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NASA NTRS1972

Neutral composition in the thermosphere.

Data obtained from the Ogo 6 neutral atmospheric composition (NAC) experiment for a period of more than 1 year are used to compare the average constituent composition at an altitude of 400 km with that predicted by the Jacchia 1971 and 1965 models. The comparison shows that the Jacchia 1971 model underestimates the molecular nitrogen densities at 400 km by a factor of 2. An atmosphere is constructed down to 120 km by means of the Stein and Walker technique. A fit is made with (1) the 400-km total densities from drag measurements and the composition from Ogo 6 NAC, (2) the 250-km measured molecular nitrogen densities, and (3) the 150-km total densities from drag. This fit shows that the Jacchia 1971 model overestimates the atomic oxygen content at 150 km.

Taeusch, D. R.↗

NASA NTRS1986

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗

NASA NTRS1986

Translucent molecular clouds: Theory and observations

Few suitable stars behind molecular clouds have been identified. A limited survey was performed of interstellar lines toward highly reddened stars in the southern sky, using the ESO 1.4 m CAT telescope with a Reticon detector, and the Cerro Tololo 4 m telescope equipped with a GEC charge coupled device (CCD) detector. Because of the reduced extinction at longer wavelengths, molecules were searched for with transitions in the red part of the spectrum such as C2 and CN. For some lines-of-sight for which C2 was detected, the 4300 A line of CH was also observed. Absorption lines of interstellar C2 around 8750 A were detected in the spectra of about 1/4 of the 36 observed stars. The inferred C2 column densities range between 10 to the 13th power and 10 to the 14th power sq. cm., and are up to an order of magnitude larger than those found for diffuse clouds. The observed column densities of CH correlate very well with those of C2 over this range. In contrast, the measured column densities of CN vary by orders of magnitude between the various regions, and they do not correlate with those of C2 and CH. The observed rotational population distribution of C2 also provides information about the physical conditions in the clouds. Models of translucent molecular clouds have been constructed along the lines described by van Dishoeck and Black (1986) for diffuse clouds. The models compute accurately the fractions of atomic and molecular hydrogen as functions of depth into the clouds, as well as the excitation of H2 by ultraviolet pumping. They also incorporate a detailed treatment of the photodissociation processes of the molecules (cf. van Dishoeck 1986), which play an important role in the chemistry up to depths of about 3 mag.

Vandishoeck, E. F.↗

NASA NTRS1994

Direct numerical simulations of turbulent non-premixed methane-air flames modeled with reduced kinetics

Turbulent non-premixed stoichiometric methane-air flames modeled with reduced kinetics have been studied using the direct numerical simulation approach. The simulations include realistic chemical kinetics, and the molecular transport is modeled with constant Lewis numbers for individual species. The effect of turbulence on the internal flame structure and extinction characteristics of methane-air flames is evaluated. Consistent with earlier DNS with simple one-step chemistry, the flame is wrinkled and in some regions extinguished by the turbulence, while the turbulence is weakened in the vicinity of the flame due to a combination of dilatation and an increase in kinematic viscosity. Unlike previous results, reignition is observed in the present simulations. Lewis number effects are important in determining the local stoichiometry of the flame. The results presented in this work are preliminary but demonstrate the feasibility of incorporating reduced kinetics for the oxidation of methane with direct numerical simulations of homogeneous turbulence to evaluate the limitations of various levels of reduction in the kinetics and to address the formation of thermal and prompt NO(x).

Card, J. M.↗

NASA NTRS1992

FDDO and DSMC analyses of rarefied gas flow through 2D nozzles

Two different approaches, the finite-difference method coupled with the discrete-ordinate method (FDDO), and the direct-simulation Monte Carlo (DSMC) method, are used in the analysis of the flow of a rarefied gas expanding through a two-dimensional nozzle and into a surrounding low-density environment. In the FDDO analysis, by employing the discrete-ordinate method, the Boltzmann equation simplified by a model collision integral is transformed to a set of partial differential equations which are continuous in physical space but are point functions in molecular velocity space. The set of partial differential equations are solved by means of a finite-difference approximation. In the DSMC analysis, the variable hard sphere model is used as a molecular model and the no time counter method is employed as a collision sampling technique. The results of both the FDDO and the DSMC methods show good agreement. The FDDO method requires less computational effort than the DSMC method by factors of 10 to 40 in CPU time, depending on the degree of rarefaction.

Chung, Chan-Hong↗

NASA NTRS1967

Dipole properties of molecular nitrogen.

Optical absorption, refractivity and electron scattering used to construct model dipole spectrum of molecular nitrogen and calculate dipole properties

MOLECULAR GAS↗

NASA NTRS1990

Photodissociation regions

Photodissociation regions are interstellar regions of predominantly neutral gas where the FUV radiation field plays a significant role in the chemistry and/or the heating. Photodissociation, grain attenuation of the FUV flux and grain photoelectric heating lead to copious emission of C II (158 microns), O I (63 microns), Si II (35 microns), C I (370,609 microns), H2 vibrotational and CO rotational transitions, and IR continuum. Theoretical models compared with observations diagnose such physical parameters as the density and temperature structure, the elemental abundances, and the FUV radiation field. Applications are made to Orion, M17 and galactic nuclei. Theoretical photodissociation models can explain the correlation in the C II (158 microns) and CO J = 1-0 emission and the correlation of the CO J = 1-0 luminosity with the molecular mass. Theoretical models also point to feedback mechanisms which may control the rate of star formation in galaxies and which may regulate the column density through giant molecular clouds.

Hollenbach, David J.↗

NASA NTRS2003

Nanolayered Features of Collagen-like Peptides

We have been investigating collagen-like model oligopeptides as molecular bases for complex ordered biomimetic materials. The collagen-like molecules incorporate aspects of native collagen sequence and secondary structure. Designed modifications to native primary and secondary structure have been incorporated to control the nanostructure and microstructure of the collagen-like materials produced. We find that the collagen-like molecules form a number of lyotropic rod liquid crystalline phases, which because of their strong temperature dependence in the liquid state can also be viewed as solvent intercalated thermotropic liquid crystals. The liquid crystalline phases formed by the molecules can be captured in the solid state by drying off solvent, resulting in solid nanopatterned (chemically and physically) thermally stable (to greater than 100 C) materials. Designed sequences which stabilize smectic phases have allowed a variety of nanoscale multilayered biopolymeric materials to be developed. Preliminary investigations suggest that chemical patterns running perpendicular to the smectic layer plane can be functionalized and used to localize a variety of organic, inorganic, and organometallic moieties in very simple multilayered nanocomposites. The phase behavior of collagen-like oligopeptide materials is described, emphasizing the correlation between mesophase, molecular orientation, and chemical patterning at the microscale and nanoscale. In many cases, the textures observed for smectic and hexatic phase collagens are remarkably similar to the complex (and not fully understood) helicoids observed in biological collagen-based tissues. Comparisons between biological morphologies and collagen model liquid crystalline (and solidified materials) textures may help us understand the molecular features which impart order and function to the extracellular matrix and to collagen-based mineralized tissues. Initial studies have utilized synthetic collagen-like peptides while future work will also focus on similar sequences generated via genetic engineering methods.

Valluzzi, Regina↗

NASA NTRS1991

Star formation and the nature of bipolar outflows

This paper presents a simple physical model for the bipolar molecular outflows that frequently accompany star formation. The model forges an intrinsic link between the bipolar flow phenomenon and the process of star formation, and it helps to explain many of the systematics known for existing sources.

Shu, Frank H.↗

NASA NTRS2006

The Origin and Evolution of Interstellar Dust

In this lecture I will discuss the many different manifestation of interstellar dust, and current dust models that satisfy interstellar extinction, diffuse infrared emission, and interstellar abundances constraints. Dust is made predominantly in AGB stars and Type I1 supernovae, and I will present observational evidence for the presence of dust in these sources. I will then present chemical evolution models that follow the abundance of dust which is determined by the combined processes of formation, destruction by interstellar shock waves, and accretion in molecular clouds. The model will be applied to the evolution of PAHs and the evolution of dust in the high-redshift galaxy (z=6.42) JD11.

Dwek, Eli↗

NASA NTRS1976

The relationship between the galactic matter distribution, cosmic ray dynamics, and gamma ray production

Theoretical considerations and analysis of the results of gamma ray astronomy suggest that the galactic cosmic rays are dynamically coupled to the interstellar matter through the magnetic fields, and hence the cosmic ray density should be enhanced where the matter density is greatest on the scale of galactic arms. This concept has been explored in a galactic model using recent 21 cm radio observations of the neutral hydrogen and 2.6 mm observations of carbon monoxide, which is considered to be a tracer of molecular hydrogen. The model assumes: (1) cosmic rays are galactic and not universal; (2) on the scale of galactic arms, the cosmic ray column (surface) density is proportional to the total interstellar gas column density; (3) the cosmic ray scale height is significantly larger than the scale height of the matter; and (4) ours is a spiral galaxy characterized by an arm to interarm density ratio of about 3:1.

Kniffen, D. A.↗

NASA NTRS1973

One- and multi-component models of the upper photosphere based on molecular spectra. I - The violet system of CN /0, 0/

Spectroheliograms taken in the CN (0, 0) violet band near 3883 A show very small scale network and cell structures with high contrast. The bandhead itself, which is a broad feature due to overlap of several CN lines, allows the diagnostic simplicity of a continuum since motions, magnetic fields, and broadening mechanisms are unimportant. We have obtained spectroheliograms in the bandhead and center-to-limb photoelectric spectra of CN (0, 0) at Kitt Peak National Observatory. From the photoelectric spectra and a detailed analysis of the formation of the CN (0, 0) spectrum we derive a best-fit one-component upper photospheric model differing from that of the HSRA and recommend a change in solar carbon abundance from the HSRA value.

Mount, G. H.↗

NASA NTRS1991

Infrared radiative energy transfer in gaseous systems

Analyses and numerical procedures are presented to investigate the radiative interactions in various energy transfer processes in gaseous systems. Both gray and non-gray radiative formulations for absorption and emission by molecular gases are presented. The gray gas formulations are based on the Planck mean absorption coefficient and the non-gray formulations are based on the wide band model correlations for molecular absorption. Various relations for the radiative flux and divergence of radiative flux are developed. These are useful for different flow conditions and physical problems. Specific plans for obtaining extensive results for different cases are presented. The procedure developed was applied to several realistic problems. Results of selected studies are presented.

Tiwari, Surendra N.↗

NASA NTRS1982

Ion-induced nucleation in a binary mixture

Recent ion-induced nucleation studies in a binary mixture of H2O and H2SO4 vapors indicate that conventional classical nucleation theories cannot account for the experimentally observed ion-H2O-H2SO4 microcluster spectra. An empirical-analytical, semi-molecular theory of nucleation of a binary mixture of vapors on ions has been developed. This theory includes molecular approach to ion-induced changes in dielectric properties in the immediate neighborhood of an ion core as well as the size dependence of the surface tension of the microcluster. In addition to gaseous sulfuric acid and water molecules, the effect of ion-hydrates and sulfuric acid hydrates has also been considered. This theory is further simplified by using an empirical correction factor for the electrostatic term. This correction factor has been obtained by comparing the simplified model with the molecular dynamics calculations for selected ion hydrate formation. These two theoretical models are then compared with the classical theory for a variety of experimental conditions.

Smith, A. C.↗

NASA NTRS1975

Conversion of laser energy to gas kinetic energy

Techniques for the gas phase absorption of laser radiation for conversion to gas kinetic energy are discussed. Absorption by inverse Bremsstrahlung, in which laser energy is converted at a gas kinetic rate in a spectrally continuous process, is briefly described, and absorption by molecular vibrational rotation bands is discussed at length. High pressure absorption is proposed as a means of minimizing gas bleaching and dissociation, the major disadvantages of the molecular absorption process. A band model is presented for predicting the molecular absorption spectra in the high pressure absorption region and is applied to the CO molecule. Use of a rare gas seeded with Fe(CO)5 for converting vibrational modes to translation modes is described.

Caledonia, G. E.↗

NASA NTRS2008

New Developments in the Embedded Statistical Coupling Method: Atomistic/Continuum Crack Propagation

A concurrent multiscale modeling methodology that embeds a molecular dynamics (MD) region within a finite element (FEM) domain has been enhanced. The concurrent MD-FEM coupling methodology uses statistical averaging of the deformation of the atomistic MD domain to provide interface displacement boundary conditions to the surrounding continuum FEM region, which, in turn, generates interface reaction forces that are applied as piecewise constant traction boundary conditions to the MD domain. The enhancement is based on the addition of molecular dynamics-based cohesive zone model (CZM) elements near the MD-FEM interface. The CZM elements are a continuum interpretation of the traction-displacement relationships taken from MD simulations using Cohesive Zone Volume Elements (CZVE). The addition of CZM elements to the concurrent MD-FEM analysis provides a consistent set of atomistically-based cohesive properties within the finite element region near the growing crack. Another set of CZVEs are then used to extract revised CZM relationships from the enhanced embedded statistical coupling method (ESCM) simulation of an edge crack under uniaxial loading.

Saether, E.↗

NASA NTRS1990

Parsec-Scale Penetration of UV into Molecular Clouds: CII 158 Micron Mapping of W3, NGC 1977, and NGC 2023

The spatial distribution of the 158 microns CII fine structure line in the galactic sources W3, NGC 1977, and NGC 2023 is mapped. The emission arises from warm (100 to 300 K), dense photodissociation regions at the surface of molecular gas. In all three sources, the emission extends over parsec scales or greater. For W3 and NGC 1977, where the UV source/molecular cloud geometry presents an edge on view of the variation of CII intensity into the molecular gas, two dimensional models of the CII emission which include the effects of gas clumping and scattering by dust on the transport of UV photons are constructed. The observed CII distribution and intensity is well modeled by a clumpy or filamentary distribution to the molecular gas, with a clump/interclump gas density ratio of 100 or more, which allows deep penetration of carbon ionizing UV photons into the clouds. The penetration of UV into clumped molecular clouds may also explain the extended far IR continuum emission from these sources. The total luminosity of CII emission from a clumpy molecular cloud with adjacent or embedded octave band stars can be as much as an order of magnitude higher than the CII luminosity of a uniform cloud. In addition, the extended penetration of UV into molecular clouds will affect the abundances of atomic and molecular species and increase the fractional ionization of interclump gas and UV illuminated clump surfaces.

Howe, J. E.↗

NASA NTRS1999

Autonomous Agents: The Origins and Co-Evolution of Reproducing Molecular Systems

The central aim of this award concerned an investigation into, and adequate formulation of, the concept of an "autonomous agent." If we consider a bacterium swimming upstream in a glucose gradient, we are willing to say of the bacterium that it is going to get food. That is, we are willing, and do, describe the bacterium as acting on its own behalf in an environment. All free living cells are, in this sense, autonomous agents. But the bacterium is "just" a set of molecules. We define an autonomous agent as a physical system able to act on its own behalf in an environment, then ask, "What must a physical system be to be an autonomous agent?" The tentative definition for a molecular autonomous agent is that it must be self-reproducing and carry out at least one thermodynamic work cycle. The work carried out in this grant involved, among other features, the development of a detailed model of a molecular autonomous agent, and study of the kinetics of this system. In particular, a molecular autonomous agent must, by the above tentative definition, not only reproduce, but must carry out at least one work cycle. I took, as a simple example of a self-reproducing molecular system, the single-stranded DNA hexamer 3'CCGCGG5' which can line up and ligate its two complementary trimers, 5'CCG3' and 5'CGG3'. But the two ligated trimers constitute the same molecular sequence in the 3' to 5' direction as the initial hexamer, hence this system is autocatalytic. On the other hand the above system is not yet an autonomous agent. At the minimum, autonomous agents, as I have defined them, are a new class of chemical reaction network. At a maximum, they may constitute a proper definition of life itself.

Kauffman, Stuart↗