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 …

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.

InfiniBand (IB) is a popular network technology for modern high-performance computing systems. MPI implementations traditionally support IB using a reliable, connection-oriented (RC) transport. However, per-process resource usage that grows linearly with the number of processes, makes this approach prohibitive for large-scale systems. IB provides an alternative in the form of a connectionless unreliable datagram transport (UD), which allows for near-constant resource usage and initialization overhead as the process count increases. This paper describes a UD-based implementation for IB in Open MPI as a scalable alternative to existing RC-based schemes. We use the software reliability capabilities of Open MPI to provide the guaranteed delivery semantics required by MPI. Results show that UD not only requires fewer resources at scale, but also allows for shorter MPI startup times. A connectionless model also improves performance for applications that tend to send small messages to many different processes.

Developing a theory of low-mass star formation ({approx} 0.1 to 3 M{sub {circle_dot}}) remains one of the most elusive and important goals of theoretical astrophysics. The star-formation process is the outcome of the complex dynamics of interstellar gas involving non-linear interactions of turbulence, gravity, magnetic field and radiation. The evolution of protostellar condensations, from the moment they are assembled by turbulent flows to the time they reach stellar densities, spans an enormous range of scales, resulting in a major computational challenge for simulations. Since the previous Protostars and Planets conference, dramatic advances in the development of new numerical algorithmic techniques have been successfully implemented on large scale parallel supercomputers. Among such techniques, Adaptive Mesh Refinement and Smooth Particle Hydrodynamics have provided frameworks to simulate the process of low-mass star formation with a very large dynamic range. It is now feasible to explore the turbulent fragmentation of molecular clouds and the gravitational collapse of cores into stars self-consistently within the same calculation. The increased sophistication of these powerful methods comes with substantial caveats associated with the use of the techniques and the interpretation of the numerical results. In this review, we examine what has been accomplished in the field and present …

Two recent papers illuminate a long sought step in DNA sliding clamp loading. One paper reveals the structure of the PCNA clamp wrapped around DNA--still open from being loaded--while a second paper discovers that the clamp may assist this process by forming a right-handed helix upon opening.

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.

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.

Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA-damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial-mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced …

An experiment aimed at the synthesis of isotopes of element 120 has been performed using the {sup 244}Pu({sup 58}Fe,xn){sup 302-x} 120 reaction. No decay chains consistent with fusion-evaporation reaction products were observed during an irradiation with a beam dose of 7.1 x 10{sup 18} 330-MeV {sup 58}Fe projectiles. The sensitivity of the experiment corresponds to a cross section of 0.4 pb for the detection of one decay.

We extend the argument of Gomis and Mehen for violation of unitarity in field theories with space-time noncommutativity to dipole field theories. In dipole field theories with a timelike dipole vector, we present 1-loop amplitudes that violate the optical theorem. A quantum mechanical system with nonlocal potential of finite extent in time also shows violation of unitarity.

Different microscanning synchrotron techniques were used to better understand the elaboration process and origins of Terra Sigillata potteries from the Roman period. A mixture Gallic slip sample cross-section showing red and yellow colors was studied. The small (micron) size of the X-ray beam available at Stanford Synchrotron Radiation Laboratory (SSRL) and Advanced Light Source (ALS) synchrotron sources, coupled with the use of a sample scanning stage allowed us to spatially resolve the distribution of the constitutive mineral phases related to the chemical composition. Results show that red color is a result of iron-rich hematite crystals and the yellow part is a result of the presence of Ti-rich rutile-type phase (brookite). Volcanic-type clay is at the origin of these marble Terra Sigillata.

The authors report on several studies of charm baryon production and decays by the BABAR collaboration. They confirm previous observations of the {Xi}'{sub c}{sup 0/+}, {Xi}{sub c}(2980){sup +} and {Xi}{sub c}(3077){sup +} baryons, measure branching ratios for Cabibbo-suppressed {Lambda}{sub c}{sup +} decays and use baryon decays to study the properties of the light-quark baryons, {Omega}{sup -} and {Xi}(1690){sup 0}.

We explore contributions to the 4D effective superpotential which arise from Euclidean D3 branes (''instantons'') that intersect space-filling D-branes. These effects can perturb the effective field theory on the space-filling branes by nontrivial operators composed of charged matter fields, changing the vacuum structure in a qualitative way in some examples. Our considerations are exemplified throughout by a careful study of a fractional brane configuration on a del Pezzo surface.

A general formalism for treating simultaneously the transverse coupled bunch and transverse coupled mode instabilities is presented. In this approach, the equations of motion of a coupled multi-bunch beam are expanded to yield a system of equations involving correlation-moments of the transverse and longitudinal motions. After a proper truncation, the system of equations is closed and can be solved. This approach allows us to formulate within one framework several known instability mechanisms including the single bunch mode coupling instability, the coupled bunch instability, the mode coupling instability, and the coupled mode coupled bunch instability as particular cases.

The Atmospheric Technologies Group (ATG) has developed an advanced atmospheric modeling capability using the Regional Atmospheric Modeling System (RAMS) and a stochastic Lagrangian particle dispersion model (LPDM) for operational use at the Savannah River Site (SRS). For local simulations concerning releases from the Central Savannah River Area (CSRA), RAMS is run in a nested grid configuration with horizontal grid spacing of 8 and 2 km for each grid, with 6-hr forecasts updated every 3 hours. An interface to allow for easy user access to LPDM had been generated, complete with post-processing results depicting surface concentration, deposition, and a variety of dose quantities. A prior weakness in this approach was that observations from the SRS tower network were only incorporated into the three-dimensional modeling effort during the initialization process. Thus, if the forecasted wind fields were in error, the resulting plume predictions would also be erroneous. To overcome this shortcoming, the procedure for generating RAMS wind fields and reading them into LPDM has been modified such that SRS wind measurements are blended with the predicted three-dimensional wind fields from RAMS using the Barnes technique. In particular, the horizontal components in RAMS are replaced with the observed values at a series of …

Many atmospheric transport and dispersion models now exist to provide consequence assessment during emergency response to near-field releases. One way of estimating the uncertainty for a given forecast is to statistically analyze an ensemble of results from several models. ENSEMBLE is a European Union program that utilizes an internet-based system to ingest transport results from numerous modeling agencies. This paper addresses the involvement of the Savannah River National Laboratory (SRNL) in ENSEMBLE, and the resulting improvements in SRNL modeling capabilities. SRNL, the only United States agency involved in the ENSEMBLE program, uses a prognostic atmospheric numerical model (the Regional Atmospheric Modeling System, RAMS) to provide three-dimensional and time-varying meteorology as input to a stochastic Lagrangian particle mode . The model design used by SRNL is discussed, including recent upgrades to the system using parallel processing which allows for finer grid resolution in the generation of the meteorology.

The accumulation of mildly deleterious missense mutations inindividual human genomes has been proposed to be a genetic basis forcomplex diseases. The plausibility of this hypothesis depends onquantitative estimates of the prevalence of mildly deleterious de novomutations and polymorphic variants in humans and on the intensity ofselective pressure against them. We combined analysis of mutationscausing human Mendelian diseases, human-chimpanzee divergence andsystematic data on human SNPs and found that about 20 percent of newmissense mutations in humans result in a loss of function, while about 27percent are effectively neutral. Thus, more than half of new missensemutations have mildly deleterious effects. These mutations give rise tomany low frequency deleterious allelic variants in the human populationas evident from a new dataset of 37 genes sequenced in over 1,500individual human chromosomes. Surprisingly, up to 70 percent of lowfrequency missense alleles are mildly deleterious and associated with aheterozygous fitness loss in the range 0.001-0.003. Thus, the low allelefrequency of an amino acid variant can by itself serve as a predictor ofits functional significance. Several recent studies have reported asignificant excess of rare missense variants in disease populationscompared to controls in candidate genes or pathways. These studies wouldbe unlikely to work if most rare variants were neutral …

Structural properties of single-phase films of {kappa}-In{sub 2}Se{sub 3} and {gamma}-In{sub 2}Se{sub 3} were investigated. Both films were polycrystalline but their microstructure differed considerably. The a-lattice parameter of {kappa}-In{sub 2}Se{sub 3} has been measured. Comparison between these two materials indicates that {kappa}-In{sub 2}Se{sub 3} has a significantly larger unit cell ({Delta}c = 2.5 {+-} 0.2 % and {Delta}a = 13.5 {+-} 0.5%) and a structure more similar to the {alpha}-phase of In{sub 2}Se{sub 3}.

Gamma-ray pulsars are among the best targets for the Large Area Telescope (LAT) aboard the GLAST mission. The higher sensitivity, time and energy resolution of the LAT will provide data of fundamental importance to understand the physics of these fascinating objects. Powerful tools for studying the LAT capabilities for pulsar science are the simulation programs developed within the GLAST Collaboration. Thanks to these simulations it is possible to produce a detailed distribution of gamma-ray photons in energy and phase that can be folded through the LAT Instrument Response Functions (IRFs). Here we present some of the main interesting results from the simulations developed to study the discovery potential of the LAT. In particular we will focus on the capability of the LAT to discover new radio-loud gamma-ray pulsars, on the discrimination between Polar Cap and Outer Gap models, and on the LAT pulsar sensitivity.

The Enriched Xenon Observatory (EXO) will search for double beta decays of 136Xe. We report the results of a systematic study of trace concentrations of radioactive impurities in a wide range of raw materials and finished parts considered for use in the construction of EXO-200, the first stage of the EXO experimental program. Analysis techniques employed, and described here, include direct gamma counting, alpha counting, neutron activation analysis, and high-sensitivity mass spectrometry.

To use type Ia supernovae as standard candles for cosmologywe need accurate broadband magnitudes. In practice the observed magnitudemay differ from the ideal magnitude-redshift relationship either throughintrinsic inhomogeneities in the type Ia supernova population or throughobservational error. Here we investigate how we can choose filterbandpasses to reduce the error caused by both these effects. We find thatbandpasses with large integral fluxes and sloping wings are best able tominimise several sources of observational error, and are also leastsensitive to intrinsic differences in type Ia supernovae. The mostimportant feature of a complete filter set for type Ia supernovacosmology is that each bandpass be a redshifted copy of the first. Wedesign practical sets of redshifted bandpasses that are matched totypical high resistivity CCD and HgCdTe infra-red detector sensitivities.These are designed to minimise systematic error in well observedsupernovae, final designs for specific missions should also considersignal-to-noise requirements and observing strategy. In addition wecalculate how accurately filters need to be calibrated in order toachieve the required photometric accuracy of future supernova cosmologyexperiments such as the SuperNova-Acceleration-Probe (SNAP), which is onepossible realisation of the Joint Dark-Energy mission (JDEM). We considerthe effect of possible periodic miscalibrations that may arise from theconstruction of an interference filter.

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Combining our results for various {Omicron}({alpha}{sub s}{sup 2}) corrections to the weak radiative B-meson decay, we are able to present the first estimate of the branching ratio at the next-to-next-to-leading order in QCD. We find {Beta}({bar B} {yields} X{sub s}{gamma}) = (3.15 {+-} 0.23) x 10{sup -4} for E{sub {gamma}} > 1.6 GeV in the {bar B}-meson rest frame. The four types of uncertainties: non-perturbative (5%), parametric (3%), higher-order (3%) and m{sub c}-interpolation ambiguity (3%) have been added in quadrature to obtain the total error.