SEARCH · Engineering Papers

Results for “Interaction Region”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,441 records · Page 80

All sources NASA NTRS DOE OSTI

NASA NTRSDate not supplied

Analysis and Prediction of VFR Vs IFR Traffic Behavior to Support Uncrewed Aircraft Flight Operations at Regional Airports

Uncrewed Aircraft flight operations at a regional airport will be affected by the uncertainty in the Visual Flight Rules traffic around. This paper analyzes Visual Flight Rules traffic behavior, compares it with Instrument Flight Rules traffic and develops traffic prediction methods to support uncrewed aircraft flight operations. The spatio-temporal distribution of traffic operating under Visual Flight Rules and Instrument Flight Rules was analyzed from one month of historical track data around Fort Worth Alliance airport as a representative regional airport. The traffic behavior was visualized as occupancy maps generated at different altitudes. The Instrument Flight Rules traffic was concentrated in fewer regions of the airspace along structured routes where the risk of interacting with one or more flights reached close to fifty percent in some areas. Visual Flight Rules traffic was spread over more regions, mostly segregated from the Instrument Flight Rules regions, and the risk of interaction was lower reaching up to twenty-five percent on average over the month in some regions. The interaction risk was predicted using predictive occupancy maps over multiple time horizons and conditioned on time and partial observation of traffic in the vicinity. The month-to-month predictability of Visual Flight Rules risk was lower than that of the Instrument Flight Rules traffic, consistently over all the conditions analyzed. However, the prediction and its accuracy were demonstrated to be sensitive to the conditions used. The predictive models generated can be used to support both strategic planning and in-flight decision-making by uncrewed aircraft during flight operations while maintaining an acceptable risk of interacting with other traffic.

VFR↗

DOE OSTI2012

Light magnetic dark matter in direct detection searches

We study a fermionic Dark Matter particle carrying magnetic dipole moment and analyze its impact on direct detection experiments. In particular we show that it can accommodate the DAMA, CoGeNT and CRESST experimental results. Assuming conservative bounds, this candidate is shown not to be ruled out by the CDMS, XENON and PICASSO experiments. We offer an analytic understanding of how the long-range interaction modifies the experimental allowed regions, in the cross section versus Dark Matter mass parameter space, with respect to the typically assumed contact interaction. Finally, in the context of a symmetric Dark Matter sector, we determine the associated thermal relic density, and further provide relevant constraints imposed by indirect searches and colliders.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2017

Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation history

Abstract. The parafluvial hyporheic zone combines the heightened biogeochemical and microbial interactions indicative of a hyporheic region with direct atmospheric/terrestrial inputs and the effects of wet–dry cycles. Therefore, understanding biogeochemical cycling and microbial interactions in this ecotone is fundamental to understanding biogeochemical cycling at the aquatic–terrestrial interface and to creating robust hydrobiogeochemical models of dynamic river corridors. We aimed to (i) characterize biogeochemical and microbial differences in the parafluvial hyporheic zone across a small spatial domain (6 lateral meters) that spans a breadth of inundation histories and (ii) examine how parafluvial hyporheic sediments respond to laboratory-simulated re-inundation. Surface sediment was collected at four elevations along transects perpendicular to flow of the Columbia River, eastern WA, USA. The sediments were inundated by the river 0, 13, 127, and 398 days prior to sampling. Spatial variation in environmental variables (organic matter, moisture, nitrate, glucose, % C, % N) and microbial communities (16S and internal transcribed spacer (ITS) rRNA gene sequencing, qPCR) were driven by differences in inundation history. Microbial respiration did not differ significantly across inundation histories prior to forced inundation in laboratory incubations. Forced inundation suppressed microbial respiration across all histories, but the degree of suppression was dramatically different between the sediments saturated and unsaturated at the time of sample collection, indicating a binary threshold response to re-inundation. We present a conceptual model in which irregular hydrologic fluctuations facilitate microbial communities adapted to local conditions and a relatively high flux of CO2. Upon rewetting, microbial communities are initially suppressed metabolically, which results in lower CO2 flux rates primarily due to suppression of fungal respiration. Following prolonged inundation, the microbial community adapts to saturation by shifting composition, and the CO2 flux rebounds to prior levels due to the subsequent change in respiration. Our results indicate that the time between inundation events can push the system into alternate states: we suggest (i) that, above some threshold of inundation interval, re-inundation suppresses respiration to a consistent, low rate and (ii) that, below some inundation interval, re-inundation has a minor effect on respiration. Extending reactive transport models to capture processes that govern such dynamics will provide more robust predictions of river corridor biogeochemical function under altered surface water flow regimes in both managed and natural watersheds.

58 GEOSCIENCES↗

DOE OSTI2018

Structural analysis of activating mutants of YfiB from Pseudomonas aeruginosa PAO1

Highlights: • Crystal structures of activating mutants of P. aeruginosa YfiB were determined. • F48S and W55L activating mutants of YfiB crystallize as dimers. • The L43P mutant of YfiB is monomeric and forms a stable complex with YfiR. • The YfiB activating region undergoes a dramatic rearrangement upon YfiR binding. • Extensive interactions are formed between the YfiB activating region and YfiR. Bacterial cyclic-di-GMP (c-di-GMP) is an important messenger molecule that influences diverse cellular processes including motility, virulence and cytotoxicity systems, polysaccharide synthesis and biofilm formation. The YfiBNR tripartite signalling system in P. aeruginosa modulates the cellular c-di-GMP levels in response to signals received from the periplasm. In this study, we analyse the structures of activating mutants of the outer membrane protein YfiB that give rise to increased surface attachment and biofilm formation. The F48S and W55L mutants of YfiB(27–168) crystallize in the same dimeric arrangement as our previously reported YfiB structures that preclude complex formation with YfiR. The L43P mutant of YfiB(27–168) is monomeric and forms a stable complex with YfiR. The YfiB(L43P)-YfiR crystal structure reveals a dramatic rearrangement of the N-terminal fragment, which is implicated in increased YfiB activation and membrane attachment, upon YfiR binding. Comparison with our previous complex structure between YfiB(59–168) and YfiR reveals extensive interactions between the N-terminal fragment of YfiB (residues 35–55) and YfiR.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2013

A first principle study for the adsorption and absorption of carbon atom and the CO dissociation on Ir(100) surface

We employ density functional theory to examine the adsorption and absorption of carbon atom as well as the dissociation of carbon monoxide on Ir(100) surface. We find that carbon atoms bind strongly with Ir(100) surface and prefer the high coordination hollow site for all coverages. In the case of 0.75 ML coverage of carbon, we obtain a bridging metal structure due to the balance between Ir–C and Ir–Ir interactions. In the subsurface region, the carbon atom prefers the octahedral site of Ir(100) surface. We find large diffusion barrier for carbon atom into Ir(100) surface (2.70 eV) due to the strong bonding between carbon atom and Ir(100) surface, whereas we find a very small segregation barrier (0.22 eV) from subsurface to the surface. The minimum energy path and energy barrier for the dissociation of CO on Ir(100) surface are obtained by using climbing image nudge elastic band. The energy barrier of CO dissociation on Ir(100) surface is found to be 3.01 eV, which is appreciably larger than the association energy (1.61 eV) of this molecule.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment

Alpaca-derived single-domain antibody fragments (VHHs) that target the influenza A virus nucleoprotein (NP) can protect cells from infection when expressed in the cytosol. We found that one such VHH, αNP-VHH1, exhibits antiviral activity similar to that of Mx proteins by blocking nuclear import of incoming viral ribonucleoproteins (vRNPs) and viral transcription and replication in the nucleus. We determined a 3.2-Å crystal structure of αNP-VHH1 in complex with influenza A virus NP. The VHH binds to a nonconserved region on the body domain of NP, which has been associated with binding to host factors and serves as a determinant of host range. Several of the NP/VHH interface residues determine sensitivity of NP to antiviral Mx GTPases. The structure of the NP/αNP-VHH1 complex affords a plausible explanation for the inhibitory properties of the VHH and suggests a rationale for the antiviral properties of Mx proteins. Such knowledge can be leveraged for much-needed novel antiviral strategies. IMPORTANCE Influenza virus strains can rapidly escape from protection afforded by seasonal vaccines or acquire resistance to available drugs. Additional ways to interfere with the virus life cycle are therefore urgently needed. The influenza virus nucleoprotein is one promising target for antiviral interventions. We have previously isolated alpaca-derived single-domain antibody fragments (VHHs) that protect cells from influenza virus infection if expressed intracellularly. We show here that one such VHH exhibits antiviral activities similar to those of proteins of the cellular antiviral defense (Mx proteins). We determined the three-dimensional structure of this VHH in complex with the influenza virus nucleoprotein and identified the interaction site, which overlaps regions that determine sensitivity of the virus to Mx proteins. Our data define a new vulnerability of influenza virus, help us to better understand the cellular antiviral mechanisms, and provide a well-characterized tool to further study them.

Hanke, Leo↗

NASA NTRS2001

Cloud and Radiation Studies during SAFARI 2000

Platnick, Steven↗

NASA NTRS1996

A Sundial-Atlas Precursor to the TIMED Mission: A Quick-Response Global Investigation into Coupled Lower Thermospheric, Ionospheric, and Mesospheric Physics

The SUNDIAL-ATLAS effort was a global-scale investigation which responded to the science priorities of the ITM Panel, the Integrated SPD Strategy Implementation Plan as a whole, and the need for potential cost-saving design criteria for the TIMED mission. The investigation focused on coupling processes in the ionospheric-thermospheric system, taking advantage of the timelines of the ATLAS-1 mission (March 1992), and the global-scale ground-based measurement and modeling activities of the SUNDIAL program. The collaborative SUNDIAL-ATLAS activity was the first opportunity for global measurements of the chemistry, kinetics, and electrodynamics which couple the E-, Fl-, and F2-regions into a single interactive system. As such, the program represented an important first step in studying global issues; and accordingly, was an important proof of concept experiment relevant to the strategic mission plans for the ITM community and the upcoming intermediate class satellite program called TIMED. To meet its projected goals, TIMED must perform a number of critical measurements and execute a number of correlations that were to be tried and tested for the first time in the SUNDIAL-ATLAS investigation. This was designed to include global correlations of thermospheric and ionospheric composition during quiet and disturbed conditions and the co-registration of global-scale ground-based measurements with along-track satellite diagnostics. The SUNDIAL component of the current investigation addressed this need by acquiring, reducing, and analyzing a multi-sensor database that complemented and extended that which was generated in the ATLAS mission (Atmospheric Laboratory for Applications and Science). The SUNDIAL data defined the state and condition of the global-scale ionosphere in the altitude range from 100 km to the F2-peak. These data specified the peak heights and densities of the E-, Fl-, and F2-regions, along with the global distributions of intermediate, descending, and sequential layers which play a critical role in the dynamo region of the lower ionospheric-thermospheric domain. The data were collected by the SUNDIAL network of more than 50 ground-based stations utilizing ionosondes, radars, photometers, Fabry-Perot interferometers, and total electron content measurements. The data were acquired during a three-week period centered on the eight-day ATLAS-1 mission, which provided image and photometric sensing of the altitude distributions of the major and minor ions and neutrals in the ITM system. This report focuses on the scientific contributions of the SUNDIAL component of the overall investigation. Specific findings are described in seven papers (attached) published in the Journal of Geophysical Research.

Szuszczewicz, E. P.↗

DOE OSTI2016

THE SPITZER SPACE TELESCOPE SURVEY OF THE ORION A AND B MOLECULAR CLOUDS. II. THE SPATIAL DISTRIBUTION AND DEMOGRAPHICS OF DUSTY YOUNG STELLAR OBJECTS

We analyze the spatial distribution of dusty young stellar objects (YSOs) identified in the Spitzer Survey of the Orion Molecular clouds, augmenting these data with Chandra X-ray observations to correct for incompleteness in dense clustered regions. We also devise a scheme to correct for spatially varying incompleteness when X-ray data are not available. The local surface densities of the YSOs range from 1 pc{sup −2} to over 10,000 pc{sup −2}, with protostars tending to be in higher density regions. This range of densities is similar to other surveyed molecular clouds with clusters, but broader than clouds without clusters. By identifying clusters and groups as continuous regions with surface densities ≥10 pc{sup −2}, we find that 59% of the YSOs are in the largest cluster, the Orion Nebula Cluster (ONC), while 13% of the YSOs are found in a distributed population. A lower fraction of protostars in the distributed population is evidence that it is somewhat older than the groups and clusters. An examination of the structural properties of the clusters and groups shows that the peak surface densities of the clusters increase approximately linearly with the number of members. Furthermore, all clusters with more than 70 members exhibit asymmetric and/or highly elongated structures. The ONC becomes azimuthally symmetric in the inner 0.1 pc, suggesting that the cluster is only ∼2 Myr in age. We find that the star formation efficiency (SFE) of the Orion B cloud is unusually low, and that the SFEs of individual groups and clusters are an order of magnitude higher than those of the clouds. Finally, we discuss the relationship between the young low mass stars in the Orion clouds and the Orion OB 1 association, and we determine upper limits to the fraction of disks that may be affected by UV radiation from OB stars or dynamical interactions in dense, clustered regions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

HUWE1 interacts with BRCA1 and promotes its degradation in the ubiquitin–proteasome pathway (Biochemical and Biophysical Research Communications, v. 444 issue 3)

Highlights: • The 2000–2634 aa region of HUWE1 mediates the interaction with BRCA1 degron. • HUWE1 promotes the degradation of BRCA1 through the ubiquitin–proteasome pathway. • HUWE1 expression is inversely correlated with BRCA1 in breast cancer cells. • RNAi inhibition of HUWE1 confers increased resistance of MCF-10F cells to IR and MMC. - Abstract: The cellular BRCA1 protein level is essential for its tumor suppression activity and is tightly regulated through multiple mechanisms including ubiquitn–proteasome system. E3 ligases are involved to promote BRCA1 for ubiquitination and degradation. Here, we identified HUWE1/Mule/ARF-BP1 as a novel BRCA1-interacting protein involved in the control of BRCA1 protein level. HUWE1binds BRCA1 through its N-terminus degron domain. Depletion of HUWE1 by siRNA-mediated interference significantly increases BRCA1 protein levels and prolongs the half-life of BRCA1. Moreover, exogenous expression of HUWE1 promotes BRCA1 degradation through the ubiquitin–proteasome pathway, which could explain an inverse correlation between HUWE1 and BRCA1 levels in MCF10F, MCF7 and MDA-MB-231 breast cancer cells. Consistent with a functional role for HUWE1 in regulating BRCA1-mediated cellular response to DNA damage, depletion of HUWE1 by siRNA confers increased resistance to ionizing radiation and mitomycin. These data indicate that HUWE1 is a critical negative regulator of BRCA1 and suggest a new molecular mechanism for breast cancer pathogenesis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

A Multi-Instrument Cloud Condensation Nuclei Spectrum Product (Final Technical Report)

A wealth of observational data exists on the characteristics of atmospheric particulate matter, over multiple years, at the DOE ARM Southern Great Plains (SGP) Central Facility site. This site is located in a region of the country that frequently experiences weather extremes, and that is removed from many local sources of pollution but is affected by transported smoke, dust, and urban emissions. The relationships between particulate matter, cloud formation and evolution, and precipitation are therefore of strong interest, and are being explored via modeling on a variety of scales. These models require as input detailed information on the characteristics of particles capable of serving as the nuclei for cloud formation. Sufficient data exist to be able to put together a picture of the nature of the total aerosol and the cloud condensation nuclei (CCN) subset, and their variability, through merged data products. This study was aimed at exploiting the multiple measurement types at SGP to develop the first such multi-year estimates. Further, the resulting data were analyzed to understand temporal patterns ranging from hourly to seasonal, thereby gaining insights into the particle sources affecting the atmosphere in this region. DOE-funded datasets that were analyzed in this study include total particle number concentrations, submicron aerosol scattering coefficients, dry aerosol size distributions, and more recently, time-resolved submicron aerosol chemical composition. Data are also available for the number concentrations of particles that are activated in a cloud condensation nucleus instrument at a series of setpoint supersaturations, providing direct observations of the number concentrations of “CCN”. This variable is the quantity that is generally desired for inclusion in numerical models that seek to represent and predict the impacts of varying aerosol characteristics on the formation and microphysical properties of clouds. One limitation of the use of direct CCN observations is that they are not available for supersaturations larger than about 1%, which is insufficient for deep convection and may be insufficient even for shallow convection, depending on the nature of the available CCN and the dynamics of the cloud. We developed a data-based approach to representing the full aerosol size spectrum with size-dependent hygroscopicity, and used this to extrapolate CCN spectra beyond the limited measurements. Five years of SGP aerosol data (2009 -2013) were analyzed. As a side product of our work, we identified and communicated several previously-unflagged data quality issues. The resulting merged aerosol distributions, along with fits for seasonal averages, were published and submitted to the ARM archive as a special value-added product (VAP; submitted as a PI product). CCN spectra were computed for the same data period and will similarly be published and submitted to the archive for use by the community. We also note that our methodologies and findings have been discussed at several Joint ARM User Facility/Atmospheric System Research (ASR) Principal Investigators Meetings and that recent ARM/ASR aerosol data reporting strategies have included similar ideas for data merging, indicating that this work has had a lasting impact on ARM aerosol data acquisition and reporting. The proposed work advances the science of the interactions of aerosols, clouds and precipitation, with direct application to improve representation of such interactions for clouds in regional and global climate models. The archived data will continue to serve research studies in the future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Optimizing DOE Opportunities to Research Land–Atmosphere Interactions in the U.S. Southeast (Workshop Report)

The southeastern United States (Southeast), with its complex and varied environments, is an area of tremendous economic, ecological, and societal importance to the country. The region is characterized by heterogeneous landscapes (i.e., geology and soil type) and a long history of human land use coupled with a warm temperature regime and high precipitation. As a result, soil erosion and deposition are pronounced, vegetation recovery is rapid, and human modification is extensive across the region. To better understand land–atmosphere interactions in this important and complex region, research communities supported by the U.S. Department of Energy’s Biological and Environmental Research (BER) program identified the Southeast as a priority region of interest. In fall 2024, the third Atmospheric Radiation Measurement Mobile Facility (AMF3), one of three mobile monitoring facilities designed to collect atmospheric and climate data from undersampled regions around the world, will begin operations in northwestern Alabama’s Bankhead National Forest (BNF). The AMF3-BNF 5-year deployment, from 2024–2029, will monitor the effects of feedbacks among aerosols, clouds, and precipitation on plant physiology and canopy-scale fluxes. It will also focus on scale aggregation to resolve the role of local forcing on larger-scale processes. To enable broader AMF3 involvement by the science community, the BER Environmental System Science (ESS) program organized the Southeast Land– Atmosphere Research Opportunities (SELARO) workshop in August 2023. The purpose was to identify gaps in scientific understanding of terrestrial processes in the Southeast (defined as states bounded by the Gulf of Mexico to the south, the Atlantic Ocean to east, the Mississippi River to the west, and extending through Tennessee and North Carolina to the north) and explore opportunities to use the AMF3-BNF deployment to coordinate and leverage research efforts across the region. Many parts of the Southeast have experienced repeated anthropogenic forcings. Farming, hunting, burning, and settlement of the region by Indigenous Peoples first shaped the distribution of plant communities, which in turn influenced European colonization patterns. Timber harvesting was common during the expansion of European settlements, and production forestry continues today. Agricultural production was extensive and then waned through the 20th century, creating a period of afforestation following agricultural abandonment. Today, many formerly agricultural landscapes are undergoing rapid urbanization and suburbanization. Overlying these patterns of anthropogenic land use are frequent disturbances from hurricanes, tornadoes, wildfires, drought, flooding, ice storms, and the occasional blizzard. An additional characteristic of the Southeast is its overall landscape complexity. Unlike the western United States, where broad expanses may share similar characteristics, Southeast topography, drainage patterns, vegetation, and development patterns vary widely across relatively small spatial scales (<1 km). This is due to the region’s underlying geology and soil development, species biodiversity patterns, and land ownership and use coupled with strong forces of erosion, weathering, and rapid plant growth in the warm, wet climate.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1992

Planet-B: A Japanese Mars aeronomy observer

An introduction is given to a Japanese Mars mission (Planet-B) which is being planned at the Institute of Space and Aeronautical Science (ISAS), Japan. Planet-B aims to study the upper atmosphere of Mars and its interaction with the solar wind. The launch of Planet-B is planned for 1996 on a new launcher, M-L, which is being developed at ISAS. In addition to the interaction with the solar wind, the structure of the Martian upper atmosphere is thought to be controlled by the meteorological condition in the lower atmosphere. The orbit of Planet-B was chosen so that it will pass two important regions, the region where the solar wind interacts with the Martian upper atmosphere and the tail region where ion acceleration is taking place. Considering the drag due to the Martian atmosphere, the periapsis altitude of 150 km and apoapsis of 10 Martian radii are planned. The orbit plane will be nearly parallel to the ecliptic plane. The altitude of the spacecraft will be spin stabilized and its spin axis will be controlled to the point of the earth. The dry weight of the spacecraft will be about 250 kg, including the scientific payload which consists of a magnetometer, plasma instruments, HF sounder, UV imaging spectrometer, and lower atmosphere monitor.

Tsuruda, K.↗

NASA NTRS2010

Optical and Microphysical Retrievals of Marine Stratocumulus Clouds off the Coast of Namibia from Satellite and Aircraft

Though the emphasis of the Southern Africa Regional Science Initiative 2000 (SAFARI-2000) dry season campaign was largely on emission sources and transport, the assemblage of aircraft (including the high altitude NASA ER-2 remote sensing platform and the University of Washington CV-580, UK MRF C-130, and South African Weather Bureau JRA in situ aircrafts) provided a unique opportunity for cloud studies. Therefore, as part of the SAFARI initiative, investigations were undertaken to assess regional aerosol-cloud interactions and cloud remote sensing algorithms. In particular, the latter part of the experiment concentrated on marine boundary layer stratocumulus clouds off the southwest coast of Africa. Associated with cold water upwelling along the Benguela current, the Namibian stratocumulus regime has received limited attention but appears to be unique for several reasons. During the dry season, outflow of continental fires and industrial pollution over this area can be extreme. From below, upwelling provides a rich nutrient source for phytoplankton (a source of atmospheric sulfur through DMS production as well as from decay processes). The impact of these natural and anthropogenic sources on the microphysical and optical properties of the stratocumulus is unknown. Continental and Indian Ocean cloud systems of opportunity were also studied during the campaign. SAFARI 2000 aircraft flights off the coast of Namibia were coordinated with NASA Terra Satellite overpasses for synergy with the Moderate Resolution Imaging Spectroradiometer (MODIS) and other Terra instruments. MODIS was developed by NASA and launched onboard the Terra spacecraft on December 18, 1999 (and Aqua spacecraft on May 4, 2002). Among the remote sensing algorithms developed and applied to this sensor are cloud optical and microphysical properties that include cloud thermodynamic phase, optical thickness, and effective particle radius of both liquid water and ice clouds. The archived products from these algorithms have applications in climate change studies, climate modeling, numerical weather prediction, and fundamental atmospheric research. The archived MODIS Collection 5 cloud products processing stream will be used to analyze low water cloud scenes off the Namibian and Angolan coasts during SAFARI 2000 time period, as well as other years. Pixel-level Terra and Aqua MODIS retrievals (l. km spatial resolution at nadir) and gridded (1' uniform grid) statistics of cloud optical thickness and effective particle radius will be presented, including joint probability distributions between the two quantities. In addition, perspectives from the MODIS Airborne Simulator, which flew on the ER-2 during SAFARI 2000 providing high spatial resolution retrievals (50 m at nadir), will be presented as appropriate. The H-SAF Program requires an experimental operational European-centric Satellite Precipitation Algorithm System (E-SPAS) that produces medium spatial resolution and high temporal resolution surface rainfall and snowfall estimates over the Greater European Region including the Greater Mediterranean Basin. Currently, there are various types of experimental operational algorithm methods of differing spatiotemporal resolutions that generate global precipitation estimates. This address will first assess the current status of these methods and then recommend a methodology for the H-SAF Program that deviates somewhat from the current approach under development but one that takes advantage of existing techniques and existing software developed for the TRMM Project and available through the public domain.

Platnick, Steven E.↗

NASA NTRS1999

Multi-Scale Interactions Associated with the Monsoon Onset Over South China Sea and Adjacent Regions during SCSMEX-98

Using data collected during The South China Sea Monsoon Experiment (SCSMEX) (1998) as well as from the TRMM Microwave-Imager (TMI) and precipitation radar (PR), we have studied the multi-scale interactions (meso-synoptic-intraseasonal) associated with monsoon onset over South China Sea (SCS) and its subsequent evolution. Results show that the monsoon onset (defined by development of steady wind direction and heavy precipitation) over the northern SCS occurred around May 15 -17. Prevailing southerlies and southwesterlies developed over the central SCS after May 20. Shortly after, monsoon convection developed over the whole SCS region around May 23-27. The entire onset process appeared to be delayed by about a week to 10 days compared with climatology. During late spring of 1998, mid-latitude frontal systems were particularly active. These systems strongly impacted the northern SCS convection and may have been instrumental in triggering the onset of the SCS monsoon. The Tropical Oceans and Global Atmosphere (TOGA) and Bureau of Meteorology Research Centre (BMRC) radar showed a wide variety of convective systems over the Intensive Flux Array, from frontal bands to shear-banded structure, deep convection, pop-corn type shallow convection, slow moving "fine lines" to water spout. Analysis of SSM/I wind and moisture data suggested that the delayed convective activity over the SCS may be linked to the weakened northward propagation of monsoon rain band, hence contributing to a persistence of the rainband south of the Yangtze River and the disastrous flood that occurred over this region during mid to late June, 1998.

Lau, William K. M.↗

DOE OSTI2015

Correlated Pc4-5 ULF waves, whistler-mode chorus, and pulsating aurora observed by the Van Allen Probes and ground-based systems

Theory and observations have linked equatorial VLF waves with pulsating aurora for decades, invoking the process of pitch angle scattering of tens of keV electrons in the equatorial magnetosphere. Recently published satellite studies have strengthened this argument, by showing strong correlation between pulsating auroral patches and both lower-band chorus and tens of keV electron modulation in the vicinity of geosynchronous orbit. Additionally, a previous link has been made between Pc4–5 compressional pulsations and modulation of whistler-mode chorus using Time History of Events and Macroscale Interactions during Substorms. In the current study, we present simultaneous in situ observations of structured chorus waves and an apparent field line resonance (in the Pc4–5 range) as a result of a substorm injection, observed by Van Allen Probes, along with ground-based observations of pulsating aurora. We demonstrate the likely scenario being one of substorm-driven Pc4–5 ULF pulsations modulating chorus waves, and thus providing the driver for pulsating particle precipitation into the Earth's atmosphere. Interestingly, the modulated chorus wave and ULF wave periods are well correlated, with chorus occurring at half the periodicity of the ULF waves. We also show, for the first time, a particular few-Hz modulation of individual chorus elements that coincides with the same modulation in a nearby pulsating aurora patch. As a result, such modulation has been noticed as a high-frequency component in ground-based camera data of pulsating aurora for decades and may be a result of nonlinear chorus wave interactions in the equatorial region.

58 GEOSCIENCES↗

DOE OSTI2016

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Quantum mechanics/molecular mechanics ( QM / MM ) methods offer a very appealing option for the computational study of enzymatic reaction mechanisms, by separating the problem into two parts that can be treated with different computational methods. Hence, in a QM / MM formalism, the part of the system in which catalysis actually occurs and that involves the active site, substrates and directly participating amino acid residues is treated at an adequate quantum mechanical level to describe the chemistry taking place. For the remaining of the enzyme, which does not participate directly in the reaction, but that typically involves a much larger number of atoms, molecular mechanics is employed, traditionally through the application of a biomolecular force field. When applied with care, QM / MM methods can be used with great advantage in comparing, at a structural and energetic level, different mechanistic proposals, discarding mechanistic alternatives and proposing new mechanistic pathways that are consistent with the available experimental data. With time, diverse flavors within the QM / MM methods have emerged, differing in a variety of technical and conceptual aspects. Hence present alternatives differ between additive and subtractive QM / MM schemes, the type of boundary schemes, and the way in which the electrostatic interactions between the two regions are accounted for. Also, single‐conformation QM / MM , multi‐ PES approaches, and QM / MM Molecular Dynamics coexist today, each type with its own advantages and limitations. This review focuses on the application of QM / MM methods in the study of enzymatic reaction mechanisms, briefly presenting also the most important technical aspects involved in these calculations. Particular attention is dedicated to the application of the single‐conformation QM / MM , multi‐ PES QM / MM studies, and QM / MM‐FEP methods and to the advantages and disadvantages of the different types of QM / MM . Recent breakthroughs are also introduced. A selection of hand‐picked examples is used to illustrate such features. WIREs Comput Mol Sci 2017, 7:e1281. doi: 10.1002/wcms.1281 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Structure and Mechanism > Reaction Mechanisms and Catalysis Electronic Structure Theory > Combined QM/MM Methods

Sousa, Sérgio Filipe↗

DOE OSTI2012

Laue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system

The high-yield expression and purification of Shewanella oneidensis cytochrome c nitrite reductase (ccNiR) and its characterization by a variety of methods, notably Laue crystallography, are reported. A key component of the expression system is an artificial ccNiR gene in which the N-terminal signal peptide from the highly expressed S. oneidensis protein 'small tetraheme c' replaces the wild-type signal peptide. This gene, inserted into the plasmid pHSG298 and expressed in S. oneidensis TSP-1 strain, generated approximately 20 mg crude ccNiR per liter of culture, compared with 0.5-1 mg/L for untransformed cells. Purified ccNiR has nitrite and hydroxylamine reductase activities comparable to those previously reported for Escherichia coli ccNiR, and is stable for over 2 weeks in pH 7 solution at 4 C. UV/vis spectropotentiometric titrations and protein film voltammetry identified five independent one-electron reduction processes. Global analysis of the spectropotentiometric data also allowed determination of the extinction coefficient spectra for the five reduced ccNiR species. The characteristics of the individual extinction coefficient spectra suggest that, within each reduced species, the electrons are distributed among the various hemes, rather than being localized on specific heme centers. The purified ccNiR yielded good-quality crystals, with which the 2.59-{angstrom}-resolution structure was solved at room temperature using the Laue diffraction method. The structure is similar to that of E. coli ccNiR, except in the region where the enzyme interacts with its physiological electron donor (CymA in the case of S. oneidensis ccNiR, NrfB in the case of the E. coli protein).

59 BASIC BIOLOGICAL SCIENCES↗