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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↗

NASA NTRS1997

Interactions of anesthetics with the water-hexane interface. A molecular dynamics study

The free energy profiles characterizing the transfer of nine solutes across the liquid-vapor interfaces of water and hexane and across the water-hexane interface were calculated from molecular dynamics simulations. Among the solutes were n-butane and three of its halogenated derivatives, as well as three halogenated cyclobutanes. The two remaining molecules, dichlorodifluoromethane and 1,2-dichloroperfluoroethane, belong to series of halo-substituted methanes and ethanes, described in previous studies (J. Chem. Phys. 1996, 104, 3760; Chem. Phys. 1996, 204, 337). Each series of molecules contains structurally similar compounds that differ greatly in anesthetic potency. The accuracy of the simulations was tested by comparing the calculated and the experimental free energies of solvation of all nine compounds in water and in hexane. In addition. the calculated and the measured surface excess concentrations of n-butane at the water liquid-vapor interface were compared. In all cases, good agreement with experimental results was found. At the water-hexane interface, the free energy profiles for polar molecules exhibited significant interfacial minima, whereas the profiles for nonpolar molecules did not. The existence of these minima was interpreted in terms of a balance between the free energy contribution arising from solute-solvent interactions and the work to form a cavity that accommodates the solute. These two contributions change monotonically, but oppositely, across the interface. The interfacial solubilities of the solutes, obtained from the free energy profiles, correlate very well with their anesthetic potencies. This is the case even when the Meyer-Overton hypothesis, which predicts a correlation between anesthetic potency and solubility in oil, fails.

NASA Center ARC↗

NASA NTRS1996

On the Evolution-Dynamics of Tropical Ocean-Atmosphere Annual-Cycle Variability

The structure of ocean-atmosphere annual-cycle variability across the global tropics is extracted from the Comprehensive Ocean-Atmosphere Data Set (COADS) surface winds and SSTs, and oceanic heat-content simulation from a nonlinear shallow water model (forced by COADS wind stress) using the co-variance based rotated principal component analysis technique.

COADS↗

NASA NTRS1961

Effect of Load-Alleviating Structure on the Landing Behavior of a Reentry-Capsule Model

[Division] Structures↗

NASA NTRS2001

Thermal Emission Spectrometer Results: Mars Atmospheric Thermal Structure and Aerosol Distribution

Infrared spectra returned by the Thermal Emission Spectrometer (TES) are well suited for retrieval of the thermal structure and the distribution of aerosols in the Martian atmosphere. Combined nadir- and limb-viewing spectra allow global monitoring of the atmosphere up to 0.01 mbar (65 km). We report here on the atmospheric thermal structure and the distribution of aerosols as observed thus far during the mapping phase of the Mars Global Surveyor mission. Zonal and temporal mean cross sections are used to examine the seasonal evolution of atmospheric temperatures and zonal winds during a period extending from northern hemisphere mid-summer through vernal equinox (L(sub s) = 104-360 deg). Temperature maps at selected pressure levels provide a characterization of planetary-scale waves. Retrieved atmospheric infrared dust opacity maps show the formation and evolution of regional dust storms during southern hemisphere summer. Response of the atmospheric thermal structure to the changing dust loading is observed. Maps of water-ice clouds as viewed in the thermal infrared are presented along with seasonal trends of infrared water-ice opacity. Uses of these observations for diagnostic studies of the dynamics of the atmosphere are discussed.

Smith, Michael D.↗

NASA NTRS2000

An Assessment of Our Ability to Model the Upper Troposphere and Lower Stratosphere in Interactive Climate Models

The physics of the upper troposphere is dominated by the different phases of water, while the lower stratosphere is governed by the presence of ozone. The tropopause may be regarded as the layer which separates the regions where stratospheric and tropospheric processes dominate the physics, but it is clearly not a smooth transition level. Modelling this region in comprehensive climate models is complicated, partly because of the constraints inherent in numerical methods (such as the finite resolution used in models) and partly because of our incomplete knowledge of the physical and chemical interactions which occur (such as the phase transitions of water and the composition of aerosols). However, studies of stratospheric impacts on climate change clearly require the tropopause region to be modelled with a high degree of accuracy. This paper will examine how well we can currently model the structure and dynamics of the tropopause region; this includes some comparisons of the simulated atmospheric composition with observational estimates of these species, some studies of discrepancies between forecasts and observations in the Data Assimilation System of the Data Assimilation office, and inferences for sparsely observed quantities. The analysis will focus on meteorological quantities, physical forcing mechanisms, and the transport and interactions of trace species.

Pawson, Steven↗

NASA NTRS1999

Early Events in the Folding of an Amphipathic Peptide A Multi- Nanosecond Molecular Dynamics Study

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations over 161.5 nanoseconds. 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 non-amphipathic structures throughout the complete trajectory indicate- 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.

Chipot, Christophe↗

NASA NTRS2022

Tropical peatland hydrology simulated with a global land surface model

Tropical peatlands are among the most carbon-dense ecosystems on Earth, and their water storage dynamics strongly control these carbon stocks. The hydrological functioning of tropical peatlands differs from that of northern peatlands, which has not yet been accounted for in global land surface models (LSMs). Here, we integrated tropical peat-specific hydrology modules into a global LSM for the first time, by utilizing the peatland-specific model structure adaptation (PEATCLSM) of the NASA Catchment Land Surface Model (CLSM). We developed literature-based parameter sets for natural (PEATCLSM(Trop,Nat)) and drained (PEATCLSM(Trop,Drain)) tropical peatlands. Simulations with PEATCLSM(Trop,Nat) were compared against those with the default CLSM version and the northern version of PEATCLSM (PEATCLSM(North,Nat)) with tropical vegetation input. All simulations were forced with global meteorological reanalysis input data for the major tropical peatland regions in Central and South America, the Congo Basin, and Southeast Asia. The evaluation against a unique and extensive data set of in situ water level and eddy covariance-derived evapotranspiration showed an overall improvement in bias and correlation compared to the default CLSM version. Over Southeast Asia, an additional simulation with PEATCLSM(Trop,Drain) was run to address the large fraction of drained tropical peatlands in this region. PEATCLSM(Trop,Drain) outperformed CLSM, PEATCLSM(North,Nat) and PEATCLSM(Trop,Nat) over drained sites. Despite the overall improvements of PEATCLSM(Trop,Nat) over CLSM, there are strong differences in performance between the three study regions. We attribute these performance differences to regional differences in accuracy of meteorological forcing data, and differences in peatland hydrologic response that are not yet captured by our model.

Peatland↗

NASA NTRS1991

Coagulation of particles in Saturn's rings - Measurements of the cohesive force of water frost

Experimental data are presented on the sticking force of water ice particles which are indicative of the role that the cohesive properties of such particles could play in the dynamics of Saturn ring particles. Sticking forces are dependent on particle impact velocities; a 'Velcro' model is devised to describe the surface structure involved in sticking. The data indicate that below the critical impact velocity of about 0.03 cm/sec, particle cohesion always occurs. Due to the optical depth of micron-sized grains in the Saturn rings, particles are hypothesized to be coated with a layer of frost which will render cohesion an important ring-dynamics process.

Hatzes, A. P.↗

NASA NTRS2019

Analyzing Seasonal Forcing Mechanisms of the Martian Polar Warming with the NASA Ames Mars Global Climate Model

The meridional transport of heat, momentum, water, dust, trace species and gases is critical for the control of Mars’ climate. Though the nature and structure of the mean meridional circulation has been previously studied, questions remain regarding the seasonal forcing mechanisms, and the implications on the combined thermal and dynamical response for Mars’ climate. A useful diagnostic of the mean meridional circulation and transport in the middle atmosphere is polar warming.

Brecht, A. S.↗

NASA NTRS1961

Effect of a Load-Alleviating Structure on the Landing Behavior of a Reentry-Capsule Model

Model tests have been made to determine the landing-impact characteristics of a parachute-supported reentry capsule that had a compliable metal structure as a load-alleviating device. A 1/6-scale dynamic model having compliable aluminum-alloy legs designed to give a low onset rate of acceleration on impact was tested at flight-path angles of 90 degrees ( vertical ) and 35 deg, at a vertical velocity of 30 ft/sec ( full scale), and at contact attitudes of 0 deg and +/-30 deg. Landings were made on concrete, sand, and water. The maximum acceleration encountered was approximately 35g and the maximum onset rate was 2,000 g/sec. on concrete a t the 55 deg flight-path, f30 contact-attitude conditions; therefore, load-alleviating devices on the canister end of the model would be required. To evaluate the scaling characteristics of compliable metal structures, models were tested with 1/4.1-scale and full-scale aluminum-alloy legs. The maximum vertical accelerations and strokes obtained from tests of the 1/4.1-scale and full-scale legs were the same within the recording accuracy of the equipment. Acceleration time histories for the 90 degree flight-path, 0 deg contact-attitude condition were computed and are in good agreement with the experimental results.

Hoffman, Edward L.↗

NASA NTRS1987

Objective method for analysis and tracking of convective cells as seen by radar

A special method has been developed for the study of cells that are embedded in convective rain systems. This method consists of a package of computer programs that use pattern recognition techniques on three-dimensional digital radar data to identify the rain cells, track them with time, and calculate their properties. The product of the computations is a comprehensive database of physically meaningful properties of rain cells, which can be used to infer the internal structure and the dynamics of convective rain systems. The cell-tracking method has been applied to the summer convective clouds of south Florida for the following purposes: (1) derivation of the relationship between the echo top height and the precipitation characteristics (e.g., area, water yield, rain intensity and duration of the rain cells); (2) study of the microphysical behaviorof cumulus clouds in relation to their cell properties; (3) evaluation of the effect of seeding on cumulus clouds on the cell scale; and (4) examination of cloud-to-ground lightning discharges in relation to convective cell intensity. The cell-tracking method is also currently being used in rain enhancement projects in Texas, Israel, and South Africa. The cell-tracking method, its products and their use in meteorological research are described in this paper.

Rosenfeld, Daniel↗

NASA NTRS2000

Molecular Dynamics Simulations of Carbon Nanotubes in Water

We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

Walther, J. H.↗

NASA NTRS2012

Modeling and Observations of the Response of Tropical Tropospheric Ozone to ENSO

The El Nino-Southern Oscillation (ENSO) is the dominant mode of tropical variability on interannual time scales. ENSO appears to extend its influence into the chemical composition of the tropical troposphere, Recent results have revealed an ENSO induced wave-1 anomaly in observed tropical tropospheric column ozone, This results in a dipole over the western and eastern tropical Pacific, whereby differencing the two regions produces an ozone anomaly with an extremely high correlation to the Nino 3.4 Index. We have successfully reproduced this result using the Goddard Earth Observing System Version 5 (GEOS-5) general circulation model coupled to a comprehensive stratospheric and tropospheric chemical mechanism forced with observed sea surface temperatures over the past 25 years, An examination of the modeled ozone field reveals the vertical contributions of tropospheric ozone to the column over the western and eastern Pacific region, We will show targeted comparisons with SHADOZ ozonesondes over these regions to provide insight into the vertical structure. Also, comparisons with NASA's Aura satellite Microwave Limb Sounder (MLS) and Tropospheric Emissions Spectrometer (TES) instruments and other appropriate data sets will be shown. In addition, the water vapor response to ENSO will be compared to help illuminate its role relative to dynamics in impacting ozone concentrations. These results indicate that the tropospheric ozone response to ENSO is potentially a very useful chemistry-climate diagnostic and should be considered in future modeling assessments.

Oman, L. D.↗

NASA NTRS2011

Validation and Simulation of Ares I Scale Model Acoustic Test - 2 - Simulations at 5 Foot Elevation for Evaluation of Launch Mount Effects

The Ares I Scale Model Acoustics Test (ASMAT) is a series of live-fire tests of scaled rocket motors meant to simulate the conditions of the Ares I launch configuration. These tests have provided a well documented set of high fidelity measurements useful for validation including data taken over a range of test conditions and containing phenomena like Ignition Over-Pressure and water suppression of acoustics. Expanding from initial simulations of the ASMAT setup in a held down configuration, simulations have been performed using the Loci/CHEM computational fluid dynamics software for ASMAT tests of the vehicle at 5 ft. elevation (100 ft. real vehicle elevation) with worst case drift in the direction of the launch tower. These tests have been performed without water suppression and have compared the acoustic emissions for launch structures with and without launch mounts. In addition, simulation results have also been compared to acoustic and imagery data collected from similar live-fire tests to assess the accuracy of the simulations. Simulations have shown a marked change in the pattern of emissions after removal of the launch mount with a reduction in the overall acoustic environment experienced by the vehicle and the formation of highly directed acoustic waves moving across the platform deck. Comparisons of simulation results to live-fire test data showed good amplitude and temporal correlation and imagery comparisons over the visible and infrared wavelengths showed qualitative capture of all plume and pressure wave evolution features.

Strutzenberg, Louise L.↗

NASA NTRS2024

Vertical Structure of a Springtime Smoky and Humid Troposphere Over the Southeast Atlantic From Aircraft and Reanalysis

The springtime atmosphere over the southeast Atlantic Ocean (SEA) is subjected to a consistent layer of biomass burning (BB) smoke from widespread fires on the African continent. An elevated humidity signal is coincident with this layer, consistently proportional to the amount of smoke present. The combined humidity and BB aerosol has potentially significant radiative and dynamic impacts. Here, we use aircraft-based observations from the NASA ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) deployments in conjunction with reanalyses to characterize covariations in humidity and BB smoke across the SEA. The observed plume–vapor relationship, and its agreement with the European Centre for Medium-Range Weather Forecasts (ECMWF) Reanalysis version 5 (ERA5) and Copernicus Atmosphere Monitoring Service (CAMS) reanalysis, persists across all observations, although the magnitude of the relationship varies as the season progresses. Water vapor is well represented by the reanalyses, while CAMS tends to underestimate carbon monoxide especially under high BB. While CAMS aerosol optical depth (AOD) is generally overestimated relative to ORACLES AOD, the observations show a consistent relationship between carbon monoxide (CO) and aerosol extinction, demonstrating the utility of the CO tracer to understanding vertical aerosol distribution. We next use k-means clustering of the reanalyses to examine multi-year seasonal patterns and distributions. We identify canonical profile types of humidity and of CO, allowing us to characterize changes in vapor and BB atmospheric structures, and their impacts as they covary. While the humidity profiles show a range in both total water vapor concentration and in vertical structure, the CO profiles primarily vary in terms of maximum concentration, with similar vertical structures in each. The distribution of profile types varies spatiotemporally across the SEA region and through the season, ranging from largely one type in the northeast and southwest to more evenly distributed between multiple types where air masses meet in the middle of the SEA. These distributions follow patterns of transport from the humid, smoky source region (greatest influence in the northeast of the SEA) and the seasonal changes in both humidity and smoke (increasing and decreasing through the season, respectively). With this work, we establish a framework for a more complete analysis of the broader radiative and dynamical effects of humid aerosols over the SEA.

Kristina Pistone↗

NASA NTRS2005

Analysis of Piezoelectric Structural Sensors with Emergent Computing Techniques

The purpose of this project was to try to interpret the results of some tests that were performed earlier this year and to demonstrate a possible use of emergence in computing to solve IVHM problems. The test data used was collected with piezoelectric sensors to detect mechanical changes in structures. This project team was included of Dr. Doug Ramers and Dr. Abdul Jallob of the Summer Faculty Fellowship Program, Arnaldo Colon-Lopez - a student intern from the University of Puerto Rico of Turabo, and John Lassister and Bob Engberg of the Structural and Dynamics Test Group. The tests were performed by Bob Engberg to compare the performance two types of piezoelectric (piezo) sensors, Pb(Zr(sub 1-1)Ti(sub x))O3, which we will label PZT, and Pb(Zn(sub 1/3)Nb(sub 2/3))O3-PbTiO, which we will label SCP. The tests were conducted under varying temperature and pressure conditions. One set of tests was done by varying water pressure inside an aluminum liner covered with carbon-fiber composite layers (a cylindrical "bottle" with domed ends) and the other by varying temperatures down to cryogenic levels on some specially prepared composite panels. This report discusses the data from the pressure study. The study of the temperature results was not completed in time for this report. The particular sensing done with these piezo sensors is accomplished by the sensor generating an controlled vibration that is transmitted into the structure to which the sensor is attached, and the same sensor then responding to the induced vibration of the structure. There is a relationship between the mechanical impedance of the structure and the resulting electrical impedance produced in the in the piezo sensor. The impedance is also a function of the excitation frequency. Changes in the real part of impendance signature relative to an original reference signature indicate a change in the coupled structure that could be the results of damage or strain. The water pressure tests were conducted by pressurizing the bottle on a test stand, and running sweeps of excitations frequencies for each of the piezo sensors and recording the resulting impedance. The sweeps were limited to 401 points by the available analyzer, and it was decided to perform individual sweeps at five different excitation frequency ranges. The frequency ranges used for the PZTs were different in two of the five ranges from the ranges used for the SCP. The bottles were pressurized to empty (no water), 0psig, 77 psig, 155 psig, 227 psig in nearly uniform increments of about 77psi. One of each of the two types of piezo sensors was fastened on to the bottle surface at two locations: about midway between the ends on cylindrical portion of the bottle and at the very edge of one of the end domes. The data was collected in files by sensor type (2 cases), by location (2 cases), by frequency range (5 cases), and pressure (5cases) to produce 100 data sets of 401 impedances. After familiarization with the piezo sensing technology and obtaining the data, the team developed a set of questions to try to answer regarding the data and made assignments of responsibilities. The next section lists the questions, and the remainder of the report describes the data analysis work performed by Dr. Ramers. This includes a discussion of the data, the approach to answering the question using statistical techniques, the use of an emergent system to investigate the data where statistical techniques were not usable, conclusions regarding the data, and recommendations.

Ramers, Douglas L.↗

NASA NTRS1989

The use of models to predict potential contamination aboard orbital vehicles

A model of fungal growth on air-exposed, nonnutritive solid surfaces, developed for utilization aboard orbital vehicles is presented. A unique feature of this testable model is that the development of a fungal mycelium can facilitate its own growth by condensation of water vapor from its environment directly onto fungal hyphae. The fungal growth rate is limited by the rate of supply of volatile nutrients and fungal biomass is limited by either the supply of nonvolatile nutrients or by metabolic loss processes. The model discussed is structurally simple, but its dynamics can be quite complex. Biofilm accumulation can vary from a simple linear increase to sustained exponential growth, depending on the values of the environmental variable and model parameters. The results of the model are consistent with data from aquatic biofilm studies, insofar as the two types of systems are comparable. It is shown that the model presented is experimentally testable and provides a platform for the interpretation of observational data that may be directly relevant to the question of growth of organisms aboard the proposed Space Station.

Boraas, Martin E.↗