Since the beginning of Run II at the Fermilab Tevatron the QCD physics groups of the CDF and D0 experiments have worked to reach unprecedented levels of precision for many QCD observables. Thanks to the large dataset--over 3 fb{sup -1} of integrated luminosity recorded by each experiment--important new measurements have recently been made public and will be summarized in this paper.

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The cyclotide MCoTI-II is a powerful trypsin inhibitor recently isolated from the seeds of Momordica cochinchinensis, a plant member of cucurbitaceae family. We report for the first time the in vivo biosynthesis of natively-folded MCoTI-II inside live E. coli cells. Our biomimetic approach involves the intracellular backbone cyclization of a linear cyclotide-intein fusion precursor mediated by a modified protein splicing domain. The cyclized peptide then spontaneously folds into its native conformation. The use of genetically engineered E. coli cells containing mutations in the glutathione and thioredoxin reductase genes considerably improves the production of folded MCoTI-II in vivo. Biochemical and structural characterization of the recombinant MCoTI-II confirmed its identity. Biosynthetic access to correctly-folded cyclotides allows the possibility of generating cell-based combinatorial libraries that can be screened inside living cells for their ability to modulate or inhibit cellular processes.

The Bio-Aerosol Mass Spectrometry (BAMS) instrument analyzes single aerosol particles using a dual-polarity time-of-flight mass spectrometer recording simultaneously spectra of thirty to a hundred thousand points on each polarity. We describe here a real-time pattern recognition algorithm developed at Lawrence Livermore National Laboratory that has been implemented on a nine Digital Signal Processor (DSP) system from Signatec Incorporated. The algorithm first preprocesses independently the raw time-of-flight data through an adaptive baseline removal routine. The next step consists of a polarity dependent calibration to a mass-to-charge representation, reducing the data to about five hundred to a thousand channels per polarity. The last step is the identification step using a pattern recognition algorithm based on a library of known particle signatures including threat agents and background particles. The identification step includes integrating the two polarities for a final identification determination using a score-based rule tree. This algorithm, operating on multiple channels per-polarity and multiple polarities, is well suited for parallel real-time processing. It has been implemented on the PMP8A from Signatec Incorporated, which is a computer based board that can interface directly to the two one-Giga-Sample digitizers (PDA1000 from Signatec Incorporated) used to record the two polarities of time-of-flight data. By using …

The authors present measurements of branching fractions for five B-meson decays to two-body charmless final states. The data, collected with the BABAR detector at the Stanford Linear Accelerator Center, represent 459 million B{bar B} pairs. The results for branching fractions are, in units of 10{sup -6} (upper limits at 90% C.L.): {Beta}(B{sup +} {yields} {eta}{rho}{sup +}) = 9.9 {+-} 1.2 {+-} 0.8, {Beta}(B{sup 0} {yields} {eta}{prime}{eta}) = 0.5 {+-} 0.4 {+-} 0.1 (< 1.2), {Beta}(B{sup 0} {yields} {eta}{pi}{sup 0}) = 0.9 {+-} 0.4 {+-} 0.1 (< 1.5), {Beta}(B{sup 0} {yields} {eta}{prime}{pi}{sup 0}) = 0.9 {+-} 0.4 {+-} 0.1 (< 1.5), and {Beta}(B{sup 0}{sup 0} {yields} {omega}{pi}{sup 0}) = {eta}{rho}{sup +} mode, they measure the charge asymmetry {Alpha}{sub ch} (B{sup +} {yields} {eta}{rho}{sup +}) = 0.13 {+-} 0.11 {+-} 0.02.

Brookhaven National Laboratory is in the process of designing a new Electron Synchrotron for scientific research using synchrotron radiation. This facility, called the 'National Synchrotron Light Source II' (NSLS-II), will provide x-ray radiation of ultra-high brightness and exceptional spatial and energy resolution. It will also provide advanced insertion devices, optics, detectors, and robotics, and a suite of scientific instruments designed to maximize the scientific output of the facility. The project scope includes the design, construction, installation, and commissioning of the following accelerators: a 200 MeV linac, a booster accelerator operating from 200 MeV to 3.0 GeV, the storage ring which stores 500 mA current of electrons at an energy of 3.0 GeV and 56 beamlines for experiments. It is planned to operate the facility primarily in a top-off mode, thereby maintaining the maximum variation in stored beam current to < 1%. Because of the very demanding requirements for beam emittance and synchrotron radiation brilliance, the beam life-time is expected to be quite low, on the order of 2 hours. Each of the 56 beamlines will be unique in terms of the source properties and configuration. The shielding designs for five representative beamlines are discussed in this paper.

Environmental contamination with a variety of pollutants hasprompted the development of effective bioremediation strategies. But howcan these processes be best monitored and controlled? One avenue underinvestigation is the development of stress response systems as tools foreffective and general process control. Although the microbial stressresponse has been the subject of intensive laboratory investigation, theenvironmental reflection of the laboratory response to specific stresseshas been little explored. However, it is only within an environmentalcontext, in which microorganisms are constantly exposed to multiplechanging environmental stresses, that there will be full understanding ofmicrobial adaptive resiliency. Knowledge of the stress response in theenvironment will facilitate the control of bioremediation and otherprocesses mediated by complex microbial communities.

To address the issue of whether tri-bimaximal mixing (TBM) is a softly-broken hidden or an accidental symmetry, we adopt a model-independent analysis in which we perturb a neutrino mass matrix leading to TBM in the most general way but leave the three texture zeros of the diagonal charged lepton mass matrix unperturbed. We compare predictions for the perturbed neutrino TBM parameters with those obtained from typical SO(10) grand unified theories with a variety of flavor symmetries. Whereas SO(10) GUTs almost always predict a normal mass hierarchy for the light neutrinos, TBM has a priori no preference for neutrino masses. We find, in particular for the latter, that the value of |U{sub e3}| is very sensitive to the neutrino mass scale and ordering. Observation of |U{sub e3}|{sup 2} > 0.001 to 0.01 within the next few years would be incompatible with softly-broken TBM and a normal mass hierarchy and would suggest that the apparent TBM symmetry is an accidental symmetry instead. No such conclusions can be drawn for the inverted and quasi-degenerate hierarchy spectra.

Desulfovibrio vulgaris ATCC 29579 is a well studied sulfate reducer that has known capabilities of reducing heavy metals and radionuclides, like chromium and uranium. Cultures grown in a defined medium (i.e. LS4D) had a lag period of approximately 40 h when exposed to 50 μMof Cr(VI). Substrate analysis revealed that although chromium is reduced within the first 5 h, growth does not resume for another 35 h. During this time, small amounts of lactate are still utilized but the reduction of sulfate does not occur. Sulfate reduction occurs concurrently with the accumulation of acetate approximately 40 h after inoculation, when growth resumes. Similar amounts of hydrogen are produced during this time compared to hydrogen production by cells not exposed to Cr(VI); therefore an accumulation of hydrogen cannot account for the utilization of lactate. There is a significant decrease in the carbohydrate to protein ratio at approximately 25 h, and this result indicated that lactate is not converted to glycogen. Most probable number analysis indicated that cell viability decreased steadily after inoculation and reached approximately 6 x 104 cells/ml 20 h post-chromium exposure. Regeneration of reducing conditions during chromium exposure does not induce growth and in fact may make the growth …

The popularity of UAVs has increased dramatically because of their successful deployment in military operations, their ability to preserve human life, and the continual improvements in wireless communication that serves to increase their capabilities. We believe the usefulness of UAVs would be dramatically increased if formation flight were added to the list of capabilities. Currently, sustained formation flight with a cluster of UAVs has only been achieved with two nodes by the Multi-UAV Testbed at the Massachusetts Institute of Technology. (Park, 2004) Formation flight is a complex operation requiring the ability to adjust the flight patterns on the fly and correct for wind gusts, terrain, and differences in node equipment. All of which increases the amount of inner node communication. Since one of the problems with MANET communication is network congestion, we believe a first step towards formation flight can be made through improved inner node communication. We have investigated current communication routing protocols and developed an altered hybrid routing protocol in order to provide communication with less network congestion.

One of the emerging computational approaches in nuclear physics is the full configuration interaction (FCI) method for solving the many-body nuclear Hamiltonian in a sufficiently large single-particle basis space to obtain exact answers - either directly or by extrapolation. The lowest eigenvalues and correspondingeigenvectors for very large, sparse and unstructured nuclear Hamiltonian matrices are obtained and used to evaluate additional experimental quantities. These matrices pose a significant challenge to the design and implementation of efficient and scalable algorithms for obtaining solutions on massively parallel computer systems. In this paper, we describe the computational strategies employed in a state-of-the-art FCI code MFDn (Many Fermion Dynamics - nuclear) as well as techniques we recently developed to enhance the computational efficiency of MFDn. We will demonstrate the current capability of MFDn and report the latest performance improvement we have achieved. We will also outline our future research directions.

We report the discovery that impacts in the Stardust cometary collector are not distributed randomly in the collecting media, but appear to be clustered on scales smaller than {approx} 10 cm. We also report the discovery of at least two populations of oblique tracks. We evaluated several hypotheses that could explain the observations. No hypothesis was consistent with all the observations, but the preponderance of evidence points toward at least one impact on the central Whipple shield of the spacecraft as the origin of both clustering and low-angle oblique tracks. High-angle oblique tracks unambiguously originate from a non-cometary impact on the spacecraft bus just forward of the collector.

Various gain models have shown the potentially great advantages of Fast Ignition (FI) Inertial Confinement Fusion (ICF) over its conventional hot spot ignition counterpart [e.g., S. Atzeni, Phys. Plasmas 6, 3316 (1999); M. Tabak et al., Fusion Sci. & Technology 49, 254 (2006)]. These gain models, however, all assume nearly uniform-density fuel assemblies. In contrast, conventional ICF implosions yield hollowed fuel assemblies with a high-density shell of fuel surrounding a low-density, high-pressure hot spot. Hence, to realize fully the advantages of FI, an alternative implosion design must be found which yields nearly isochoric fuel assemblies without substantial hot spots. Here, it is shown that a self-similar spherical implosion of the type originally studied by Guderley [Luftfahrtforschung 19, 302 (1942)] may be employed to yield precisely such quasi-isochoric imploded states. The difficulty remains, however, of accessing these self-similarly imploding configurations from initial conditions representing an actual ICF target, namely a uniform, solid-density shell at rest. Furthermore, these specialized implosions must be realized for practicable drive parameters and at the scales and energies of interest in ICF. A direct-drive implosion scheme is presented which meets all of these requirements and reaches a nearly isochoric assembled density of 300 g=cm{sup 3} and areal …

We attempt to predict the observed morphology, column density and velocity gradient of Pillar II of the Eagle Nebula, using Rayleigh Taylor (RT) models in which growth is seeded by an initial perturbation in density or in shape of the illuminated surface, and cometary models in which structure is arises from a initially spherical cloud with a dense core. Attempting to mitigate suppression of RT growth by recombination, we use a large cylindrical model volume containing the illuminating source and the self-consistently evolving ablated outflow and the photon flux field, and use initial clouds with finite lateral extent. An RT model shows no growth, while a cometary model appears to be more successful at reproducing observations.

Carbon nanotubes offer an outstanding platform for studying molecular transport at nanoscale, and have become promising materials for nanofluidics and membrane technology due to their unique combination of physical, chemical, mechanical, and electronic properties. In particular, both simulations and experiments have proved that fluid flow through carbon nanotubes of nanometer size diameter is exceptionally fast compared to what continuum hydrodynamic theories would predict when applied on this length scale, and also, compared to conventional membranes with pores of similar size, such as zeolites. For a variety of applications such as separation technology, molecular sensing, drug delivery, and biomimetics, selectivity is required together with fast flow. In particular, for water desalination, coupling the enhancement of the water flux with selective ion transport could drastically reduce the cost of brackish and seawater desalting. In this work, we study the ion selectivity of membranes made of aligned double-walled carbon nanotubes with sub-2 nm diameter. Negatively charged groups are introduced at the opening of the carbon nanotubes by oxygen plasma treatment. Reverse osmosis experiments coupled with capillary electrophoresis analysis of permeate and feed show significant anion and cation rejection. Ion exclusion declines by increasing ionic strength (concentration) of the feed and by lowering solution …

This paper presents a 3-axis gimbal whose three rotational axes are actuated by a novel drive system: linear piezoelectric motors whose linear output is converted to rotation by using drive disks. Advantages of this technology are: fast response, high accelerations, dither-free actuation and backlash-free positioning. The gimbal was developed to house a laser range finder for the purpose of tracking and guiding unmanned aerial vehicles during landing maneuvers. The tilt axis was built and the test results indicate excellent performance that meets design specifications.

Modern single molecule fluorescence microscopy offers new, highly quantitative ways of studying the systems biology of cells while keeping the cells healthy and alive in their natural environment. In this context, a quantum optical technique, photon antibunching, has found a small niche in the continuously growing applications of single molecule techniques to small molecular complexes. Here, we review some of the most recent applications of photon antibunching in biophotonics, and we provide a guide for how to conduct photon antibunching experiments at the single molecule level by applying techniques borrowed from time-correlated single photon counting. We provide a number of new examples for applications of photon antibunching to the study of multichromophoric molecules and small molecular complexes.

The objectives of the program during the past year was to complete Technical Objectives 2 and 3 and initiate Technical Objective 4 are described. To assist the Department of Energy in the development of a low cost, reliable and high performance air compressor/expander. Technical Objective 1: Perform a turbocompressor systems PEM fuel cell trade study to determine the enhanced turbocompressor approach. Technical Objective 2: Using the results from technical objective 1, an enhanced turbocompressor will be fabricated. The design may be modified to match the flow requirements of a selected fuel cell system developer. Technical Objective 3: Design a cost and performance enhanced compact motor and motor controller. Technical Objective 4: Turbocompressor/motor controller development.

Homologous recombination (HR) repairs chromosome damage and is indispensable for tumor suppression in humans. RAD51 mediates the DNA strand pairing step in HR. RAD51AP1 (RAD51 Associated Protein 1) is a RAD51-interacting protein whose function has remained elusive. Knockdown of RAD51AP1 in human cells by RNA interference engenders sensitivity to different types of genotoxic stress. Moreover, RAD51AP1-depleted cells are impaired for the recombinational repair of a DNA double-strand break and exhibit chromatid breaks both spontaneously and upon DNA damaging treatment. Purified RAD51AP1 binds dsDNA and RAD51, and it greatly stimulates the RAD51-mediated D-loop reaction. Biochemical and cytological results show that RAD51AP1 functions at a step subsequent to the assembly of the RAD51-ssDNA nucleoprotein filament. Our findings provide the first evidence that RAD51AP1 helps maintain genomic integrity via RAD51 recombinase enhancement.

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We compare four algorithms from the latest LAPACK 3.1 release for computing eigenpairs of a symmetric tridiagonal matrix. These include QR iteration, bisection and inverse iteration (BI), the Divide-and-Conquer method (DC), and the method of Multiple Relatively Robust Representations (MR). Our evaluation considers speed and accuracy when computing all eigenpairs, and additionally subset computations. Using a variety of carefully selected test problems, our study includes a variety of today's computer architectures. Our conclusions can be summarized as follows. (1) DC and MR are generally much faster than QR and BI on large matrices. (2) MR almost always does the fewest floating point operations, but at a lower MFlop rate than all the other algorithms. (3) The exact performance of MR and DC strongly depends on the matrix at hand. (4) DC and QR are the most accurate algorithms with observed accuracy O({radical}ne). The accuracy of BI and MR is generally O(ne). (5) MR is preferable to BI for subset computations.

Efficient utilization of carbon inputs is critical to the economic viability of the current forest products sector. Input carbon losses occur in various locations within a pulp mill, including losses as volatile organics and wastewater . Opportunities exist to capture this carbon in the form of value-added products such as biodegradable polymers. Waste activated sludge from a pulp mill wastewater facility was enriched for 80 days for a methanol-utilizing consortium with the goal of using this consortium to produce biopolymers from methanol-rich pulp mill waste streams. Five enrichment conditions were utilized: three high-methanol streams from the kraft mill foul condensate system, one methanol-amended stream from the mill wastewater plant, and one methanol-only enrichment. Enrichment reactors were operated aerobically in sequencing batch mode at neutral pH and 25°C with a hydraulic residence time and a solids retention time of four days. Non-enriched waste activated sludge did not consume methanol or reduce chemical oxygen demand. With enrichment, however, the chemical oxygen demand reduction over 24 hour feed/decant cycles ranged from 79 to 89 %, and methanol concentrations dropped below method detection limits. Neither the non-enriched waste activated sludge nor any of the enrichment cultures accumulated polyhydroxyalkanoates (PHAs) under conditions of nitrogen sufficiency. …

The ATLAS experiment at the Large Hadron Collider at CERN has a substantial collaborative Education and Outreach project. This article describes its activities and how it promotes physics to students around the world. With the extraordinary possibility to make groundbreaking discoveries, the ATLAS Experiment [1] at the Large Hadron Collider at CERN can play an important role in promoting contemporary physics at school. For many years ATLAS has had a substantial collaborative Education and Outreach (E&O) project in which physicists from various parts of the world take part. When the experiment begins in 2007, students from around the world will be analyzing data using cutting-edge technology. The unprecedented collision energies of the Large Hadron Collider allow ATLAS to decode the 'events' that unfold after the head-on collisions of protons (Fig. 1). The scientific results from these events will reveal much about the basic nature of matter, energy, space, and time. Students and others will be excited as they try to find events that may be signs for dark matter, extra dimensions of space, mini-black holes, string theory, and other fundamental discoveries. Science education and outreach and the promotion of awareness and appreciation of physics research have become important tasks for …

It is shown in this work that basic measurements made from well defined source detector configurations can be readily converted in to benchmark quality results by which Monte Carlo N-Particle (MCNP) input stacks can be validated. Specifically, a recent measurement made in support of national security at the Nevada Test Site (NTS) is described with sufficient detail to be submitted to the American Nuclear Society’s (ANS) Joint Benchmark Committee (JBC) for consideration as a radiation measurement benchmark. From this very basic measurement, MCNP input stacks are generated and validated both in predicted signal amplitude and spectral shape. Not modeled at this time are those perturbations from the more recent pulse height light (PHL) tally feature, although what spectral deviations are seen can be largely attributed to not including this small correction. The value of this work is as a proof-of-concept demonstration that with well documented historical testing can be converted into formal radiation measurement benchmarks. This effort would support virtual testing of algorithms and new detector configurations.