Gravity Wave and Turbulence Transport in the Mesopause Region

Vertical transport due to dissipating gravity waves and turbulence in the mesopause region (85-100 km) are analyzed with observational data obtained from a narrow-band sodium wind/temperature lidar located at Andes Lidar Observatory (ALO), Cerro Pach´on (30.25 S, 70.73 W), Chile. The Na lidar at ALO has been in regular operation since 2010. The upgrade of the lidar system in May 2014 resulted in great improvements of the signal levels, which enabled data acquisition of high temporal and vertical resolutions reaching 6 s and 25 m. Traditional data processing utilizes signals at lower resolutions, typically at 60 s and 500 m, to reduce the measurement errors caused by photon noise. By using the high quality signals at much higher resolutions, the lidar is capable determined. of resolving smallest scale gravity waves and even turbulence. This dissertation focuses on characterizing the vertical heat flux induced by both dissipating gravity waves and turbulence with observations after the upgrade. The vertical heat flux is defined as the covariance between vertical wind and temperature perturbations (also called sensible heat flux or enthalpy flux if it is potential temperature). The associated cooling and heating effects on the atmosphere due to this heat transport are also determined. Starting from the observational data, the increased signal of ALO Na lidar significantly reduces the photon noise error but leads to challenges with photomultiplier tube (PMT) saturation at the same time. Corrections to this effect can be measured in a laboratory setting but may have large uncertainties at high photon count rates. Results show that this laboratory-correction can induce large errors for temperature, wind, and Na density measurements, which generates significant bias in the heat flux calculation due to the inherent correlation between vertical wind and temperature errors. A calibration procedure is developed to remove such PMT correction errors from laboratory measurements; then, the revised PMT correction curves are applied to reprocess the data. The corresponding heat flux bias is also calculated with numerical simulations and observations, and both conclude that it is necessary to eliminate this bias from heat flux calculations. Next, the seasonal variation of gravity wave vertical fluxes is calculated from over 400 hours of observations. The flux of potential temperature (enthalpy flux) and sensible heat are related through energy flux. The energy flux is estimated from vertical wavenumber (m) and frequency (w) spectra of temperature perturbations. Flux of potential temperature exhibits a strong semi-annual variation with maximum downward transport appears at 95 km in Jan and 88 km in Aug. Energy flux decreases exponentially with altitude from 10 2 to 10 4 Wm 2 and is larger during southern hemisphere winter. In order to investigate the dissipation of different scale gravity waves and their contributions to the vertical transports, perturbations are separated into three scale ranges. Results show that shorter period gravity waves tend to dissipate at higher altitudes and generate more heat transports. Wave vertical group velocity is estimated from energy flux and total wave energy. The averaged vertical group velocities for high, medium, and low frequency waves are 3.9ms 1, 0.9ms 1, and 0.3ms 1, respectively. In the end, with the high resolution raw data, a new method is developed to derive the turbulence by relating the turbulent perturbations to the photon count fluctuations. Using 150h of lidar observations kH is directly derived for the first time from eddy heat transport. Other key parameters such as the energy dissipation rate and the associated heating rate are also derived from the measurements without resorting to complex turbulence theory. Turbulence w and m spectra are calculated, which follow the power law with slopes consistent with theoretical models. The eddy heat flux generally decreases with altitude from about 0:5Kms 1 at 85km to 0:1Kms 1 at 100km, with a local maximum of 0:6Kms 1 at 93km. The derived mean turbulence thermal diffusivity and energy dissipation rate are 43m2s 1 and 37mWkg 1, respectively. The mean net cooling resulted from the heat transport and energy dissipation is 4:9 1:5Kd 1, comparable to that due to gravity wave transport at 7:9 1:9Kd 1. Turbulence key parameters show consistency with turbulence theories. The results presented in this dissertation can contribute to a more comprehensive parameterization scheme in terms of the thermal structure and wave dissipation for the general circulation models (GCMs). The derived turbulence parameters and cooling/heating rates can provide significant references for parameterizing the wave-driven residual circulation by generating more realistic global thermal structures

gravity waves, na lidar

Vertical energy transports due to dissipating gravity waves in the mesopause region (85–100 km) are analyzed using over 400 h of observational data obtained from a narrow-band sodium wind-temperature lidar located at Andes Lidar Observatory (ALO), Cerro Pachón (30.25°S, 70.73°W), Chile. Sensible heat flux is directly estimated using measured temperature and vertical wind; energy flux is estimated from the vertical wavenumber and frequency spectra of temperature perturbations; and enthalpy flux is derived based on its relationship with sensible heat and energy fluxes. Sensible heat flux is mostly downward throughout the region. Enthalpy flux exhibits an annual oscillation with maximum downward transport in July above 90 km. The dominant feature of energy flux is the exponential decrease from 10-2 to 10-4W m-2 with the altitude increases from 85 to 100 km and is larger during austral winter. The annual mean thermal diffusivity inferred from enthalpy flux decreases from 303m2 s-1 at 85 km to minimum 221m2 s-1 at 90 km then increases to 350m2 s-1 at 99 km. Results also show that shorter period gravity waves tend to dissipate at higher altitudes and generate more heat transport. The averaged vertical group velocities for high, medium, and low frequency waves are 4.15 m s-1, 1.15 m s-1, and 0.70 m s-1, respectively. Gravity wave heat transport brings significant cooling in the mesopause region at an average cooling rate of 6.7 ± 1.1 K per da

First Na Lidar Measurements of Turbulence Heat Flux, Thermal Diffusivity, and Energy Dissipation Rate in the Mesopause Region

Turbulence is ubiquitous in the mesopause region, where the atmospheric stability is low and wave breaking is frequent. Measuring turbulence is challenging in this region and is traditionally done by rocket soundings and radars. In this work, we show for the first time that the modern Na wind/temperature lidar located at Andes Lidar Observatory in Cerro Pachón, Chile, is able to directly measure the turbulence perturbations in temperature and vertical wind between 85 and 100 km. Using 150 h of lidar observations, we derived the frequency (ω) and vertical wave number (m) spectra for both gravity wave and turbulence, which follow the power law with slopes consistent with theoretical models. The eddy heat flux generally decreases with altitude from about −0.5 Km s−1 at 85 km to −0.1 Km s−1 at 100 km, with a local maximum of −0.6 Km s−1 at 93 km. The derived mean turbulence thermal diffusivity and energy dissipation rate are 43 m2 s−1 and 37 mW kg−1, respectively. The mean net cooling resulted from the heat transport and energy dissipation is −4.9 ± 1.5 K d−1, comparable to that due to gravity wave transport at −7.9 ± 1.9 K d−1. Turbulence key parameters show consistency with turbulence theories

First Measurement of Horizontal Wind and Temperature in the Lower Thermosphere (105–140 km) with a Na Lidar at Andes Lidar Observatory

We report the first measurement of nighttime atmospheric temperature and horizontal wind profiles in the lower thermosphere up to 140 km with the Na lidar at Andes Lidar Observatory in Cerro Pachón, Chile (30.25°S, 70.74°W), when enhanced thermospheric Na was observed. Temperature and horizontal wind were derived up to 140 km using various resolutions, with the lowest resolution of about 2.7 hr and 15 km above 130 km. Thus, the measurements span 60 km in vertical, more than double the traditional 25 km. On the night of 17 April 2015, the horizontal wind magnitude in the thermosphere exceeds 150 ms−1, consistent with past rocket measurements. The meridional wind shows a clear transition from the diurnal-tide-dominant mesopause to the semidiurnal-tide-dominant lower thermosphere. A lidar with a 100 times the power aperture product will be able to measure wind and temperature above 160 km and cover longer time span, providing key measurements for the study of atmosphere-space interactions in this region

Transcriptional Regulation of opaR, qrr2–4 and aphA by the Master Quorum-Sensing Regulator OpaR in Vibrio parahaemolyticus

Background: Vibrio parahaemolyticus is a leading cause of infectious diarrhea and enterogastritis via the fecal-oral route. V. harveyi is a pathogen of fishes and invertebrates, and has been used as a model for quorum sensing (QS) studies. LuxR is the master QS regulator (MQSR) of V. harveyi, and LuxR-dependent expression of its own gene, qrr2–4 and aphA have been established in V. harveyi. Molecular regulation of target genes by the V. parahaemolyticus MQSR OpaR is still poorly understood. Methodology/Principal Findings: The bioinformatics analysis indicated that V. parahaemolyticus OpaR, V. harveyi LuxR, V. vulnificu SmcR, and V. alginolyticus ValR were extremely conserved, and that these four MQSRs appeared to recognize the same conserved cis-acting signals, which was represented by the consensus constructs manifesting as a position frequency matrix and as a 20 bp box, within their target promoters. The MQSR box-like sequences were found within the upstream DNA regions of opaR, qrr2–4 and aphA in V. parahaemolyticus, and the direct transcriptional regulation of these target genes by OpaR were further confirmed by multiple biochemical experiments including primer extension assay, gel mobility shift assay, and DNase I footprinting analysis. Translation and transcription starts, core promoter elements for sigma factor recognition, Shine-Dalgarno sequences for ribosome recognition, and OpaR-binding sites were determined for the five target genes of OpaR, which gave a structural map of the OpaR-dependent promoters. Further computational promote

Observation and Modeling of Gravity Wave Propagation through Reflection and Critical Layers above Andes Lidar Observatory at Cerro Pachón, Chile

A complex gravity wave event was observed from 04:30 to 08:10 UTC on 16 January 2015 by a narrow-band sodium lidar and an all-sky airglow imager located at Andes Lidar Observatory (ALO) in Cerro Pachón (30.25∘S, 70.73∘W), Chile. The gravity wave packet had a period of 18–35 min and a horizontal wavelength of about 40–50 km. Strong enhancements of the vertical wind perturbation, exceeding10 m s−1, were found at ∼90 km and ∼103 km, consistent with nearly evanescent wave behavior near a reflection layer. A reduction in vertical wavelength was found as the phase speed approached the background wind speed near ∼93 km. A distinct three-layered structure was observed in the lidar data due to refraction of the wave packet. A fully nonlinear model was used to simulate this event, which successfully reproduced the amplitudes and layered structure seen in observations. The model results provide dynamical insight, suggesting that a double reflection occurring at two separate heights caused the large vertical wind amplitudes, while the three-layered structure in the temperature perturbation was a result of relatively stable regions at those altitudes. The event provides a clear perspective on the filtering processes to which short-period, small-scale gravity waves are subject in mesosphere and lower thermosphere

Reactive uptake coefficients for multiphase reactions determined by a dynamic chamber system

Dynamic flow-through chambers are frequently used to measure gas exchange rates between the atmosphere and biosphere on the Earth's surface such as vegetation and soils. Here, we explore the performance of a dynamic chamber system in determining the uptake coefficient γ of exemplary gases (O3 and SO2) on bulk solid-phase samples. After characterization of the dynamic chamber system, the derived γ is compared with that determined from a coated-wall flow tube system. Our results show that the dynamic chamber system and the flow tube method show a good agreement for γin the range of 10−8 to 10−3. The dynamic chamber technique can be used for liquid samples and real atmospheric aerosol samples without complicated coating procedures, which complements the existing techniques in atmospheric kinetic studies.</p

Even Visually Intact Cell Walls in Waterlogged Archaeological Wood Are Chemically Deteriorated and Mechanically Fragile : A Case of a 170 Year-Old Shipwreck

Structural and chemical deterioration and its impact on cell wall mechanics were investigated for visually intact cell walls (VICWs) in waterlogged archaeological wood (WAW). Cell wall mechanical properties were examined by nanoindentation without prior embedding. WAW showed more than 25% decrease of both hardness and elastic modulus. Changes of cell wall composition, cellulose crystallite structure and porosity were investigated by ATR-FTIR imaging, Raman imaging, wet chemistry, C-13-solid state NMR, pyrolysis-GC/MS, wide angle X-ray scattering, and N-2 nitrogen adsorption. VICWs in WAW possessed a cleavage of carboxyl in side chains of xylan, a serious loss of polysaccharides, and a partial breakage of beta -O-4 interlinks in lignin. This was accompanied by a higher amount of mesopores in cell walls. Even VICWs in WAW were severely deteriorated at the nanoscale with impact on mechanics, which has strong implications for the conservation of archaeological shipwrecks.Peer reviewe

Even Visually Intact Cell Walls in Waterlogged Archaeological Wood Are Chemically Deteriorated and Mechanically Fragile: A Case of a 170 Year-Old Shipwreck

Structural and chemical deterioration and its impact on cell wall mechanics were investigated for visually intact cell walls (VICWs) in waterlogged archaeological wood (WAW). Cell wall mechanical properties were examined by nanoindentation without prior embedding. WAW showed more than 25% decrease of both hardness and elastic modulus. Changes of cell wall composition, cellulose crystallite structure and porosity were investigated by ATR-FTIR imaging, Raman imaging, wet chemistry, 13C-solid state NMR, pyrolysis-GC/MS, wide angle X-ray scattering, and N2 nitrogen adsorption. VICWs in WAW possessed a cleavage of carboxyl in side chains of xylan, a serious loss of polysaccharides, and a partial breakage of β-O-4 interlinks in lignin. This was accompanied by a higher amount of mesopores in cell walls. Even VICWs in WAW were severely deteriorated at the nanoscale with impact on mechanics, which has strong implications for the conservation of archaeological shipwrecks

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

<p>Abstract</p> <p>Background</p> <p>The osmotic regulator OmpR in <it>Escherichia coli </it>regulates differentially the expression of major porin proteins OmpF and OmpC. In <it>Yersinia enterocolitica </it>and <it>Y. pseudotuberculosis</it>, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in <it>Y. pestis </it>are not yet fully understood.</p> <p>Results</p> <p><it>Y. pestis </it>OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The <it>ompR </it>mutation likely did not affect the virulence of <it>Y. pestis </it>strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the <it>ompR </it>mutation, indicating the global regulatory role of OmpR in <it>Y. pestis</it>. Real-time RT-PCR or <it>lacZ </it>fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner.</p> <p>Conclusion</p> <p>OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. <it>Y. pestis </it>OmpR regulates <it>ompC</it>, <it>F</it>, <it>X</it>, and <it>R </it>directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and × at high osmolarity in <it>Y. pestis</it>, in contrast to the reciprocal regulation of them in <it>E. coli</it>. The main difference is that <it>ompF </it>expression is not repressed at high osmolarity in <it>Y. pestis</it>, which is likely due to the absence of a promoter-distal OmpR-binding site for <it>ompF</it>.</p