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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
NASA NTRS1986

An improved approach to the analysis of drug-protein binding by distance geometry

The calculation of side chain centers of coordinates and the subsequent generation of side chain-side chain and side chain-backbone distance matrices is suggested as an improved method for viewing interactions inside proteins and for the comparison of protein structures. The use of side chain distance matrices is demonstrated with free PTI, and the use of difference distance matrices for side chains is shown for free and trypsin-bound PTI as well as for the X-ray structures of trypsin complexes with PTI and with benzamidine. It is found that conformational variations are reflected in the side chain distance matrices much more than in the standard C-C distance representations.

NASA Discipline Exobiology↗
DOE OSTI2025

Extended molecular eigenmodes treatment of dipole–dipole NMR relaxation in real fluids

Traditional models of NMR relaxation fail to account for the complex, multi-exponential behavior of the autocorrelation function in realistic systems characterized by soft-interactions and molecules that are chemically and physically complex. Here, in this study, we describe the relative diffusion of the spin dipoles by means of a Fokker–Planck equation that includes an interaction potential of mean force to account for the response of the physical/chemical environment around the dipoles. By numerically solving the Fokker–Planck equation for the diffusion propagator, we estimate dipole–dipole NMR relaxation for like- and unlike-spin systems via its eigenmode solution. We test the model against molecular simulations of diffusing dipoles with harmonic potentials and also validate using experimental longitudinal relaxation data from real systems, including Gd(III)–aqua and Gd(III)–DO3A–butrol complexes, the latter being an important MRI contrast agent. Using this novel approach, we predict both the inner- and outer-shell contributions to the relaxivity rates with excellent accuracy at frequencies relevant to MRI. We also show that, under the appropriate assumptions, our framework naturally recovers the Bloembergen–Purcell–Pound, the Solomon–Bloembergen–Morgan, and the Hwang–Freed models. Our implementation is general and publicly available for application to a broad range of systems.

Pinheiro dos Santos, Thiago J. [Rice Univ., Housto↗
DOE OSTI2022

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model

We report molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. The SLIC/CDC multiscale model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). The SLIC/CDC model predicts Gibbs energies of solvation for a database of 500 solutes in water with average accuracy better than 1 kcal/mol both for experimental measurements and for explicit-solvent molecular dynamics simulations. The separate SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent accessible surface area (SASA) nonpolar energy mode. The SLIC/SASA model predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems and better than 1.6 kcal/mol average accuracy in ionic liquids. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Modeling study on the cleavage step of the self-splicing reaction in group I introns

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

NASA Discipline Exobiology↗
NASA NTRS1989

Photoionization-regulated star formation and the structure of molecular clouds

A model for the rate of low-mass star formation in Galactic molecular clouds and for the influence of this star formation on the structure and evolution of the clouds is presented. The rate of energy injection by newly formed stars is estimated, and the effect of this energy injection on the size of the cloud is determined. It is shown that the observed rate of star formation appears adequate to support the observed clouds against gravitational collapse. The rate of photoionization-regulated star formation is estimated and it is shown to be in agreement with estimates of the observed rate of star formation if the observed molecular cloud parameters are used. The mean cloud extinction and the Galactic star formation rate per unit mass of molecular gas are predicted theoretically from the condition that photionization-regulated star formation be in equilibrium. A simple model for the evolution of isolated molecular clouds is developed.

Mckee, Christopher F.↗
NASA NTRS2001

Computer Simulation of the Forces Acting on a Submerged Polystyrene Probe as it Approaches the Succinonitrile Melt-Solid Interface

A Modeling approach to simulate both mesoscale and microscopic forces acting in a typical AFM experiment is presented. A 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. Ultimately, the goal is to measure the forces between a particle and the crystal-melt interface. Two modes of AFM operation are considered in this paper - a stationary and a "tapping" one. The continuous mechanics approach to model tip-surface interaction is presented. At microscopic levels, tip contamination and details of tip-surface interaction are modeled using a molecular dynamics approach for the case of polystyrene - succinonitrile contact. Integration of the mesoscale model with a molecular dynamic model is discussed.

Bune, Andris V.↗
DOE OSTI2020

Model for photothermal ionization and molecular recombination during pulsed ablation of polyethylene

The surface erosion of polyethylene is studied under conditions characteristic of extremely high-rate heating expected in laser-driven and high energy density experiments. A coupled model for photoionization and volumetric photothermal degradation of polyethylene is developed that includes finite rate chemistry and molecular recombination of radicals. First, the model is used to explore the evolution of radicals and hydrocarbons during isochoric heating, for which it is found that polyethylene is not in chemical equilibrium for rates >108K/s. Then, the model is used to explore the cooperativity between photoionization and photothermal ionization during one-dimensional ablation from a pulsed heating source, accounting for coupled energy deposition, thermokinetics, thermochemistry, hydrodynamics, mechanics, and thermal conduction in the ALEGRA multi-physics code. The ablation depth per energy pulse is found to agree with an analytical model for instantaneous energy deposition and absent molecular recombination or photoionization. Otherwise, molecular recombination of radicals reduces the depth of ablation per pulse, owing to thermal stabilization on forming branched molecules. Radical formation through photoionization can be compensated for by recombination, but it accelerates ablation at high enough photoionization rates. Finally, the influence of molecular recombination on the ablation depth is found to decrease for long pulses, owing to decreased recombination reaction rates at lower vapor densities near the ablated surface. These and other findings highlight competition between the processes of scission, recombination, and photoionization during pulsed ablation of polyethylene.

Moore, N. W. (ORCID:0000000272259674)↗
DOE OSTI2021

Numerically exact generalized Green's function cluster expansions for electron-phonon problems

We generalize the family of approximate momentum average methods to formulate a numerically exact, convergent hierarchy of equations whose solution provides an efficient algorithm to compute the Green's function of a particle dressed by bosons suitable in the entire parameter regime. We use this approach to extract ground-state properties and spectral functions. Our approximation-free framework, dubbed the generalized Green's function cluster expansion (GGCE), allows access to exact numerical results in the extreme adiabatic limit, where many standard methods struggle or completely fail. We showcase the performance of the method, specializing three important models of charge-boson coupling in solids and molecular complexes: the molecular Holstein model, which describes coupling between charge density and local distortions, the Peierls model, which describes modulation of charge hopping due to intersite distortions, and a more complex Holstein + Peierls system with couplings to two different phonon modes, paradigmatic of charge-lattice interactions in organic crystals. Furthermore, the GGCE serves as an efficient approach that can be systematically extended to different physical scenarios, thus providing a tool to model the frequency dependence of dressed particles in realistic settings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS2003

The Chemistry and Excitation of Water in Molecular Clouds

We model the chemistry and thermal balance of opaque molecular clouds exposed to an external flux of ultraviolet photons. We include the processes of gas phase and grain surface chemical reactions; in particular we examine closely the freezing of atoms and molecules onto grain surfaces and the desorption of molecules from grain surfaces as a function of depth into a molecular cloud. We find that on the surface of a molecular cloud the gas phase water abundances are low because of photodissociation, and the grain phase water (ice) abundance is low because of photodesorption of water from the grain surfaces. Deeper into the cloud, at A(sub v) less than or approximately 2-8 depending on the strength of the external ultraviolet flux, the gas phase water abundance increases with depth as the photodissociation rates decline due to dust attenuation of the ultraviolet field. However, beyond A(sub v) less than or approximately 2-8 the gas phase water abundance declines because the water freezes as water ice on the grains, and photodesorption is no longer effective in clearing the ice. A peak water abundance of about 10(exp -6) to 10(exp -7) occurs at about A(sub v) approximately 2-8, relatively independent of the gas density and the ultraviolet field. We show that such a model matches very closely the observations of the Submillimeter Wave Astronomical Satellite (SWAS), a NASA Small Explorer Mission. The model elucidates several mechanisms that have been recently invoked to understand gas phase chemistry in clouds, including-the freeze-out of molecules onto grain surface, the desorption of these molecules from the surfaces, and the abundance gradients of molecules as functions of depth into molecular clouds.

Hollenbach, David↗
NASA NTRS1983

Modeling correlation with flight data

The molecular contamination flow model (space 2 program) predicts the induced environment of the space shuttle orbiter/payload on orbit as well as the induced gas flow between the orbiter and payload surfaces. This computer program relates the input parameters which characterize the time dependent status of the orbiter/payload to the required output parameters. An application of the model to data from space transportation system flights 1, 2, and 3 shows that the model correlates well for direct flow and for return flux (STS-2/H2O). Correlation for return flux from other molecular sources/species appears to be within expectations but more analysis is required. The space 2 model seems to be an adequate predictive tool.

Ehlers, H. K. F.↗
DOE OSTI2024

Reaction Pathways and Energy Consumption in NH 3 Decomposition for H 2 Production by Low Temperature, Atmospheric Pressure Plasma

Pathways for NH 3 decomposition to N 2 and N 2 H 4 by atmospheric pressure nonthermal plasma are analyzed using a combination of molecular beam mass spectrometry measurements and zero-dimensional kinetic modeling. Experimental measurements show that NH 3 conversion and selectivity towards N 2 formation scale monotonically with the specific energy input into the plasma with ~ 100% selectivity to N 2 formation achieved at specific energy inputs above 0.12 J cm −3 (3.1 eV (molecule NH 3 ) −1 ). The kinetic model recovers these trends, although it underpredicts N 2 selectivity at low specific energy input. These discrepancies can be explained by the underestimation of reaction rate coefficients for reactions that consume N 2 H x species in collisions with H radicals and/or radial nonuniformities in power deposition, gas temperature, and species concentrations that are not represented by the plug flow approximation used in the model. The kinetic model shows that N 2 formation proceeds through N 2 H x decomposition pathways rather than NH x decomposition pathways in low temperature, atmospheric pressure plasma. Higher selectivity toward N 2 production can be achieved by operating at higher NH 3 conversion and with a higher gas temperature. Furthermore, the high energy cost of NH 3 decomposition by atmospheric pressure nonthermal plasma found in this work (25–50 eV (molecule NH 3 converted) −1 ; 17–33 eV (molecule H 2 formed) −1 ) is a result of the energy requirement for electron-impact dissociation of NH 3 and the significant re-formation of NH 3 by three-body recombination reactions between NH 2 and H.

Nonthermal plasma↗