Gravity gradient preliminary investigations on exhibit ''A'' Final report

Quartz microbalance gravity gradiometer performance test

Measurement of conditional phase shifts for quantum logic

Measurements of the birefringence of a single atom strongly coupled to a high-finesse optical resonator are reported, with nonlinear phase shifts observed for intracavity photon number much less than one. A proposal to utilize the measured conditional phase shifts for implementing quantum logic via a quantum-phase gate (QPG) is considered. Within the context of a simple model for the field transformation, the parameters of the "truth table" for the QPG are determined.Comment: 4 pages in Postscript format, including 4 figures (attached as uuencoded version of a gzip-file

Magnetars vs. high magnetic field pulsars: a theoretical interpretation of the apparent dichotomy

Highly magnetized neutron stars (NSs) are characterized by a bewildering range of astrophysical manifestations. Here, building on our simulations of the evolution of magnetic stresses in the NS crust and its ensuing fractures (Perna & Pons 2011), we explore in detail, for the middle-age and old NSs, the dependence of starquake frequency and energetics on the relative strength of the poloidal (B_p) and toroidal (B_tor) components. We find that, for B_p >~10^{14}G, since a strong crustal toroidal field B_tor B_p is quickly formed on a Hall timescale, the initial toroidal field needs to be B_tor >> B_p to have a clear influence on the outbursting behaviour. For initial fields B_p <~ 10^{14}G, it is very unlikely that a middle-age (t~10^5 years) NS shows any bursting activity. This study allows us to solve the apparent puzzle of how NSs with similar dipolar magnetic fields can behave in a remarkably different way: an outbursting 'magnetar' with a high X-ray luminosity, or a quiet, low-luminosity, "high-$B$" radio pulsar. As an example, we consider the specific cases of the magnetar 1E2259+586 and the radio pulsar PSRJ1814-1744, which at present have a similar dipolar field ~6x10^{13}G. We determine for each object an initial magnetic field configuration that reproduces the observed timing parameters at their current age. The same two configurations also account for the differences in quiescent X-ray luminosity and for the 'magnetar/outbursting' behaviour of 1E2259+586 but not of PSRJ1814-1744. We further use the theoretically predicted surface temperature distribution to compute the light-curve for these objects. In the case of 1E2259+586, for which data are available, our predicted temperature distribution gives rise to a pulse profile whose double-peaked nature and modulation level is consistent with the observations.Comment: 8 pages emulateapj, 5 figures, accepted to Ap

Identification of a new member of the phage shock protein response in Escherichia coli, the phage shock protein g (PspG)

The phage shock protein operon (pspABCDE) of Escherichia coli is strongly up-regulated in response to overexpression of the filamentous phage secretin protein IV (pIV) and by many other stress conditions including defects in protein export. PspA has an established role in maintenance of the proton-motive force of the cell under stress conditions. Here we present evidence for a new member of the phage shock response in E. coli. Using transcriptional profiling, we show that the synthesis of pIV in E. coli leads to a highly restricted response limited to the up-regulation of the psp operon genes and yjbO. The psp operon and yjbO are also up-regulated in response to pIV in Salmonella enterica serovar Typhimurium. yjbO is a highly conserved gene found exclusively in bacteria that contain a psp operon but is physically unlinked to the psp operon. yjbO encodes a putative inner membrane protein that is co-controlled with the psp operon genes and is predicted to be an effector of the psp response in E. coli. We present evidence that yjbO expression is driven by sigma(54)-RNA polymerase, activated by PspF and integration host factor, and negatively regulated by PspA. PspF specifically regulates only members of the PspF regulon: pspABCDE and yjbO. We found that increased expression of YjbO results in decreased motility of bacteria. Because yjbO is co-conserved and co-regulated with the psp operon and is a member of the phage shock protein F regulon, we propose that yjbO be renamed pspG

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

An external-shock origin of the E_p-E_gamma relation for Gamma-Ray Bursts

We investigate the possibility that the E_p propto E_gamma^{1/2} relation between the peak energy E_p of the nuF_nu spectrum and energy output E_gamma for long-duration GRBs arises from the external shock produced by the interaction of a relativistic outflow with the ambient medium. To that aim, we take into account the dependence of all parameters which determine E_p and E_gamma on the radial distribution of the ambient medium density and find that the E_p-E_gamma relation can be explained if the medium around GRBs has a universal radial stratification. For various combinations of GRB radiative process (synchrotron or inverse-Compton) and dissipation mechanism (reverse or forward shock), we find that the circumburst medium must have a particle density with a radial distribution different than the R^{-2} expected for constant mass-loss rate and terminal speed.Comment: 6 pages, to appear in MNRA

The evolution of ultraviolet emission lines from the circumstellar material surrounding SN 1987A

The presence of narrow high-temperature emission lines from nitrogen-rich gas close to SN 1987A has been the principal observational constraint on the evolu- tionary status of the supernova's progenitor. A new analysis of the complete five-year set of low and high resolution IUE ultraviolet spectra of SN 1987A (1987.2--1992.3) provide fluxes for the N V 1240, N IV] 1486, He II 1640, OIII] 1665, NIII] 1751, and CIII] 1908 lines with significantly reduced random and systematic errors and reveals significant short-term fluctuations in the light curves. The N V, N IV] and N III] lines turn on sequentially over 15 to 20 days and show a progression from high to low ionization potential, implying an ioni- zation gradient in the emitting region. The line emission turns on suddenly at 83+/-4 days after the explosion, as defined by N IV]. The N III] line reaches peak luminosity at 399+/-15 days. A ring radius of (6.24+/-0.20)E{17} cm and inclination of 41.0+/-3.9 is derived from these times, assuming a circular ring. The probable role of resonant scattering in the N V light curve introduces systematic errors that leads us to exclude this line from the timing analysis. A new nebular analysis yields improved CNO abundance ratios N/C=6.1+/-1.1 and N/O=1.7+/-0.5, confirming the nitrogen enrichment found in our previous paper. From the late-time behavior of the light curves we find that the emission origi- nates from progressively lower density gas. We estimate the emitting mass near maximum (roughly 400 days) to be roughly 4.7E{-2} solar masses, assuming a filling factor of unity and an electron density of 2.6E4 cm^{-3}. These results are discussed in the context of current models for the emission and hydrodynamics of the ring.Comment: 38 pages, AASTeX v.4.0, 13 Postscript figures; ApJ, in pres

Accelerated large-scale multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware.</p> <p>Results</p> <p>We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor.</p> <p>Conclusions</p> <p>Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from <url>http://dna.cs.byu.edu/msa/</url>.</p