On the kinematic deconvolution of the local neighbourhood luminosity function

A method for inverting the statistical star counts equation, including proper motions, is presented; in order to break the degeneracy in that equation it uses the supplementary constraints required by dynamical consistency. The inversion gives access to both the kinematics and the luminosity function of each population in three r\'egimes: the singular ellipsoid, the constant ratio Schwarzschild ellipsoid plane parallel models and the epicyclic model. This more realistic model is taylored to account for local neighbourhood density and velocity distribution. The first model is fully investigated both analytically and via means of a non-parametric inversion technique, while the second model is shown to be formally its equivalent. The effect of noise and incompleteness in apparent magnitude is investigated. The third model is investigated via a 5D+2D non-parametric inversion technique where positivity of the underlying luminosity function is explicitely accounted for. It is argued that its future application to data such as the Tycho catalogue (and in the upcoming satellite GAIA) could lead -- provided the vertical potential, and/or the asymmetric drift or w_0 are known -- to a non-parametric determination of the local neighbourhood luminosity function without any reference to stellar evolution tracks. It should also yield the proportion of stars for each kinematic component and a kinematic diagnostic to split the thin disk from the thick disk or the halo.Comment: 18 pages, LateX (or Latex, etc), mnras, accepted for publicatio

Towards the Rosetta Stone of planet formation

Transiting exoplanets (TEPs) observed just about 10 Myrs after formation of their host systems may serve as the Rosetta Stone for planet formation theories. They would give strong constraints on several aspects of planet formation, e.g. time-scales (planet formation would then be possible within 10 Myrs), the radius of the planet could indicate whether planets form by gravitational collapse (being larger when young) or accretion growth (being smaller when young). We present a survey, the main goal of which is to find and then characterise TEPs in very young open clusters.Comment: Poster contribution to Detection and Dynamics of Transiting Exoplanets (Haute Provence Observatory Colloquium, 23-27 August 2010

Early post-metamorphic, Carboniferous blastoid reveals the evolution and development of the digestive system in echinoderms

Inferring the development of the earliest echinoderms is critical to uncovering the evolutionary assembly of the phylum-level body plan but has long proven problematic because early ontogenetic stages are rarely preserved as fossils. Here, we use synchrotron tomography to describe a new early post-metamorphic blastoid echinoderm from the Carboniferous (approx. 323 Ma) of China. The resulting three-dimensional reconstruction reveals a U-shaped tubular structure in the fossil interior, which is interpreted as the digestive tract. Comparisons with the developing gut of modern crinoids demonstrate that crinoids are an imperfect analogue for many extinct groups. Furthermore, consideration of our findings in a phylogenetic context allows us to reconstruct the evolution and development of the digestive system in echinoderms more broadly; there was a transition from a straight to a simple curved gut early in the phylum's evolution, but additional loops and coils of the digestive tract (as seen in crinoids) were not acquired until much later

Transit Timing Analysis in the HAT-P-32 system

We present the results of 45 transit observations obtained for the transiting exoplanet HAT-P-32b. The transits have been observed using several telescopes mainly throughout the YETI network. In 25 cases, complete transit light curves with a timing precision better than $1.4\:$min have been obtained. These light curves have been used to refine the system properties, namely inclination $i$, planet-to-star radius ratio $R_\textrm{p}/R_\textrm{s}$, and the ratio between the semimajor axis and the stellar radius $a/R_\textrm{s}$. First analyses by Hartman et al. (2011) suggest the existence of a second planet in the system, thus we tried to find an additional body using the transit timing variation (TTV) technique. Taking also literature data points into account, we can explain all mid-transit times by refining the linear ephemeris by 21ms. Thus we can exclude TTV amplitudes of more than $\sim1.5$min.Comment: MNRAS accepted; 13 pages, 10 figure

Constraints on a second planet in the WASP-3 system

There have been previous hints that the transiting planet WASP-3 b is accompanied by a second planet in a nearby orbit, based on small deviations from strict periodicity of the observed transits. Here we present 17 precise radial velocity measurements and 32 transit light curves that were acquired between 2009 and 2011. These data were used to refine the parameters of the host star and transiting planet. This has resulted in reduced uncertainties for the radii and masses of the star and planet. The radial-velocity data and the transit times show no evidence for an additional planet in the system. Therefore, we have determined the upper limit on the mass of any hypothetical second planet, as a function of its orbital period.Comment: Accepted for publication in The Astronomical Journa

YETI observations of the young transiting planet candidate CVSO 30 b

CVSO 30 is a unique young low-mass system, because, for the first time, a close-in transiting and a wide directly imaged planet candidates are found around a common host star. The inner companion, CVSO 30 b, is the first possible young transiting planet orbiting a previously known weak-lined T-Tauri star. With five telescopes of the 'Young Exoplanet Transit Initiative' (YETI) located in Asia, Europe and South America we monitored CVSO 30 over three years in a total of 144 nights and detected 33 fading events. In two more seasons we carried out follow-up observations with three telescopes. We can confirm that there is a change in the shape of the fading event between different observations and that the fading event even disappears and reappears. A total of 38 fading event light curves were simultaneously modelled. We derived the planetary, stellar, and geometrical properties of the system and found them slightly smaller but in agreement with the values from the discovery paper. The period of the fading event was found to be 1.36 s shorter and 100 times more precise than the previous published value. If CVSO 30 b would be a giant planet on a precessing orbit, which we cannot confirm, yet, the precession period may be shorter than previously thought. But if confirmed as a planet it would be the youngest transiting planet ever detected and will provide important constraints on planet formation and migration time-scales.Comment: 14 pages (20 with appendix), 7 figures (16 with appendix), 6 tables (7 with appendix

Multi-site campaign for transit timing variations of WASP-12 b: possible detection of a long-period signal of planetary origin

The transiting planet WASP-12 b was identified as a potential target for transit timing studies because a departure from a linear ephemeris was reported in the literature. Such deviations could be caused by an additional planet in the system. We attempt to confirm the existence of claimed variations in transit timing and interpret its origin. We organised a multi-site campaign to observe transits by WASP-12 b in three observing seasons, using 0.5-2.6-metre telescopes. We obtained 61 transit light curves, many of them with sub-millimagnitude precision. The simultaneous analysis of the best-quality datasets allowed us to obtain refined system parameters, which agree with values reported in previous studies. The residuals versus a linear ephemeris reveal a possible periodic signal that may be approximated by a sinusoid with an amplitude of 0.00068+/-0.00013 d and period of 500+/-20 orbital periods of WASP-12 b. The joint analysis of timing data and published radial velocity measurements results in a two-planet model which better explains observations than single-planet scenarios. We hypothesize that WASP-12 b might be not the only planet in the system and there might be the additional 0.1 M_Jup body on a 3.6-d eccentric orbit. A dynamical analysis indicates that the proposed two-planet system is stable over long timescales.Comment: Accepted for publication in A&

Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles

The ability to interact with different partners is one of the most important features in proteins. Proteins that bind a large number of partners (hubs) have been often associated with intrinsic disorder. However, many examples exist of hubs with an ordered structure, and evidence of a general mechanism promoting promiscuity in ordered proteins is still elusive. An intriguing hypothesis is that promiscuous binding sites have specific dynamical properties, distinct from the rest of the interface and pre-existing in the protein isolated state. Here, we present the first comprehensive study of the intrinsic dynamics of promiscuous residues in a large protein data set. Different computational methods, from coarse-grained elastic models to geometry-based sampling methods and to full-atom Molecular Dynamics simulations, were used to generate conformational ensembles for the isolated proteins. The flexibility and dynamic correlations of interface residues with a different degree of binding promiscuity were calculated and compared considering side chain and backbone motions, the latter both on a local and on a global scale. The study revealed that (a) promiscuous residues tend to be more flexible than nonpromiscuous ones, (b) this additional flexibility has a higher degree of organization, and (c) evolutionary conservation and binding promiscuity have opposite effects on intrinsic dynamics. Findings on simulated ensembles were also validated on ensembles of experimental structures extracted from the Protein Data Bank (PDB). Additionally, the low occurrence of single nucleotide polymorphisms observed for promiscuous residues indicated a tendency to preserve binding diversity at these positions. A case study on two ubiquitin-like proteins exemplifies how binding promiscuity in evolutionary related proteins can be modulated by the fine-tuning of the interface dynamics. The interplay between promiscuity and flexibility highlighted here can inspire new directions in protein-protein interaction prediction and design methods. © 2013 American Chemical Society

MOLA: a bootable, self-configuring system for virtual screening using AutoDock4/Vina on computer clusters

<p>Abstract</p> <p>Background</p> <p>Virtual screening of small molecules using molecular docking has become an important tool in drug discovery. However, large scale virtual screening is time demanding and usually requires dedicated computer clusters. There are a number of software tools that perform virtual screening using AutoDock4 but they require access to dedicated Linux computer clusters. Also no software is available for performing virtual screening with Vina using computer clusters. In this paper we present MOLA, an easy-to-use graphical user interface tool that automates parallel virtual screening using AutoDock4 and/or Vina in bootable non-dedicated computer clusters.</p> <p>Implementation</p> <p>MOLA automates several tasks including: ligand preparation, parallel AutoDock4/Vina jobs distribution and result analysis. When the virtual screening project finishes, an open-office spreadsheet file opens with the ligands ranked by binding energy and distance to the active site. All results files can automatically be recorded on an USB-flash drive or on the hard-disk drive using VirtualBox. MOLA works inside a customized Live CD GNU/Linux operating system, developed by us, that bypass the original operating system installed on the computers used in the cluster. This operating system boots from a CD on the master node and then clusters other computers as slave nodes via ethernet connections.</p> <p>Conclusion</p> <p>MOLA is an ideal virtual screening tool for non-experienced users, with a limited number of multi-platform heterogeneous computers available and no access to dedicated Linux computer clusters. When a virtual screening project finishes, the computers can just be restarted to their original operating system. The originality of MOLA lies on the fact that, any platform-independent computer available can he added to the cluster, without ever using the computer hard-disk drive and without interfering with the installed operating system. With a cluster of 10 processors, and a potential maximum speed-up of 10x, the parallel algorithm of MOLA performed with a speed-up of 8,64× using AutoDock4 and 8,60× using Vina.</p