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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions

Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. In this paper, we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge–dipole and CH–π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Finally and hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations

DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

All-optical phase conjugation using diffractive wavefront processing

Abstract Optical phase conjugation (OPC) is a nonlinear technique used for counteracting wavefront distortions, with applications ranging from imaging to beam focusing. Here, we present a diffractive wavefront processor to approximate all-optical phase conjugation. Leveraging deep learning, a set of diffractive layers was optimized to all-optically process an arbitrary phase-aberrated input field, producing an output field with a phase distribution that is the conjugate of the input wave. We experimentally validated this wavefront processor by 3D-fabricating diffractive layers and performing OPC on phase distortions never seen during training. Employing terahertz radiation, our diffractive processor successfully performed OPC through a shallow volume that axially spans tens of wavelengths. We also created a diffractive phase-conjugate mirror by combining deep learning-optimized diffractive layers with a standard mirror. Given its compact, passive and multi-wavelength nature, this diffractive wavefront processor can be used for various applications, e.g., turbidity suppression and aberration correction across different spectral bands.

42 ENGINEERING↗
DOE OSTI2020

Structural basis for dimerization quality control

Most quality control pathways target misfolded proteins to prevent toxic aggregation and neurodegeneration 1 . Dimerization quality control further improves proteostasis by eliminating complexes of aberrant composition 2 , but how it detects incorrect subunits remains unknown. Here we provide structural insight into target selection by SCF-FBXL17, a dimerization-quality-control E3 ligase that ubiquitylates and helps to degrade inactive heterodimers of BTB proteins while sparing functional homodimers. We find that SCF-FBXL17 disrupts aberrant BTB dimers that fail to stabilize an intermolecular β-sheet around a highly divergent β-strand of the BTB domain. Furthermore, complex dissociation allows SCF-FBXL17 to wrap around a single BTB domain, resulting in robust ubiquitylation. SCF-FBXL17 therefore probes both shape and complementarity of BTB domains, a mechanism that is well suited to establish quality control of complex composition for recurrent interaction modules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Methods to capture proteomic and metabolomic signatures from cerebrospinal fluid and serum of healthy individuals

Discovery of reliable signatures for the empirical diagnosis of neurological diseases—both infectious and non-infectious—remains unrealized. One of the primary challenges encountered in such studies is the lack of a comprehensive database representative of a signature background that exists in healthy individuals, and against which an aberrant event can be assessed. For neurological insults and injuries, it is important to understand the normal profile in the neuronal (cerebrospinal fluid) and systemic fluids (e.g., blood). Here, we present the first comparative multi-omic human database of signatures derived from a population of 30 individuals (15 males, 15 females, 23–74 years) of serum and cerebrospinal fluid. In addition to empirical signatures, we also assigned common pathways between serum and CSF. Together, our findings provide a cohort against which aberrant signature profiles in individuals with neurological injuries/disease can be assessed—providing a pathway for comprehensive diagnostics and therapeutics discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Vacancy structures and melting behavior in rock-salt GeSbTe

Ge-Sb-Te alloys have been widely used in optical/electrical memory storage. Because of the extremely fast crystalline-amorphous transition, they are also expected to play a vital role in next generation nonvolatile microelectronic memory devices. However, the distribution and structural properties of vacancies have been one of the key issues in determining the speed of melting (or amorphization), phase-stability, and heat-dissipation of rock-salt GeSbTe, which is crucial for its technological breakthrough in memory devices. Using spherical aberration-aberration corrected scanning transmission electron microscopy and atomic scale energy-dispersive X-ray mapping, we observe a new rock-salt structure with high-degree vacancy ordering (or layered-like ordering) at an elevated temperature, which is a result of phase transition from the rock-salt phase with randomly distributed vacancies. First-principles calculations reveal that the phase transition is an energetically favored process. Furthermore, molecular dynamics studies suggest that the melting of the cubic rock-salt phases is initiated at the vacancies, which propagate to nearby regions. The observation of multi-rock-salt phases suggests another route for multi-level data storage using GeSbTe.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Precision controlled atomic resolution scanning transmission electron microscopy using spiral scan pathways

Atomic-resolution imaging in an aberration-corrected scanning transmission electron microscope (STEM) can enable direct correlation between atomic structure and materials functionality. The fast and precise control of the STEM probe is, however, challenging because the true beam location deviates from the assigned location depending on the properties of the deflectors. To reduce these deviations, i.e. image distortions, we use spiral scanning paths, allowing precise control of a sub-Å sized electron probe within an aberration-corrected STEM. Although spiral scanning avoids the sudden changes in the beam location (fly-back distortion) present in conventional raster scans, it is not distortion-free. “Archimedean” spirals, with a constant angular frequency within each scan, are used to determine the characteristic response at different frequencies. We then show that such characteristic functions can be used to correct image distortions present in more complicated constant linear velocity spirals, where the frequency varies within each scan. Through the combined application of constant linear velocity scanning and beam path corrections, spiral scan images are shown to exhibit less scan distortion than conventional raster scan images. The methodology presented here will be useful for in situ STEM imaging at higher temporal resolution and for imaging beam sensitive materials.

47 OTHER INSTRUMENTATION↗
DOE OSTI2014

Planck 2013 results. XXVII. Doppler boosting of the CMB: Eppur si muove

Our velocity relative to the rest frame of the cosmic microwave background (CMB) generates a dipole temperature anisotropy on the sky which has been well measured for more than 30 years, and has an accepted amplitude of v/c = 1.23 × 10 -3 , or v = 369 s -1 . In addition to this signal generated by Doppler boosting of the CMB monopole, our motion also modulates and aberrates the CMB temperature fluctuations (as well as every other source of radiation at cosmological distances). This is an order 10 -3 effect applied to fluctuations which are already one part in roughly 10 5 , so it is quite small. Nevertheless, it becomes detectable with the all-sky coverage, high angular resolution, and low noise levels of the Planck satellite. Here we report a first measurement of this velocity signature using the aberration and modulation effects on the CMB temperature anisotropies, finding a component in the known dipole direction, ( l,b ) = (264°,48°), of 384 km s -1 ± 78 km s -1 (stat.) ± 115 km s -1 (syst.). This is a significant confirmation of the expected velocity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Using the Gerchberg-Saxton algorithm to reconstruct nonmodulated pyramid wavefront sensor measurements

Adaptive optics (AO) is a technique to improve the resolution of ground-based telescopes by correcting, in real-time, optical aberrations due to atmospheric turbulence and the telescope itself. With the rise of Giant Segmented Mirror Telescopes (GSMT), AO is needed more than ever to reach the full potential of these future observatories. One of the main performance drivers of an AO system is the wavefront sensing operation, consisting of measuring the shape of the above mentioned optical aberrations. Aims. The non-modulated pyramid wavefront sensor (nPWFS) is a wavefront sensor with high sensitivity, allowing the limits of AO systems to be pushed. The high sensitivity comes at the expense of its dynamic range, which makes it a highly non-linear sensor. We propose here a novel way to invert nPWFS signals by using the principle of reciprocity of light propagation and the Gerchberg-Saxton (GS) algorithm. We test the performance of this reconstructor in two steps: the technique is first implemented in simulations, where some of its basic properties are studied. Then, the GS reconstructor is tested on the Santa Cruz Extreme Adaptive optics Laboratory (SEAL) testbed located at the University of California Santa Cruz. This new way to invert the nPWFS measurements allows us to drastically increase the dynamic range of the reconstruction for the nPWFS, pushing the dynamics close to a modulated PWFS. The reconstructor is an iterative algorithm requiring heavy computational burden, which could be an issue for real-time purposes in its current implementation. However, this new reconstructor could still be helpful in the case of many wavefront control operations. In conclusion, this reconstruction technique has also been successfully tested on the Santa Cruz Extreme AO Laboratory (SEAL) bench where it is now used as the standard way to invert nPWFS signal.

47 OTHER INSTRUMENTATION↗
DOE OSTI2013

Defects in paramagnetic Co-doped ZnO films studied by transmission electron microscopy

We study planar defects in epitaxial Co:ZnO dilute magnetic semiconductor thin films deposited on c-plane sapphire (Al{sub 2}O{sub 3}), as well as the Co:ZnO/Al{sub 2}O{sub 3} interface, using aberration-corrected transmission electron microscopy and electron energy-loss spectroscopy. Co:ZnO samples that were deposited using pulsed laser deposition and reactive magnetron sputtering are both found to contain extrinsic stacking faults, incoherent interface structures, and compositional variations within the first 3–4 Co:ZnO layers next to the Al{sub 2}O{sub 3} substrate. The stacking fault density is in the range of 10{sup 17} cm{sup −3}. We also measure the local lattice distortions around the stacking faults. It is shown that despite the relatively high density of planar defects, lattice distortions, and small compositional variation, the Co:ZnO films retain paramagnetic properties.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Non-descanned multifocal multiphoton microscopy with a multianode photomultiplier tube

Multifocal multiphoton microscopy (MMM) improves imaging speed over a point scanning approach by parallelizing the excitation process. Early versions of MMM relied on imaging detectors to record emission signals from multiple foci simultaneously. For many turbid biological specimens, the scattering of emission photons results in blurred images and degrades the signal-to-noise ratio (SNR). We have recently demonstrated that a multianode photomultiplier tube (MAPMT) placed in a descanned configuration can effectively collect scattered emission photons from each focus into their corresponding anodes significantly improving image SNR for highly scattering specimens. Unfortunately, a descanned MMM has a longer detection path resulting in substantial emission photon loss. Optical design constraints in a descanned geometry further results in significant optical aberrations especially for large field-of-view (FOV), high NA objectives. Here, we introduce a non-descanned MMM based on MAPMT that substantially overcomes most of these drawbacks. We show that we improve signal efficiency up to fourfold with limited image SNR degradation due to scattered emission photons. The excitation foci can also be spaced wider to cover the full FOV of the objective with minimal aberrations. The performance of this system is demonstrated by imaging interneuron morphological structures deep in the brains of living mice.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Amphoteric doping of praseodymium Pr{sup 3+} in SrTiO{sub 3} grain boundaries

Charge compensation in rare-earth Praseodymium (Pr{sup 3+}) doped SrTiO{sub 3} plays an important role in determining the overall photoluminescence properties of the system. Here, the Pr{sup 3+} doping behavior in SrTiO{sub 3} grain boundaries (GBs) is analyzed using aberration corrected scanning transmission electron microscopy. The presence of Pr{sup 3+} induces structural variations and changes the statistical prevalence of the GB structures. In contrast to the assumption that Pr{sup 3+} substitutes on the Sr site in the bulk, Pr{sup 3+} is found to substitute on both Sr and Ti sites inside the GBs, with the highest concentration at the Ti sites. This amphoteric doping behavior in the boundary plane is further confirmed by first principles theoretical calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Design and fabrication of a duoplasmatron extraction geometry and LEBT for the LANSCE H{sup +} RFQ project

The 750-keV H{sup +} Cockcroft-Walton at LANSCE will be replaced with a recently fabricated 4-rod Radio Frequency Quadrupole (RFQ) with injection energy of 35 keV. The existing duoplasmatron source extraction optics need to be modified to produce up to 35 mA of H{sup +} current with an emittance <0.02 π-cm-mrad (rms, norm) for injection into the RFQ. Parts for the new source have been fabricated and assembly is in process. We will use the existing duoplasmatron source with a newly designed extraction system and low energy beam transport (LEBT) for beam injection into the RFQ. In addition to source modifications, we need a new LEBT for transport and matching into the RFQ. The LEBT uses two magnetic solenoids with enough drift space between them to accommodate diagnostics and a beam deflector. The LEBT is designed to work over a range of space-charge neutralized currents and emittances. The LEBT is optimized in the sense that it minimizes the beam size in both solenoids for a point design of a given neutralized current and emittance. Special attention has been given to estimating emittance growth due to source extraction optics and solenoid aberrations. Examples of source-to-RFQ matching and emittance growth (due to both non-linear space charge and solenoid aberrations) are presented over a range of currents and emittances about the design point. A mechanical layout drawing will be presented along with the status of the source and LEBT, design, and fabrication.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Direct observation of oxygen-vacancy-enhanced polarization in a SrTiO{sub 3}-buffered ferroelectric BaTiO{sub 3} film on GaAs

The integration of functional oxide thin-films on compound semiconductors can lead to a class of reconfigurable spin-based optoelectronic devices if defect-free, fully reversible active layers are stabilized. However, previous first-principles calculations predicted that SrTiO{sub 3} thin films grown on Si exhibit pinned ferroelectric behavior that is not switchable, due to the presence of interfacial vacancies. Meanwhile, piezoresponse force microscopy measurements have demonstrated ferroelectricity in BaTiO{sub 3} grown on semiconductor substrates. The presence of interfacial oxygen vacancies in such complex-oxide/semiconductor systems remains unexplored, and their effect on ferroelectricity is controversial. Here, we use a combination of aberration-corrected scanning transmission electron microscopy and first-principles density functional theory modeling to examine the role of interfacial oxygen vacancies on the ferroelectric polarization of a BaTiO{sub 3} thin film grown on GaAs. We demonstrate that interfacial oxygen vacancies enhance the polar discontinuity (and thus the single domain, out-of-plane polarization pinning in BaTiO{sub 3}), and propose that the presence of surface charge screening allows the formation of switchable domains.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

The role of chemical structure on the magnetic and electronic properties of Co{sub 2}FeAl{sub 0.5}Si{sub 0.5}/Si(111) interface

We show that Co{sub 2}FeAl{sub 0.5}Si{sub 0.5} film deposited on Si(111) has a single crystal structure and twin related epitaxial relationship with the substrate. Sub-nanometer electron energy loss spectroscopy shows that in a narrow interface region there is a mutual inter-diffusion dominated by Si and Co. Atomic resolution aberration-corrected scanning transmission electron microscopy reveals that the film has B2 ordering. The film lattice structure is unaltered even at the interface due to the substitutional nature of the intermixing. First-principles calculations performed using structural models based on the aberration corrected electron microscopy show that the increased Si incorporation in the film leads to a gradual decrease of the magnetic moment as well as significant spin-polarization reduction. These effects can have significant detrimental role on the spin injection from the Co{sub 2}FeAl{sub 0.5}Si{sub 0.5} film into the Si substrate, besides the structural integrity of this junction.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging

Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. As a result, the use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO 3 , a material that is traditionally difficult to image by TEM/STEM because of dose issues.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Atomic scale study of surface orientations and energies of Ti 2 O 3 crystals

For nanostructured particles, the faceting planes and their terminating chemical species are two critical factors that govern their chemical behavior. In this paper, the surface atomistic structure and termination of Ti 2 O 3 crystals were analyzed using atomic-scale aberration-corrected scanning transmission electron microscopy (STEM) combined with density functional theory (DFT) calculations. STEM imaging reveals that the Ti 2 O 3 crystals are most often faceted along (001), (012), (-114), and (1–20) planes. The DFT calculation indicates that the (012) surface with TiO-termination has the lowest cleavage energy and correspondingly the lowest surface energy, indicating that (012) will be the most stable and prevalent surfaces in Ti 2 O 3 nanocrystals. Finally, these observations provide insights for exploring the interfacial process involving Ti 2 O 3 nanoparticles.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Short spatial filters with spherical lenses for high-power pulsed lasers

We report possible employment of short spatial filters based on spherical lenses in a pulsed laser source (neodymium glass, 300 J, 1 ns). The influence of the spherical aberration on the quality of output radiation and coefficient of conversion to the second harmonics is studied. The ultra-short aberration spatial filter of length 1.9 m with an aperture of 122 mm is experimentally tested. A considerable shortening of multi-cascade pump lasers for modern petawatt laser systems is demonstrated by the employment of short spatial filters without expensive aspherical optics. (elements of laser systems)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗