Single-molecule pulling: phenomenology and interpretation

Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level processes that are familiar from our macroscopic thermodynamic experience. In this Chapter, we summarize the essential phenomenology that is typically observed during single-molecule pulling, provide a general statistical mechanical framework for the interpretation of the equilibrium force spectroscopy and illustrate how to simulate single-molecule pulling experiments using molecular dynamics.Comment: arXiv admin note: text overlap with arXiv:0908.220

Magnetic fields from reionisation

We present a complementary study to a new model for generating magnetic fields of cosmological interest. The driving mechanism is the photoionisation process by photons provided by the first luminous sources. Investigating the transient regime at the onset of inhomogeneous reionisation, we show that magnetic field amplitudes as high as $2 \times 10^{-16}$ Gauss can be obtained within a source lifetime. Photons with energies above the ionisation threshold accelerate electrons, inducing magnetic fields outside the Stroemgren spheres which surround the ionising sources. Thanks to their mean free path, photons with higher energies propagate further and lead to magnetic field generation deeper in the neutral medium. We find that soft X-ray photons could contribute to a significant premagnetisation of the intergalactic medium at a redshift of z=15.Comment: accepted for publication in A&

HST/NICMOS Paschen-alpha Survey of the Galactic Center: Overview

We have recently carried out the first wide-field hydrogen Paschen-alpha line imaging survey of the Galactic Center (GC), using the NICMOS instrument aboard the Hubble Space Telescope. The survey maps out a region of 2253 pc^2 around the central supermassive black hole (Sgr A*) in the 1.87 and 1.90 Micron narrow bands with a spatial resolution of 0.01 pc at a distance of 8 kpc. Here we present an overview of the observations, data reduction, preliminary results, and potential scientific implications, as well as a description of the rationale and design of the survey. We have produced mosaic maps of the Paschen-alpha line and continuum emission, giving an unprecedentedly high resolution and high sensitivity panoramic view of stars and photo-ionized gas in the nuclear environment of the Galaxy. We detect a significant number of previously undetected stars with Paschen-alpha in emission. They are most likely massive stars with strong winds, as confirmed by our initial follow-up spectroscopic observations. About half of the newly detected massive stars are found outside the known clusters (Arches, Quintuplet, and Central). Many previously known diffuse thermal features are now resolved into arrays of intriguingly fine linear filaments indicating a profound role of magnetic fields in sculpting the gas. The bright spiral-like Paschen-alpha emission around Sgr A* is seen to be well confined within the known dusty torus. In the directions roughly perpendicular to it, we further detect faint, diffuse Paschen-alpha emission features, which, like earlier radio images, suggest an outflow from the structure. In addition, we detect various compact Paschen-alpha nebulae, probably tracing the accretion and/or ejection of stars at various evolutionary stages.Comment: accepted for publication in MNRAS; a version of higher resolution images may be found at http://www.astro.umass.edu/~wqd/papers/hst/paper1.pd

Gene banks offer breeders access to germplasm: Germplasm collections help to preserve genetic diversity

Although most of us would agree that access to germplasm is the lifeblood of our nursery industry, how many of us know that behind the scenes there is a coordinated public and private effort to deal with germplasm issues

Photoionization of the Be isoelectronic sequence: total cross sections

The photoionization of the four-electron beryllium-like isoelectronic series from the neutral to Fe^{+22} has been studied for ground ^1S and metastable ^3P initial states. The wave functions of the final-state (target) ions were built using the CIV3 code. Both nonrelativistic LS-coupling R-matrix and relativistic Breit-Pauli (BP) R-matrix methods were used to calculate the cross sections in the photon-energy range between the first ionization threshold and the 1s^2 4f_{7/2} threshold for each ion. Our total cross sections compare well with experiment which is available for Be, B^+, C^{+2}, N^{+3}, and O^{+4}. The agreement between the present work and previous calculations is discussed in detail. The importance of relativistic effects is seen by the comparison between the LS and the BP results.Comment: 45 pages, 3 tables, 22 figure

Spitzer Spectral Mapping of Supernova Remnant Cassiopeia A

We present the global distribution of fine structure infrared line emission in the Cassiopeia A supernova remnant using data from the Spitzer Space Telescope's Infrared Spectrograph. We identify emission from ejecta materials in the interior, prior to their encounter with the reverse shock, as well as from the post-shock bright ring. The global electron density increases by >~100 at the shock to ~10^4 cm^-3, providing evidence for strong radiative cooling. There is also a dramatic change in ionization state at the shock, with the fading of emission from low ionization interior species like [SiII], giving way to [SIV] and, at even further distances, high-energy X-rays from hydrogenic silicon. Two compact, crescent-shaped clumps with highly enhanced neon abundance are arranged symmetrically around the central neutron star. These neon crescents are very closely aligned with the "kick" direction of the compact object from the remnant's expansion center, tracing a new axis of explosion asymmetry. They indicate that much of the apparent macroscopic elemental mixing may arise from different compositional layers of ejecta now passing through the reverse shock along different directions.Comment: 9 pages, 8 figures, accepted by Ap

The High-Density Ionized Gas in the Central Parsecs of the Galaxy

We report the results from observations of H30$\alpha$ line emission in Sgr A West with the Submillimeter Array at a resolution of 2\arcsec and a field of view of about 40\arcsec. The H30$\alpha$ line is sensitive to the high-density ionized gas in the minispiral structure. We compare the velocity field obtained from H30$\alpha$ line emission to a Keplerian model, and our results suggest that the supermassive black hole at Sgr A* dominates the dynamics of the ionized gas. However, we also detect significant deviations from the Keplerian motion, which show that the impact of strong stellar winds from the massive stars along the ionized flows and the interaction between Northern and Eastern arms play significant roles in the local gas dynamics.Comment: 4 pages, 2 figure

Analysis of alpha Centauri AB including seismic constraints

Detailed models of alpha Cen A and B based on new seismological data for alpha Cen B by Carrier & Bourban (2003) have been computed using the Geneva evolution code including atomic diffusion. Taking into account the numerous observational constraints now available for the alpha Cen system, we find a stellar model which is in good agreement with the astrometric, photometric, spectroscopic and asteroseismic data. The global parameters of the alpha Cen system are now firmly constrained to an age of t=6.52+-0.30 Gyr, an initial helium mass fraction Y_i=0.275+-0.010 and an initial metallicity (Z/X)_i=0.0434+-0.0020. Thanks to these numerous observational constraints, we confirm that the mixing-length parameter alpha of the B component is larger than the one of the A component, as already suggested by many authors (Noels et al. 1991, Fernandes & Neuforge 1995 and Guenther & Demarque 2000): alpha_B is about 8% larger than alpha_A (alpha_A=1.83+-0.10 and alpha_B=1.97+-0.10). Moreover, we show that asteroseismic measurements enable to determine the radii of both stars with a very high precision (errors smaller than 0.3%). The radii deduced from seismological data are compatible with the new interferometric results of Kervella et al. (2003) even if they are slightly larger than the interferometric radii (differences smaller than 1%).Comment: 13 pages, 9 figures, accepted for publication in A&

Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers

Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (\u3c96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96)