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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 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
NASA NTRS1992

Realization of high quality production schedules: Structuring quality factors via iteration of user specification processes

This paper describes an architecture for realizing high quality production schedules. Although quality is one of the most important aspects of production scheduling, it is difficult, even for a user, to specify precisely. However, it is also true that the decision as to whether a scheduler is good or bad can only be made by the user. This paper proposes the following: (1) the quality of a schedule can be represented in the form of quality factors, i.e. constraints and objectives of the domain, and their structure; (2) quality factors and their structure can be used for decision making at local decision points during the scheduling process; and (3) that they can be defined via iteration of user specification processes.

Hamazaki, Takashi↗
DOE OSTI2020

The carboxylation status of osteocalcin has important consequences for its structure and dynamics

The carboxylation status of Osteocalcin (Ocn) not only influences formation and structure in bones but also has important endocrine functions affecting energy metabolism and expenditure. In this study, the role of γ-carboxylation of the glutamate residues in the structure-dynamics-function relationship in Ocn is investigated. Three forms of Ocn, differentially carboxylated at the Glu-17, 21 and 24 residues, along with a mutated form of Ocn carrying Glu/Ala mutations, are modeled and simulated using molecular dynamics (MD) simulation in the presence of calcium ions. Characterization of the global conformational dynamics of Ocn, described in terms of the orientational variations within its 3-helical domain, highlights large structural variations in the non-carboxylated osteocalcin (nOcn). The bi-carboxylated Ocn (bOcn) and tri-carboxylated (tOcn) species, in contrast, display relatively rigid tertiary structures, with the dynamics of most regions strongly correlated. Radial distribution functions calculated for both bOcn and tOcn show long-range ordering of the calcium ion distribution around the carboxylated glutamate (γGlu) residues, likely playing an important role in promoting stability of these Ocns. Additionally, the same calcium ions are observed to coordinate with neighboring γGlu, better shielding their negative charges and in turn stabilizing these systems more than do the singly coordinating calcium ions observed in the case of nOcn. bOcn is also found to exhibit a more helical C-terminal structure, that has been shown to activate its cellular receptor GPRC6A, highlighting the allosteric role of Ocn carboxylation in modulating the stability and binding potential of the active C-terminal. Furthermore, the carboxylation status of Ocn as well and its calcium coordination appear to have a direct influence on Ocn structure and dynamics, possibly leading to the known differences in Ocn biological function.

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

Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS

RNA-binding protein with multiple splicing (designated RBPMS) is a higher vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM). RBPMS has been shown to be involved in mRNA transport, localization and stability, with key roles in axon guidance, smooth muscle plasticity, as well as regulation of cancer cell proliferation and migration. We report on structure-function studies of the RRM domain of RBPMS bound to a CAC-containing single-stranded RNA. These results provide insights into potential topologies of complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites as detected by photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation. These studies establish that the RRM domain of RBPMS forms a symmetrical dimer in the free state, with each monomer binding sequence-specifically to all three nucleotides of a CAC segment in the RNA bound state. Structure-guided mutations within the dimerization and RNA-binding interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of dimerization and a decrease in RNA-binding affinity as observed by size exclusion chromatography and isothermal titration calorimetry. Here, as anticipated from biochemical binding studies, over-expression of dimerization or RNA-binding mutants of Flag-HA-tagged RBPMS were no longer able to track with stress granules in HEK293 cells, thereby documenting the deleterious effects of such mutations in vivo .

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Generalized Symbolic Execution for Model Checking and Testing

Modern software systems, which often are concurrent and manipulate complex data structures must be extremely reliable. We present a novel framework based on symbolic execution, for automated checking of such systems. We provide a two-fold generalization of traditional symbolic execution based approaches: one, we define a program instrumentation, which enables standard model checkers to perform symbolic execution; two, we give a novel symbolic execution algorithm that handles dynamically allocated structures (e.g., lists and trees), method preconditions (e.g., acyclicity of lists), data (e.g., integers and strings) and concurrency. The program instrumentation enables a model checker to automatically explore program heap configurations (using a systematic treatment of aliasing) and manipulate logical formulae on program data values (using a decision procedure). We illustrate two applications of our framework: checking correctness of multi-threaded programs that take inputs from unbounded domains with complex structure and generation of non-isomorphic test inputs that satisfy a testing criterion. Our implementation for Java uses the Java PathFinder model checker.

Khurshid, Sarfraz↗
DOE OSTI2021

Antiphase-Boundary-Engineered Domain Switching in a (110)-Oriented BiFeO 3 Film

A ferroelectric domain wall memory device exploits the presence (or absence) of domain walls as the basis for information storage. Although structural defects strongly influence ferroelectric domain wall nucleation and growth, this correlation is far from being fully understood. For example, a single defect can play opposing roles: it can act as a nucleation site to initiate domain switching or, conversely, serve as a pinning center inhibiting domain wall motion. This is particularly the case for antiphase boundaries (APBs), whose influence on switching remains relatively unexplored despite being ubiquitous in oxide perovskite ferroelectrics. Here, we use aberration-corrected scanning transmission microscopy and in situ transmission electron microscopy under an applied bias to extensively characterize the influence of an APB on the switching behavior in a (110)-oriented BiFeO 3 thin film. We demonstrate that deterministic nucleation occurs in the proximity of a vertically oriented APB, following which domain growth occurs laterally in a symmetric fashion. Atomic-scale structural analysis reveals that the shear operation vector for the APB is 1/2[110]; this half-unit-cell shift extends over a few nanometers, implying that the APB plane is inclined toward the imaging direction. The symmetric switching observation is attributed to local inhomogeneous lattice strain and a reduction of polarization caused by the APB. These results demonstrate that an extended structural defect can be used as an active switching element rather than a stumbling block in reprogrammable domain-wall-based devices. Ultimately, this will expand the capabilities of ferroelectric thin films for future electronic devices based on ferroelectric domain walls.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Magnetic pinning in a superconducting film by a ferromagnetic layer with stripe domains

A magnetic study of superconductor/ferromagnet bilayers was performed by hysteresis loops and temperature-dependent magnetization measurements. The superconductor/ferromagnet bilayers consist of a Nb film deposited on a Py film with weak perpendicular magnetic anisotropy. By comparing the temperature-dependent magnetization data obtained on samples with different ferromagnetic layer thickness, a decrease of the magnetic pinning with increasing thickness of the ferromagnetic layer has been found. This is confirmed by the reduction of the Nb film critical current density at low fields extracted by using the magnetic irreversibility of the hysteresis loops. Here, the reduction of the pinning can be related to the increase of the stripe width in the ferromagnetic layer observed by magnetic force microscopy (MFM) measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1994

Physical state of the western U.S. upper mantle

Using observed P wave images of the western U.S. upper mantle, which show lateral variations of up to 8%, and existing scaling relations, we infer that the low-velocity mantle is hot and partially molten to depths of 100-200 km, and that the high-velocity upper mantle is subsolidus. Most the high-velocity upper mantle within a few hundred kilometers of the coastline appears to be relatively dense, suggesting that it is relatively cool (i.e., a thermal lithosphere). This is expected for features associated with the subducting Juan de Fuca and Gorda slabs, and the high velocity upper mantle beneath the Transverse Ranges has been attributed to the sinking of negatively buoyant mantle lithosphere. Other high-velocity mantle structures near the continental margin are consistent with this interpretation. In contrast, the generally high elevations of the continental interior imply a buoyant upper mantle there, an inference that holds for both the high- and the low-velocity upper mantle. The only resonable way to produce the high-velocity low-density upper mantle is through basalt depletion, thereby creating mantle of increased solidus temperature and decreased density. We distinguish a marginal domain, within approximately 250 km of the Pacific coast, from an interior domain. This is based on the inferred upper mantle compositional difference and regional associations: beneath the marginal domain, upper mantle structures trend parallel to the surface physiography and young tectonic structures, whereas upper mantle structures beneath the continental interior trend northeasterly. This northeast orientation is discordant with the young tectonic structures, but aligns with young volcanic activity. The high lateral gradients in observed upper mantle seismic structure found throughout the western United States imply high lateral gradients in the associated temperature or partial melt fields. Because these fields diffuse on time scales of less than a few tens of millions of years, the imaged upper mantle structure is young. The following upper mantle processes are hypothesized to account for these findings and inferences. Away from the plate margin, small-scale upper mantle convection driven by partial melt-induced buoyancy of hot upper mantle leads to the production and segregation of melt and the creation of compositional variations. The heterogeneous upper mantle P wave structure of the elevated continental interior is largely a consequence of partial melt variations that are modulated by the compositional variations, and throughout this region we infer high temperatures and low densities. Near the plate margin, relative plate motions force upper mantle flow, although upper mantle flow driven by the positive buoyancy of melt and the negative bouyancy lithosphere is important locally.

Humphreys, Eugene D.↗
DOE OSTI2015

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

ABSTRACT Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ- d -Glu-A 2 pm (A 2 pm is diaminopimelic acid) cysteine amidase (or dl -endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l -Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. IMPORTANCE Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.

Xu, Qingping↗
DOE OSTI2021

Condensation of collective polar vortex modes

The dynamics of extended objects such as domain walls, domain bubbles, vortex structures, etc., can be described by their equations of motion associated with their effective mass and spring constant. Here we analytically derive the equations of motion for the polarization dynamics and elastodynamics for the structural responses of ferroelectric polar vortices, and theoretically extract their effective mass, spring constant, and mode frequencies. We demonstrate two subterahertz phonon modes and predicted their frequencies, both consistent with our recent experimental measurements and phase-field simulations. We show that elastic modulation of the energy function and spring constants leads to a condensation of a collective mode upon a second-order structural transition from symmetric to asymmetric vortices at a critical strain, analogous to the ferroelectric soft phonon mode at a ferroelectric transition. Furthermore, the present work offers a theoretical framework for predicting and manipulating the ultrafast collective dynamics of polar nanostructures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases

The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases remove methyl groups from tri- and dimethylated lysine 4 of histone H3. Accumulating evidence from primary tumors and model systems supports a role for KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) as oncogenic drivers. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC). Here we demonstrate that internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. We present a crystal structure of the linked JmjN-JmjC domain from KDM5A, which reveals that the linked domain fully reconstitutes the cofactor (metal ion and α-ketoglutarate) binding characteristics of other structurally characterized Jumonji domain demethylases. Docking studies with GSK-J1, a selective inhibitor of the KDM6/KDM5 subfamilies, identify critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. Further, we found that GSK-J1 inhibited the demethylase activity of KDM5C with 8.5-fold increased potency compared with that of KDM5B at 1 mm α-ketoglutarate. In contrast, JIB-04 (a pan-inhibitor of the Jumonji demethylase superfamily) had the opposite effect and was ~8-fold more potent against KDM5B than against KDM5C. Interestingly, the relative selectivity of JIB-04 toward KDM5B over KDM5C in vitro translates to a ~10–50-fold greater growth-inhibitory activity against breast cancer cell lines. Here, these data define the minimal requirements for enzymatic activity of the KDM5 family to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain and provide structural characterization of the linked JmjN-JmjC domain for the KDM5 family, which should prove useful in the design of KDM5 demethylase inhibitors with improved potency and selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Domain Nucleation and Growth in an Epitaxially Grown Wurtzite Ferroelectric

Ferroelectric domain nucleation and growth in epitaxial (Al, B, Sc)N films grown on n-GaN substrates are explored using a combination of ferroelectric property measurements and scanning transmission electron microscopy, including novel in situ switching studies. The films are electrically switched to nitrogen-polar (N-polar) and metal-polar (M-polar) configurations, attaining a remanent polarization of 120 µC cm −2 with coercive fields of ≈6 MV cm −1 . In the initial switching cycle, the ferroelectric domains nucleate near the bottom n-GaN electrode and develop domain walls with zigzag morphologies, while residual “dead layers” that do not switch from the as-deposited orientation persist at the top and bottom electrodes. The in situ microscopy experiments reveal that domain walls propagate fastest in the lateral direction, parallel to the electrode/film interface. These findings provide insights into the domain dynamics and structural evolution of wurtzite ferroelectrics, offering implications for next-generation electronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Gel polymer electrolytes for batteries

Nanostructured gel polymer electrolytes that have both high ionic conductivity and high mechanical strength are disclosed. The electrolytes have at least two domains--one domain contains an ionically-conductive gel polymer and the other domain contains a rigid polymer that provides structure for the electrolyte. The domains are formed by block copolymers. The first block provides a polymer matrix that may or may not be conductive on by itself, but that can soak up a liquid electrolyte, thereby making a gel. An exemplary nanostructured gel polymer electrolyte has an ionic conductivity of at least 1.times.10.sup.-4 S cm.sup.-1 at 25.degree. C.

25 ENERGY STORAGE↗
DOE OSTI2024

Theory of strain phase equilibria and diagrams

Chemical phase equilibria and phase diagrams are well established and have served as indispensable guides for designing materials through chemical tuning. However, a general thermodynamic theory for strain phase equilibria remains elusive despite extensive studies which have revealed dramatic impacts of mechanical strain on the stability of phases and domain states in solid-state materials. Here, we establish the thermodynamic theory of strain equilibria and a general framework for efficiently constructing multidomain and multiphase diagrams of arbitrarily strained solids under incoherent conditions. As examples, we obtain temperature-strain phase diagrams of ferroelectric PbTiO 3 , strongly correlated VO 2 , and unconventional ferroelectric Hf 0.5 Zr 0.5 O 2 . We reveal the analogs of the Gibbs phase rules, multiple- and multi-critical points, common-tangent construction, and level rule in strain equilibria to those in the familiar chemical phase equilibria. Finally, our strain equilibria theory offers a powerful framework for predicting the thermodynamic stability of structural phases and domains in strained solids and for guiding the strain engineering of their functional properties.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Effects of rigidity on the selectivity of protein kinase inhibitors

Established strategies for discovering selective kinase inhibitors are target-centric as they often target certain structural or reactive features in the target kinase. In the absence of such prominent features, there is a lack of general methods for discovering selective inhibitors. As such, here we describe a new strategy that exploits conformational flexibility of kinases for achieving selective kinase inhibition. Through ring closure, we designed and synthesized a panel of isoquinoline-containing compounds as rigidified analogs of an amidophenyl-containing parent compound. These analogs potently inhibit kinases including Abl and BRAF but have diminished inhibition against some other kinases compared to the parent compound. Sequence analysis reveals that many of the kinases that are potently inhibited by the isoquonoline-containing compounds contain a long insertion within their catalytic domains. A crystal structure of one rigid compound bound to BRAF confirmed its binding mode. Our findings highlight the potential of a novel strategy of rigidification for improving the selectivity of kinase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Origin of Phase Separation in Ni-Rich Layered Oxide Cathode Materials During Electrochemical Cycling

In intercalation materials, the kinetics and uniformity of mass transport across the nanocrystalline domains dictate the structural reversibility and transport capability at the macroscopic level. (De)intercalation-induced interlayer disintegrations exhibit anisotropic crystallite size change. Due to the anisotropic mass transport mechanism, separated phases are inherently crystallographically oriented. One such material is LiNi $1–x–y$ Mn $x$ Co $y$ O 2 , which plays a pivotal role in advanced Li-ion batteries but suffers from severe phase inhomogeneities under fast charge or electrochemical aging. Here, using operando synchrotron techniques, we probe the mechanistic origins of the compositional and orientational-dependent phase separations during the electrochemical cycling of LiNi 0.8 Mn 0.1 Co 0.1 O 2 by comprehensive analysis of both in-plane and out-of-plane reflections. In the H2/H3 phase regime, in-plane domain propagation occurs due to increased covalency despite the severe decay of interlayer crystallographic order, resulting in the change of crystalline domain shape from 3D spheres to two-dimensional nanosheets. The crystallographically selective XRD line splitting is linked to the geometry of the facets as mass transfers along the ab plane. In conclusion, this work provides mechanistic insights into crystallographic orientation-dependent phase inhomogeneity under fast charge and extended cycling.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural and Optical Properties of High Entropy (La,Lu,Y,Gd,Ce)AlO 3 Perovskite Thin Films

Mixtures of Ce-doped rare-earth aluminum perovskites are drawing a significant amount of attention as potential scintillating devices. However, the synthesis of complex perovskite systems leads to many challenges. Designing the A-site cations with an equiatomic ratio allows for the stabilization of a single-crystal phase driven by an entropic regime. This work describes the synthesis of a highly epitaxial thin film of configurationally disordered rare-earth aluminum perovskite oxide (La 0.2 Lu 0.2 Y 0.2 Gd 0.2 Ce 0.2 )AlO 3 and characterizes the structural and optical properties. The thin films exhibit three equivalent epitaxial domains having an orthorhombic structure resulting from monoclinic distortion of the perovskite cubic cell. An excitation of 286.5 nm from Gd 3+ and energy transfer to Ce 3+ with 405 nm emission are observed, which represents the potential for high-energy conversion. These experimental results also offer the pathway to tunable optical properties of high-entropy rare-earth epitaxial perovskite films for a range of applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural insights into photoactivation of plant Cryptochrome-2

Cryptochromes (CRYs) are evolutionarily conserved photoreceptors that mediate various light-induced responses in bacteria, plants, and animals. Plant cryptochromes govern a variety of critical growth and developmental processes including seed germination, flowering time and entrainment of the circadian clock. CRY’s photocycle involves reduction of their flavin adenine dinucleotide (FAD)-bound chromophore, which is completely oxidized in the dark and semi to fully reduced in the light signaling-active state. Despite the progress in characterizing cryptochromes, important aspects of their photochemistry, regulation, and light-induced structural changes remain to be addressed. In this study, we determine the crystal structure of the photosensory domain of Arabidopsis CRY2 in a tetrameric active state. Systematic structure-based analyses of photo-activated and inactive plant CRYs elucidate distinct structural elements and critical residues that dynamically partake in photo-induced oligomerization. Our study offers an updated model of CRYs photoactivation mechanism as well as the mode of its regulation by interacting proteins.

59 BASIC BIOLOGICAL SCIENCES↗