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At least 235 records · Page 13

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DOE OSTI2023

7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system

Abstract The modified nucleosides 2′-deoxy-7-cyano- and 2′-deoxy-7-amido-7-deazaguanosine (dPreQ0 and dADG, respectively) recently discovered in DNA are the products of the bacterial queuosine tRNA modification pathway and the dpd gene cluster, the latter of which encodes proteins that comprise the elaborate Dpd restriction–modification system present in diverse bacteria. Recent genetic studies implicated the dpdA, dpdB and dpdC genes as encoding proteins necessary for DNA modification, with dpdD–dpdK contributing to the restriction phenotype. Here we report the in vitro reconstitution of the Dpd modification machinery from Salmonella enterica serovar Montevideo, the elucidation of the roles of each protein and the X-ray crystal structure of DpdA supported by small-angle X-ray scattering analysis of DpdA and DpdB, the former bound to DNA. While the homology of DpdA with the tRNA-dependent tRNA-guanine transglycosylase enzymes (TGT) in the queuosine pathway suggested a similar transglycosylase activity responsible for the exchange of a guanine base in the DNA for 7-cyano-7-deazaguanine (preQ0), we demonstrate an unexpected ATPase activity in DpdB necessary for insertion of preQ0 into DNA, and identify several catalytically essential active site residues in DpdA involved in the transglycosylation reaction. Further, we identify a modification site for DpdA activity and demonstrate that DpdC functions independently of DpdA/B in converting preQ0-modified DNA to ADG-modified DNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Constraints on the polarization angle oscillations of the Crab Nebula with the Simons Array and its applications to the search for axionlike particles

Here, we present a search for polarization oscillation of the Crab Nebula, also known as Tau A, at millimeter wavelengths using observations with the Simons Array, the successor experiment to POLARBEAR. We follow up on previous work by POLARBEAR using 90 GHz band data of the 2023 observing season of the Simons Array to evaluate the variability of Tau A’s polarization angle. Tau A is widely used as a polarization angle calibration source in millimeter-wave astronomy, and thus it is necessary to validate the stability. Additionally, an interesting application of the time-resolved polarimetry of Tau A is to search for axionlike particles (ALPs). We do not detect a global signal across the frequencies considered in this analysis and place a median 95% upper bound of polarization oscillation amplitude A < 0.12° over oscillation frequencies from 3.39 yr -1 to 1.50 day -1 . This constrains the ALP-photon coupling at a median 95% upper bound of g aγγ < 3.84 × 10 -12 × (m a /10 -21 eV) in the mass range from 4.4 × 10 -22 to 7.2 × 10 -20 eV, assuming the ALP constitutes all of dark matter, its field is a stochastic Gaussian field, and it is the sole source of Tau A’s polarization angle oscillation. Additionally, we do not detect signal at the frequencies where 2.5σ hints were previously reported by POLARBEAR, but we do not exclude these signals at the 95% confidence level.

Adkins, Tylor [University of California, Berkeley]↗

DOE OSTI2024

Dielectronic satellite emission from a solid-density Mg plasma: Relationship to models of ionization potential depression

Here, we report on experiments where solid-density Mg plasmas are created by heating with the focused output of the Linac Coherent Light Source x-ray free-electron laser. We study the K-shell emission from the helium- and lithium-like ions using Bragg crystal spectroscopy. Observation of the dielectronic satellites in lithium-like ions confirms that the M-shell electrons appear bound for these high charge states. An analysis of the intensity of these satellites indicates that when modeled with an atomic-kinetics code, the ionization potential depression model employed needs to produce depressions for these ions which lie between those predicted by the well known Stewart-Pyatt and Ecker-Kroll models. These results are largely consistent with recent density functional theory calculations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Hydration-driven stabilization and volume collapse of grain boundaries in Mg2SiO4 forsterite predicted by first-principles simulations

Grain boundaries in mantle minerals are of critical importance to geophysical and geochemical processes of the Earth’s interior. One of the fundamental issues is to understand how the water (H 2 O) component influences the properties of grain boundaries in silicate materials. Here, we report the results of the structure and stability of several tilt grain boundaries in Mg 2 SiO 4 forsterite over the pressure range 0 to 15 GPa using density functional theory-based first-principles simulations. Here, the results suggest greater energetic stability and hydration-driven volume collapse (negative excess volume) at zero pressure for the majority of hydrous grain boundaries relative to the anhydrous (dry) ones. All the hydrous grain boundaries become increasingly favorable at elevated pressures as the calculated hydration enthalpy systematically decreases with increasing pressure. The hydrous components at the interfacial regions are predominantly in the hydroxyl form and, to a lesser extent, in the molecular H 2 O form. Their calculated ratio ranges from 1.6 to 8.7 among the different grain boundary configurations. Our structural analysis also reveals that the hydroxyls are bound to either both Mg and Si or to Mg only. In comparison, the molecular species are bound only to Mg sites. Besides direct oxygen-hydrogen bonding, intermolecular hydrogen bonding becomes important with compression. On the basis of our results, we suggest that local atomic rearrangements caused by dissociative adsorption of water facilitate efficient compaction of the boundary interfaces, which, in turn, results in greater relative stability of hydrous grain boundaries. This means that water prefers to be incorporated within the grain boundaries over the bulk of silicate materials.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

FY2020 performance assessment annual review for the E-area low-level waste facility

The Savannah River Site (SRS) E-Area Low-Level Waste Facility (ELLWF) consists of six types of disposal units described in the Performance Assessment (PA) (WSRC, 2008): Low Activity Waste Vault (LAWV), Intermediate Level Vault (ILV), Trenches [Slit Trenches (STs), Engineered Trenches (ETs), and Component-in-Grout (CIG) Trenches], and Naval Reactor Component Disposal Areas (NRCDAs). The ELLWF is a part of the Solid Waste Management Facility (SWMF). SWMF is managed and operated by the SRS Management and Operations prime contractor, Savannah River Nuclear Solutions (SRNS). Within SRNS, the Solid Waste Management (SWM) organization is responsible for operating the SWMF, and the Savannah River National Laboratory (SRNL) is the technical agency responsible for preparing and maintaining the PA. SWMF operations have been performed at SRS since 1952. The mission of the SWMF is to provide storage, processing, disposal, and shipment of radioactive, hazardous, and mixed waste. The SWMF is committed to treat, store, and dispose of these waste products in a manner that protects the environment and the health and safety of the facility worker, the co-located worker, and the offsite general public. Wastes handled in the SWMF include low level waste, transuranic waste, hazardous waste, Toxic Substances Control Act waste, and mixed waste (containing both hazardous and radioactive constituents). The FY2020 PA Annual Review for the ELLWF affirms that the disposal facility continued to operate within the bounds of the current PA and Composite Analysis (CA) baseline and the subsequent SA’s and satisfied all the requirements, conditions, and limitations identified in the 2008 DAS (DOE 2008a), RWMB SRNL_STI-2020-00588 Revision 0 vi (McGill, 2020), and ELLWF Low-Level Waste Acceptance Criteria (SRS-1S, 2014). This annual review affirms that the supporting studies performed in FY2020 do not alter the conclusions of the ELLWF PA (WSRC, 2008) and that there is a reasonable expectation that the ELLWF will meet the performance objectives delineated in DOE Manual 435.1-1 (DOE 2011)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Nuclear Physics Multimessenger Astrophysics Constraints on the Neutron Star Equation of State: Adding NICER’s PSR J0740+6620 Measurement

In the past few years, new observations of neutron stars (NSs) and NS mergers have provided a wealth of data that allow one to constrain the equation of state (EOS) of nuclear matter at densities above nuclear saturation density. However, most observations were based on NSs with masses of about 1.4 M ⊙ , probing densities up to ~three to four times the nuclear saturation density. Even higher densities are probed inside massive NSs such as PSR J0740+6620. Very recently, new radio observations provided an update to the mass estimate for PSR J0740+6620, and X-ray observations by the NICER and XMM telescopes constrained its radius. Based on these new measurements, we revisit our previous nuclear physics multimessenger astrophysics constraints and derive updated constraints on the EOS describing the NS interior. By combining astrophysical observations of two radio pulsars, two NICER measurements, the two gravitational-wave detections GW170817 and GW190425, detailed modeling of the kilonova AT 2017gfo, and the gamma-ray burst GRB 170817A, we are able to estimate the radius of a typical 1.4 M ⊙ NS to be ${11.94}_{-0.87}^{+0.76}\,\mathrm{km}$ at 90% confidence. Finally, our analysis allows us to revisit the upper bound on the maximum mass of NSs and disfavors the presence of a strong first-order phase transition from nuclear matter to exotic forms of matter, such as quark matter, inside NSs.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1981

Application of unconnected phase narrowband Delta VLBI to deep space navigation

Unconnected phase narrowband Delta VLBI data strategies are evaluated for enhancing deep space cruise navigation and for rapidly redetermining the spacecraft trajectory after a midcourse correction maneuver. Results of a covariance analysis study are presented for a Jupiter bound spacecraft based on a simulated data strategy consisting of daily 10 minute narrowband scans from two baselines augmented with conventional two way range and Doppler passes. For post-maneuver recovery, the narrowband strategy achieves a factor of two improvement in orbit determination performance. Cruise OD performance is also significantly enhanced due to the ability of the narrowband data to accurately sense the orientation of the orbital plane.

Ellis, J.↗

NASA NTRS1983

Consistent Tolerance Bounds for Statistical Distributions

Assumption that sample comes from population with particular distribution is made with confidence C if data lie between certain bounds. These "confidence bounds" depend on C and assumption about distribution of sampling errors around regression line. Graphical test criteria using tolerance bounds are applied in industry where statistical analysis influences product development and use. Applied to evaluate equipment life.

Mezzacappa, M. A.↗

NASA NTRS1981

A general analysis of anti-jam communication systems

A general error bound is derived for a general anti-jam communication system which will serve as the basis for evaluating the performance of all such complex communication systems. The two most common spread spectrum techniques, coherent DS/BPSK and noncoherent FH/MFSK, are analyzed. Pulse jamming represents the worst type of jammer for DS/BPSK systems, and several receiver structures against such a jammer are examined. It is found that for low values of chip energy-to-noise ratios of O dB or less there is little difference between having or not having jammer state knowledge with a hard decision receiver. Soft decision receivers are shown to be useless against very narrow pulses without jammer state knowledge. Partial band jammers are close to the worst case jammer for FH/MFSK systems. The conclusions found for these systems are similar to those for the DS/BPSK systems.

Omura, J. K.↗

NASA NTRS1984

Three unusual strokes in a triggered lightning flash

Time-resolved photographic records of three strokes of a triggered lightning flash are examined. These strokes exhibit several examples of novel behavior that include (1) the abrupt transformation of dart leaders to stepped leaders and (2) the partial 'reflection' of dart leader luminosity back up the channel. Both phenomena are associated with an apparent discontinuity in channel characteristics between the natural and artificial (wire) sections of the channel. We estimate the ratio of characteristic impedances for these sections to have an upper bound of about a factor of 3. Analysis of one of the dart leader 'reflections' yields a propagation speed of 9.6 x 10 to the 7th m/s whereas the dart leader and return stroke speeds (two-dimensional) over the same channel section are 1.7 x 10 to the 7th and 13 x 10 to the seventh m/s, respectively. Also, one of the return strokes reveals the occurrence of two distinct waves of luminosity that are separated by only 5 microns and that travel up nearly identical channels that differ only in the channel terminus.

Idone, V. P.↗

NASA NTRS1985

Fast and optimal solution to the Rankine-Hugoniot problem

A new, definitive, reliable and fast iterative method is described for determining the geometrical properties of a shock (i.e., theta sub Bn, yields N, V sub s and M sub A), the conservation constants and the self-consistent asymptotic magnetofluid variables, that uses the three dimensional magnetic field and plasma observations. The method is well conditioned and reliable at all theta sub Bn angles regardless of the shock strength or geometry. Explicit proof of uniqueness of the shock geometry solution by either analytical or graphical methods is given. The method is applied to synthetic and real shocks, including a bow shock event and the results are then compared with those determined by preaveraging methods and other iterative schemes. A complete analysis of the confidence region and error bounds of the solution is also presented.

Vinas, A. F.↗

NASA NTRS1986

Fast and optimal solution to the 'Rankine-Hugoniot problem'

Vinas, A. F.↗

NASA NTRS1988

International Conference on Advances in Communication and Control Systems, 1st, Washington, DC, June 18-20, 1987, Proceedings

Theoretical models of communication and control systems are discussed in reviews and reports. Topics addressed include smoothing and identification for random fields, the information and coding capacities of mismatched Gaussian channels, recursive least-squares estimation and Kalman filtering by systolic arrays, Kemp echo digital filters, a periodic test-scheduling scheme for communication and queuing processes, and receivers for direct-sequence systems. Consideration is given to a distributed-parameter model for detecting cracks in rotors, active control of aeroelastic systems governed by functional differential equations, robust multivariable control of large space structures, finite-rank relatively bounded perturbations of semigroup generators, and sensitivity analysis of convex optimal-control problems.

Declaris, Nicholas↗

NASA NTRS1998

Failure of Laminated Composites at Thickness Discontinuities: An Experimental and Analytical Study

Failure initiation of laminated composites at a thickness discontinuity is studied experimentally with the aid of an optical microscope under combined loading of tension, transverse shear and bending, making use of three- and four-point bending arrangements. Because transverse shear produced relatively small effects in failure initiation results are presented as tension-bending interactions. Two loading frames for three- and four-point bending were designed to apply moment and tension simultaneously to produce failure by generating a ply crack; this initiation was evaluated by finite element analysis using ABAQUS. For cross-plies bounding the interface at the base of the step it is found that a maximum strain criterion applied to the continuing (long) ply describes the failure initiation. Ultimate failure resulted at loads on the order of 25 to 35% higher than those at failure initiation.

Lee, Sangwook↗

NASA NTRS2001

Rayleigh Scattering Diagnostic for Dynamic Measurement of Velocity Fluctuations in High Speed Jets

A flow diagnostic technique based on the molecular Rayleigh scattering of laser light is used to obtain dynamic density and velocity data in a high speed flow. The technique is based on analyzing the Rayleigh scattered light with a Fabry-Perot interferometer used in the static, imaging mode. An analysis is presented that established a lower bound for measurement uncertainty of about 20 m/sec for individual velocity measurements obtained in a 100 microsecond time interval. Software and hardware interfaces were developed to allow computer control of all aspects of the experiment and data acquisition. The signals from three photomultiplier tubes were simultaneously recorded using photon counting at a 10 kHz sampling rate and 10 second recording periods. Density and velocity data, including distribution functions and power spectra, taken in a Mach 0.8 free jet, are presented.

Seasholtz, Richard G.↗

NASA NTRS2010

Verifiable Adaptive Control with Analytical Stability Margins by Optimal Control Modification

This paper presents a verifiable model-reference adaptive control method based on an optimal control formulation for linear uncertain systems. A predictor model is formulated to enable a parameter estimation of the system parametric uncertainty. The adaptation is based on both the tracking error and predictor error. Using a singular perturbation argument, it can be shown that the closed-loop system tends to a linear time invariant model asymptotically under an assumption of fast adaptation. A stability margin analysis is given to estimate a lower bound of the time delay margin using a matrix measure method. Using this analytical method, the free design parameter n of the optimal control modification adaptive law can be determined to meet a specification of stability margin for verification purposes.

Nguyen, Nhan T.↗

DOE OSTI2023

Towards resolving protein structures at the atomic scale using atom probe tomography

In the field of Structural Biology, Atom Probe Tomography (APT) is in the nascent stages of development wherein coarse-grained visuals of proteins have been captured. The characterization of organic samples or biomolecules through the technique is currently limited to the detection of a few dominant signatures. The problem of indecipherable characterization can inherently be traced back to multiple forms of technique-specific responses to organic samples and consequent triggers leading to organic-sample and sample-medium interactions. While it is possible for captured manifestations of protein reconstructions to seemingly appear intact from a basic visual purview, the parameter-protein associative responses throughout the structure as a direct consequence of the inherent workings of the technique (until harmonized with organic sample complexity and behavior) and field evaporation-based factors make non-aberrative atomic associations infeasible. The work focused on identifying and theorizing the (above stated and other) fundamental mechanisms that stronghold the study of intricate atomic to higher order associations in proteins through APT. Attempts at structure elucidation of the cryogenic sample under study, through indirect associations (and methods) based on other imaging techniques, further revealed the distinct and highly distortive nature at the atomic scale deterring structural tunability and thus characterization of APT based cryogenic samples under analysis. As a direct counter to the atomic scale characterization problem, by taking the experiment-specific uncertainties, and probable APT-centric organic sample-based variabilities into account, a basic result is extracted and presented. Through mass-spectrometric and computational analysis, specific individual amino acids (Sulfur-containing protein-bound amino acids) in proteins and aspects of protein structure (probable backbone fragments, partial sequence - partial backbone portions) have been identified and characterized. Under analysis considerations, a few of the simplest known and easily inferable segments that favor structural deteriorations in the reconstructions are stated. Additionally, to overcome technique-specific deterrents to the characterization of biomolecules in cryogenic sample medium, the development of a protein-labeling strategy tailored to APT is suggested.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Interpretation of high-harmonic fast-wave propagation in the scrape-off layer of NSTX-U as a geometrically bounded-waveguide mode

This paper revisits the onset of high-harmonic fast-wave (HHFW) propagation in the scrape-off layer (SOL) plasma of the NSTX/NSTX-U spherical tokamak, motivated by past HHFW heating and current drive experiments and modelling. Previously, the fast-wave propagation in the SOL was correlated with the opening (suppression) of the fast-wave right-hand cutoff layer in front of the antenna. In this work, the SOL propagation is interpreted as a geometric waveguide mode guided by the SOL geometry, whose radial width can be comparable to the wave’s perpendicular wavelength in the HHFW regime. A two-dimensional circular model is first employed using full-wave solvers to characterise the poloidal eigenmode structures and to clarify their relationship to annulus resonance. By progressively adding a tokamak-like magnetic-field configuration, starting from a uniform axial field, the effects of magnetic-field gradients and pitch on the SOL waveguide mode are characterised. The poloidal mode numbers supported by the SOL plasma agree well with analytic estimates, indicating that an anisotropic plasma in a bounded geometry selectively supports and amplifies the resonant poloidal mode number. Additionally, two-dimensional axisymmetric NSTX-U simulations demonstrate that the SOL eigenmode features identified in the circular model persist in the experimentally relevant configurations. A control approach based on lengthening the wave perpendicular wavelength relative to the SOL width, including a higher magnetic (B)-field operation, is discussed. The analysis here shows the key role of a bounded geometry in interpreting HHFW eigenmode coupling and propagation in the NSTX-U SOL plasma.

plasma heating↗