Machine Learning Nucleation Collective Variables with Graph Neural Networks

The efficient calculation of nucleation collective variables (CVs) is one of the main limitations to the application of enhanced sampling methods to the investigation of nucleation processes in realistic environments. Here we discuss the development of a graph-based model for the approximation of nucleation CVs that enables orders-of-magnitude gains in computational efficiency in the on-the-fly evaluation of nucleation CVs. By performing simulations on a nucleating colloidal system mimicking a multistep nucleation process from solution, we assess the model's efficiency in both postprocessing and on-the-fly biasing of nucleation trajectories with pulling, umbrella sampling, and metadynamics simulations. Moreover, we probe and discuss the transferability of graph-based models of nucleation CVs across systems using the model of a CV based on sixth-order Steinhardt parameters trained on a colloidal system to drive the nucleation of crystalline copper from its melt. Our approach is general and potentially transferable to more complex systems as well as to different CVs

Nernst branes in gauged supergravity

We study static black brane solutions in the context of N = 2 U(1) gauged supergravity in four dimensions. Using the formalism of first-order flow equations, we construct novel extremal black brane solutions including examples of Nernst branes, i.e. extremal black brane solutions with vanishing entropy density. We also discuss a class of non-extremal generalizations which is captured by the first-order formalism.Comment: 44 pages, 3 figures, v2: added appendix B and references, minor typographic changes, v3: added some clarifying remarks, version published in JHE

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Vertical Aerosol Distribution and Mesospheric Clouds From ExoMars UVIS

The vertical opacity structure of the martian atmosphere is important for understanding the distribution of ice (water and carbon dioxide) and dust. We present a new data set of extinction opacity profiles from the NOMAD/UVIS spectrometer aboard the ExoMars Trace Gas Orbiter, covering one and a half Mars Years (MY) including the MY 34 Global Dust Storm and several regional dust storms. We discuss specific mesospheric cloud features and compare with existing literature and a Mars Global Climate Model (MGCM) run with data assimilation. Mesospheric opacity features, interpreted to be water ice, were present during the global and regional dust events and correlate with an elevated hygropause in the MGCM, providing evidence that regional dust storms can boost transport of vapor to mesospheric altitudes (with potential implications for atmospheric escape). The season of the dust storms also had an apparent impact on the resulting lifetime of the cloud features, with events earlier in the dusty season correlating with longer‐lasting mesospheric cloud layers. Mesospheric opacity features were also present during the dusty season even in the absence of regional dust storms, and interpreted to be water ice based on previous literature. The assimilated MGCM temperature structure agreed well with the UVIS opacities, but the MGCM opacity field struggled to reproduce mesospheric ice features, suggesting a need for further development of water ice parameterizations. The UVIS opacity data set offers opportunities for further research into the vertical aerosol structure of the martian atmosphere, and for validation of how this is represented in numerical models

Expected Performances of the NOMAD/ExoMars instrument

NOMAD (Nadir and Occultation for MArs Discovery) is one of the four instruments on board the ExoMars Trace Gas Orbiter, scheduled for launch in March 2016. It consists of a suite of three high-resolution spectrometers – SO (Solar Occultation), LNO (Limb, Nadir and Occultation) and UVIS (Ultraviolet and Visible Spectrometer). Based upon the characteristics of the channels and the values of Signal-to-Noise Ratio obtained from radiometric models discussed in [Vandaele et al., Optics Express, 2015] and [Thomas et al., Optics Express, 2015], the expected performances of the instrument in terms of sensitivity to detection have been investigated. The analysis led to the determination of detection limits for 18 molecules, namely CO, H2O, HDO, C2H2, C2H4, C2H6, H2CO, CH4, SO2, H2S, HCl, HCN, HO2, NH3, N2O, NO2, OCS, O3. NOMAD should have the ability to measure methane concentrations <25 parts per trillion (ppt) in solar occultation mode, and 11 parts per billion in nadir mode. Occultation detections as low as 10 ppt could be made if spectra are averaged [Drummond et al., Planetary Space and Science, 2011]. Results have been obtained for all three channels in nadir and in solar occultation

Water heavily fractionated as it ascends on Mars as revealed by ExoMars/NOMAD

sotopic ratios and, in particular, the water D/H ratio are powerful tracers of the evolution and transport of water on Mars. From measurements performed with ExoMars/NOMAD, we observe marked and rapid variability of the D/H along altitude on Mars and across the whole planet. The observations (from April 2018 to April 2019) sample a broad range of events on Mars, including a global dust storm, the evolution of water released from the southern polar cap during southern summer, the equinox phases, and a short but intense regional dust storm. In three instances, we observe water at very high altitudes (>80 km), the prime region where water is photodissociated and starts its escape to space. Rayleigh distillation appears the be the driving force affecting the D/H in many cases, yet in some instances, the exchange of water reservoirs with distinctive D/H could be responsible

Focus on collagen: in vitro systems to study fibrogenesis and antifibrosis _ state of the art

Fibrosis represents a major global disease burden, yet a potent antifibrotic compound is still not in sight. Part of the explanation for this situation is the difficulties that both academic laboratories and research and development departments in the pharmaceutical industry have been facing in re-enacting the fibrotic process in vitro for screening procedures prior to animal testing. Effective in vitro characterization of antifibrotic compounds has been hampered by cell culture settings that are lacking crucial cofactors or are not holistic representations of the biosynthetic and depositional pathway leading to the formation of an insoluble pericellular collagen matrix. In order to appreciate the task which in vitro screening of antifibrotics is up against, we will first review the fibrotic process by categorizing it into events that are upstream of collagen biosynthesis and the actual biosynthetic and depositional cascade of collagen I. We point out oversights such as the omission of vitamin C, a vital cofactor for the production of stable procollagen molecules, as well as the little known in vitro tardy procollagen processing by collagen C-proteinase/BMP-1, another reason for minimal collagen deposition in cell culture. We review current methods of cell culture and collagen quantitation vis-à-vis the high content options and requirements for normalization against cell number for meaningful data retrieval. Only when collagen has formed a fibrillar matrix that becomes cross-linked, invested with ligands, and can be remodelled and resorbed, the complete picture of fibrogenesis can be reflected in vitro. We show here how this can be achieved. A well thought-out in vitro fibrogenesis system represents the missing link between brute force chemical library screens and rational animal experimentation, thus providing both cost-effectiveness and streamlined procedures towards the development of better antifibrotic drugs

No detection of methane on Mars from early ExoMars Trace Gas Orbiter observations

The detection of methane on Mars has been interpreted as indicating that geochemical or biotic activities could persist on Mars today. A number of different measurements of methane show evidence of transient, locally elevated methane concentrations and seasonal variations in background methane concentrations. These measurements, however, are difficult to reconcile with our current understanding of the chemistry and physics of the Martian atmosphere, which-given methane's lifetime of several centuries-predicts an even, well mixed distribution of methane. Here we report highly sensitive measurements of the atmosphere of Mars in an attempt to detect methane, using the ACS and NOMAD instruments onboard the ESA-Roscosmos ExoMars Trace Gas Orbiter from April to August 2018. We did not detect any methane over a range of latitudes in both hemispheres, obtaining an upper limit for methane of about 0.05 parts per billion by volume, which is 10 to 100 times lower than previously reported positive detections. We suggest that reconciliation between the present findings and the background methane concentrations found in the Gale crater would require an unknown process that can rapidly remove or sequester methane from the lower atmosphere before it spreads globally

Martian dust storm impact on atmospheric H₂O and D/H observed by ExoMars Trace Gas Orbiter

Global dust storms on Mars are rare but can affect the Martian atmosphere for several months. They can cause changes in atmospheric dynamics and inflation of the atmosphere, primarily owing to solar heating of the dust. In turn, changes in atmospheric dynamics can affect the distribution of atmospheric water vapour, with potential implications for the atmospheric photochemistry and climate on Mars. Recent observations of the water vapour abundance in the Martian atmosphere during dust storm conditions revealed a high-altitude increase in atmospheric water vapour that was more pronounced at high northern latitudes, as well as a decrease in the water column at low latitudes. Here we present concurrent, high-resolution measurements of dust, water and semiheavy water (HDO) at the onset of a global dust storm, obtained by the NOMAD and ACS instruments onboard the ExoMars Trace Gas Orbiter. We report the vertical distribution of the HDO/H O ratio (D/H) from the planetary boundary layer up to an altitude of 80 kilometres. Our findings suggest that before the onset of the dust storm, HDO abundances were reduced to levels below detectability at altitudes above 40 kilometres. This decrease in HDO coincided with the presence of water-ice clouds. During the storm, an increase in the abundance of H2O and HDO was observed at altitudes between 40 and 80 kilometres. We propose that these increased abundances may be the result of warmer temperatures during the dust storm causing stronger atmospheric circulation and preventing ice cloud formation, which may confine water vapour to lower altitudes through gravitational fall and subsequent sublimation of ice crystals. The observed changes in H2O and HDO abundance occurred within a few days during the development of the dust storm, suggesting a fast impact of dust storms on the Martian atmosphere