A class of symplectic integrators with adaptive timestep for separable Hamiltonian systems

Symplectic integration algorithms are well-suited for long-term integrations of Hamiltonian systems because they preserve the geometric structure of the Hamiltonian flow. However, this desirable property is generally lost when adaptive timestep control is added to a symplectic integrator. We describe an adaptive-timestep symplectic integrator that can be used if the Hamiltonian is the sum of kinetic and potential energy components and the required timestep depends only on the potential energy (e.g. test-particle integrations in fixed potentials). In particular, we describe an explicit, reversible, symplectic, leapfrog integrator for a test particle in a near-Keplerian potential; this integrator has timestep proportional to distance from the attracting mass and has the remarkable property of integrating orbits in an inverse-square force field with only "along-track" errors; i.e. the phase-space shape of a Keplerian orbit is reproduced exactly, but the orbital period is in error by O(1/N^2), where N is the number of steps per period.Comment: 24 pages, 3 figures, submitted to Astronomical Journal; minor errors in equations and one figure correcte

Vombat: An Open Source Tool for Creating Stratigraphic Logs from Virtual Outcrops

An open source tool, Vombat , is presented that is designed to operate on Virtual Outcrop Models of sedimentary rocks, with the specific aim of assisting the stratigraphic analysis and interpretation. Vombat makes it possible to estimate the average attitude of the bedding and to create one or more attitude-aligned stratigraphic reference frames. This allows Vombat to extract continuous stratigraphic logs of any property associated with the point clouds (e.g. the lidar intensity or RGB color). Stratigraphic logs produced by Vombat can be compared and correlated to typical outcrop logs and petrophysical logs obtained from boreholes (e.g. gamma ray logs) and can provide information about the lithological variations in a stratigraphic succession. Furthermore, Vombat stratigraphic reference frames can be used to associate a stratigraphic position (a depth in the stratigraphic column) to any observation made on the outcrop, allowing visualization in 3D (on the virtual outcrop model) and 1D (on a stratigraphic column) for any collected data. All the geological objects created in the virtual environment can then be saved. The tool has been developed to be user-friendly and is constituted by a dynamically loaded plugin for the open source software CloudCompare

Carnian (Late Triassic) C-isotope excursions, environmental changes, and biotic turnover: a global perturbation of the Earth's surface system

Here we present the second part of the special thematic issue on the Carnian Pluvial Episode (CPE). In this issue, two works on terrestrial sedimentological and floral changes linked to the CPE, and new carbon isotope records from Oman and China are presented. The papers published in this issue complement those contained in volume 175 issue 6; they altogether give an almost complete vision of the state-of-the-art about the CPE, including the many conundrums

Evaluating the use of amber in palaeoatmospheric reconstructions: The carbon-isotope variability of modern and Cretaceous conifer resins.

Stable carbon-isotope geochemistry of fossilized tree resin (amber) potentially could be a very useful tool to infer the composition of past atmospheres. To test the reliability of amber as a proxy for the atmosphere, we studied the variability of modern resin d13C at both local and global scales. An amber d13C curve was then built for the Cretaceous, a period of abundant resin production, and interpreted in light of data from modern resins. Our data show that hardening changes the pristine d13C value by causing a 13C-depletion in solid resin when compared to fresh liquid-viscous resin, probably due to the loss of 13C-enriched volatiles. Modern resin d13C values vary as a function of physiological and environmental parameters in ways that are similar to those described for leaves and wood. Resin d13C varies between plant species and localities, within the same tree and between different plant tissues by up to 6¿, and in general increases with increasing altitudes of the plant-growing site. We show that, as is the case with modern resin, Cretaceous amber d13C has a high variability, generally higher than that of other fossil material. Despite the high natural variability, amber shows a negative 2.5-3¿ d13C trend from the middle Early Cretaceous to the Maastrichtian that parallels published terrestrial d13C records. This trend mirrors changes in the atmospheric d13C calculated from the d13C and d18O of benthic foraminiferal tests, although the magnitude of the shift is larger in plant material than in the atmosphere. Increasing mean annual precipitation and pO2 could have enhanced plant carbon-isotope fractionation during the Late Cretaceous, whereas changing pCO2 levels seem to have had no effect on plant carbon-isotope fractionation. The results of this study suggest that amber is a powerful fossil plant material for palaeoenvironmental and palaeoclimatic reconstructions. Improvement of the resolution of the existing data coupled with more detailed information about botanical source and environmental growing conditions of the fossil plant material will probably allow a more faithful interpretation of amber d13C records and a wider understanding of the composition of the past atmosphere

The origin of variability of the intermediate-mass black-hole ULX system HLX-1 in ESO 243-49

The ultra-luminous intermediate-mass black-hole system HLX-1 in the ESO 243-49 galaxy exhibits variability with a possible recurrence time of a few hundred days. Finding the origin of this variability would constrain the still largely unknown properties of this extraordinary object. Since it exhibits an intensity-hardness behavior characteristic of black-hole X-ray transients, we have analyzed the variability of HLX-1 in the framework of the disk instability model that explains outbursts of such systems. We find that the long-term variability of HLX-1 is unlikely to be explained by a model in which outbursts are triggered by thermal-viscous instabilities in an accretion disc. Possible alternatives include the instability in a radiation-pressure dominated disk but we argue that a more likely explanation is a modulated mass-transfer due to tidal stripping of a star on an eccentric orbit around the intermediate-mass black hole. We consider an evolutionary scenario leading to the creation of such a system and estimate the probability of its observation. We conclude, using a simplified dynamical model of the post-collapse cluster, that no more than 1/100 to 1/10 of Mbh < 10^4 Msun IMBHs - formed by run-away stellar mergers in the dense collapsed cores of young clusters - could have a few times 1 Msun Main-Sequence star evolve to an AGB on an orbit eccentric enough for mass transfer at periapse, while avoiding collisional destruction or being scattered into the IMBH by 2-body encounters. The finite but low probability of this configuration is consistent with the uniqueness of HLX-1. We note, however, that the actual response of a standard accretion disk to bursts of mass transfer may be too slow to explain the observations unless the orbit is close to parabolic (and hence even rarer) and/or additional heating, presumably linked to the highly time-dependent gravitational potential, are invoked.Comment: 8 pages, 2 figures. Additional figure, extended discussion. To be published in ApJ, June 10, 2011, v734 -

The S-Star Cluster at the Center of the Milky Way: On the nature of diffuse NIR emission in the inner tenth of a parsec

Sagittarius A*, the super-massive black hole at the center of the Milky Way, is surrounded by a small cluster of high velocity stars, known as the S-stars. We aim to constrain the amount and nature of stellar and dark mass associated with the cluster in the immediate vicinity of Sagittarius A*. We use near-infrared imaging to determine the $K_\mathrm{s}$-band luminosity function of the S-star cluster members, and the distribution of the diffuse background emission and the stellar number density counts around the central black hole. This allows us to determine the stellar light and mass contribution expected from the faint members of the cluster. We then use post-Newtonian N-body techniques to investigate the effect of stellar perturbations on the motion of S2, as a means of detecting the number and masses of the perturbers. We find that the stellar mass derived from the $K_\mathrm{s}$-band luminosity extrapolation is much smaller than the amount of mass that might be present considering the uncertainties in the orbital motion of the star S2. Also the amount of light from the fainter S-cluster members is below the amount of residual light at the position of the S-star cluster after removing the bright cluster members. If the distribution of stars and stellar remnants is strongly enough peaked near Sagittarius A*, observed changes in the orbital elements of S2 can be used to constrain both their masses and numbers. Based on simulations of the cluster of high velocity stars we find that at a wavelength of 2.2 $\mu$m close to the confusion level for 8 m class telescopes blend stars will occur (preferentially near the position of Sagittarius A*) that last for typically 3 years before they dissolve due to proper motions.Comment: 14 pages, 11 figures, minor changes to match the published version in Astronomy & Astrophysic

Extinction and dawn of the modern world in the Carnian (Late Triassic)

The Carnian Pluvial Episode (Late Triassic) was a time of global environmental changes and possibly substantial coeval volcanism. The extent of the biological turnover in marine and terrestrial ecosystems is not well understood. Here, we present a meta-analysis of fossil data that suggests a substantial reduction in generic and species richness and the disappearance of 33% of marine genera. This crisis triggered major radiations. In the sea, the rise of the first scleractinian reefs and rock-forming calcareous nannofossils points to substantial changes in ocean chemistry. On land, there were major diversifications and originations of conifers, insects, dinosaurs, crocodiles, lizards, turtles, and mammals. Although there is uncertainty on the precise age of some of the recorded biological changes, these observations indicate that the Carnian Pluvial Episode was linked to a major extinction event and might have been the trigger of the spectacular radiation of many key groups that dominate modern ecosystems

Uncovering the Cyanobacterial Chemical Diversity: The Search for Novel Anticancer Compounds

This article belongs to the Proceedings of The 7th Iberian Congress on Cyanotoxins/3rd Iberoamerican Congress on Cyanotoxins[Abstract] Cancer has a tremendous negative socio-economic impact on our society. Thus, the discovery of new and more effective anticancer drugs is of utmost importance. To address this societal challenge, the main goal of the CYANCAN project was the discovery of anticancer compounds from cyanobacteria. These photosynthetic bacteria are considered among the most promising groups capable of producing metabolites with pharmaceutical applications. A valuable and underexplored natural resource that can underpin the discovery of promising compounds can be found in the Blue Biotechnology and Ecotoxicology Culture Collection (LEGE-CC) at CIIMAR (Interdisciplinary Centre of Marine and Environmental Research), comprising more than 700 different cyanobacterial strains. Herein, we present the recent advances implemented for finding robust anticancer lead compounds from LEGE-CC cyanobacteria. For this purpose, we developed a natural product library. Sixty cyanobacterial strains, representative of LEGE-CC biodiversity, were chromatographed to yield 480 fractions that were tested for their cytotoxic activity against 2D and 3D models of human colon carcinoma (HCT 116). The conjugation of monolayer assays and 3D cancer spheroids led to the selection of 11 active fractions, of which the chemical space was studied using an untargeted metabolomics approach. The putative annotation and identification of several compounds led to the selection of two marine strains for compound isolation: Leptothoe sp. and Lusitaniella coriacea. The isolation of the compounds was guided through bioactivity assays and mass spectrometry. These molecules were purified from the crudes by employing several chromatography methods, and the chemical structures were determined by means of NMR (nuclear magnetic resonance) and MS/MS (tandem mass spectrometry) experiments. Thus, a novel macrolide-type compound was isolated from Leptothoe sp., which presented a highly cytotoxic activity against our cancer cell models. Its effects on cancer vascularization and metastasis were studied using the zebrafish model. Moreover, from L. coriacea, five unprecedented salicyl-capped thiazol(in)e NRPs-PKs (nonribosomal peptides-polyketides) compounds were isolated. These compounds showed the potential to act as reversers of P-glycoprotein efflux activity.CIIMAR strategic funds UIDB/04423/2020 and UIDP/04423/2020; CYANCAN PTDC/MED-QUI/30944/2017, co-financed by NORTE 2020, Portugal 2020, and the European Union through the ERDF. EMERTOX: EU Horizon 2020 R&I programme under the Marie Skłodowska-Curie grant agreement No 778,069. Ribeiro, T: FCT grant SFRH/BD/139131/2018. Castelo-Branco, R: FCT grant SFRH/BD/136367/2018Centro Interdisciplinar de Investigação Marinha e Ambiental (Porto); UIDB/04423/2020Portugal. Fundação para a Ciência e a Tecnologia; PTDC/MED-QUI/30944/2017Portugal. Fundação para a Ciência e a Tecnologia; SFRH/BD/139131/2018Portugal. Fundação para a Ciência e a Tecnologia; SFRH/BD/136367/201