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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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NASA NTRS2021

Intercomparison of Middle Atmospheric Meteorological Analyses for the Northern Hemisphere Winter 2009-2010

Detailed meteorological analyses based on observations extending through the middle atmosphere (~15 to 100 km altitude) can provide key information to whole atmosphere modelling systems regarding the physical mechanisms linking day-to-day changes in ionospheric electron density to meteorological variability near the Earth’s surface. However, the extent to which independent middle atmosphere analyses differ in their representation of wave-induced coupling to the ionosphere is unclear. To begin to address this issue, we present the first intercomparison among four such analyses, JAGUAR-DAS, MERRA-2, NAVGEM-HA, and WACCMX+DART, focusing on the Northern Hemisphere (NH) 2009-2010 winter, which includes a major sudden stratospheric warming (SSW). This intercomparison examines the altitude, latitude, and time dependences of zonal mean zonal winds and temperatures among these four analyses over the 1 December 2009 – 31 March 2010 period, as well as latitude and altitude dependences of monthly mean amplitudes of the diurnal and semidiurnal migrating solar tides, the eastward propagating diurnal zonal wave number 3 nonmigrating tide, and traveling planetary waves associated with the quasi-5-day and quasi-2-day Rossby modes. Our results show generally good agreement among the four analyses up to the stratopause (~50 km altitude). Large discrepancies begin to emerge in the mesosphere and lower thermosphere owing to (1) differences in the types of satellite data assimilated by each system and (2) differences in the details of the global atmospheric models used by each analysis system. The results of this intercomparison provide initial estimates of uncertainty in analyses commonly used to constrain middle atmospheric meteorological variability in whole atmosphere model simulations.

John P Mccormack↗
NASA NTRS2009

Synthesis and Assimilation Systems - Essential Adjuncts to the Observing System

Assimilation systems synthesize diverse in-situ and satellite data streams into full four-dimensional state estimates by combining the strengths of each data set and also of the model. The resulting analysis provides an integrated view of the information in the various observations as well as derived estimates of unobserved quantities. Assimilation systems are particularly important for the ocean where subsurface observations, even today, are sparse and intermittent compared with the scales needed to represent ocean variability and where satellites only sense the surface. Increasingly, models and assimilation systems are being used to provide information about the current observing system and to help in the design plans for new observations. Whether it is as a user of observations or a contributor to evaluation of the observing system, ocean synthesis and assimilation systems are now an integral part of the global ocean observing and information system. Major advances have been made over the last decade under the auspices of WCRP's Climate Variability and Predictability Project (CLIVAR) and the Global Ocean Data Assimilation Experiment (GODAE). In addition to advances in the assimilation systems, there have been major developments in the observing system, with satellite altimetry, the tropical moored buoy arrays in the Pacific and Atlantic, and more recently Argo. These developments have led to significant advances in our understanding and prediction of ocean variations at both mesoscale and climate scales. Many challenges remain. Some of these challenges lie in the observations themselves, some in the assimilation systems that, even in the more recent era of unprecedented observations from satellite altimetry and Argo, provide different views of climate variations. Yet there are many examples of successful applications from ocean assimilation products. Use of these systems for assessing the observing system helps identify the strengths of each observation type, and indicates that none of the current observations is redundant. Indeed, the indication is that the ocean remains under-sampled and that further improvements in the observing system are needed for both climate monitoring and prediction. Future developments will be increasingly towards consistent analyses across components of the Earth system using, e.g., coupled atmosphere-ocean models.

Rienecker, Michele M.↗
NASA NTRS2015

Chlorophyll Variability in the Oligotrophic Gyres: Mechanisms, Seasonality and Trends

A 16-year (1998-2013) analysis of trends and seasonal patterns was conducted for the 5 subtropical ocean gyres using chlorophyll-a (Chl-a) retrievals from ocean color satellite data, sea surface temperature (SST) obtained from optimally interpolated Advanced Very High Resolution Radiometer (AVHRR) data, and sea-level anomaly (SLA) from Aviso multi-sensor altimetry data. Trend analysis was also performed on mixed-layer data derived from gridded temperature and salinity profiles (1998-2010) from the Simple Ocean Data Assimilation (SODA) model. The Chl-a monthly composites were constructed from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate-resolution Imaging Spectroradiometer (MODIS) on Aqua using two different algorithms: the standard algorithm (STD) that has been in use since the start of the SeaWiFS mission in 1997, and a more recently developed Ocean Color Index (OCI) algorithm that is purported to provide improved accuracy in low chlorophyll waters such as the oligotrophic regions of the subtropical gyres. Trends were obtained for all gyres using both STD and OCI algorithms, which demonstrated generally consistent results. The North Pacific, Indian Ocean, North Atlantic and South Atlantic gyres showed significant downward trends in Chl-a, while the South Pacific gyre has a much weaker upward trend with no statistical significance. Time series of satellite-derived net primary production (NPP) showed downward trends for all the gyres, while all 5 gyres exhibited positive trends in SST and SLA. The seasonal variability of Chl-a in each gyre is tightly coupled to the variability in mixed layer depth (MLD) with peak values in winter in both hemispheres when vertical mixing is more vigorous, reaching depths approaching the nutricline (ZNO3, here defined as the depth of the 0.2 micron nitrate concentration). On a seasonal basis, Chl-a concentrations increase when the MLD approaches or is deeper than the nutricline depth, in agreement with the concept that vertical mixing is the major driving mechanism for phytoplankton photosynthesis in the interior of the gyres. In addition, MLD and SST seasonal changes are well correlated indicating that SST is a reasonable index of vertical mixing in the gyres. The combination of surface warming trends and biomass reduction over the 16-year period has the potential to reduce atmospheric CO2 uptake by the gyres and therefore influence the global carbon cycle.

Long-term trends↗
NASA NTRS1998

Arctic Sea Ice Motion from Wavelet Analysis of Satellite Data

Wavelet analysis of DMSP SSM/I (Special Sensor Microwave/Imager) 85 GHz and 37 GHz radiance data, SMMR (Scanning Multichannel Microwave Radiometer) 37 GHz, and NSCAT (NASA Scatterometer) 13.9 GHZ data can be used to obtain daily sea ice drift information for both the northern and southern polar regions. The derived maps of sea ice drift provide both improved spatial coverage over the existing array of Arctic Ocean buoys and better temporal resolution over techniques utilizing data from satellite synthetic aperture radars (SAR). Examples of derived ice-drift maps in the Arctic illustrate large-scale circulation reversals within a period of a couple weeks. Comparisons with ice displacements derived from buoys show good quantitative agreement. NASA Scatterometer (NSCAT) 13.9 GHZ data have been also used for wavelet analysis to derive sea-ice drift. First, the 40' incidence-angle, sigma-zero (surface roughness) daily map of whole Arctic region with 25 km of pixel size from satellite's 600 km swath has been constructed. Then, the similar wavelet transform procedure to SSM/I data can be applied. Various scales of wavelet transform and threshold have been tested. By overlaying , neighbor filtering, and block-averaging the results of multiscale wavelet transforms, the final sea ice drift vectors are much smooth and representative to the sea ice motion. This wavelet analysis procedure is robust and can make a major contribution to the understanding of ice motion over large areas at relatively high temporal resolutions. The results of wavelet analysis of SSM/I and NSCAT images and buoy data can be merged by some data fusion techniques and will help to improve our current knowledge of sea ice drift and related processes through the data assimilation of ocean-ice numerical model.

Liu, Antony K.↗
DOE OSTI2024

Spatio–Temporal Machine Learning for Regional to Continental Scale Terrestrial Hydrology

Integrated hydrologic models can simulate coupled surface and subsurface processes but are computationally expensive to run at high resolutions over large domains. Here we develop a novel deep learning model to emulate subsurface flows simulated by the integrated ParFlow–CLM model across the contiguous US. We compare convolutional neural networks like ResNet and UNet run autoregressively against our novel architecture called the Forced SpatioTemporal RNN (FSTR). The FSTR model incorporates separate encoding of initial conditions, static parameters, and meteorological forcings, which are fused in a recurrent loop to produce spatiotemporal predictions of groundwater. We evaluate the model architectures on their ability to reproduce 4D pressure heads, water table depths, and surface soil moisture over the contiguous US at 1 km resolution and daily time steps over the course of a full water year. The FSTR model shows superior performance to the baseline models, producing stable simulations that capture both seasonal and event–scale dynamics across a wide array of hydroclimatic regimes. The emulators provide over 1,000× speedup compared to the original physical model, which will enable new capabilities like uncertainty quantification and data assimilation for integrated hydrologic modeling that were not previously possible. Our results demonstrate the promise of using specialized deep learning architectures like FSTR for emulating complex process–based models without sacrificing fidelity.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1999

Real-Time Assimilation of Goes-Derived Products into A Mesoscale Model and It's Impact on Short-Term (06-36hr) Forecasts from 17 October 1998 through the Present

As the parameterizations of surface energy budgets in regional models have become more complete physically, models have the potential to be much more realistic in simulations of coupling between surface radiation, hydrology, and surface energy transfer. Realizing the importance of properly specifying the surface energy budget, many institutions are using land-surface models to represent the lower boundary forcing associated with biophysical processes and soil hydrology. However, the added degrees of freedom due to inclusion of such land-surface schemes require the specification of additional parameters within the model system such as vegetative resistances, green vegetation fraction, leaf area index, soil physical and hydraulic characteristics, stream flow, runoff, and the vertical distribution of soil moisture. Spatial heterogeneity of these parameters makes correct specification problematic since measurements are not routinely available. A technique has been developed for assimilating GOES-IR skin temperature tendencies, solar insolation, and surface albedo into the surface energy budget equation of a mesoscale model so that the simulated rate of temperature change closely agrees with the satellite observations. The technique has been successfully employed in a number of mesoscale models in case-study mode. We have taken the next step and developed a study to determine if assimilating these types of data into mesoscale models in real-time can improve short-term (648h) forecasts of temperature, relative humidity, and QPF on a daily basis over relatively large regions. Therefore, an operational modeling/assimilation system has been developed at the GHCC during the past summer that allows us to produce simulations out to 48 hours in a timely manor. The PSU/NCAR MM5 is used in a nested configuration with a 25 km grid covering the southeastern third of the US. The model has been on-line since 1 July 1998 and forecast products are posted on our web site. The satellite algorithms that generate data to be assimilated came on-line 17 October 1998. Quantitative assessment of the forecast quality is performed via traditional verification statistics. In addition, invaluable qualitative information is obtained through close collaboration with several NWSFO's who are using the MM5 products in real-time on a daily basis. The assimilation technique has been applied in an off-line mode since 17 October. Results based on bulk statistical verification of surface meteorology over the entire Southeastern US show that assimilating the GOES-derived land surface tendencies and solar radiation results in a significant reduction of the shelter air temperature and RH bias on a daily basis. In fact, the assimilation technique has produced improved temperature and RH forecasts for 97% of the 100 simulations performed to date. Work is currently underway to determine the sensitivity of the assimilation procedure to the availability of satellite data, length of assimilation period, model initialization, and synoptic-scale meteorological conditions. In addition, results from a detailed energy budget analysis using the Early Eta, our operational MM5, and the assimilation runs will help us to better understand the satellite assimilation the land-surface energy budge. Research during the spring-summer of 1999 will focus on the impact of the assimilation technique during the warm season where it is hypothesized that it can have a positive impact on QPF during conditions of weak synoptic-scale forcing.

Lapenta, William M.↗
NASA NTRS2024

Calculating the High-Latitude Ionospheric Electrodynamics Using A Machine Learning-Based Field-Aligned Current Model

We introduce a new framework called Machine Learning (ML) based Auroral Ionospheric electrodynamics Model (ML-AIM). ML-AIM solves a current continuity equation by utilizing the ML model of Field Aligned Currents of Kunduri et al. (2020, https://doi.org/10.1029/2020JA027908), the FAC-derived auroral conductance model of Robinson et al. (2020, https://doi.org/10.1029/2020JA028008), and the solar irradiance conductance model of Moen and Brekke (1993, https://doi.org/10.1029/92gl02109). The ML-AIM inputs are 60-min time histories of solar wind plasma, interplanetary magnetic fields (IMF), and geomagnetic indices, and its outputs are ionospheric electric potential, electric fields, Pedersen/Hall currents, and Joule Heating. We conduct two ML-AIM simulations for a weak geomagnetic activity interval on 14 May 2013 and a geomagnetic storm on 7–8 September 2017. ML-AIM produces physically accurate ionospheric potential patterns such as the two-cell convection pattern and the enhancement of electric potentials during active times. The cross polar cap potentials (ΦPC) from ML-AIM, the Weimer (2005, https://doi.org/10.1029/2004ja010884) model, and the Super Dual Auroral Radar Network (SuperDARN) data-assimilated potentials, are compared to the ones from 3204 polar crossings of the Defense Meteorological Satellite Program F17 satellite, showing better performance of ML-AIM than others. ML-AIM is unique and innovative because it predicts ionospheric responses to the time-varying solar wind and geomagnetic conditions, while the other traditional empirical models like Weimer (2005, https://doi.org/10.1029/2004ja010884) designed to provide a quasi-static ionospheric condition under quasi-steady solar wind/IMF conditions. Plans are underway to improve ML-AIM performance by including a fully ML network of models of aurora precipitation and ionospheric conductance, targeting its characterization of geomagnetically active times.

auroral electrodynamics↗
NASA NTRS2011

Quantifying the Aerosol Semi-Direct Effect in the NASA GEOS-5 AGCM

Aerosols such as black carbon, dust, and some organic carbon species both scatter and absorb incoming solar radiation. This direct aerosol radiative forcing (DARF) redistributes solar energy both by cooling the surface and warming the atmosphere. As a result, these aerosols affect atmospheric stability and cloud cover (the semi-direct effect, or SDE). Furthermore, in regions with persistent high loadings of absorbing aerosols (e.g. Asia), regional circulation patterns may be altered, potentially resulting in changes in precipitation patterns. Here we investigate aerosol-climate coupling using the NASA Goddard Earth Observing System model version 5 (GEOS-5) atmospheric general circulation model (AGCM), in which we have implemented an online version of the Goddard Chemistry, Aerosol, Radiation and Transport (GOCART) model. GOCART includes representations of the sources, sinks, and chemical transformation of externally mixed dust, sea salt, sulfate, and carbonaceous aerosols. We examine a series of free-running ensemble climate simulations of the present-day period (2000-2009) forced by observed sea surface temperatures to determine the impact of aerosols on the model climate. The SDE and response of each simulation is determined by differencing with respect to the control simulation (no aerosol forcing). In a free-running model, any estimate of the SDE includes changes in clouds due both to atmospheric heating from aerosols and changes in circulation. To try and quantify the SDE without these circulation changes we then examine the DARF and SDE in GEOS-5 with prescribed meteorological analyses introduced by the MERRA analysis. By doing so, we are able to examine changes in model clouds that occur on shorter scales (six hours). In the GEOS-5 data assimilation system (DAS), the analysis is defined as the best estimate of the atmospheric state at any given time, and it is determined by optimally combining a first-guess short-term GCM forecast with all available observations. The Incremental Analysis Update (IAU) is added to the model forecast tendencies to align them with the analysis every six hours, thus preventing longer timescale feedbacks due to the aerosol forcing. We calculate the SDE by comparing model runs with and without aerosols, and the difference in the IAU between these runs is a useful metric with which to evaluate the impact of the SDE on the model atmosphere and clouds. Decreasing the IAU indicates that the aerosol direct and semi-direct effects act to reduce the bias between the model and observations and vice versa.

Randles, Cynthia A.↗
NASA NTRS2019

Global Ocean Primary Production Trends in the Modern Ocean Color Satellite Record (1998-2015)

Ocean primary production (PP), representing the uptake of inorganic carbon through photosynthesis, supports marine life and affects carbon exchange with the atmosphere. It is difficult to ascertain its magnitude, variability, and trends due to our inability to measure it directly at large scales. Yet it is paramount for understanding changes in marine health, fisheries, and the global carbon cycle. Using assimilation of ocean color satellite data into an ocean biogeochemical model, we estimate that global net ocean PP has experienced a small but significant decline −0.8 PgC/y (−2.1%) per decade (P < 0.05) in the 18-year satellite record from 1998 to 2015. This decline is associated with shallowing surface mixed layer depth (−2.4% per decade) and decreasing nitrate concentrations (−3.2% per decade). Relative contributions to PP by various types of ocean phytoplankton have changed, with decreases in production by intermediate-sized phytoplankton represented by chlorophytes (−14.3% per decade). This is partially compensated by increases from the unique, more nutrient-efficient, coccolithophores (8.4% per decade). Geographically, the North and Equatorial Indian Oceans are responsible for much of the decline in PP, falling 0.16 and 0.69 PgC/y per decade, respectively. Reduced production by large, fast-growing diatoms along with chlorophytes characterizes the decline here. In contrast, increases in PP are found in the North and North Central Pacific. The increases here are led by chlorophytes in the North Pacific and the small cyanobacteria in the North Central Pacific. These results suggest that the multi-decadal satellite observational record, coupled with an underlying representation of marine biodiversity in a model, can monitor the uptake of carbon by phytoplankton and that changes, although small, are occurring in the global oceans.

Watson W Gregg↗
NASA NTRS2017

Upper Blue Nile Basin Water Budget from a Multi-Model Perspective

Improved understanding of the water balance in the Blue Nile is of critical importance because of increasingly frequent hydroclimatic extremes under a changing climate. The intercomparison and evaluation of multiple land surface models (LSMs) associated with different meteorological forcing and precipitation datasets can offer a moderate range of water budget variable estimates. In this context, two LSMs, Noah version 3.3 (Noah3.3) and Catchment LSM version Fortuna 2.5 (CLSMF2.5) coupled with the Hydrological Modeling and Analysis Platform (HyMAP) river routing scheme are used to produce hydrological estimates over the region. The two LSMs were forced with different combinations of two reanalysis-based meteorological datasets from the Modern-Era Retrospective analysis for Research and Applications datasets (i.e., MERRA-Land and MERRA-2) and three observation-based precipitation datasets, generating a total of 16 experiments. Modeled evapotranspiration (ET), streamflow, and terrestrial water storage estimates were evaluated against the Atmosphere-Land Exchange Inverse (ALEXI) ET, in-situ streamflow observations, and NASA Gravity Recovery and Climate Experiment (GRACE) products, respectively. Results show that CLSMF2.5 provided better representation of the water budget variables than Noah3.3 in terms of Nash-Sutcliffe coefficient when considering all meteorological forcing datasets and precipitation datasets. The model experiments forced with observation-based products, the Climate Hazards group Infrared Precipitation with Stations (CHIRPS) and the Tropical Rainfall Measuring Mission (TRMM) Multi-Satellite Precipitation Analysis (TMPA), outperform those run with MERRA-Land and MERRA-2 precipitation. The results presented in this paper would suggest that the Famine Early Warning Systems Network (FEWS NET) Land Data Assimilation System incorporate CLSMF2.5 and HyMAP routing scheme to better represent the water balance in this region.

Rainfall↗
DOE OSTI2024

Earth System Reanalysis in Support of Climate Model Improvements

Recent climate model developments, established through increased model resolution, have led to substantial improvements in model simulations of the time-evolving, coupled Earth system and its subcomponents. However, regardless of resolution, climate models will always produce climate features and variability that differ from the real world and will be prone to biases. This is due to many remaining uncertainties, such as in parametric and structural model uncertainty, in the initial conditions prescribed, and in the prescribed (scenario) forcing which varies on decadal to centennial timescales. Further model improvements are expected to arise specifically from improved representation of physical processes realized through model-data fusion. This will create an unprecedented opportunity to better exploit a large array of Earth observations, from in situ measurements to weather radars and satellite observations, as the resolved scales of the models approach those of the observations. For this, climate DA will be the central tool to bring models and observations into consistency, by improving initial conditions, inferring uncertain model parameters and structure, and quantifying uncertainty. Generally, there will be advantages and complementarities of adjoint-based smoother approaches, ensemble-based filter approaches, or new ML-inspired approaches. Yet, the ever-increasing model resolution will present growing challenges arising from computational cost, calling for new ways of performing data assimilation and model optimization. Using the complementarity in a hybrid approach, blending tools and concepts from variational, ensemble and ML methods might be what is required in the future. In this context ML could be important to handle non-linear responses, and to better approximate non-Gaussian distributions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

ABSTRACTSulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources, and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

Trotter, Valentine V↗
DOE OSTI2023

Methanogens acquire and bioaccumulate nickel during reductive dissolution of nickelian pyrite

ABSTRACT Nickel (Ni) is a key component of the active site metallocofactors of numerous enzymes required for methanogenesis, including [NiFe]-hydrogenase, carbon monoxide dehydrogenase, and methyl CoM reductase, leading to a high demand for Ni among methanogens. However, methanogens often inhabit euxinic environments that favor the sequestration of nickel as metal-sulfide minerals, such as nickelian pyrite [(Ni,Fe)S 2 ], that have low solubilities and that are not considered bioavailable. Recently, however, several different model methanogens ( Methanosarcina barkeri , Methanococcus voltae , Methanococcus maripaludis ) were shown to reductively dissolve pyrite (FeS 2 ) and to utilize dissolution products to meet iron and sulfur biosynthetic demands. Here, using M. barkeri Fusaro, and laboratory-synthesized (Ni,Fe)S 2 that was physically isolated from cells using dialysis membranes, we show that trace nickel (<20 nM) abiotically solubilized from the mineral can support methanogenesis and limited growth, roughly fivefold less than the minimum concentration known to support methanogenesis. Furthermore, when provided direct contact with (Ni,Fe)S 2 , M. barkeri promoted the reductive dissolution of (Ni,Fe)S 2 and assimilated solubilized nickel, iron, and sulfur as its sole source of these elements. Cells that reductively dissolved (Ni,Fe)S 2 bioaccumulated approximately fourfold more nickel than those grown with soluble nickel and sulfide but had similar metabolic coupling efficiencies. While the mechanism for Ni uptake in archaeal methanogens is not known, homologs of the bacterial Nik uptake system were shown to be ubiquitous across methanogen genomes. Collectively, these observations indicate that (Ni,Fe)S 2 is bioavailable in anoxic environments and that methanogens can convert this mineral into nickel-, iron-, and sulfur-containing metalloenzymes to support methanogenesis and growth. IMPORTANCE Nickel is an essential metal, and its availability has changed dramatically over Earth history due to shifts in the predominant type of volcanism in the late Archean that limited its availability and an increase in euxinic conditions in the early Proterozoic that favored its precipitation as nickel sulfide minerals. Observations presented herein indicate that the methanogen, Methanosarcina barkeri , can acquire nickel at low concentration (<20 nM) from soluble and mineral sources. Furthermore, M. barkeri was shown to actively reduce nickelian pyrite; use dissolution products to meet their iron, sulfur, and nickel demands; and bioaccumulate nickel. These data help to explain how M. barkeri (and possibly other methanogens and anaerobes) can acquire nickel in contemporary and past anoxic or euxinic environments.

(NiFe)S2↗
DOE OSTI2023

Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

Sulfate-reducing bacteria (SRB) are obligate anaerobes that can couple their growth to the reduction of sulfate. Despite the importance of SRB to global nutrient cycles and their damage to the petroleum industry, our molecular understanding of their physiology remains limited. To systematically provide new insights into SRB biology, we generated a randomly barcoded transposon mutant library in the model SRB Desulfovibrio vulgaris Hildenborough (DvH) and used this genome-wide resource to assay the importance of its genes under a range of metabolic and stress conditions. In addition to defining the essential gene set of DvH, we identified a conditional phenotype for 1,137 non-essential genes. Through examination of these conditional phenotypes, we were able to make a number of novel insights into our molecular understanding of DvH, including how this bacterium synthesizes vitamins. For example, we identified DVU0867 as an atypical L-aspartate decarboxylase required for the synthesis of pantothenic acid, provided the first experimental evidence that biotin synthesis in DvH occurs via a specialized acyl carrier protein and without methyl esters, and demonstrated that the uncharacterized dehydrogenase DVU0826:DVU0827 is necessary for the synthesis of pyridoxal phosphate. In addition, we used the mutant fitness data to identify genes involved in the assimilation of diverse nitrogen sources and gained insights into the mechanism of inhibition of chlorate and molybdate. Our large-scale fitness dataset and RB-TnSeq mutant library are community-wide resources that can be used to generate further testable hypotheses into the gene functions of this environmentally and industrially important group of bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Analysis of the tropospheric water distribution during FIRE 2

The Penn State/NCAR mesoscale model, as adapted for use at ARC, was used as a testbed for the development and validation of cloud models for use in General Circulation Models (GCM's). This modeling approach also allows us to intercompare the predictions of the various cloud schemes within the same dynamical framework. The use of the PSU/NCAR mesoscale model also allows us to compare our results with FIRE-II (First International Satellite Cloud Climatology Project Regional Experiment) observations, instead of climate statistics. Though a promising approach, our work to date revealed several difficulties. First, the model by design is limited in spatial coverage and is only run for 12 to 48 hours at a time. Hence the quality of the simulation will depend heavily on the initial conditions. The poor quality of upper-tropospheric measurements of water vapor is well known and the situation is particularly bad for mid-latitude winter since the coupling with the surface is less direct than in summer so that relying on the model to spin-up a reasonable moisture field is not always successful. Though one of the most common atmospheric constituents, water vapor is relatively difficult to measure accurately, especially operationally over large areas. The standard NWS sondes have little sensitivity at the low temperatures where cirrus form and the data from the GOES 6.7 micron channel is difficult to quantify. For this reason, the goals of FIRE Cirrus II included characterizing the three-dimensional distribution of water vapor and clouds. In studying the data from FIRE Cirrus II, it was found that no single special observation technique provides accurate regional distributions of water vapor. The Raman lidar provides accurate measurements, but only at the Hub, for levels up to 10 km, and during nighttime hours. The CLASS sondes are more sensitive to moisture at low temperatures than are the NWS sondes, but the four stations only cover an area of two hundred kilometers on a side. The aircraft give the most accurate measurements of water vapor, but are limited in spatial and temporal coverage. This problem is partly alleviated by the use of the MAPS analyses, a four-dimensional data assimilation system that combines the previous 3-hour forecast with the available observations, but its upper-level moisture analyses are sometimes deficient because of the vapor measurement problem. An attempt was made to create a consistent four-dimensional description of the water vapor distribution during the second IFO by subjectively combining data from a variety of sources, including MAPS analyses, CLASS sondes, SPECTRE sondes, NWS sondes, GOES satellite analyses, radars, lidars, and microwave radiometers.

Westphal, Douglas L.↗
NASA NTRS2007

Coupled Stochastic Time-Inverted Lagrangian Transport/Weather Forecast and Research/Vegetation Photosynthesis and Respiration Model: Simulations of Tower-Based and Airborne CO2 Measurements - Part II

This paper evaluates simulations of atmospheric CO2 measured in 2004 at continental surface and airborne receptors, intended to test the capability to use data with high temporal and spatial resolution for analyses of carbon sources and sinks at regional and continental scales. The simulations were performed using the Stochastic Time-Inverted Lagrangian Transport (STILT) model driven by the Weather Forecast and Research (WRF) model, and linked to surface fluxes from the satellite-driven Vegetation Photosynthesis and Respiration Model (VPRM). The simulations provide detailed representations of hourly CO2 tower data and reproduce the shapes of airborne vertical profiles with high fidelity. WRF meteorology gives superior model performance compared with standard meteorological products, and the impact of including WRF convective mass fluxes in the STILT trajectory calculations is significant in individual cases. Important biases in the simulation are associated with the nighttime CO2 build-up and subsequent morning transition to convective conditions, and with errors in the advected lateral boundary condition. Comparison of STILT simulations driven by the WRF model against those driven by the Brazilian variant of the Regional Atmospheric Modeling System (BRAMS) shows that model-to-model differences are smaller than between an individual transport model and observations, pointing to systematic errors in the simulated transport. Future developments in the WRF model s data assimilation capabilities, basic research into the fundamental aspects of trajectory calculations, and intercomparison studies involving other transport models, are possible venues for reducing these errors. Overall, the STILT/WRF/VPRM offers a powerful tool for continental and regional scale carbon flux estimates.

Eluszkiewicz, Janusz↗
DOE OSTI2021

Joint CO 2 Mole Fraction and Flux Analysis Confirms Missing Processes in CASA Terrestrial Carbon Uptake Over North America

Terrestrial biosphere models (TBMs) play a key role in the detection and attribution of carbon cycle processes at local to global scales and in projections of the coupled carbon-climate system. TBM evaluation commonly involves direct comparison to eddy-covariance flux measurements. This study uses atmospheric CO 2 mole fraction ([CO 2 ]) measured in situ from aircraft and tower, in addition to flux-measurements from summer 2016 to evaluate the CASA TBM. WRF-Chem is used to simulate [CO 2 ] using biogenic CO 2 fluxes from a CASA parameter-based ensemble and CarbonTracker version 2017 (CT2017) in addition to transport and CO 2 boundary condition ensembles. The resulting “super ensemble” of modeled [CO 2 ] demonstrates that the biosphere introduces the majority of uncertainty to the simulations. Both aircraft and tower [CO 2 ] data show that the CASA ensemble net ecosystem exchange (NEE) of CO 2 is biased high (NEE too positive) and identify the maximum light use efficiency E max a key parameter that drives the spread of the CASA ensemble in summer 2016. These findings are verified with flux-measurements. The direct comparison of the CASA flux ensemble with flux-measurements confirms missing sink processes in CASA. Separating the daytime and nighttime flux, we discover that the underestimated net uptake results from missing sink processes that result in overestimation of respiration. NEE biases are smaller in the CT2017 posterior biogenic fluxes, which assimilates observed [CO 2 ]. Flux tower analyses, however, reveal an unrealistic overestimation of nighttime respiration in CT2017 due to the limitation of inversion strategy.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2012

Ground and Airborne Methane Measurements using Optical Parametric Amplifiers

We report on an initial airborne demonstration of atmospheric methane column measurements at 1.65 micrometers using a widely tunable, seeded optical parametric amplifier (OPA) lidar and a photon counting detector. Methane is an important greenhouse gas and accurate knowledge of its sources and sinks is needed for climate modeling. Our lidar system uses 20 pulses at increasing wavelengths and integrated path differential absorption (IPDA) to map a methane line at 1650.9 nanometers. The wavelengths are generated by using a Nd:YAG pump laser at 1064.5 nanometers and distributed feedback diode laser at 1650.9 nanometers and a periodically-poled lithium niobate (PPLN) crystal. The pulse width was 3 nanoseconds and the pulse repetition rate was 6.28 KHz. The outgoing energy was approximately 13 microJoules/pulse. A commercial 20 nanometer diameter fiber-coupled telescope with a photon counting detector operated in analog mode with a 0.8 nanometer bandpass filter was used as the lidar receiver. The lidar system was integrated on NASA's DC-8 flying laboratory, based at Dryden Airborne operations Facility (DAOF) in Palmdale CA. Three flights were performed in the central valley of California. Each flight lasted about 2.5 hours and it consisted of several flight segments at constant altitudes at approximately 3, 4.5, 6, 7.6, 9.1, 10.6 km (l0, 15, 20, 25, 30, 35 kft). An in-situ cavity ring down spectrometer made by Picarro Inc. was flown along with the lidar instrument provided us with the "truth" i.e. the local CH4, CO2 and H2O concentrations at the constant flight altitude segments. Using the aircraft's altitude, GPS, and meteorological data we calculated the theoretical differential optical depth of the methane absorption at increasing altitudes. Our results showed good agreement between the experimentally derived optical depth measurements from the lidar instrument and theoretical calculations as the flight altitude was increased from 3 to 10.6 kilometers, assuming a constant methane mixing ratio of 1.8 parts per million. The in-situ spectrometer did not show any significant deviations from the ambient concentrations. Further analysis using meteorological data from the Global Modeling and Assimilation Office (http://gmao.gsfc.nasa.gov/) to derive the theoretical optical depth also showed good agreement with the experimentally derived values. The OPA lidar system with slight modifications has also been used to measure CO2, water vapor, and CO in the near and mid-infrared spectral regions on the ground.

Riris, Haris↗