Analysis of Accordion DNA Stretching Revealed by The Gold Cluster Ruler

A promising new method for measuring intramolecular distances in solution uses small-angle X-ray scattering interference between gold nanocrystal labels (Mathew-Fenn et al, Science, 322, 446 (2008)). When applied to double stranded DNA, it revealed that the DNA length fluctuations are strikingly strong and correlated over at least 80 base pair steps. In other words, the DNA behaves as accordion bellows, with distant fragments stretching and shrinking concertedly. This hypothesis, however, disagrees with earlier experimental and computational observations. This Letter shows that the discrepancy can be rationalized by taking into account the cluster exclusion volume and assuming a moderate long-range repulsion between them. The long-range interaction can originate from an ion exclusion effect and cluster polarization in close proximity to the DNA surface.Comment: 9 pages, 4 figures, to appear in Phys. Rev.

Optimization approaches for the design and operation of open-loop shallow geothermal systems

The optimization of open-loop shallow geothermal systems, which includes both design and operational aspects, is an important research area aimed at improving their efficiency and sustainability and the effective management of groundwater as a shallow geothermal resource. This paper investigates various approaches to address optimization problems arising from such research questions. The identified optimization approaches are thoroughly analyzed based on criteria such as computational efficiency and applicability. Moreover, a novel classification scheme is introduced that categorizes the approaches according to the type of groundwater simulation model (numerical or simplified) and the optimization algorithm used (gradient-based or derivative-free). Finally, a comprehensive review of existing approaches is provided, highlighting their strengths and limitations and offering recommendations for both the use of existing approaches and the development of new ones in this field.Comment: 16 pages, 3 figures; submitted to Advances in Geoscience

Subordination model of anomalous diffusion leading to the two-power-law relaxation responses

We derive a general pattern of the nonexponential, two-power-law relaxation from the compound subordination theory of random processes applied to anomalous diffusion. The subordination approach is based on a coupling between the very large jumps in physical and operational times. It allows one to govern a scaling for small and large times independently. Here we obtain explicitly the relaxation function, the kinetic equation and the susceptibility expression applicable to the range of experimentally observed power-law exponents which cannot be interpreted by means of the commonly known Havriliak-Negami fitting function. We present a novel two-power relaxation law for this range in a convenient frequency-domain form and show its relationship to the Havriliak-Negami one.Comment: 5 pages; 3 figures; corrected versio

Electronic structure and magnetic properties of cobalt intercalated in graphene on Ir(111)

Using a combination of photoemission and x-ray magnetic circular dichroism (XMCD), we characterize the growth and the electronic as well as magnetic structure of cobalt layers intercalated in between graphene and Ir(111). We demonstrate that magnetic ordering exists beyond one monolayer intercalation, and determine the Co orbital and spin magnetic moments. XMCD from the carbon edge shows an induced magnetic moment in the graphene layer, oriented antiparallel to that of cobalt. The XMCD experimental data are discussed in comparison to our results of first-principles electronic structure calculations. It is shown that good agreement between theory and experiment for the Co magnetic moments can be achieved when the local-spin-density approximation plus the Hubbard U (LSDA+U) is used

Composition, structure and stability of RuO_2(110) as a function of oxygen pressure

Using density-functional theory (DFT) we calculate the Gibbs free energy to determine the lowest-energy structure of a RuO_2(110) surface in thermodynamic equilibrium with an oxygen-rich environment. The traditionally assumed stoichiometric termination is only found to be favorable at low oxygen chemical potentials, i.e. low pressures and/or high temperatures. At realistic O pressure, the surface is predicted to contain additional terminal O atoms. Although this O excess defines a so-called polar surface, we show that the prevalent ionic model, that dismisses such terminations on electrostatic grounds, is of little validity for RuO_2(110). Together with analogous results obtained previously at the (0001) surface of corundum-structured oxides, these findings on (110) rutile indicate that the stability of non-stoichiometric terminations is a more general phenomenon on transition metal oxide surfaces.Comment: 12 pages including 5 figures. Submitted to Phys. Rev. B. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Modeling the Emission Processes in Blazars

Blazars are the most violent steady/recurrent sources of high-energy gamma-ray emission in the known Universe. They are prominent emitters of electromagnetic radiation throughout the entire electromagnetic spectrum. The observable radiation most likely originates in a relativistic jet oriented at a small angle with respect to the line of sight. This review starts out with a general overview of the phenomenology of blazars, including results from a recent multiwavelength observing campaign on 3C279. Subsequently, issues of modeling broadband spectra will be discussed. Spectral information alone is not sufficient to distinguish between competing models and to constrain essential parameters, in particular related to the primary particle acceleration and radiation mechanisms in the jet. Short-term spectral variability information may help to break such model degeneracies, which will require snap-shot spectral information on intraday time scales, which may soon be achievable for many blazars even in the gamma-ray regime with the upcoming GLAST mission and current advances in Atmospheric Cherenkov Telescope technology. In addition to pure leptonic and hadronic models of gamma-ray emission from blazars, leptonic/hadronic hybrid models are reviewed, and the recently developed hadronic synchrotron mirror model for TeV gamma-ray flares which are not accompanied by simultaneous X-ray flares (``orphan TeV flares'') is revisited.Comment: Invited Review at "The Multimessenger Approach to Gamma-Ray Sources", Barcelona, Spain, July 2006; submitted to Astrophysics and Space Science. 10 pages, including 6 eps figures. Uses Springer's ApSS macro

Stability of sub-surface oxygen at Rh(111)

Using density-functional theory (DFT) we investigate the incorporation of oxygen directly below the Rh(111) surface. We show that oxygen incorporation will only commence after nearly completion of a dense O adlayer (\theta_tot = 1.0 monolayer) with O in the fcc on-surface sites. The experimentally suggested octahedral sub-surface site occupancy, inducing a site-switch of the on-surface species from fcc to hcp sites, is indeed found to be a rather low energy structure. Our results indicate that at even higher coverages oxygen incorporation is followed by oxygen agglomeration in two-dimensional sub-surface islands directly below the first metal layer. Inside these islands, the metastable hcp/octahedral (on-surface/sub-surface) site combination will undergo a barrierless displacement, introducing a stacking fault of the first metal layer with respect to the underlying substrate and leading to a stable fcc/tetrahedral site occupation. We suggest that these elementary steps, namely, oxygen incorporation, aggregation into sub-surface islands and destabilization of the metal surface may be more general and precede the formation of a surface oxide at close-packed late transition metal surfaces.Comment: 9 pages including 9 figure files. Submitted to Phys. Rev. B. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Theory of solvation in polar nematics

We develop a linear response theory of solvation of ionic and dipolar solutes in anisotropic, axially symmetric polar solvents. The theory is applied to solvation in polar nematic liquid crystals. The formal theory constructs the solvation response function from projections of the solvent dipolar susceptibility on rotational invariants. These projections are obtained from Monte Carlo simulations of a fluid of dipolar spherocylinders which can exist both in the isotropic and nematic phase. Based on the properties of the solvent susceptibility from simulations and the formal solution, we have obtained a formula for the solvation free energy which incorporates experimentally available properties of nematics and the length of correlation between the dipoles in the liquid crystal. Illustrative calculations are presented for the Stokes shift and Stokes shift correlation function of coumarin-153 in 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4,4-n-heptyl-cyanopiphenyl (7CB) solvents as a function of temperature in both the nematic and isotropic phase.Comment: 19 pages, 9 figure

High-Energy Neutrinos from Photomeson Processes in Blazars

An important radiation field for photomeson neutrino production in blazars is shown to be the radiation field external to the jet. Assuming that protons are accelerated with the same power as electrons and injected with a -2 number spectrum, we predict that km^2 neutrino telescopes will detect about 1-to-several neutrinos per year from flat spectrum radio quasars (FSRQs) such as 3C 279. The escaping high-energy neutron and photon beams transport inner jet energy far from the black-hole engine, and could power synchrotron X-ray jets and FR II hot spots and lobes.Comment: revised paper (minor revisions), accepted for publication in PR

The HERMES Back Drift Chambers

The tracking system of the HERMES spectrometer behind the bending magnet consists of two pairs of large planar 6-plane drift chambers. The design and performance of these chambers is described. This description comprises details on the mechanical and electronical design, information about the gas mixture used and its properties, results on alignment, calibration, resolution, and efficiencies, and a discussion of the experience gained through the first three years of operation.Comment: 21 pages, LaTex, 16 figures include