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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

A full-dimensional quantum dynamics study of the mode specificity in the H + HOD abstraction reaction

We employ the initial state-selected time-dependent wave packet approach to an atom-triatom reaction to study the H + HOD → OH + HD/OD + H{sub 2} reaction without the centrifugal sudden approximation, based on an accurate potential energy surface which was recently developed by neural network fitting to high level ab initio energy points. The total reaction probabilities and integral cross sections, which are the exact coupled-channel results, are calculated for the HOD reactant initially in the ground and several vibrationally excited states, including the bending excited state, OD stretching excited states, OH stretching excited states, and combined excitations of them. The reactivity enhancements from different initial states of HOD are presented, which feature strong bond-selective effects of the reaction dynamics. The current results for the product branching ratios, reactivity enhancements, and relative cross sections are largely improved over the previous calculations, in quantitatively good agreement with experiment. The thermal rate constant for the title reaction and the contributions from individual vibrational states of HOD are also obtained.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS2007

Interactions of the SAP Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku70/80 complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The SAP domain of Ku70 (residues 556-609), contains an a helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the SAP/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the SAP domain of Ku70 and a 10 base pairs DNA duplex. Large-scale conformational changes were observed and some putative binding modes were suggested based on energetic analysis. These modes are consistent with previous experimental investigations. In addition, the results indicate that cooperation of SAP with other domains of Ku70/80 is necessary to explain the high affinity of binding as observed in experiments.

Hu, Shaowen↗
NASA NTRS2007

Interactions of the C-terminal Domain of Human Ku70 with DNA Substrate: A Molecular Dynamics Study

NASA is developing a systems biology approach to improve the assessment of health risks associated with space radiation. The primary toxic and mutagenic lesion following radiation exposure is the DNA double strand break (DSB), thus a model incorporating proteins and pathways important in response and repair of this lesion is critical. One key protein heterodimer for systems models of radiation effects is the Ku(sub 70/80) complex. The Ku70/80 complex is important in the initial binding of DSB ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. The C-terminal domain of Ku70 (Ku70c, residues 559-609), contains an helix-extended strand-helix motif and similar motifs have been found in other nucleic acid-binding proteins critical for DNA repair. However, the exact mechanism of damage recognition and substrate specificity for the Ku heterodimer remains unclear in part due to the absence of a high-resolution structure of the Ku70c/DNA complex. We performed a series of molecular dynamics (MD) simulations on a system with the subunit Ku70c and a 14 base pairs DNA duplex, whose starting structures are designed to be variable so as to mimic their different binding modes. By analyzing conformational changes and energetic properties of the complex during MD simulations, we found that interactions are preferred at DNA ends, and within the major groove, which is consistent with previous experimental investigations. In addition, the results indicate that cooperation of Ku70c with other subunits of Ku(sub 70/80) is necessary to explain the high affinity of binding as observed in experiments.

Hu, Shaowen↗
DOE OSTI2015

Ab initio molecular dynamics study of liquid sodium and cesium up to critical point

Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Features of the microstructure development under conditions, reproducing the process of friction stir welding. Molecular-dynamics study

Friction stir welding is a recently developed technology which is used in various branches of modern engineering. The basis of this technology is the friction of the rotating cylindrical or specially shaped tool between two metal plates brought together either to meet their ends of one above another with the overlap. When applying the FSW process in various economical sectors, the important task is to study the mechanisms and identify the physical laws and factors leading to formation of structural inhomogeneities and discontinuities in the weld seam. This paper analyzes the basic mechanisms behind the structural state generation in the material subjected to severe plastic deformation and heating. To investigate the atomic mechanisms of structural changes in FSW, the modeling at atomic scale has been carried out. Results of work can be a basis for new knowledge about the microstructure evolution in FSW.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

The RAVE-on Catalog of Stellar Atmospheric Parameters and Chemical Abundances for Chemo-dynamic Studies in the Gaia Era

The orbits, atmospheric parameters, chemical abundances, and ages of individual stars in the Milky Way provide the most comprehensive illustration of galaxy formation available. The Tycho- Gaia Astrometric Solution (TGAS) will deliver astrometric parameters for the largest ever sample of Milky Way stars, though its full potential cannot be realized without the addition of complementary spectroscopy. Among existing spectroscopic surveys, the RAdial Velocity Experiment (RAVE) has the largest overlap with TGAS (≳200,000 stars). We present a data-driven re-analysis of 520,781 RAVE spectra using The Cannon . For red giants, we build our model using high-fidelity APOGEE stellar parameters and abundances for stars that overlap with RAVE. For main sequence and sub-giant stars, our model uses stellar parameters from the K2/EPIC . We derive and validate effective temperature T {sub eff}, surface gravity log g , and chemical abundances of up to seven elements (O, Mg, Al, Si, Ca, Fe, and Ni). We report a total of 1,685,851 elemental abundances with a typical precision of 0.07 dex, a substantial improvement over previous RAVE data releases. The synthesis of RAVE-on and TGAS is the most powerful data set for chemo-dynamic analyses of the Milky Way ever produced.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Secondary structure and dynamics study of the intrinsically disordered silica-mineralizing peptide P 5 S 3 during silicic acid condensation and silica decondensation

The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5S3, a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains five protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated ortho silicic acid P5S3 strongly enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2) at globally undersaturated concentrations. The secondary structure of P5S3 during these different functions was studied by circular dichroism (CD), complemented by nuclear magnetic resonance (NMR) studies of the peptide in the absence of silicate. The NMR studies of dual-labeled (13C, 15N) P5S3 revealed a disordered structure at pH 2.8 and 4.5. Within the pH range of 4.5 to 9.5, the CD data verified the disordered secondary structure but also suggested the presence of some polyproline II character in the absence of silicic acid. Upon silicic acid polymerization and during dissolution of preformed silica, the CD spectrum of P5S3 indicated partial transition into an α-helical conformation which was transient during silica-dissolution. Consequently, the secondary structural changes observed for P5S3 correlate with the presence of oli-gomeric/polymeric silicic acid, presumably due to P5S3-silicic acid interactions. These interactions appear, at least in part, ionic in nature since dodecylsulfate micelles, which are negatively charged, cause similar conformational shifts to P5S3 in the absence of silica while ß-D-dodecyl maltoside micelles, which are neutral, do not. Thus, P5S3 influences both the condensation of silicic acid into silica and its decondensation back to silicic acid. Moreover, the dynamics of these pro-cesses may be indirectly monitored by following structural changes to P5S3 with CD spectroscopy.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Computational Fluid Dynamics Study on the Effects of RATO Timing on the Scale Model Acoustic Test

The Scale Model Acoustic Test (SMAT) is a 5% scale test of the Space Launch System (SLS), which is currently being designed at Marshall Space Flight Center (MSFC). The purpose of this test is to characterize and understand a variety of acoustic phenomena that occur during the early portions of lift off, one being the overpressure environment that develops shortly after booster ignition. The SLS lift off configuration consists of four RS-25 liquid thrusters on the core stage, with two solid boosters connected to each side. Past experience with scale model testing at MSFC (in ER42), has shown that there is a delay in the ignition of the Rocket Assisted Take Off (RATO) motor, which is used as the 5% scale analog of the solid boosters, after the signal to ignite is given. This delay can range from 0 to 16.5ms. While this small of a delay maybe insignificant in the case of the full scale SLS, it can significantly alter the data obtained during the SMAT due to the much smaller geometry. The speed of sound of the air and combustion gas constituents is not scaled, and therefore the SMAT pressure waves propagate at approximately the same speed as occurs during full scale. However, the SMAT geometry is much smaller allowing the pressure waves to move down the exhaust duct, through the trench, and impact the vehicle model much faster than occurs at full scale. To better understand the effect of the RATO timing simultaneity on the SMAT IOP test data, a computational fluid dynamics (CFD) analysis was performed using the Loci/CHEM CFD software program. Five different timing offsets, based on RATO ignition delay statistics, were simulated. A variety of results and comparisons will be given, assessing the overall effect of RATO timing simultaneity on the SMAT overpressure environment.

Nielsen, Tanner↗
DOE OSTI2015

Thermal conductivity of Bi{sub 2}Te{sub 3} tilted nanowires, a molecular dynamics study

Evidence for an excellent compromise between structural stability and low thermal conductivity has been achieved with tilted Bi{sub 2}Te{sub 3} nanowires. The latter ones were recently fabricated and there is a need in modeling and characterization. The structural stability and the thermal conductivity of Bi{sub 2}Te{sub 3} nanowires along the tilted [015]* direction and along the [010] direction have been explored. For the two configurations of nanowires, the effect of the length and the cross section on the thermal conductivity is discussed. The thermal conductivity of infinite size tilted nanowire is 0.34 W/m K, significantly reduced compared to nanowire along the [010] direction (0.59 W/m K). This reveals that in Bi{sub 2}Te{sub 3} nanowires the structural anisotropy can be as important as size effects to reduce the thermal conductivity. The main reason is the reduction of the phonon mean free path which is found to be 1.7 nm in the tilted nanowires, compared to 5.3 nm for the nanowires along the [010] direction. The fact that tilted Bi{sub 2}Te{sub 3} nanowire is mechanically stable and it has extremely low thermal conductivity suggests these nanowires as a promising material for future thermoelectric generation application.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics

Protons are used throughout the biological world for a number of functions, from charge balance to energy carriers. Metalloenzymes use protons as energy carriers and control proton movement both temporally and spatially. Despite the interest and need for controlled proton movement in other systems, the scientific community has not been able to develop extensive general rules for developing synthetic proton pathways. In part this is due to the challenging nature of studying these large and complex molecules experimentally, although experiments have gleaned extensive critical insight. While computational methods are also challenging because of the large size of the molecules, they have been critical in advancing our knowledge of proton movement through pathways, but even further, they have advanced our knowledge in how protonation and proton movement is correlated with large and small scale molecular motions and electron movement. These studies often complement experimental studies but provide insight and depth simply not possible in many cases in the absence of theory. In this chapter, we will discuss advances and methods used in understanding proton movement in hydrogenases.

Electron Transport↗