The SiC problem: astronomical and meteoritic evidence

Pre-solar grains of silicon carbide found in meteorites and interpreted as having had an origin around carbon stars from their isotopic composition, have all been found to be of the beta-SiC polytype. Yet to date fits to the 11.3 microns SiC emission band of carbon stars had been obtained only for alpha-SiC grains. We present thin film infrared (IR) absorption spectra measured in a diamond anvil cell for both the alpha- and beta- polymorphs of synthetic SiC and compare the results with previously published spectra taken using the KBr matrix method. We find that our thin film spectra have positions nearly identical to those obtained previously from finely ground samples in KBr. Hence, we show that this discrepancy has arisen from inappropriate `KBr corrections' having been made to laboratory spectra of SiC particles dispersed in KBr matrices. We re-fit a sample of carbon star mid-IR spectra, using laboratory data with no KBr correction applied, and show that beta-SiC grains fit the observations, while alpha-SiC grains do not. The discrepancy between meteoritic and astronomical identifications of the SiC-type is therefore removed. This work shows that the diamond anvil cell thin film method can be used to produce mineral spectra applicable to cosmic environments without further manipulation.Comment: to be published in Astrophysical Journal Letter 4 pages, 3 figure

The Structure of the Oligomerization Domain of Lsr2 from Mycobacterium tuberculosis Reveals a Mechanism for Chromosome Organization and Protection

Lsr2 is a small DNA-binding protein present in mycobacteria and related actinobacteria that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). A recent structure of the C-terminal DNA-binding domain of Lsr2 provides a rationale for its interaction with the minor groove of DNA, its preference for AT-rich tracts, and its similarity to other bacterial nucleoid-associated DNA-binding domains. In contrast, the details of Lsr2 dimerization (and oligomerization) via its N-terminal domain, and the mechanism of Lsr2-mediated chromosomal cross-linking and protection is unknown. We have solved the structure of the N-terminal domain of Lsr2 (N-Lsr2) at 1.73 Å resolution using crystallographic ab initio approaches. The structure shows an intimate dimer of two ß-ß-a motifs with no close homologues in the structural databases. The organization of individual N-Lsr2 dimers in the crystal also reveals a mechanism for oligomerization. Proteolytic removal of three N-terminal residues from Lsr2 results in the formation of an anti-parallel β-sheet between neighboring molecules and the formation of linear chains of N-Lsr2. Oligomerization can be artificially induced using low concentrations of trypsin and the arrangement of N-Lsr2 into long chains is observed in both monoclinic and hexagonal crystallographic space groups. In solution, oligomerization of N-Lsr2 is also observed following treatment with trypsin. A change in chromosomal topology after the addition of trypsin to full-length Lsr2-DNA complexes and protection of DNA towards DNAse digestion can be observed using electron microscopy and electrophoresis. These results suggest a mechanism for oligomerization of Lsr2 via protease-activation leading to chromosome compaction and protection, and concomitant down-regulation of large numbers of genes. This mechanism is likely to be relevant under conditions of stress where cellular proteases are known to be upregulated

Estimated optical constants of gypsum in the regions of weak absorptions: Application of scattering theories and comparisons to independent measurements

Diffuse reflectance spectra of multiple grain size fractions are used to estimate the optical constants of gypsum over the 0.4–15 μm wavelength region. Two independent scattering theories are used to iteratively determine the imaginary index of refraction from the measured reflectance. We compare the results of these two with each other and with imaginary indices of gypsum reported in the literature. We find that the scattering theory results are more sensitive in the infrared to weak spectral features that are clearly distinguished in the diffuse reflectance spectra. However, we find the scattering results provide a poor determination of the optical constants in the regions of relatively strong absorptions. At visible and near-infrared wavelengths we provide a comparison to the results obtained from analysis of the diffuse reflectance to results obtained from direct transmission measurements of several gypsum crystals having different sample thicknesses. We find the simplest models of the transmission reproduce the observed spectra. The different sample thicknesses for the transmission measurements and different grain sizes in the scattering theories allow evaluation of the imaginary index of refraction over a wide range of values. We find the imaginary index of refraction determined from scattering theories is in remarkable agreement with those obtained from transmission spectra. Different models of the reflectance and transmittance have associated strengths and weaknesses, and we conclude that combining these models provides a more accurate determination of the optical constants of a material when compared to using each separately. We combine the resulting real and imaginary indices of refraction with those reported at infrared wavelengths to provide values covering visual, near-infrared, and infrared wavelengths (0.4–333 μm, 25000–30 cm^(−1))

Deterministic model of battery, uphill currents, and nonequilibrium phase transitions

We consider point particles in a table made of two circular cavities connected by two rectangular channels, forming a closed loop under periodic boundary conditions. In the first channel, a bounce-back mechanism acts when the number of particles flowing in one direction exceeds a given threshold T. In that case, the particles invert their horizontal velocity, as if colliding with vertical walls. The second channel is divided in two halves parallel to the first but located in the opposite sides of the cavities. In the second channel, motion is free. We show that, suitably tuning the sizes of cavities of the channels and of T, nonequilibrium phase transitions take place in the N→∞ limit. This induces a stationary current in the circuit, thus modeling a kind of battery, although our model is deterministic, conservative, and time reversal invariant

Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans

Very little is known about the growth and mutation rates of Mycobacterium tuberculosis during latent infection in humans. However, studies in rhesus macaques have suggested that latent infections have mutation rates that are higher than that observed during active tuberculosis disease. Elevated mutation rates are presumed risk factors for the development of drug resistance. Therefore, the investigation of mutation rates during human latency is of high importance. We performed whole genome mutation analysis of M. tuberculosis isolates from a multi-decade tuberculosis outbreak of the New Zealand Rangipo strain. We used epidemiological and phylogenetic analysis to identify four cases of tuberculosis acquired from the same index case. Two of the tuberculosis cases occurred within two years of exposure and were classified as recently transmitted tuberculosis. Two other cases occurred more than 20 years after exposure and were classified as reactivation of latent M. tuberculosis infections. Mutation rates were compared between the two recently transmitted pairs versus the two latent pairs. Mean mutation rates assuming 20 hour generation times were 5.5X10⁻¹⁰ mutations/bp/generation for recently transmitted tuberculosis and 7.3X10⁻¹¹ mutations/bp/generation for latent tuberculosis. Generation time versus mutation rate curves were also significantly higher for recently transmitted tuberculosis across all replication rates (p = 0.006). Assuming identical replication and mutation rates among all isolates in the final two years before disease reactivation, the u20hr mutation rate attributable to the remaining latent period was 1.6×10⁻¹¹ mutations/bp/generation, or approximately 30 fold less than that calculated during the two years immediately before disease. Mutations attributable to oxidative stress as might be caused by bacterial exposure to the host immune system were not increased in latent infections. In conclusion, we did not find any evidence to suggest elevated mutation rates during tuberculosis latency in humans, unlike the situation in rhesus macaques

Transport and nonequilibrium phase transitions in polygonal urn models

We study the deterministic dynamics of N point particles moving at a constant speed in a 2D table made of two polygonal urns connected by an active rectangular channel, which applies a feedback control on the particles, inverting the horizontal component of their velocities when their number in the channel exceeds a fixed threshold. Such a bounce-back mechanism is non-dissipative: it preserves volumes in phase space. An additional passive channel closes the billiard table forming a circuit in which a stationary current may flow. Under specific constraints on the geometry and on the initial conditions, the large N limit allows nonequilibrium phase transitions between homogeneous and inhomogeneous phases. The role of ergodicity in making a probabilistic theory applicable is discussed for both rational and irrational urns. The theoretical predictions are compared with the numerical simulation results. Connections with the dynamics of feedback-controlled biological systems are highlighted

A New Measurement of the Average FUV Extinction Curve

We have measured the extinction curve in the far-ultraviolet wavelength region of (900 -- 1200 A) using spectra obtained with the Berkeley EUV/FUV spectrometer during the ORFEUS-I and the ORFEUS-II missions in 1993 and 1996. From the complete sample of early-type stars observed during these missions, we have selected pairs of stars with the same spectral type but different reddenings to measure the differential FUV extinction. We model the effects of molecular hydrogen absorption and exclude affected regions of the spectrum to determine the extinction from dust alone. We minimize errors from inaccuracies in the cataloged spectral types of the stars by making our own determinations of spectral types based on their IUE spectra. We find substantial scatter in the curves of individual star pairs and present a detailed examination of the uncertainties and their effects on each extinction curve. We find that, given the potentially large uncertainties inherent in using the pair method at FUV wavelengths, a careful analysis of measurement uncertainties is critical to assessing the true dust extinction. We present a new measurement of the average far-ultraviolet extinction curve to the Lyman limit; our new measurement is consistent with an extrapolation of the standard extinction curve of Savage & Mathis (1979).Comment: 13 pages text, 7 figures 4 tables. Sent as gzipped tar, with ms.tex and 7 figure

Linear characterization and modeling of GaN-on-Si HEMT technologies with 100 nm and 60 nm gate lengths

Motivated by the growing interest towards low-cost, restriction-free MMIC processes suitable for multi-function, possibly space-qualified applications, this contribution reports the extraction of reliable linear models for two advanced GaN-on-Si HEMT technologies, namely OMMIC’s D01GH (100 nm gate length) and D006GH (60 nm gate length). This objective is pursued by means of both classical and more novel approaches. In particular, the latter include a nondestructive method for determining the extrinsic resistances and an optimizaion-based approach to extracting the remaining parasitic elements: these support standard DC and RF measurements in order to obtain a scalable, bias-dependent equivalent-circuit model capturing the small-signal behavior of the two processes. As to the noise model, this is extracted by applying the well known noise-temperature approach to noise figure measurements performed in two different frequency ranges: a lower band, where a standard Y-factor test bench is used, and an upper band, where a custom cold-source test bench is set up and described in great detail. At 5 V drain-source voltage, minimum noise figures as low as 1.5 dB and 1.1 dB at 40 GHz have been extracted for the considered 100 nm and 60 nm HEMTs, respectively: this testifies the maturity of both processes and the effectiveness of the gate length reduction. The characterization and modeling campaign, here presented for the first time, has been repeatedly validated by published designs, a couple of which are reviewed for the Reader’s convenience