Exoplanet atmospheres with EChO: spectral retrievals using EChOSim

We demonstrate the effectiveness of the Exoplanet Characterisation Observatory mission concept for constraining the atmospheric properties of hot and warm gas giants and super Earths. Synthetic primary and secondary transit spectra for a range of planets are passed through EChOSim (Waldmann & Pascale 2014) to obtain the expected level of noise for different observational scenarios; these are then used as inputs for the NEMESIS atmospheric retrieval code and the retrieved atmospheric properties (temperature structure, composition and cloud properties) compared with the known input values, following the method of Barstow et al. (2013a). To correctly retrieve the temperature structure and composition of the atmosphere to within 2 {\sigma}, we find that we require: a single transit or eclipse of a hot Jupiter orbiting a sun-like (G2) star at 35 pc to constrain the terminator and dayside atmospheres; 20 transits or eclipses of a warm Jupiter orbiting a similar star; 10 transits/eclipses of a hot Neptune orbiting an M dwarf at 6 pc; and 30 transits or eclipses of a GJ1214b-like planet.Comment: 13 pages, 15 figures, 1 table. Accepted by Experimental Astronomy. The final publication will shortly be available at Springer via http://dx.doi.org/10.1007/s10686-014-9397-

Cryo-EM map interpretation and protein model-building using iterative map segmentation.

A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a Cα model. The Cα model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo-EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps

Surface localization of gas sources on comet 67P/Churyumov-Gerasimenko based on DFMS/COPS data

We reconstruct the temporal evolution of the source distribution for the four major gas species H2O, CO2, CO, and O2 on the surface of comet 67P/Churyumov-Gerasimenko during its 2015 apparition. The analysis applies an inverse coma model and fits to data between August 6th 2014 and September 5th 2016 measured with the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS). The spatial distribution of gas sources with their temporal variation allows one to construct surface maps for gas emissions and to evaluate integrated productions rates. For all species peak production rates and integrated productions rates per orbit are evaluated separately for the northern and the southern hemisphere. The nine most active emitting areas on the comet's surface are defined and their correlation to emissions for each of the species is discussed.Comment: 11 page

Observation of a New Type of Low Frequency Waves at Comet 67P/Churyumov-Gerasimenko

We report on magnetic field measurements made in the innermost coma of 67P/Churyumov-Gerasimenko in its low activity state. Quasi-coherent, large-amplitude ($\delta B/B \sim 1$), compressional magnetic field oscillations at $\sim$ 40 mHz dominate the immediate plasma environment of the nucleus. This differs from previously studied comet-interaction regions where waves at the cometary ion gyro-frequencies are the main feature. Thus classical pick-up ion driven instabilities are unable to explain the observations. We propose a cross-field current instability associated with newborn cometary ion currents as a possible source mechanism.Comment: 6 pages, 3 Figure

Skipping orbits and enhanced resistivity in large-diameter InAs/GaSb antidot lattices

We investigated the magnetotransport properties of high-mobility InAs/GaSb antidot lattices. In addition to the usual commensurability features at low magnetic field we found a broad maximum of classical origin around 2.5 T. The latter can be ascribed to a class of rosetta type orbits encircling a single antidot. This is shown by both a simple transport calculation based on a classical Kubo formula and an analysis of the Poincare surface of section at different magnetic field values. At low temperatures we observe weak 1/B-periodic oscillations superimposed on the classical maximum.Comment: 4 pages, 4 Postscript figures, REVTeX, submitted to Phys Rev

Generation of an optimal target list for the Exoplanet Characterisation Observatory (EChO)

The Exoplanet Characterisation Observatory (EChO) has been studied as a space mission concept by the European Space Agency in the context of the M3 selection process. Through direct measurement of the atmospheric chemical composition of hundreds of exoplanets, EChO would address fundamental questions such as: What are exoplanets made of? How do planets form and evolve? What is the origin of exoplanet diversity? More specifically, EChO is a dedicated survey mission for transit and eclipse spectroscopy capable of observing a large, diverse and well-defined planetary sample within its four to six year mission lifetime. In this paper we use the end-to-end instrument simulator EChOSim to model the currently discovered targets, to gauge which targets are observable and assess the EChO performances obtainable for each observing tier and time. We show that EChO would be capable of observing over 170 relativity diverse planets if it were launched today, and the wealth of optimal targets for EChO expected to be discovered in the next 10 years by space and ground-based facilities is simply overwhelming. In addition, we build on previous molecular detectability studies to show what molecules and abundances will be detectable by EChO for a selection of real targets with various molecular compositions and abundances. EChO's unique contribution to exoplanetary science will be in identifying the main constituents of hundreds of exoplanets in various mass/temperature regimes, meaning that we will be looking no longer at individual cases but at populations. Such a universal view is critical if we truly want to understand the processes of planet formation and evolution in various environments. In this paper we present a selection of key results. The full results are available online (http://www.ucl.ac.uk/exoplanets/echotargetlist/).Comment: Accepted for publication in Experimental Astronomy, 20 pages, 10 figures, 3 table

Assessing Protein Conformational Sampling Methods Based on Bivariate Lag-Distributions of Backbone Angles

Despite considerable progress in the past decades, protein structure prediction remains one of the major unsolved problems in computational biology. Angular-sampling-based methods have been extensively studied recently due to their ability to capture the continuous conformational space of protein structures. The literature has focused on using a variety of parametric models of the sequential dependencies between angle pairs along the protein chains. In this article, we present a thorough review of angular-sampling-based methods by assessing three main questions: What is the best distribution type to model the protein angles? What is a reasonable number of components in a mixture model that should be considered to accurately parameterize the joint distribution of the angles? and What is the order of the local sequence–structure dependency that should be considered by a prediction method? We assess the model fits for different methods using bivariate lag-distributions of the dihedral/planar angles. Moreover, the main information across the lags can be extracted using a technique called Lag singular value decomposition (LagSVD), which considers the joint distribution of the dihedral/planar angles over different lags using a nonparametric approach and monitors the behavior of the lag-distribution of the angles using singular value decomposition. As a result, we developed graphical tools and numerical measurements to compare and evaluate the performance of different model fits. Furthermore, we developed a web-tool (http://www.stat.tamu.edu/∼madoliat/LagSVD) that can be used to produce informative animations

Structure of the CLC-1 chloride channel from Homo sapiens.

CLC channels mediate passive Cl- conduction, while CLC transporters mediate active Cl- transport coupled to H+ transport in the opposite direction. The distinction between CLC-0/1/2 channels and CLC transporters seems undetectable by amino acid sequence. To understand why they are different functionally we determined the structure of the human CLC-1 channel. Its 'glutamate gate' residue, known to mediate proton transfer in CLC transporters, adopts a location in the structure that appears to preclude it from its transport function. Furthermore, smaller side chains produce a wider pore near the intracellular surface, potentially reducing a kinetic barrier for Cl- conduction. When the corresponding residues are mutated in a transporter, it is converted to a channel. Finally, Cl- at key sites in the pore appear to interact with reduced affinity compared to transporters. Thus, subtle differences in glutamate gate conformation, internal pore diameter and Cl- affinity distinguish CLC channels and transporters