This paper discusses configuration scripts in general and the scripting language issues involved. A brief description of GNU autoconf is provided along with a contrasting overview of autokonf, a configuration script generator implemented in Perl, whose macros are implemented in Perl, generating a configuration script in Perl. It is very portable, easily extensible, and readily mastered.

It is shown that a quantum kinetic theory approach to line broadening, extended to stationary non-equilibrium states, yields corrections to the standard electron impact widths of isolated lines that depend on the population of the radiator internal levels. A consistent classical limit from a general quantum treatment of the perturbing electrons also introduces corrections to the isolated line widths. Both effects are essential in preserving detailed-balance relations. Preliminary analysis indicates that these corrections may resolve existing discrepancies between theoretical and experimental widths of isolated lines. An experimental test of the results is proposed.

The main focus of the work is to develop a better understanding of the distribution of the elements B, Be and Li in melilite, fassaitic clinop clinopy-roxene, anorthite and spinel, which are the primary constituents of calcium-aluminum-rich inclusions (CAIs). These elements are the parent or decay products of short-lived nuclides (specifically, {sup 7}Be and {sup 10}Be) formed by cosmic ray spallation reactions on silicon and oxygen. Recent observations suggest that some CAIs contain ''fossil'' {sup 7}Be and {sup 10}Be in the form of ''excess'' amounts of their decay products (B and Li). The exact timing of {sup 7}Be and {sup 10}Be production is unknown, but if it occurred early in CAI history, it could constrain the birthplace of CAIs to be within a limited region near the infant sun. Other interpretations are possible, however, and bear little significance to early CAI genesis. In order to interpret the anomalies as being ''primary'', and thus originating at high temperature, information on the intermineral partitioning of both parent and daughter elements is required.

The pseudorapidity asymmetry and centrality dependence of charged hadron spectra in d+Au collisions at {radical}s{sub NN} = 200 GeV are presented. The charged particle density at mid-rapidity, its pseudorapidity asymmetry and centrality dependence are reasonably reproduced by a Multi-Phase Transport model, by HIJING, and by the latest calculations in a saturation model. Ratios of transverse momentum spectra between backward and forward pseudorapidity are above unity for p{sub T} below 5 GeV/c. The ratio of central to peripheral spectra in d+Au collisions shows enhancement at 2 < p{sub T} < 6 GeV/c, with a larger effect at backward rapidity than forward rapidity. Our measurements are in qualitative agreement with gluon saturation and in contrast to calculations based on incoherent multiple partonic scatterings.

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The precipitation characteristics of tetrahedrally close-packed (TCP) phases during the welding and the subsequent solution annealing process of Alloy 22 1 1/2 inch thick plate double-U prototypical welds are investigated. Electron backscatter diffraction (EBSD) was used to provide large scale microstructural observation of the weld cross section, and scanning electron microscopy (SEM) was used to map the location of the TCP phases. Analysis shows that TCP precipitation occurs congruent to the weld passes, with the solution annealing reducing the sizes of coarser precipitates.

This article discusses conversions of Ruthenium(III) alkyl complexes.

I review recent progress in lattice QCD at finite temperature. Results on the transition temperature will be summarized. Recent progress in understanding in-medium modifications of interquark forces and quarkonia spectral functions at finite temperatures is discussed.

Accelerator mass spectrometry (AMS) is a highly sensitive analytical methodology used to quantify the content of radioisotopes, such as {sup 14}C, in a sample. The primary goals of this work were to demonstrate the utility of AMS in determining cellular [{sup 14}C]doxorubicin (DOX) concentrations and to develop a sensitive assay that is superior to high performance liquid chromatography (HPLC) for the quantification of DOX at the tumor level. In order to validate the superior sensitivity of AMS versus HPLC with fluorescence detection, we performed three studies comparing the cellular accumulation of DOX: one in vitro cell line study, and two in vivo xenograft mouse studies. Using AMS, we quantified cellular DOX content up to 4 hours following in vitro exposure at concentrations ranging from 0.2 pg/ml (345 fM) to 2 {micro}g/ml (3.45 {micro}M) [{sup 14}C]DOX. The results of this study show that, compared to standard fluorescence-based HPLC, the AMS method was over five orders of magnitude more sensitive. Two in vivo studies compared the sensitivity of AMS to HPLC using a nude mouse xenograft model in which breast cancer cells were implanted subcutaneously. After sufficiently large tumors formed, DOX was administered intravenously at two dose levels. Additionally, we tested the …

VisIt is a richly featured visualization tool that is used to visualize some of the largest simulations ever run. The scale of these simulations requires that optimizations are incorporated into every operation VisIt performs. But the set of applicable optimizations that VisIt can perform is dependent on the types of operations being done. Complicating the issue, VisIt has a plugin capability that allows new, unforeseen components to be added, making it even harder to determine which optimizations can be applied. We introduce the concept of a contract to the standard data flow network design. This contract enables each component of the data flow network to modify the set of optimizations used. In addition, the contract allows for new components to be accommodated gracefully within VisIt's data flow network system.

We have developed an algorithm that extends the possible size-parameter range for the calculation of plane-wave light scattering from infinite homogeneous circular cylinders using a Mie-type analysis. Our algorithm is based on the calculation of the ratios of Bessel functions instead of calculating the Bessel functions or their logarithmic derivatives directly. We have found that this algorithm agrees with existing methods (when those methods converge). We have also found that our algorithm converges in cases of very large size parameters, in which case other algorithms often do not.

We report on the first experimental demonstration of Compton imaging of gamma rays with a single coaxial high-purity germanium (HPGe) detector. This imaging capability is realized by two-dimensional segmentation of the outside contact in combination with digital pulse-shape analysis, which enables to image gamma rays in 4{pi} without employing a collimator. We are able to demonstrate the ability to image the 662keV gamma ray from a {sup 137}Cs source with preliminary event selection with an angular accuracy of 5 degree with an relative efficiency of 0.2%. In addition to the 4{pi} imaging capability, such a system is characterized by its excellent energy resolution and can be implemented in any size possible for Ge detectors to achieve high efficiency.

We present the application of hardware accelerated volume rendering algorithms to the simulation of radiographs as an aid to scientists designing experiments, validating simulation codes, and understanding experimental data. The techniques presented take advantage of 32 bit floating point texture capabilities to obtain validated solutions to the radiative transport equation for X-rays. An unsorted hexahedron projection algorithm is presented for curvilinear hexahedra that produces simulated radiographs in the absorption-only regime. A sorted tetrahedral projection algorithm is presented that simulates radiographs of emissive materials. We apply the tetrahedral projection algorithm to the simulation of experimental diagnostics for inertial confinement fusion experiments on a laser at the University of Rochester. We show that the hardware accelerated solution is faster than the current technique used by scientists.

Mycoplasma genitalium (Mg) and M. pneumoniae (Mp) are human pathogens with two of the smallest genomes sequenced to date ({approx} 480 and 680 genes, respectively). The Berkeley Structural Genomics Center is determining representative structures for gene products in these organisms, helping to understand the set of protein folds needed to sustain this minimal organism. The protein coded by gene MG354 (gi3844938) from M. genitalium has a relatively unique sequence, related only to MPN530 from M. pneumoniae (68% identity, coverage 99%) and MGA{_}0870 from the avian pathogen M. gallisepticum (23% identity, coverage 94%), has no homologue with a determined structure, and no functional annotations.

Although operons are often subject to horizontal gene transfer (HGT), non-HGT genes are particularly likely to be in operons. To resolve this apparent discrepancy and to determine whether HGT is involved in operon formation, we examined the evolutionary history of the genes and operons in Escherichia coli K12. We show that genes that have homologs in distantly related bacteria but not in close relatives of E. coli (indicating HGTi) form new operons at about the same rates as native genes. Furthermore, genes in new operons are no more likely than other genes to have phylogenetic trees that are inconsistent with the species tree. In contrast, essential genes and ubiquitous genes without paralogs (genes believed to undergo HGT rarely) often form new operons. We conclude that HGT is not associated with operon formation, but instead promotes the prevalence of pre-existing operons. To explain operon formation, we propose that new operons reduce the amount of regulatory information required to specify optimal expression patterns. Consistent with this hypothesis, operons have greater amounts of conserved regulatory sequences than do individually transcribed genes.

Smoothed Particle Hydrodynamics (SPH) is a meshless Lagrangian technique for modeling hydrodynamics, and as such offers some unique advantages when applied to problems of material failure and breakup. The two most important of these advantages are: (1) SPH is Lagrangian and robust--i.e., it is never necessary to advect or remap. Damage models typically involve a number of complex history variables (such as the damage associated with the Lagrangian mass, crack orientations, etc.), and advecting these quantities as is required in a mesh based algorithm is a very challenging problem. (2) SPH allows the Lagrangian points to move about, reconnect, or separate as dictated by the material flow. This naturally allows for the points to move apart as distinct fragments of material form, resulting in gaps or cracks between the fragments. Typically mesh based algorithms represent the ''cracks'' between fragments as zones of failed material, which is quite different than allowing voids devoid of material to form.

The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of 4-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.

Progress in structural biology very much depends upon the development of new high-resolution techniques and tools. Despite decades of study of viruses, bacteria and bacterial spores and their pressing importance in human medicine and biodefense, many of their structural properties are poorly understood. Thus, characterization and understanding of the architecture of protein surface and internal structures of pathogens is critical to elucidating mechanisms of disease, immune response, physicochemical properties, environmental resistance and development of countermeasures against bioterrorist agents. Furthermore, even though complete genome sequences are available for various pathogens, the structure-function relationships are not understood. Because of their lack of symmetry and heterogeneity, large human pathogens are often refractory to X-ray crystallographic analysis or reconstruction by cryo-electron microscopy (cryo-EM). An alternative high-resolution method to examine native structure of pathogens is atomic force microscopy (AFM), which allows direct visualization of macromolecular assemblies at near-molecular resolution. The capability to image single pathogen surfaces at nanometer scale in vitro would profoundly impact mechanistic and structural studies of pathogenesis, immunobiology, specific cellular processes, environmental dynamics and biotransformation.

We present X-ray light curves for the cataclysmic variable EX Hydrae obtained with the Chandra High Energy Transmission Grating Spectrometer and the Extreme Ultraviolet Explorer Deep Survey photometer. We confirm earlier results on the shape and amplitude of the binary light curve and discuss a new feature: the phase of the minimum in the binary light curve, associated with absorption by the bulge on the accretion disk, increases with wavelength. We discuss several scenarios that could account for this trend and conclude that, most likely, the ionization state of the bulge gas is not constant, but rather decreases with binary phase. We also conclude that photoionization of the bulge by radiation originating from the white dwarf is not the main source of ionization, but that it is heated by shocks originating from the interaction between the in-flowing material from the companion and the accretion disk. The findings in this paper provide a strong test for accretion disk models in close binary systems.

Beamline 7.2 of the Advanced Light Source (ALS) at theLawrence Berkeley National Laboratory (LBNL) is a beam diagnostics systemthat uses the synchrotron radiation emitted by a dipole magnet. Itconsists of two branches; in the first one the x-ray portion of theradiation is used in a pinhole camera system for measuring the transverseprofile of the beam. The second branch is equipped with an x-ray beamposition monitor (BPM) and with a multipurpose port where the visible andthe far-infrared part of the radiation can be used for variousapplications such as bunch length measurements and IR coherentsynchrotron radiation experiments. The pinhole system has been operatingsuccessfully since the end of 2003. The installation of the second branchhas been completed recently and the results of its commissioning arepresented in this paper together with examples of beam measurementsperformed at BL 7.2.

Colloidal nanocrystals are nanometer-sized, solution-grown inorganic particles stabilized by a layer of surfactants attached to their surface. The inorganic cores exhibit useful properties controlled by composition as well as size and shape, while the surfactant coating ensures that these structures are easy to fabricate and process. It is this combination of features that makes colloidal nanocrystals attractive and promising building blocks for advanced materials and devices. But their full potential can only be exploited if we achieve exquisite control over their composition, size, shape, crystal structure and surface properties. Here we review what is known about nanocrystal growth and outline strategies for controlling it.

Lawrence Livermore National Laboratory (LLNL) is evaluating design alternatives to improve the voltage regulation in our Flash X-Ray (FXR) accelerator cell and pulse-power system. The goal is to create a more mono-energetic electron beam. When an electron beam crosses the energized gap of an accelerator cell, the electron energy is increased. However, the beam with the associated electromagnetic wave also looses a small amount of energy because of the increased impedance seen across the gap. The beam-induced voltage at the gap is time varying. This creates beam energy variations that we need to understand and control. A high-fidelity computer simulation of the beam and cell interaction has been completed to quantify the time varying induced voltage at the gap. The cell and pulse-power system was characterized using a Time-domain Reflectometry (TDR) measurement technique with a coaxial air-line to drive the cell gap. The beam-induced cell voltage is computed by convoluting the cell impedance with measured beam current. The voltage was checked against other measurements to validate the accuracy.

Lawrence Livermore National Laboratory (LLNL) is evaluating design alternatives to improve the voltage regulation in our injector and accelerator cells of our Flash X-Ray (FXR) machine. The operational peak electron beam current and energy at the x-ray generating target are 3.2 kA and 17 MeV. The goal is to create a more mono-energetic electron beam with variation of less than 1%-root-mean-squared (rms). This would allow the beam to be focused more tightly and create an x-ray source with a smaller spot-size. Our injector appears to have significant voltage-variation, and this report describes a technique to appreciably correct the deviations. When an electron beam crosses the energized gap of an accelerator cell, the energy increases. However, the beam with the associated electromagnetic wave also loses a small amount of energy because of the increased impedance seen across each gap. The phenomenon is sometimes called beam loading. It can also be described as a beam-induced voltage at the gap which is time varying. The polarity of this induced voltage is the opposite of the voltage in the injector. The time varying profiles of the injector and induced gap voltage are related through the beam current. However, while the change in magnitude is …

High energy scattering in the QCD parton model was recently shown to be a reaction-diffusion process, and thus to lie in the universality class of the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation. We recall that the latter appears naturally in the context of the parton model. We provide a thorough numerical analysis of the mean field approximation, given in QCD by the Balitsky-Kovchegov equation. In the framework of a simple stochastic toy model that captures the relevant features of QCD, we discuss and illustrate the universal properties of such stochastic models. We investigate in particular the validity of the mean field approximation and how it is broken by fluctuations. We find that the mean field approximation is a good approximation in the initial stages of the evolution in rapidity.