the mammary microenvironment (3). They demonstrated that cells isolated from the seminiferous tubules of the mature testis, mixed with normal mammary epithelial cells, contributed a sizable number of epithelial progeny to normal mammary outgrowths in transplanted mammary fat pads. However, in those experiments they …

We report the scaling behavior of Barkhausen avalanches for every small field step along the hysteresis loop in CoCrPt alloy film having perpendicular magnetic anisotropy. Individual Barkhausen avalanche is directly observed utilizing a high-resolution soft X-ray microscopy that provides real space images with a spatial resolution of 15 nm. Barkhausen avalanches are found to exhibit power-law scaling behavior at all field steps along the hysteresis loop, despite their different patterns for each field step. Surprisingly, the scaling exponent of the power-law distribution of Barkhausen avalanches is abruptly altered from 1 {+-} 0.04 to 1.47 {+-} 0.03 as the field step is close to the coercive field. The contribution of coupling among adjacent domains to Barkhausen avalanche process affects the sudden change of the scaling behavior observed at the coercivity-field region on the hysteresis loop of CoCrPt alloy film.

In this project we developed further a twin approach to the study of regional-scale climate variability and change. The two approaches involved probabilistic network (PN) models (sometimes called dynamic Bayesian networks) and intermediate-complexity coupled ocean-atmosphere models (ICMs). We thus made progress in identifying the predictable modes of climate variability and investigating their impacts on the regional scale. In previous work sponsored by DOE’s Climate Change Prediction Program (CCPP), we had developed a family of PNs (similar to Hidden Markov Models) to simulate historical records of daily rainfall, and used them to downscale seasonal predictions of general circulation models (GCMs). Using an idealized atmospheric model, we had established a novel mechanism through which ocean-induced sea-surface temperature (SST) anomalies might influence large-scale atmospheric circulation patterns on interannual and longer time scales; similar patterns were found in a hybrid coupled ocean–atmosphere–sea-ice model. In this continuation project, we built on these ICM results and PN model development to address prediction of rainfall and temperature statistics at the local scale, associated with global climate variability and change, and to investigate the impact of the latter on coupled ocean–atmosphere modes. Our main project results consist of extensive further development of the hidden Markov models for rainfall …

This report is an analysis of slice transverse emittance evolution in a photocathode RF gun

Uranium dioxide (UO2) is the most common fuel material in commercial nuclear power reactors. UO2 has the advantages of a high melting point, good high-temperature stability, good chemical compatibility with cladding and coolant, and resistance to radiation. The main disadvantage of UO2 is its low thermal conductivity. During a reactor’s operation, because the thermal conductivity of UO2 is very low, for example, about 2.8 W/m-K at 1000 oC [1], there is a large temperature gradient in the UO2 fuel pellet, causing a very high centerline temperature, and introducing thermal stresses, which lead to extensive fuel pellet cracking. These cracks will add to the release of fission product gases after high burnup. The high fuel operating temperature also increases the rate of fission gas release and the fuel pellet swelling caused by fission gases bubbles. The amount of fission gas release and fuel swelling limits the life time of UO2 fuel in reactor. In addition, the high centerline temperature and large temperature gradient in the fuel pellet, leading to a large amount of stored heat, increase the Zircaloy cladding temperature in a lost of coolant accident (LOCA). The rate of Zircaloy-water reaction becomes significant at the temperature above 1200 oC [2]. …

The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 {angstrom} resolution, respectively. These structures reveal a core fold that is comprised of an {alpha}-helix lying diagonally across a five-stranded, mixed {beta}-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the {beta}-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

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This report describes a study conducted by Pacific Northwest National Laboratory to identify populations of migrating juvenile salmonids with a potential to be impacted by repeated exposure to turbine passage conditions. This study is part of a research program supported by the U.S. Department of Energy Wind/Hydropower Program. The program's goal is to increase hydropower generation and capacity while enhancing environmental performance. Our study objective is to determine whether the incremental effects of turbine passage during downstream migration impact populations of salmonids. When such a potential is found to exist, a secondary objective is to determine what level of effect of passing multiple turbines is required to decrease the number of successful migrants by 10%. This information will help identify whether future laboratory or field studies are feasible and design those studies to address conditions that present the greatest potential to improve dam survival and thus benefit fish and power generation.

Conventional annular Hall thrusters become inefficient when scaled to low power. Cylindrical Hall thrusters, which have lower surface-to-volume ratio, are more promising for scaling down. They presently exhibit performance comparable with conventional annular Hall thrusters. The present paper gives a review of the experimental and numerical investigations of electron crossfield transport in the 2.6 cm miniaturized cylindrical Hall thruster (100 W power level). We show that, in order to explain the discharge current observed for the typical operating conditions, the electron anomalous collision frequency {nu}{sub b} has to be on the order of the Bohm value, {nu}{sub B} {approx} {omega}{sub c}/16. The contribution of electron-wall collisions to cross-field transport is found to be insignificant. The optimal regimes of thruster operation at low background pressure (below 10{sup -5} Torr) in the vacuum tank appear to be different from those at higher pressure ({approx} 10{sup -4} Torr).

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Ion tracking and ion-track lithography have been performed almost exclusively using ions with energies near or above the maximum in electronic stopping, which occurs at {approx}1 MeV/amu. In this paper, ion-track lithography using ions with energies well below this maximum is discussed. The results of etching ion tracks created in polycarbonate films by ions with energies just above the anticipated threshold for creating etchable latent tracks with cylindrical geometry have been examined. Low-energy neon and argon ions with 18-60 keV/amu and fluences of {approx}10{sup 8}/cm{sup 2} were used to examine the limits for producing useful, etchable tracks in polycarbonate films. By concentrating on the early stages of etching (i.e., {approx}20 nm < SEM hole diameter < {approx}100 nm), the energy deposition calculated for the incident ion was correlated with the creation of etchable tracks. The experimental results are discussed with regard to the energy losses of the ions in the polycarbonate films and to the formation of continuous latent tracks through the entire thickness of the films. The probability distributions for large-angle scattering events were calculated to assess their importance as a function of ion energy. All these results have significant implications with respect to the threshold for formation of …

Cell communication modulates numerous biological processes including proliferation, apoptosis, motility, invasion and differentiation. Correspondingly, there has been significant interest in the development of surface display strategies for the presentation of signaling molecules to living cells. This effort has primarily focused on naturally surface-bound ligands, such as extracellular matrix components and cell membranes. Soluble ligands (e.g. growth factors and cytokines) play an important role in intercellular communications, and their display in a surface-bound format would be of great utility in the design of array-based live cell assays. Recently, several cell microarray systems that display cDNA, RNAi, or small molecules in a surface array format were proven to be useful in accelerating high-throughput functional genetic studies and screening therapeutic agents. These surface display methods provide a flexible platform for the systematic, combinatorial investigation of genes and small molecules affecting cellular processes and phenotypes of interest. In an analogous sense, it would be an important advance if one could display soluble signaling ligands in a surface assay format that allows for systematic, patterned presentation of soluble ligands to live cells. Such a technique would make it possible to examine cellular phenotypes of interest in a parallel format with soluble signaling ligands as one …

A. ABSTRACT The importance of lateral gene transfer (LGT) in the evolution of microbial species has become increasingly evident with each completed microbial genome sequence. Most significantly, the genome of Thermotoga maritima MSB8, a hyperthermophilic bacterium isolated by Karl Stetter and workers from Vulcano Italy in 1986, and sequenced at The Institute for Genomic Research (TIGR) in Rockville Maryland in 1999, revealed extensive LGT between % . this bacterium and members of the archaeal domain (in particular Archaeoglobus fulgidus, and Pyracoccus frcriosus species). Based on whole genome comparisons, it was estimated that 24% of the genetic information in this organism was acquired by genetic exchange with archaeal species, Independent analyses including periodicity analysis of the T. maritimu genomic DNA sequence, phylogenetic reconstruction based on genes that appear archaeal-like, and codon and amino acid usage, have provided additional evidence for LGT between T. maritima and the archaea. More recently, DiRuggiero and workers have identified a very recent LGT event between two genera of hyperthermophilic archaea, where a nearly identical DNA fragment of 16 kb in length flanked by insertion sequence (IS) elements, exists. Undoubtedly, additional examples of LGT will be identified as more microbial genomes are completed. For the present moment …

We consider the class of effective supergravity theories from the weakly coupled heterotic string in which local supersymmetry is broken by gaugino condensation in a hidden sector, with dilaton stabilization achieved through corrections to the classical dilaton Kahler potential. If there is a single hidden condensing (simple) gauge group, the axion is massless (up to contributions from higher dimension operators) above the QCD condensation scale. We show how the standard relation between the axion mass and its Planck scale coupling constant is modified in this class of models due to a contribution to the axion-gluon coupling that appears below the scale of supersymmetry breaking when gluinos are integrated out. In particular there is a point of enhanced symmetry in parameter space where the axion mass is suppressed. We revisit the question of the universal axion as the Peccei-Quinn axion in the light of these results, and find that the strong CP problem is avoided in most compactifications of the weakly coupled heterotic string.