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.

Constraining Relativistic Bow Shock Properties in Rotation-Powered Millisecond Pulsar Binaries

Multiwavelength followup of unidentified Fermi sources has vastly expanded the number of known galactic-field "black widow" and "redback" millisecond pulsar binaries. Focusing on their rotation-powered state, we interpret the radio to X-ray phenomenology in a consistent framework. We advocate the existence of two distinct modes differing in their intrabinary shock orientation, distinguished by the phase-centering of the double-peaked X-ray orbital modulation originating from mildly-relativistic Doppler boosting. By constructing a geometric model for radio eclipses, we constrain the shock geometry as functions of binary inclination and shock stand-off $R_0$. We develop synthetic X-ray synchrotron orbital light curves and explore the model parameter space allowed by radio eclipse constraints applied on archetypal systems B1957+20 and J1023+0038. For B1957+20, from radio eclipses the stand-off is $R_0 \sim 0.15$ -- $0.3$ fraction of binary separation from the companion center, depending on the orbit inclination. Constructed X-ray light curves for B1957+20 using these values are qualitatively consistent with those observed, and we find occultation of the shock by the companion as a minor influence, demanding significant Doppler factors to yield double peaks. For J1023+0038, radio eclipses imply $R_0 \lesssim 0.4$ while X-ray light curves suggest $0.1\lesssim R_0 \lesssim 0.3$ (from the pulsar). Degeneracies in the model parameter space encourage further development to include transport considerations. Generically, the spatial variation along the shock of the underlying electron power-law index should yield energy-dependence in the shape of light curves motivating future X-ray phase-resolved spectroscopic studies to probe the unknown physics of pulsar winds and relativistic shock acceleration therein.Comment: Accepted to ApJ, 36 pages, 15 figures; comments welcom

Metastable precursors during the oxidation of the Ru(0001) surface

Using density-functional theory, we predict that the oxidation of the Ru(0001) surface proceeds via the accumulation of sub-surface oxygen in two-dimensional islands between the first and second substrate layer. This leads locally to a decoupling of an O-Ru-O trilayer from the underlying metal. Continued oxidation results in the formation and stacking of more of these trilayers, which unfold into the RuO_2(110) rutile structure once a critical film thickness is exceeded. Along this oxidation pathway, we identify various metastable configurations. These are found to be rather close in energy, indicating a likely lively dynamics between them at elevated temperatures, which will affect the surface chemical and mechanical properties of the material.Comment: 11 pages including 9 figures. Submitted to Phys. Rev. B. Related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

X-ray variability patterns in blazars

We study the expected variability patterns of blazars within the two-zone acceleration model putting special emphasis on flare shapes and spectral lags. We solve semi-analytically the kinetic equations which describe the particle evolution in the acceleration and radiation zone. We then perturb the solutions by introducing Lorentzian variations in its key parameters and examine the flaring behavior of the system. We apply the above to the X-ray observations of blazar 1ES 1218+304 which exhibited a hard lag behavior during a flaring episode and discuss possibilities of producing it within the context of our model. The steady-state radio to X-rays emission of 1ES 1218+304 can be reproduced with parameters which lie well within the ones generally accepted from blazar modeling. Additionally, we find that the best way to explain its flaring behavior is by varying the rate of particles injected in the acceleration zone.Comment: accepted by A&

Feller Processes: The Next Generation in Modeling. Brownian Motion, L\'evy Processes and Beyond

We present a simple construction method for Feller processes and a framework for the generation of sample paths of Feller processes. The construction is based on state space dependent mixing of L\'evy processes. Brownian Motion is one of the most frequently used continuous time Markov processes in applications. In recent years also L\'evy processes, of which Brownian Motion is a special case, have become increasingly popular. L\'evy processes are spatially homogeneous, but empirical data often suggest the use of spatially inhomogeneous processes. Thus it seems necessary to go to the next level of generalization: Feller processes. These include L\'evy processes and in particular Brownian motion as special cases but allow spatial inhomogeneities. Many properties of Feller processes are known, but proving the very existence is, in general, very technical. Moreover, an applicable framework for the generation of sample paths of a Feller process was missing. We explain, with practitioners in mind, how to overcome both of these obstacles. In particular our simulation technique allows to apply Monte Carlo methods to Feller processes.Comment: 22 pages, including 4 figures and 8 pages of source code for the generation of sample paths of Feller processe

Computational Simulations of the Lateral-Photovoltage-Scanning-Method

The major task for the Lateral-Photovoltage-Scanning-Method is to detect doping striations and the shape of the solid-liquid-interface of an indirect semiconductor crystal. This method is sensitive to the gradient of the charge carrier density. Attempting to simulate the signal generation of the LPS-Method, we are using a three dimensional Finite Volume approach for solving the van Roosbroeck equations with COMSOL Multiphysics in a silicon sample. We show that the simulated LPS-voltage is directly proportional to the gradient of a given doping distribution, which is also the case for the measured LPS-voltage

Photon-induced oxidation of graphene/Ir(111) by SO₂ adsorption

We prepare a single layer of graphene oxide by adsorption and subsequent photo-dissociation of SO2 on graphene/Ir(111). Epoxidic oxygen is formed as the main result of this process on graphene, as judged from the appearance of characteristic spectroscopic features in the C 1s and O 1s core level lines. The different stages of decomposition of SO2 into its photo-fragments are examined during the oxidation process. NEXAFS at the carbon K edge reveals a strong disturbance of the graphene backbone after oxidation and upon SO adsorption. The oxide phase is stable up to room temperature, and is fully reversible upon annealing at elevated temperatures. A band gap opening of 330 ± 60 meV between the valence and conduction bands is observed in the graphene oxide phase

Photon-Photon Absorption of Very High Energy Gamma-Rays from Microquasars: Application to LS 5039

Very high energy (VHE) gamma-rays have recently been detected from the Galactic black-hole candidate and microquasar LS 5039. A plausible site for the production of these VHE gamma-rays is the region close to the mildly relativistic outflow. However, at distances comparable to the binary separation, the intense photon field of the stellar companion will lead to substantial gamma-gamma absorption of VHE gamma-rays. If the system is viewed at a substantial inclination (i > 0), this absorption feature will be modulated on the orbital period of the binary as a result of a phase-dependent stellar-radiation intensity and pair-production threshold. We apply our results to LS 5039 and find that (1) gamma-gamma absorption effects will be substantial if the photon production site is located at a distance from the central compact object of the order of the binary separation (~ 2.5e12 cm) or less; (2) the gamma-gamma absorption depth will be largest at a few hundred GeV, leading to a characteristic absorption trough; (3) the gamma-gamma absorption feature will be strongly modulated on the orbital period of the binary, characterized by a spectral hardening accompanying periodic dips of the VHE gamma-ray flux; and (4) gamma rays can escape virtually unabsorbed, even from within ~ 10^{12} cm, when the star is located behind the production site as seen by the observer.Comment: Submitted to ApJ Letters. AASTeX, 12 ms pages, including 4 eps figure