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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
NASA NTRS1988

Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

Owenson, Brian↗
NASA NTRS1987

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↗
NASA NTRS1989

Tidal disruption of open clusters in their parent molecular clouds

A simple model of tidal encounters has been applied to the problem of an open cluster in a clumpy molecular cloud. The parameters of the clumps are taken from the Blitz, Stark, and Long (1988) catalog of clumps in the Rosette molecular cloud. Encounters are modeled as impulsive, rectilinear collisions between Plummer spheres, but the tidal approximation is not invoked. Mass and binding energy changes during an encounter are computed by considering the velocity impulses given to individual stars in a random realization of a Plummer sphere. Mean rates of mass and binding energy loss are then computed by integrating over many encounters. Self-similar evolutionary calculations using these rates indicate that the disruption process is most sensitive to the cluster radius and relatively insensitive to cluster mass. The calculations indicate that clusters which are born in a cloud similar to the Rosette with a cluster radius greater than about 2.5 pc will not survive long enough to leave the cloud. The majority of clusters, however, have smaller radii and will survive the passage through their parent cloud.

Long, Kevin↗
NASA NTRS1975

Depletion of the F2 region ionosphere and the protonosphere by the release of molecular hydrogen

Theoretical models have been used to investigate the effects of artificially injected H2 gas on plasma densities in the ionospheric F region and the overlying protonosphere. Owing to large reaction rates between H2 and ionospheric O(+) ions, plasma densities in both daytime and nighttime ionospheres can be greatly reduced by modest amounts of released H2 gas. One hundred kg of H2 released at 300-km altitude reduces local O(+) densities by more than three orders of magnitude and produces about a 5% depression in H(+) densities in the overlying protonosphere. These results suggest that it should be possible to conduct controlled chemical-modification experiments for investigation of many outstanding ionospheric and magnetospheric problems.

Bernhardt, P. A.↗
NASA NTRS2002

Equivalent-Continuum Modeling With Application to Carbon Nanotubes

A method has been proposed for developing structure-property relationships of nano-structured materials. This method serves as a link between computational chemistry and solid mechanics by substituting discrete molecular structures with equivalent-continuum models. It has been shown that this substitution may be accomplished by equating the vibrational potential energy of a nano-structured material with the strain energy of representative truss and continuum models. As important examples with direct application to the development and characterization of single-walled carbon nanotubes and the design of nanotube-based devices, the modeling technique has been applied to determine the effective-continuum geometry and bending rigidity of a graphene sheet. A representative volume element of the chemical structure of graphene has been substituted with equivalent-truss and equivalent continuum models. As a result, an effective thickness of the continuum model has been determined. This effective thickness has been shown to be significantly larger than the interatomic spacing of graphite. The effective thickness has been shown to be significantly larger than the inter-planar spacing of graphite. The effective bending rigidity of the equivalent-continuum model of a graphene sheet was determined by equating the vibrational potential energy of the molecular model of a graphene sheet subjected to cylindrical bending with the strain energy of an equivalent continuum plate subjected to cylindrical bending.

Odegard, Gregory M.↗
NASA NTRS1991

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↗
NASA NTRS1989

Dust emission in the Sagittarius B2 molecular cloud core

A model is presented for the dust emission from the Sagittarius B2 molecular cloud core which reproduces the observed spectrum between 30 and 1300 micron, as well as the distribution of the emission at 1300 micron. The model is based on the assumption that Sgr B2(N) continuum source is located behind the dust cloud associated with Sgr B2(M) continuum source. The fact that Sgr B2(N) is stronger at 1300 micron can be attributed to a local column density maximum at the position of this source. Absence of a 53 micron emission peak at the position of Sgr B2(N) suggests that the luminosity of the north source is lower than that of the middle source.

Lis, Dariusz C.↗
NASA NTRS1996

Red Fluorescent Line Emission from Hydrogen Molecules in Diffuse Molecular Clouds

We have modeled the fluorescent pumping of electronic and vibrational emissions of molecular hydrogen (H2) within diffuse molecular clouds that are illuminated by ultraviolet continuum radiation. Fluorescent line intensities are predicted for transitions at ultraviolet, infrared, and red visible wavelengths as functions of the gas density, the visual extinction through the cloud, and the intensity of the incident UV continuum radiation. The observed intensity in each fluorescent transition is roughly proportional to the integrated rate of H2 photodissociation along the line of sight. Although the most luminous fluorescent emissions detectable from ground-based observatories lie at near-infrared wavelengths, we argue that the lower sky brightness at visible wavelengths makes the red fluorescent transitions a particularly sensitive probe. Fabry-Perot spectrographs of the type that have been designed to observe very faint diffuse Ha emissions are soon expected to yield sensitivities that will be adequate to detect H2 vibrational emissions from molecular clouds that are exposed to ultraviolet radiation no stronger than the mean radiation field within the Galaxy. Observations of red H2 fluorescent emission together with cospatial 21 cm H I observations could serve as a valuable probe of the gas density in diffuse molecular clouds.

Neufeld, David A.↗
NASA NTRS2001

Computer Simulation of the Forces Acting on the Polystyrene Probe Submerged into the Succinonitrile Near Phase Transition

Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. At mesoscale level interaction between the cantilever tip and the sample surface is primarily described by the balance of attractive Van der Waals and repulsive forces. The model of cantilever oscillations is applicable to both non-contact and "tapping" AFM. This model can be farther enhanced to describe nanoparticle manipulation by cantilever. At microscopic level tip contamination and details of tip-surface interaction can be simulated using molecular dynamics approach. Integration of mesoscale model with molecular dynamic model is discussed.

Bune, Andris V.↗
NASA NTRS2022

Building and Breaking Carbon Composites with REACTER

Carbon-based composites have become indispensable materials in aerospace and other high-performance applications, yet obtaining a detailed, nanoscale understanding of their morphology and failure mechanisms using only experimental methods remains a difficult challenge. REACTER is a versatile computational modeling tool for atomistic molecular dynamics simulations designed to model chemical reactions at the speed and length scales of classical force fields. In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites: carbon nanotube (CNT) composites and carbon fiber reinforced polymers (CFRP). A network of CNTs was grown dynamically using the new ‘create atoms’ feature of REACTER. The CNT filler was embedded into a polyarylacetylene (PAA) matrix by simulated in situ polymerization to obtain the final composite model. To generate the second class of carbon composite, fully carbonized (graphitic) carbon fiber morphologies were created by the method of Desai et al. [1], but using the advanced reaction constraints framework of REACTER. Two fiber models were created, representing a circular carbon fiber core and a flat surface, and similarly infiltrated with resin to obtain the final CFRP structure. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third order DFT-based tight-binding simulations, via a reaction constraint on the total potential energy of the involved atoms.

Polymer↗
NASA NTRS1972

A band model formulation for very nonuniform paths.

Anomalous behavior has been observed when molecular band-models incorporating the Curtis-Godson or similar approximations are applied to problems characterized by a large variation in temperature along the optical path. The nature of this misbehavior has been examined and a procedure has been developed for its suppression by the introduction of a less restrictive assumption in the derivation of the band model from the basic equation of transfer.

Lindquist, G. H.↗
NASA NTRS2019

Testbed Results for Scalar and Vector Radiative Transfer Computations of Light in Atmosphere-Ocean Systems

We generate and tabulate reflectance values of the Stokes parameters I, Q, and U of upwelling radiance just above a rough ocean surface and at the top of the atmosphere (TOA) for 100 scattering geometries, four atmosphere-ocean systems, and four wavelengths. The atmosphere-ocean systems increase in complexity from (a) a molecular atmosphere above a rough ocean surface (AOS-I model); to (b) a pure water body below a rough ocean surface (AOS-II model); to (c) a fully-coupled simple atmosphere-ocean system (AOS-III model) containing a molecular atmosphere, rough ocean surface, and pure water; to (d) a fully-coupled complex atmosphere-ocean system (AOS-IV model) that includes scattering by molecules, rough ocean surface, pure water, and hydrosols. Our wavelengths (350, 450, 550, and 650 nm) capture the ultraviolet-visible range. Our tables provide radiative transfer (RT) testbed results for atmosphere-ocean systems with an accuracy that surpasses the measurement accuracy of state-of-the-art polarimeters. To validate the accuracy of these tables we performed computations using three independent RT codes that provide deterministic numerical solutions for the RT equation. The agreement is 10(exp –5) for AOS-IV model, and 10(exp –6) for the other models. The degree of linear polarization computed by these RT codes differs by ≤0.2% for 15 isolated cases of tabulated reflectance values, and by ≤0.1% for all remaining cases. We also provide comparisons with results obtained by a stochastic RT code for AOS-I model. The agreement between the deterministic and stochastic results for this model is 10(exp –5) at TOA, and 10(exp –6) above the ocean surface.

Polarimeters↗
NASA NTRS1976

Calculations of molecular ionization energies using a self-consistent-charge Hartree-Fock-Slater method

A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.

Rosen, A.↗
NASA NTRS2021

Sputtering of Surfaces by Ion Irradiation: A Comparison of Molecular Dynamics and Binary Collision Approximation Models to Laboratory Measurements

We compare various sputtering simulation methods to experimental results in both the low energy (<1 keV) and high energy (≥1 keV) impact regimes for argon ions impacting a pure copper substrate at normal incidence. Our results indicate that for high energy impacts, both binary collision approximation (BCA) and molecular dynamics methods can be used to generate reasonable predictions for the yield and energy distribution of the sputtered atoms. We also find reasonable agreement between the theoretical and experimental results down to impact energies of 600 eV. However, at 200 eV impact energies, significant discrepancies appear between the experimental and theoretical ejecta energy distributions in the peak position, the width of the energy distribution, and the magnitude of the high energy tail. These discrepancies appear to arise from the experimental results being only for atoms sputtered normal to the substrate surface, whereas the theoretical results are integrated over all 2π solid angles above the surface. Using the BCA code SDTrimSP and limiting the results to only atoms emitted within ±15° of the surface normal brings theory and experiment into reasonable agreement. These results suggest that for low energy impacts, the energy distribution of sputtered atoms is highly dependent on the emission angle of the ejecta.

Solar wind↗
NASA NTRS1979

A statistical model for the initial stellar mass function

The nonlinear stages of the fragmentation of a collapsing molecular cloud are modeled by coagulation theory. Several distinct physical processes are discussed, including protostellar fragment coalescence, gas accretion, and binary formation. This work confirms and extends the earlier result of Nakano (1966) that an approximately self-similar limiting form of the mass spectrum develops after several mean initial collision times. An approximate solution to the velocity-averaged coagulation equation is given for an arbitrary power-law dependence of the coalescence rate on mass, with dimensional dependence proportional to m to the power lambda; i.e., the asymptotic mass spectrum varies as m to the -3 lambda/2 power at small masses and cuts off exponentially at large masses, the characteristic mass depending on the number of collision times elapsed. Simple physical arguments suggest that lambda may increase with increasing mass, but is restricted to the range from 2/3 to 4/3. A large fraction of collisions could result in binary formation.

Silk, J.↗
NASA NTRS1987

Low Reynolds number modeling of turbulent flows with and without wall transpiration

A full Reynolds-stress closure that is capable of describing the flow all the way to the wall is formulated. The closure is based on the conventional high Reynolds number form of the redistribution model, the inclusion of molecular diffusion, and a modified dissipation model to account for viscous effects near a wall. Two dissipation models are investigated along with two gradient diffusion and two redistribution models. Their respective effects on the calculated flow properties are assessed by comparing them with the data of fully developed turbulent flows and a developing pipe flow with wall transpiration. The near-wall behavior is very well predicted; however, the wall correction to the redistribution modeling is found to have little effect on the calculated results. The overall behavior of the fully developed turbulent flows is best described by a nonisotropic gradient diffusion model, a return-to-isotropy redistribution model, and a dissipation model that accounts for viscous behavior near a wall. This same closure also gives the best prediction of the axial pressure drop behavior along a pipe with a uniform wall suction. Furthermore, the near-wall behavior of such a flow is very well predicted by this closure.

So, Ronald M. C.↗
NASA NTRS1993

The abundance of CH(+) in translucent molecular clouds - Further tests of shock models

Observations of interstellar absorption lines of CH(+) in the (0, 0) and (1, 0) bands of the A 1Pi - X 1Sigma(+) system are presented for 17 stars with reddenings up to E(B-V) about 1.5 mag. Complementary data on interstellar CH in the (0, 0) bands of the A 2Delta - X 2Pi and B 2Sigma(-) - X 2Pi systems and C2 in the A 1Pi(u) - X 1Sigma(g)(+) red system have been obtained as well. The derived CH(+) column densities continue to increase with total column density, and values up to 10 exp 14/sq cm are reported for highly-reddened lines of sight. In most cases, the CH(+) and CH absorptions are dominated by a single strong component, with weaker features displaced by a few km/s. No significant velocity difference is found between CH(+) and neutral species such as CH and CN for this sample of randomly oriented lines of sight. In contrast with CN, the CH(+) abundance does not increase with the density in the cloud as derived from the observed C2 excitation. For the two clouds with the largest density, HD 62542 and HD 94413, no CH(+) absorption is found with CH(+)/CH less than 0.03 and 0.14, respectively. The CH(+) findings do not support a single-shock origin for the formation of the ion.

Gredel, R.↗