Discovery of Multi-Phase Cold Accretion in a Massive Galaxy at z=0.7

We present detailed photo+collisional ionization models and kinematic models of the multi-phase absorbing gas, detected within the HST/COS, HST/STIS, and Keck/HIRES spectra of the background quasar TON 153, at 104 kpc along the projected minor axis of a star-forming spiral galaxy (z=0.6610). Complementary g'r'i'Ks photometry and stellar population models indicate that the host galaxy is dominated by a 4 Gyr stellar population with slightly greater than solar metallicity and has an estimated log(M*)=11 and a log(Mvir)=13. Photoionization models of the low ionization absorption, (MgI, SiII, MgII and CIII) which trace the bulk of the hydrogen, constrain the multi-component gas to be cold (logT=3.8-5.2) and metal poor (-1.68<[X/H]<-1.64). A lagging halo model reproduces the low ionization absorption kinematics, suggesting gas coupled to the disk angular momentum, consistent with cold accretion mode material in simulations. The CIV and OVI absorption is best modeled in a separate collisionally ionized metal-poor (-2.50<[X/H]<-1.93) warm phase with logT=5.3. Although their kinematics are consistent with a wind model, given the 2-2.5dex difference between the galaxy stellar metallicity and the absorption metallicity indicates the gas cannot arise from galactic winds. We discuss and conclude that although the quasar sight-line passes along the galaxy minor axis at projected distance of 0.3 virial radii, well inside its virial shock radius, the combination of the relative kinematics, temperatures, and relative metallicities indicated that the multi-phase absorbing gas arises from cold accretion around this massive galaxy. Our results appear to contradict recent interpretations that absorption probing the projected minor axis of a galaxy is sampling winds.Comment: 16 pages, 11 figures, accepted for publication in MNRA

Photoionization and Photoelectric Loading of Barium Ion Traps

Simple and effective techniques for loading barium ions into linear Paul traps are demonstrated. Two-step photoionization of neutral barium is achieved using a weak intercombination line (6s2 1S0 6s6p 3P1, 791 nm) followed by excitation above the ionization threshold using a nitrogen gas laser (337 nm). Isotopic selectivity is achieved by using a near Doppler-free geometry for excitation of the triplet 6s6p 3P1 state. Additionally, we report a particularly simple and efficient trap loading technique that employs an in-expensive UV epoxy curing lamp to generate photoelectrons.Comment: 5 pages, Accepted to PRA 3/20/2007 -fixed typo -clarified figure 3 caption -added reference [15

Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus

<p>Abstract</p> <p>Background</p> <p>The Sydney blood bank cohort (SBBC) of long-term survivors consists of multiple individuals infected with <it>nef</it>-deleted, attenuated strains of human immunodeficiency virus type 1 (HIV-1). Although the cohort members have experienced differing clinical courses and now comprise slow progressors (SP) as well as long-term nonprogressors (LTNP), longitudinal analysis of <it>nef</it>/long-terminal repeat (LTR) sequences demonstrated convergent <it>nef</it>/LTR sequence evolution in SBBC SP and LTNP. Thus, the <it>in vivo </it>pathogenicity of attenuated HIV-1 strains harboured by SBBC members is dictated by factors other than <it>nef</it>/LTR. Therefore, to determine whether defects in other viral genes contribute to attenuation of these HIV-1 strains, we characterized dominant HIV-1 <it>rev </it>alleles that persisted in 4 SBBC subjects; C18, C64, C98 and D36.</p> <p>Results</p> <p>The ability of Rev derived from D36 and C64 to bind the Rev responsive element (RRE) in RNA binding assays was reduced by approximately 90% compared to Rev derived from HIV-1_NL4-3, C18 or C98. D36 Rev also had a 50–60% reduction in ability to express Rev-dependent reporter constructs in mammalian cells. In contrast, C64 Rev had only marginally decreased Rev function despite attenuated RRE binding. In D36 and C64, attenuated RRE binding was associated with rare amino acid changes at 3 highly conserved residues; Gln to Pro at position 74 immediately N-terminal to the Rev activation domain, and Val to Leu and Ser to Pro at positions 104 and 106 at the Rev C-terminus, respectively. In D36, reduced Rev function was mapped to an unusual 13 amino acid extension at the Rev C-terminus.</p> <p>Conclusion</p> <p>These findings provide new genetic and mechanistic insights important for Rev function, and suggest that Rev function, not Rev/RRE binding may be rate limiting for HIV-1 replication. In addition, attenuated <it>rev </it>alleles may contribute to viral attenuation and long-term survival of HIV-1 infection in a subset of SBBC members.</p

Geometry-dependent critical currents in superconducting nanocircuits

In this paper we calculate the critical currents in thin superconducting strips with sharp right-angle turns, 180-degree turnarounds, and more complicated geometries, where all the line widths are much smaller than the Pearl length $\Lambda = 2 \lambda^2/d$. We define the critical current as the current that reduces the Gibbs free-energy barrier to zero. We show that current crowding, which occurs whenever the current rounds a sharp turn, tends to reduce the critical current, but we also show that when the radius of curvature is less than the coherence length this effect is partially compensated by a radius-of-curvature effect. We propose several patterns with rounded corners to avoid critical-current reduction due to current crowding. These results are relevant to superconducting nanowire single-photon detectors, where they suggest a means of improving the bias conditions and reducing dark counts. These results also have relevance to normal-metal nanocircuits, as these patterns can reduce the electrical resistance, electromigration, and hot spots caused by nonuniform heating.Comment: 29 pages, 24 figure

Heat exchange mediated by a quantum system

We consider heat transfer between two thermal reservoirs mediated by a quantum system using the generalized quantum Langevin equation. The thermal reservoirs are treated as ensembles of oscillators within the framework of the Drude-Ullersma model. General expressions for the heat current and thermal conductance are obtained for arbitrary coupling strength between the reservoirs and the mediator and for different temperature regimes. As an application of these results we discuss the origin of Fourier's law in a chain of large, but finite subsystems coupled to each other by the quantum mediators. We also address a question of anomalously large heat current between the STM tip and substrate found in a recent experiment. The question of minimum thermal conductivity is revisited in the framework of scaling theory as a potential application of the developed approach.Comment: 16 pages, 6 figure

The Spatial, Ionization, and Kinematic Conditions of the z=1.39 Damped Ly-alpha Absorber in Q0957+561 A,B

We examined the sizes of the absorption clouds in a z=1.3911 damped Ly-alpha absorber (DLA) in the double image lensed quasar Q0957+561 A,B (separation 135 pc at the absorber redshift). Using HIRES/Keck spectra, we studied the MgII 2796,2803 doublet, FeII multiplet, and MgI 2853 transition in absorption. We defined six "clouds" in the system of sightline A and seven clouds in the system of sightline B. An examination of the N(v) profiles, using the apparent optical depth method, reveals no clear physical connection between the clouds in A and those in B. The observed column density ratios of all clouds is log[N(MgI)/N(FeII)] ~ -2 across the full velocity range in both systems and also spatially (in both sightlines). This is a remarkable uniformity not seen in Lyman limit systems. The uniformity of the cloud properties suggests that the multiple clouds are not part of a "halo". Based upon photoionization modeling, we constrain the ionization parameters in the range -6.2 < log(U) < -5.1, where the range brackets known abundance ratio and dust depletion patterns. The inferred cloud properties are densities of 2 < n_H < 20 cm^-3, and line of sight sizes of 1 < D < 25 pc. The masses of the clouds in system A are 10 < M/M_sun < 1000 and in system B are 1 < M/M_sun < 60 for spherical clouds. For planar clouds, the upper limits are 400 M_sun and 160 M_sun for A and B, respectively. We favor a model of the absorber in which the DLA region itself is a single cloud in thiscomplex, which could be a parcel of gas in a galactic ISM. A spherical cloud of ~10 pc would be limited to one of the sightlines (A) and imply a covering factor less than 0.1 for the DLA complex. We infer that the DLA cloud properties are consistent with those of lower density, cold clouds in the Galactic interstellar medium.Comment: Accepted for publication in the Astrophysical Journal; final versio

A Bayesian model selection approach to mediation analysis.

Genetic studies often seek to establish a causal chain of events originating from genetic variation through to molecular and clinical phenotypes. When multiple phenotypes share a common genetic association, one phenotype may act as an intermediate for the genetic effects on the other. Alternatively, the phenotypes may be causally unrelated but share genetic loci. Mediation analysis represents a class of causal inference approaches used to determine which of these scenarios is most plausible. We have developed a general approach to mediation analysis based on Bayesian model selection and have implemented it in an R package, bmediatR. Bayesian model selection provides a flexible framework that can be tailored to different analyses. Our approach can incorporate prior information about the likelihood of models and the strength of causal effects. It can also accommodate multiple genetic variants or multi-state haplotypes. Our approach reports posterior probabilities that can be useful in interpreting uncertainty among competing models. We compared bmediatR with other popular methods, including the Sobel test, Mendelian randomization, and Bayesian network analysis using simulated data. We found that bmediatR performed as well or better than these alternatives in most scenarios. We applied bmediatR to proteome data from Diversity Outbred (DO) mice, a multi-parent population, and demonstrate the power of mediation with multi-state haplotypes. We also applied bmediatR to data from human cell lines to identify transcripts that are mediated through or are expressed independently from local chromatin accessibility. We demonstrate that Bayesian model selection provides a powerful and versatile approach to identify causal relationships in genetic studies using model organism or human data