Copper ions for the 2005 run [1] of the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory (BNL) are accelerated in the Tandem, Booster and AGS prior to injection into RHIC. The setup and performance of these accelerators with copper are reviewed in this paper.

None

We summarize four of our group's high-risk/high-payoff research projects funded by the Intelligence Technology Innovation Center (ITIC) in conjunction with our DHS-funded pathogen informatics activities. These are (1) quantitative assessment of genomic sequencing needs to predict high quality DNA and protein signatures for detection, and comparison of draft versus finished sequences for diagnostic signature prediction; (2) development of forensic software to identify SNP and PCR-RFLP variations from a large number of viral pathogen sequences and optimization of the selection of markers for maximum discrimination of those sequences; (3) prediction of signatures for the detection of virulence, antibiotic resistance, and toxin genes and genetic engineering markers in bacteria; (4) bioinformatic characterization of virulence factors to rapidly screen genomic data for potential genes with similar functions and to elucidate potential health threats in novel organisms. The results of (1) are being used by policy makers to set national sequencing priorities. Analyses from (2) are being used in collaborations with the CDC to genotype and characterize many variola strains, and reports from these collaborations have been made to the President. We also determined SNPs for serotype and strain discrimination of 126 foot and mouth disease virus (FMDV) genomes. For (3), currently >1000 probes …

We read with interest the paper by Michiels et al on the prediction of cancer with microarrays and the commentary by Ioannidis listing the potential as well as the limitations of this approach (February 5, p 488 and 454). Cancer is a disease characterized by complex, heterogeneous mechanisms and studies to define factors that can direct new drug discovery and use should be encouraged. However, this is easier said than done. Casti teaches that a better understanding does not necessarily extrapolate to better prediction, and that useful prediction is possible without complete understanding (1). To attempt both, explanation and prediction, in a single nonmathematical construct, is a tall order (Figure 1).

The WW{gamma} triple gauge boson coupling parameters are studied using p{bar p} {yields} {ell}{nu}{gamma} + X({ell} = e, {mu}) events at {radical}s = 1.96 TeV. The data were collected with the D0 detector from an integrated luminosity of 162 pb{sup -1} delivered by the Fermilab Tevatron Collider. The cross section times branching fraction for p{bar p} {yields} W({gamma}) + X {yields} {ell}{nu}{gamma} + X with E{sub T}{sup {gamma}} > 8 GeV and {Delta}R{sub {ell}{gamma}} > 0.7 is 14.8 {+-} 1.6(stat) {+-} 1.0(syst) {+-} 1.0(lum) pb. The one-dimensional 95% confidence level limits on anomalous couplings are -0.88 < {Delta}{kappa}{sub {gamma}} < 0.96 and -0.20 < {lambda}{sub {gamma}} < 0.20.

The RHIC spin program requires 2 x 10{sup 11} proton/bunch with 70% polarization. As the injector to RHIC, AGS is the bottleneck for preserving polarization: there is no space for a full snake to overcome numerous depolarizing resonances. An ac dipole and a partial snake have been used to preserve beam polarization in the past few years. Two helical snakes have been built and installed in the AGS. With careful setup of optics at injection and along the ramp, this combination can eliminate all depolarizing resonances encountered during acceleration. This paper presents the setup and preliminary results.

High-energy ion colliders (hadron colliders operating with ions other than protons) are premier research tools for nuclear physics. The collision energy and high luminosity are important design and operations considerations. The experiments also expect flexibility with frequent changes in the collision energy, detector fields, and ion species, including asymmetric collisions. For the creation, acceleration, and storage of bright intense ion beams limits are set by space charge, charge exchange, and intrabeam scattering effects. The latter leads to luminosity lifetimes of only a few hours for intense heavy ions beams. Currently, the Relativistic Heavy Ion Collider (RHIC) at BNL is the only operating high-energy ion collider. Later this decade the Large Hadron Collider (LHC), under construction at CERN, will also run with heavy ions.

The thermodynamics and kinetics of the fcc (delta) to monoclinic (alpha-prime) phase transformation and its reversion in a plutonium-gallium alloy have been studied using differential scanning calorimetry, resistometry, and dilatometry. Under ambient conditions, the delta phase is metastable in a Pu-2.0 at% Ga alloy. Thermal cycling to below the ambient temperature results in a partial transformation to the alpha-prime phase; this transformation is composition-invariant and exhibits martensitic behavior. Because this transformation results in an unusually invariant large 25% volume contraction that cannot be fully accommodated by purely elastic adjustments, the transformation mode is expected to involve burst formation of individual alpha-prime particles. However, upon cooling, these individual bursts were not resolved by the above techniques, although signals corresponding to the overall accumulation of many alpha-prime particles were observed. On the other hand, upon heating, signals from differential scanning calorimetry, resistometry, and dilatometry showed a series of discrete changes occurring in periodic increments beginning at approximately 32 C. These features correspond to the cooperative reversion of many alpha-prime particles to the delta phase; they appear to be the result of an interplay between the autocatalytically driven reversion of a cascade of individual martensite units, and self-quenching caused by small changes of …

A variety of H{sup -} ion sources are in use at accelerator laboratories around the world. A list of these ion sources includes surface plasma sources with magnetron, Penning and surface converter geometries as well as magnetic-multipole volume sources with and without cesium. Just as varied is the means of igniting and maintaining magnetically confined plasmas. Hot and cold cathodes, radio frequency, and microwave power are all in use, as well as electron tandem source ignition. The extraction systems of accelerator H{sup -} ion sources are highly specialized utilizing magnetic and electric fields in their low energy beam transport systems to produce direct current, as well as pulsed and/or chopped beams with a variety of time structures. Within this paper, specific ion sources utilized at accelerator laboratories shall be reviewed along with the physics of surface and volume H{sup -} production in regard to source emittance. Current research trends including aperture modeling, thermal modeling, surface conditioning, and laser diagnostics will also be discussed.

Initial- and final-state interactions from gluon exchange, normally neglected in the parton model, have a profound effect in QCD hard-scattering reactions, leading to leading-twist single-spin asymmetries, diffractive deep inelastic scattering, diffractive hard hadronic reactions, as well as nuclear shadowing and antishadowing-leading-twist physics not incorporated in the light-front wavefunctions of the target computed in isolation. The physics of such processes thus require the understanding of QCD at the amplitude level; in particular, the physics of spin requires an understanding of the phase structure of final-state and initial-state interactions, as well as the structure of the basic wavefunctions of hadrons themselves. I also discuss transversity in exclusive channels, including how one can use single-spin asymmetries to determine the relative phases of the timelike baryon form factors, as well as the anomalous physics of the normal-normal spin-spin correlation observed in large-angle proton-proton elastic scattering. As an illustration of the utility of light-front wavefunctions, the transversity distribution of a single electron is computed, as defined from its two-particle QED quantum fluctuations.

The exit from mitosis is the last critical decision a cell has to make during a division cycle. A complex regulatory system has evolved to evaluate the success of mitotic events and control this decision. Whereas outstanding genetic work in yeast has led to rapid discovery of a large number of interacting genes involved in the control of mitotic exit, it has also become increasingly difficult to comprehend the logic and mechanistic features embedded in the complex molecular network. Our view is that this difficulty stems in part from the attempt to explain mitotic exit control using concepts from traditional top-down engineering design, and that exciting new results from evolutionary engineering design applied to networks and electronic circuits may lend better insights. We focus on four particularly intriguing features of the mitotic exit control system: the two-stepped release of Cdc14; the self-activating nature of Tem1 GTPase; the spatial sensor associated with the spindle pole body; and the extensive redundancy in the mitotic exit network. We attempt to examine these design features from the perspective of evolutionary design and complex system engineering.

A first set of laser-plasma interaction, hohlraum energetics and hydrodynamic experiments have been performed using the first 4 beams of the National Ignition Facility (NIF), in support of indirect drive Inertial Confinement Fusion (ICF) and High Energy Density Physics (HEDP). In parallel, a robust set of optical and x-ray spectrometers, interferometer, calorimeters and imagers have been activated. The experiments have been undertaken with laser powers and energies of up to 8 TW and 17 kJ in flattop and shaped 1-9 ns pulses focused with various beam smoothing options.

A novel sample preparation technique is reported to fabricate electron transparent samples from devices utilizing a FIB process with a successive wet etching step. The high quality of the obtained samples allows for band gap--and chemical composition measurements of In{sub x}Ga{sub 1-x}N quantum wells where electron beam induced damage can be controlled and shown to be negligible. The results reveal indium enrichment in nanoclusters and defects that cause fluctuations of the band gap energy and can be measured by low loss Electron Energy Spectroscopy with nm resolution. Comparing our time, energy, and spatially resolved measurements of band gap energies, chemical composition, and their related fluctuations with literature data, we find quantitative agreement if the band gap energy of InN is 1.5-2 eV.

Using data collected by the FOCUS experiment at Fermilab, the authors present a new measurement of the charm semileptonic branching ratio BR(D{sup +} {yields} {rho}{sup 0}{mu}{sup +}{nu})/BR(D{sup +}{yields}{bar K}*{sup 0} {mu}{sup +}{nu}). From a sample of 320 {+-} 44 and 11,372 {+-} 161 D{sup +} {yields} {rho}{sup 0}{mu}{sup +}{nu} and D{sup +} {yields} K{sup -}{pi}{sup +}{mu}{sup +}{nu} events respectively, they find BR(D{sup +} {yields} {rho}{sup 0}{mu}{sup +}{nu})/BR(D{sup +}{yields}{bar K}*{sup 0} {mu}{sup +}{nu}) = 0.041 {+-} 0.006(stat) {+-} 0.004(syst).

The authors apply a genetic programming technique to search for the doubly Cabibbo suppressed decays {Lambda}{sub c}{sup +} {yields} pK{sup +} {pi}{sup -} and D{sub s}{sup +} {yields} K{sup +}K{sup +}{pi}{sup -}. They normalize these decays to their Cabibbo favored partners and find BR({Lambda}{sub c}{sup +} {yields} pK{sup +}{pi}{sup -})/BR({Lambda}{sub c}{sup +} {yields} pK{sup -}{pi}{sup +}) = (0.05 {+-} 0.26 {+-} 0.02)% and BR(D{sub s}{sup +} {yields} K{sup +}K{sup +}{pi}{sup -})/BR(D{sub s}{sup +} {yields} K{sup -}K{sup +}{pi}{sup +}) = (0.52 {+-} 0.17 {+-} 0.11)% where the first errors are statistical and the second are systematic. Expressed as 90% confidence levels (CL), they find < 0.46% and < 0.78% respectively. This is the first successful use of genetic programming in a high energy physics data analysis.

Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set of ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket …

The Relativistic Heavy Ion Collider provides not only collisions of ions but also collisions of polarized protons. In a circular accelerator, the polarization of polarized proton beam can be partially or fully lost when a spin depolarizing resonance is encountered. To preserve the beam polarization during acceleration, two full Siberian snakes were employed in RHIC. In 2002, polarized proton beams were first accelerated to 100 GeV and collided in RHIC. Beams were brought into collisions with longitudinal polarization at the experiments STAR and PHENIX by using spin rotators. Optimizing polarization transmission efficiency and improving luminosity performance are significant challenges. Currently, the luminosity lifetime in RHIC is limited by the beam-beam effect. The current state of RHIC polarized proton program, including its dedicated physics run in 2005 and efforts to optimize luminosity production in beam-beam limited conditions are reported.

The AdS/CFT correspondence has led to important insights into the properties of quantum chromodynamics even though QCD is a broken conformal theory. We have recently shown how a holographic model based on a truncated AdS space can be used to obtain the hadronic spectrum of light q{bar q}, qqq and gg bound states. Specific hadrons are identified by the correspondence of string modes with the dimension of the interpolating operator of the hadron's valence Fock state, including orbital angular momentum excitations. The predicted mass spectrum is linear M {proportional_to} L at high orbital angular momentum, in contrast to the quadratic dependence M{sup 2} {proportional_to} L found in the description of spinning strings. Since only one parameter, the QCD scale LQCD, is introduced, the agreement with the pattern of physical states is remarkable. In particular, the ratio of D to nucleon trajectories is determined by the ratio of zeros of Bessel functions. The light-front quantization of gauge theories in light-cone gauge provides a frame-independent wavefunction representation of relativistic bound states, simple forms for current matrix elements, explicit unitarity, and a trivial vacuum. The light-front Fock-state wavefunctions encode the bound state properties of hadrons in terms of their quark and gluon degrees …

We construct and analyze a u-band selected galaxy sample from the SDSS Southern Survey, which covers 275 deg{sup 2}. The sample includes 43223 galaxies with spectroscopic redshifts in the range 0.005 < z < 0.3 and with 14.5 < u < 20.5. The S/N in the u-band Petrosian aperture is improved by coadding multiple epochs of imaging data and by including sky-subtraction corrections. Luminosity functions for the near-UV {sup 0.1}u band ({lambda} {approx} 322 {+-} 26 nm) are determined in redshift slices of width 0.02, which show a highly significant evolution in M* of -0.8 {+-} 0.1 mag between z = 0 and 0.3; with M* - 5 log h{sub 70} = -18.84 {+-} 0.05 (AB mag), log {phi}* = -2.06 {+-} 0.03 (h{sub 70}{sup 3} Mpc{sup -3}) and log {rho}{sub L} = 19.11 {+-} 0.02 (h{sub 70} W Hz{sup -1}Mpc{sup -3}) at z = 0.1. The faint-end slope determined for z < 0.06 is given by {alpha} = -1.05 {+-} 0.08. This is in agreement with recent determinations from GALEX at shorter wavelengths. Comparing our z < 0.3 luminosity density measurements with 0.2 < z < 1.2 from COMBO-17, we find that the 280-nm density evolves as {rho}{sub L} …

None

We present a K{pi} mass spectrum analysis of the four-body semileptonic charm decay D{sup +} {yields} K{sup -}{pi}{sup +}{mu}{sup +}{nu} in the range of 0.65 GeV/c{sup 2} < m{sub K{pi}} < 1.5 GeV/c{sup 2}. We observe a non-resonant contribution of 5.30 {+-} 0.74{sub -0.51}{sup +0.99}% with respect to the total D{sup +} {yields} K{sup -} {pi}{sup +}{mu}{sup +}{nu} decay. For the K*(892){sup 0} resonance, we obtain a mass of 895.41 {+-} 0.32{sub -0.36}{sup +0.35} NeV/c{sup 2}, a width of 47.79 {+-} 0.86{sub -1.1}{sup +1.3} MeV/c{sup 2}, and a Blatt-Weisskopf damping factor parameter of 3.96 {+-} 0.54{sub -0.90}{sup +0.72} GeV{sup -1}. We also report 90% CL upper limits of 1.60% and 1.90% for the branching ratios {Lambda}(D{sup +} {yields} {bar K}*(1680){sup 0} {mu}{sup +}{nu})/{Lambda}(D{sup +} {yields} K{sup -} {pi}{sup +}{mu}{sup +}{nu}) and {Lambda}(D{sup +} {yields} {bar K}*{sub 0}(1430){sup 0}) {mu}{sup +}{nu}/{Lambda}(D{sup +} {yields} K{sup -}{pi}{sup +}) {mu}{sup +}{nu}, respectively.

A high statistics measurement of the D{sub s}{sup +} lifetime from the Fermilab fixed-target FOCUS photoproduction experiment is presented. They describe the analysis of the two decay modes, D{sub s}{sup +} {yields} {phi}(1020){pi}{sup +} and D{sub s}{sup +} {yields} {bar K}*(892){sup 0}K{sup +}, used for the measurement. The measured lifetime is 507.4 {+-} 5.5(stat.) {+-} 5.1(syst.) is using 8961 {+-} 105 D{sub s}{sup +} {yields} {phi}(1020){pi}{sup +} and 4680 {+-} 90 D{sub s}{sup +} {yields} {bar K}*(892){sup 0} K{sup +} decays. This is a significant improvement over the present world average.

Using data from the FOCUS experiment (FNAL-E831), they study the decay of {Lambda}{sub c}{sup +} baryons into final states contain a {Lambda} hyperon. The branching fractions of {Lambda}{sub c}{sup +} into {Lambda}{pi}{sup +}, {Lambda}{pi}{sup +}{pi}{sup +}{pi}{sup -} and {Lambda}{bar K}{sup 0}K{sup +} relative to that into pK{sup -} {pi}{sup +} are measured to be 0.217 {+-} 0.013 {+-} 0.020, 0.508 {+-} 0.024 {+-} 0.024 and 0.142 {+-} 0.018 {+-} 0.022, respectively. New measurements are also reported. Further, an analysis of the subresonant structure for the {Lambda}{sub c}{sup +} {yields} {Lambda}{pi}{sup +}{pi}{sup +}{pi}{sup -} decay mode is presented.

Using data from the FOCUS (E831) experiment, they have searched for T violation in charm meson decays using the four-body decay channels D{sup 0} {yields} K{sup -}K{sup +} {pi}{sup -}{pi}{sup +}, D{sup +} {yields} K{sub S}{sup 0}K{sup +}{pi}{sup -}{pi}{sup +}, and D{sub s}{sup +} {yields} K{sub S}{sup 0}K{sup +}{pi}{sup -}{pi}{sup +}. The T violation asymmetry is obtained using triple-product correlations and assuming the validity of the CPT theorem. They find the asymmetry values to be A{sub T{sub viol}}(D{sup 0}) = 0.010 {+-} 0.057(stat.) {+-} 0.037(syst.), A{sub T{sub viol}}(D{sup +}) = 0.023 {+-} 0.062(stat.) {+-} 0.022(syst.), and A{sub T{sub viol}}(D{sub s}{sup +}) = -0.036 {+-} 0.067(stat.) {+-} 0.023(syst.). Each measurement is consistent with no T violation. New measurements of the CP asymmetries for some of these decay modes are also presented.