We discuss the recent results on open charm measurements at RHIC. The heavy flavor upgrade program for both PHENIX and STAR experiments are briefly discussed. The completion of the program will yield important information on light flavor thermalization of the partonic matter created in high-energy nuclear collisions at RHIC. A new era of RHIC is ahead of us with the progress of the upgrade program.

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ), and predicted genes using two popular gene finding pipelines (fgenesb and CRITICA/GLIMMER). The phylogenetic origins of the assembled contigs were predicted using one sequence similarity--based (blast hit distribution) and two sequence composition--based (PhyloPythia, oligonucleotide frequencies) binning methods. We explored the effects of the simulated community structure and method combinations on the fidelity of each processing step by comparison to the corresponding isolate genomes. The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis.

Most cosmic-ray air shower arrays have focused on detectingelectromagnetic shower particles and low energy muons. A few groups (mostnotably MACRO + EASTOP and SPASE + AMANDA) have studied the high energymuon component of showers. However, these experiments had small solidangles, and did not study muons far from the core. The IceTop + IceCubecombination, with its 1 km$^2$ muon detection area can study muons farfrom the shower core. IceCube can measure their energy loss ($dE/dx$),and hence their energy. With the energy, and the known distribution ofproduction heights, the transverse momentum ($p_T$) spectrum of high$p_T$ muons can be determined. The production of the semuons iscalculable in perturbative QCD, so the measured muon spectra can be usedto probe the composition of incident cosmic-rays.

I study the incorporation of renormalization group (RG)improved BFKL kernels in the Balitsky-Kovchegov (BK) equation whichdescribes parton saturation. The RG improvement takes into accountimportant parts of the next-to-leading and higher order logarithmiccorrections to the kernel. The traveling wave front method for analyzingthe BK equation is generalized to deal with RG-resummed kernels,restricting to the interesting case of fixed QCD coupling. The resultsshow that the higher order corrections suppress the rapid increase of thesaturation scale with increasing rapidity. I also perform a "diffusive"differential equation approximation, which illustrates that someimportant qualitative properties of the kernel change when including RGcorrections.

An RFQ-based neutron generator system is described that produces pulsed neutrons for the active screening of sea-land cargo containers for the detection of shielded special nuclear materials (SNM). A microwave-driven deuteron source is coupled to an electrostatic LEBT that injects a 40 mA D+ beam into a 6 MeV, 5.1 meter-long 200 MHz RFQ. The RFQ has a unique beam dynamics design and is capable of operating at duty factors of 5 to 10% accelerating a D+ time-averaged current of up to 1.5 mA at 5% duty factor, including species and transmission loss. The beam is transported through a specially-designed thin-window into a 2.5-atmosphere deuterium gas target. A high-frequency dipole magnet is used to scan the beam over the long dimension of the 5 by 35 cm target window. The source will deliver a neutron flux of 1x10$sup 7$ n/(cm$sup 2$s) to the center of an empty cargo container. Details of the ion source, LEBT, RFQ beam dynamics and gas target design are presented.

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The alignment system for the CMS Muon Endcap detector employs several hundred sensors such as optical 1-D CCD sensors illuminated by lasers and analog distance- and tilt-sensors to monitor the positions of one sixth of 468 large Cathode Strip Chambers. The chambers mounted on the endcap yoke disks undergo substantial deformation on the order of centimeters when the 4T field is switched on and off. The Muon Endcap alignment system is required to monitor chamber positions with 75-200 {micro}m accuracy in the R? plane, {approx}400 {micro}m in the radial direction, and {approx}1 mm in the z-direction along the beam axis. The complete alignment hardware for one of the two endcaps has been installed at CERN. A major system test was performed when the 4T solenoid magnet was ramped up to full field for the first time in August 2006. We present the overall system design and first results on disk deformations, which indicate that the measurements agree with expectations.

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NbTi accelerator dipoles are limited to magnetic fields (H)of about 10 T, due to an intrinsic upper critical field(Hc2) limitationof 14 T. To surpass this restriction, prototype Nb3Sn magnets are beingdeveloped which have reached 16 T. We show that Nb3Sn dipole technologyis practically limited to 17 to 18 T due to insufficient high fieldpinning, and intrinsically to 20 to 22 T due to Hc2 limitations.Therefore, to obtain magnetic fields approaching 20 T and higher, amaterial is required with a higher Hc2 and sufficient high field pinningcapacity. A realistic candidate for this purpose is Bi-2212, which isavailable in roundwires and sufficient lengths for the fabrication ofcoils based on Rutherford-type cables. We initiated a program to developthe required technology to construct accelerator magnets from'windand-react' (W&R) Bi-2212 coils. We outline the complicationsthat arise through the use of Bi-2212, describe the development paths toaddress these issues, and conclude with the design of W&R Bi-2212sub-scale magnets.

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

In the event of a short-term, large-scale toxic chemical release to the atmosphere, shelter-in-place (SIP) may be used as an emergency response to protect public health. We modeled hypothetical releases using realistic, empirical parameters to explore how key factors influence SIP effectiveness for single-family dwellings in a residential district. Four classes of factors were evaluated in this case-study: (a) time scales associated with release duration, SIP implementation delay, and SIP termination; (b) building air-exchange rates, including air infiltration and ventilation; (c) the degree of sorption of toxic chemicals to indoor surfaces; and (d) the shape of the dose-response relationship for acute adverse health effects. Houses with lower air leakage are more effective shelters, and thus variability in the air leakage of dwellings is associated with varying degrees of SIP protection in a community. Sorption on indoor surfaces improves SIP effectiveness by lowering the peak indoor concentrations and reducing the amount of contamination in the indoor air. Nonlinear dose-response relationships imply substantial reduction in adverse health effects from lowering the peak exposure concentration. However, if the scenario is unfavorable for sheltering (e.g. sheltering in leaky houses for protection against a nonsorbing chemical with a linear dose-response), the community must implement SIP …

Biclustering has many applications in text mining, web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L{sub 1} constraint to L{sub p} constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithm to solve the generalized Motzkin-Straus optimization problem. The algorithm is provably convergent and has a computational complexity of O(|E|) where |E| is the number of edges. It relies on a matrix vector multiplication and runs efficiently on most current computer architectures. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.

Using a large sample of D{sup +} {yields} K{sup -}K{sup +}{pi}{sup +} decays collected by the FOCUS photoproduction experiment at Fermilab, we present the first non-parametric analysis of the K{sup -} {pi}{sup +} amplitudes in D{sup +} {yields} K{sup -}K{sup +}{pi}{sup +} decay. The technique is similar to the technique used for our non-parametric measurements of the D{sup +} {yields} {bar K}*{sup 0} e{sup +}{nu} form factors. Although these results are in rough agreement with those of E687, we observe a wider S-wave contribution for the {bar K}*{sub 0}{sup 0}(1430) contribution than the standard, PDG [1] Breit-Wigner parameterization. We have some weaker evidence for the existence of a new, D-wave component at low values of the K{sup -} {pi}{sup +} mass.

The D0 Collaboration presents first evidence for the production of single top quarks at the Fermilab Tevatron p{bar p} collider. Using a 0.9 fb{sup -1} dataset, we apply a multivariate analysis to separate signal from background and measure {sigma}(p{bar p} {yields} tb + X, tqb + X) = 4.9 {+-} 1.4 pb. The probability to measure a cross section at this value or higher in the absence of signal is 0.035%, corresponding to a 3.4 standard deviation significance. We use the cross section measurement to directly determine the CKM matrix element that describes the W tb coupling and find 0.68 < |V{sub tb}| {le} 1 at 95% C.L.

TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system to its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.

We describe methods to identify {tau} leptons produced in high energy p{bar p} collisions ({radical}s = 1.96 GeV) at the Tevatron, using the D0 detector. Different procedures used for discrimination against background particles misidentified as taus are also discussed. Finally, we present some physics results obtained by applying these methods to illustrate their performance.

Long baseline neutrino oscillation physics in the U.S. is centered at the Fermi National Accelerator Laboratory (FNAL), in particular at the Neutrinos at the Main Injector (NuMI) beamline commissioned in 2004-2005. Already, the MINOS experiment has published its first results confirming the disappearance of {nu}{sub {mu}}'s across a 735 km baseline. The forthcoming NOvA experiment will search for the transition {nu}{sub {mu}} {yields} {nu}{sub e} and use this transition to understand the mass heirarchy of neutrinos. These, as well as other conceptual ideas for future experiments using the NuMI beam, will be discussed. The turn-on of the NuMI facility has been positive, with over 310 kW beam power achieved. Plans for increasing the beam intensity once the Main Injector accelerator is fully-dedicated to the neutrino program will be presented.

ILC project will be the next large high energy physics tool that will use polarized electrons (and positrons). For this machine spin physics will play an important role. The polarized electron source design is based on electron injectors built for the Stanford Linear Collider (polarized) and Tesla Test Facility (un-polarized). The ILC polarized electron source will provide a 5GeV spin polarized electron beam for injection into the ILC damping ring. Although most ILC machine parameters have been achieved by the SLC or TTF source, features of both must be integrated into one design. The bunch train structure presents unique challenges to the source laser drive system. A suitable laser system has not yet been demonstrated and is part of the ongoing R&D program for ILC at SLAC. Furthermore, ILC injector R&D incorporates photocathode development, increasing available polarization, and improving operational properties in gun vacuum systems. Another important area of research and development is advancing the design of DC and RF electron gun technology for polarized sources. This presentation presents the current status of the design and outlines aspects of the relevant R&D program carried out within the ILC community.

The authors present a new method for studying high-p{sub T} dilepton events (e{sup {+-}}e{sup {-+}}, {mu}{sup {+-}}{mu}{sup {-+}}, e{sup {+-}}{mu}{sup {-+}}) and simultaneously extracting the production cross sections of p{bar p} {yields} t{bar t}, p{bar p} {yields} W{sup +}W{sup -}, and p{bar p} {yields} Z{sup 0} {yields} {tau}{sup +}{tau}{sup -} at a center-of-mass energy of {radical}s = 1.96 TeV. They perform a likelihood fit to the dilepton data in a parameter space defined by the missing transverse energy and the number of jets in the event. The results, which use 360 pb{sup -1} of data recorded with the CDF II detector at the Fermilab Tevatron Collider, are {sigma}(t{bar t}) = 8.5{sub -2.2}{sup +2.7} pb, {sigma}(W{sup +}W{sup -}) = 16.3{sub -4.4}{sup +5.2} pb, and {sigma}(Z{sup 0} {yields} {tau}{sup +}{tau}{sup -}) = 291{sub -46}{sup +50} pb.

We show that under a new U(1) gauge symmetry, which is non-anomalous in the presence of one ''right-handed neutrino'' per generation and consistent with the standard model Yukawa couplings, the most general fermion charges are determined in terms of four rational parameters. This generalization of the B-L symmetry with generation-dependent lepton charges leads to neutrino masses induced by operators of high dimensionality. Neutrino masses are thus naturally small without invoking physics at energies above the TeV scale, whether neutrinos are Majorana or Dirac fermions. This ''Leptocratic'' Model predicts the existence of light quasi-sterile neutrinos with consequences for cosmology, and implies that collider experiments may reveal the origin of neutrino masses.

Presented are the latest results of jet fragmentation studies at the Tevatron using the CDF Run II detector. Studies include the distribution of transverse momenta (Kt) of particles jets, two-particle momentum correlations, and indirectly global event shapes in p{bar p} collisions. Results are discussed within the context of recent Next-to-Leading Log calculations as well as earlier experimental results from the Tevatron and e{sup +}e{sup -} colliders.

Neutrino Factories offer an exciting option for the long-term neutrino physics program. This new type of neutrino facility will provide beams with unique properties. Low systematic uncertainties at a Neutrino Factory, together with a unique and precisely known neutrino flavor content, will enable neutrino oscillation measurements to be made with unprecedented sensitivity and precision. Over recent years, the resulting neutrino factory physics potential has been discussed extensively in the literature. In addition, over the last six years the R&D necessary to realize a Neutrino Factory has been progressing, and has developed into a significant international activity. It is expected that, within about five more years, the initial phase of this R&D program will be complete and, if the community chooses to build this new type of neutrino source within the following decade, neutrino factory technology will be ready for the final R&D phase prior to construction. In this paper (1) an overview is given of the technical ingredients needed for a Neutrino Factory, (2) beam properties are described, (3) the resulting neutrino oscillation physics potential is summarized, (4) a more detailed description is given for one representative Neutrino Factory design, and (5) the ongoing R&D program is summarized, and future …

Today’s society relies greatly upon an array of complex national and international infrastructure networks such as transportation, utilities, telecommunication, and even financial networks. While modeling and simulation tools have provided insight into the behavior of individual infrastructure networks, a far less understood area is that of the interrelationships among multiple infrastructure networks including the potential cascading effects that may result due to these interdependencies. This paper first describes infrastructure interdependencies as well as presenting a formalization of interdependency types. Next the paper describes a modeling and simulation framework called CIMS© and the work that is being conducted at the Idaho National Laboratory (INL) to model and simulate infrastructure interdependencies and the complex behaviors that can result.

In this paper recent results from the CDF and D0 experiments on heavy flavor spectroscopy are reported. Both experiments are using up to 1.1 fb{sup -1} of data delivered by the Tevatron proton-antiproton collider at the Fermi National Accelerator Laboratory, Batavia, IL, USA. The CDF and D0 detectors are described in references [1,2].