A 2-stage detector was designed to find rho-independent transcription terminators in the Escherichia coli genome. The detector includes a Stochastic Context Free Grammar (SCFG) component and a Support Vector Machine (SVM) component. To find terminators, the SCFG searches the intergenic regions of nucleotide sequence for local matches to a terminator grammar that was designed and trained utilizing examples of known terminators. The grammar selects sequences that are the best candidates for terminators and assigns them a prefix, stem-loop, suffix structure using the Cocke-Younger-Kasaami (CYK) algorithm, modified to incorporate energy affects of base pairing. The parameters from this inferred structure are passed to the SVM classifier, which distinguishes terminators from non-terminators that score high according to the terminator grammar. The SVM was trained with negative examples drawn from intergenic sequences that include both featureless and RNA gene regions (which were assigned prefix, stem-loop, suffix structure by the SCFG), so that it successfully distinguishes terminators from either of these. The classifier was found to be 96.4% successful during testing.

We study the two-point correlation function of a uniformly selected sample of 4,428 optically selected luminous quasars with redshift 2.9 {le} z {le} 5.4 selected over 4041 deg{sup 2} from the Fifth Data Release of the Sloan Digital Sky Survey. We fit a power-law to the projected correlation function w{sub p}(r{sub p}) to marginalize over redshift space distortions and redshift errors. For a real-space correlation function of the form {zeta}(r) = (r/r{sub 0}){sup -{gamma}}, the fitted parameters in comoving coordinates are r{sub 0} = 15.2 {+-} 2.7 h{sup -1} Mpc and {gamma} = 2.0 {+-} 0.3, over a scale range 4 {le} r{sub p} {le} 150 h{sup -1} Mpc. Thus high-redshift quasars are appreciably more strongly clustered than their z {approx} 1.5 counterparts, which have a comoving clustering length r{sub 0} {approx} 6.5 h{sup -1} Mpc. Dividing our sample into two redshift bins: 2.9 {le} z {le} 3.5 and z {ge} 3.5, and assuming a power-law index {gamma} = 2.0, we find a correlation length of r{sub 0} = 16.9 {+-} 1.7 h{sup -1} Mpc for the former, and r{sub 0} = 24.3 {+-} 2.4 h{sup -1} Mpc for the latter. Strong clustering at high redshift indicates that quasars are …

The Fourier transform of the deeply virtual Compton scattering amplitude (DVCS) with respect to the skewness parameter {zeta} = Q{sup 2}/2p {center_dot} q can be used to provide an image of the target hadron in the boost-invariant variable {sigma}, the coordinate conjugate to light-front time {tau} = t + z/c. As an illustration, we construct a consistent covariant model of the DVCS amplitude and its associated generalized parton distributions using the quantum fluctuations of a fermion state at one loop in QED, thus providing a representation of the light-front wave functions of a lepton in {sigma} space. A consistent model for hadronic amplitudes can then be obtained by differentiating the light-front wave functions with respect to the bound-state mass. The resulting DVCS helicity amplitudes are evaluated as a function of {sigma} and the impact parameter {rvec b}{sub {perpendicular}}, thus providing a light-front image of the target hadron in a frame-independent three-dimensional light-front coordinate space. Models for the LFWFs of hadrons in (3 + 1) dimensions displaying confinement at large distances and conformal symmetry at short distances have been obtained using the AdS/CFT method. We also compute the LFWFs in this model in invariant three dimensional coordinate space. We find that …

ILC designers are exploring new packaging standards for Accelerator Controls and Instrumentation, particularly high-speed serial interconnect systems for intelligent instruments versus the existing parallel backplanes of VME, VXI and CAMAC. The High Availability Advanced Telecom Computing Architecture (ATCA) system is a new industrial open standard designed to withstand single-point hardware or software failures. The standard crate, controller, applications module and sub-modules are being investigated. All modules and sub-modules are hot-swappable. A single crate is designed for a data throughput in communications applications of 2 Tb/s and an Availability of 0.99999, which translates into a downtime of five minutes per year. The ILC is planning to develop HA architectures for controls, beam instrumentation and detector systems.

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We present branching fraction measurements of charged and neutral B decays to D{pi}{sup -}, D*{pi}{sup -} and D**{pi}{sup -} with a missing mass method, based on a sample of 231 million {Upsilon}(4S) {yields} B{bar B} pairs collected by the BABAR detector at the PEP-II e{sup +}e{sup -} collider. One of the B mesons is fully reconstructed and the other one decays to a reconstructed charged {pi} and a companion charmed meson identified by its recoil mass, inferred by kinematics. Here D** refers to the sum of all the non-strange charm meson states with masses in the range 2.2-2.8 GeV/c{sup 2}.

Pulsed power machines capable of producing tremendous energy face various diagnostic and characterizing challenges. Such devices, which may produce 10 - 100MAs, have traditionally relied on Faraday rotation and Rogowski coil technology for time-varying current measurements. Faraday rotation requires a host of costly optical components, including fibers, polarizers, retarders, lasers, and detectors, as well as setup, alignment, and time-consuming post-processing to unwrap the time-dependent current signal. Rogowski coils face potential problems such as physical distortion to the sensor itself due to the tremendous strain caused by magnetically induced pressures, which is proportional to the magnetic field squared (B2). Electrical breakdown in the intense field region is also a major concern. Other related challenges include, but are not limited to, bandwidth and inductance limitations and susceptibility issues related to electrical magnetic interference (EMI).

Uniaxial compression experiments on copper single crystals, oriented to maximize the shear for one slip system, show some unexpected results. In addition to the expected activity on the primary slip system, the results show appreciable activity perpendicular to the primary system. The magnitude of the activity orthogonal to the primary varies from being equal to the primary for the as-fabricated samples to 1/5 of the primary in the samples annealed after fabrication.

The authors report measurements of the decays B{sup +} {yields} {phi}{phi}K{sup +} and B{sup 0} {yields} {phi}{phi}K{sup 0} using a sample of 231 million B{bar B} pairs collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The branching fractions are measured to be {Beta}(B{sup +} {yields} {phi}{phi}K{sup +}) = (7.5 {+-} 1.0(stat) {+-} 0.7(syst)) x 10{sup -6} and {Beta}(B{sup 0} {yields} {phi}{phi}K{sup 0}) = (4.1{sub -1.4}{sup +1.7}(stat) {+-} 0.4(syst)) x 10{sup -6} for a {phi}{phi} invariant mass below 2.85 GeV/c{sup 2}.

We study the processes e{sup +}e{sup -} {yields} (J/{psi}{gamma}{gamma}){gamma} and e{sup +}e{sup -} {yields} (J/{psi}{pi}{sup -}{pi}{sup +}){gamma} where the hard photon radiated from an initial e{sup +}e{sup -} collision with center-of-mass (CM) energy near 10.58 GeV is detected. In the final state J/{psi}{gamma}{gamma} we consider J/{psi}{pi}{sup 0}, J/{psi}{eta}, {chi}{sub c1}{gamma}, and {chi}c{sub 2}{gamma} candidates. The invariant mass of the hadronic final state defines the effective e{sup +}e{sup -} CM energy in each event, so these data can be compared with direct e{sup +}e{sup -} measurements. We report 90% CL upper limits for the integrated cross section times branching fractions of the J/{psi}{gamma}{gamma} channels in the Y (4260) mass region.

Spin dynamics in crossing a single depolarization resonance is a well-studied subject. One well-known example is that of Froissart and Stora in 1960. More is needed to complete the understanding, particularly of the transient effects, when crossing a single resonance, but question arises what happens if we cross two resonances or cross a single resonance twice. When a resonance is crossed twice, the particle's spin dynamics encounters two additional phenomena. First, the two crossings will interfere with each other, leading to an interference effect. Second, there will be a spin echo effect. We discuss these two effects in this report. Two proposals to test these effects experimentally are made at the end.

Carbon coating has proven to be a successful approach toimprove the rate capability of LiFePO4 used in rechargeable Li-ionbatteries. Investigations of the microstructure of carbon coated LiFePO4after charge discharge cycling shows that the carbon surface layerremains intact over 100 cycles. We find micro cracks in the cycledmaterial that extend parallel to low indexed lattice planes. Ourobservations differ from observations made by other authors. However thedifferences between the orientations of crack surfaces in both studiescan be reconciled considering the location of weak bonds in the unit celland specimen geometry as well as elastic stress fields ofdislocation.

Minority carrier lifetime was measured by time-resolved photoluminescence (TRPL) method in sets of p-type and n-type InGaAs double heterostructures (DH) moderately doped with Zn and Te, respectively. Contributions of the radiative and non-radiative recombination terms were separated by fitting experimental data to temperature dependences of the radiative term. The latter was modeled with measured fundamental absorption spectrum and the temperature dependence of the photon recycling effect was taken into account. Different temperature dependences of radiative terms for electron and hole materials were obtained. It was concluded that in 0.6 eV Te-doped InGaAs structures the radiative recombination controls the hole lifetime at liquid nitrogen temperatures, while Auger recombination dominates at room and above room temperatures. In similar 0.6 eV InGaAs with Zn-doped active regions Shockley-Read-Hall (SRH) recombination was found dominant in a wide temperature range from liquid nitrogen to above-room temperatures. Rapid decrease of electron lifetime with decrease of excess carrier concentration was observed and attributed to recombination through partially-ionized deep donor centers. The obtained data allows for more adequate modeling of the performance and design optimization of narrow-gap photonic devices based on InGaAs Indium-rich compounds.

Magnetic soft X-ray microscopy images magnetism in nanoscale systems with a spatial resolution down to 15nm provided by state-of-the-art Fresnel zone plate optics. X-ray magnetic circular dichroism (X-MCD) is used as element-specific magnetic contrast mechanism similar to photoemission electron microscopy (PEEM), however, with volume sensitivity and the ability to record the images in varying applied magnetic fields which allows to study magnetization reversal processes at fundamental length scales. Utilizing a stroboscopic pump-probe scheme one can investigate fast spin dynamics with a time resolution down to 70 ps which gives access to precessional and relaxation phenomena as well as spin torque driven domain wall dynamics in nanoscale systems. Current developments in zone plate optics aim for a spatial resolution towards 10nm and at next generation X-ray sources a time resolution in the fsec regime can be envisioned.

Suspended carbon nanotube devices are a promising platform for future bio-electronic applications. Suspended carbon nanotube transistors have been previously fabricated in air; however all previous attempts to bring them into liquid failed. We analyze forces acting on the suspended nanotube devices during immersion into liquids and during device operation and show that surface tension forces acting on the suspended nanotubes during transfer into the liquid phase are responsible for the nanotube damage. We have developed a new strategy that circumvents these limitations by coating suspended nanotubes with a rigid inorganic shell in the gas phase. The coating reinforces the nanotubes and allows them to survive transfer through the interface. Subsequent removal of the coating in the solution phase restores pristine suspended nanotubes. We demonstrate that devices fabricated using this technique preserve their original electrical characteristics.

We study J/{psi} production at RHIC and LHC energies with both initial production and regeneration. We solve the coupled set of transport equation for the J/{psi} distribution in phase space and the hydrodynamic equation for evolution of quark-gluon plasma. At RHIC, continuous regeneration is crucial for the J/{psi} momentum distribution while the elliptic flow is still dominated by initial production. At LHC energy, almost all the initially created J/{psi}s are dissociated in the medium and regeneration dominates the J/{psi} properties.

We present a second-order accurate algorithm for solving thefree-space Poisson's equation on a locally-refined nested grid hierarchyin three dimensions. Our approach is based on linear superposition oflocal convolutions of localized charge distributions, with the nonlocalcoupling represented on coarser grids. There presentation of the nonlocalcoupling on the local solutions is based on Anderson's Method of LocalCorrections and does not require iteration between different resolutions.A distributed-memory parallel implementation of this method is observedto have a computational cost per grid point less than three times that ofa standard FFT-based method on a uniform grid of the same resolution, andscales well up to 1024 processors.

In order to utilize hard x-ray free electron lasers (XFEL's) when they are extended to attosecond pulse lengths, it is necessary to choose optical elements with minimal response time. Specular grazing incidence optics made of low-Z materials are popular candidates for reflectors since they are likely to withstand x-ray damage and provide sufficiently large reflectivities. Using linear-optics reflection theory, we calculated the transient reflectivity of a delta-function electric pulse from a homogeneous semi-infinite medium as a function of angle of incidence for s- and p-polarized light. We specifically considered the pulse response of Be, diamond, silicon carbide, and silicon, all of which are of relevance to the XFEL's that are currently being built. We found that the media emit energy in a damped oscillatory way, and that the impulse-response times are shorter than 0.3 fs for normal incidence. For grazing incidence, the impulse-response time is substantially shorter, making grazing-incidence mirrors a good choice for deep-sub-femtosecond reflective optics.

The Rayleigh-Taylor (RT) instability is an important factor in bounding the performance envelope of ignition targets. This paper describes an experiment for ablative RT instability that for the first time achieves growth factors close to those expected to occur in ignition targets at the National Ignition Facility (NIF). The large growth allows small seed perturbations to be detected and can be used to place an upper bound on perturbation growth at the ablation front resulting from microstructure in the preferred Be ablator. The experiments were performed on the Omega laser using a halfraum 1.2 mm long by 2 mm diameter with a 75% laser entrance hole. The halfraum was filled with {approx} 1 atm of neopentane to delay gold plasma from closing the diagnostic line of sight down the axis of the halfraum. The ablator was mounted at the base of the halfraum, and was accelerated by a two stepped X-ray pulse consisting of an early time section {approx} 100 eV to emulate the NIF foot followed by an approximately constant {approx} 150 eV drive sustained over an additional 5-7ns. It is this long pulse duration and late time observation that distinguishes the present work from previous experiments, and is …

During the past several years, an International Scoping Study (ISS) of a Neutrino Factory was carried out, with the aim of developing an internationally accepted baseline facility design. Progress toward that goal will be described. Many of the key technical aspects of a Neutrino Factory facility design are presently being investigated experimentally, and the status of these investigations will be mentioned. Plans for the recently launched International Design Study (IDS), which serves as a follow-on to the ISS, will be briefly described.

We are developing a frequency-multiplexed readout for arrays of high-resolution Gamma detectors based on superconducting transition edge sensors (TESs). Each sensor is part of an LCR resonant circuit and is biased at an identifying carrier frequency. Several carrier signals are added and amplified with a single SQUID preamplifier at 4 K. Gamma absorption modulates the amplitude of the carrier, and demodulation at room temperature retrieves the initial temperature evolution of the sensor. This multiplexing system has originally been developed to read out large arrays of bolometers for cosmic microwave background studies. To accommodate the faster Gamma-ray signals, its demodulator bandwidth is being extended to 20 kHz to allow reading out up to eight TESs with a detector bandwidth of 10 kHz. Here we characterize the system noise performance and show how this multiplexing scheme can be adapted to read out arrays of superconducting Gamma-ray detectors.

The threats of bio-terrorism and newly emerging infectious diseases pose serious challenges to the national security infrastructure. Rapid detection and diagnosis of infectious disease in human populations, as well as characterizing pathogen biology, are critical for reducing the morbidity and mortality associated with such threats. One of the key challenges in managing an infectious disease outbreak, whether through natural causes or acts of overt terrorism, is detection early enough to initiate effective countermeasures. Much recent attention has been directed towards the utility of biomarkers or molecular signatures that result from the interaction of the pathogen with the host for improving our ability to diagnose and mitigate the impact of a developing infection during the time window when effective countermeasures can be instituted. Host responses may provide early signals in blood even from localized infections. Multiple innate and adaptive immune molecules, in combination with other biochemical markers, may provide disease-specific information and new targets for countermeasures. The presence of pathogen specific markers and an understanding of the molecular capabilities and adaptations of the pathogen when it interacts with its host may likewise assist in early detection and provide opportunities for targeting countermeasures. An important question that needs to be addressed is …

We present a set of 11 type Ia supernova (SN Ia) lightcurves with dense, pre-maximum sampling. These supernovae (SNe), in galaxies behind the Large Magellanic Cloud (LMC), were discovered by the SuperMACHO survey. The SNe span a redshift range of z = 0.11-0.35. Our lightcurves contain some of the earliest pre-maximum observations of SNe Ia to date. We also give a functional model that describes the SN Ia lightcurve shape (in our V R-band). Our function uses the ''expanding fireball'' model of Goldhaber et al. (1998) to describe the rising lightcurve immediately after explosion but constrains it to smoothly join the remainder of the lightcurve. We fit this model to a composite observed V R-band lightcurve of three SNe between redshifts of 0.135 to 0.165. These SNe have not been K-corrected or adjusted to account for reddening. In this redshift range, the observed V R-band most closely matches the rest frame V-band. Using the best fit to our functional description of the lightcurve, we find the time between explosion and observed V R-band maximum to be 19.2 {+-} 1.3-1.6 {+-} 0.07(red.) rest-frame days for a SN Ia with a V R-band {Delta}m{sub -10} of 0.52. For the redshifts sampled, the …

We report on the first measurements to the angle {gamma} of the Unitarity Triangle in B meson decays collected by the BABAR detector at the SLAC PEP-II asymmetric-energy B factory in the years 1999-2004.