A Hydrophobic Gate in an Ion Channel: The Closed State of the Nicotinic Acetylcholine Receptor

The nicotinic acetylcholine receptor (nAChR) is the prototypic member of the `Cys-loop' superfamily of ligand-gated ion channels which mediate synaptic neurotransmission, and whose other members include receptors for glycine, gamma-aminobutyric acid, and serotonin. Cryo-electron microscopy has yielded a three dimensional structure of the nAChR in its closed state. However, the exact nature and location of the channel gate remains uncertain. Although the transmembrane pore is constricted close to its center, it is not completely occluded. Rather, the pore has a central hydrophobic zone of radius about 3 A. Model calculations suggest that such a constriction may form a hydrophobic gate, preventing movement of ions through a channel. We present a detailed and quantitative simulation study of the hydrophobic gating model of the nicotinic receptor, in order to fully evaluate this hypothesis. We demonstrate that the hydrophobic constriction of the nAChR pore indeed forms a closed gate. Potential of mean force (PMF) calculations reveal that the constriction presents a barrier of height ca. 10 kT to the permeation of sodium ions, placing an upper bound on the closed channel conductance of 0.3 pS. Thus, a 3 A radius hydrophobic pore can form a functional barrier to the permeation of a 1 A radius Na+ ion. Using a united atom force field for the protein instead of an all atom one retains the qualitative features but results in differing conductances, showing that the PMF is sensitive to the detailed molecular interactions.Comment: Accepted by Physical Biology; includes a supplement and a supplementary mpeg movie can be found at http://sbcb.bioch.ox.ac.uk/oliver/download/Movies/watergate.mp

Semliki Forest virus induced, immune mediated demyelination: the effect of irradiation

International audienceThe Dark Energy Camera has captured a large set of images as part of Science Verification (SV) for the Dark Energy Survey (DES). The SV footprint covers a large portion of the outer Large Magellanic Cloud (LMC), providing photometry 1.5 mag fainter than the main sequence turn-off of the oldest LMC stellar population. We derive geometrical and structural parameters for various stellar populations in the LMC disc. For the distribution of all LMC stars, we find an inclination of i = -38.14° ± 0.08° (near side in the north) and a position angle for the line of nodes of θ0 = 129.51° ± 0.17°. We find that stars younger than ∼4 Gyr are more centrally concentrated than older stars. Fitting a projected exponential disc shows that the scale radius of the old populations is R>4 Gyr = 1.41 ± 0.01 kpc, while the younger population has R = 0.72 ± 0.01 kpc. However, the spatial distribution of the younger population deviates significantly from the projected exponential disc model. The distribution of old stars suggests a large truncation radius of Rt = 13.5 ± 0.8 kpc. If this truncation is dominated by the tidal field of the Galaxy, we find that the LMC is {∼eq } 24^{+9}_{-6} times less massive than the encircled Galactic mass. By measuring the Red Clump peak magnitude and comparing with the best-fitting LMC disc model, we find that the LMC disc is warped and thicker in the outer regions north of the LMC centre. Our findings may either be interpreted as a warped and flared disc in the LMC outskirts, or as evidence of a spheroidal halo component

Brown dwarf census with the Dark Energy Survey year 3 data and the thin disc scale height of early L types

27 pages, 18 figuresIn this paper we present a catalogue of 11 745 brown dwarfs with spectral types ranging from L0 to T9, photometrically classified using data from the Dark Energy Survey (DES) year 3 release matched to the Vista Hemisphere Survey (VHS) DR3 and Wide-field Infrared Survey Explorer (WISE) data, covering ≈2400 deg2 up to iAB = 22. The classification method follows the same phototype method previously applied to SDSS-UKIDSS-WISE data. The most significant difference comes from the use of DES data instead of SDSS, which allow us to classify almost an order of magnitude more brown dwarfs than any previous search and reaching distances beyond 400 pc for the earliest types. Next, we also present and validate the GalmodBD simulation, which produces brown dwarf number counts as a function of structural parameters with realistic photometric properties of a given survey. We use this simulation to estimate the completeness and purity of our photometric LT catalogue down to iAB = 22, as well as to compare to the observed number of LT types. We put constraints on the thin disc scale height for the early L (L0–L3) population to be around 450 pc, in agreement with previous findings. For completeness, we also publish in a separate table a catalogue of 20 863 M dwarfs that passed our colour cut with spectral types greater than M6. Both the LT and the late M catalogues are found at DES release page https://des.ncsa.illinois.edu/releases/other/y3-mlt.Peer reviewedFinal Published versio

Forward Global Photometric Calibration of the Dark Energy Survey

Many scientific goals for the Dark Energy Survey (DES) require calibration of optical/NIR broadband $b = grizY$ photometry that is stable in time and uniform over the celestial sky to one percent or better. It is also necessary to limit to similar accuracy systematic uncertainty in the calibrated broadband magnitudes due to uncertainty in the spectrum of the source. Here we present a "Forward Global Calibration Method (FGCM)" for photometric calibration of the DES, and we present results of its application to the first three years of the survey (Y3A1). The FGCM combines data taken with auxiliary instrumentation at the observatory with data from the broad-band survey imaging itself and models of the instrument and atmosphere to estimate the spatial- and time-dependence of the passbands of individual DES survey exposures. "Standard" passbands are chosen that are typical of the passbands encountered during the survey. The passband of any individual observation is combined with an estimate of the source spectral shape to yield a magnitude $m_b^{\mathrm{std}}$ in the standard system. This "chromatic correction" to the standard system is necessary to achieve sub-percent calibrations. The FGCM achieves reproducible and stable photometric calibration of standard magnitudes $m_b^{\mathrm{std}}$ of stellar sources over the multi-year Y3A1 data sample with residual random calibration errors of $\sigma=5-6\,\mathrm{mmag}$ per exposure. The accuracy of the calibration is uniform across the $5000\,\mathrm{deg}^2$ DES footprint to within $\sigma=7\,\mathrm{mmag}$. The systematic uncertainties of magnitudes in the standard system due to the spectra of sources are less than $5\,\mathrm{mmag}$ for main sequence stars with $0.5<g-i<3.0$.Comment: 25 pages, submitted to A

Astrometric calibration and performance of the Dark Energy Camera

We characterize the ability of the Dark Energy Camera (DECam) to perform relative astrometry across its 500~Mpix, 3 deg^2 science field of view, and across 4 years of operation. This is done using internal comparisons of ~4x10^7 measurements of high-S/N stellar images obtained in repeat visits to fields of moderate stellar density, with the telescope dithered to move the sources around the array. An empirical astrometric model includes terms for: optical distortions; stray electric fields in the CCD detectors; chromatic terms in the instrumental and atmospheric optics; shifts in CCD relative positions of up to ~10 um when the DECam temperature cycles; and low-order distortions to each exposure from changes in atmospheric refraction and telescope alignment. Errors in this astrometric model are dominated by stochastic variations with typical amplitudes of 10-30 mas (in a 30 s exposure) and 5-10 arcmin coherence length, plausibly attributed to Kolmogorov-spectrum atmospheric turbulence. The size of these atmospheric distortions is not closely related to the seeing. Given an astrometric reference catalog at density ~0.7 arcmin^{-2}, e.g. from Gaia, the typical atmospheric distortions can be interpolated to 7 mas RMS accuracy (for 30 s exposures) with 1 arcmin coherence length for residual errors. Remaining detectable error contributors are 2-4 mas RMS from unmodelled stray electric fields in the devices, and another 2-4 mas RMS from focal plane shifts between camera thermal cycles. Thus the astrometric solution for a single DECam exposure is accurate to 3-6 mas (0.02 pixels, or 300 nm) on the focal plane, plus the stochastic atmospheric distortion.Comment: Submitted to PAS

Evidence for Color Dichotomy in the Primordial Neptunian Trojan Population

In the current model of early Solar System evolution, the stable members of the Jovian and Neptunian Trojan populations were captured into resonance from the leftover reservoir of planetesimals during the outward migration of the giant planets. As a result, both Jovian and Neptunian Trojans share a common origin with the primordial disk population, whose other surviving members constitute today's trans-Neptunian object (TNO) populations. The cold classical TNOs are ultra-red, while the dynamically excited "hot" population of TNOs contains a mixture of ultra-red and blue objects. In contrast, Jovian and Neptunian Trojans are observed to be blue. While the absence of ultra-red Jovian Trojans can be readily explained by the sublimation of volatile material from their surfaces due to the high flux of solar radiation at 5AU, the lack of ultra-red Neptunian Trojans presents both a puzzle and a challenge to formation models. In this work we report the discovery by the Dark Energy Survey (DES) of two new dynamically stable L4 Neptunian Trojans,2013 VX30 and 2014 UU240, both with inclinations i >30 degrees, making them the highest-inclination known stable Neptunian Trojans. We have measured the colors of these and three other dynamically stable Neptunian Trojans previously observed by DES, and find that 2013 VX30 is ultra-red, the first such Neptunian Trojan in its class. As such, 2013 VX30 may be a "missing link" between the Trojan and TNO populations. Using a simulation of the DES TNO detection efficiency, we find that there are 162 +/- 73 Trojans with Hr < 10 at the L4 Lagrange point of Neptune. Moreover, the blue-to-red Neptunian Trojan population ratio should be higher than 17:1. Based on this result, we discuss the possible origin of the ultra-red Neptunian Trojan population and its implications for the formation history of Neptunian Trojans

Photometric redshifts and clustering of emission line galaxies selected jointly by DES and eBOSS

We present the results of the first test plates of the extended Baryon Oscillation Spectroscopic Survey. This paper focuses on the emission line galaxies (ELG) population targetted from the Dark Energy Survey (DES) photometry. We analyse the success rate, efficiency, redshift distribution, and clustering properties of the targets. From the 9000 spectroscopic redshifts targetted, 4600 have been selected from the DES photometry. The total success rate for redshifts between 0.6 and 1.2 is 71\% and 68\% respectively for a bright and faint, on average more distant, samples including redshifts measured from a single strong emission line. We find a mean redshift of 0.8 and 0.87, with 15 and 13\% of unknown redshifts respectively for the bright and faint samples. In the redshift range 0.6<z<1.2, for the most secure spectroscopic redshifts, the mean redshift for the bright and faint sample is 0.85 and 0.9 respectively. Star contamination is lower than 2\%. We measure a galaxy bias averaged on scales of 1 and 10~Mpc/h of 1.72 \pm 0.1 for the bright sample and of 1.78 \pm 0.12 for the faint sample. The error on the galaxy bias have been obtained propagating the errors in the correlation function to the fitted parameters. This redshift evolution for the galaxy bias is in agreement with theoretical expectations for a galaxy population with MB-5\log h < -21.0. We note that biasing is derived from the galaxy clustering relative to a model for the mass fluctuations. We investigate the quality of the DES photometric redshifts and find that the outlier fraction can be reduced using a comparison between template fitting and neural network, or using a random forest algorithm

H0LiCOW X: Spectroscopic/imaging survey and galaxy-group identification around the strong gravitational lens system WFI2033-4723

Galaxies and galaxy groups located along the line of sight towards gravitationally lensed quasars produce high-order perturbations of the gravitational potential at the lens position. When these perturbation are too large, they can induce a systematic error on $H_0$ of a few-percent if the lens system is used for cosmological inference and the perturbers are not explicitly accounted for in the lens model. In this work, we present a detailed characterization of the environment of the lens system WFI2033-4723 ($z_{\rm src} = 1.662$, $z_{\rm lens}$ = 0.6575), one of the core targets of the H0LICOW project for which we present cosmological inferences in a companion paper (Rusu et al. 2019). We use the Gemini and ESO-Very Large telescopes to measure the spectroscopic redshifts of the brightest galaxies towards the lens, and use the ESO-MUSE integral field spectrograph to measure the velocity-dispersion of the lens ($\sigma_{\rm {los}}= 250^{+15}_{-21}$ km/s) and of several nearby galaxies. In addition, we measure photometric redshifts and stellar masses of all galaxies down to $i < 23$ mag, mainly based on Dark Energy Survey imaging (DR1). Our new catalog, complemented with literature data, more than doubles the number of known galaxy spectroscopic redshifts in the direct vicinity of the lens, expanding to 116 (64) the number of spectroscopic redshifts for galaxies separated by less than 3 arcmin (2 arcmin) from the lens. Using the flexion-shift as a measure of the amplitude of the gravitational perturbation, we identify 2 galaxy groups and 3 galaxies that require specific attention in the lens models. The ESO MUSE data enable us to measure the velocity-dispersions of three of these galaxies. These results are essential for the cosmological inference analysis presented in Rusu et al. (2019).Comment: Matches the version accepted for publication by MNRAS. Note that this paper previously appeared as H0LICOW X