Two models of the influenza A M2 channel domain: verification by comparison

Background: The influenza M2 protein is a simple membrane protein, containing a single transmembrane helix. It is representative of a very large family of single-transmembrane helix proteins. The functional protein is a tetramer, with the four transmembrane helices forming a proton-permeable channel across the bilayer. Two independently derived models of the M2 channel domain are compared, in order to assess the success of applying molecular modelling approaches to simple membrane proteins.Results: The Cα RSMD between the two models is 1.7 å. Both models are composed of a left-handed bundle of helices, with the helices tilted roughly 15° relative to the (presumed) bilayer normal. The two models have similar pore radius profiles, with a pore cavity lined by the Ser31 and Gly34 residues and a pore constriction formed by the ring of His37 residues.Conclusions:Independent studies of M2 have converged on the same structural model for the channel domain. This model is in agreement with solid state NMR data. In particular, both model and NMR data indicate that the M2 helices are tilted relative to the bilayer normal and form a left-handed bundle. Such convergence suggests that, at least for simple membrane proteins, restraints-directed modelling might yield plausible models worthy of further computational and experimental investigation

Probing the cosmic star formation using long Gamma-Ray Bursts: New constraints from the Spitzer Space Telescope

We report on IRAC-4.5mic, IRAC-8.0mic and MIPS-24mic deep observations of 16 Gamma-Ray Burst (GRBs) host galaxies performed with the Spitzer Space Telescope, and we investigate in the thermal infrared the presence of evolved stellar populations and dust-enshrouded star-forming activity associated with these objects. Our sample is derived from GRBs that were identified with sub-arcsec localization between 1997 and 2001, and only a very small fraction (~20%) of the targeted sources is detected down to f_4.5mic ~3.5microJy and f_24mic ~85microJy (3sigma). This likely argues against a population dominated by massive and strongly-starbursting (i.e., SFR > ~100 Msol/yr) galaxies as it has been recently suggested from submillimeter/radio and optical studies of similarly-selected GRB hosts. Furthermore we find evidence that some GRBs do not occur in the most infrared-luminous regions -- hence the most actively star-forming environments -- of their host galaxies. Should the GRB hosts be representative of all star-forming galaxies at high redshift, models of infrared galaxy evolution indicate that > ~50% of GRB hosts should have f_24mic > ~100microJy. Unless the identification of GRBs prior to 2001 was prone to strong selection effects biasing our sample against dusty galaxies, we infer in this context that the GRBs identified with the current techniques can not be directly used as unbiased probes of the global and integrated star formation history of the Universe.Comment: ApJ in press, 23 pages, 8 figures (scheduled for the ApJ 10 May 2006, v642 2 issue). Full resolution available at http://perceval.as.arizona.edu/~elefloch/Publis/ms_grb_spitzer.pd

Improved method for implicit Monte Carlo

The Implicit Monte Carlo (IMC) method has been used for over 30 years to analyze radiative transfer problems, such as those encountered in stellar atmospheres or inertial confinement fusion. Reference [2] provided an exact error analysis of IMC for 0-D problems and demonstrated that IMC can exhibit substantial errors when timesteps are large. These temporal errors are inherent in the method and are in addition to spatial discretization errors and approximations that address nonlinearities (due to variation of physical constants). In Reference [3], IMC and four other methods were analyzed in detail and compared on both theoretical grounds and the accuracy of numerical tests. As discussed in, two alternative schemes for solving the radiative transfer equations, the Carter-Forest (C-F) method and the Ahrens-Larsen (A-L) method, do not exhibit the errors found in IMC; for 0-D, both of these methods are exact for all time, while for 3-D, A-L is exact for all time and C-F is exact within a timestep. These methods can yield substantially superior results to IMC

The Truncated Disk of CoKu Tau/4

We present a model of a dusty disk with an inner hole which accounts for the Spitzer Space Telescope Infrared Spectrograph observations of the low-mass pre-main sequence star CoKu Tau/4. We have modeled the mid-IR spectrum (between 8 and 25 mic) as arising from the inner wall of a disk. Our model disk has an evacuated inner zone of radius ~ 10 AU, with a dusty inner ``wall'', of half-height ~ 2 AU, that is illuminated at normal incidence by the central star. The radiative equilibrium temperature decreases from the inner disk edge outward through the optically-thick disk; this temperature gradient is responsible for the emission of the silicate bands at 10 and 20 mic. The observed spectrum is consistent with being produced by Fe-Mg amorphous glassy olivine and/or pyroxene, with no evidence of a crystalline component. The mid-infrared spectrum of CoKu Tau/4 is reminiscent of that of the much older star TW Hya, where it has been suggested that the significant clearing of its inner disk is due to planet formation. However, no inner disk remains in CoKu Tau/4, consistent with the star being a weak-emission (non-accreting) T Tauri star. The relative youth of CoKu Tau/4 (~ 1 Myr) may indicate much more rapid planet formation than typically assumed.Comment: 32 pages, 9 figures, accepted in Ap

A Spitzer IRS Spectral Atlas of Luminous 8 micron Sources in the Large Magellanic Cloud

We present an atlas of Spitzer Space Telescope Infrared Spectrograph (IRS) spectra of highly luminous, compact mid-infrared sources in the Large Magellanic Cloud. Sources were selected on the basis of infrared colors and 8 micron (MSX) fluxes indicative of highly evolved, intermediate- to high-mass stars with current or recent mass loss at large rates. We determine the chemistry of the circumstellar envelope from the mid-IR continuum and spectral features and classify the spectral types of the stars. In the sample of 60 sources, we find 21 Red Supergiants (RSGs), 16 C-rich Asymptotic Giant Branch (AGB) stars, 11 HII regions, 4 likely O-rich AGB stars, 4 Galactic O-rich AGB stars, 2 OH/IR stars, and 2 B[e] supergiants with peculiar IR spectra. We find that the overwhelming majority of the sample AGB stars (with typical IR luminosities ~1.0E4 L_sun) have C-rich envelopes, while the O-rich objects are predominantly luminous RSGs with L_IR ~ 1.0E5 L_sun. We determine mean bolometric corrections to the stellar K-band flux densities and find that for carbon stars, the bolometric corrections depend on the infrared color, whereas for RSGs, the bolometric correction is independent of IR color. Our results reveal that objects previously classified as PNe on the basis of IR colors are in fact compact HII regions with very red IRS spectra that include strong atomic recombination lines and PAH emission features. We demonstrate that the IRS spectral classes in our sample separate clearly in infrared color-color diagrams that use combinations of 2MASS data and synthetic IRAC/MIPS fluxes derived from the IRS spectra. On this basis, we suggest diagnostics to identify and classify, with high confidence levels, IR-luminous evolved stars and HII regions in nearby galaxies using Spitzer and near-infrared photometry.Comment: 46 pages, 9 figures; accepted for publication in AJ; abstract abridge

Planetary Candidates Observed by Kepler IV: Planet Sample From Q1-Q8 (22 Months)

We provide updates to the Kepler planet candidate sample based upon nearly two years of high-precision photometry (i.e., Q1-Q8). From an initial list of nearly 13,400 Threshold Crossing Events (TCEs), 480 new host stars are identified from their flux time series as consistent with hosting transiting planets. Potential transit signals are subjected to further analysis using the pixel-level data, which allows background eclipsing binaries to be identified through small image position shifts during transit. We also re-evaluate Kepler Objects of Interest (KOI) 1-1609, which were identified early in the mission, using substantially more data to test for background false positives and to find additional multiple systems. Combining the new and previous KOI samples, we provide updated parameters for 2,738 Kepler planet candidates distributed across 2,017 host stars. From the combined Kepler planet candidates, 472 are new from the Q1-Q8 data examined in this study. The new Kepler planet candidates represent ~40% of the sample with Rp~1 Rearth and represent ~40% of the low equilibrium temperature (Teq<300 K) sample. We review the known biases in the current sample of Kepler planet candidates relevant to evaluating planet population statistics with the current Kepler planet candidate sample.Comment: 12 pages, 8 figures, Accepted ApJ Supplemen

Evaluating the GeoSnap 13-μ\mum Cut-Off HgCdTe Detector for mid-IR ground-based astronomy

New mid-infrared HgCdTe (MCT) detector arrays developed in collaboration with Teledyne Imaging Sensors (TIS) have paved the way for improved 10-$\mu$m sensors for space- and ground-based observatories. Building on the successful development of longwave HAWAII-2RGs for space missions such as NEO Surveyor, we characterize the first 13-$\mu$m GeoSnap detector manufactured to overcome the challenges of high background rates inherent in ground-based mid-IR astronomy. This test device merges the longwave HgCdTe photosensitive material with Teledyne's 2048x2048 GeoSnap-18 (18-$\mu$m pixel) focal plane module, which is equipped with a capacitive transimpedance amplifier (CTIA) readout circuit paired with an onboard 14-bit analog-to-digital converter (ADC). The final assembly yields a mid-IR detector with high QE, fast readout (>85 Hz), large well depth (>1.2 million electrons), and linear readout. Longwave GeoSnap arrays would ideally be deployed on existing ground-based telescopes as well as the next generation of extremely large telescopes. While employing advanced adaptive optics (AO) along with state-of-the-art diffraction suppression techniques, instruments utilizing these detectors could attain background- and diffraction-limited imaging at inner working angles <10 $\lambda/D$, providing improved contrast-limited performance compared to JWST MIRI while operating at comparable wavelengths. We describe the performance characteristics of the 13-$\mu$m GeoSnap array operating between 38-45K, including quantum efficiency, well depth, linearity, gain, dark current, and frequency-dependent (1/f) noise profile.Comment: 17 pages, 17 figures. Accepted for publication in special addition of Astronomische Nachrichten / Astronomical Notes as a contribution to SDW202

Detection of Potential Transit Signals in the First Three Quarters of Kepler Mission Data

We present the results of a search for potential transit signals in the first three quarters of photometry data acquired by the Kepler Mission. The targets of the search include 151,722 stars which were observed over the full interval and an additional 19,132 stars which were observed for only 1 or 2 quarters. From this set of targets we find a total of 5,392 detections which meet the Kepler detection criteria: those criteria are periodicity of the signal, an acceptable signal-to-noise ratio, and a composition test which rejects spurious detections which contain non-physical combinations of events. The detected signals are dominated by events with relatively low signal-to-noise ratio and by events with relatively short periods. The distribution of estimated transit depths appears to peak in the range between 40 and 100 parts per million, with a few detections down to fewer than 10 parts per million. The detected signals are compared to a set of known transit events in the Kepler field of view which were derived by a different method using a longer data interval; the comparison shows that the current search correctly identified 88.1% of the known events. A tabulation of the detected transit signals, examples which illustrate the analysis and detection process, a discussion of future plans and open, potentially fruitful, areas of further research are included