A three-state model with loop entropy for the over-stretching transition of DNA

We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the exponent c in the asymptotic expression S ~ - c ln n for the entropy of a loop of length n. Force extension curves are derived exactly employing a generalized Poland-Scheraga approach and compared to experimental data. Simultaneous fitting to force-extension data at room temperature and to the denaturation phase transition at zero force is possible and allows to establish a global phase diagram in the force-temperature plane. Under a stretching force, the effects of the stacking energy, entering as a domain-wall energy between paired and unpaired bases, and the loop entropy are separated. Therefore we can estimate the loop exponent c independently from the precise value of the stacking energy. The fitted value for c is small, suggesting that nicks dominate the experimental force extension traces of natural DNA.Comment: 12 pages, 5 figures + Supplementary informatio

Heterotic Models from Vector Bundles on Toric Calabi-Yau Manifolds

We systematically approach the construction of heterotic E_8 X E_8 Calabi-Yau models, based on compact Calabi-Yau three-folds arising from toric geometry and vector bundles on these manifolds. We focus on a simple class of 101 such three-folds with smooth ambient spaces, on which we perform an exhaustive scan and find all positive monad bundles with SU(N), N=3,4,5 structure groups, subject to the heterotic anomaly cancellation constraint. We find that anomaly-free positive monads exist on only 11 of these toric three-folds with a total number of bundles of about 2000. Only 21 of these models, all of them on three-folds realizable as hypersurfaces in products of projective spaces, allow for three families of quarks and leptons. We also perform a preliminary scan over the much larger class of semi-positive monads which leads to about 44000 bundles with 280 of them satisfying the three-family constraint. These 280 models provide a starting point for heterotic model building based on toric three-folds.Comment: 41 pages, 5 figures. A table modified and a table adde

Influence of point defects on magnetic vortex structures

We employed micro-Hall magnetometry and micromagnetic simulations to investigate magnetic vortex pinning at single point defects in individual submicron-sized permalloy disks. Small ferromagnetic particles containing artificial point defects can be fabricated by using an image reversal electron beam lithography process. Corresponding micromagnetic calculations, modeling the defects within the disks as holes, give reasonable agreement between experimental and simulated pinning and depinning field values

Toric Construction of Global F-Theory GUTs

We systematically construct a large number of compact Calabi-Yau fourfolds which are suitable for F-theory model building. These elliptically fibered Calabi-Yaus are complete intersections of two hypersurfaces in a six dimensional ambient space. We first construct three-dimensional base manifolds that are hypersurfaces in a toric ambient space. We search for divisors which can support an F-theory GUT. The fourfolds are obtained as elliptic fibrations over these base manifolds. We find that elementary conditions which are motivated by F-theory GUTs lead to strong constraints on the geometry, which significantly reduce the number of suitable models. The complete database of models is available at http://hep.itp.tuwien.ac.at/f-theory/. We work out several examples in more detail.Comment: 35 pages, references adde

Physisorption of an electron in deep surface potentials off a dielectric surface

We study phonon-mediated adsorption and desorption of an electron at dielectric surfaces with deep polarization-induced surface potentials where multi-phonon transitions are responsible for electron energy relaxation. Focusing on multi-phonon processes due to the nonlinearity of the coupling between the external electron and the acoustic bulk phonon triggering the transitions between surface states, we calculate electron desorption times for graphite, MgO, CaO, (\text{Al}_2\text{O}_3), and (\text{SiO}_2) and electron sticking coefficients for (\text{Al}_2\text{O}_3), CaO, and (\text{SiO}_2). To reveal the kinetic stages of electron physisorption, we moreover study the time evolution of the image state occupancy and the energy-resolved desorption flux. Depending on the potential depth and the surface temperature we identify two generic scenarios: (i)adsorption via trapping in shallow image states followed by relaxation to the lowest image state and desorption from that state via a cascade through the second strongly bound image state in not too deep potentials and (ii)adsorption via trapping in shallow image states but followed by a relaxation bottleneck retarding the transition to the lowest image state and desorption from that state via a one step process to the continuum in deep potentials.Comment: 12 pages, 7 figure

Excitation Enhancement of a Quantum Dot Coupled to a Plasmonic Antenna

Plasmonic antennas are key elements to control the luminescence of quantum emitters. However, the antenna's influence is often hidden by quenching losses. Here, the luminescence of a quantum dot coupled to a gold dimer antenna is investigated. Detailed analysis of the multiply excited states quantifies the antenna's influence on the excitation intensity and the luminescence quantum yield separately

Methane-suppressing effect of myristic acid in sheep as affected by dietary calcium and forage proportion

The efficiency of myristic acid (14:0) as a feed additive to suppress CH4 emissions of ruminants was evaluated under different dietary conditions. Six sheep were subjected to a 6 × 6 Latin square arrangement. A supplement of non-esterified 14: 0 (50 g/kg DM) was added to two basal diets differing in their forage:concentrate values (1:1/5 and 1: 0/5), which were adjusted to dietary Ca contents of 4/2 and 9/0 g/ kg DM, respectively. Comparisons were made with the unsupplemented basal diets (4/2 g Ca/kg DM). The 14:0 supplementation decreased (P < 0/001) total tract CH4 release depending on basal diet type (interaction, P < 0/001) and dietary Ca level (P < 0/05, post hoc test). In the concentrate-based diet, 14:0 suppressed CH4 emission by 58 and 47% with 4/2 and 9/0 g Ca/kg DM, respectively. The 14:0 effect was lower (22%) in the forage-based diet and became insignificant with additional Ca. Myristic acid inhibited (P < 0/05) rumen archaea without significantly altering proportions of individual methanogen orders. Ciliate protozoa concentration was decreased (P < 0/05, post hoc test) by 14:0 only in combination with 9/0 g Ca/kg DM. Rumen fluid NH3 concentration and acetate:pro-pionate were decreased (P < 0/05) and water consumption was lower (P < 0/01) with 14:0. The use of 14:0 had no clear effects on total tract organic matter and fibre digestion; this further illustrates that the suppressed methanogenesis resulted from direct effects against methanogens. The present study demonstrated that 14:0 is a potent CH4 inhibitor but, to be effective in CH4 mitigation feeding strategies, interactions with other diet ingredients have to be considere

Late laying hens deposit dietary antioxidants preferentially in the egg and not in the body

The allocation of nutrients in the metabolism of laying hens favors the egg over the body. It is unclear whether this programming also includes micronutrients and antioxidants. This was tested with five by seven 76-wk-old Heisdorf & Nelson Brown Nick layers. They were fed a basal diet low in antioxidants either unchanged (control) or supplemented with 40 IU of α-tocopherylacetate/kg of diet (vitamin E) or 2.5% chokeberry pomace, rose hip, or sage in the last 4 wk before slaughter. The traits measured were subjected to ANOVA. The additives did not affect ADFI, performance, egg quality, carcass, or meat quality. Yolk tocopherol contents were higher with vitamin E and sage compared with control and rose hip treatments. Oxidative stability was more affected in egg yolk powder than in the meat. After 12 wk of storage, yolks from vitamin E-treated hens were lowest in TBA levels (5.0 mg of malondialdehyde/kg), followed by chokeberry (8.7) and sage (8.8). Rose hip (18.1) and control (18.9) treatments were similar. In meat, TBA was slightly decreased after 9 d of storage in meat from chokeberry- and sage-supplemented hens (contrast analysis). In conclusion, antioxidant deposition to the egg seems to be part of the genetic determination of the hen. Adding antioxidants is therefore interesting for layer nutrition in general, and herbal additives allow performing this in a natural way. The programming for partitioning, however, renders the strategic feeding of antioxidants before slaughter, with the goal to increase oxidative stability of spent hen meat rather inefficien

Enteric and manure-derived methane and nitrogen emissions as well as metabolic energy losses in cows fed balanced diets based on maize, barley or grass hay

Ruminant husbandry constitutes the most important source of anthropogenic methane (CH4). In addition to enteric (animal-derived) CH4, excreta are another source of CH4, especially when stored anaerobically. Increasing the proportion of dietary concentrate is often considered as the primary CH4 mitigation option. However, it is unclear whether this is still valid when diets to be compared are energy-balanced. In addition, non-structural carbohydrates and side effects on nitrogen (N) emissions may be important. In this experiment, diet types representing either forage-only or mixed diets were examined for their effects on CH4 and N emissions from animals and their slurries in 18 lactating cows. Apart from a hay-only diet, treatments included two mixed diets consisting of maize stover, pelleted whole maize plants and gluten or barley straw and grain and soy bean meal. The diets were balanced in crude protein and net energy for lactation. After adaptation, data and samples were collected for 8 days including a 2-day CH4 measurement in respiratory chambers. Faeces and urine, combined proportionately according to excretion, were used to determine slurry-derived CH4 and N emissions. Slurry was stored for 15 weeks at either 14°C or 27°C, and temperatures were classified as ‘cool' and ‘warm', respectively. The low-starch hay-only diet had high organic matter and fibre digestibility and proved to be equally effective on the cows' performance as mixed diets. The enteric CH4 formation remained unaffected by the diet except when related to digested fibre. In this case emission was lowest with the hay-only diet (61 v. 88 to 101 g CH4/kg digested NDF). Feeding the hay diet resulted in the highest slurry-CH4 production after 7 weeks of storage at 14°C and 27°C, and after 15 weeks at 14°C. CH4 emissions were, in general, about 10-fold higher at 27°C compared with 14°C but only after 15 weeks of storage. Urinary N losses were highest with the barley diet and lowest with the maize diet. There was a trend towards similar differences in N losses from the slurry of these cows (significant at 14°C). However, contrary to CH4, slurry-N emissions seemed to be temperature-independent. In conclusion, energetically balanced diets proved to be widely equivalent in their emission potential when combining animal and their slurry, this even at a clearly differing forage : concentrate ratio. The variation in CH4 emission from slurry stored shortly or at cold temperature for 15 weeks was of low importance as such conditions did not support methanogenesis in slurry anywa