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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.

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At least 19 records

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NASA NTRS1993

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

NASA Discipline Number 52-20↗

NASA NTRS1996

Interactions of anesthetics with the membrane-water interface

Although the potency of conventional anesthetics correlates with lipophilicity, an affinity to water also is essential. It was recently found that compounds with very low affinities to water do not produce anesthesia regardless of their lipophilicity. This finding implies that clinical anesthesia might arise because of interactions at molecular sites near the interface of neuronal membranes with the aqueous environment and, therefore, might require increased concentrations of anesthetic molecules at membrane interfaces. As an initial test of this hypothesis, we calculated in molecular dynamics simulations the free energy profiles for the transfer of anesthetic 1,1,2-trifluoroethane and nonanesthetic perfluoroethane across water-membrane and water-hexane interfaces. Consistent with the hypothesis, it was found that trifluoroethane, but not perfluoroethane, exhibits a free energy minimum and, therefore, increased concentrations at both interfaces. The transfer of trifluoroethane from water to the nonpolar hexane or interior of the membrane is accompanied by a considerable, solvent-induced shift in the conformational equilibrium around the C-C bond.

NASA Center ARC↗

NASA NTRS1988

Computer modeling of polymers

A Polymer Molecular Analysis Display System (p-MADS) was developed for computer modeling of polymers. This method of modeling allows for the theoretical calculation of molecular properties such as equilibrium geometries, conformational energies, heats of formations, crystal packing arrangements, and other properties. Furthermore, p-MADS has the following capabilities: constructing molecules from internal coordinates (bonds length, angles, and dihedral angles), Cartesian coordinates (such as X-ray structures), or from stick drawings; manipulating molecules using graphics and making hard copy representation of the molecules on a graphics printer; and performing geometry optimization calculations on molecules using the methods of molecular mechanics or molecular orbital theory.

Green, Terry J.↗

NASA NTRS1999

Boronate affinity adsorption of RNA: possible role of conformational changes

Batch equilibrium adsorption isotherm determination is used to characterize the adsorption of mixed yeast RNA on agarose-immobilized m-aminophenylboronic acid. It is shown that the affinity-enhancing influence of divalent cations depends strongly on the precise nature of the cation used, with barium being far more effective than the conventionally-used magnesium. This adsorption-promoting influence of barium is suggested to arise primarily from ionic influences on the structure and rigidity of the RNA molecule, as the adsorption of ribose-based small molecules is not similarly affected. The substitution of barium for the standard magnesium counterion does not greatly promote the adsorption of DNA, implying that the effect is specific to RNA and may be useful in boronate-based RNA separations. RNA adsorption isotherms exhibit sharp transitions as functions of temperature, and these transitions occur at different temperatures with Mg2+ and with Ba2+. Adsorption affinity and capacity were found to increase markedly at lower temperatures, suggestive of an enthalpically favored interaction process. The stoichiometric displacement parameter, Z, in Ba2+ buffer is three times the value in Mg2+ buffer, and is close to unity.

NASA Discipline Environmental Health↗

NASA NTRS1981

One-dimensional models of quasi-neutral parallel electric fields

Parallel electric fields can exist in the magnetic mirror geometry of auroral field lines if they conform to the quasineutral equilibrium solutions. Results on quasi-neutral equilibria and on double layer discontinuities were reviewed and the effects on such equilibria due to non-unique solutions, potential barriers and field aligned current flows using as inputs monoenergetic isotropic distribution functions were examined.

Stern, D. P.↗

NASA NTRS1995

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Karpas, Z.↗

NASA NTRS1979

An improved supersonic, three-dimensional, external, inviscid flow field code

A numerical procedure was developed to compute the inviscid super/hypersonic flow fields about complex vehicle geometries accurately and efficiently. A second-order accurate finite difference scheme is used to integrate the three-dimensional Euler equations in regions of continuous flow, while all shock waves are computed as discontinuities via the Rankine-Hugoniot jump conditions. Conformal mappings are used to develop a computational grid. The effects for equilibrium air are included using curve fits of Mollier charts. This report deals only with modifications to these procedures in four specific areas: inlet mass ingestion, subsonic axial Mach number, improved conformal mappings, and vehicles flying at yaw. In each area both the modifications to the computational procedures and computer code are discussed.

Marconi, F.↗

NASA NTRS1978

Infrared spectra of molecules and materials of astrophysical interest

The Raman spectra of gaseous, liquid and solid, and infrared spectra of gaseous and solid isopropylamine-d sub 0 and -d sub 2 was investigated between 4000 and 50 cm superscript -1. Differences between the spectrum of the solid phase and that of the fluid phases were interpreted in terms of an equilibrium between low energy s-trans and high energy gauche conformers, and a complete vibrational assignment was proposed for the s-trans conformer. The far infrared spectra of the gaseous compounds contained bands due to the asymmetric amino and coupled methyl torsions; the assignment of these bands was aided by observation of a number of two quantum transitions for each vibrational mode. The asymmetric potential functions were calculated, which resulted in values for the enthalpy differences between conformers in the gaseous phase of 446 and 523 callmole for the sub 0 -d and -d sub 2 compounds, respectively. The methyl torsional potential function of isopropylamine-d sub 0 was calculated which led to a value for the barrier height to internal rotation of the methyl rotors of 4.23 + or - 0.06 kcal/mole. Values for the ideal gas thermodynamic functions were calculated over a range of temperatures.

Durig, J. R.↗

NASA NTRS1977

Galilean satellites - Anomalous temperatures disputed

Anomalous averaged infrared brightness temperatures of the Galilean satellites of Jupiter reported by Gross (1975) are rejected as falsely conceived and lacking physical reality. It is argued that the calculations of equilibrium temperatures should be corrected, whereupon predictions would be in satisfactory agreement with observations, in conformity with the radiometric method of determining the diameters of asteroids and satellites. The IR irradiance and the related disk-averaged brightness temperature for the spectral band are recommended as more relevant. Attention is drawn to some interesting discrepancies between calculated and observed temperatures of the Jovian satellites which merit further investigation.

Morrison, D.↗

NASA NTRS1988

Numerical simulation of hypersonic flow over an aeroassist flight experiment vehicle

Solutions of wind-tunnel and entry-flight flow around the vehicle are obtained from the Navier-Stokes equations coupled with the chemical species continuity equations if needed. The time-iterative method employs several techniques: shock fitting, chemistry-split ADI and an algebraic grid in conformal spherical-polar space. Sensitivities of the results to numerical parameters and to frozen, equilibrium and finite rate reactions are investigated in the forebody computation. Quantitative results are obtained for the shock layer and the near wake for the entire vehicle corresponding to both ground test and flight conditions. Complex flow characteristics are analyzed on the basis of the complete flowfield over the aerobrake and simplified afterbodies. The method is stable and cost effective, and has yielded shock locations and wall pressure distributions which are in good agreement with wind-tunnel data.

Li, C. P.↗

NASA NTRS1997

Kinetics, Ca2+ dependence, and biophysical properties of integrin-mediated mechanical modulation of transmitter release from frog motor nerve terminals

Neurotransmitter release from frog motor nerve terminals is strongly modulated by change in muscle length. Over the physiological range, there is an approximately 10% increase in spontaneous and evoked release per 1% muscle stretch. Because many muscle fibers do not receive suprathreshold synaptic inputs at rest length, this stretch-induced enhancement of release constitutes a strong peripheral amplifier of the spinal stretch reflex. The stretch modulation of release is inhibited by peptides that block integrin binding of natural ligands. The modulation varies linearly with length, with a delay of no more than approximately 1-2 msec and is maintained constant at the new length. Moreover, the stretch modulation persists in a zero Ca2+ Ringer and, hence, is not dependent on Ca2+ influx through stretch activated channels. Eliminating transmembrane Ca2+ gradients and buffering intraterminal Ca2+ to approximately normal resting levels does not eliminate the modulation, suggesting that it is not the result of release of Ca2+ from internal stores. Finally, changes in temperature have no detectable effect on the kinetics of stretch-induced changes in endplate potential (EPP) amplitude or miniature EPP (mEPP) frequency. We conclude, therefore, that stretch does not act via second messenger pathways or a chemical modification of molecules involved in the release pathway. Instead, there is direct mechanical modulation of release. We postulate that tension on integrins in the presynaptic membrane is transduced mechanically into changes in the position or conformation of one or more molecules involved in neurotransmitter release, altering sensitivity to Ca2+ or the equilibrium for a critical reaction leading to vesicle fusion.

Non-NASA Center↗

NASA NTRS1999

Stoichiometry of the large conductance bacterial mechanosensitive channel of E. coli. A biochemical study

MscL, a 15 kDa transmembrane protein, is the only component involved in the formation of a 3 nS channel in the inner membrane of Escherichia coli that opens in response to mechanical or osmotic stress. While previous data had suggested that the functional MscL complex might be a hexamer, a recent crystallographic study of the MscL homologue from M. tuberculosis reveals a pentameric structure. The present work further examines the stoichiometry of the E. coli MscL using a variety of biochemical approaches. Detergent-purified 6His-MscL in solution and MscL in the membrane could be chemically crosslinked with the products displaying ladderlike patterns on SDS gels. Three crosslinking agents (EDC, DMS, and DMA) used at saturating concentrations invariably generated pentamers as the largest product. DSS produced additional bands corresponding to larger complexes although the pentamer band appeared to be the predominant product at high levels of crosslinker. It is not clear whether these extra bands reflect a difference in the crosslinking chemistry of DSS or whether its spacer arm is the longest of those used, or a combination of both facts. For the detergent-solubilized 6His-MscL both sedimentation equilibrium and gel chromatography showed the presence of multiple species. Thus the longer spacer arm could permit both intra- and intercomplex linkages. Nonetheless, the patterns obtained with all agents are consistent with and strongly suggest a pentameric organization for the MscL channel. Expression of MscL as genetically engineered double or triple subunit tandems yields low numbers of functional channels as compared to expressed monomers. The double-tandem assemblies must have an even number of subunits and crosslinking in the membrane confirmed hexamerization. Gel chromatography clearly demonstrated that the channels formed from the double tandems were larger than those formed from WT MscL, consistent with the native channel being pentameric. The observation that both double and triple tandems form channels of normal conductance implies that the pentameric assembly is to some degree independent of the number of subunit repeats in the polypeptide precursor. The channel is thus a pentameric core with the 'extra' subunits left out of the functional complex. From sedimentation equilibrium and size-exclusion chromatography, we also conclude that MscL complexes are not in a dynamic equilibrium with monomers, but are pre-assembled; and thus, their gating properties must result from changes in the conformation of the entire complex induced by the mechanical stress.

NASA Discipline Cell Biology↗

NASA NTRS1972

Extended chain crystals of linear high polymers.

Studies of extended chain crystals carried out over the last 10 years have been reviewed. Crystallization in an extended chain conformation is possible either by chain folding followed by extension in the solid state, or by crystallization during polymerization. The equilibrium isometric crystal habit is only rarely exhibited. Crystals which derive from folded chain macroconformation by subsequent chain extension have lamellar habit, crystals which crystallize during polymerization often show fibrillar habit because of nucleation limitation. The morphology of extended chain crystals is analogous to folded chain crystals. Their properties have been shown to be close to the extrapolated equilibrium properties.

Wunderlich, B.↗

NASA NTRS1989

Application of unstructured grid methods to steady and unsteady aerodynamic problems

The purpose is to describe the development of unstructured grid methods which have several advantages when compared to methods which make use of structured grids. Unstructured grids, for example, easily allow the treatment of complex geometries, allow for general mesh movement for realistic motions and structural deformations of complete aircraft configurations which is important for aeroelastic analysis, and enable adaptive mesh refinement to more accurately resolve the physics of the flow. Steady Euler calculations for a supersonic fighter configuration to demonstrate the complex geometry capability; unsteady Euler calculations for the supersonic fighter undergoing harmonic oscillations in a complete-vehicle bending mode to demonstrate the general mesh movement capability; and vortex-dominated conical-flow calculations for highly-swept delta wings to demonstrate the adaptive mesh refinement capability are discussed. The basic solution algorithm is a multi-stage Runge-Kutta time-stepping scheme with a finite-volume spatial discretization based on an unstructured grid of triangles in 2D or tetrahedra in 3D. The moving mesh capability is a general procedure which models each edge of each triangle (2D) or tetrahedra (3D) with a spring. The resulting static equilibrium equations which result from a summation of forces are then used to move the mesh to allow it to continuously conform to the instantaneous position or shape of the aircraft. The adaptive mesh refinement procedure enriches the unstructured mesh locally to more accurately resolve the vortical flow features. These capabilities are described in detail along with representative results which demonstrate several advantages of unstructured grid methods. The applicability of the unstructured grid methodology to steady and unsteady aerodynamic problems and directions for future work are discussed.

Batina, John T.↗

NASA NTRS1976

Development of a computer code for calculating the steady super/hypersonic inviscid flow around real configurations. Volume 1: Computational technique

A numerical procedure has been developed to compute the inviscid super/hypersonic flow field about complex vehicle geometries accurately and efficiently. A second order accurate finite difference scheme is used to integrate the three dimensional Euler equations in regions of continuous flow, while all shock waves are computed as discontinuities via the Rankine Hugoniot jump conditions. Conformal mappings are used to develop a computational grid. The effects of blunt nose entropy layers are computed in detail. Real gas effects for equilibrium air are included using curve fits of Mollier charts. Typical calculated results for shuttle orbiter, hypersonic transport, and supersonic aircraft configurations are included to demonstrate the usefulness of this tool.

Marconi, F.↗

NASA NTRS1976

Development of a computer code for calculating the steady super/hypersonic inviscid flow around real configurations. Volume 2: Code description

A numerical procedure was developed to compute the inviscid super/hypersonic flow field about complex vehicle geometries accurately and efficiently. A second-order accurate finite difference scheme is used to integrate the three-dimensional Euler equations in regions of continuous flow, while all shock waves are computed as discontinuities via the Rankine-Hugoniot jump conditions. Conformal mappings are used to develop a computational grid. The effects of blunt nose entropy layers are computed in detail. Real gas effects for equilibrium air are included using curve fits of Mollier charts. Typical calculated results for shuttle orbiter, hypersonic transport, and supersonic aircraft configurations are included to demonstrate the usefulness of this tool.

Marconi, F.↗

NASA NTRS1998

The Effects of Impurities on Protein Crystal Growth and Nucleation: A Preliminary Study

Kubota and Mullin (1995) devised a simple model to account for the effects of impurities on crystal growth of small inorganic and organic molecules in aqueous solutions. Experimentally, the relative step velocity and crystal growth of these molecules asymptotically approach zero or non-zero values with increasing concentrations of impurities. Alternatively, the step velocity and crystal growth can linearly approach zero as the impurity concentration increases. The Kubota-Mullin model assumes that the impurity exhibits Langmuirian adsorption onto the crystal surface. Decreases in step velocities and subsequent growth rates are related to the fractional coverage (theta) of the crystal surface by adsorbed impurities; theta = Kx / (I +Kx), x = mole fraction of impurity in solution. In the presence of impurities, the relative step velocity, V/Vo, and the relative growth rate of a crystal face, G/Go, are proposed to conform to the following equations: V/Vo approx. = G/Go = 1 - (alpha)(theta). The adsorption of impurity is assumed to be rapid and in quasi-equilibrium with the crystal surface sites available. When the value of alpha, an effectiveness factor, is one the growth will asymptotically approach zero with increasing concentrations of impurity. At values less than one, growth approaches a non-zero value asymptotically. When alpha is much greater than one, there will be a linear relationship between impurity concentration and growth rates. Kubota and Mullin expect alpha to decrease with increasing supersaturation and shrinking size of a two dimensional nucleus. It is expected that impurity effects on protein crystal growth will exhibit behavior similar to that of impurities in small molecule growth. A number of proteins were added to purified chicken egg white lysozyme, the effect on crystal nucleation and growth assessed.

Schall, Constance A.↗

NASA NTRS1994

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

Smith, Grant D.↗