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At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Optimal Transfer Operators in Algebraic Two-Level Methods for Nonsymmetric and Indefinite Problems

Consider an algebraic two-level method applied to the 𝑛-dimensional linear system 𝐴⁢𝒙 = 𝒃 using fine-space preconditioner (i.e., “relaxation” or “smoother”) 𝑀, with 𝑀 ≈ 𝐴, restriction and interpolation 𝑅 and 𝑃, and algebraic coarse-space operator 𝐴 𝑐 : = 𝑅 ∗ ⁢𝐴⁢𝑃. Then, what are the best possible transfer operators 𝑅 and 𝑃 of a given dimension 𝑛 𝑐 < 𝑛? Brannick et al. [12] showed that when 𝐴 and 𝑀 are Hermitian positive definite (HPD), the optimal interpolation is such that its range contains the 𝑛 𝑐 smallest generalized eigenvectors of the matrix pencil (𝐴, 𝑀). Recently, in Ali et al. [5] we generalized this framework to the non-HPD setting, by considering both right (interpolation) and left (restriction) generalized eigenvectors of (𝐴, 𝑀) and defining corresponding nonsymmetric transfer operators {𝑅#, 𝑃#}. Tight convergence bounds for {𝑅#, 𝑃#} are derived in spectral radius, as well as a proof of pseudo-optimality. Note, {𝑅#, 𝑃#} are typically complex valued, which is not practical for real-valued problems. Here, in this work, we build on [5], first characterizing all inner products in which the coarse-space correction defined by {𝑅#, 𝑃#} is orthogonal. We then develop tight two-level convergence bounds in these norms, and prove that the underlying transfer operators {𝑅#, 𝑃#} are genuinely optimal. As a special case, our theory both recovers and extends the HPD results from [12]. Finally, we show how to construct optimal, real-valued transfer operators in the case of that 𝐴 and 𝑀 are real valued, but are not HPD. Numerical examples arising from a discretized advection-reaction equation, wave-equation, and Stokes equations are used to verify and illustrate the theory.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

INTERDUNE DEPOSITS AND STRATIGRAPHIC FRAMEWORK OF THE NAVAJO SANDSTONE IN THE LAKE POWELL AREA, UTAH, USA

The Western Interior of the USA was dominated by desert environments for much of the Jurassic. Of these desert environments, the most extensive by far was the Navajo Sandstone erg, which, in conjunction with its correlative Nugget and Aztec Sandstones, is thought to have covered well over 500,000 km2, and is one of the largest ergs preserved in the rock record. The Navajo Sandstone is also one of a few geologic units which show promise as a potential CO2 sequestration reservoir in Utah. It outcrops along the eastern and southern margin of the state, and subcrops throughout most of the central area. The Navajo Sandstone consists of stacked eolian deposits, composed of well sorted, clean sandstone, deposited in commonly tabular, high angle cross bedded paleodunes, which are on average 15 m thick. Interspersed between these paleodunes are interdune deposits. Interdune deposits consist of sandy to calcareous, predominantly planar bedded, lensoid units, ranging from <1 m up to 7 m thick. In some cases, these interdune deposits occur along more extensive stratigraphic bounding surfaces. Dating within the Navajo Sandstone has historically been very difficult, as a result of its predominantly clean, aeolian sandstone composition. In addition, complexity of internal stratigraphic surfaces coupled with a low structural dip and generally flat topography has resulted in a poor understanding of the internal stratigraphy of the Navajo Sandstone. Exceptional three-dimensional exposures of the Navajo Sandstone in the upper portions of Lake Powell permit us to relate interdune carbonates to a hierarchical bounding surfaces model. Here we use this combined approach to interpret the internal stratigraphy of the Navajo Sandstone in this region. This work forms part of a larger study of the Navajo Sandstone across Utah and its potential as a CO2 reservoir, by developing a more comprehensive stratigraphic framework, and increasing understanding of stratigraphic complexity within one of the most significant eolian systems in the world.

Mahon, Elizabeth↗
DOE OSTI2020

Direct functionalization of C-H bonds by electrophilic anions

Bond formation between two of the most inert molecules, alkanes and [B12X12]2- (X = Cl, Br), is performed in a two step process. Fragmentation of [B12X12]2- in the gas phase generates highly reactive [B12X11]- ions which spontaneously react with alkanes. The reaction mechanism was investigated using tandem mass spectrometry and gas-phase vibrational spectroscopy combined with electronic structure calculations. This effort revealed the unprecedented and counterintuitive electrophilic substitution of a proton in an alkane by a negatively charged ion resulting in a B-C bond formation. The product is a dianionic [B12X11CnH2n+1]2- species, in which H+ is electrostatically bound to the dianion. High flux ion soft-landing was performed to co-deposit [B12X11]- and complex organic molecules (phthalates) in thin layers on surfaces. Molecular structure analysis of the product films revealed that C-H functionalization by [B12X11]- occured in the presence of other more reactive functional groups. This observation demonstrates the utility of highly reactive fragment ions for defined bond formation processes and may pave the way to the use of gas phase ion chemistry for chemical synthesis in the condensed phase.

Warneke, Jonas↗
DOE OSTI2019

Unexpected Roles of Triethanolamine in the Photochemical Reduction of CO 2 to Formate by Ruthenium Complexes

We show a series of 4,4'-dimethyl-2,2'-bipyridyl ruthenium complexes with carbonyl ligands were prepared and studied using a combination of electrochemical and spectroscopic methods with infrared detection to provide structural information on reaction intermediates in the photochemical reduction of CO 2 to formate in acetonitrile (CH 3 CN). An unsaturated 5-coordinate intermediate was characterized, and the hydride-transfer step to CO 2 from a singly reduced metal-hydride complex was observed with kinetic resolution. While triethanolamine (TEOA) was expected to act as a proton acceptor to ensure the sacrificial behavior of 1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]imidazole as an electron donor, time-resolved infrared measurements revealed that about 90% of the photogenerated one-electron reduced complexes undergo unproductive back electron transfer. Furthermore, TEOA showed the ability to capture CO 2 from CH 3 CN solutions to form a zwitterionic alkylcarbonate adduct and was actively engaged in key catalytic steps such as metal-hydride formation, hydride transfer to CO 2 to form the bound formate intermediate, and dissociation of formate ion product. Collectively, the data provide an overview of the transient intermediates of Ru(II) carbonyl complexes and emphasize the importance of considering the participation of TEOA when investigating and proposing catalytic pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structure, substrate binding and activity of a unique AAA+ protein: the BrxL phage restriction factor

Abstract Bacteriophage exclusion (‘BREX’) systems are multi-protein complexes encoded by a variety of bacteria and archaea that restrict phage by an unknown mechanism. One BREX factor, termed BrxL, has been noted to display sequence similarity to various AAA+ protein factors including Lon protease. In this study we describe multiple CryoEM structures of BrxL that demonstrate it to be a chambered, ATP-dependent DNA binding protein. The largest BrxL assemblage corresponds to a dimer of heptamers in the absence of bound DNA, versus a dimer of hexamers when DNA is bound in its central pore. The protein displays DNA-dependent ATPase activity, and ATP binding promotes assembly of the complex on DNA. Point mutations within several regions of the protein-DNA complex alter one or more in vitro behaviors and activities, including ATPase activity and ATP-dependent association with DNA. However, only the disruption of the ATPase active site fully eliminates phage restriction, indicating that other mutations can still complement BrxL function within the context of an otherwise intact BREX system. BrxL displays significant structural homology to MCM subunits (the replicative helicase in archaea and eukaryotes), implying that it and other BREX factors may collaborate to disrupt initiation of phage DNA replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The ghost in the radiation: robust encodings of the black hole interior

We reconsider the black hole firewall puzzle, emphasizing that quantum error-correction, computational complexity, and pseudorandomness are crucial concepts for understanding the black hole interior. We assume that the Hawking radiation emitted by an old black hole is pseudorandom, meaning that it cannot be distinguished from a perfectly thermal state by any efficient quantum computation acting on the radiation alone. We then infer the existence of a subspace of the radiation system which we interpret as an encoding of the black hole interior. This encoded interior is entangled with the late outgoing Hawking quanta emitted by the old black hole, and is inaccessible to computationally bounded observers who are outside the black hole. Specifically, efficient operations acting on the radiation, those with quantum computational complexity polynomial in the entropy of the remaining black hole, commute with a complete set of logical operators acting on the encoded interior, up to corrections which are exponentially small in the entropy. Thus, under our pseudorandomness assumption, the black hole interior is well protected from exterior observers as long as the remaining black hole is macroscopic. On the other hand, if the radiation is not pseudorandom, an exterior observer may be able to create a firewall by applying a polynomial-time quantum computation to the radiation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Complex Functional Materials

The Complex Functional Materials (CFM) area of leadership focuses on the identification and development of materials comprised of multiple components or building blocks that are integrated or chemically bound together to achieve a desired function or response. Soft materials, such as polymers, as well as structural properties at the meso- and micro-scale that control materials function are particularly emphasized in this leadership area. Further, complex functional materials are generally developed to satisfy multiple materials design criteria all of which are essential to the overall application. CFM supports applications that are aligned with all three Los Alamos National Laboratory mission areas. These mission areas are: materials for nuclear deterrence, materials for energy security, and materials for global security

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure and bonding of a radium coordination compound in the solid state

The structure and bonding of radium (Ra) is poorly understood because of challenges arising from its scarcity and radioactivity. Here we report the synthesis of a molecular Ra 2+ complex using 226 Ra and the organic ligand dibenzo-30-crown-10, and its characterization in the solid state by single-crystal X-ray diffraction. The crystal structure of the Ra 2+ complex shows an 11-coordinate arrangement comprising the 10 donor O atoms of dibenzo-30-crown-10 and that of a bound water molecule. Under identical crystallization conditions, barium (Ba 2+ ) yielded a 10-coordinate ‘Pac-Man’-shaped structure lacking water. Furthermore, the bond distance between the Ra centre and the O atom of the coordinated water is substantially longer than would be predicted from the ionic radius of Ra 2+ and by analogy with Ba 2+ , supporting greater water lability in Ra 2+ complexes than in their Ba 2+ counterparts. In conclusion, barium often serves as a non-radioactive surrogate for radium, but our findings show that Ra 2+ chemistry cannot always be predicted using Ba 2+ .

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

Spread Spectrum Time Domain Reflectometry and Steepest Descent Inversion to Measure Complex Impedance

In this paper, we present a method for estimating complex impedances using reflectometry and a modified steepest descent inversion algorithm. We simulate spread spectrum time domain reflectometry (SSTDR), which can measure complex impedances on energized systems for an experimental setup with resistive and capacitive loads. A parametric function, which includes both a misfit function and stabilizer function, is created. The misfit function is a least squares estimate of how close the model data matches observed data. The stabilizer function prevents the steepest descent algorithm from becoming unstable and diverging. Steepest descent iteratively identifies the model parameters that minimize the parametric function. We validate the algorithm by correctly identifying the model parameters (capacitance and resistance) associated with simulated SSTDR data, with added 3 dB white Gaussian noise. With the stabilizer function, the steepest descent algorithm estimates of the model parameters are bounded within a specified range. Furthermore, the errors for capacitance (220pF to 820pF) and resistance (50 Ω to 270 Ω) are < 10%, corresponding to a complex impedance magnitude |R +1/jωC| of 53 Ω to 510 Ω.

14 SOLAR ENERGY↗
DOE OSTI2024

Uranyl Naphthylsalophen and Pyrasal Complexes: Oxo Ligands Acting as Hydrogen Bond Acceptors in the Solid State

Uranium is most stable when it is exposed to oxygen or water in its +6 oxidation state as the uranyl (UO 2 2+ ) ion. This ion is subsequently particularly stable and very resistant to functionalization due to the inverse trans effect. Uranyl oxo ligands are typically not considered good hydrogen bond acceptors due to their weak Lewis basicity; however, the ligands bound in the equatorial plane greatly affect the strength of the oxo ligands’ hydrogen bonding. Here, in this work, new naphthylsalophen and pyrasal complexes of uranium were synthesized and crystallized for characterization in the solid state. The bond lengths and angles of the uranyl ion and the ligand conformation are compared. In the solid state, one of the pyrasal complexes showed a hydrogen bond directly from a water molecule to the uranyl oxo ligand, which resulted in an asymmetric lengthening of the U–O yl bonds from 1.789 to 1.862 Å and 1.784 to 1.844 Å.

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

Microscopic Theory of Nuclear Fission

Nuclear fission represents the ultimate test for microscopic theories of nuclear structure and reactions. Fission is a large-amplitude, time-dependent phenomenon taking place in a self-bound, strongly interacting many-body system. It should, at least in principle, emerge from the complex interactions of nucleons within the nucleus. The goal of microscopic theories is to build a consistent and predictive theory of nuclear fission by using as only ingredients protons and neutrons, nuclear forces, and quantum many-body methods. Thanks to a constant increase in computing power, such a goal has never seemed more within reach. This chapter gives an overview both of the set of techniques used in microscopic theories to describe the fission process and of some recent successes achieved by this class of methods.

Nuclear physics and radiation physics↗
DOE OSTI2021

How structural differences influence cross-model consistency: An electric sector case study

Multiple models are often employed to describe a range of possible outcomes for one or more scenarios, yielding insights into causal relationships and their uncertainties. Electric sector capacity expansion scenarios are a common topic of such efforts due to the economic influence of the electric sector, but model results typically span a broad solution space despite efforts to harmonize input assumptions, making decision implications difficult to discern. This study investigates the relationship between input harmonization and cross-model scenario consistency under disparate electric sector scenarios. We compare cross-model consistency between two state-of-the-art electric sector capacity expansion models (GCAM-USA and ReEDS) for six electric sector scenarios comprising alternate assumptions about fossil fuel resource availability, technology innovation, and long-term economy-wide transitions under four harmonization configurations varying model representations of electricity demand, fuel prices, renewable resources, and capacity retirements. These comparisons reveal that cross-model consistency can vary across scenarios under a given harmonization configuration, suggesting that harmonization efforts must often be scenario-specific if comparable cross-model consistency is desired. Model structural differences can hinder consistency, and the impact of these differences can depend on the scenario. Ultimately, thorough harmonization can reveal insights into cross-model consistency, which can be used to tighten uncertainty bounds and improve the decision-making implications of multi-model activities.

Cohen, Stuart↗
DOE OSTI2021

Mapping glyceride species in biodiesel by high-temperature gas chromatography combined with chemical ionization mass spectrometry.

Accurate and comprehensive identification of residual glycerides in biodiesel is an important part of the fuel characterization, due to the impact of glycerides on the fuel physicochemical properties. However, analysis of bound glycerol in biodiesel samples faces challenges due to lack of readily available standards of structurally complex glyceride species in non-traditional biodiesel feedstocks, and a risk of misannotation in the presence of impurities in gas chromatographic separations. Here we evaluate methane and isobutane chemical ionization – single quadrupole mass spectrometry combined with high temperature gas chromatography separations for mapping monoacylglycerols, diacylglycerols and triacylglycerols in biodiesel. Unlike the electron impact ionization which produces mostly in-source fragments, isobutane chemical ionization spectra of tetramethylsilyl (TMS) derivatized monoacylglycerols and diacylglycerols are dominated by molecular ions and M-SiO(CH3)3+ ions, which provide important diagnostic information. We demonstrate the utility of isobutane chemical ionization in identifying structurally complex glycerolipid standards as well as species in biodiesel samples from different plant and animal feedstocks.

biodiesel, chemcial ionization mass spectrometry↗
DOE OSTI2022

Iodination of PEGylated Polymers Counteracts the Inhibition of Fibrinogen Adsorption by PEG

Poly(ethylene glycol), PEG, known to inhibit protein adsorption, is widely used on the surfaces of biomedical devices when biofilm formation is undesirable. Poly(desaminotyrosyl-tyrosine ethyl ester carbonate), PDTEC, PC for short, has been a promising coating polymer for insertion devices, and it has been anticipated that PEG plays a similar role if it is copolymerized with PC. Earlier studies show that no fibrinogen (Fg) is adsorbed onto PC polymers with PEG beyond the threshold weight percentage. This is attributed to the phase separation of PEG. Further, iodination of the PC units in the PC polymer, (I 2 PC), has been found to counteract this Fg-repulsive effect by PEG. Here, in this study, we employ surface-sensitive X-ray techniques to demonstrate the surface affinity of Fg toward the air–water interface, particularly in the presence of self-assembled PC-based film, in which its constituent polymer units are assumed to be much more mobile as a free-standing film. Fg is found to form a Gibbs monolayer with its long axis parallel to the aqueous surface, thus maximizing its interactions with hydrophobic interfaces. It influences the amount of insoluble, surface-bound I 2 PC likely due to the desorption of the formed Fg–I 2 PC complex and/or the penetration of Fg onto the I 2 PC film. The results show that the phase behavior at the liquid–polymer interface shall be taken into account for the surface behavior of bulk polymers surrounded by tissue. The ability of PEG units rearranging into a protein-blocking layer, rather than its mere presence in the polymer, is the key to antifouling characteristics desired for polymeric coating on insertion devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Biosynthesis of Minimal C-Phycocyanin Chromophore Assemblies in E. coli Provides a Platform to Dissect Protein-Mediated Tuning of Exciton Transfer

Cyanobacteria are arguably among the most evolutionarily successful organisms on Earth, inhabiting a wide range of ocean, freshwater, soil, and even desert environments on every continent. The cyanobacterial phycobilisome consists of stacks of disk-like light-collecting moieties, allophycocyanin (APC) and phycocyanin (CPC), with covalently bound phycocyanobilin (PCB) pigments. The ways in which the energies of the specific chromophores in these complexes are tuned by the protein to achieve its highly efficient and directional energy transfer are not fully understood, as complex combinations of decay pathways are occurring simultaneously and competitively through this elaborate light-harvesting system. This makes it difficult to extract information about isolated protein-pigment interactions. We provide herein a description of a useful new experimental platform in which we have recombinantly expressed a fully functioning CPC complex and selectively created minimal chromophore sets to study their individual contributions to the overall CPC spectra. Structural and computational analysis of this protein system have provided a greater understanding of how the protein environment serves to alter the photophysics of each of these chromophores. Introduction of a quencher into various positions within CPC confirmed the ability of the protein environment to tune the directionality of energy transport in this assembly. Further mutational analysis suggested the roles of key amino acids surrounding the chromophores, showcasing the utility of heterologous expression techniques for understanding the effects of structure on EET mechanisms in the phycobilisome.

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

Crystal structure of active CDK4-cyclin D and mechanistic basis for abemaciclib efficacy

Despite the biological and therapeutic relevance of CDK4/6 for the treatment of HR+, HER2- advanced breast cancer, the detailed mode of action of CDK4/6 inhibitors is not completely understood. Of particular interest, phosphorylation of CDK4 at T172 (pT172) is critical for generating the active conformation, yet no such crystal structure has been reported to date. We describe here the x-ray structure of active CDK4-cyclin D3 bound to the CDK4/6 inhibitor abemaciclib and discuss the key aspects of the catalytically-competent complex. Furthermore, the effect of CDK4/6 inhibitors on CDK4 T172 phosphorylation has not been explored, despite its role as a potential biomarker of CDK4/6 inhibitor response. We show mechanistically that CDK4/6i stabilize primed (pT172) CDK4-cyclin D complex and selectively displace p21 in responsive tumor cells. Stabilization of active CDK4-cyclin D1 complex can lead to pathway reactivation following alternate dosing regimen. Consequently, sustained binding of abemaciclib to CDK4 leads to potent cell cycle inhibition in breast cancer cell lines and prevents rebound activation of downstream signaling. Overall, our study provides key insights demonstrating that prolonged treatment with CDK4/6 inhibitors and composition of the CDK4/6-cyclin D complex are both critical determinants of abemaciclib efficacy, with implications for this class of anticancer therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA

Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA, among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively ‘featureless’ surface dominated by the peptide’s backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA-mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA-derived public NeoAg.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantifying unitary flow efficiency and entanglement for many-body localization

Holography tells us that there should be a mapping between a boundary Hamiltonian and bulk degrees of freedom. We probe the bulk geometry of the Wegner Wilson Flow (WWF) in the context of many-body localization by addressing efficiency and bulk entanglement growth measures through approximating upper bounds on the boundary entanglement entropy. Here, we connect these upper bounds to the Fubini-Study metric and clarify how a central quantity, the information fluctuation complexity, distinguishes bulk unitary rotation from entanglement production. We also give a short new proof of the small incremental entangling theorem in the absence of ancillas, achieving a dimension independent, universal factor of c = 2.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗