Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular evolution”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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

At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

H and K maps of two star-forming regions: S 140 and CEP A OB3

The molecular clouds near S 140 and Cep A OB3 both contain regions that emit strongly in the infrared but which have relatively little or no emission in radio wavelengths. The lack of radio emission is usually interpreted to mean that little ionization has taken place, and that the IR emission comes from dust heated by a central pre-main sequence object. We have made high resolution maps of these two areas with H and K broadband filters with the 2.3m telescope of the Wyoming Infrared Observatory (WIRO). Our observations were made with an InSb detector using the standard WIRO mapping technique of multiple scanning to construct a series of 64x64 pictures. Our scanning was made in one arcsec steps with a 7 inch aperture to produce a resolution of about 6 sec FWHM. Observations of S 140 by Blair et al (1978) with moderate resolution in J, H, and K, revealed a prominent IR source that they called S 140IR. We have scanned an area surrounding their S 140IR region and have obtained total IR fluxes which are in close agreement with Blair et al. Additional detail corresponds to that seen by Dinerstein et al (1979) at 0.9 microns and Campbell (1986) at 1.0 microns. The large (H-K) values for all components of S 140IR indicates that they are probably embedded in the parent molecular cloud with A(v) = 25 mag and A(K) = 2.2 mag. Recent radio studies of Cep A by Hughes and Wouterloot (1984) and FIR studies by Evans et al (1981) have shown the similarity of Cep A to S 140. There is, however, some emission detected from ionized regions by the radio observations, indicating a slightly more advanced stage of evolution for Cep A. We observed an area around the strongest source in Cep A in both H and K, and the K map is presented. We have identified three sources separate from the main source.

Graadalen, G. L.↗
NASA NTRS1992

Growing protein crystals in microgravity - The NASA Microgravity Science and Applications Division (MSAD) Protein Crystal Growth (PCG) program

In collaboration with a medical researcher at the University of Alabama at Birmingham, NASA's Marshall Space Flight Center in Huntsville, Alabama, under the sponsorship of the Microgravity Science and Applications Division (MSAD) at NASA Headquarters, is continuing a series of space experiments in protein crystal growth which could lead to innovative new drugs as well as basic science data on protein molecular structures. From 1985 through 1992, Protein Crystal Growth (PCG) experiments will have been flown on the Space Shuttle a total of 14 times. The first four hand-held experiments were used to test hardware concepts; later flights incorporated these concepts for vapor diffusion protein crystal growth with temperature control. This article provides an overview of the PCG program: its evolution, objectives, and plans for future experiments on NASA's Space Shuttle and Space Station Freedom.

Herren, B.↗
NASA NTRS1979

Molecular phylogenetic trees - On the validity of the Goodman-Moore augmentation algorithm

A response is made to the reply of Nei and Tateno (1979) to the letter of Holmquist (1978) supporting the validity of the augmentation algorithm of Moore (1977) in reconstructions of nucleotide substitutions by means of the maximum parsimony principle. It is argued that the overestimation of the augmented numbers of nucleotide substitutions (augmented distances) found by Tateno and Nei (1978) is due to an unrepresentative data sample and that it is only necessary that evolution be stochastically uniform in different regions of the phylogenetic network for the augmentation method to be useful. The importance of the average value of the true distance over all links is explained, and the relative variances of the true and augmented distances are calculated to be almost identical. The effects of topological changes in the phylogenetic tree on the augmented distance and the question of the correctness of ancestral sequences inferred by the method of parsimony are also clarified.

Holmquist, R.↗
NASA NTRS2000

The Survival of Meteorite Organic Compounds with Increasing Impact Pressure

The majority of carbonaceous meteorites studied today are thought to originate in the asteroid belt. Impacts among asteroidal objects generate heat and pressure that may have altered or destroyed pre-existing organic matter in both targets and projectiles to a greater or lesser degree depending upon impact velocities. Very little is known about the shock related chemical evolution of organic matter relevant to this stage of the cosmic history of biogenic elements and compounds. The present work continues our study of the effects of shock impacts on selected classes of organic compounds utilizing laboratory shock facilities. Our approach was to subject mixtures of organic compounds, embedded in a matrix of the Murchison meteorite, to a simulated hypervelocity impact. The molecular compositions of products were then analyzed to determine the degree of survival of the original compounds. Insofar as results associated with velocities < 8 km/sec may be relevant to impacts on planetary surfaces (e.g., oblique impacts, impacts on small outer planet satellites) or grain-grain collisions in the interstellar medium, then our experiments will be applicable to these environments as well.

Cooper, George↗
NASA NTRS1992

Protein sequences and redox titrations indicate that the electron acceptors in reaction centers from heliobacteria are similar to Photosystem I

Photosynthetic reaction centers isolated from Heliobacillus mobilis exhibit a single major protein on SDS-PAGE of 47 000 Mr. Attempts to sequence the reaction center polypeptide indicated that the N-terminus is blocked. After enzymatic and chemical cleavage, four peptide fragments were sequenced from the Heliobacillus mobilis apoprotein. Only one of these sequences showed significant specific similarity to any of the protein and deduced protein sequences in the GenBank data base. This fragment is identical with 56% of the residues, including both cysteines, found in highly conserved region that is proposed to bind iron-sulfur center Fx in the Photosystem I reaction center peptide that is the psaB gene product. The similarity to the psaA gene product in this region is 48%. Redox titrations of laser-flash-induced photobleaching with millisecond decay kinetics on isolated reaction centers from Heliobacterium gestii indicate a midpoint potential of -414 mV with n = 2 titration behavior. In membranes, the behavior is intermediate between n = 1 and n = 2, and the apparent midpoint potential is -444 mV. This is compared to the behavior in Photosystem I, where the intermediate electron acceptor A1, thought to be a phylloquinone molecule, has been proposed to undergo a double reduction at low redox potentials in the presence of viologen redox mediators. These results strongly suggest that the acceptor side electron transfer system in reaction centers from heliobacteria is indeed analogous to that found in Photosystem I. The sequence similarities indicate that the divergence of the heliobacteria from the Photosystem I line occurred before the gene duplication and subsequent divergence that lead to the heterodimeric protein core of the Photosystem I reaction center.

NASA Discipline Number 52-30↗
NASA NTRS1974

Evolution of models for evolution

The paper discusses models of evolution and their values, and some critiques of these models and the value of these critiques. A model is investigated which involves the formation of prebiotic protein from amino acids. Its formation by four theoretical critiques that suggest alternative environmental conditions is discussed. Experiments are reviewed so as to illustrate the experimental testing of the possible weaknesses of a model for a single molecular evolutionary phase and to suggest some necessary changes in the model.

Rohlfing, D. L.↗
NASA NTRS1994

An investigation of solar wind effects on the evolution of the Martian atmosphere

This investigation concentrated on the question of how atmosphere escape, related to both photochemistry and the Mars solar wind interaction, may have affected the evolution of Mars' atmosphere over time. The principal investigator and postdoctoral researcher adopted the premise that contemporary escape processes have dominated the losses to space over the past 3.5 billion years, but that the associated loss rates have been modified by solar evolution. A model was constructed for the contemporary escape scenario based on knowledge gained from both Venus in-situ measurements from Pioneer Venus Orbiter and Mars measurements from Phobos-2. Venus provided a valuable second example of a weakly magnetized planet having a similar solar wind interaction where we have more knowledge from observations. The model included photochemical losses from recombining ionospheric molecular ions, scavenging Martian upper atmosphere ('pickup') ions by the solar wind, and sputtering of the atmosphere by reentering pickup ions. The existence of the latter mechanism was realized during the course of the supported investigation, and is now thought by Jakosky and Pepin to explain some of the Martian noble gas isotope ratios.

Luhmann, Janet G.↗
NASA NTRS2000

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗
NASA NTRS2018

New O+CO2 Scattering Cross Sections and Their Impact on Photochemical Atmospheric Escape of Oxygen from Mars

Dissociative recombination of O2+ and CO2+ molecular ions in the upper atmosphere of Mars is a major source of suprathermal (hot) oxygen atoms. A significant fraction of hot O atoms are sufficiently fast to overcome Mars' gravitational potential and escape to space. This mechanism is known as photochemical escape (PE) and found to be one of the major escape mechanisms presently active on Mars. The Mars Atmosphere and Volatile Evolution Mission (MAVEN) can constrain the PE rate from measurements of electron temperature and density and ion temperature and density. Escape probabilities of hot O can then be constructed from in-situ neutral densities and escaping O flux loss due to collisions with atmospheric background gases. Due to CO2 abundance in the upper atmosphere, O+CO2 scattering is the most important sink of the escaping hot O flux that strongly affects estimates of total atomic oxygen escape rate obtained from MAVEN data, as outlined above. New O+CO2 elastic and inelastic cross sections were constructed from first principles for collision energies from 0.01-5 eV. O(3P)+CO2 collisions were described using new 4D electronic potential energy surfaces (PESs) for restricted geometries. Three lowest triplet states of CO2 were considered for symmetric, bending, and asymmetric vibrational modes. The cross sections were determined from close-coupling calculations performed on individual surfaces using vibrating rotor approximations for CO2 molecule. Differential and momentum transfer cross sections, of use in energy transfer atmospheric models, were also constructed. The obtained cross sections are in excellent agreement with published results. Our new elastic cross sections are significantly smaller than assumed in earlier atmospheric escape models, resulting in larger photochemical escape rate of O from Mars, as estimated from a 1D escape model. Our results agree well with estimated hot O flux (about 9 x 10(sup 25) s(sup -1)) derived from altitude profiles of 130.4 nm O emission measured up to ~4,000 km by the Imaging Ultraviolet Spectrograph on MAVEN orbiter.

Atmospheric↗
NASA NTRS2019

Measuring the D/H Ratios of Exoplanets and Brown Dwarfs

The relative abundance of deuterium and hydrogen is a potent tracer of planet formation and evolution. Jupiter and Saturn have protosolar atmospheric D/H ratios, a relic of substantial gas accretion from the nebula, while the atmospheres of Neptune and Uranus are enhanced in D by accretion of ices into their envelopes. For terrestrial planets, D/H ratios are used to determine the mechanisms of volatile delivery and subsequent atmosphere loss over the lifetime of the planet. Planets and brown dwarfs more massive than ~13 M(J) quickly fuse their initial D reservoir. Here, we simulate spectra for giant exoplanets and brown dwarfs (2 M(Neptune) to ~10 M(Jupiter)) from T(eff) = 200–1800 K including both CH3D and HDO to determine the observability of these dominant deuterium isotopologues in mid-infrared thermal emission spectra. Colder objects have stronger molecular features in their spectra, due to the temperature dependence of molecular cross sections. CH3D is easier to observe than HDO at all temperatures considered, due to the strength of its absorption bands and locations of features at wavelengths with few other strong absorption features. We predict that for nearby cool brown dwarfs, the CH3D abundance can be measured at high signal to noise with the James Webb Space Telescope (JWST); for objects from 200 to 800 K closer than 10 pc, a protosolar D/H ratio would be readily observable in 2.5 hr. Moderately young Jupiter-mass planets (100–300 Myr) and young Neptunes (10 Myr) may be discovered with JWST and provide the best targets for detecting deuterium on an exoplanet in the coming decade. Future telescope designs should consider the importance of isotopes for understanding the formation and evolution of planetary atmospheres.

Caroline V. Morley↗
NASA NTRS1986

Intramolecular interactions in aminoacyl nucleotides: Implications regarding the origin of genetic coding and protein synthesis

Cellular organisms store information as sequences of nucleotides in double stranded DNA. This information is useless unless it can be converted into the active molecular species, protein. This is done in contemporary creatures first by transcription of one strand to give a complementary strand of mRNA. The sequence of nucleotides is then translated into a specific sequence of amino acids in a protein. Translation is made possible by a genetic coding system in which a sequence of three nucleotides codes for a specific amino acid. The origin and evolution of any chemical system can be understood through elucidation of the properties of the chemical entities which make up the system. There is an underlying logic to the coding system revealed by a correlation of the hydrophobicities of amino acids and their anticodonic nucleotides (i.e., the complement of the codon). Its importance lies in the fact that every amino acid going into protein synthesis must first be activated. This is universally accomplished with ATP. Past studies have concentrated on the chemistry of the adenylates, but more recently we have found, through the use of NMR, that we can observe intramolecular interactions even at low concentrations, between amino acid side chains and nucleotide base rings in these adenylates. The use of this type of compound thus affords a novel way of elucidating the manner in which amino acids and nucleotides interact with each other. In aqueous solution, when a hydrophobic amino acid is attached to the most hydrophobic nucleotide, AMP, a hydrophobic interaction takes place between the amino acid side chain and the adenine ring. The studies to be reported concern these hydrophobic interactions.

Lacey, J. C., Jr.↗
NASA NTRS2018

Marginal protein stability drives subcellular proteome isoelectric point

There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome—a highly acidic compartment in the cell—have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.

Kaiser Loell↗
NASA NTRS1984

Mass loss from red giants - A simple evolutionary model for NGC 7027

NGC 7027 is a young planetary nebula with the remnants of a red giant circumstellar envelope surrounding the central, ionized region. By comparing the outer molecular envelope with the inner ionized material, it is argued that the mass loss rate has decreased by at least a factor of 3, and more probably by about a factor of 10, during the past 1000 years. From this result, it is argued that the luminosity of the central star has also decreased substantially during the same time, consistent with models for the rapid evolution of stars just after they evolve off the asymptotic giant branch. In this picture, the distance to NGC 7027 is less than 1300 pc. NGC 7027 was the last (and best) example of a star where apparently the momentum in the outflowing mass /M(dot)v/ is considerably greater than the momentum in the radiation field (L/c). With the above description of this object, the evidence is now strong that quite often the mass lost from late-type giants is ultimately driven to infinity by radiation pressure on grains. If M(dot)v is as large as L/c for asymptotic branch stars, then it is expected that the total amount of mass lost during this stage of evolution is of the same magnitude as the initial mass of the star, and therefore this mass loss can profoundly affect the star's ultimate fate.

Jura, M.↗
NASA NTRS1988

The formation of interstellar jets

The formation of interstellar jets by convergence of supersonic conical flows and the further dynamical evolution of these jets are investigated theoretically by means of numerical simulations. The results are presented in extensive graphs and characterized in detail. Strong radiative cooling is shown to result in jets with Mach numbers 2.5-29 propagating to lengths 50-100 times their original widths, with condensation of swept-up interstellar matter at Mach 5 or greater. The characteristics of so-called molecular outflows are well reproduced by the simulations of low-Mach-number and quasi-adiabatic jets.

Tenorio-Tagle, G.↗
NASA NTRS1994

Evolution of macromolecular dust: Far-ultraviolet spectral dust extinction and gas absorption of stellar light as measured with the Hopkins Ultraviolet Telescope

From far-ultraviolet (FUV) spectra of B stars taken with the Hopkins Ultraviolet Telescope (HUT) and Voyager space observations, we determine the far-ultraviolet extinction by Galactic dust and hydrogen absorption in the local spiral-arm clouds towards HD 25443 (B0.5 III), HD 37903 (B1.5 V), and HD 200775 (B3 Ve). We find that the (n (H)) = 1.3 cu cm and number fraction (f = 0.31) of H atoms in molecular hydrogen relative to the total hydrogen indicates a mostly diffuse medium toward HD 25443. We also determine f = 0.56 for the gas in the photodissociation region (PDR) in front of HD 37903 and f approximately equals 0.36 for the HD 200775 PDR. The inferred ratios of N(H2)/I(CO) = 2.4 to 2.8 x 10(exp 20)/K(km/s)/sq cm for cool gas in dark clouds agree with previous canonical estimates of N(H2)/I(CO) = 2 to 3 x 10(exp 20)/K(km/s)/sq cm and support the use of the ratio for determining masses of molecular clouds. We find that the shape and strength of the HD 25443 FUV extinction is the same as a diffuse-medium mean extinction (R(sub nu) = 2.95) extrapolated from mid-UV wavelengths (normal). The HD 37903 FUV extinction through a bright H2 photodissociation region is higher than a mean FUV extinction(R(sub nu) = 4.11), as is the HD 200775 extinction. Another star from the literature rho Oph, probes the dense medium and exhibits an FUV extinction of normal mean strength (R(sub nu) = 4.55) but steeper shape. The normal FUV -extinction of HD 25443 implies that the small FUV-extinction dust in the diffuse medium forms in p art from larger grains as the grains shatter under shocks. The normal strength of the rho Oph FUV-extinction indicates that the minute dust condenses onto or coagulates into larger grains in the dense medium. The high extinction deviation of the HD 37903 PDR (and HD 200775 PDR) shows that FUV radiation from hot stars with T(sub eff) approximately equals 20,000 to 23,000 K in PDRs can evaporate some of the FUV-extinction dust from grain surfaces. In contrast, previously measured extinctions in Galactic H(+) (H II) regions shows that FUV radiation at T(sub eff) greater than 25,000 K can destroy some of the dust in H(+) regions. Thus, some of the FUV-extinction dust is highly volatile. We find that the dust carrier of the variable FUV-extinction is correlated (r = 0.99) with the mid-IR (12 micrometers) radiation from hydrocarbon dust. The volatile FUV-extinction component could thus be due to minute hydrocarbon dust particles or macromolecules, probably PAHs, which are known to condense onto larger grains in the dense medium. Larger grains compsed of PAHs clustered into a solid could thus produce the steep FUV extinction of the rho Oph dense medium. After exposure to FUV photons wihtin approximately 1 pc of HD 37903, PAHs with about 30 carbon atoms would evaporate off the larger grains, increasing gaseous PAH abundance by approximately 14%. Also, after receiving shocks in the diffuse medium toward HD 25443, the larger hydrocarbon grains would shatter into PAH molecules. In summary, as the Galactic medium cycles betwee n the diffuse and dense medium, hydrocarbon dust cycles into and out of larger grains under the influence of shocks, radiation, and condensation.

Buss, Richard H., Jr.↗
NASA NTRS1977

Absorption of X-rays in the interstellar medium

The X-ray photoabsorption cross sections (per hydrogen atom) of interstellar clouds and the intercloud medium are calculated separately, taking into account abundance evolution, self-blanketing by grains, molecule formation, and ionization structure. A reference cross section describing a neutral monatomic gas of elements in solar abundances is computed for purposes of comparison, the cross section of the intercloud medium is calculated by assuming that 15% of the hydrogen is ionized, and the cross section of the clouds is computed for the cases where all hydrogen is in either molecular or atomic form. A comparison of the reference cross section with the others shows that a cross section is increased relative to the reference if abundances are enhanced or if molecular hydrogen exists and is decreased if atoms exist in grains or if hydrogen is ionized. It is noted that the total cross section will be a linear combination of the cross sections of the clouds and the intercloud medium and can reflect the characteristics of a particular line of sight.

Ride, S. K.↗
NASA NTRS2012

Wide-Field Infrared Survey Explorer Observations of the Evolution of Massive Star-Forming Regions

We present the results of a mid-infrared survey of II outer Galaxy massive star-forming regions and 3 open clusters with data from the Wide-field Infrared Survey Explorer (WISE). Using a newly developed photometric scheme to identify young stellar objects and exclude extragalactic contamination, we have studied the distribution of young stars within each region. These data tend to support the hypothesis that latter generations may be triggered by the interaction of winds and radiation from the first burst of massive star formation with the molecular cloud material leftover from that earlier generation of stars. We dub this process the "fireworks hypothesis" since star formation by this mechanism would proceed rapidly and resemble a burst of fireworks. We have also analyzed small cutout WISE images of the structures around the edges of these massive star-forming regions. We observe large (1-3 pc size) pillar and trunk-like structures of diffuse emission nebulosity tracing excited polycyclic aromatic hydrocarbon molecules and small dust grains at the perimeter of the massive star-forming regions. These structures contain small clusters of emerging Class I and Class II sources, but some are forming only a single to a few new stars.

Koenig, X. P.↗
NASA NTRS2011

Wide-Field Infrared Survey Explorer Observations of the Evolution of Massive Star-Forming Regions

We present the results of a mid-infrared survey of 11 outer Galaxy massive star-forming regions and 3 open clusters with data from the Wide-field Infrared Survey Explorer (WISE). Using a newly developed photometric scheme to identify young stellar objects and exclude extragalactic contamination, we have studied the distribution of young stars within each region. These data tend to support the hypothesis that latter generations may be triggered by the interaction of winds and radiation from the first burst of massive star formation with the molecular cloud material leftover from that earlier generation of stars.We dub this process the "fireworks hypothesis" since star formation by this mechanism would proceed rapidly and resemble a burst of fireworks.We have also analyzed small cutout WISE images of the structures around the edges of these massive star-forming regions. We observe large (1-3 pc size) pillar and trunk-like structures of diffuse emission nebulosity tracing excited polycyclic aromatic hydrocarbon molecules and small dust grains at the perimeter of the massive star-forming regions. These structures contain small clusters of emerging Class I and Class II sources, but some are forming only a single to a few new stars.

Koenig, X. P.↗