Infrared measurements of atmospheric constituents

The objective of this program is to obtain data concerning the concentration versus altitude of various constituents of interest in the photochemistry of the stratospheric ozone layer. Data pertinent to this objective are obtained using balloon-borne instruments to measure the atmospheric transmission and emission in the mid infrared. In addition to obtaining constituent profile information, the spectral data obtained are also used to identify absorption or emission features which may interfere with the retrieval of constituent data from satellite instruments using lower spectral resolution. The spectral resolution obtained with the solar spectral system is 0.0025 cm(exp -1) and represents about a factor of 5 greater resolution than any solar spectra previously obtained in this spectral region. As a result of the increase in spectral resolution, a large number of features are observed in these spectra which were not observed in previous studies. Identification and analysis of these features is in progress. The results of this analysis to date shows a number of HNO3 features which have not been observed before, and these occur where they will interfere with the retrieval of other constituents. An example of the interference is the occurrence of features in the 780.2 cm(exp -1) region which overlap the ClONO2 feature which will be used for retrieval of ClONO2 by the CLAES instrument on UARS. A number of features due to COF2 were also identified in the 1250 cm(exp -1) region which may interfere with retrieval of N2O5

Chemical ozone loss in the Arctic winter 1991–1992

Chemical ozone loss in winter 1991–1992 is recalculated based on observations of the HALOE satellite instrument, Version 19, ER-2 aircraft measurements and balloon data. HALOE satellite observations are shown to be reliable in the lower stratosphere below 400 K, at altitudes where the measurements are most likely disturbed by the enhanced sulfate aerosol loading, as a result of the Mt.~Pinatubo eruption in June 1991. Significant chemical ozone loss (13–17 DU) is observed below 380 K from Kiruna balloon observations and HALOE satellite data between December 1991 and March 1992. For the two winters after the Mt. Pinatubo eruption, HALOE satellite observations show a stronger extent of chemical ozone loss towards lower altitudes compared to other Arctic winters between 1991 and 2003. In spite of already occurring deactivation of chlorine in March 1992, MIPAS-B and LPMA balloon observations indicate that chlorine was still activated at lower altitudes, consistent with observed chemical ozone loss occurring between February and March and April. Large chemical ozone loss of more than 70 DU in the Arctic winter 1991–1992 as calculated in earlier studies is corroborated here

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl

ASaiM: A Galaxy-based framework to analyze microbiota data

Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable

A Method for Calculating the Structure of (Singular) Spacetimes in the Large

A formalism and its numerical implementation is presented which allows to calculate quantities determining the spacetime structure in the large directly. This is achieved by conformal techniques by which future null infinity (\Scri{}^+) and future timelike infinity ($i^+$) are mapped to grid points on the numerical grid. The determination of the causal structure of singularities, the localization of event horizons, the extraction of radiation, and the avoidance of unphysical reflections at the outer boundary of the grid, are demonstrated with calculations of spherically symmetric models with a scalar field as matter and radiation model.Comment: 29 pages, AGG2

Validation and data characteristics of methane and nitrous oxide profiles observed by MIPAS and processed with Version 4.61 algorithm

The ENVISAT validation programme for the atmospheric instruments MIPAS, SCIAMACHY and GOMOS is based on a number of balloon-borne, aircraft, satellite and ground-based correlative measurements. In particular the activities of validation scientists were coordinated by ESA within the ENVISAT Stratospheric Aircraft and Balloon Campaign or ESABC. As part of a series of similar papers on other species [this issue] and in parallel to the contribution of the individual validation teams, the present paper provides a synthesis of comparisons performed between MIPAS CH4 and N2O profiles produced by the current ESA operational software (Instrument Processing Facility version 4.61 or IPF v4.61, full resolution MIPAS data covering the period 9 July 2002 to 26 March 2004) and correlative measurements obtained from balloon and aircraft experiments as well as from satellite sensors or from ground-based instruments. In the middle stratosphere, no significant bias is observed between MIPAS and correlative measurements, and MIPAS is providing a very consistent and global picture of the distribution of CH4 and N2O in this region. In average, the MIPAS CH4 values show a small positive bias in the lower stratosphere of about 5%. A similar situation is observed for N2O with a positive bias of 4%. In the lower stratosphere/upper troposphere (UT/LS) the individual used MIPAS data version 4.61 still exhibits some unphysical oscillations in individual CH4 and N2O profiles caused by the processing algorithm (with almost no regularization). Taking these problems into account, the MIPAS CH4 and N2O profiles are behaving as expected from the internal error estimation of IPF v4.61 and the estimated errors of the correlative measurements

Sedimentation and Flow Through Porous Media: Simulating Dynamically Coupled Discrete and Continuum Phases

We describe a method to address efficiently problems of two-phase flow in the regime of low particle Reynolds number and negligible Brownian motion. One of the phases is an incompressible continuous fluid and the other a discrete particulate phase which we simulate by following the motion of single particles. Interactions between the phases are taken into account using locally defined drag forces. We apply our method to the problem of flow through random media at high porosity where we find good agreement to theoretical expectations for the functional dependence of the pressure drop on the solid volume fraction. We undertake further validations on systems undergoing gravity induced sedimentation.Comment: 22 pages REVTEX, figures separately in uudecoded, compressed postscript format - alternatively e-mail '[email protected]' for hardcopies

The UV-A and visible solar irradiance spectrum: inter-comparison of absolutely calibrated, spectrally medium resolution solar irradiance spectra from balloon- and satellite-borne measurements

International audienceWithin the framework of the ENVISAT/-SCIAMACHY satellite validation, solar irradiance spectra are absolutely measured at moderate resolution in the UV/visible spectral range (in the UV from 316.7–418 nm and the visible from 400–652 nm at a full width half maximum resolution of 0.55 nm and 1.48 nm, respectively) from aboard the azimuth-controlled LPMA/DOAS balloon gondola at around 32 km balloon float altitude. After accounting for the atmospheric extinction due to Rayleigh scattering and gaseous absorption (O3, and NO2), the measured solar spectra are compared with previous observations. Our solar irradiance is +1.6% larger than the re-calibrated Kurucz et al. (1984) solar spectrum (Fontenla et al., 1999, called MODTRAN 3.5) in the visible spectral range (435–650 nm), +1.5% larger in the (370–415 nm) wavelength interval, but -4% smaller in the UV spectral range (316.7–370 nm), when the Kurucz spectrum is convolved to the spectral resolution of our instrument. The same comparison with the SOLSPEC solar spectrum (Thuillier et al., 1997, 1998a, b) confirms the somewhat larger solar irradiance (+1.7%) measured by the balloon instrument from 435–500 nm, but not from 500–650 nm, where the SOLSPEC is -1.3% lower than MODTRAN 3.5. Comparison of the SCIAMACHY solar spectrum from channels 1 to 4 (– re-calibrated by the University of Bremen –) with MODTRAN 3.5 indicates an agreement of +0.2% in the visible spectral range (435–585 nm). With this calibration, the SCIAMACHY solar spectrum is congruent with the balloon observations (-1%) in the 316.7–370 nm wavelength range, but both are up to -5%/-3% smaller than MODTRAN 3.5 and SOLSPEC, respectively. In agreement with findings of Skupin et al. (2002) our study emphasizes that the present ESA SCIAMACHY level 1 calibration is systematically +15% larger in the considered wavelength intervals when compared to all available other solar irradiance measurements

Viscous-Inviscid Interactions in a Boundary-Layer Flow Induced by a Vortex Array

In this paper we investigate the asymptotic validity of boundary layer theory. For a flow induced by a periodic row of point-vortices, we compare Prandtl's solution to Navier-Stokes solutions at different $Re$ numbers. We show how Prandtl's solution develops a finite time separation singularity. On the other hand Navier-Stokes solution is characterized by the presence of two kinds of viscous-inviscid interactions between the boundary layer and the outer flow. These interactions can be detected by the analysis of the enstrophy and of the pressure gradient on the wall. Moreover we apply the complex singularity tracking method to Prandtl and Navier-Stokes solutions and analyze the previous interactions from a different perspective

Balloon-borne stratospheric BrO measurements: comparison with Envisat/SCIAMACHY BrO limb profiles

International audienceFor the first time, results of four stratospheric BrO profiling instruments, are presented and compared with reference to the SLIMCAT 3-dimensional chemical transport model (3-D CTM). Model calculations are used to infer a BrO profile validation set, measured by 3 different balloon sensors, for the new Envisat/SCIAMACHY (ENVIronment SATellite/SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY) satellite instrument. The balloon observations include (a) balloon-borne in situ resonance fluorescence detection of BrO (Triple), (b) balloon-borne solar occultation DOAS measurements (Differential Optical Absorption Spectroscopy) of BrO in the UV, and (c) BrO profiling from the solar occultation SAOZ (Systeme d'Analyse par Observation Zenithale) balloon instrument. Since stratospheric BrO is subject to considerable diurnal variation and none of the measurements are performed close enough in time and space for a direct comparison, all balloon observations are considered with reference to outputs from the 3-D CTM. The referencing is performed by forward and backward air mass trajectory calculations to match the balloon with the satellite observations. The diurnal variation of BrO is considered by 1-D photochemical model calculation along the trajectories. The 1-D photochemical model is initialised with output data of the 3-D model with additional constraints on the vertical transport, the total amount and photochemistry of stratospheric bromine as given by the various balloon observations. Total [Bry]=(20.1±2.5) pptv obtained from DOAS BrO observations at mid-latitudes in 2003, serves as an upper limit of the comparison. Most of the balloon observations agree with the photochemical model predictions within their given error estimates. First retrieval exercises of BrO limb profiling from the SCIAMACHY satellite instrument on average agree to around 20% with the photochemically-corrected balloon observations of the remote sensing instruments (SAOZ and DOAS). An exception is the in situ Triple profile, in which the balloon and satellite data mostly does not agree within the given errors. In general, the satellite measurements show systematically higher values below 25 km than the balloon data and a change in profile shape above about 25 km