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All sourcesNASA NTRSDOE OSTI
NASA NTRS2015

Empirical InfraRed Line Lists for Five SO2 Isotopologues: 32/33/34/36S16O2 and 32S18O2

Using the latest published, empirically refined potential energy surface (PES) Ames-1 and purely ab initio CCSD(T)/aug-cc-pVQZ dipole moment surface (DMS), we have computed Infrared line lists for five symmetric isotopologues of sulfur dioxide: 32S16O2 (626), 33S16O2 (636), 34S16O2 (646), 36S16O2 (666), and 32S18O2 (828). The line lists are based on J=0-80 rovibrational variational calculations with E’ ≤ 8000 cm-1. The 34S16O2 and 33S16O2 line lists are compared to the experiment-based models in the HIgh-resolution TRANsmission molecular absorption database (HITRAN2012, http://www.cfa.harvard.edu/hitran/) and the Cologne Database for Molecular Spectroscopy, CDMS (http://www.astro.uni-koeln.de/cdms/). The accuracy for computed 646 band origins is similar to what has been reported for the main isotopologue, i.e. 0.01 – 0.03 cm-1 for bands up to 5500 cm-1. For rovibrational transitions, the 646 line position and intensity deviation patterns are much simpler and more self-consistent than those of the main isotopologue 626. The discrepancies are mainly found for higher Ka/J transitions. 626 and 646 exhibit comparable line position and intensity agreement for lower Ka/J transitions. The line position deviations for the 636 purely rotational band are parallel to those of 626 and 646, while its line intensity deviations do not show branching patterns as we found in the 626 and 646 cases. Predictions for the other minor isotopologues are expected to exhibit similar accuracy. These line lists are accurate enough to provide alternatives for missing bands of 626 and the minor isotopologues. It may significantly facilitate the laboratory spectroscopic measurement and analysis, as well as to identify these isotopologues in various astrophysical environments.

Sulfur Dioxide↗
NASA NTRS1978

Compatibility of seasonal variations in mid-latitude thermospheric models at solar maximum and low geomagnetic activity

Satellite drag data, in situ mass spectrometer data, Fabry Perot interferometer data, and incoherent scatter data were used to produce models of the concentration of atomic oxygen and molecular nitrogen in the thermosphere and of the exospheric temperature. Incoherent scatter data from two stations near 45 deg N were used. The three techniques provide similar patterns for the annual variations of the atomic oxygen concentration at 400 km, and the mean annual temperatures are within 20 K of each other for five of the six models involved. Four of the models are in good agreement concerning the annual temperature variation. There is fair agreement between incoherent scatter models and mass spectrometer models for the N2 concentrations at 400 km but disagreement between these models and the satellite drag model. It is shown that most disagreements can be resolved by changing both the vertical temperature profile and the lower-thermosphere oxygen concentration in the direction indicated by previous incoherent scatter measurements.

Alcayde, D.↗
NASA NTRS1999

Research on Spectroscopy, Opacity, and Atmospheres

A web site has been set up to make the calculations accessible; (i.e., cfakus.harvard.edu) This data can also be accessed by FTP. It has all of the atomic and diatomic molecular data, tables of distribution function opacities, grids of model atmospheres, colors, fluxes, etc, programs that are ready for distribution, and most of recent papers developed during this grant. Atlases and computed spectra will be added as they are completed. New atomic and molecular calculations will be added as they are completed. The atomic programs that had been running on a Cray at the San Diego Supercomputer Center can now run on the Vaxes and Alpha. The work started with Ni and Co because there were new laboratory analyses that included isotopic and hyperfine splitting. Those calculations are described in the appended abstract for the 6th Atomic Spectroscopy and oscillator Strengths meeting in Victoria last summer. A surprising finding is that quadrupole transitions have been grossly in error because mixing with higher levels has not been included. All levels up through n=9 for Fe I and II, the spectra for which the most information is available, are now included. After Fe I and Fe II, all other spectra are "easy". ATLAS12, the opacity sampling program for computing models with arbitrary abundances, has been put on the web server. A new distribution function opacity program for workstations that replaces the one used on the Cray at the San Diego Supercomputer Center has been written. Each set of abundances would take 100 Cray hours costing $100,000.

Kurucz, Robert L.↗
NASA NTRS1980

Neutral cometary atmospheres. I - An average random walk model for photodissociation in comets

A method for constructing physically realistic photochemical models, taking into account the isotropic ejection of dissociated molecular fragments as well as radiation pressure acceleration, has been developed using Monte Carlo techniques. The effect of the isotropic ejection, as opposed to the radial motion arbitrarily assumed in Haser's model, is adequately described by a simple average random walk model. It is shown that measured radial (Haser) scale lengths are in fact only lower limits to a range of possible true scale lengths for a given brightness profile, which explains the current discrepancies between observed scale lengths and those predicted by photochemistry.

Combi, M. R.↗
NASA NTRS2018

Coalescence of DNA Double Strand Breaks Induced by Galactic Cosmic Radiation is Modulated by Genetics in 15 Inbred Strains of Mice

In this manuscript we address the challenges associated with the ability to predict radiation sensitivity associated with exposure to either cosmic radiation or X-rays in a population study, by monitoring DNA damage sensing protein 53BP1 forming small nuclear radiation-induced foci (RIF) as a surrogate biomarker of DNA double strand breaks (DSB). 76 primary skin fibroblasts were isolated from 10 collaborative cross strains and five reference inbred mice (C57Bl/6, BALB/CByJ, B6C3, C3H and CBA/CaJ) and exposed to three different charged nuclei of increasing LET (350 MeV/n Si, 350 MeV/n Ar and 600 MeV/n Fe) and X-ray. Our data brings strong evidence against the classic "contact-first" model where DSBs are assumed to be immobile and repaired at the lesion site. In contrast, our model suggests nearby DSBs move into single repair unit characterized by large RIF before the repair machinery kicks in. Such model has the advantage of being much more efficient molecularly but is poorly suited to deal with cosmic radiation, where energy is concentrated along the particle trajectory, inducing a large density of DSBs along each particle track. In accordance with this model, RIF quantification after X-ray exposition showed a saturated dose response for early time points post-irradiation for all strains. Similarly, the high-LET response showed that RIF number matched the number of track per cell, not the number of expected DSB per cell (1). At the temporal level, we noted that the percentage of unrepaired high-LET tracks over a 48 hour time-course increased with LET, confirming that the DNA repair process becomes more difficult as more DSB coalesce into single RIF. There was also good agreement between persistent RIF levels measured in-vitro in the primary skin cultures and survival levels of T-cells and B-cells collected in blood samples from 10 CC strains 24 hours after 0.1 Gy whole-body dose of X-ray. This suggests that persistent RIF 24 hour post-IR is a good surrogate in-vitro biomarker for in-vivo radiation toxicity. Finally, at the genomic level, large differences in repair rates between strains for high-LET allowed us to identify suggestive genetic loci associated with radiation sensitivity. Interestingly, the two highest LETs provided the most strain variation with a common locus on Chromosome 10 highly enriched for DNA repair associated genes we discussed in detail.

Radiation-Induced Foci↗
NASA NTRS2001

Calcium-stimulated autophosphorylation site of plant chimeric calcium/calmodulin-dependent protein kinase

The existence of two molecular switches regulating plant chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK), namely the C-terminal visinin-like domain acting as Ca(2+)-sensitive molecular switch and calmodulin binding domain acting as Ca(2+)-stimulated autophosphorylation-sensitive molecular switch, has been described (Sathyanarayanan, P. V., Cremo, C. R., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 30417-30422). Here we report the identification of Ca(2+)-stimulated autophosphorylation site of CCaMK by matrix-assisted laser desorption ionization time of flight-mass spectrometry. Thr(267) was confirmed as the Ca(2+)-stimulated autophosphorylation site by post-source decay experiments and by site-directed mutagenesis. The purified T267A mutant form of CCaMK did not show Ca(2+)-stimulated autophosphorylation, autophosphorylation-dependent variable calmodulin affinity, or Ca(2+)/calmodulin stimulation of kinase activity. Sequence comparison of CCaMK from monocotyledonous plant (lily) and dicotyledonous plant (tobacco) suggests that the autophosphorylation site is conserved. This is the first identification of a phosphorylation site specifically responding to activation by second messenger system (Ca(2+) messenger system) in plants. Homology modeling of the kinase and calmodulin binding domain of CCaMK with the crystal structure of calcium/calmodulin-dependent protein kinase 1 suggests that the Ca(2+)-stimulated autophosphorylation site is located on the surface of the kinase and far from the catalytic site. Analysis of Ca(2+)-stimulated autophosphorylation with increasing concentration of CCaMK indicates the possibility that the Ca(2+)-stimulated phosphorylation occurs by an intermolecular mechanism.

Non-NASA Center↗
NASA NTRS2018

Simple Ion Channels: From Structure to Electrophysiology and Back

A reliable way to establish whether our understanding of a channel is satisfactory is to reproduce its measured ionic conductance over a broad range of applied voltages in computer simulations. In molecular dynamics (MD), this can be done by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. Since this approach is computationally very expensive, we have developed a markedly more efficient alternative in which MD is combined with the electrodiffusion (ED) equation. In this approach, the assumptions of the ED equation can be rigorously tested, and the precision and consistency of the calculated conductance can be determined. We have demonstrated that the full current/voltage dependence and the underlying free energy profile for a simple channel can be reliably calculated from equilibrium or non-equilibrium MD simulations at a single voltage. To carry out MD simulations, a structural model of a channel has to be assumed, which is an important constraint, considering that high-resolution structures are available for only very few simple channels. If the comparison of calculated ionic conductance with electrophysiological data is satisfactory, it greatly increases our confidence that the structure and the function are described sufficiently accurately. We examined the validity of the ED for several channels embedded in phospholipid membranes - four naturally occurring channels: trichotoxin, alamethicin, p7 from hepatitis C virus (HCV) and Vpu from the HIV-1 virus, and a synthetic, hexameric channel, formed by a 21-residue peptide that contains only leucine and serine. All these channels mediate transport of potassium and chloride ions. It was found that the ED equation is satisfactory for these systems. In some of them experimental and calculated electrophysiological properties are in good agreement, whereas in others there are strong indications that the structural models are incorrect.

molecular dynamics (MD↗
NASA NTRS1985

The thermal structure of the dayside upper atmosphere of Venus above 125 km

A one-dimensional model of the Venus thermosphere has been constructed which includes computation of the heating efficiency of solar ultraviolet radiation, heat loss by radiation to space of infrared-active species, thermal transport by molecular and eddy conduction, and viscous dissipation. By comparing model predictions with results obtained from the Pioneer Venus Orbiter spacecraft, the results indicate that energy transport parameterized by eddy heat conduction plays a dominant role in determining thermospheric temperature. It is suggested that there exists a feedback mechanism linking heating and thermospheric circulation such that eddy cooling maintains an asymptotic temperature of about 300 K for both solar-maximum and solar-minimum conditions. The variation in thermospheric temperature with solar zenith angle, atomic oxygen-mixing ratio, rate of vibrational excitation of CO2 by ground-state O atoms, and the assumed transfer of O(1D) electronic energy to CO2 vibrational energy are also studied.

Hollenbach, D. J.↗
NASA NTRS2014

Ames Culture Chamber System: Enabling Model Organism Research Aboard the international Space Station

Understanding the genetic, physiological, and behavioral effects of spaceflight on living organisms and elucidating the molecular mechanisms that underlie these effects are high priorities for NASA. Certain organisms, known as model organisms, are widely studied to help researchers better understand how all biological systems function. Small model organisms such as nem-atodes, slime mold, bacteria, green algae, yeast, and moss can be used to study the effects of micro- and reduced gravity at both the cellular and systems level over multiple generations. Many model organisms have sequenced genomes and published data sets on their transcriptomes and proteomes that enable scientific investigations of the molecular mechanisms underlying the adaptations of these organisms to space flight.

culture chamber system↗
NASA NTRS2023

Polarization Calibration Using Solar Radiation Background Signal Scattered from Dense Cirrus Clouds in the Visible and Ultraviolet Wavelength Regimes

In this presentation we describe the application of a previously developed technique that is now being used to correct the daytime polarization calibration of the CALIPSO lidar. The technique leverages the fact that the solar radiation background signals from dense cirrus clouds are largely unpolarized due to the internal multiple reflections within the non-spherical ice particles and the multiple scattering that occurs among these particles. Therefore, the ratio of polarization components of the cirrus background signals provides a good estimate for the polarization gain ratio (PGR) of the lidar. Using airborne backscatter lidar measurements, this technique was demonstrated to work well in the infrared regime. However, in the visible and ultraviolet regime, the molecular contribution is too large to be ignored, and thus corrections must be applied to account for the highly polarizing characteristics of the molecular scattering. Ignoring molecular scattering contributions can cause PGR errors of 2-3% at 532 nm, where the CALIPSO lidar makes its depolarization measurement. Because of the wavelength dependence of -4 of the molecular scattering, the PGR error can be even larger at the 355 nm wavelength that will be used by ESA’s EarthCARE lidar. To correct the molecular scattering contributions to the lidar received solar background signal, a look-up table has been created using a polarization-sensitive radiative transfer model. This presentation describes the theory and implementation of the molecular scattering correction.

Zhaoyan Liu↗
NASA NTRS1997

Mesospheric Observations and Modeling of the Zeeman Split 233.9 GHz O-18O-16 line

Observations made from Kitt Peak, AZ, of the 233.9 GHz emission line of O-18O-16 in the upper stratosphere and lower mesosphere are reported. A good model fit to the line is obtained by incorporation of pressure and temperature broadening effects, as well as a Zeeman splitting algorithm that uses a standard geomagnetic field model and a paramagnetic Hamiltonian description of the molecular energy states. These observations are used, along with the well known O-18O-16 mixing ratio, to establish absolute calibration for observations of other chemical species from Kitt Peak. Repeated measurements show no change in this absolute calibration between observation dates. The wide magnetic splitting (+/-1.8 MHz) exhibited by this line with only six Zeeman components provides a unique test of middle atmosphere Zeeman effect model calculations, supporting the use Of 02 lines by microwave atmospheric sounders to measure pressure and temperature.

Sandor, Brad J.↗
NASA NTRS1974

Direct integration transmittance model

A transmittance model has been developed for interpretation of high spectral resolution measurements of laboratory absorption and of planetary thermal emission. The high spectral resolution requires transmittances to be computed monochromatically by summing the contribution of individual molecular absorption lines. A magnetic tape atlas of H2O, O3, and CO2 molecular line parameters serves as input to the transmittance model with simple empirical representations used for continuum regions wherever suitable laboratory data exist. The theoretical formulation of the transmittance model and the computational procedures used for the evaluation of the transmittances are discussed, and application of the model to several homogeneous-path laboratory absorption examples is demonstrated.

Kunde, V. G.↗
NASA NTRS2012

Comparison of MSL RCS Jet Computations With Flow Visualization and Velocimetry

Numerical predictions of the Mars Science Laboratory (MSL) reaction control system (RCS) jets interacting with a Mach 10 hypersonic flow are compared to experimental nitric oxide (NO) planar laser-induced fluorescence (PLIF) data. The steady Reynolds Averaged Navier Stokes (RANS) equations using the Baldwin-Barth one-equation turbulence model were solved using the OVERFLOW code. The experimental PLIF data used for comparison consists of qualitative two-dimensional visualization images, qualitative reconstructed three-dimensional flow structures, and quantitative two-dimensional distributions of streamwise velocity. Through modeling of the PLIF signal equation, computational flow images (CFI) were produced and directly compared to the qualitative PLIF data. Post processing of the experimental and simulation data enabled the jet trajectory to be extracted for a more quantitative comparison. The two-dimensional velocity fields were reconstructed through interpolation of a series of single-component velocity profiles. Each distribution of single-component velocity was obtained using molecular tagging velocimetry (MTV). After validating the numerical model, the numerical solution was further examined to gain insight into hypersonic jet-in-crossflow interaction. Future NO-PLIF experiments are proposed based on this analysis.

Johansen, Craig T.↗
NASA NTRS1993

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Non-NASA Center↗
NASA NTRS1977

The structure of the planets Jupiter and Saturn

Planetary models for Jupiter and Saturn are computed using a fourth-order theory and an equation of state for the molecular hydrogen and helium planetary envelopes taken from the Monte Carlo calculations of Slattery and Hubbard (1976). Models for Jupiter are found that have a small amount of heavy elements either mixed with hydrogen and helium throughout the interior of the planet or concentrated in a small dense core. Saturn is modeled with a solar-composition hydrogen and helium envelope and a small dense core. It is concluded that the molecular equation of state linked with suitable interior equations of state can produce Jovian models which satisfy the observational data. The planetary models show that the enrichment of heavy elements (relative to solar composition) is approximately 3 times for Jupiter and 10 times for Saturn.

Slattery, W. L.↗
NASA NTRS2004

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗
NASA NTRS1992

Warm neutral halos around molecular clouds. IV - H I and continuum: Aperture synthesis observations towards the molecular cloud B5

We present aperture synthesis observations of H I (21 cm) line radiation and continuum emission at 408 and 1420 MHz towards a field centered on the molecular cloud B5. The H I emission shows an extended atomic halo around the molecular cloud. The opacity of the halo is derived using H I absorption toward several background sources and a simple source model is presented. The model indicates that the halo is not gravitationally bound to the molecular cloud and that it is in fact expanding away from it. Approximately 350 solar masses are contained in the H I halo. Flux densities and spectral indices for the sources detected in both of the continuum bands are given.

Andersson, B.-G.↗
NASA NTRS1990

An outgassing model of non-metallic materials for the ascent of a Titan 4 launch vehicle

Outgassing of nonmetallic materials and components inside Titan IV's 2A compartment during ascent may present a problem to the payload community in relation to molecular deposition and degradation of sensitive payload surfaces. The procedure currently being developed to model the amounts, transport, and deposition of outgassed molecular contaminants onto a payload's sensitive surface consists of three phases. The first phase involves the development of a thermogravimetric method that recreates the increasing temperature and decreasing pressure profiles expected in the 2A compartment of the TIV launch vehicle during ascent. The second phase involves the determination of deposition rates of outgassed materials onto a payload surface, and the subsequent evaporation rate as a function of temperature of deposited material. The third phase takes the temperature and pressure profiles from phase one, the deposition and evaporation rates and kinetic coefficients determined in phase two, and incorporates them into the SPACE II computer program to determine which payload surfaces are most susceptible to molecular deposition from TIV's outgassing sources, and the level of permanent deposition expected on those surfaces.

Barrows, R. D.↗