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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 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b)

We present the results of a high-statistics equilibrium study of the folding/unfolding transition for the 20-residue mini-protein Trp-cage (TC5b) in water. The ECEPP/3 force field is used and the interaction with water is treated by a solvent-accessible surface area method. A Wang-Landau type simulation is used to calculate the density of states and the conditional probabilities for the various values of the radius of gyration and the number of native contacts at fixed values of energy—along with a systematic check on their convergence. All thermodynamic quantities of interest are calculated from this information. The folding-unfolding transition corresponds to a peak in the temperature dependence of the computed specific heat. This is corroborated further by the structural signatures of folding in the distributions for radius of gyration and the number of native contacts as a function of temperature. The potentials of mean force are also calculated for these variables, both separately and jointly. A local free energy minimum, in addition to the global minimum, is found in a temperature range substantially below the folding temperature. The free energy at this second minimum is approximately 5 k{sub B}T higher than the value at the global minimum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A thermodynamical analysis of rf current drive with fast electrons

The problem of rf current drive (CD) by pushing fast electrons with high-parallel-phase-velocity waves, such as lower-hybrid (LH) or electron-cyclotron (EC) waves, is revisited using the first and second laws, the former to retrieve the well-known one-dimensional (1D) steady-state CD efficiency, and the latter to calculate a lower bound for the rate of entropy production when approaching steady state. The laws of thermodynamics are written in a form that explicitly takes care of frictional dissipation and are thus applied to a population of fast electrons evolving under the influence of a dc electric field, rf waves, and collisions while in contact with a thermal, Maxwellian reservoir with a well-defined temperature. Besides the laws of macroscopic thermodynamics, there is recourse to basic elements of kinetic theory only, being assumed a residual dc electric field and a strong rf drive, capable of sustaining in the resonant region, where waves interact with electrons, a raised fast-electron tail distribution, which becomes an essentially flat plateau in the case of the 1D theory for LHCD. Within the 1D model, particularly suited for LHCD as it solely retains fast-electron dynamics in velocity space parallel to the ambient magnetic field, an H theorem for rf CD is also derived, which is written in different forms, and additional physics is recovered, such as the synergy between the dc and rf power sources, including the rf-induced hot conductivity, as well as the equation for electron-bulk heating. As much as possible 1D results are extended to 2D, to account for ECCD by also considering fast-electron velocity-space dynamics in the direction perpendicular to the magnetic field, which leads to a detailed discussion on how the definition of an rf-induced conductivity may depend on whether one works at constant rf current or power. Moreover, working out the collisional dissipated power and entropy-production rate written in terms of the fast-electron distribution, it is shown that the well-known formula for the steady-state CD efficiency, usually obtained from the first law in the form of power balance between the external sources and collisional losses, emerges as a lower bound for that CD figure of merit, in what can be interpreted as an instance of the second law.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis

A microbe’s ecological niche and biotechnological utility are confirmed by its specific set of co-evolved metabolic pathways. The acquisition of new pathways, through horizontal gene transfer or genetic engineering, can have unpredictable consequences. In this work, we show that two different pathways for coumarate catabolism failed to function when initially transferred into Escherichia coli . Using laboratory evolution, we elucidated the factors limiting activity of the newly acquired pathways and the modifications required to overcome these limitations. Both pathways required host mutations to enable effective growth with coumarate, but the necessary mutations differed. In one case, a pathway intermediate inhibited purine nucleotide biosynthesis, and this inhibition was relieved by single amino acid replacements in IMP dehydrogenase. A strain that natively contains this coumarate catabolism pathway, Acinetobacter baumannii , is resistant to inhibition by the relevant intermediate, indicating that natural pathway transfers have faced and overcome similar challenges. Molecular dynamics simulation of the wild type and a representative single-residue mutant provide insight into the structural and dynamic changes that relieve inhibition. These results reflect how deleterious interactions can limit pathway transfer, that these interactions can be traced to specific molecular interactions between host and pathway, and how evolution or engineering can alleviate these limitations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2010

Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways

Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli. Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation. The faithful transmission of information through two-component pathways and the avoidance of unwanted cross-talk require exquisite specificity of histidine kinase-response regulator interactions to ensure that cells mount the appropriate response to external signals. To identify putative specificity-determining residues, we have analyzed amino acid coevolution in two component proteins and identified a set of residues that can be used to rationally rewire a model signaling pathway, EnvZOmpR. To explore how a relatively small set of residues can dictate partner selectivity, we combined alanine-scanning mutagenesis with an approach we call trajectory-scanning mutagenesis, in which all mutational intermediates between the specificity residues of EnvZ and another kinase, RstB, were systematically examined for phosphotransfer specificity. The same approach was used for the response regulators OmpR and RstA. Collectively, the results begin to reveal the molecular mechanism by which a small set of amino acids enables an individual kinase to discriminate amongst a large set of highlyrelated response regulators and vice versa. Our results also suggest that the mutational trajectories taken by two component signaling proteins following gene or pathway duplication may be constrained and subject to differential selective pressures. Only some trajectories allow both the maintenance of phosphotransfer and the avoidance of unwanted cross-talk.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

Nuclear gamma rays from 720-MeV alpha-induced reactions on Al-27 and Si-28

Prompt gamma rays from the interaction of 720-MeV alpha particles with Al-27 and Si-28 were detected and analyzed to identify residual nuclei and to determine cross sections for production of specific levels. No gamma-ray transitions were detected from nuclei heavier than the target. From Doppler broadening, the momentum of the residual nuclei was estimated. The results are compared with previous results for 140- and 1600-MeV alphas on Al-27 and approximately 200-MeV positive or negative pions on Al-27 and Si-28 and fitted to a spallation-yield formula.

Lieb, B. J.↗
NASA NTRS1985

Effects of Rayleigh and Newtonian damping on wave-mean flow interaction

A theoretical study is made of the effects of mean damping on wave-mean flow interactions. A condition is derived for the Eliassen-Palm flux divergence to balance the steady-state residual circulations induced by eddies in the presence of mean damping. It is shown by a simple analytical model that this balance holds for stratospheric planetary waves when the Rayleigh friction coefficient is one order smaller than the Newtonian cooling coefficient, although the tall mean flow condition is not violated. In this case, the Eliassen-Palm flux divergence can be interpreted as approximating the steady residual circulation (approximately equal to Lagrangian-mean circulations) induced by eddies as well as the net mean acceleration in the absence of mean damping. This balance is consistent with the stratospheric circulations of a dynamical model.

Hayashi, Y.↗
NASA NTRS1989

Multi-grid for structures analysis

In structural analysis the amount of computational time necessary for a solution is proportional to the number of degrees of freedom times the bandwidth squared. In implicit time analysis, this must be done at each discrete point in time. If, in addition, the problem is nonlinear, then this solution must be iterated at each point in time. If the bandwidth is large, the size of the problem that can be analyzed is severely limited. The multi-grid method is a possible algorithm which can make this solution much more computationally efficient. This method has been used for years in computational fluid mechanics. It works on the fact that relaxation is very efficient on the high frequency components of the solution (nearest neighbor interactions) and not very good on low frequency components of the solution (far interactions). The multi-grid method is then to relax the solution on a particular model until the residual stops changing. This indicates that the solution contains the higher frequency components. A coarse model is then generated for the lower frequency components to the solution. The model is then relaxed for the lower frequency components of the solution. These lower frequency components are then interpolated to the fine model. In computational fluid mechanics the equations are usually expressed as finite differences.

Kascak, Albert F.↗
NASA NTRS1994

Erratum: The 2.27 day period of WR-134 (HD 191765)

The original temporal analysis of a 12 night spectral timeseries of Wolf-Rayet (WR)-134 has been found to be flawed and a re-analysis shows that the line profile variations are indeed periodic. When combined with a 4 night timeseries taken 45 days earlier, a period near 2.27 d is found in periodograms of the He II lambda 5412 line centroid, rms line width, and line skew variations. When the emission line residuals are ordered as a function of phase, a sinuous feature appears to 'snake' about the line center with an amplitude of +/-500 km/s. This is approximately equal to 20 larger than the line centroid amplitude; the calculation of which is heavily weighted by static portions of the line profile. In addition to the 'snake,' emission residuals appear that move away from line center on unbound trajectories and are thought to result from the interaction of a periodic driver with the unstable flow of the radiation driven wind.

Mccandliss, Stephan R.↗
DOE OSTI2012

Understanding the Mechanism of Solvent-Mediated Adhesion of Vacuum Deposited Au and Pt Thin Films onto PMMA Substrates

The adhesion of 100 nm thick electron-beam deposited Au and Pt and magnetron sputtered Au thin films onto poly(methyl methacrylate) (PMMA) substrates can be significantly enhanced to over 90% adhesion by either spin-casting or vapor-exposure to hydrohalocarbon solvents prior to metal deposition compared to samples that are either cleaned in isopropyl alcohol or pre-treated with a remote O2 plasma. X-ray photoelectron spectroscopy (XPS) and evolved gas Fourier transform infrared spectroscopy (EGA-FTIR) reveal the presence of residual halogenated solvent molecules at the PMMA surface which chemically activates the surface to produce a stable chemical interaction between the noble metal film and the PMMA. Density functional theory (DFT) calculations show that the halogenated solvent molecules preferentially form a Lewis acid-base adduct with the oxygen atoms in the ester group in PMMA which is consistent with the measured enthalpy of desorption of chloroform (CHCl3) on PMMA determined by EGA-FTIR to be 36 kJ mol-1. The DFT model also supports the experimentally observed change in the high resolution XPS O 1s peak at 533.77 eV after metallization attributed to a change in the local bonding environment of the bridging O in the PMMA ester group. DFT also predicts that the deposited metal atom (M) inserts into the C-X bond where X is the halogen atom on either CHCl3 or bromoform (CHBr3) to form a O M X interaction that is observed by a M-X bond in the high resolution XPS Cl 2p3/2 peak at 198.03 eV and Br 3p3/2 peak at 182.06 eV. A range of solvents with differing polarities for PMMA pre-treatment have been used and it is proposed that non-complexing solvents result in significant metal adhesion improvement. The Gutmann acceptor number can be used to predict the effectiveness of solvent treatment for noble metal adhesion. A model is proposed in which the bond energy of the C-X bond of the solvent must be sufficiently low so that the C-X bond can be cleaved to form the M-X bond. Supporting this model, a negative control of vapor phase exposure to fluoroform (CHF3) is shown to have no effect on noble metal adhesion due to the higher bond dissociation energy of the C-F bond compared to the C-Cl and C-Br bond energy. The surface activation of vapor-phase exposed PMMA surfaces is technologically significant for the fabrication of polymer microdevices requiring Au or Pt metallization.

Mo, Alan K↗
NASA NTRS1984

An Analysis of Wave Interactions in Swept-Wing Flows

Crossflow instabilities dominate disturbance growth in the leading-edge region of swept wings. Streamwise vortices in a boundary layer strongly influence the behavior of other disturbances. Amplification of crossflow vortices near the leading edge produces a residual spanwise nonuniformity in the mid-chord regions where Tollmien-Schlichting (T-S) waves are strongly amplified. Should the T-S wave undergo double-exponential growth because of this effect, the usual transition prediction methods would fail. The crossflow/Tollmien-Schlichting wave interaction was modeled as a secondary instability. The effects of suction are included, and different stability criteria are examined. The results are applied to laminar flow control wings characteristic of energy-efficient aircraft designs.

Reed, H. L.↗
DOE OSTI2024

Activation of polycystin-1 signaling by binding of stalk-derived peptide agonists

Polycystin-1 (PC1) is the protein product of thePKD1gene whose mutation causes autosomal dominant Polycystic Kidney Disease (ADPKD). PC1 is an atypical G protein-coupled receptor (GPCR) with an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal and membrane-embedded C-terminal (CTF) fragments. Recently, activation of PC1 CTF signaling was shown to be regulated by a stalk tethered agonist (TA), resembling the mechanism observed for adhesion GPCRs. Here, synthetic peptides of the first 9- (p9), 17- (p17), and 21-residues (p21) of the PC1 stalk TA were shown to re-activate signaling by a stalkless CTF mutant in human cell culture assays. Novel Peptide Gaussian accelerated molecular dynamics (Pep-GaMD) simulations elucidated binding conformations of p9, p17, and p21 and revealed multiple specific binding regions to the stalkless CTF. Peptide agonists binding to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of stalk TA-mediated PC1 CTF activation. Additional sequence coevolution analyses showed the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. These insights into the structural dynamic mechanism of PC1 activation by TA peptide agonists provide an in-depth understanding that will facilitate the development of therapeutics targeting PC1 for ADPKD treatment.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2013

Partitioning Behavior of Organic Contaminants in Carbon Storage Environments: A Critical Review

Carbon capture and storage is a promising strategy for mitigating the CO{sub 2} contribution to global climate change. The large scale implementation of the technology mandates better understanding of the risks associated with CO{sub 2} injection into geologic formations and the subsequent interactions with groundwater resources. The injected supercritical CO{sub 2} (sc-CO{sub 2}) is a nonpolar solvent that can potentially mobilize organic compounds that exist at residual saturation in the formation. Here, we review the partitioning behavior of selected organic compounds typically found in depleted oil reservoirs in the residual oil–brine–sc-CO{sub 2} system under carbon storage conditions. The solubility of pure phase organic compounds in sc-CO{sub 2} and partitioning of organic compounds between water and sc-CO{sub 2} follow trends predicted based on thermodynamics. Compounds with high volatility and low aqueous solubility have the highest potential to partition to sc-CO{sub 2}. The partitioning of low volatility compounds to sc-CO{sub 2} can be enhanced by cosolvency due to the presence of higher volatility compounds in the sc-CO{sub 2}. The effect of temperature, pressure, salinity, pH, and dissolution of water molecules into sc-CO{sub 2} on the partitioning behavior of organic compounds in the residual oil–brine–sc-CO{sub 2} system is discussed. Data gaps and research needs for models to predict the partitioning of organic compounds in brines and from complex mixtures of oils are presented. Models need to be able to better incorporate the effect of salinity and cosolvency, which will require more experimental data from key classes of organic compounds.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2011

Crystal Structure of a Phosphorylated Light Chain Domain of Scallop Smooth-Muscle Myosin

We have determined the crystal structure of a phosphorylated smooth-muscle myosin light chain domain (LCD). This reconstituted LCD is of a sea scallop catch muscle myosin with its phosphorylatable regulatory light chain (RLC SmoA). In the crystal structure, Arg{sup 16}, an arginine residue that is present in this isoform but not in vertebrate smooth-muscle RLC, stabilizes the phosphorylation site. This arginine interacts with the carbonyl group of the phosphorylation-site serine in the unphosphorylated LCD (determined previously), and with the phosphate group when the serine is phosphorylated. However, the overall conformation of the LCD is essentially unchanged upon phosphorylation. This result provides additional evidence that phosphorylation of the RLC is unlikely to act as an on-switch in regulation of scallop catch muscle myosin.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2004

High-Resolution Mesoscale Simulations of the 6-7 May 2000 Missouri Flash Flood: Impact of Model Initialization and Land Surface Treatment

High-resolution mesoscale model simulations of the 6-7 May 2000 Missouri flash flood event were performed to test the impact of model initialization and land surface treatment on timing, intensity, and location of extreme precipitation. In this flash flood event, a mesoscale convective system (MCS) produced over 340 mm of rain in roughly 9 hours in some locations. Two different types of model initialization were employed: 1) NCEP global reanalysis with 2.5-degree grid spacing and 12-hour temporal resolution, and 2) Eta reanalysis with 40- km grid spacing and $hour temporal resolution. In addition, two different land surface treatments were considered. A simple land scheme. (SLAB) keeps soil moisture fixed at initial values throughout the simulation, while a more sophisticated land model (PLACE) allows for r interactive feedback. Simulations with high-resolution Eta model initialization show considerable improvement in the intensity of precipitation due to the presence in the initialization of a residual mesoscale convective vortex (hlCV) from a previous MCS. Simulations with the PLACE land model show improved location of heavy precipitation. Since soil moisture can vary over time in the PLACE model, surface energy fluxes exhibit strong spatial gradients. These surface energy flux gradients help produce a strong low-level jet (LLJ) in the correct location. The LLJ then interacts with the cold outflow boundary of the MCS to produce new convective cells. The simulation with both high-resolution model initialization and time-varying soil moisture test reproduces the intensity and location of observed rainfall.

Baker, R. David↗
DOE OSTI2012

Structures of NodZ [alpha]1,6-fucosyltransferase in complex with GDP and GDP-fucose

Rhizobial NodZ {alpha}1,6-fucosyltransferase ({alpha}1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5'-diphosphate-{beta}-L-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signaling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two {alpha}1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of {alpha}1,6-FucT in complex with its substrate GDP-Fuc and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 {angstrom} resolution. The fucose residue is exposed to solvent and is disordered. The enzyme-product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-L-glucosamine (penta-NAG). The structure has been determined at 1.98 {angstrom} resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among {alpha}1,2-, {alpha}1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop located between strand {beta}C2 and helix {alpha}C3. In addition, there is a shift of the {alpha}C3 helix itself upon GDP-Fuc binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Sympathetic cooling of the Ba{sup +} ion by collisions with ultracold Rb atoms: Theoretical prospects

State-of-the-art ab initio techniques have been applied to compute the potential energy curves of the (BaRb){sup +} molecular ion in the Born-Oppenheimer approximation for the singlet and triplet states dissociating into the ground-state {sup 1}S Rb{sup +} ion and the Ba atom in the ground {sup 1}S state or the lowest singlet or triplet d excited states, and for the singlet and triplet states dissociating into the ground-state {sup 2}S Rb atom and the ground-state {sup 2}S Ba{sup +} ion. The ground-state potential energy was obtained with the coupled-cluster method restricted to single, double, and nonperturbative triple excitations. The first triplet states in the {Sigma}, {Pi}, and {Delta} symmetries were computed with the restricted open-shell coupled-cluster method restricted to single, double, and nonperturbative triple excitations. All other excited-state potential energy curves were computed using the equation of motion approach within the coupled-cluster singles, doubles, and linear triples framework. The long-range coefficients describing the electrostatic, induction, and dispersion interactions at large interatomic distances are also reported. The electric transition dipole moments governing the x {sup 1{Sigma}{yields}1{Sigma}},{sup 1{Pi}} transitions have been obtained as the first residue of the polarization propagator computed with the linear response coupled-cluster method restricted to single and double excitations. Nonadiabatic radial and angular coupling matrix elements as well as the spin-orbit coupling matrix elements have been evaluated using the multireference configuration-interaction method restricted to single and double excitations with a large active space. With these couplings, the spin-orbit-coupled (relativistic) potential energy curves for the 0{sup +} and 1 states relevant for the running experiments have been obtained. Finally, relativistic transition moments and nonadiabatic coupling matrix elements were obtained from the nonrelativistic results and spin-orbit eigenvectors. The electronic structure input has been employed in the single-channel scattering calculations of the collisional cross sections between the Ba{sup +} ion and Rb atom. Both nonrelativistic and relativistic potentials were used in these calculations. Our results show that the inelastic cross section corresponding to the charge transfer from the Rb atom to the Ba{sup +} ion is much smaller than the elastic one over a wide range of energies up to 1 mK. This suggests that sympathetic cooling of the Ba{sup +} ion by collisions with ultracold Rb atoms should be possible.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2010

Crystal Structures of Mutant Forms of the Yeast F[subscript 1] ATPase Reveal Two Modes of Uncoupling

The mitochondrial ATP synthase couples the flow of protons with the phosphorylation of ADP. A class of mutations, the mitochondrial genome integrity (mgi) mutations, has been shown to uncouple this process in the yeast mitochondrial ATP synthase. Four mutant forms of the yeast F{sub 1} ATPase with mgi mutations were crystallized; the structures were solved and analyzed. The analysis identifies two mechanisms of structural uncoupling: one in which the empty catalytic site is altered and in doing so, apparently disrupts substrate (phosphate) binding, and a second where the steric hindrance predicted between {gamma}Leu83 and {beta}{sub DP} residues, Leu-391 and Glu-395, located in Catch 2 region, is reduced allowing rotation of the {gamma}-subunit with less impedance. Overall, the structures provide key insights into the critical interactions in the yeast ATP synthase involved in the coupling process.

36 MATERIALS SCIENCE↗