We have utilized atomic force microscopy (AFM) to visualize the native surface topology and ultrastructure of Bacillus thuringiensis and Bacillus cereus spores in water and in air. AFM was able to resolve the nanostructure of the exosporium and three distinctive classes of appendages. Removal of the exosporium exposed either a hexagonal honeycomb layer (B. thuringiensis) or a rodlet outer spore coat layer (B. cereus). Removal of the rodlet structure from B. cereus spores revealed an underlying honeycomb layer similar to that observed with B. thuringiensis spores. The periodicity of the rodlet structure on the outer spore coat of B. cereus was {approx}8 nm, and the length of the rodlets was limited to the cross-patched domain structure of this layer to {approx}200 nm. The lattice constant of the honeycomb structures was {approx}9 nm for both B. cereus and B. thuringiensis spores. Both honeycomb structures were composed of multiple, disoriented domains with distinct boundaries. Our results demonstrate that variations in storage and preparation procedures result in architectural changes in individual spore surfaces, which establish AFM as a useful tool for evaluation of preparation and processing ''fingerprints'' of bacterial spores. These results establish that high-resolution AFM has the capacity to reveal species-specific assembly …

High-energy electron cooling for RHIC presents many unique features and challenges. An accurate estimate of the cooling times requires detailed simulation of the electron cooling process. The first step towards such calculations is to have an accurate description of the cooling force. Numerical simulations are being used to explore various features of the friction force which appear due to several effects, including the anisotropy of the electron distribution in velocity space and the effect of a strong solenoidal magnetic field. These aspects are being studied in detail using the VORFAL code, which explicitly resolves close binary collisions. Results are compared with available asymptotic and empirical formulas and also, using the BETACOOL code, with direct numerical integration of less approximate expressions over the specified electron distribution function.

High-energy electron cooling, presently considered as essential tool for several applications in high-energy and nuclear physics, requires accurate description of the friction force. A series of measurements were performed at CELSIUS with the goal to provide accurate data needed for the benchmarking of theories and simulations. Some results of accurate comparison of experimental data with the friction force formulas are presented.

A 3D solid model-aided object cueing method that matches phase angles of directional derivative vectors at image pixels to phase angles of vectors normal to projected model edges is described. It is intended for finding specific types of objects at arbitrary position and orientation in overhead images, independent of spatial resolution, obliqueness, acquisition conditions, and type of imaging sensor. It is shown that the phase similarity measure can be efficiently evaluated over all combinations of model position and orientation using the FFT. The highest degree of similarity over all model orientations is captured in a match surface of similarity values vs. model position. Unambiguous peaks in this surface are sorted in descending order of similarity value, and the small image thumbnails that contain them are presented to human analysts for inspection in sorted order.

The summary of this paper is: (1) The conundrum in the title is whether to treat radiation in the lab frame or the comoving frame in a radiation-hydrodynamic problem; (2) Several of the difficulties are associated with combining a somewhat relativistic treatment of radiation with a non-relativistic treatment of hydrodynamics; (3) The principal problem is a tradeoff between easily obtaining the correct diffusion limit and describing free-streaming radiation with the correct wave speed; (4) The computational problems of the comoving-frame formulation in more than one dimension, and the difficulty of obtaining both exact conservation and full u/c accuracy argue against this method; (5) As the interest in multi-D increases, as well as the power of computers, the lab-frame method is becoming more attractive; and (6) The Monte Carlo method combines the advantages of both lab-frame and comoving-frame approaches, its only disadvantage being cost.

We have developed a novel method for patterning surface chemistry: Photocatalytic Lithography. This technique relies on inexpensive stamp materials and light; it does not necessitate mass transport or specified substrates, and the wavelength of light should not limit feature resolution. We have demonstrated the utility of this technique through the patterning of proteins, single cells and bacteria.

CdZnTe (CZT) has been traditionally used as substrate for HgCdTe (MCT) epitaxy. The constraint of good lattice matching plays a fundamental role in the use of this substrate. In, fact, despite the difficulties in growing large area of affordable high-quality substrates, CZT wafers remain the best choice for high yield infrared devices. Nevertheless, material quality of the substrate and epilayer play a limiting role in IR focal plane array (FPA) detector technology. Furthermore, data suggest that the quality of the epilayer is affected by imperfections in the CZT substrate. In addition the pixel size for the current generation of FPAs (less than 20 {micro}m) suggests a need for detailed microscale characterization and an understanding of the substrates and epilayers on at least the spatial scale of the pixel dimensions. In an effort to understand the correlation between material quality and device performances, we have begun to study CZT substrates to investigate bulk and surface properties. The National Synchrotron Light Source (NSLS, BNL) permits a wide variety of material investigations that take advantage of the highly collimated photon radiation emitted from the X-ray and VUV-IR rings. Synchrotron radiation offers the capability to combine good resolution and shorter exposure times than conventional …

The main performance limitation for RHIC is emittance growth caused by IntraBeam Scattering during the store. We have developed a longitudinal bunched-beam stochastic cooling system in the 5-8 GHz band which will be used to counteract IBS longitudinal emittance growth and prevent de-bunching during the store. Solutions to the technical problems of achieving sufficient kicker voltage and overcoming the electronic saturation effects caused by coherent components within the Schottky spectrum are described. Results from tests with copper ions in RHIC during the FY05 physics run, including the observation of signal suppression, are presented.

We are developing an all fiber laser system optimized for providing input pulses for short pulse (1-10ps), high energy ({approx}1kJ) glass laser systems. Fiber lasers are ideal solutions for these systems as they are highly reliable and once constructed they can be operated with ease. Furthermore, they offer an additional benefit of significantly reduced footprint. In most labs containing equivalent bulk laser systems, the system occupies two 4'x8' tables and would consist of 10's if not a 100 of optics which would need to be individually aligned and maintained. The design requirements for this application are very different those commonly seen in fiber lasers. High energy lasers often have low repetition rates (as low as one pulse every few hours) and thus high average power and efficiency are of little practical value. What is of high value is pulse energy, high signal to noise ratio (expressed as pre-pulse contrast), good beam quality, consistent output parameters and timing. Our system focuses on maximizing these parameters sometimes at the expense of efficient operation or average power. Our prototype system consists of a mode-locked fiber laser, a compressed pulse fiber amplifier, a ''pulse cleaner'', a chirped fiber Bragg grating, pulse selectors, a transport …

Zinc oxide is a very attractive material for a range of optoelectronic devices including blue light-emitting diodes and laser diodes. Though n-type doping has been successfully achieved, p-type doing of ZnO is still a challenge that must be overcome before p-n junction devices can be realized. Ion implantation is widely used in the microelectronics industry for selective area doping and device isolation. Understanding damage accumulation and recrystallization processes is important for achieving selective area doping. In this study, As (potential p-type dopant) ion implantation and annealing studies were carried out. ZnO samples were implanted with high dose (1.4 x 10{sup 17} ions/cm{sup 2}) 300 keV As ions at room temperature. Furnace annealing of samples in the range of 900 C to 1200 C was employed to achieve recrystallization of amorphous layers and electrical activation of the dopant. Rutherford backscattering/channeling spectrometry, transmission electron microscopy and cathodolumiescence spectroscopy were used to monitor damage accumulation and annihilation behavior in ZnO. Results of this study have significant implications for p-type doing of ZnO by ion implantation.

Unlike other fuels, hydrogen (H{sub 2}) can be generated and consumed without generating carbon dioxide (CO{sub 2}). This creates both significant engineering challenges and unsurpassed ecological advantages for H{sub 2} as a fuel, while enabling an inexhaustible (closed) global fuel cycle based on the cleanest, most abundant, natural, and elementary substances: H{sub 2}, O{sub 2}, and H{sub 2}O. If generated using light, heat, and/or electrical energy from solar, wind, fission, or (future) fusion power sources, H{sub 2} becomes a versatile, storable, and universal carbonless energy carrier, a necessary element for future global energy system(s) aimed at being free of air and water pollution, CO{sub 2}, and other greenhouse gases. The case for hydrogen rests fundamentally on the need to eliminate pollution and stabilize Earth's atmosphere and climate system.

Studies of beam halo became unavoidable feature of high-intensity machines where uncontrolled beam loss should be kept to extremely small level. For a well controlled stable beam such a loss is typically associated with the low density halo surrounding beam core. In order to minimize uncontrolled beam loss or improve performance of an accelerator, it is very important to understand what are the sources of halo formation in a specific machine of interest. The dominant mechanisms are, in fact, different in linear accelerators, circular machines or Energy Recovering Linacs (ERL). In this paper, we summarize basic mechanisms of halo formation in high-intensity beams and discuss their application to various types of accelerators of interest, such as linacs, rings and ERL.

The design of an electron cooler must take into account both electron beam dynamics issues as well as the electron cooling physics. Research towards high-energy electron cooling of RHIC is in its 3rd year at Brookhaven National Laboratory. The luminosity upgrade of RHIC calls for electron cooling of various stored ion beams, such as 100 GeV/A gold ions at collision energies. The necessary electron energy of 54 MeV is clearly out of reach for DC accelerator system of any kind. The high energy also necessitates a bunched beam, with a high electron bunch charge, low emittance and small energy spread. The Collider-Accelerator Department adopted the Energy Recovery Linac (ERL) for generating the high-current, high-energy and high-quality electron beam. The RHIC electron cooler ERL will use four Superconducting RF (SRF) 5-cell cavities, designed to operate at ampere-class average currents with high bunch charges. The electron source will be a superconducting, 705.75 MHz laser-photocathode RF gun, followed up by a superconducting Energy Recovery Linac (ERL). An R&D ERL is under construction to demonstrate the ERL at the unprecedented average current of 0.5 amperes. Beam dynamics performance and luminosity enhancement are described for the case of magnetized and non-magnetized electron cooling of RHIC.

Porous rock on the earth's surface often contains more than one fluid phase, and an important case is partial saturation with air and water. We implemented a pore-scale, percolation model coupled with a continuum model for water vapor diffusion in order to create a simulated tomographic image of water distribution within a rock core during drying. As drying proceeds, the initial, continuous water cluster breaks up into smaller and smaller clusters with an increasing surface-area-to-volume ratio. Drying times are a function of the number and location of boundary surfaces, but the surface-area-to-volume ratio is approximately the same for a given saturation. By applying a Voigt volume average of the elastic properties of water-filled and air-filled cells, and by introducing the ad hoc rule that water-filled pores on the air-water interface of a cluster behave in a drained manner, we find elastic moduli as a function of saturation that mimic laboratory experimental data.

In this paper I first address the question of whether theseat of the power radiated by an antenna made of conducting members isdistributed over the "arms" of the antenna according to $ - \bf J \cdotE$, where $\bf J$ is the specified current density and $\bf E$ is theelectric field produced by that source. Poynting's theorem permits only aglobal identification of the total input power, usually from a localizedgenerator, with the total power radiated to infinity, not a localcorrespondence of $- \bf J \cdot E\ d^3x $ with some specific radiatedpower, $r^2 \bf S \cdot \hat r\ d\Omega $. I then describe a modelantenna consisting of two perfectly conducting hemispheres of radius\emph a separated by a small equatorial gap across which occurs thedriving oscillatory electric field. The fields and surface current aredetermined by solution of the boundary value problem. In contrast to thefirst approach (not a boundary value problem), the tangential electricfield vanishes on the metallic surface. There is no radial Poyntingvector at the surface. Numerical examples are shown to illustrate how theenergy flows from the input region of the gap and is guided near theantenna by its "arms" until it is launched at larger \emph r/a into theradiation pattern …

We present a patch-based direct Eulerian adaptive mesh refinement (AMR) algorithm for modeling real equation-of-state, multimaterial compressible flow with strength. Our approach to AMR uses a hierarchical, structured grid approach first developed by (Berger and Oliger 1984), (Berger and Oliger 1984). The grid structure is dynamic in time and is composed of nested uniform rectangular grids of varying resolution. The integration scheme on the grid hierarchy is a recursive procedure in which the coarse grids are advanced, then the fine grids are advanced multiple steps to reach the same time, and finally the coarse and fine grids are synchronized to remove conservation errors during the separate advances. The methodology presented here is based on a single grid algorithm developed for multimaterial gas dynamics by (Colella et al. 1993), refined by(Greenough et al. 1995), and extended to the solution of solid mechanics problems with significant strength by (Lomov and Rubin 2003). The single grid algorithm uses a second-order Godunov scheme with an approximate single fluid Riemann solver and a volume-of-fluid treatment of material interfaces. The method also uses a non-conservative treatment of the deformation tensor and an acoustic approximation for shear waves in the Riemann solver. This departure from a strict …

We present a family of ordering algorithms that can be used as a preprocessing step prior to performing sparse LU factorization. The ordering algorithms simultaneously achieve the objectives of selecting numerically good pivots and preserving the sparsity. We describe the algorithmic properties and challenges in their implementation. By mixing the two objectives we show that we can reduce the amount of fill-in in the factors and reduce the number of numerical problems during factorization. On a set of large unsymmetric real problems, we obtained the median reductions of 12% in the factorization time, of 13% in the size of the LU factors, of 20% in the number of operations performed during the factorization phase, and of 11% in the memory needed by the multifrontal solver MA41-UNS. A byproduct of this ordering strategy is an incomplete LU-factored matrix that can be used as a preconditioner in an iterative solver.

Similar to the radiative parton energy loss due to gluonbremsstrahlung, elastic energy loss of a parton undergoing multiplescattering in a finite medium is demonstrated to be sensitive tointerference effect. The interference between amplitudes of elasticscattering via a gluon exchange and that of gluon radiation reduces theeffective elastic energy loss in a finite medium and gives rise to anon-trivial length dependence. The reduction is most significant for apropagation length L<4/\pi T in a medium with a temperature T. Thoughthe finite size effect is not significant for the average partonpropagation in the most central heavy-ion collisions, it will affect thecentrality dependence of its effect on jet quenching.

The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

A multi-wavelength laser based system has been constructed to measure defect induced beam modulation (diffraction) from ICF class laser optics. The Nd:YLF-based modulation measurement system (MMS) uses simple beam collimation and imaging to capture diffraction patterns from optical defects onto an 8-bit digital camera at 1053, 527 and 351 nm. The imaging system has a field of view of 4.5 x 2.8 mm{sup 2} and is capable of imaging any plane from 0 to 30 cm downstream from the defect. The system is calibrated using a 477 micron chromium dot on glass for which the downstream diffraction patterns were calculated numerically. Under nominal conditions the system can measure maximum peak modulations of approximately 7:1. An image division algorithm is used to calculate the peak modulation from the diffracted and empty field images after the baseline residual light background is subtracted from both. The peak modulation can then be plotted versus downstream position. The system includes a stage capable of holding optics up to 50 pounds with x and y translation of 40 cm and has been used to measure beam modulation due to solgel coating defects, surface digs on KDP crystals, lenslets in bulk fused silica and laser damage sites …

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We present first-principles total-energy density-functional theory electronic structure calculations for the neutral and charge states of an oxygen vacancy in KH{sub 2}PO{sub 4} (KDP). Even though the overall DOS profiles for the defective KDP are quite similar to those of the perfect KDP, the oxygen vacancy in the neutral and +1 charge states induces defect states in the band gap. For the neutral oxygen vacancy, the gap states are occupied by two electrons. The difference between the integral of the total density of states (DOS) and the sum of the DOS projected on the atoms of 0.98 |e|, indicates that one of the two electrons resulting from the removal of the oxygen atom is trapped in the vacancy, while the other tends to delocalize in the neighboring atoms. For the +1 charge oxygen vacancy, the addition of the hole reduces the occupation of the filled gap-states in the neutral case from two to one electron and produces new empty states in the gap. The new empty gap states are very close to the highest occupied states, leading to a dramatic decrease of the band gap. The difference between the integral of the total DOS and the sum of the DOS …

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The 32 pixel laboratory microcalorimeter spectrometer built by the NASA/Goddard Space Flight Center is now an integral part of the spectroscopy suite used routinely by the electron beam ion trap and radiative properties group at the Lawrence Livermore National Laboratory. The second generation laboratory instrument, dubbed the XRS/EBIT, is nearly identical to the XRS instrument on the Suzaku X-ray Observatory, formerly Astro-E2. The detector array is from the same processed wafer and uses the same HgTe absorbers. it is being used to measure the photon emission from a variety of radiation sources. These include x-ray emission from laboratory simulated celestial sources, x-ray emission from highly charged ions of Au, and x-ray emission following charge exchange and radiative electron capture. The wide range of applications demonstrates the versatility of a high-resolution, high-efficiency low temperature detector that is able to collect data continually with minimal operator servicing.