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At least 451 records · Page 25

Relation between bond-length alternation and second electronic hyperpolarizability of conjugated organic molecules

The solvent dependence of the second hyperpolarizability, gamma, of a variety of unsaturated organic compounds has been measured by third harmonic generation at 1907 nanometers. It is seen that the measured gamma is a function of solvent polarity. These solvent-dependent hyperpolarizabilities are associated with changes in molecular geometry from a highly bond-length alternated, polyenelike structure for a formyl-substituted compound in nonpolar solvents, to a cyaninelike structure, with little bond-length alternation, for a dicyanovinyl-substituted compound in polar solvents. By tuning bond-length alternation, gamma can be optimized in either a positive or negative sense for polymethine dyes of a given conjugation length.

Marder, Seth R.↗

Molecular abundances and low-mass star formation. 1: Si- and S-bearing species toward IRAS 16293-2422

Results from millimeter and submillimeter spectral line surveys of the protobinary source Infrared Astronomical Satellite (IRAS) 16293-2422 are presented. Here we outline the abundances of silicon- and sulfur-containing species. A combination of rotation diagram and full statistical equilibrium/radiative transfer calculations is used to constrain the physical conditions toward IRAS 16293 and to construct its beam-averaged chemical composition over a 10 to 20 sec (1600 to 3200 AU) scale. The chemical complexity as judged by species such as SiO, OCS, and H2S, is intermediate between that of dark molecular clouds such as L134N and hot molecular cloud cores such as Orion KL. From the richness of the spectra compared to other young stellar objects of similar luminosity, it is clear that molecular abundances do not scale simply with mass; rather, the chemistry is a strong function of evolutionary state, i.e., age.

Blake, Geoffrey A.↗

Preliminary Work in Obtaining Site-Directed Mutants of Hen Egg White Lysozyme

Protein crystal growth studies are recognized as a critical endeavor in the field of molecular biotechnology. The scientific applications of this field include the understanding of how enzymes function and the accumulation of accurate information of atomic structures, a key factor in the process of rational drug design. NASA has committed substantial investment and resources to the field of protein crystal growth and has conducted many microgravity protein crystal growth experiments aboard shuttle flights. Crystals grown in space tend to be larger, denser and have a more perfect habit and geometry. These improved properties gained in the microgravity environment of space result largely from the reduction of solutal convection, and the elimination of sedimentation at the growing crystal surface. Shuttle experiments have yielded many large, high quality crystals that are suitable for high resolution X-ray diffraction analysis. Examples of biologically important macromolecules which have been successfully crystallized during shuttle missions include: lysozyme, isocitrate lyase, gamma-interferon, insulin, human serum albumin and canavalin. Numerous other examples are also available. In addition to obtaining high quality crystals, investigators are also interested in learning the mechanisms by which the growth events take place. Crystallization experiments indicate that for the enzyme HEWL, measured growth rates do not follow mathematical models for 2D nucleation and dislocation-led growth of tetragonal protein crystals. As has been suggested by the laboratory of Marc L. Pusey, a possible explanation for the disagreement between observation and data is that HEWL tetraconal crystals form by aggregated units of lysozyme in supersaturated solutions. Surface measurement data was shown to fit very well with a model using an octamer unit cell as the growth unit. According to this model, the aggregation pathway and subsequent crystal growth is described by: monomer < ------ > dimer < ------- > tetramer < ------ > octamer < ------ > higher order. It is believed that multimer aggregation of lysozyme occurs by interaction at specific binding sites on the surface of the protein crystals. If the presence of discrete binding sites and the aggregation hypothesis is true, then it follows that the alteration of the binding site(s) should have significant effect on the measurements obtained during growth experiments. Site-directed mutagenesis allows the specific alteration of proteins by replacement, deletion or addition of specific amino acid residues. This report outlines the approach for this strategy and the progress made thus far toward that end.

Holmes, Leonard D.↗

Radiative Cooling of Warm Molecular Gas

We consider the radiative cooling of warm (T >= 100 K), fully molecular astrophysical gas by rotational and vibrational transitions of the molecules H2O, CO, and H2. Using an escape probability method to solve for the molecular level populations, we have obtained the cooling rate for each molecule as a function of temperature, density, and an optical depth parameter. A four-parameter expression proves useful in fitting the run of cooling rate with density for any fixed values of the temperature and optical depth parameter. We identify the various cooling mechanisms which are dominant in different regions of the astrophysically relevant parameter space. Given the assumption that water is very abundant in warm regions of the interstellar medium, H2O rotational transitions are found to dominate the cooling of warm interstellar gas over a wide portion of the parameter space considered. While chemical models for the interstellar medium make the strong prediction that water will be produced copiously at temperatures above a few hundred degrees, our assumption of a high water abundance has yet to be tested observationally. The Infrared Space Observatory and the Submillimeter Wave Astronomy Satellite will prove ideal instruments for testing whether water is indeed an important coolant of interstellar and circumstellar gas.

Neufeld, David A.↗

Optical Properties of Thin Film Molecular Mixtures

Thin films composed of molecular mixtures of metal and dielectric are being considered for use as solar selective coatings for a variety of space power applications. By controlling the degree of molecular mixing, the solar selective coatings can be tailored to have the combined properties of high solar absorptance, alpha, and low infrared emittance, epsilon. On orbit, these combined properties would simultaneously maximize the amount of solar energy captured by the coating and minimize the amount of thermal energy radiated. Mini-satellites equipped with solar collectors coated with these cermet coatings may utilize the captured heat energy to power a heat engine to generate electricity, or to power a thermal bus that directs heat to remote regions of the spacecraft. Early work in this area identified the theoretical boundary conditions needed to operate a Carnot cycle in space, including the need for a solar concentrator, a solar selective coating at the heat inlet of the engine, and a radiator. A solar concentrator that can concentrate sunlight by a factor of 100 is ideal. At lower values, the temperature of the solar absorbing surface becomes too low for efficient heat engine operation, and at higher values, cavity type heat receivers become attractive. In designing the solar selective coating, the wavelength region yielding high solar absorptance must be separated from the wavelength region yielding low infrared emittance by establishing a sharp transition in optical properties. In particular, a sharp transition in reflectance is desired in the infrared to achieve the desired optical performance. For a heat engine operating at 450C, a sharp transition at 1.8 micrometers is desired. The radiator completes the heat flow through the Carnot cycle. Additional work has been done supporting the use of molecular mixtures for terrestrial applications. Sputter deposition provides a means to apply coatings to the tubes that carry a working fluid at the focus of trough-style collectors. Sputtering offers considerable flexibility in coating conditions, including a wide variety of metal and dielectric targets. Coating designs range from simple two or three layer coatings to complex coatings that are purposely graded to be metal-rich at their base and oxide-rich at their surface in order to yield the desired solar selective properties. In these cermet coatings, molecular islands of metal are thought to be embedded in a three dimensional matrix of dielectric. Recent work has identified the use of custom made ion beam sputter deposition targets to produce coatings containing molecular mixtures of metal and dielectric. The targets are cylindrical and the surface consists of a gradually changing composition of metal and dielectric. Rotating the cylinder under the beam during ion beam sputter deposition yields a coating that is a molecular mixture of metal and dielectric, with the composition changing through the thickness of the coating. The optical properties of these coatings are not only dependent on their thickness and chemical composition, but are also dependent on the extent of the through thickness gradient established during deposition. This paper presents a summary of the optical properties of several thin film molecular mixtures designed as solar selective coatings. Optical performance is first identified as a function of wavelength, from the ultraviolet to the visible and infrared. Coating composition, thickness, and gradient from metal to dielectric also play an important role. Additional work for future activities is also identified.

Jaworske, Donald A.↗

Cloud Algorithm Design and Performance for the 2002 Geoscience Laser Altimeter System Mission

A satellite borne lidar instrument, the Geoscience Laser Altimeter System (GLAS), is to be launched in late 2002 and will provide continuous profiling of atmospheric clouds and aerosol on a global basis. Data processing algorithms have been developed to provide operational data products in near real time. Basic data products for cloud observations are the height of the top and bottom of single to multiple cloud layers and the lidar calibrated observed backscatter cross section up to the level of signal attenuation. In addition the optical depth and vertical profile of visible extinction cross section of many transmissive cloud layers and most haze layers are to be derived. The optical thickness is derivable in some cases from the attenuation of the molecular scattering below cloud base. In other cases an assumption of the scattering phase function is required. In both cases a estimated correction for multiple scattering is required. The data processing algorithms have been tested in part from aircraft measurements used to simulated satellite data. The GLAS lidar observations will be made from an orbit that will allow inter comparison with all other existing satellite cloud measurements.

Spinhirne, J. D.↗

Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

Kikuchi, Hideaki↗

Finding Uncertainties that Cause the Age Dependence of Dose Limits to Be Immature

Space radiation permissible exposure limits (PEL) are intended to set acceptable levels of cancer risks, and avoid any clinical significant non-cancer effects. The 1989 recommendation of the National Council of Radiation Protection and Measurements (NCRP) recommended a strong age dependence of dose limits that departed drastically from the then mature 1970 dose limits recommendations from the National Academy of Science, which were independent of age. In 2000, the NCRP recommended revised limits that showed a similar trend of risk with age to the 1989 report. In this model, the cancer risk per Sv varies by more than 2-fold for ages between 30- and 50-yr. Therefore for galactic cosmic rays exposure, astronaut age has a larger influence on risk then radiation shielding mass or material composition, vehicle propulsion method, or position in the solar cycle. For considering the control of mission costs and resources, the possibility of using astronaut age as a trade variable in mission design could be considered. However, the uncertainties in describing the age dependence on risk have not been fully explored. We discuss biological factors that influence the age dependence of radiation risks, including susceptibility, expression and latency, and radiation quality. These factors depend not only on the individual s age, but also their genetic sensitivity and interaction with other environmental factors. Epidemiological data is limited in describing the age dependence on risk. The 2005, BEIR VII report recommends an age dependence for cancer risk attributable solely to the life-table disagreeing strongly with the NCRP model. However, BEIR VII also noted the limited power of human data for concomitantly describing both age and age after exposure dependences of cancer risks. Many experimental studies have shown that high LET radiation (e.g., high charge and energy (HZE) nuclei and neutrons) display reduced latency compared to low LET radiation, suggesting distinct biological factors are important. We discuss potential molecular mechanisms that would influence the age dependence of radiation risks. A probability distribution function for the uncertainties in age-dependence of risk models is described and predictions for Mars missions discussed. Our report suggests that theoretical considerations based on new experimental studies are needed to ensure the correct age dependence in space radiation risk models and the resulting Astronaut PEL.

Cucinotta, Francis A.↗

Norbornene-Based Polymer Electrolytes for Lithium Cells

Norbornene-based polymers have shown promise as solid electrolytes for lithium-based rechargeable electrochemical cells. These polymers are characterized as single-ion conductors. Single-ion-conducting polymers that can be used in lithium cells have long been sought. Single-ion conductors are preferred to multiple-ion conductors as solid electrolytes because concentration gradients associated with multiple-ion conduction lead to concentration polarization. By minimizing concentration polarization, one can enhance charge and discharge rates. Norbornene sulfonic acid esters have been synthesized by a ring-opening metathesis polymerization technique, using ruthenium-based catalysts. The resulting polymer structures (see figure) include sulfonate ionomers attached to the backbones of the polymer molecules. These molecules are single-ion conductors in that they conduct mobile Li+ ions only; the SO3 anions in these polymers, being tethered to the backbones, do not contribute to ionic conduction. This molecular system is especially attractive in that it is highly amenable to modification through functionalization of the backbone or copolymerization with various monomers. Polymers of this type have been blended with poly(ethylene oxide) to lend mechanical integrity to free-standing films, and the films have been fabricated into solid polymer electrolytes. These electrolytes have been demonstrated to exhibit conductivity of 2 10(exp -5)S/cm (which is high, relative to the conductivities of other solid electrolytes) at ambient temperature, plus acceptably high stability. This type of norbornene-based polymeric solid electrolyte is in the early stages of development. Inasmuch as the method of synthesis of these polymers is inherently flexible and techniques for the fabrication of the polymers into solid electrolytes are amenable to optimization, there is reason to anticipate further improvements.

Cheung, Iris↗

A quantitative analysis of IRAS maps of molecular clouds

We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

Wiseman, Jennifer J.↗

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

Rein, Robert↗

Membrane-Based Functions in the Origin of Cellular Life

How simple membrane peptides performed such essential proto-cellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we investigate how these peptides insert into membranes, self-assemble into higher-order structures and acquire functions. We have studied the insertion of an a-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)S into a model membrane. The transmembrane state is metastable, and approximately 15 kcal/mol is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)S and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self- assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to reengineering the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Wilson, Michael A.↗

Automatic Molecular Design using Evolutionary Techniques

Molecular nanotechnology is the precise, three-dimensional control of materials and devices at the atomic scale. An important part of nanotechnology is the design of molecules for specific purposes. This paper describes early results using genetic software techniques to automatically design molecules under the control of a fitness function. The fitness function must be capable of determining which of two arbitrary molecules is better for a specific task. The software begins by generating a population of random molecules. The population is then evolved towards greater fitness by randomly combining parts of the better individuals to create new molecules. These new molecules then replace some of the worst molecules in the population. The unique aspect of our approach is that we apply genetic crossover to molecules represented by graphs, i.e., sets of atoms and the bonds that connect them. We present evidence suggesting that crossover alone, operating on graphs, can evolve any possible molecule given an appropriate fitness function and a population containing both rings and chains. Prior work evolved strings or trees that were subsequently processed to generate molecular graphs. In principle, genetic graph software should be able to evolve other graph representable systems such as circuits, transportation networks, metabolic pathways, computer networks, etc.

Globus, Al↗

Seawater Debye Model Function at L-Band and Its Impact on Salinity Retrieval From Aquarius Satellite Data

A model function of seawater, which specifies the dielectric constant of seawater as a function of salinity, temperature, and frequency, is important for the retrieval of sea surface salinity using satellite data. In 2017, a model function has been developed based on measurement data at 1.4134 GHz using a third-order polynomial expression in salinity ( S ) and temperature ( T ). Although the model showed improvements in salinity retrieval, it had an inconsistent behavior between partitioned salinities. To improve the stability of the model, new dielectric measurements of seawater have been made recently over a broad range of salinities and temperatures to expand the data set used for developing the model function. The structure of the model function has been changed from a polynomial expansion in S and T to a physics-based model consisting of a Debye molecular resonance term plus a conductivity term. Each unknown parameter is expressed in S and T based on the expanded measurement data set. Physical arguments have been used to limit the number of unknown coefficients in these expressions to improve the stability of the model function. The new model function has been employed in the retrieval algorithm of the Aquarius satellite mission to obtain a global salinity map. The retrieved salinity using a different model function is compared with in situ data collected by Argo floats to evaluate the impact and the performance of model functions. The results indicate that the new model function has significant improvements in salinity retrieval compared with other existing models.

Seawater↗

Pharmacological activities in thermal proteins: relationships in molecular evolution

The model of protobiological events that has been presented in these pages has increasing relevance to pharmacological research. The thermal proteins that function as key substances in the proteinoid theory have recently been found to prolong the survival of rat forebrain neurons in culture and to stimulate the growth of neurites. A search for such activity in thermal proteins added to cultures of modern neurons was suggested by the fact that some of the microspheres assembled from proteinoids rich in hydrophobic amino acids themselves generate fibrous outgrowths.

NASA Discipline Exobiology↗

Characterization of the major cyanogen bromide fragment of alpha-A crystallin

Alpha crystallin from the bovine lens has been digested with cyanogen bromide, and the major fragment (CB-1) has been purified using reverse phase HPLC. Characterization of this fragment by Edman degradation and antisera to synthetic peptides indicates that it originates from alpha-A crystallin, but lacks the N-terminal methionine and the last 35 amino acids from the C-terminus of the molecule. The purified CB-1 fragment binds as well as native alpha crystallin to lens membrane, but is unable to self-assemble into the correct size of high molecular weight oligomeric complexes characteristic of the intact alpha-A chain. Together, these results demonstrate that the alpha-A chain is comprised of at least two functional domains, one of which is involved in binding of alpha-A crystallin to lens membrane, and another which is necessary for correct self-assembly of the molecule into high molecular weight oligomers.

Non-NASA Center↗

Vacuum-ultraviolet excitation cross sections by electron impact on NO.

Absolute excitation functions were measured for the NO(+) A l super Pi-Chi 1 super Sigma (+) molecular band system, the nitrogen 1200-, 1243-, and 1493-A multiplets, and oxygen 1304-A multiplet. Excitation was by electron impact on NO from threshold to approximately 250 eV. Results are plotted and tabulated.

Mentall, J. E.↗

Electric discharges in air - Near infrared emission spectrum.

The emission from glow discharges in flowing air has been investigated in the 1- to 5-micron wavelength region with a vacuum spectrometer. Most of the spectral features observed in the pressure range of .5 to 10 torr are identified, including atomic lines of OI, NI, and HI and molecular bands of N2, NO, N2O, CO2, and CO. The spectra are presented as a function of pressure and a table compiled of the atomic lines. Of particular interest are the contrasts between the emission of the air discharge and that of the pure gases, nitrogen and oxygen. In addition, the results of studies of several discharge modes, employing steady voltages and pulsed, provide data on details of the energy flow within the plasma.

Benesch, W. M.↗