Can one predict DNA Transcription Start Sites by studying bubbles?

It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the Peyrard-Bishop-Dauxois model, seems to point in this direction. However, sufficiently large bubbles appear only seldom which makes an accurate calculation difficult even for minimal models. In this letter, we introduce a new method that is orders of magnitude faster than MD. Using this method we show that the present evidence is unsubstantiated.Comment: 4 pages, 3 figures, accepted for publication in physical review letter

Evidence of non-thermal X-ray emission from HH 80

Protostellar jets appear at all stages of star formation when the accretion process is still at work. Jets travel at velocities of hundreds of km/s, creating strong shocks when interacting with interstellar medium. Several cases of jets have been detected in X-rays, typically showing soft emission. For the first time, we report evidence of hard X-ray emission possibly related to non-thermal processes not explained by previous models of the post-shock emission predicted in the jet/ambient interaction scenario. HH 80 is located at the south head of the jet associated to the massive protostar IRAS 18162-2048. It shows soft and hard X-ray emission in regions that are spatially separated, with the soft X-ray emission region situated behind the region of hard X-ray emission. We propose a scenario for HH 80 where soft X-ray emission is associated to thermal processes from the interaction of the jet with denser ambient matter and the hard X-ray emission is produced by synchrotron radiation at the front shock.Comment: Accepted for publication in ApJ

A likely magnetic activity cycle for the exoplanet host M dwarf GJ 3512

Current radial velocity data from specialized instruments contain a large amount of information that may pass unnoticed if their analysis is not accurate. The joint use of Bayesian inference tools and frequency analysis has been shown effective to reveal exoplanets but they have been used less frequently to investigate stellar activity. We intend to use radial velocity data of the exoplanet host star GJ 3512 to investigate its magnetic activity. Our study includes the analysis of the photometric data available. The main objectives of our work are to constrain the orbital parameters of the exoplanets in the system, to determine the current level of activity of the star and to derive an activity cycle length for it. An adaptive importance sampling method was used to determine the parameters of the exoplanets orbit. Generalized Lomb-Scargle periodograms were constructed with both radial velocity curve and photometric data. A careful analysis of the harmonic frequencies was conducted in each periodogram. Our fit to multiple Keplerian orbits constrained the orbital parameters of two giant gas planets orbiting the star GJ 3512. The host star showed an increase of its magnetic activity during the last observing campaign. The accurate fit of the radial velocity curve data to the multi-Keplerian orbit permitted to reveal the star rotation in the residuals of the best fit and estimate an activity cycle length of ~ 14 years.Comment: Accepted for publication in the Astronomical Journal. 15 pages, 11 figure

AE Aurigae: first detection of non-thermal X-ray emission from a bow shock produced by a runaway star

Runaway stars produce shocks when passing through interstellar medium at supersonic velocities. Bow shocks have been detected in the mid-infrared for several high-mass runaway stars and in radio waves for one star. Theoretical models predict the production of high-energy photons by non-thermal radiative processes in a number sufficiently large to be detected in X-rays. To date, no stellar bow shock has been detected at such energies. We present the first detection of X-ray emission from a bow shock produced by a runaway star. The star is AE Aur, which was likely expelled from its birthplace by the encounter of two massive binary systems and now is passing through the dense nebula IC 405. The X-ray emission from the bow shock is detected at 30" to the northeast of the star, coinciding with an enhancement in the density of the nebula. From the analysis of the observed X-ray spectrum of the source and our theoretical emission model, we confirm that the X-ray emission is produced mainly by inverse Compton upscattering of infrared photons from dust in the shock front.Comment: Accepted for publication in the Astrophysical Journal with number ApJ, 757, L6. Four figure

The ultracool dwarf DENIS-P J104814.7-395606. Chromospheres and coronae at the low-mass end of the main-sequence

We have obtained an XMM-Newton observation and a broad-band spectrum from the ultraviolet to the near infrared with X-Shooter for one of the nearest M9 dwarfs, DENIS-P J1048-3956 (4pc). We integrate these data by a compilation of activity parameters for ultracool dwarfs from the literature with the aim to advance our understanding of these objects by comparing them to early-M type dwarf stars and the Sun. Our deep XMM-Newton observation has led to the first X-ray detection of DENIS-P J1048-3956 (log Lx = 25.1) as well as the first measurement of its V band brightness (V = 17.35mag). Flux-flux relations between X-ray and chromospheric activity indicators are here for the first time extended into the regime of the ultracool dwarfs. The approximate agreement of DENIS-P J1048-3956 and other ultracool dwarfs with flux-flux relations for early-M dwarfs suggests that the same heating mechanisms work in the atmospheres of ultracool dwarfs, albeit weaker as judged from their lower fluxes. The observed Balmer decrements of DENIS-P J1048-3956 are compatible with optically thick plasma in LTE at low, nearly photospheric temperature or optically thin LTE plasma at 20000K. Describing the decrements with CaseB recombination requires different emitting regions for Halpha and the higher Balmer lines. The high observed Halpha/Hbeta flux ratio is also poorly fitted by the optically thin models. We derive a similarly high value for the Halpha/Hbeta ratio of vB10 and LHS2065 and conclude that this may be a characteristic of ultracool dwarfs. We add DENIS-P J1048-3956 to the list of ultracool dwarfs detected in both the radio and the X-ray band. The Benz-Guedel relation between radio and X-ray luminosity of late-type stars is well-known to be violated by ultracool dwarfs. We speculate on the presence of two types of ultracool dwarfs with distinct radio and X-ray behavior.Comment: accepted for publication in Astronomy & Astrophysic

An X-ray study of the SNR G344.7-0.1 and the central object CXOU J170357.8-414302

Aims. We report results of an X-ray study of the supernova remnant (SNR) G344.7-0.1 and the point-like X-ray source located at the geometrical center of the SNR radio structure. Methods. The morphology and spectral properties of the remnant and the central X-ray point-like source were studied using data from the XMM-Newton and Chandra satellites. Archival radio data and infrared Spitzer observations at 8 and 24 $\mu$m were used to compare and study its multi-band properties at different wavelengths. Results. The XMM-Newton and Chandra observations reveal that the overall X-ray emission of G344.7-0.1 is extended and correlates very well with regions of bright radio and infrared emission. The X-ray spectrum is dominated by prominent atomic emission lines. These characteristics suggest that the X-ray emission originated in a thin thermal plasma, whose radiation is represented well by a plane-parallel shock plasma model (PSHOCK). Our study favors the scenario in which G344.7-0.1 is a 6 x 10^3 year old SNR expanding in a medium with a high density gradient and is most likely encountering a molecular cloud on the western side. In addition, we report the discovery of a soft point-like X-ray source located at the geometrical center of the radio SNR structure. The object presents some characteristics of the so-called compact central objects (CCO). However, its neutral hydrogen absorption column (N_{H}) is inconsistent with that of the SNR. Coincident with the position of the source, we found infrared and optical objects with typical early-K star characteristics. The X-ray source may be a foreground star or the CCO associated with the SNR. If this latter possibility were confirmed, the point-like source would be the farthest CCO detected so far and the eighth member of the new population of isolated and weakly magnetized neutron stars.Comment: 9 pages, 8 figures, accepted for publication in Astronomy and Astrophysics. Higher resolution figures can be seen on A&

Electrical characterization of single molecule and Langmuir–Blodgett monomolecular films of a pyridine-terminated oligo(phenylene-ethynylene) derivative

Monolayer Langmuir–Blodgett (LB) films of 1,4-bis(pyridin-4-ylethynyl)benzene (1) together with the “STM touch-to-contact” method have been used to study the nature of metal–monolayer–metal junctions in which the pyridyl group provides the contact at both molecule–surface interfaces. Surface pressure vs area per molecule isotherms and Brewster angle microscopy images indicate that 1 forms true monolayers at the air–water interface. LB films of 1 were fabricated by deposition of the Langmuir films onto solid supports resulting in monolayers with surface coverage of 0.98 × 10-9 mol·cm-2. The morphology of the LB films that incorporate compound 1 was studied using atomic force microscopy (AFM). AFM images indicate the formation of homogeneous, monomolecular films at a surface pressure of transference of 16 mN·m-1. The UV–vis spectra of the Langmuir and LB films reveal that 1 forms two dimensional J-aggregates. Scanning tunneling microscopy (STM), in particular the “STM touch-to-contact” method, was used to determine the electrical properties of LB films of 1. From these STM studies symmetrical I–V curves were obtained. A junction conductance of 5.17 × 10-5 G0 results from the analysis of the pseudolinear (ohmic) region of the I–V curves. This value is higher than that of the conductance values of LB films of phenylene-ethynylene derivatives contacted by amines, thiols, carboxylate, trimethylsilylethynyl or acetylide groups. In addition, the single molecule I–V curve of 1 determined using the I(s) method is in good agreement with the I–V curve obtained for the LB film, and both curves fit well with the Simmons model. Together, these results not only indicate that the mechanism of transport through these metal–molecule–metal junctions is non-reso- nant tunneling, but that lateral interactions between molecules within the LB film do not strongly influence the molecule conduc- tance. The results presented here complement earlier studies of single molecule conductance of 1 using STM-BJ methods, and support the growing evidence that the pyridyl group is an efficient and effective anchoring group in sandwiched metal–monolayer–metal junctions prepared under a number of different conditions