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Results for “Complexity bounding”

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 OSTI2024

Mechanisms in the Synthesis of S -Alcohols with 1,4-NADH Biomimetic Co-factor N-Benzyl-1,4-dihydronicotinamide using Horse Liver Alcohol Dehydrogenase: A Hybrid Computational Study

The enantioselective reduction of prochiral ketones catalyzed by horse liver alcohol dehydrogenase (HLADH), was investigated via a hybrid computational approach, for molecular reactions involved in chiral synthesis of S-alcohols, when the natural co-factor, 1,4-dihyronicotinamide adenine dinucleotide, 1,4-NADH, was replaced with biomimetic co-factor, N-benzyl-1,4-dihydronicotinamide, 1. We surmised that different hydride and proton transfer mechanisms were involved using co-factor, 1. An alternative mechanism, where the hydride transfer step occurred, via an η 1 -keto-S-η 2 -5,6-1,4-dihydronicotinamide-Zn(II) complex, was previously investigated with a model of the HLADH-Zn(II) catalytic site (J. Organometal. Chem. 2021, 943, 121810). Presently, we studied canonical and alternative mechanisms compared to models of the entire enzyme structure. We disproved the η 2 -Zn(II) complex, and discovered a canonical hydride transfer from biomimetic 1,4-NADH, 1, to the Zn(II) bound prochiral ketone substrate, followed by a new proton relay, consisting of a water chain connecting His51 to Ser48 that accomplished the S-alkoxy anion's protonation to yield the final S-alcohol product. The HLADH catalysis, with biomimetic co-factor, 1, that replaced the ribose group, the 5'-diphosphate groups, and the adenine nucleotide with a N-benzyl group, has provided a new paradigm for the design of other structures of 1,4-NADH biomimetic co-factors, including their economic value in biocatalysis reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Reduced order models for Lagrangian hydrodynamics

It is reported, as a mathematical model of high-speed flow and shock wave propagation in a complex multimaterial setting, Lagrangian hydrodynamics is characterized by moving meshes, advection-dominated solutions, and moving shock fronts with sharp gradients. These challenges hinder the existing projection-based model reduction schemes from being practical. We develop several variations of projection-based reduced order model techniques for Lagrangian hydrodynamics by introducing three different reduced bases for position, velocity, and energy fields. A time-windowing approach is also developed to address the challenge imposed by the advection-dominated solutions. Lagrangian hydrodynamics is formulated as a nonlinear problem, which requires a proper hyper-reduction technique. Therefore, we apply the over-sampling DEIM and SNS approaches to reduce the complexity due to the nonlinear terms. Finally, we also present both a posteriori and a priori error bounds associated with our reduced order model. We compare the performance of the spatial and time-windowing reduced order modeling approaches in terms of accuracy and speed-up with respect to the corresponding full order model for several numerical examples, namely Sedov blast, Gresho vortices, Taylor-Green vortices, and triple-point problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Mapping strain and structural heterogeneities around bubbles in amorphous ionically conductive Bi 2 O 3

While amorphous materials are often approximated to have a statistically homogeneous atomic structure, they frequently exhibit localized structural heterogeneity that challenges simplified models. This study uses 4D scanning transmission electron microscopy to investigate the strain and structural modifications around gas bubbles in amorphous Bi 2 O 3 induced by argon irradiation. We present a method for determining strain fields surrounding bubbles that can be used to measure the internal pressure of the gas. Compressive strain is observed around the cavities, with higher-order crystalline symmetries emerging near the cavity interfaces, suggesting paracrystalline ordering as a result of bubble coarsening. This ordering, along with a compressive strain gradient, indicates that gas bubbles induce significant localized changes in atomic packing. By analyzing strain fields with maximum compressive strains of 3%, we estimate a lower bound on the internal pressure of the bubbles at 2.5 GPa. These findings provide insight into the complex structural behavior of amorphous materials under stress, particularly in systems with gas inclusions, and offer new methods for probing the local atomic structure in disordered materials. Although considering structural heterogeneity in amorphous systems is non-trivial, these features have crucial impacts on material functionalities, such as mechanical strength, ionic conductivity, and electronic mobility.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Potent Inhibition of E. coli DXP Synthase by a gem -Diaryl Bisubstrate Analog

New antimicrobial strategies are needed to address pathogen resistance to currently used antibiotics. Bacterial central metabolism is a promising target space for the development of agents that selectively target bacterial pathogens. 1-Deoxy- D -xylulose 5-phosphate synthase (DXPS) converts pyruvate and d-glyceraldehyde 3-phosphate ( D -GAP) to DXP, which is required for synthesis of essential vitamins and isoprenoids in bacterial pathogens. Thus, DXPS is a promising antimicrobial target. Toward this goal, our lab has demonstrated selective inhibition of Escherichia coli DXPS by alkyl acetylphosphonate (alkylAP)-based bisubstrate analogs that exploit the requirement for ternary complex formation in the DXPS mechanism. Here, we present the first DXPS structure with a bisubstrate analog bound in the active site. Insights gained from this cocrystal structure guided structure–activity relationship studies of the bisubstrate scaffold. A low nanomolar inhibitor (compound 8) bearing a gem-dibenzyl glycine moiety conjugated to the acetylphosphonate pyruvate mimic via a triazole-based linker emerged from this study. Compound 8 was found to exhibit slow, tight-binding inhibition, with contacts to E. coli DXPS residues R99 and R478 demonstrated to be important for this behavior. This work has discovered the most potent DXPS inhibitor to date and highlights a new role of R99 that can be exploited in future inhibitor designs toward the development of a novel class of antimicrobial agents.

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

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗
NASA NTRS1987

Magnetic reorientation and spontaneous formation of tangential discontinuities in deformed magnetic fields

This paper provides an explicit illustration of the formation of tangential discontinuities (current sheets) in a force-free magnetic field whose footpoints have been subjected to bounded continuous displacement and shuffling so that the lines of force are wound about each other in complex but continuous patterns. The discontinuities appear spontaneously because of the reorientation of the field under the enhanced pressure where two regions of different field topology are pressed together by the general winding and wrapping.

Parker, E. N.↗
NASA NTRS1994

The Balmer-dominated northeast limb of the Cygnus loop supernova remnant

We present a comprehensive investigation of the Balmar-dominated northeast limb of the Cygnus Loop supernova remnant. Data presented include H alpha (O III), and X-ray images, UV and visible spectrophotometry, and high-resolution spectroscophy. The two relatively bright Balmer-dominated filaments visible on the POSS prints are seen to be part of a very smooth and regular complex of filaments. These filaments mark the current location of the blast wave and are seen to bound the sharply limb-brightened X-ray emission, including the previously reported X-ray, 'halo.' The (O III)/h beta ratio throughout the region is approximately 0.1, except for regions in which the shock is undergoing a transition from nonradiative to incomplete radiative to incomplete radiative conditions. At these locations (O III) emission from the cooling region is quite strong, while collisionally excited Balmer-line emission can be weak because of photoionization of the preshock medium by UV from the nascent cooling region. As a result (O III)/H beta is greater than 100 in some locations. The nonradiative/radiative transition is best studied along the length of the northwestern of the two brightest filaments, where the shock velocity and swept-up column go from approximately 180 km/s and 10(exp 17)/sq cm at one end to approximately 140 km/s and 8 x 10(exp 17)/cm at the other. There are also a number of locations of such incomplete radiative emission where the shock has recently encountered denser regions with characteristic sizes of approximately 10(exp 18) cm. There is a considerable amount of evidence that the shock has decelerated from approximately 400 km/s to less than 200 km/s in the last 1000 yr. We interpret this as the result of the blast wave hitting the wall of a cavity which surround the supernova precursor and succeed in matching a wide range of data with a reflected shock model in which the density ofthe cavity wall is approximately 1.2/cu cm and the density in the interior of the cavity is about 0.09/cu cm. This analysis supports previous suggestions that the Cygnus Loop was a cavity explosion. We opredict that the X-ray shell will continue to brighten for the next 1000 years or so, during which time the shock front will become radiative throughout the northeast region. The similarity of the time scales for post-shock cooling, shock deceleration, and the 1ressure evolution of the region violates assumptions of steady flow, and greatly complicated interpretation of shock specptra in the region. This may be a common and important effect in many supernova remnants. High-resolutoin spectroscopy of the H alpha line profile shows that the broad component is surprisingly narrow (approximately 130 km/s). Consistency between this line width and the shock velocity inferred from spectrophotometry requires either rapid postshock equilibration of T(sub i) and T(sub e), or that the shock front has declerated from 180 km/s to 150 km/s in the last approximately 200 yr. While we cannot unambiguously distinquish between these models, the required deceleration is consistent with extrapolation of the shock decleration rate inferred over the last 1000 years. The width of the narrow component of the h alpha line profile is approximately 3 km/s, which indicates that the preshock medium has been heated to approximately 25,000 K by a shock precursor. The most promising types of precursor are heating either by fast neutrals which overtake the shock or by cosmic rays. In the latter case the observed properties of the precursor constrain the cosmic-ray diffusion coefficient to be between about 10(exp 23) sq cm/s. The characteristics of the precursor seem to be about right to explain the presence of weak (S II) and (N II) emission previously reported by Fesen & Itoh (1985).

Hester, J. Jeff↗
NASA NTRS2002

A Dissimilarity Measure for Clustering High- and Infinite Dimensional Data that Satisfies the Triangle Inequality

The cosine or correlation measures of similarity used to cluster high dimensional data are interpreted as projections, and the orthogonal components are used to define a complementary dissimilarity measure to form a similarity-dissimilarity measure pair. Using a geometrical approach, a number of properties of this pair is established. This approach is also extended to general inner-product spaces of any dimension. These properties include the triangle inequality for the defined dissimilarity measure, error estimates for the triangle inequality and bounds on both measures that can be obtained with a few floating-point operations from previously computed values of the measures. The bounds and error estimates for the similarity and dissimilarity measures can be used to reduce the computational complexity of clustering algorithms and enhance their scalability, and the triangle inequality allows the design of clustering algorithms for high dimensional distributed data.

Socolovsky, Eduardo A.↗
NASA NTRS1996

Latency and activation in the control of TGF-beta

The biological activity of the transforming growth factor-beta's (TGF-beta)3 is tightly controlled by their persistence in the extracellular compartment as latent complexes. Each of the three mammalian isoform genes encodes a product that is cleaved intracellularly to form two polypeptides, each of which dimerizes. Mature TGF-beta, a 24 kD homodimer, is noncovalently associated with the 80 kD latency-associated peptide (LAP). LAP is a fundamental component of TGF-beta that is required for its efficient secretion, prevents it from binding to ubiquitous cell surface receptors, and maintains its availability in a large extracellular reservoir that is readily accessed by activation. This latent TGF-beta complex (LTGF-beta) is secreted by all cells and is abundant both in circulating forms and bound to the extracellular matrix. Activation describes the collective events leading to the release of TGF-beta. Despite the importance of TGF-beta regulation of growth and differentiation in physiological and malignant tissue processes, remarkably little is known about the mechanisms of activation in situ. Recent studies of irradiated mammary gland reveal certain features of TGF-beta 1 activation that may shed light on its regulation and potential roles in the normal and neoplastic mammary gland.

Non-NASA Center↗
DOE OSTI2024

Structural insights into the formation of repulsive netrin guidance complexes

Netrins dictate attractive and repulsive responses during axon growth and cell migration, where the presence of the receptor Uncoordinated-5 (UNC-5) on target cells results in repulsion. Here, we showed that UNC-5 is a heparin-binding protein, determined its structure bound to a heparin fragment, and could modulate UNC-5–heparin affinity using a directed evolution platform or structure-based rational design. We demonstrated that UNC-5 and UNC-6/netrin form a large, stable, and rigid complex in the presence of heparin, and heparin and UNC-5 exclude the attractive UNC-40/DCC receptor from binding to UNC-6/netrin to a large extent. Caenorhabditis elegans with a heparin-binding–deficient UNC-5 fail to establish proper gonad morphology due to abrogated cell migration, which relies on repulsive UNC-5 signaling in response to UNC-6. Combining UNC-5 mutations targeting heparin and UNC-6/netrin contacts results in complete cell migration and axon guidance defects. Our findings establish repulsive netrin responses to be mediated through a glycosaminoglycan-regulated macromolecular complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Regulation of Absorption and Emission in a Protein/Fluorophore Complex

Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore’s aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Active conformation of the p97-p47 unfoldase complex

The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a “hand-over-hand” mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Photoinduced charge transfer in the Zn-methanol cation studied with selected-ion photofragment imaging

The Zn + (methanol) ion molecule complex produced by laser vaporization is studied with photofragment imaging at 280 and 266 nm. Photodissociation produces the methanol cation CH 3 OH + via excitation of a charge-transfer excited state. Surprisingly, excitation of bound excited states produces the same fragment via a curve crossing prior to separation of products. Significant kinetic energy release is detected at both wavelengths with isotropic angular distributions. Similar experiments are conducted on the perdeuterated methanol complex. The Zn + cation is a minor product channel that also exhibits significant kinetic energy release. Finally, an energetic cycle using the ionization energies of zinc and methanol together with the kinetic energy release produces an upper limit on the Zn + -methanol bond energy of 33.7 ± 4.2 kcal/mol (1.46 ± 0.18 eV).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Lucina pectinata oxyhemoglobin (II-III) heterodimer pH susceptibility

Lucina pectinata live in high concentrations of hydrogen sulfide (H 2 S) and contains one hemoglobin, Hemoglobin I (HbI), transporting H 2 S and two hemoglobins, Hemoglobin II (HbII) and Hemoglobin (HbIII), transferring dioxygen to symbionts. HbII and HbIII contain B10 tyrosine (Tyr) and E7 glutamine (Gln) in the heme pocket generating an efficient hydrogen bonding network with the (HbII-HbIII)-O 2 species, leading to very low ligand dissociation rates. The results indicate that the oxy-hemeprotein is susceptible to pH from 4 to 9, at acidic conditions, and as a function of the potassium ferricyanide concentration, 100% of the met-aquo derivative is produced. Without a strong oxidant, pH 5 generates a small concentration of the met-aquo complex. The process is accelerated by the presence of salts, as indicated by the crystallization structures and UV–Vis spectra. The results suggest that acidic pH generates conformational changes associated with B10 and E7 heme pocket amino acids, weakening the (HbII-HbIII)-O 2 hydrogen bond network. The observation is supported by X-ray crystallography, since at pH 4 and 5, the heme-Fe tends to oxidize, while at pH 7, the oxy-heterodimer is present. Additionally, conformational changes are observed at higher pH by the presence of a 605 nm transition associated with the iron heme-Tyr interaction. Therefore, pH is one crucial factor regulating the (HbII-HbIII)-O 2 complex hydrogen-bonding network. Thus, it can be proposed that the hydrogen bonding adjustments between the heme bound O 2 and the Tyr and Gln amino acids contribute to oxygen dissociation from the (HbII-HbIII)-O 2 system.

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

Dynamic Features of Cu-Ceria Interface under CO 2 Hydrogenation to Methanol

It is generally accepted that metal–support interaction is very important for the hydrogenation of CO 2 to methanol, but little has been revealed about the feature of interfacial active sites under real reaction conditions since there are only limited techniques that can be applied under high-pressure conditions. Here, in this work, by combining multiple in situ and operando techniques on a model Cu/ceria catalyst, we have tracked Cu and ceria sites for methanol formation. Under the reaction condition, it is found that upon reaching the reaction temperature, oxidized Cu species in the as-synthesized catalyst immediately change into metallic Cu species. Following this, it is the gradual formation of methanol, the changing rate of which coincides with the formation of a unique Ce 3+ species. The combined experimental results and density functional theory (DFT) calculations have determined that the formed Ce 3+ sites driven by the reaction conditions are bound to hydrides, adsorbed carbonate species, and interfacial active Cu sites. The Cu-ceria interaction in this complex moiety is weak and can be easily disturbed with reaction environment variations, leading to dynamic changes at the interface upon the hydrogenation of active carbonate intermediates, which are precursors for the formation of methanol. The formation of this unique Cu–Ce 3+ interface and its dynamicity lead to an increase of methanol selectivity from less than 20% to 60%. These results suggest that reactant-derived species (H – and carbonate in this work) can be essential components of the active center with the functions of manipulating the metal−oxide interaction and directing reaction pathways.

CO2 hydrogenation to methanol↗
DOE OSTI2025

Metal–Metal Bonding Influences Hydride Reactivity in [Sn–Rh] 3+ and [Sn–Ni] 2+ Bimetallics

Heavier group 14 metal hydrides serve as key intermediates in catalytic transformations, such as hydroboration. Regenerating such intermediates via a clean hydride source like dihydrogen could provide catalytic processes with a more economical alternative to, e.g., silanes and hydridoborane reagents. Herein, we report our efforts toward this goal using a [Sn–Rh] 3+ bimetallic system with the formal Rh I center acting as a potential dihydrogen activator. Targeting the introduction of a hydride ligand to the bimetallic core, our reactivity studies have revealed a preference for the hydride ligand to be bound to the Rh center, instead of the Sn center. Finally, examination of the electronic structures of these complexes via theoretical and experimental methods has revealed the electron acceptor nature of the Rh center within the bimetallic core and offers an explanation for the localization of the hydride between metal centers.

anions↗
DOE OSTI2020

Quantum Hamiltonian for the surface charge density on a ring torus and radiative decay of plasmons

Photon scattering and the ensuing excitation of surface plasmons in single rings, single composite rings, and many-ring systems was recently shown to provide dispersion and field distributions [K. V. Garapati et al., J. Phys. Commun. 2, 015031 (2018)] of potential for specific applications in particle and molecular trapping [R. Alaee et al., Appl. Phys. Lett. 109, 141102 (2016); M. Salhi et al., Phys. Rev. A 92, 033416 (2015)], in addition to metamaterials and sensing. Furthermore, following photon or electron interactions with metallic nanorings, both radiative and nonradiative decay channels are important in the consideration of the nanoparticle as a photon or phonon source, and in related applications. In this work, we quantize the electronic normal modes of the ring torus and obtain the radiative decay of plasmons. Due to a geometry-related complexity, we employ a perturbation approach to obtain analytical expressions for the radiative decay channel for a vacuum bounded single solid nanoring. In quantizing the fields, the frequency spectrum of the charge density normal modes of the nanoring is obtained and shown to agree with the exact quasistatic plasmon dispersion relations. Higher-order corrections beyond the presented zero- and first-order calculations may be obtained following the presented results. The results are of potential interest in quantum sensing such as entangling photons and plasmons, or plasmons and trapped molecules.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

LANL Phase 3 Container Loading in Support of the Fire-Induced Pressure Response and Failure Characterization of PCV/SCV/3013 Containers

The PCV/SCV/3013 Thermal Test Program is intended to determine the pressure response of packaged 3013 containers when exposed to a facility fire in the K-Area Complex (KAC) at the Savannah River Site. The fire tests support the KAC safety basis and must be bounding of the maximum pressure that would result from any 3013 container exposed to a KAC facility fire. The testing program has the following objectives: “To increase understanding of the pressure and temperature conditions at which failure occurs; To determine the allowable moisture for which failure will not occur under specified fire conditions, and; To increase understanding regarding the effects of salts on the pressurization, corrosion, and potential failure of the container.”

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗