Two-dimensional confined systems, such as substrate-supported incommensurate layers, are of interest because their structural and electronic properties may differ from those of bulk materials. While advances in experimental techniques have resulted in the growth of many such interesting systems, progress can often be hampered by the lack of an atomistic-scale understanding of the structure, especially for incommensurate systems. In this work, we develop an atomic-scale model for an ordered incommensurate gold-sulfide (AuS) adlayer that has been previously demonstrated to exist on the Au(111) surface, following sulfur deposition and annealing to 450 K. We introduce theoretical techniques within density functional theory to take into account charge transfer in an incommensurate system and model scanning tunneling microscopy images, which are in good agreement with experiment. Our simulations indicate that this model is remarkably robust. We analyze the nature of bonding in this structure using state-of-the-art Wannier-function based techniques. Our analysis provides a natural explanation for the extraordinary robustness and unusual stoichiometry of this layer. This structure and its chemistry have implications for related S-Au interfaces, such as those in self-assembled monolayers of thiols on Au substrates.

We have studied pressure-induced chemical reactions in carbon monoxide using both a diamond-anvil cell and a modified large volume press. Our spectroscopic data reveal that carbon monoxide disproportionates into molecular CO{sub 2} and a solid lactone-type polymer; photochemically above 3.2 GPa, thermochemically above 5 GPa at 300K, or at 3 GPa and {approx}2000K as achieved by laser heating. The solid product can be recovered at ambient conditions with a high degree of conversion, measured to be up to 95% of the original CO. Its fundamental chemical structure includes {beta}-lactone and conjugated C=C, which can be considered a severely modified polymeric carbon suboxide with open ladders and smaller five-membered rings. The polymer is metastable at ambient conditions, spontaneously liberating CO{sub 2} gases exothermically. We find that the recovered polymer has a high energy density, 1-8 KJ/g, and is very combustible. We estimate the density of recovered CO polymer to be at least 1.65 g/cm cm{sup 3}.

This research describes a non-invasive, non-contact method used to quantitatively analyze the functional characteristics of tissue. Multi-spectral images collected at several near-infrared wavelengths are input into a mathematical optical skin model that considers the contributions from different analytes in the epidermis and dermis skin layers. Through a reconstruction algorithm, we can quantify the percent of blood in a given area of tissue and the fraction of that blood that is oxygenated. Imaging normal tissue confirms previously reported values for the percent of blood in tissue and the percent of blood that is oxygenated in tissue and surrounding vasculature, for the normal state and when ischemia is induced. This methodology has been applied to assess vascular Kaposi's sarcoma lesions and the surrounding tissue before and during experimental therapies. The multi-spectral imaging technique has been combined with laser Doppler imaging to gain additional information. Results indicate that these techniques are able to provide quantitative and functional information about tissue changes during experimental drug therapy and investigate progression of disease before changes are visibly apparent, suggesting a potential for them to be used as complementary imaging techniques to clinical assessment.

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We have developed and tested a fully autonomous pathogen detection system (APDS) capable of continuously monitoring the environment for airborne biological threat agents. The system was developed to provide early warning to civilians in the event of a bioterrorism incident and can be used at high profile events for short-term, intensive monitoring or in major public buildings or transportation nodes for long-term monitoring. The APDS is completely automated, offering continuous aerosol sampling, in-line sample preparation fluidics, multiplexed detection and identification immunoassays, and nucleic-acid based polymerase chain reaction (PCR) amplification and detection. Highly multiplexed antibody-based and duplex nucleic acid-based assays are combined to reduce false positives to a very low level, lower reagent costs, and significantly expand the detection capabilities of this biosensor. This article provides an overview of the current design and operation of the APDS. Certain sub-components of the ADPS are described in detail, including the aerosol collector, the automated sample preparation module that performs multiplexed immunoassays with confirmatory PCR, and the data monitoring and communications system. Data obtained from an APDS that operated continuously for seven days in a major U.S. transportation hub is reported.

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For this study, an extensive suite of mineral particles analogous to components of cosmic dust were tested to determine if their Raman signatures can be recognized after hypervelocity capture in aerogel. The mineral particles were mainly of greater than 20 micrometers in size and were accelerated onto the silica aerogel by light gas gun shots. It was found that all the individual minerals captured in aerogel could be subsequently identified using Raman (or fluorescent) spectra. The beam spot size used for the laser illumination was of the order of 5 micrometers, and in some cases the captured particles were of a similar small size. In some samples fired into aerogel there was observed a shift in the wavenumbers of some of the Raman bands, a result of the trapped particles being at quite high temperatures due to heating by the laser. Temperatures of samples under laser illumination were estimated from the relative intensities of Stokes and anti-Stokes Raman bands, or, in the case of ruby particles, from the wavenumber of fluorescence bands excited by the laser. It was found that the temperature of particles in aerogel varied greatly, dependent upon laser power and the nature of the particle. In the …

Lawrence Berkeley National Laboratory (LBNL) is working to address the needs of the primary scientific Grand Challenges now being considered by the U.S. Department of Energy, Office of Basic Energy Sciences: we are exploring scientific discovery opportunities, and new areas of science, to be unlocked with the use of advanced photon sources. A partnership of several divisions at LBNL is working to define the science and instruments needed in the future. To meet these needs, we propose a seeded, high-repetition-rate, free-electron laser (FEL) facility. Temporally and spatially coherent photon pulses, of controlled duration ranging from picosecond to sub-femtosecond, are within reach in the vacuum ultraviolet (VUV) to soft X-ray regime, and LBNL is developing critical accelerator physics and technologies toward this goal. We envision a facility with an array of FELs, each independently configurable and tunable, providing a range of photon-beam properties with high average and peak flux and brightness.

Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog(TM) system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.

The Linac Coherent Light Source (LCLS) at SLAC will be the brightest X-ray laser in the world when it comes on line. In order to achieve the brightness a 200fS length electron bunch is passed through an undulator. To create the 200fS, 3kA bunch, a 10pS electron bunch, created from a photo cathode in an RF gun, is run off crest on the RF to set up a position to energy correlation. The bunch is then compressed by chicanes. The stability of the RF system is critical in setting up the position to energy correlation. Specifications derived from simulations require the RF system to be stable to below 200fS in several critical injector stations and the last kilometer of linac. The SLAC linac RF system is being upgraded to meet these requirements.

{sup 137}Cs transfer factors were computed for small mammals collected from the dried sediment areas of a partially drained, contaminated reservoir. Soil {sup 137}Cs concentrations were heterogeneous on small and large spatial scales, with a geometric mean of 253.1 Bq/kg dry weight. About 50% of the variance in cotton rat Sigmodon hispidus tissue {sup 137}Cs levels was explained by variation in soil {sup 137}Cs levels. Soil to animal transfer factors (whole body dry weight) averaged 6.0 for cotton rats and 1.2 for cotton mice Peromyscus gossypinus. These values are similar to {sup 137}Cs transfer factors for herbivorous, homeothermic animals from other contaminated ecosystems. Site-specific transfer factors can significantly affect the estimation of dose. In the RESRAD-BIOTA dose model, the default transfer factor for {sup 137}Cs in terrestrial animals is 110 resulting in an estimate of radiation dose to terrestrial biota that is 16 times more than the dose calculated with the actual measured transfer factor.

We have directly probed the plasma conditions in which the Ni-like Pd transient collisional x-ray laser is generated and propagates by measuring the near-field image and by utilizing picosecond resolution soft x-ray laser interferometry of the preformed Pd plasma gain medium. The electron density and gain region of the plasma have been determined experimentally and are found to be in good agreement with simulations. We observe a strong dependence of the laser pump-gain medium coupling on the laser pump parameters. The most efficient coupling of laser pump energy into the gain region occurs with the formation of lower density gradients in the pre-formed plasma and when the duration of the main heating pulse is comparable to the gain lifetime ({approx}10ps for mid-Z Ni-like schemes). This increases the output intensity by more than an order of magnitude relative to the commonly utilized case where the same pumping energy is delivered within a shorter heating pulse duration (< 3ps). In contrast, the higher intensity heating pulses are observed to be absorbed at higher electron densities and in regions where steep density gradients limit the effective length of the gain medium.

In a recent article it was argued that dynamic heterogeneity in d-dimensional glass formers is a manifestation of an order-disorder phenomenon in the d+1 dimensions of spacetime. By considering a dynamical analogue of the free energy, evidence was found for phase coexistence between active and inactive regions of spacetime, and it was suggested that this phenomenon underlies the glass transition. Here we develop these ideas further by investigating in detail the one-dimensional Fredrickson-Andersen (FA) model in which the active and inactive phases originate in the reducibility of the dynamics. We illustrate the phase coexistence by considering the distributions of mesoscopic spacetime observables. We show how the analogy with phase coexistence can be strengthened by breaking microscopic reversibility in the FA model, leading to a non-equilibrium theory in the directed percolation universality class.

The preequilibrium reaction mechanism makes an important contribution to neutron-induced reactions above E{sub n} {approx} 10 MeV. The preequilibrium process has been studied exclusively via the characteristic high energy neutrons produced at bombarding energies greater than 10 MeV. They are expanding the study of the preequilibrium reaction mechanism through {gamma}-ray spectroscopy. Cross-section measurements were made of prompt {gamma}-ray production as a function of incident neutron energy (E{sub n} = 1 to 250 MeV) on a {sup 48}Ti sample. Energetic neutrons were delivered by the Los Alamos National Laboratory spallation neutron source located at the Los Alamos Neutron Science Center facility. The prompt-reaction {gamma} rays were detected with the large-scale Compton-suppressed Germanium Array for Neutron Induced Excitations (GEANIE). Neutron energies were determined by the time-of-flight technique. The {gamma}-ray excitation functions were converted to partial {gamma}-ray cross sections taking into account the dead-time correction, target thickness, detector efficiency and neutron flux (monitored with an in-line fission chamber). Residual state population was predicted using the GNASH reaction code, enhanced for preequilibrium. The preequilibrium reaction spin distribution was calculated using the quantum mechanical theory of Feshback, Kerman, and Koonin (FKK). The multistep direct part of the FKK theory was calculated for a one-step process. …

It will be challenging to measure the temporal profile of the hard X-ray SASE beam independently from the electron beam in the LCLS and other 4th generation light sources. A fast interaction mechanism is needed that can be probed by an ultrafast laser pulse in a pump-probe experiment. It is proposed to exploit the rotation in polarization of light reflected from a thin magnetized film, known as the surface magneto optic Kerr effect (SMOKE), to witness the absorption of the x-ray pulse in the thin film. The change in spin orbit coupling induced by the x-ray pulse occurs on the subfemtosecond time scale and changes the polarization of the probe beam. The limitation to the technique lies with the bandwidth of the probe laser pulse and how short the optical pulse can be made. The SMOKE mechanism will be described and the choices of materials for use with 1.5 {angstrom} x-rays. A schematic description of the pump-probe geometry for x-ray diagnosis is also described.

At Stanford Linear Accelerator Center (SLAC) a Bunch Length Measurement system has been developed to measure the length of the electron bunch for its new Linac Coherent Light Source (LCLS). This destructive measurement uses a transverse-mounted RF deflector (TCAV) to vertically streak the electron beam and an image taken with an insertable screen and a camera. The device control software was implemented with the Experimental Physics and Industrial Control System (EPICS) toolkit. The analysis software was implemented in Matlab{trademark} using the EPICS/Channel Access Interface for Scilab{trademark} and Matlab{trademark} (labCA). This architecture allowed engineers and physicists to develop and integrate their control and analysis without duplication of effort.

The automatic alignment system for the National Ignition Facility (NIF) is a large-scale parallel system that directs all 192 laser beams along the 300-m optical path to a 50-micron focus at target chamber in less than 30 minutes. The system commands 9,000 stepping motors to adjust mirrors and other optics. Twenty-two control loops per beamline request image processing services running on a LINUX cluster to analyze high-resolution images of the beam and references. Process-leveling assures the computational load is evenly spread on the cluster. Algorithms also estimate measurement accuracy and reject off-normal images. One challenge to achieving rapid alignment of beams in parallel is the efficient coordination of shared laser devices, such as sensors that are configurable to monitor multiple beams. Contention for shared resources is managed by the Component Mediation System, which precludes deadlocks and optimizes device motions using a hierarchical component structure. A reservation service provided by the software framework prevents interference from competing instances of automated controls or from the actions of system operators. The design, architecture and performance of the system will be discussed.

A four-dimensional field theory with a qualitatively new type of nonlocality is constructed from a setting where Kaluza-Klein particles probe toroidally compactified string theory with twisted boundary conditions. In this theory fundamental particles are not pointlike and occupy a volume proportional to their R-charge. The theory breaks Lorentz invariance but appears to preserve spatial rotations. At low energies, it is approximately N=4 Super Yang-Mills theory, deformed by an operator of dimension seven. The dispersion relation of massless modes in vacuum is unchanged, but under certain conditions in this theory, particles can travel at superluminal velocities.

A two-color two-photon atomic double ionization experiment using subfemtosecond UV pulses can be designed such that the sequential two-color process dominates and one electron is ejected by each pulse. Nonetheless, ab initio calculations show that, for sufficiently short pulses, a prominent interference pattern in the joint energy distribution of the sequentially ejected electrons can be observed that is due to their indistinguishability and the exchange symmetry of the wave function.

The signals that determine the correct polarity of breast epithelial structures in vivo are not understood. We have shown previously that luminal epithelial cells can be polarized when cultured within a reconstituted basement membrane gel. We reasoned that such cues in vivo may be given by myoepithelial cells. Accordingly, we used an assay where luminal epithelial cells are incorrectly polarized to test this hypothesis. We show that culturing human primary luminal epithelial cells within collagen-I gels leads to formation of structures with no lumina and with reverse polarity as judged by dual stainings for sialomucin, epithelial specific antigen or occludin. No basement membrane is deposited, and {beta}4-integrin staining is negative. Addition of purified human myoepithelial cells isolated from normal glands corrects the inverse polarity, and leads to formation of double-layered acini with central lumina. Among the laminins present in the human breast basement membrane (laminin-1, -5 and -10/11), laminin-1 was unique in its ability to substitute for myoepithelial cells in polarity reversal. Myoepithelial cells were purified also from four different breast cancer sources including a biphasic cell line. Three out of four samples either totally lacked the ability to interact with luminal epithelial cells, or conveyed only correction of polarity …

The Advanced Oxidation Process (AOP) with OH radicals are the most efficient to mineralize organic compounds, and there are various methods to generate OH radicals as the use of ozone, hydrogen peroxide and ultra-violet radiation and ionizing radiation. The irradiation of aqueous solutions with high-energy electrons results in the excitation and ionizing of the molecules and rapid (10{sup -14} - 10{sup -9} s) formation of reactive intermediates. These reactive species will react with organic compounds present in industrial effluent inducing their decomposition. Titanium dioxide (TiO{sub 2}) catalyzed photoreaction is used to remove a wide range of pollutants in air and water media, combined to UV/VIS light, FeO{sub 2}, and H{sub 2}O{sub 2}, but as far as known there is no report on the combination with ionizing radiation. In some recent studies, the removal of organic pollutants in industrial effluent, such as Benzene, Toluene, and Xylene from petroleum production using ionizing radiation was investigated. It has been ob served that none of the methods can be used individually in wastewater treatment applications with good economics and high degree of energy efficiency. In the present work, the efficiency of ionizing radiation in presence of TiO{sub 2} to treat industrial effluent was evaluated. …

The flowing fluid electric conductivity (FEC) logging method, wellbore fluid is replaced with de-ionized water, following which FEC profiles in the wellbore are measured at a series of times while the well is pumped at a constant rate. Locations were fluid enters the wellbore show peaks in the FEC logs, which may be analyzed to infer inflow strengths and salinities of permeable features intersected by the wellbore. In multi-rate flowing FEC logging, the flowing FEC logging method is repeated using two or more pumping rates, which enables the transmissivities and inherent pressure heads of these features to be estimated as well. We perform multi-rate FEC logging on a deep borehole in fractured granitic rock, using three different pumping rates. Results identify 19 hydraulically conducting fractures and indicate that transmissivity, pressure head, and salinity vary significantly among them. By using three pumping rates rather than the minimum number of two, we obtain an internal consistency check on the analysis that provides a measure of the uncertainty of the results. Good comparisons against static FEC profiles and against independent chemical, geological, and hydrogeological data have further enhanced confidence in the results of the multi-rate flowing FEC logging method.

Beams for heavy-ion fusion (HIF) are expected to require substantial neutralization in a target chamber. Present targets call for higher beam currents and smaller focal spots than most earlier designs, leading to high space-charge fields. Collisional stripping by the background gas expected in the chamber further increases the beam charge. Simulations with no electron sources other than beam stripping and background-gas ionization show an acceptable focal spot only for high ion energies or for currents far below the values assumed in recent HIF power-plant scenarios. Much recent research has, therefore, focused on beam neutralization by electron sources that were neglected in earlier simulations, including emission from walls and the target, photoionization by radiation from the target, and pre-neutralization by a plasma generated along the beam path. The simulations summarized here indicate that these effects can significantly reduce the beam focal-spot size.