We construct the microstates of near-extremal black holes in AdS_5 x S5 as gases of defects distributed in heavy BPS operators in the dual SU(N) Yang-Mills theory. These defects describe open strings on spherical D3-branes in the S5, and we show that they dominate the entropy by directly enumerating them and comparing the results with a partition sum calculation. We display new decoupling limits in which the field theory of the lightest open strings on the D-branes becomes dual to a near-horizon region of the black hole geometry. In the single-charge black hole we find evidence for an infrared duality between SU(N) Yang-Mills theories that exchanges the rank of the gauge group with an R-charge. In the two-charge case (where pairs of branes intersect on a line), the decoupled geometry includes an AdS_3 factor with a two-dimensional CFT dual. The degeneracy in this CFT accounts for the black hole entropy. In the three-charge case (where triples of branes intersect at a point), the decoupled geometry contains an AdS_2 factor. Below a certain critical mass, the two-charge system displays solutions with naked timelike singularities even though they do not violate a BPS bound. We suggest a string theoretic resolution of these …

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged …

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 …

Beamlines have been designed for coherence experiments at the ALS based on brightness preserving spherical grating monochromators. The operation is almost paraxial so that a very simple scheme can deliver the modest spectral resolution required, with just two focusing optics, one of which is the spherical grating.

The PHOBOS experiment at RHIC has measured the multiplicity of primary charged particles as a function of centrality and pseudorapidity in Au+Au collisions at {radical}(s{sub NN}) = 19.6, 130 and 200 GeV. Two observations indicate universal behavior of charged particle production in heavy ion collisions. The first is that forward particle production, over a range of energies, follows a universal limiting curve with a non-trivial centrality dependence. The second arises from comparisons with pp/{bar p}p and e{sup +}e{sup -} data. <Nch>/<N{sub part}/2> in nuclear collisions at high energy scales with {radical}s in a similar way as N{sub ch} in e{sup +}e{sup -} collisions and has a very weak centrality dependence. These features may be related to a reduction in the leading particle effect due to the multiple collisions suffered per participant in heavy ion collisions.

The cylindrical Hall thruster features high ionization efficiency, quiet operation, and ion acceleration in a large volume-to-surface ratio channel with performance comparable with the state-of-the-art annular Hall thrusters. These characteristics were demonstrated in low and medium power ranges. Optimization of miniaturized cylindrical thrusters led to performance improvements in the 50-200W input power range, including plume narrowing, increased thruster efficiency, reliable discharge initiation, and stable operation. __________________________________________________

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Tritium clean-up systems typically deploy gas processing technologies between stages of palladium-silver (Pd/Ag) diffusers/permeators. The number of diffusers positioned before and after a gas clean-up process to obtain optimal system performance will vary with feed gas inert composition. A simple method to analyze optimal diffuser configuration is presented. The method assumes equilibrium across the Pd/Ag tubes and system flows are limited by diffuser vacuum pump speeds preceding or following the clean-up process. A plot of system feed as a function of inert feed gas composition for various diffuser configuration allows selection of a diffuser configuration for maximum throughput based on feed gas composition.

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From examination of only 4 deg{sup 2} of sky in the NOAO Deep Wide-Field Survey (NDWFS) region, we have identified the first radio-loud quasar at a redshift z > 6. The object, FIRST J1427385+331241, was discovered by matching the FLAMEX IR survey to FIRST survey radio sources with NDWFS counterparts. One candidate z > 6 quasar was found, and spectroscopy with the Keck II telescope confirmed its identification, yielding a redshift z = 6.12. The object is a Broad Absorption Line (BAL) quasar with an optical luminosity of M{sub B} {approx} -26.9 and a radio-to-optical flux ratio {approx} 60. Two Mg II absorptions systems are present at redshifts of z = 2.18 and z = 2.20. We briefly discuss the implications of this discovery for the high-redshift quasar population.

Jet quenching in the matter created in high energy nucleus/nucleus collisions provides a tomographic tool to probe the medium properties. Recent experimental results from the Relativistic Heavy-Ion Collider (RHIC) on characterization of jet production via dihadron correlations at high transverse momentum are reviewed. Expectations from the dihadron measurements for the lower energy {radical}s{sub NN} = 62.4 GeV RHIC run are discussed.

The PHOBOS experiment at RHIC has measured the multiplicity of primary charged particles as a function of centrality and pseudorapidity in Au+Au collisions at {radical}(s{sub NN}) = 19.6, 130 and 200 GeV. Two observations indicate universal behavior of charged particle production in heavy ion collisions. The first is that forward particle production, over a range of energies, follows a universal limiting curve with a non-trivial centrality dependence. The second arises from comparisons with pp/{bar p}p and e{sup +}e{sup -} data. <N{sub ch}>/<N{sub part}/2> in nuclear collisions at high energy scales with {radical}s in a similar way as N{sub ch} in e{sup +}e{sup -} collisions and has a very weak centrality dependence. These features may be related to a reduction in the leading particle effect due to the multiple collisions suffered per participant in heavy ion collisions.

Ground surface subsidence resulting from the March 1992 JUNCTION underground nuclear test at the Nevada Test Site (NTS) imaged by satellite synthetic aperture radar interferometry (InSAR) wholly occurred during a period of several months after the shot (Vincent et al., 1999) and after the main cavity collapse event. A significant portion of the subsidence associated with the small (less than 20 kt) GALENA and DIVIDER tests probably also occurred after the shots, although the deformation detected in these cases contains additional contributions from coseismic processes, since the radar scenes used to construct the deformation interferogram bracketed these two later events, The dimensions of the seas of subsidence resulting from all three events are too large to be solely accounted for by processes confined to the damage zone in the vicinity of the shot point or the collapse chimney. Rather, the subsidence closely corresponds to the span dimensions predicted by Patton's (1990) empirical relationship between spall radius and yield. This suggests that gravitational settlement of damaged rock within the spall zone is an important source of post-shot subsidence, in addition to settlement of the rubble within the collapse chimney. These observations illustrate the potential power of InSAR as a tool for …

Adaptive Mesh Refinement (AMR) is a numerical technique for locally tailoring the resolution computational grids. Multilevel algorithms for solving elliptic problems on adaptive grids include the Fast Adaptive Composite grid method (FAC) and its parallel variants (AFAC and AFACx). Theory that confirms the independence of the convergence rates of FAC and AFAC on the number of refinement levels exists under certain ellipticity and approximation property conditions. Similar theory needs to be developed for AFACx. The effectiveness of multigrid-based elliptic solvers such as FAC, AFAC, and AFACx on adaptively refined overlapping grids is not clearly understood. Finally, a non-trivial eye model problem will be solved by combining the power of using overlapping grids for complex moving geometries, AMR, and multilevel elliptic solvers.

The objective of this project is to develop improved seismic event location techniques that can be used to generate more and better quality reference events using data from local and regional seismic networks. Their approach is to extend existing methods of multiple-event location with more general models of the errors affecting seismic arrival time data, including picking errors and errors in model-based travel-times (path corrections). Toward this end, they are integrating a grid-search based algorithm for multiple-event location (GMEL) with a new parameterization of travel-time corrections and new kriging method for estimating the correction parameters from observed travel-time residuals. Like several other multiple-event location algorithms, GMEL currently assumes event-independent path corrections and is thus restricted to small event clusters. The new parameterization assumes that travel-time corrections are a function of both the event and station location, and builds in source-receiver reciprocity and correlation between the corrections from proximate paths as constraints. The new kriging method simultaneously interpolates travel-time residuals from multiple stations and events to estimate the correction parameters as functions of position. They are currently developing the algorithmic extensions to GMEL needed to combine the new parameterization and kriging method with the simultaneous location of events. The result will …

Free electron lasers operating in the 0.1 to 1.5 nm wavelength have been proposed for the Stanford Linear Accelerator Center and DESY (Germany). The unprecedented brightness and associated fluence predicted for pulses <300 fs pose new challenges for optical components. A criterion for optical component design is required, implying an understanding of x-ray-matter interactions at these extreme conditions. In our experimental effort, the extreme conditions are simulated by currently available sources ranging from optical lasers, through x-ray lasers (at 14.7 nm) down to K-alpha sources ({approx}0.15 nm). In this paper we present an overview of our research program, including (a) Results from the experimental campaign at a short pulse (100 fs-5 ps) power laser at 800 nm, (b) K-a experiments, and (c) Computer modeling and experimental project using a tabletop high brightness ps x-ray laser at the Lawrence Livermore National Laboratory.

As with all electromagnet radiation, polarization of x-rays is a general phenomenon. Such polarization has been known since the classic experiments of Barkla in 1906. The general implementation of polarization to x-ray analysis had to await the fixed geometry of energy-dispersive systems. The means of optimizing these systems is shown in this review paper. Improved detection limits are the result.

Contemporary microprocessors provide a rich set of integrated performance counters that allow application developers and system architects alike the opportunity to gather important information about workload behaviors. These counters can capture instruction, memory, and operating system behaviors. Current techniques for analyzing data produced from these counters use raw counts, ratios, and visualization techniques to help users make decisions about their application source code. While these techniques are appropriate for analyzing data from one process, they do not scale easily to new levels demanded by contemporary computing systems. Indeed, the amount of data generated by these experiments is on the order of tens of thousands of data points. Furthermore, if users execute multiple experiments, then we add yet another dimension to this already knotty picture. This flood of multidimensional data can swamp efforts to harvest important ideas from these valuable counters. Very simply, this paper addresses these concerns by evaluating several multivariate statistical techniques on these datasets. We find that several techniques, such as statistical clustering, can automatically extract important features from this data. These derived results can, in turn, be feed directly back to an application developer, or used as input to a more comprehensive performance analysis environment, such as …

Gated, microchannel-plate-based (MCP) framing cameras have been deployed worldwide for 0.2 - 9 keV x-ray imaging and spectroscopy of transient plasma phenomena. For a variety of spectroscopic and imaging applications, the angular sensitivity of MCPs must be known for correctly interpreting the data. We present systematic measurements of angular sensitivity at discrete relevant photon energies and arbitrary MCP gain. The results can been accurately predicted by using a simple 2D approximation to the 3D MCP geometry and by averaging over all possible photon ray paths.

As evidenced by the popularity of MPI (Message Passing Interface), message passing is an effective programming technique for managing coarse-grained concurrency on distributed computers. Unfortunately, debugging message-passing applications can be difficult. Software complexity, data races, and scheduling dependencies can make programming errors challenging to locate with manual, interactive debugging techniques. This article describes Umpire, a new tool for detecting programming errors at runtime in message passing applications. Umpire monitors the MPI operations of an application by interposing itself between the application and the MPI runtime system using the MPI profiling layer. It, then, checks its MPI behavior for specific errors. The initial collection of programming errors includes deadlock detection, mismatched collective operations, and resource exhaustion. They present an evaluation that demonstrates the effectiveness of this approach.

Although programming models and languages appear to be converging, the computational workloads and communication patterns for scientific applications vary dramatically, depending, in part, on the nature of the problem the applications are solving. In this paper, we investigate the scalability, architectural requirements, and inherent behavioral characteristics of eight scalable scientific applications. We provide a comparative analysis of these applications and isolate their performance characteristics using empirical measurements. We refine our analysis into precise explanations of the factors that influence performance and scalability for each application; we distill these factors into common traits and overall recommendations. Initially, we examine the overall scalability of each application. Then, based on these results, we iteratively investigate the primary factors that affect scalability and performance using a combination of measurement techniques, such as message tracing and monitoring hardware counters, until we can understand each application's primary performance properties and the root causes of those properties.

We present first principle molecular dynamics simulations for selected point defects on the (001) stoichiometric carbon terminated surface of cubic Silicon Carbide. In particular we investigated missing units and coordination defects. The results of our calculations are compared with recent experiments, in particular we discuss simulated STM images, which are in good agreement with measured ones.

In this paper, the adaptive optics (AO) system at Keck Observatory is characterized. The AO system is described in detail. The physical parameters of the lenslets, CCD and deformable mirror, the calibration procedures and the signal processing algorithms are explained. Results of sky performance tests are presented: the AO system is shown to deliver images with an average Strehl ratio of up to 0.37 at 1.59 {micro}m using a bright guide star. An error budget that is consistent with the observed image quality is presented.

The growing processor/memory performance gap causes the performance of many codes to be limited by memory accesses. If known to exist in an application, strided memory accesses forming streams can be targeted by optimizations such as prefetching, relocation, remapping, and vector loads. Undetected, they can be a significant source of memory stalls in loops. Existing stream-detection mechanisms either require special hardware, which may not gather statistics for subsequent analysis, or are limited to compile-time detection of array accesses in loops. Formally, little treatment has been accorded to the subject; the concept of locality fails to capture the existence of streams in a program's memory accesses. The contributions of this paper are as follows. First, we define spatial regularity as a means to discuss the presence and effects of streams. Second, we develop measures to quantify spatial regularity, and we design and implement an on-line, parallel algorithm to detect streams - and hence regularity - in running applications. Third, we use examples from real codes and common benchmarks to illustrate how derived stream statistics can be used to guide the application of profile-driven optimizations. Overall, we demonstrate the benefits of our novel regularity metric as a low-cost instrument to detect potential …