This contribution addresses various aspects of nuclear waste vitrification. Nuclear wastes have a variety of components and composition ranges. For each waste composition, the glass must be formulated to possess acceptable processing and product behavior defined in terms of physical and chemical properties that guarantee the glass can be easily made and resist environmental degradation. Glass formulation is facilitated by developing property-composition models, and the strategy of model development and application is reviewed. However, the large variability of waste compositions presents numerous additional challenges: insoluble solids and molten salts may segregate; foam may hinder heat transfer and slow down the process; molten salts may accumulate in container refractory walls; the glass on cooling may precipitate crystalline phases. These problems need targeted exploratory research. Examples of specific problems and their possible solutions are discussed.

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest …

Computer-aided materials research is now an integral part of science and technology. It becomes particularly valuable when comprehensive experimental investigations and materials testing are too costly, hazardous, or of excessive duration; then, theoretical and computational studies can supplement and enhance the information gained from limited experimental data. Such is the case for improving our fundamental understanding of the properties of aging plutonium in the nuclear weapons stockpile. The question of the effects of plutonium aging on the safety, security, and reliability of the nuclear weapons stockpile emerged after the United States closed its plutonium manufacturing facility in 1989 and decided to suspend any further underground testing of nuclear weapons in 1992. To address this, the Department of Energy's National Nuclear Security Administration (NNSA) initiated a research program to investigate plutonium aging, i.e., the changes with time of properties of Pu-Ga alloys employed in the nuclear weapons and to develop models describing these changes sufficiently reliable to forecast them for several decades. The November 26, 2006 press release by the NNSA summarizes the conclusions of the investigation, '...there appear to be no serious or sudden changes occurring, or expected to occur, in plutonium that would affect performance of pits beyond the …

The initial stages of wet thermal oxidation of Si(100)-(2x1) have been investigated by in-situ ambient pressure x-ray photoemission spectroscopy (APXPS), including chemical-state resolution via Si 2p core-level spectra. Real-time growth rates of silicon dioxide have been monitored at 100 mTorr of water vapor. This pressure is considerably higher than in any prior study using XPS. Substrate temperatures have been varied between 250 and 500 C. Above a temperature of {approx} 400 C, two distinct regimes, a rapid and a quasi-saturated one, are identified and growth rates show a strong temperature dependence which cannot be explained by the conventional Deal-Grove model.

The orientation relationship, habit plane, parent-product interface at the atomic level, twin relationship, and plastic deformation resulting from the {delta} {yields} {alpha}{prime} isothermal martensitic transformation in Pu-Ga alloys are examined using optical microscopy, transmission electron microscopy, and finite element calculations. The {delta} {yields} {alpha}{prime} transformation exhibits a {approx}20% volume collapse when the face-centered cubic {delta} phase transforms to the monoclinic {alpha}{prime} phase, which results in unique and intriguing crystallography and morphology. Here, we show that the orientation relationship is very close to that previously reported by Zocco et al. (1990), but has small rotational misalignments between the two phases both parallel and perpendicular to the [110]{sub {delta}} {parallel}[100]{sub {alpha}{prime}} direction. The amount of plastic deformation is exceedingly large due to the {approx}20% volume collapse and transmission electron microscopy is used to quantify the difference in dislocation density between untransformed {delta}-matrix and regions of {delta} adjacent to the transformed {alpha}{prime}. The twins contained in {alpha}{prime} plates are shown to have a (205){sub {alpha}} orientation as the lattice invariant deformation and are found to be composed of two alternating variants that share a common <020>{sub {alpha}{prime}} direction, but differ by a 60 degree rotation about <020>{sub {alpha}{prime}}. A combination of electron diffraction …

Incoherent electron effects could seriously limit the beam lifetime in proton or ion storage rings, such as LHC, SPS, or RHIC, or blow up the vertical emittance of positron beams, e.g., at the B factories or in linear-collider damping rings. Different approaches to modeling these effects each have their own merits and drawbacks. We describe several simulation codes which simplify the descriptions of the beam-electron interaction and of the accelerator structure in various different ways, and present results for a toy model of the SPS. In addition, we present evidence that for positron beams the interplay of incoherent electron-cloud effects and synchrotron radiation can lead to a significant increase in vertical equilibrium emittance. The magnitude of a few incoherent e{sup +}e{sup -} scattering processes is also estimated. Options for future code development are reviewed.

Research at Stanford Linear Accelerator Center (SLAC) is in progress on a TeV-scale linear collider that will operate at 5-10 times the energy of present generation accelerators. This will require development of high power X-Band sources generating 50-100 MW per source. Conventional pillbox window designs are capable of transmitting peak rf powers up to about 30 MW, well below the desired level required for the use of a single window per tube. SLAC has developed a 75 MW TE{sub 01} window [1] that uses a 'traveling wave' design to minimize fields at the window face. Irises match to the dielectric window impedance, resulting in a pure traveling wave in the ceramic and minimum fields on the window face. The use of the TE{sub 01} mode also has zero electric field on the braze fillet. Unfortunately, in-band resonances prevented this window design from achieving the desired 75MW power level. It was believed the resonances resulted from sudden steps in the circular guide to match the 38mm input diameter to the overmoded (TE{sub 01} and TE{sub 02} mode propagating) 65 mm diameter of the window ceramic. Calabazas Creek Research Inc. is currently developing a traveling wave window using compact, numerically optimized, parabolic …

We completed estimates of neutron cross section covariances for {sup 55}Mn and {sup 90}Zr, from keV range to 25 MeV, considering the most important reaction channels, total, elastic, inelastic, capture, and (n,2n). The nuclear reaction model code EMPIRE was used to calculate sensitivity to model parameters by perturbation of parameters that define the optical model potential, nuclear level densities and strength of the pre-equilibrium emission. The sensitivity analysis was performed with the set of parameters which reproduces the ENDF/B-VII.0 cross sections. The experimental data were analyzed and both statistical and systematic uncertainties were extracted from almost 30 selected experiments. Then, the Bayesian code KALMAN was used to combine the sensitivity analysis and the experiments to obtain the evaluated covariance matrices.

Over the last decade the electron density of plasmas has been measured using X-ray laser interferometers in the 14 to 47 nm wavelength regime. With the same formula used in decades of experiments with optical interferometers, the data analysis assumes the index of refraction is due only to the free electrons, which makes the index less than one. Over the last several years, interferometer experiments in C, Al, Ag, and Sn plasmas have observed plasmas with index of refraction greater than one at 14 or 47 nm and demonstrated unequivocally that the usual formula for calculating the index of refraction is not always valid as the contribution from bound electrons can dominate the free electrons in certain cases. In this paper we search for other materials with strong anomalous dispersion that could be used in X-ray laser interferometer experiments to help understand this phenomena. An average atom code is used to calculate the plasma properties. This paper discusses the calculations of anomalous dispersion in Ne and Na plasmas near 47 nm and Xe plasmas near 14 nm. With the advent of the FLASH X-ray free electron laser in Germany and the LCLS X-FEL coming online at Stanford in 2 years …

Available methods for developing and screening small drug-like molecules able to knockout toxins or pathogenic microorganisms have some limitations. In order to be useful, these new methods must provide high-throughput analysis and identify specific binders in a short period of time. To meet this need, we are developing an approach that uses living cells to generate libraries of small biomolecules, which are then screened inside the cell for activity. Our group is using this new, combined approach to find highly specific ligands capable of disabling anthrax Lethal Factor (LF) as proof of principle. Key to our approach is the development of a method for the biosynthesis of libraries of cyclic peptides, and an efficient screening process that can be carried out inside the cell.

Laser-plasma interactions (LPI) have been studied experimentally in high-temperature, high-energy density plasmas. The studies have been performed using the Omega laser at the Laboratory for Laser Energetics (LLE), Rochester, NY. Up to 10 TW of power was incident upon reduced-scale hohlraums, distributed in three laser beam cones. The hot hohlraums fill quickly with plasma. Late in the laser pulse, most of the laser energy is deposited at the laser entrance hole, where most of the LPI takes place. Due to the high electron temperature, the stimulated Raman scattering (SRS) spectrum extends well beyond {omega}{sub 0}/2, due to the Bohm-Gross shift. This high-temperature, high-energy density regime provides a unique opportunity to study LPI beyond inertial confinement fusion (ICF) conditions.

The ubiquity of modular structure in real-world complex networks is being the focus of attention in many trials to understand the interplay between network topology and functionality. The best approaches to the identification of modular structure are based on the optimization of a quality function known as modularity. However this optimization is a hard task provided that the computational complexity of the problem is in the NP-hard class. Here we propose an exact method for reducing the size of weighted (directed and undirected) complex networks while maintaining invariant its modularity. This size reduction allows the heuristic algorithms that optimize modularity for a better exploration of the modularity landscape. We compare the modularity obtained in several real complex-networks by using the Extremal Optimization algorithm, before and after the size reduction, showing the improvement obtained. We speculate that the proposed analytical size reduction could be extended to an exact coarse graining of the network in the scope of real-space renormalization.

The connection between the Bessel discrete variable basis expansion and a specific form of an orthogonal set of Jacobi polynomials is demonstrated. These so-called Zernike polynomials provide alternative series expansions of suitable functions over the unit interval. Expressing a Bessel function in a Zernike expansion provides a straightforward method of generating series identities. Furthermore, the Zernike polynomials may also be used to efficiently evaluate the Hankel transform for rapidly decaying functions or functions with finite support.

I review recent progress in finite temperature lattice calculations, including the determination of the transition temperature, equation of state, screening of static quarks and meson spectral functions.

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Recent experiments at SLAC have shown that high gradient acceleration of electrons is achievable in meter scale plasmas. Results from these experiments show that the wakefield is sensitive to parameters in the electron beam which drives it. In the experiment the bunch lengths were varied systematically at constant charge. The effort to extract a measurement of the decelerating wake from the maximum energy loss of the electron beam is discussed.

In order to reach the high peak current required for an x-ray FEL, two separate magnetic dipole chicanes are used in the LCLS accelerator to compress the electron bunch length in stages. In these bunch compressors, coherent synchrotron radiation (CSR) can be emitted-induced either by a short electron bunch, or by any longitudinal density modulation that may be on the bunch. We present measurements, simulations, and analysis of (1) the CSR-induced energy loss, (2) the related transverse emittance growth, and (3) the microbunching-induced CSR directly observed at optical wavelengths.

A large exchange splitting of the conduction band in ultrathin films of the ferromagnetic semiconductor EuO was determined quantitatively, by using EuO as a tunnel barrier and fitting the current-voltage characteristics and temperature dependence to tunneling theory. This exchange splitting leads to different tunnel barrier heights for spin-up and spin-down electrons, and is large enough to produce a near fully spin-polarized current. Moreover, the magnetic properties of these ultrathin films (<6 nm) show a reduction in Curie temperature with decreasing thickness, in agreement with theoretical calculation [R. Schiller et al., Phys. Rev. Lett. 86, 3847 (2001)].

We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to Sparse Matrix Vector Multiplication (SpMV), the explicit heat equation PDE on a regular grid (Stencil), and a lattice Boltzmann application (LBMHD). We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Xeon Clovertown, AMD Opteron Barcelona, Sun Victoria Falls, and the Sony-Toshiba-IBM (STI) Cell. Rather than hand-tuning each kernel for each system, we develop a code generator for each kernel that allows us to identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto-tuned kernel applications often achieve a better than 4X improvement compared with the original code. Additionally, we analyze a Roofline performance model for each platform to reveal hardware bottlenecks and software challenges for future multicore systems and applications.

Supermassive black holes (SMBHs) are a ubiquitous component of the nuclei of galaxies. It is normally assumed that, following the merger of two massive galaxies, a SMBH binary will form, shrink due to stellar or gas dynamical processes and ultimately coalesce by emitting a burst of gravitational waves. However, so far it has not been possible to show how two SMBHs bind during a galaxy merger with gas due to the difficulty of modeling a wide range of spatial scales. Here we report hydrodynamical simulations that track the formation of a SMBH binary down to scales of a few light years following the collision between two spiral galaxies. A massive, turbulent nuclear gaseous disk arises as a result of the galaxy merger. The black holes form an eccentric binary in the disk in less than a million years as a result of the gravitational drag from the gas rather than from the stars.

Despite the rapid accumulation of systems-level biological data, understanding the dynamic nature of cellular activity remains a difficult task. The reason is that most biological data are static, or only correspond to snapshots of cellular activity. In this study, we explicitly attempt to detangle the temporal complexity of biological networks by using compilations of time-series gene expression profiling data.We define a dynamic network module to be a set of proteins satisfying two conditions: (1) they form a connected component in the protein-protein interaction (PPI) network; and (2) their expression profiles form certain structures in the temporal domain. We develop the first efficient mining algorithm to discover dynamic modules in a temporal network, as well as frequently occurring dynamic modules across many temporal networks. Using yeast as a model system, we demonstrate that the majority of the identified dynamic modules are functionally homogeneous. Additionally, many of them provide insight into the sequential ordering of molecular events in cellular systems. We further demonstrate that identifying frequent dynamic network modules can significantly increase the signal to noise separation, despite the fact that most dynamic network modules are highly condition-specific. Finally, we note that the applicability of our algorithm is not limited to the …

Libraries of cDNA clones are valuable resources foranalysing the expression, structure, and regulation of genes, as well asfor studying protein functions and interactions. Full-length cDNA clonesprovide information about intron and exon structures, splice junctionsand 5'- and 3'-untranslated regions (UTRs). Open reading frames (ORFs)derived from cDNA clones can be used to generate constructs allowingexpression of native proteins and N- or C-terminally tagged proteins.Thus, obtaining full-length cDNA clones and sequences for most or allgenes in an organism is critical for understanding genome functions.Expressed sequence tag (EST) sequencing samples cDNA libraries at random,which is most useful at the beginning of large-scale screening projects.However, as projects progress towards completion, the probability ofidentifying unique cDNAs via EST sequencing diminishes, resulting in poorrecovery of rare transcripts. We describe an adapted, high-throughputprotocol intended for recovery of specific, full-length clones fromplasmid cDNA libraries in five days.

An explosive growth of online news has taken place. Users are inundated with thousands of news articles, only some of which are interesting. A system to filter out uninteresting articles would aid users that need to read and analyze many articles daily, such as financial analysts and government officials. The most obvious approach for reducing the amount of information overload is to learn keywords of interest for a user (Carreira et al., 2004). Although filtering articles based on keywords removes many irrelevant articles, there are still many uninteresting articles that are highly relevant to keyword searches. A relevant article may not be interesting for various reasons, such as the article's age or if it discusses an event that the user has already read about in other articles. Although it has been shown that collaborative filtering can aid in personalized recommendation systems (Wang et al., 2006), a large number of users is needed. In a limited user environment, such as a small group of analysts monitoring news events, collaborative filtering would be ineffective. The definition of what makes an article interesting--or its 'interestingness'--varies from user to user and is continually evolving, calling for adaptable user personalization. Furthermore, due to the nature …

Over the past quarter century, light-source user facilities have transformed research in areas ranging from gas-phase chemical dynamics to materials characterization. The ever-improving capabilities of these facilities have revolutionized our ability to study the electronic structure and dynamics of atoms, molecules, and even the most complex new materials, to understand catalytic reactions, to visualize magnetic domains, and to solve protein structures. Yet these outstanding facilities still have limitations well understood by their thousands of users. Accordingly, over the past several years, many proposals and conceptual designs for"next-generation" x-ray light sources have been developed around the world. In order to survey the scientific problems that might be addressed specifically by those new light sources operating below a photon energy of about 3 keV and to identify the scientific requirements that should drive the design of such facilities, a workshop"Science for a New Class of Soft X-Ray Light Sources" was held in Berkeley in October 2007. From an analysisof the most compelling scientific questions that could be identified and the experimental requirements for answering them, we set out to define, without regard to the specific technologies upon which they might be based, the capabilities such light sources would have to deliver in …