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NASA NTRS2009

NASA Tech Briefs, March 2009

Topics covered include: Improved Instrument for Detecting Water and Ice in Soil; Real-Time Detection of Dust Devils from Pressure Readings; Determining Surface Roughness in Urban Areas Using Lidar Data; DSN Data Visualization Suite; Hamming and Accumulator Codes Concatenated with MPSK or QAM; Wide-Angle-Scanning Reflectarray Antennas Actuated by MEMS; Biasable Subharmonic Membrane Mixer for 520 to 600 GHz; Hardware Implementation of Serially Concatenated PPM Decoder; Symbolic Processing Combined with Model-Based Reasoning; Presentation Extensions of the SOAP; Spreadsheets for Analyzing and Optimizing Space Missions; Processing Ocean Images to Detect Large Drift Nets; Alternative Packaging for Back-Illuminated Imagers; Diamond Machining of an Off-Axis Biconic Aspherical Mirror; Laser Ablation Increases PEM/Catalyst Interfacial Area; Damage Detection and Self-Repair in Inflatable/Deployable Structures; Polyimide/Glass Composite High-Temperature Insulation; Nanocomposite Strain Gauges Having Small TCRs; Quick-Connect Windowed Non-Stick Penetrator Tips for Rapid Sampling; Modeling Unsteady Cavitation and Dynamic Loads in Turbopumps; Continuous-Flow System Produces Medical-Grade Water; Discrimination of Spore-Forming Bacilli Using spoIVA; nBn Infrared Detector Containing Graded Absorption Layer; Atomic References for Measuring Small Accelerations; Ultra-Broad-Band Optical Parametric Amplifier or Oscillator; Particle-Image Velocimeter Having Large Depth of Field; Enhancing SERS by Means of Supramolecular Charge Transfer; Improving 3D Wavelet-Based Compression of Hyperspectral Images; Improved Signal Chains for Readout of CMOS Imagers; SOI CMOS Imager with Suppression of Cross-Talk; Error-Rate Bounds for Coded PPM on a Poisson Channel; Biomorphic Multi-Agent Architecture for Persistent Computing; and Using Covariance Analysis to Assess Pointing Performance.

Source record↗

NASA NTRS2001

Simulation of Peptides at Aqueous Interfaces

Behavior of peptides at water-membrane interfaces is of great interest in studies on cellular transport and signaling, membrane fusion, and the action of toxins and antibiotics. Many peptides, which exist in water only as random coils, can form sequence-dependent, ordered structures at aqueous interfaces, incorporate into membranes and self-assembly into functional units, such as simple ion channels. Multi -nanosecond molecular dynamics simulations have been carried out to study the mechanism and energetics of interfacial folding of both non-polar and amphiphilic peptides, their insertion into membranes and association into higher-order structures. The simulations indicate that peptides fold non-sequentially, often through a series of amphiphilic intermediates. They further incorporate into the membrane in a preferred direction as folded monomers, and only then aggregate into dimers and, possibly, further into "dimers of dimers".

Pohorille, Andrew↗

NASA NTRS2019

Mitigation of Silver Ion Loss from Solution by Polymer Coating of Metal Surfaces

Spacecraft potable water systems require a biocidal agent that effectively provides both immediate and residual disinfection over long periods of time. Ionic silver (Ag+) is a leading candidate for this application, but suffers from rapid concentration loss due interactions with the metal storage containers and tubing. In order to maintain biocidal efficacy in systems with long periods of dormancy and to reduce the required rate of Ag+ injection, it is necessary to develop alternative materials and coatings for certified metal alloys that significantly reduce the Ag+ loss. In this work, we investigate the performance of two unusual polymers, Teflon AF 2400 and parylene-AF4, as barrier coatings under immersion in 400 ppb Ag+. We show that 25 m-thick parylene-AF4 is a promising coating with Ag+ losses similar to PTFE. Key challenges with this material include maintenance of adhesion under long-term immersion and control of deposition during the internal coating of high-aspect ratio tubing. Solutions to these problems may including surface structuring of substrates for mechanical anchoring or an alternative parylene-C chemistry (with more stable adhesion), and dynamic spatio-temporal control of substrate temperature, respectively.

water↗

NASA NTRS1984

The global distribution and variability of stratospheric constituents measured by LIMS

The purpose of the Nimbus 7 LIMS experiment was to sound the composition and structure of the upper atmosphere and provide data for study of photochemistry, radiation, and dynamics processes. Vertical profiles were measured of temperature and ozone (O3) over the 10-km to 65-km range and water vapor, nitrogen dioxide, and nitric acid over the 10-km to 50-km range. Latitude coverage extended from 64 deg S to 84 deg N. Several general features of the atmosphere have emerged from data analyzes thus far. Nitrogen dioxide exhibits rapid latitudinal variations in winter and shows hemispheric asymmetry with generally higher vertical column amount in the summer hemisphere. HNO3 data show that this gas is highly variable with altitude, latitude, and season. Smallest mixing ratios occur in the tropics, and the largest values occur in the high latitude winter hemisphere. The results show that O3, NO2, and HNO3 are strongly affected during a stratospheric warming.

Russell, J. M., III↗

NASA NTRS2007

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

Carra, Claudio↗

NASA NTRS2018

Improved Hydrology over Peatlands in a Global Land Modeling System

Peatlands of the Northern Hemisphere represent an important carbon pool that mainly accumulated since the last ice age under permanently wet conditions in specific geological and climatic settings. The carbon balance of peatlands is closely coupled to water table dynamics. Consequently, the future carbon balance over peatlands is strongly dependent on how hydrology in peatlands will react to changing boundary conditions, e.g. due to climate change or regional water level drawdown of connected aquifers or streams. Global land surface modeling over organic-rich regions can provide valuable global-scale insights on where and how peatlands are in transition due to changing boundary conditions. However, the current global land surface models are not able to reproduce typical hydrological dynamics in peatlands well. We implemented specific structural and parametric changes to account for key hydrological characteristics of peatlands into NASA's GEOS-5 Catchment Land Surface Model (CLSM, Koster et al. 2000). The main modifications pertain to the modeling of partial inundation, and the definition of peatland-specific runoff and evapotranspiration schemes. We ran a set of simulations on a high performance cluster using different CLSM configurations and validated the results with a newly compiled global in-situ dataset of water table depths in peatlands. The results demonstrate that an update of soil hydraulic properties for peat soils alone does not improve the performance of CLSM over peatlands. However, structural model changes for peatlands are able to improve the skill metrics for water table depth. The validation results for the water table depth indicate a reduction of the bias from 2.5 to 0.2 m, and an improvement of the temporal correlation coefficient from 0.5 to 0.65, and from 0.4 to 0.55 for the anomalies. Our validation data set includes both bogs (rain-fed) and fens (ground and/or surface water influence) and reveals that the metrics improved less for fens. In addition, a comparison of evapotranspiration and soil moisture estimates over peatlands will be presented, albeit only with limited ground-based validation data. We will discuss strengths and weaknesses of the new model by focusing on time series of specific validation sites.

Bechtold, M.↗

NASA NTRS1981

A molecular model for ice nucleation and growth, attachment 2

The central field empirical pair potential model is applied to studying the effects of kinks, ledges, and vacancies on the absorption of water molecules from the vapor. Molecular dynamics simulations indicate that cluster and/or surface modes play a primary role in the absorption process, the flexibility of the hydrogen bond serves to decrease the energy required for structural interconversion, and the rapid distribution of added energy in a hydrogen bonded system lead to aggregate stability which greatly exceeds that predicted by static energy calculations.

Hale, B. N.↗

NASA NTRS1995

Comets and the KAO

Seven comets have been observed from the Kuiper Airborne Observatory (KAO) in its twenty year history. Of these, comets p/Halley (1986 3) and Comet Wilson (1987 7) produced significant scientific results. Comet Halley was a bright and highly predictable comet that allowed a well-planned and coordinated observing program. Comet Wilson, on the other hand, was a dynamically new comet discovered only a few months before perihelion. In this paper we review the scientific discoveries made by the airborne program and the KAO on these comets, including the discovery of water, new structure in the silicate emission band, and a number of as yet unexplained spectral features.

Lynch, David K.↗

NASA NTRS2004

Spin-Down of the North Atlantic Subpolar Circulation

Dramatic changes have occurred in the mid-to-high-latitude North Atlantic Ocean as evidenced by TOPEX/Poseidon observations of sea surface height (SSH) in the subpolar gyre and the Gulf Stream. Analysis of altimeter data shows that subpolar SSH has increased during the 1990s and the geostrophic velocity derived from altimeter data shows a decline in the gyre circulation. Direct current-meter observations in the boundary current of the Labrador Sea support the trend in the 199Os, and, together with hydrographic data show that in the mid-late 1990s the trend extends deep in the water column. We find that buoyancy forcing over the northern North Atlantic has a dynamic effect consistent with the altimeter data and hydrographic observations: a weak thermohaline forcing and the subsequent decay of the domed structure of the subpolar isopycnals would give rise to the observed anticyclonic circulation trend.

Hakkinen, S.↗

NASA NTRSDate not supplied

The Seasonal Evolution of Atmospheric Vertical Structure of Smoke and Humidity Over the Southeast Atlantic Biomass Burning Region

The atmosphere over the southeast Atlantic Ocean (SEA) sees a consistent springtime biomass burning (BB) smoke from widespread agricultural fires on the African continent. This smoke layer is initially lofted high in a continental mixed layer (~5-6km) and is then transported westward in the free troposphere, where it overlies and ultimately mixes into the SEA stratocumulus-topped oceanic boundary layer. Coincident with this smoke is an elevated humidity signal which is present from the time a given airmass is over the continental source region; this correlation is persistent through the biomass burning season, although varying through the course of the season. ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) was a NASA Earth Venture Suborbital mission with the goal of measuring aerosol, cloud, and atmospheric properties over this region during three deployments in September 2016, August 2017, and October 2018. We use the ORACLES observations to assess this smoke-vapor relationship. First, we discuss the good agreement between the airborne ORACLES dataset and the ECMWF ERA5 and CAMS reanalyses, as well as results from NASA’s MERRA-2, as seen over the three deployment years. We then use the reanalyses to develop a framework in which to understand more broadly the radiative and dynamical interactions between the elevated smoke and water vapor over the SEA through the biomass burning season, beyond the three ORACLES observation periods. Looking at seven years of reanalysis data for the BB season, we find distinct variations between each month/deployment in terms of vertical smoke distribution and correlation to atmospheric specific humidity, due to changing conditions through the BB season. Using k-means clustering of these climatological reanalyses, we identify six canonical atmospheric profile types of varying total atmospheric humidity and vertical structure and describe their changing incidence spatially and throughout the season, and six analogous profile types for carbon monoxide, allowing us to characterize the atmospheric structure of both vapor and BB over time throughout the SEA region. The radiative heating of both aerosol and water vapor has potential to influence the cloud-top entrainment and atmospheric turbulence, thus modifying the underlying stratocumulus cloud properties. We next discuss how these smoke-humidity variations influence both the low-cloud fraction (as observed by MODIS and VIIRS, and output by ERA5) and the boundary layer height in the region. This classification will ultimately allow for a more complete analysis of the broader radiative and dynamical effects of humid aerosols overlying stratocumulus clouds.

Kristina Marie Myers Pistone↗

NASA NTRS1977

Effect of compliant wall motion on turbulent boundary layers

A critical analysis of available compliant wall data which indicated drag reduction under turbulent boundary layers is presented. Detailed structural dynamic calculations suggest that the surfaces responded in a resonant, rather than a compliant, manner. Alternate explanations are given for drag reductions observed in two classes of experiments: (1) flexible pipe flows and (2) water-backed membranes in air. Analysis indicates that the wall motion for the remaining data is typified by short wavelengths in agreement with the requirements of a possible compliant wall drag reduction mechanism recently suggested by Langley.

Bushnell, D. M.↗

NASA NTRS1999

Computer Simulation Studies of Ion Channel Gating: Characteristics of the M2 Channel of Influenza-A Virus in a Phospholipid Bilayer

The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.

Schweighofer, Karl J.↗

NASA NTRS1989

The outflow speed of the coma of Halley's comet

Data concerning the outflow speed of the coma of Comet Halley are studied in relation to a generalization of the coupled pure-gas-dynamic/Monte Carlo model of Combi and Smyth (1988) to include the dusty-gas dynamics of the inner coma. Measurements made by the Giotto neutral-gas spectrometer, IR water observations from the Kuiper Airborne Observatory, and Doppler radio line profiles of HCN and OH are used to examine the radial dependence of the outflow speed, the asymmetry in the outflow speed, and the overall heliocentric distance dependence of the Doppler profiles, respectively. The results suggest that the model makes it possible to understand the gross long-term behavior and radial structure of the dynamics of the cometary coma.

Combi, Michael R.↗

NASA NTRS2011

CFD Study of the Hydrocarbon Boost Low-Pressure Inducer and Kicker in the Presence of a Circumferential Groove

Results are presented of a computational fluid dynamics (CFD) study done in support of Marshall Space Flight Center's (MSFC) sub-scale water flow experiments of the Hydrocarbon Boost (HCB) Oxidizer Turbopump (OTP) being developed by the Air Force Research Laboratory (AFRL) and Aerojet. A circumferential groove may be added to the pump to reduce synchronous cavitation and subsequent bearing loads at a minimal performance cost. However, the energy may reappear as high order cavitation (HOC) that spans a relatively large frequency range. Thus, HOC may have implications for the full-scale OTP inducer in terms of reduced structural margin at higher mode frequencies. Simulations using the LOCI/Stream CFD program were conducted in order to explore the fluid dynamical impact of the groove on the low-pressure inducer and kicker. It was found that the circumferential groove has minimal head performance impact, but causes back-flowing high-swirl fluid to interact with the nearly-axial incoming fluid just above the inducer blades. The high-shear interface between the fluids is Kelvin-Helmholtz unstable, resulting in trains of low pressure regions or 'pearls' forming near the upstream edge of the groove. When the static pressure in these regions becomes low enough and they get cut by the blade leading edge, HOC is thought to occur. Although further work is required, the numerical models indicate that HOC will occur in the runbox of the AFRL/Aerojet HCB OTP. Comparisons to the ongoing water flow experiments will be discussed, as well as possible designs that may mitigate HOC while continuing to reduce synchronous cavitation. December 2011 MSS/LPS/SPS Joint Subcommittee Meeting ABSTRACT SUBMITTAL FORM

Coker, Robert↗

NASA NTRS1988

On the interpretation of integrated water vapor patterns in midlatitude cyclones derived from the Nimbus 7 scanning multichannel microwave radiometer

The present exploration of methods for the interpretation of the Nimbus 7 satellite's Scanning Multichannel Microwave Radiometer (SMMR) vapor patterns and the ways in which they relate to the dynamical structure of individual midlatitude storms employs gridded meteorological data from the First GARP Global Experiment special observing period in order to calculate diagnostic quantities. SMMR patterns for a storm at a weak stage determined from the diagnostic quantities are compared with SMMR patterns for the storm at a stronger stage. A more complete interpretation of the SMMR patterns emerges from these considerations.

Mcmurdie, Lynn A.↗

NASA NTRS1988

Microscale ocean dynamics

The detailed dynamics of the micro-scale ocean surface phenomena are studied along with the relationships among the surface signatures with the underlying dynamical processes. The approach to advance the understanding in this area is as follows: (1) Conduct rigorous theoretical studies of the ocean surface wave dynamics and statistical properties; (2) Conduct process-oriented laboratory experiments to verify the theoretical results, and to provide guidance for further studies; and (3) Prepare testable hypotheses for field verifications and comparisons during the ONR/NASA sponsored Surface Wave Dynamics Experiment (SWADE). An analytic model was established for wave breaking probability to study the influence of wave breaking on the spectrum shape in both deep and finite-depth waters. The spectrum was processed along with the structures of the water surface under the influence of wind and existing waves.

Huang, N.↗

NASA NTRS1991

Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

Wilson, Michael A.↗

NASA NTRS1999

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399. Copyright 1999 Wiley-Liss, Inc.

NASA Center ARC↗