Dyadobacter fermentans (Chelius MK and Triplett EW, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order 'Sphingobacteriales'. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in ageing cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the 'sphingobacterial' genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

SLAC has developed a multi-physics simulation code TEM3P for simulating integrated effects of electromagnetic, thermal and structural loads. TEM3P shares the same software infrastructure with SLAC's parallel finite element electromagnetic codes, thus enabling all physics simulations within a single framework. The finite-element approach allows high-fidelity, high-accuracy simulations and the parallel implementation facilitates large-scale computation with fast turnaround times. In this paper, TEM3P is used to analyze thermal loading at coupler end of the JLAB SRF cavity.

The primary purpose of this 3-year DOE-funded research effort, now completed, was to develop consistent, theoretical foundations of computations on discrete geometry, to realize the promise of predictive and scalable management of large geometric datasets as handled routinely in applied sciences. Geometry (be it simple 3D shapes or higher dimensional manifolds) is indeed a central and challenging issue from the modeling and computational perspective in several sciences such as mechanics, biology, molecular dynamics, geophysics, as well as engineering. From digital maps of our world, virtual car crash simulation, predictive animation of carbon nano-tubes, to trajectory design of space missions, knowing how to process and animate digital geometry is key in many cross-disciplinary research areas.

Many modern scientific applications rely on highly parallel calculations, which scale to 10's of thousands processors. However, most applications do not concentrate on parallelizing input/output operations. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab initio nuclear structure calculations. In this paper, we develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient input/output of large datasets along with their portability and ease of use in the downstream processing.

Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically adequately accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of Leptotrichia are large fusiform non-motile, non-sporulating rods, which often populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and saccharolytic. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the order 'Fusobacteriales' and no more than the second sequence from the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds …

The broad purpose of this project was to work cooperatively with the DOE to explore technology nad policy issues associated with more efficient, reliable, and affordable electric transmission and distribution use.

The behavior of aftershock sequences around the Nevada Test Site in the southern Great Basin is characterized as a potential discriminant between explosions and earthquakes. The aftershock model designed by Reasenberg and Jones (1989, 1994) allows for a probabilistic statement of earthquake-like aftershock behavior at any time after the mainshock. We use this model to define two types of aftershock discriminants. The first defines M{sub X}, or the minimum magnitude of an aftershock expected within a given duration after the mainshock with probability X. Of the 67 earthquakes with M > 4 in the study region, 63 of them produce an aftershock greater than M{sub 99} within the first seven days after a mainshock. This is contrasted with only six of 93 explosions with M > 4 that produce an aftershock greater than M{sub 99} for the same period. If the aftershock magnitude threshold is lowered and the M{sub 90} criteria is used, then no explosions produce an aftershock greater than M{sub 90} for durations that end more than 17 days after the mainshock. The other discriminant defines N{sub X}, or the minimum cumulative number of aftershocks expected for given time after the mainshock with probability X. Similar to the …

This project was a molecular dynamics study of the relevant issues associated with the structure and transport of lithium in polymer electrolytes such as polyethylene oxide(PEO). In close collaboration with quantum chemist Larry Curtiss and neutron scatterers David Lee Price and Marie-Louise Saboungi at Argonne, we used molecular dynamics to study the local structure and dynamics and ion transport in the polymer. The studies elucidated the mechanism of Li transport in PEO, revealing that the rate limiting step is extremely sensitive to the magnitude of the torsion forces in the backbone of the polymer. Because the torsion forces are difficult to manipulate chemically, this makes it easier to understand why improving the conductivity of PEO based electrolytes has proven to be very difficult. We studied the transport properties of cations in ionic liquids as possible additives to polymer membranes for batteries and fuel cells and found preliminary indications that the transport is enhanced near phase separation in acid-ionic liquid mixtures.

High power gyrotrons are used for electron cyclotron heating, current drive and parasitic mode suppression in tokamaks for fusion energy research. These devices are crucial for successful operation of many research programs around the world, including the ITER program currently being constructed in France. Recent gyrotron failures resulted from cyclic fatigue of the copper material used to fabricated the collectors. The techniques used to collect the spent beam power is common in many gyrotrons produced around the world. There is serious concern that these tubes may also be at risk from cyclic fatigue. This program addresses the cause of the collector failure. The Phase I program successfully demonstrated feasibility of a mode of operation that eliminates the cyclic operation that caused the failure. It also demonstrated that new material can provide increased lifetime under cyclic operation that could increase the lifetime by more than on order of magnitude. The Phase II program will complete that research and develop a collector that eliminates the fatigue failures. Such a design would find application around the world.

The Linac Coherent Light Source at the SLAC National Accelerator Laboratory (operated by Stanford University for the US Department of Energy) is the world's first hard X-ray Free Electron Laser machine. It uses high energy electrons delivered by a linac to create ultrafast and brilliant X-ray pulses that can be used as a 'high-speed' camera to obtain images of atoms and molecules. LCLS is a pioneer machine and, as such, its design has encountered unprecedented challenges, the solutions to which will benefit future facilities of its kind across the globe. This article describes the radiation protection aspects of LCLS electron beamlines. Special emphasis is put on the successful commissioning of the LCLS electron line, where, for all examined loss sources, the measured prompt and residual dose rates are in agreement with or below the values predicted through detailed Monte Carlo simulations, used earlier to design the shielding.

Cryptobacterium curtum Nakazawa et al. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodontitis, inflammations and abscesses. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

The cylindrical ideal magnetohydrodynamic (MHD) stability problem, including ow and a resistive wall, is cast in the standard mathematical form, ωA⋅x = B⋅x, without discretizing the vacuum regions surrounding the plasma. This is accomplished by means of a finite element expansion for the plasma perturbations, by coupling the plasma surface perturbations to the resistive wall using a Green's function approach, and by expanding the unknown vector, x, to include the perturbed current in the resistive wall as an additional degree of freedom. The ideal MHD resistive wall mode (RWM) can be stabilized when the plasma has a uniform equilibrium ow such that the RWM frequency resonates with the plasma's Doppler-shifted sound continuum modes. The resonance induces a singularity in the parallel component of the plasma perturbations, which must be adequately resolved. Complete stabilization within the ideal MHD model (i.e. without parallel damping being added) is achieved as the grid spacing in the region of the resonance is extrapolated to 0 step size

A new method for solving relativistic ideal hydrodynamics in (1+3)D is developed. Longitudinal and transverse radial flows are explicitly embedded into the ansatz for velocity field and the hydrodynamic equations are reduced to a single equation for the transverse velocity field only, which is analytically more tractable as compared with the full hydrodynamic equations. As an application we use the method to find analytically all possible solutions whose transverse velocity fields have power dependence on proper time and transverse radius. Possible application to the Relativistic Heavy Ion Collisions and possible generalizations of the method are discussed.

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

DOE requires sources for testing of high gradient accelerator structures. A power of 50 MW is required at K and Ka band. The pulse length must be ~ 1 microsecond and the pulse repetition frequency at least 100 Hz. At least some applications may require phase stability not offered by a free running oscillator. CCR proposed to build a 50 MW 30 GHz gyrklystron amplifier. This approach would give the required phase stability. The frequency was at the second harmonic of the cycltron frequency and used the TE02 mode. This makes it possible to design a device without an inner conductor, and with a conventional (non-inverted) MIG. This minimizes cost and the risk due to mechanical alignment issues. A detailed design of the gyroklystron was produced. The design was based on simulations of the cavity(ies), electron gun, output coupler and output window. Two designs were produced. One was at the fundamental of the cyclotron frequency. Simulations predicted an output power of 72 MW with an efficiency of 48%. The other was at the second harmonic, producing 37 MW with an efficiency of 37%.

Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmark the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.

Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified amongst the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer?s lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

We present an improved design for a SuperB interaction region. The new design minimizes local bending of the two colliding beams by separating all beam magnetic elements near the Interaction Point (IP). The total crossing angle at the IP is increased from 48 mrad to 60 mrad. The first magnetic element is a six slice Permanent Magnet (PM) quadrupole with an elliptical aperture allowing us to increase the vertical space for the beam. This magnet starts 36 cm from the Interaction Point (IP). This magnet is only seen by the Low-Energy Beam (LEB), the High-Energy Beam (HEB) has a drift space at this location. This allows the preliminary focusing of the LEB which has a smaller beta y* at the IP than the HEB. The rest of the final focusing for both beams is achieved by two super-conducting side-by-side quadrupoles (QD0 and QF1). These sets of magnets are enclosed in a warm bore cryostat located behind the PM quadrupole for the LEB. We describe this design for the interaction region.

Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically yet uncharted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic organism with the ability to grow under anaerobic as well as under aerobic conditions (oxygen concentration larger than 15percent), here only in the presence of 5percent CO2. Strain VPI 2845T, the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

This project assessed the advantages and limitations of using minor actinides as a fuel component to achieve ultra-long life Very High Temperature Reactor (VHTR) configurations. Researchers considered and compared the capabilities of pebble-bed and prismatic core designs with advanced actinide fuels to achieve ultra-long operation without refueling. Since both core designs permit flexibility in component configuration, fuel utilization, and fuel management, it is possible to improve fissile properties of minor actinides by neutron spectrum shifting through configuration adjustments. The project studied advanced actinide fuels, which could reduce the long-term radio-toxicity and heat load of high-level waste sent to a geologic repository and enable recovery of the energy contained in spent fuel. The ultra-long core life autonomous approach may reduce the technical need for additional repositories and is capable to improve marketability of the Generation IV VHTR by allowing worldwide deployment, including remote regions and regions with limited industrial resources. Utilization of minor actinides in nuclear reactors facilitates developments of new fuel cycles towards sustainable nuclear energy scenarios.

Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and is of interest because of the rather isolated phylogenetic location of the genomically little studied suborder Catenulisporineae within the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic lifestyle, but can also grow scantly under anaerobic conditions. Under regular conditions C. acidiphilia grows in long filaments of relatively short aerial hyphae with marked septation. It is a free living, non motile, Gram-positive bacterium isolated from a forest soil sample taken from a wooded area in Gerenzano, Italy. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the actinobacterial family Catenulisporaceae, and the 10,467,782 bp long single replicon genome with its 9056 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.