Effect of Cluster Formation on Isospin Asymmetry in the Liquid-Gas Phase Transition Region

Nuclear matter within the liquid-gas phase transition region is investigated in a mean-field two-component Fermi-gas model. Following largely analytic considerations, it is shown that: (1) Due to density dependence of asymmetry energy, some of the neutron excess from the high-density phase could be expelled into the low-density region. (2) Formation of clusters in the gas phase tends to counteract this trend, making the gas phase more liquid-like and reducing the asymmetry in the gas phase. Flow of asymmetry between the spectator and midrapidity region in reactions is discussed and a possible inversion of the flow direction is indicated.Comment: 9 pages,3 figures, RevTe

Dust in the wind: Crystalline silicates, corundum and periclase in PG 2112+059

We have determined the mineralogical composition of dust in the Broad Absorption Line (BAL) quasar PG 2112+059 using mid-infrared spectroscopy obtained with the Spitzer Space Telescope. From spectral fitting of the solid state features, we find evidence for Mg-rich amorphous silicates with olivine stoichiometry, as well as the first detection of corundum (Al_2O_3) and periclase (MgO) in quasars. This mixed composition provides the first direct evidence for a clumpy density structure of the grain forming region. The silicates in total encompass 56.5% of the identified dust mass, while corundum takes up 38 wt.%. Depending on the choice of continuum, a range of mass fractions is observed for periclase ranging from 2.7% in the most conservative case to 9% in a less constrained continuum. In addition, we identify a feature at 11.2 micron as the crystalline silicate forsterite, with only a minor contribution from polycyclic aromatic hydrocarbons. The 5% crystalline silicate fraction requires high temperatures such as those found in the immediate quasar environment in order to counteract rapid destruction from cosmic rays.Comment: 2 figure

On the evolution of the molecular line profiles induced by the propagation of C-shock waves

We present the first results of the expected variations of the molecular line emission arising from material recently affected by C-shocks (shock precursors). Our parametric model of the structure of C-shocks has been coupled with a radiative transfer code to calculate the molecular excitation and line profiles of shock tracers such as SiO, and of ion and neutral molecules such as H13CO+ and HN13C, as the shock propagates through the unperturbed medium. Our results show that the SiO emission arising from the early stage of the magnetic precursor typically has very narrow line profiles slightly shifted in velocity with respect to the ambient cloud. This narrow emission is generated in the region where the bulk of the ion fluid has already slipped to larger velocities in the precursor as observed toward the young L1448-mm outflow. This strongly suggests that the detection of narrow SiO emission and of an ion enhancement in young shocks, is produced by the magnetic precursor of C-shocks. In addition, our model shows that the different velocity components observed toward this outflow can be explained by the coexistence of different shocks at different evolutionary stages, within the same beam of the single-dish observations.Comment: 7 pages, 4 figures, accepted for publication in Ap

Atmospheric and oceanic impacts of Antarctic glaciation across the Eocene-Oligocene transition

The glaciation of Antarctica at the Eocene–Oligocene transition (approx. 34 million years ago) was a major shift in the Earth’s climate system, but the mechanisms that caused the glaciation, and its effects, remain highly debated. A number of recent studies have used coupled atmosphere–ocean climate models to assess the climatic effects of Antarctic glacial inception, with often contrasting results. Here, using the HadCM3L model, we show that the global atmosphere and ocean response to growth of the Antarctic ice sheet is sensitive to subtle variations in palaeogeography, using two reconstructions representing Eocene and Oligocene geological stages. The earlier stage (Eocene; Priabonian), which has a relatively constricted Tasman Seaway, shows a major increase in sea surface temperature over the Pacific sector of the Southern Ocean in response to the ice sheet. This response does not occur for the later stage (Oligocene; Rupelian), which has a more open Tasman Seaway. This difference in temperature response is attributed to reorganization of ocean currents between the stages. Following ice sheet expansion in the earlier stage, the large Ross Sea gyre circulation decreases in size. Stronger zonal flow through the Tasman Seaway allows salinities to increase in the Ross Sea, deep-water formation initiates and multiple feedbacks then occur amplifying the temperature response. This is potentially a model-dependent result, but it highlights the sensitive nature of model simulations to subtle variations in palaeogeography, and highlights the need for coupled ice sheet–climate simulations to properly represent and investigate feedback processes acting on these time scales

Mid-infrared spectra of PAH emission in Herbig AeBe stars

We present spectra of four Herbig AeBe stars obtained with the Infrared Spectrograph (IRS). on the Spitzer Space Telescope. All four of the sources show strong emission from polycyclic aromatic hydrocarbons (PAHs), with the 6.2 um emission feature shifted to 6.3 um and the strongest C-C skeletal-mode feature occuring at 7.9 um instead of at 7.7 um as is often seen. Remarkably, none of the four stars have silicate emission. The strength of the 7.9 um feature varies with respect to the 11.3 um feature among the sources, indicating that we have observed PAHs with a range of ionization fractions. The ionization fraction is higher for systems with hotter and brighter central stars. Two sources, HD 34282 and HD 169142, show emission features from aliphatic hydrocarbons at 6.85 and 7.25 um. The spectrum of HD 141569 shows a previously undetected emission feature at 12.4 um which may be related to the 12.7 um PAH feature. The spectrum of HD 135344, the coolest star in our sample, shows an unusual profile in the 7-9 um region, with the peak emission to the red of 8.0 um and no 8.6 um PAH feature.Comment: Accepted by ApJ 23 June, 2005, 8 pages (emulateapj), 5 figures (3 in color

Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7–2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations

The shape and composition of interstellar silicate grains

We investigate the composition and shape distribution of silicate dust grains in the interstellar medium. The effect of the amount of magnesium in the silicate lattice is studied. We fit the spectral shape of the interstellar 10 mu extinction feature as observed towards the galactic center. We use very irregularly shaped coated and non-coated porous Gaussian Random Field particles as well as a statistical approach to model shape effects. For the dust materials we use amorphous and crystalline silicates with various composition and SiC. The results of our analysis of the 10 mu feature are used to compute the shape of the 20 mu silicate feature and to compare this with observations. By using realistic particle shapes we are, for the first time, able to derive the magnesium fraction in interstellar silicates. We find that the interstellar silicates are highly magnesium rich (Mg/(Fe+Mg)>0.9) and that the stoichiometry lies between pyroxene and olivine type silicates. This composition is not consistent with that of the glassy material found in GEMS in interplanetary dust particles indicating that these are, in general, not unprocessed remnants from the interstellar medium. Also, we find a significant fraction of SiC (~3%). We discuss the implications of our results for the formation and evolutionary history of cometary and circumstellar dust. We argue that the fact that crystalline silicates in cometary and circumstellar grains are almost purely magnesium silicates is a natural consequence of our findings that the amorphous silicates from which they were formed were already magnesium rich.Comment: Accepted for publication in A&

Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Three-micron spectra of AGB stars and supergiants in nearby galaxies

The dependence of stellar molecular bands on the metallicity is studied using infrared L-band spectra of AGB stars (both carbon-rich and oxygen-rich) and M-type supergiants in the Large and Small Magellanic Clouds (LMC and SMC) and in the Sagittarius Dwarf Spheroidal Galaxy. The spectra cover SiO bands for oxygen-rich stars, and acetylene (C2H2), CH and HCN bands for carbon-rich AGB stars. The equivalent width of acetylene is found to be high even at low metallicity. The high C2H2 abundance can be explained with a high carbon-to-oxygen (C/O) ratio for lower metallicity carbon stars. In contrast, the HCN equivalent width is low: fewer than half of the extra-galactic carbon stars show the 3.5micron HCN band, and only a few LMC stars show high HCN equivalent width. HCN abundances are limited by both nitrogen and carbon elemental abundances. The amount of synthesized nitrogen depends on the initial mass, and stars with high luminosity (i.e. high initial mass) could have a high HCN abundance. CH bands are found in both the extra-galactic and Galactic carbon stars. None of the oxygen-rich LMC stars show SiO bands, except one possible detection in a low quality spectrum. The limits on the equivalent widths of the SiO bands are below the expectation of up to 30angstrom for LMC metallicity. Several possible explanations are discussed. The observations imply that LMC and SMC carbon stars could reach mass-loss rates as high as their Galactic counterparts, because there are more carbon atoms available and more carbonaceous dust can be formed. On the other hand, the lack of SiO suggests less dust and lower mass-loss rates in low-metallicity oxygen-rich stars. The effect on the ISM dust enrichment is discussed.Comment: accepted for A&