We development a general framework for information-passing and concurrent discrete to continuum scale bridging and applied it to biological, electro-mechanical and thermo-electrical systems. Funds were used for partial support of two post-doctoral research associates (Aiqin Li, Dawei Zhang) and three graduate students (Renge Li, Mohan Nuggehally, Joseph Riendeau).

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The cereus group represents sporulating soil bacteriacontaining pathogenic strains which may cause diarrheic or emetic foodpoisoning outbreaks. Multiple locus sequence typing revealed a presencein natural samples of these bacteria of about thirty clonal complexes.Application of genomic methods to this group was however biased due tothe major interest for representatives closely related to B. anthracis.Albeit the most important food-borne pathogens were not yet defined,existing dataindicate that they are scattered all over the phylogenetictree. The preliminary analysis of the sequences of three genomesdiscussed in this paper narrows down the gaps in our knowledge of thecereus group. The strain NVH391-98 is a rare but particularly severefood-borne pathogen. Sequencing revealed that the strain must be arepresentative of a novel bacterial species, for which the name Bacilluscytotoxis is proposed. This strain has a reduced genome size compared toother cereus group strains. Genome analysis revealed absence of sigma Bfactor and the presence of genes encoding diarrheic Nhe toxin, notdetected earlier. The strain B. cereus F837/76 represents a clonalcomplex close to that of B. anthracis. Including F837/76, three such B.cereus strains had been sequenced. Alignment of genomes suggests that B.anthracis is their common ancestor. Since such strains often emerge fromclinical cases, they merit a special attention. The …

An attempt has been made to derive a version of the virial integral that would describe average properties of the interstellar medium (ISM). It is suggested to eliminate the (large) contribution of stellar matter by introducing 'exclusion zones' surrounding stars. Such an approach leads to the appearance of several types of additional surface integrals in the general expression. Their contribution depends on the rate of energy and matter exchange between the stars and ISM. If this exchange is weak, one can obtain a desired virial integral for ISM. However, the presence of intermittent large-scale energetic events significantly constrains the applicability of the virial theorem. If valid, the derived virial integral is dominated by cold molecular/atomic clouds, with only minor contribution of the global magnetic field and low-density warm part.

One way to reduce the effects of anthropogenic greenhousegases on climate is to inject carbon dioxide (CO2) from industrialsources into deep geological formations such as brine formations ordepleted oil or gas reservoirs. Research has and is being conducted toimprove understanding of factors affecting particular aspects ofgeological CO2 storage, such as performance, capacity, and health, safetyand environmental (HSE) issues, as well as to lower the cost of CO2capture and related processes. However, there has been less emphasis todate on system-level analyses of geological CO2 storage that considergeological, economic, and environmental issues by linking detailedrepresentations of engineering components and associated economic models.The objective of this study is to develop a system-level model forgeological CO2 storage, including CO2 capture and separation,compression, pipeline transportation to the storage site, and CO2injection. Within our system model we are incorporating detailedreservoir simulations of CO2 injection and potential leakage withassociated HSE effects. The platform of the system-level modelingisGoldSim [GoldSim, 2006]. The application of the system model is focusedon evaluating the feasibility of carbon sequestration with enhanced gasrecovery (CSEGR) in the Rio Vista region of California. The reservoirsimulations are performed using a special module of the TOUGH2 simulator,EOS7C, for multicomponent gas mixtures of methane and CO2 or methane andnitrogen. …

The authors present Sigma, a Web-rich application which provides user-friendly access in processing and plotting of the evaluated and experimental nuclear reaction data stored in the ENDF-6 and EXFOR formats. The main interface includes browsing using a periodic table and a directory tree, basic and advanced search capabilities, interactive plots of cross sections, angular distributions and spectra, comparisons between evaluated and experimental data, computations between different cross section sets. Interactive energy-angle, neutron cross section uncertainties plots and visualization of covariance matrices are under development. Sigma is publicly available at the National Nuclear Data Center website at www.nndc.bnl.gov/sigma.

Long-range as well as head-on beam-beam effects are expected to limit the LHC performance with design parameters. They are also important consideration for the LHC upgrades. To mitigate long-range effects current carrying wires parallel to the beam were proposed. Two such wires are installed in RHIC where they allow studying the effect of strong long-range beam-beam effects, as well as the compensation of a single long-range interaction. The tests provide benchmark data for simulations and analytical treatments. To reduce the head-on beam-beam effect electron lenses were proposed for both RIDC and the LHC. We present the experimental long-range beam-beam program at RHIC and report on head-on compensations studies based on simulations.

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 …

The 100-F-36 waste site is the location of the former 108-F Biological Laboratory. The building was closed in 1973, decontaminated, decommissioned, and eventually demolished in 1999. In accordance with this evaluation, the confirmatory sampling results support a reclassification of this site to No Action. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of confirmatory sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

We present a method to measure self-diffusion acrossmembranes without the need for concentration or pressure gradients.Hyperpolarized xenon in combination with remote detection of NMR allowsthe measurement of membrane permeation, even in the gas phase. Theresulting images allow quantification of the amount of fluid diffusedthrough the membrane, and represent an alternative, potentially moreprecise way of measuring a membrane diffusion coefficient. The use ofremote detection of NMR allows for non-invasive signal encoding coupledto sensitive detection, making this approach ideal for the study ofdiffusion in intact devices such as fuel cells or separationsystems.

Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria iscatalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes polarized X-ray absorption spectroscopy measurements of PS II single crystals. Analysis of those results has constrained the Mn4Ca cluster geometry to a setof three similar high-resolution structures. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 Angstrom-resolution X-ray structures or other previously proposed models. The differences between the models derived from X-rayspectroscopy and crystallography are predominantly because of damage to the Mn4Ca cluster by X-rays under the conditions used for structure determination by X-ray crystallography. X-ray spectroscopy studies are also used for studying the changes in the structure of the Mn4Ca catalytic center as it cycles through the five intermediate states known as the Si-states (i=0-4). The electronic structure of the Mn4Ca cluster has been studied more recently using resonant inelastic X-ray …

In recent experiments plasma electrons became trapped in a plasma wakefield accelerator (PWFA). The transverse size of these trapped electrons on a downstream diagnostic yields an upper limit measurement of transverse normalized emittance divided by peak current, {var_epsilon}{sub N,x}/I. The lowest upper limit for {var_epsilon}{sub N,x}/I measured in the experiment is 1.3 {center_dot} 10{sup -10} m/A.

We report on design studies for a seeded FEL light source that is responsive to the scientific needs of the future. The FEL process increases radiation flux by several orders of magnitude above existing incoherent sources, and offers the additional enhancements attainable by optical manipulations of the electron beam: control of the temporal duration and bandwidth of the coherent output, reduced gain length in the FEL, utilization of harmonics to attain shorter wavelengths, and precise synchronization of the x-ray pulse with seed laser systems. We describe an FEL facility concept based on a high repetition rate RF photocathode gun, that would allow simultaneous operation of multiple independent FEL's, each producing high average brightness, tunable over the VUV-soft x-ray range, and each with individual performance characteristics determined by the configuration of the FEL. SASE, enhanced-SASE (ESASE), seeded, harmonic generation, and other configurations making use of optical manipulations of the electron beam may be employed, providing a wide range of photon beam properties to meet varied user demands.

In this report we derive a model for a highly scattering medium, implemented as a set of MATLAB functions. This model is used to analyze an approach for using time-reversal to enhance the detection of a single frequency source in a highly scattering medium. The basic approach is to apply the singular value decomposition to the multistatic response matrix for a time-reversal array system. We then use the array in a purely passive mode, measuring the response to the presence of a source. The measured response is projected onto the singular vectors, creating a time-reversal pseudo-spectrum. We can then apply standard detection techniques to the pseudo-spectrum to determine the presence of a source. If the source is close to a particular scatterer in the medium, then we would expect an enhancement of the inner product between the array response to the source with the singular vector associated with that scatterer. In this note we begin by deriving the Foldy-Lax model of a highly scattering medium, calculate both the field emitted by the source and the multistatic response matrix of a time-reversal array system in the medium, then describe the initial analysis approach.

We are now well-advanced in our development, prototyping and deployment of a high performance next generation Integrated Environment for Collaborative Work. The system, aimed at using the capability of ESnet and Internet2 for rapid data exchange, is based on the Virtual Room Videoconferencing System (VRVS) developed by Caltech. The VRVS system has been chosen by the Internet2 Digital Video (I2-DV) Initiative as a preferred foundation for the development of advanced video, audio and multimedia collaborative applications by the Internet2 community. Today, the system supports high-end, broadcast-quality interactivity, while enabling a wide variety of clients (Mbone, H.323) to participate in the same conference by running different standard protocols in different contexts with different bandwidth connection limitations, has a fully Web-integrated user interface, developers and administrative APIs, a widely scalable video network topology based on both multicast domains and unicast tunnels, and demonstrated multiplatform support. This has led to its rapidly expanding production use for national and international scientific collaborations in more than 60 countries. We are also in the process of creating a 'testbed video network' and developing the necessary middleware to support a set of new and essential requirements for rapid data exchange, and a high level of interactivity in …

If carbon dioxide capture and storage (CCS) technologies areimplemented on a large scale, the amounts of CO2 injected and sequesteredunderground could be extremely large. The stored CO2 then replaces largevolumes of native brine, which can cause considerable pressureperturbation and brine migration in the deep saline formations. Ifhydraulically communicating, either directly via updipping formations orthrough interlayer pathways such as faults or imperfect seals, theseperturbations may impact shallow groundwater or even surface waterresources used for domestic or commercial water supply. Possibleenvironmental concerns include changes in pressure and water table,changes in discharge and recharge zones, as well as changes in waterquality. In compartmentalized formations, issues related to large-scalepressure buildup and brine displacement may also cause storage capacityproblems, because significant pressure buildup can be produced. Toaddress these issues, a three-year research project was initiated inOctober 2006, the first part of which is summarized in this annualreport.

Currently, most of our thinking about the defects responsible for initiating laser damage considers them as featureless absorbers. However, an increasing body of evidence, particularly involving multi-wavelength irradiation, suggests electronic structure of damage initiators is important in determining both initiation and conditioning behaviors in KDP. The effective absorption coefficient of energy under multi-wavelength irradiation cannot be accounted for by a structureless absorber, but is consistent with an initiator with a multi-level structure. We outline the evidence and assess the ability of such a simple multi-level model to explain these and other experimentally observed behaviors.

We present an experimental realization of the classical Jeffery-Hamel flows inside a wedge-shaped channel. We compare the measured velocity fields with the predictions of Jeffery-Hamel theory. A detailed experimental study of bifurcation diagrams for the solutions reveals the absolute stability of the pure outflow solution and an interesting hysteretic structure for bifurcations. We also observe a multiple vortex flow regime predicted earlier numerically and analytically. Experimental studies of the stability of the flow to perturbations at the channel exit are also conducted.

The {tau}{sup -} {yields} {eta}{pi}{sup -}{pi}{sup +}{pi}{sup -}{nu}{sub {tau}} decay with the {eta} {yields} {gamma}{gamma} mode is studied using 384 fb{sup -1} of data collected by the BABAR detector. The branching fraction is measured to be (1.60 {+-} 0.05 {+-} 0.11) x 10{sup -4}. It is found that {tau}{sup -} {yields} f{sub 1}(1285){pi}{sup -} {nu}{sub {tau}} {yields} {eta}{pi}{sup -}{pi}{sup +}{pi}{sup -}{nu}{sub {tau}} is the dominant decay mode with a branching fraction of (1.11 {+-} 0.06 {+-} 0.05) x 10{sup -4}. The first error on the branching fractions is statistical and the second systematic. In addition, a 90% confidence level upper limit on the branching fraction of the {tau}{sup -} {yields} {eta}{prime}(958){pi}{sup -}{nu}{sub {tau}} decay is measured to be 7.2 x 10{sup -6}. This last decay proceeds through a second-class current and is expected to be forbidden in the limit of isospin symmetry.

The 100-F-31 waste site is a former septic system that supported the inhalation laboratories, also referred to as the 144-F Particle Exposure Laboratory (132-F-2 waste site), which housed animals exposed to particulate material. The 100-F-31 waste site has been remediated to achieve the remedial action objectives specified in the Remaining Sites ROD. The results of verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River.

This article examines the impact of retail electricity rate design on the economic value of grid-connected photovoltaic (PV) systems, focusing on commercial customers in California. Using 15-min interval building load and PV production data from a sample of 24 actual commercial PV installations, we compare the value of the bill savings across 20 commercial-customer retail electricity rates currently offered in the state. Across all combinations of customers and rates, we find that the annual bill savings from PV, per kWh generated, ranges from $0.05 to $0.24/kWh. This sizable range in rate-reduction value reflects differences in rate structures, revenue requirements, the size of the PV system relative to building load, and customer load shape. The most significant rate design issue for the value of commercial PV is found to be the percentage of total utility bills recovered through demand charges, though a variety of other factors are also found to be of importance. The value of net metering is found to be substantial, but only when energy from commercial PV systems represents a sizable portion of annual customer load. Though the analysis presented here is specific to California, our general results demonstrate the fundamental importance of retail rate design for the …

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Distinct maxima and minima in the neutron total cross section uncertainties were observed in our large scale covariance calculations using a spherical optical potential. In this contribution we investigate the physical origin of this oscillating structure. Specifically, we analyze the case of neutron reactions on {sup 56}Fe, for which total cross section uncertainties are characterized by the presence of five distinct minima at 0.1, 1.1, 5, 25, and 70 MeV. To investigate their origin, we calculated total cross sections by perturbing the real volume depth V{sub v} by its expected uncertainty {+-}{Delta}V{sub v}. Inspecting the effect of this perturbation on the partial wave cross sections we found that the first minimum (at 0.1 MeV) is exclusively due to the contribution of the s-wave. On the other hand, the same analysis at 1.1 MeV showed that the minimum is the result of the interplay between s-, p-, and d-waves; namely the change in the s-wave happens to be counterbalanced by changes in the p- and d-waves. Similar considerations can be extended for the third minimum, although it can be also explained in terms of the Ramsauer effect as well as the other ones (at 25 and 70 MeV). We discuss the …