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.

Timing Signatures of the Internal-Shock Model for Blazars

We investigate the spectral and timing signatures of the internal-shock model for blazars. For this purpose, we develop a semi-analytical model for the time-dependent radiative output from internal shocks arising from colliding relativistic shells in a blazar jet. The emission through synchrotron and synchrotron-self Compton (SSC) radiation as well as Comptonization of an isotropic external radiation field are taken into account. We evaluate the discrete correlation function (DCF) of the model light curves in order to evaluate features of photon-energy dependent time lags and the quality of the correlation, represented by the peak value of the DCF. The almost completely analytic nature of our approach allows us to study in detail the influence of various model parameters on the resulting spectral and timing features. This paper focuses on a range of parameters in which the gamma-ray production is dominated by Comptonization of external radiation, most likely appropriate for gamma-ray bright flat-spectrum radio quasars (FSRQs) or low-frequency peaked BL Lac objects (LBLs). In most cases relevant for FSRQs and LBLs, the variability of the optical emission is highly correlated with the X-ray and high-energy (HE: > 100 MeV) gamma-ray emission. Our baseline model predicts a lead of the optical variability with respect to the higher-energy bands by 1 - 2 hours and of the HE gamma-rays before the X-rays by about 1 hour. We show that variations of certain parameters may lead to changing signs of inter-band time lags, potentially explaining the lack of persistent trends of time lags in most blazars.Comment: Accepted for publication in Ap

A New Model for the Hard Time Lags in Black Hole X-Ray Binaries

The time-dependent Comptonized output of a cool soft X-ray source drifting inward through an inhomogeneous hot inner disk or corona is numerically simulated. We propose that this scenario can explain from first principles the observed trends in the hard time lags and power spectra of the rapid aperiodic variability of the X-ray emission of Galactic black-hole candidates.Comment: 10 pages, including 2 figures; uses epsf.sty, rotate.sty; accepted for ApJ Letter

Conversion of relativistic pair energy into radiation in the jets of active galactic nuclei

It is generally accepted that relativistic jet outflows power the nonthermal emission from active galactic nuclei (AGN). The composition of these jets -- leptonic versus hadronic -- is still under debate. We investigate the microphysical details of the conversion process of the kinetic energy in collimated relativistic pair outflows into radiation through interactions with the ambient interstellar medium. Viewed from the coordinate system comoving with the pair outflow, the interstellar protons and electrons represent a proton-electron beam propagating with relativistic speed in the pair plasma. We demonstrate that the beam excites both electrostatic and low-frequency magnetohydrodynamic Alfven-type waves via a two-stream instability in the pair background plasma, and we calculate the time evolution of the distribution functions of the beam particles and the generated plasma wave turbulence power spectra. For standard AGN jet outflow and environment parameters we show that the initial beam distributions of interstellar protons and electrons quickly relax to plateau-distributions in parallel momentum, transferring thereby one-half of the initial energy density of the beam particles to electric field fluctuations of the generated electrostatic turbulence. On considerably longer time scales, the plateaued interstellar electrons and protons will isotropise by their self-generated transverse turbulence and thus be picked-up in the outflow pair plasma. These longer time scales are also characteristic for the development of transverse hydromagnetic turbulence from the plateaued electrons and protons. This hydromagnetic turbulence upstream and downstream is crucial for diffusive shock acceleration to operate at external or internal shocks associated with pair outflows.Comment: A&A in pres

Microphase separation in polyelectrolytic diblock copolymer melt : weak segregation limit

We present a generalized theory of microphase separation for charged-neutral diblock copolymer melt. Stability limit of the disordered phase for salt-free melt has been calculated using Random Phase Approximation (RPA) and self-consistent field theory (SCFT). Explicit analytical free energy expressions for different classical ordered microstructures (lamellar, cylinder and sphere) are presented. We demonstrate that chemical mismatch required for the onset of microphase separation ($\chi^{\star} N$) in charged-neutral diblock melt is higher and the period of ordered microstructures is lower than those for the corresponding neutral-neutral diblock system. Theoretical predictions on the period of ordered structures in terms of Coulomb electrostatic interaction strength, chain length, block length, and the chemical mismatch between blocks are presented. SCFT has been used to go beyond the stability limit, where electrostatic potential and charge distribution are calculated self-consistently. Stability limits calculated using RPA are in perfect agreement with the corresponding SCFT calculations. Limiting laws for stability limit and the period of ordered structures are presented and comparisons are made with an earlier theory. Also, transition boundaries between different morphologies have been investigated

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

Equation of Motion for the Solvent Polarization Apparent Charges in the Polarizable Continuum Model: Application to Time-Dependent CI

The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion (EOM) for the apparent solvent polarization charges that generate the reaction field in the Polarizable Continuum Model (PCM) for solvation and we have coupled them to a real-time time-dependent density functional theory (RT TDDFT) description of the solute [Corni et al. J. Phys. Chem. A 119, 5405 (2014)]. Here we present an extension of the EOM-PCM approach to a Time-Dependent Configuration Interaction (TD CI) description of the solute dynamics, which is free from the qualitative artifacts of RT TDDFT in the adiabatic approximation. As tests of the developed approach, we investigate the solvent Debye relaxation after an electronic excitation of the solute obtained either by a $\pi$ pulse of light or by assuming the idealized sudden promotion to the excited state. Moreover, we present EOM for the Onsager solvation model and we compare the results with PCM. The developed approach provides qualitatively correct real-time evolutions and is promising as a general tool to investigate the electron dynamics elicited by external electromagnetic fields for molecules in solution.Comment: This is the final peer-reviewed manuscript accepted for publication in The Journal of Chemical Physics. Copyright by AIP, the final published version can be found at http://scitation.aip.org/content/aip/journal/jcp/146/6/10.1063/1.497562

The long-term optical spectral variability of BL Lacertae

We present the results from a study of the long-term optical spectral variations of BL Lacertae, using the long and well-sampled B and R-band light curves of the Whole Earth Blazar Telescope (WEBT) collaboration, binned on time intervals of 1 day. The relation between spectral slope and flux (the spectrum gets bluer as the source flux increases) is well described by a power-law model, although there is significant scatter around the best-fitting model line. To some extent, this is due to the spectral evolution of the source (along well-defined loop-like structures) during low-amplitude events, which are superimposed on the major optical flares, and evolve on time scales of a few days. The "bluer-when-brighter" mild chromatism of the long-term variations of the source can be explained if the flux increases/decreases faster in the B than in the R band. The B and R-band variations are well correlated, with no significant, measurable delays larger than a few days. On the other hand, we find that the spectral variations lead those in the flux light curves by ~ 4 days. Our results can be explained in terms of Doppler factor variations due to changes in the viewing angle of a curved and inhomogeneous emitting jet.Comment: 7 pages, 5 figures, accepted for publication in A&