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DOE OSTI2014

Crystal structure of a DNA/Ba 2+ G-quadruplex containing a water-mediated C-tetrad

We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA CNV KGCGTGG) ( CNV K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba 2+ . The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba 2+ ions to occupy adjacent steps in the central ion channel. One ordered Mg 2+ facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the CNV K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson–Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA

The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal Lamodule binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear.We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study thus confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine

The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome—an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'- 0 CG- 1 CA- 2 CG- 3 TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2 CG has very little effect on TCF4 binding, E-box 1 CA modification has a negative influence on binding, while modification of the flanking 0 CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2011

Quantum tagging for tags containing secret classical data

Various authors have considered schemes for quantum tagging, that is, authenticating the classical location of a classical tagging device by sending and receiving quantum signals from suitably located distant sites, in an environment controlled by an adversary whose quantum information processing and transmitting power is potentially unbounded. All of the schemes proposed elsewhere in the literature assume that the adversary is able to inspect the interior of the tagging device. All of these schemes have been shown to be breakable if the adversary has unbounded predistributed entanglement. We consider here the case in which the tagging device contains a finite key string shared with distant sites but kept secret from the adversary, and show this allows the location of the tagging device to be authenticated securely and indefinitely. Our protocol relies on quantum key distribution between the tagging device and at least one distant site, and demonstrates a new practical application of quantum key distribution. It also illustrates that the attainable security in position-based cryptography can depend crucially on apparently subtle details in the security scenario considered.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Dirac's equation and its implications for density functional theory based calculations of materials containing heavy elements

Electronic structure calculations based on density functional theory (DFT) give quantitatively accurate predictions of properties of most materials containing light elements. For heavy materials, and in particular for f -electron systems, DFT based methods can fail both qualitatively and quantitatively for two distinct reasons: their failure to describe confinement effects arising from localized f -electron behavior and their incomplete or approximate treatment of relativity. In addition, different methods for incorporating relativistic effects, which give identical results in most light materials, can give different predictions in heavy elements. In order to develop a quantitative capability for calculating the properties of these materials, it is essential to separate the predictions of the underlying equations from the uncertainty introduced in approximations used in computation. Working toward that goal, here we have developed a code, called dirac-fp , which is based directly on solving the Dirac-Kohn-Sham equations and uses the full-potential linear muffin-tin orbital (FP-LMTO) approach to electronic structure. In order to assess the performance of dirac-fp , we perform calculations on three different face-centered cubic materials using different approximate treatments of relativity: the scalar relativistic (SR) approach commonly used in most solid-state DFT codes, the scalar relativistic plus spin-orbit coupling corrections (SR+SO) approach which includes spin-orbit coupling self-consistently using the SR states inside the muffin tins, and the Dirac-Kohn-Sham (Dirac) approach implemented in dirac-fp . Performing calculations on thorium, in which relativistic effects should be strong, aluminum, in which relativistic effects should be negligible, and gold, in which relativistic effects play an intermediate role, we find that the Dirac approach is able to provide theoretically consistent results in the electronic structure and ground-state properties across all three materials.

3-dimensional systems↗

DOE OSTI2016

Number of holes contained within the Fermi surface volume in underdoped high-temperature superconductors

Here, we provide a potential solution to the longstanding problem relating Fermi surface reconstruction to the number of holes contained within the Fermi surface volume in underdoped high T c superconductors. On considering uniaxial and biaxial charge-density wave order, we show that there exists a relationship between the ordering wave vector, the hole doping, and the cross-sectional area of the reconstructed Fermi surface whose precise form depends on the volume of the starting Fermi surface. We consider a “large” starting Fermi surface comprising 1+p hole carriers, as predicted by band structure calculations, and a “small” starting Fermi surface comprising p hole carriers, as proposed in models in which the Coulomb repulsion remains the dominant energy. Using the reconstructed Fermi surface cross-sectional area obtained in quantum oscillation experiments in YBa 2 Cu 3 O 6+x and HgBa 2 CuO 4+x and the established methods for estimating the chemical hole doping, we find the ordering vectors obtained from x-ray scattering measurements to show a close correspondence with those expected for the small starting Fermi surface. We therefore show the quantum oscillation frequency and charge-density wave vectors provide accurate estimates for the number of holes contributing to the Fermi surface volume in the pseudogap regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Nonlinear Sigma model amplitudes to all loop orders are contained in the Tr ( Φ 3 ) theory

Scattering amplitudes for the simplest theory of colored scalar particles—the Tr ( Φ 3 ) theory—have recently been the subject of active investigations. In this work we describe an unanticipated wider implication of this work: the Tr ( Φ 3 ) theory secretly contains nonlinear sigma model (NLSM) amplitudes to all loop orders. The NLSM amplitudes are obtained from Tr ( Φ 3 ) amplitudes by a unique shift of kinematic variables. We show that this shifted kinematics produces amplitudes for a cubic theory with a linear term in the potential, with extrema spontaneously breaking U ( N ) → U ( N − k ) × U ( k ) . The Goldstone amplitudes for this theory coincide with those of pions in the U ( N ) × U ( N ) → U ( N ) chiral Lagrangian to all orders in the planar limit. We also give a purely on-shell understanding of this correspondence, showing that integrands defined by the kinematic shifts have the correct residues on poles and appropriately produce the Adler zero. Finally, we discuss how similar kinematic shifts produce certain infinite classes of mixed amplitudes of pions and Tr ( Φ 3 ) scalars, most of which are not interpretable from the Lagrangian description. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2011

DNA compaction by azobenzene-containing surfactant

We report on the interaction of cationic azobenzene-containing surfactant with DNA investigated by absorption and fluorescence spectroscopy, dynamic light scattering, and atomic force microscopy. The properties of the surfactant can be controlled with light by reversible switching of the azobenzene unit, incorporated into the surfactant tail, between a hydrophobic trans (visible irradiation) and a hydrophilic cis (UV irradiation) configuration. The influence of the trans-cis isomerization of the azobenzene on the compaction process of DNA molecules and the role of both isomers in the formation and colloidal stability of DNA-surfactant complexes is discussed. It is shown that the trans isomer plays a major role in the DNA compaction process. The influence of the cis isomer on the DNA coil configuration is rather small. The construction of a phase diagram of the DNA concentration versus surfactant/DNA charge ratio allows distancing between three major phases: colloidally stable and unstable compacted globules, and extended coil conformation. There is a critical concentration of DNA above which the compacted globules can be hindered from aggregation and precipitation by adding an appropriate amount of the surfactant in the trans configuration. This is because of the compensation of hydrophobicity of the globules with an increasing amount of the surfactant. Below the critical DNA concentration, the compacted globules are colloidally stable and can be reversibly transferred with light to an extended coil state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Down-regulation of kelch domain-containing F-box protein in Arabidopsis enhances the production of (poly)phenols and tolerance to ultraviolet radiation

Phenylpropanoid biosynthesis in plants engenders myriad phenolics with diverse biological functions. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the pathway, directing primary metabolic flux into a phenylpropanoid branch. Previously, we demonstrated that the Arabidopsis Kelch-domain containing F-box proteins, AtKFB01, -20, and -50, function as the negative regulators controlling phenylpropanoid biosynthesis via mediating PAL’s ubiquitination and subsequent degradation. Here, we reveal that Arabidopsis KFB39, a close homolog of AtKFB50, also interacts physically with PAL isozymes and modulates PALs' stability and activity. Disturbing the expression of KFB39 reciprocally affects the accumulation/deposition of a set of phenylpropanoid end products, suggesting that KFB39 is an additional post-translational regulator responsible for the turnover of PAL and negatively controlling phenylpropanoid biosynthesis. Furthermore, we discover that exposure of Arabidopsis to UV-B radiation suppresses the expression of all four KFB genes while inducing the transcription of PAL isogenes; these data suggest that Arabidopsis consolidates both transcriptional and post-translational regulation mechanisms to maximize its responses to UV stress. Simultaneous down-regulation of all four identified KFBs significantly enhances the production of (poly)phenols and the plant’s tolerance to UV irradiation. This study offers a biotechnological approach for engineering the production of useful phenolic chemicals and for increasing a plant’s resistance to environmental stress.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

HLB1 Is a Tetratricopeptide Repeat Domain-Containing Protein That Operates at the Intersection of the Exocytic and Endocytic Pathways at the TGN/EE in Arabidopsis

The endomembrane system plays essential roles in plant development, but the proteome responsible for its function and organization remains largely uncharacterized in plants. For this study, we identified and characterized the HYPERSENSITIVE TO LATRUNCULIN B1 (HLB1) protein isolated through a forward-genetic screen in Arabidopsis thaliana for mutants with heightened sensitivity to actin-disrupting drugs. HLB1 is a plant-specific tetratricopeptide repeat domain-containing protein of unknown function encoded by a single Arabidopsis gene. HLB1 associated with the trans-Golgi network (TGN)/early endosome (EE) and tracked along filamentous actin, indicating that it could link post-Golgi traffic with the actin cytoskeleton in plants. HLB1 was found to interact with the ADP-ribosylation-factor guanine nucleotide exchange factor, MIN7/BEN1 (HOPM INTERACTOR7/BREFELDIN A-VISUALIZED ENDOCYTIC TRAFFICKING DEFECTIVE1) by coimmunoprecipitation. The min7/ben1 mutant phenocopied the mild root developmental defects and latrunculin B hypersensitivity of hlb1, and analyses of a hlb1/ min7/ben1 double mutant showed that hlb1 and min7/ben1 operate in common genetic pathways. Based on these data, we propose that HLB1 together with MIN7/BEN1 form a complex with actin to modulate the function of the TGN/EE at the intersection of the exocytic and endocytic pathways in plants.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2019

Extraction of Plutonium-Containing Microcrystals from Hanford Soil using a Focused Ion Beam for Single-Crystal X-ray Diffraction Analysis

Herein we report the successful use of a focused ion beam/scanning electron microscope (FIB/SEM) to prepare microsamples of radioactive single-crystals for X-ray diffraction analysis. This technique was used to extract and analyze crystalline Pu-containing particles as small as 28 µm3 from Hanford soil taken from the 216-Z-9 waste crib which were then crystallographically characterized using single-crystal X-ray diffraction (SCXRD) to confirm the cubic structure of PuO2. As a systematic proof of concept, the technique was first tested using UO2 crystals milled into cubic shapes with approximate volumes 4620, 1331, 125, 8 and 1 µm3, respectively, in order to empirically determine the crystal size limits for characterization by a laboratory-based diffractometer with a sealed tube Mo or Ag anode X-ray source and a charge-coupled device (CCD) detector.

microcrystals, Plutomium, focused ion beam/scannin↗

DOE OSTI2021

Chemical state mapping of simulant Chernobyl lava-like fuel containing material using micro-focused synchrotron X-ray spectroscopy

Uranium speciation and redox behaviour is of critical importance in the nuclear fuel cycle. X-ray absorption near-edge spectroscopy (XANES) is commonly used to probe the oxidation state and speciation of uranium, and other elements, at the macroscopic and microscopic scale, within nuclear materials. Two-dimensional (2D) speciation maps, derived from microfocus X-ray fluorescence and XANES data, provide essential information on the spatial variation and gradients of the oxidation state of redox active elements such as uranium. In the present work, we elaborate and evaluate approaches to the construction of 2D speciation maps, in an effort to maximize sensitivity to the U oxidation state at the U L 3 -edge, applied to a suite of synthetic Chernobyl lava specimens. Our analysis shows that calibration of speciation maps can be improved by determination of the normalized X-ray absorption at excitation energies selected to maximize oxidation state contrast. The maps are calibrated to the normalized absorption of U L 3 XANES spectra of relevant reference compounds, modelled using a combination of arctangent and pseudo-Voigt functions (to represent the photoelectric absorption and multiple-scattering contributions). We validate this approach by microfocus X-ray diffraction and XANES analysis of points of interest, which afford average U oxidation states in excellent agreement with those estimated from the chemical state maps. This simple and easy-to-implement approach is general and transferrable, and will assist in the future analysis of real lava-like fuel-containing materials to understand their environmental degradation, which is a source of radioactive dust production within the Chernobyl shelter.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Synthesis and structure determination of Ce 6 Cd 23 Te: a new chalcogen-containing member of the RE 6 Cd 23 T family ( RE is a rare-earth metal and T is a late group 14, 15 and 16 element)

The ternary phase hexacerium tricosacadmium telluride, Ce 6 Cd 23 Te, was synthesized by a high-temperature reaction of the elements in sealed Nb ampoules and was structurally characterized by powder and single-crystal X-ray diffraction. The structure, established from single-crystal X-ray diffraction methods, is isopointal with the Zr 6 Zn 23 Si structure type (Pearson symbol cF 120, cubic space group Fm -3 m ), a filled version of the Th 6 Mn 23 structure with the same space group and Pearson symbol cF 116. Though no Cd-containing rare-earth metal binaries are known to form with this structure, it appears that the addition of small amounts of a p -block element allows the formation of such interstitially stabilized ternary compounds. Temperature-dependent direct current (dc) magnetization measurements suggest local-moment magnetism arising from the Ce 3+ ground state, with possible valence fluctuations at low temperature, inferred from the deviations from the Curie–Weiss law.

Chemistry↗

DOE OSTI2023

Time-Frequency Warped Waveforms for Well-Contained Massive Machine Type Communications

Herein this paper proposes a novel time-frequency warped waveform for short symbols, massive machine-type communication (mMTC), and internet of things (IoT) applications. The waveform is composed of asymmetric raised cosine (RC) pulses to increase the signal containment in time and frequency domains. The waveform has low power tails in the time domain, hence better performance in the presence of delay spread and time offsets. The time-axis warping unitary transform is applied to control the waveform occupancy in time-frequency space and to compensate for the usage of high roll-off factor pulses at the symbol edges. The paper explains a step-by-step analysis for determining the roll-off factors profile and the warping functions. Gains are presented over the conventional Zero-tail Discrete Fourier Transform-spread-Orthogonal Frequency Division Multiplexing (ZT-DFT-s-OFDM), and Cyclic prefix (CP) DFT-s-OFDM schemes in the simulations section.

42 ENGINEERING↗

DOE OSTI2016

Investigation of Sb-Containing Precursors for Cu(In, Ga)Se2 Thin Films Through Design of Experiments

The Design of Experiments (DoE) module in JMP statistical software was used to determine the best parameters for Sb-containing CIGS precursors with a fixed selenization step. Solar cells were fabricated and measured for all completed films. The most important factor influencing the current-voltage device parameters was identified as the temperature and antimony flux interaction. The DoE prediction profiler and predictive contour plots provided guidance to further improve the device parameters. In one follow-up run, we increased device efficiency from 14.9% to 15.5% Additional gains in efficiency to 16.9% were realized by introducing an intentional Ga gradient and an antireflective coating.

14 SOLAR ENERGY↗

DOE OSTI2019

Thermal neutron-induced single-event upsets in microcontrollers containing boron-10

Single-event upsets (SEUs) were measured in thermal neutron-irradiated microcontrollers with 65-nm node and 130-nm node SRAMs. The suspected upset mechanism is charge deposition from the energetic byproducts of 10 B thermal neutron capture. Although elemental analysis confirmed that both microcontrollers contain 10 B, only the 65-nm node microcontroller exhibited a strong response to thermal neutrons. Monte Carlo simulations were performed to investigate the effects of 11 B enrichment on thermal neutron-induced SEUs in a 65-nm SRAM node when boron is present in the p -type well, p -type source and drain, or tungsten plug. Simulations indicate that the byproducts of 10 B(n,α) 7 Li reactions are capable of generating sufficient charge to upset a 65-nm SRAM. Finally, the highest amount of charge deposition from 10 B(n,α) 7 Li reaction byproducts occurs when natural boron is used to dope the p -type source and drain regions. Simulations also show that the SEU cross section is non-negligible when 11 B-enriched boron is used for doping.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Cyanobacterial carboxysomes contain an unique rubisco–activase–like protein

In plants, rubisco activase (Rca) regulates rubisco by removing inhibitory molecules such as ribulose–1,5–bisphosphate (RuBP). In cyanobacteria, a homologous protein (activase–like cyanobacterial protein, ALC), contains a distinctive C–terminal fusion resembling the small–subunit of rubisco. Although cyanobacterial rubisco is believed to be less sensitive to RuBP inhibition, the ALC is widely distributed among diverse cyanobacteria. Using microscopy, biochemistry and molecular biology, the cellular localization of the ALC, its effect on carboxysome/cell ultrastructure in Fremyella diplosiphon, and its function in vitro were studied. Bioinformatic analysis uncovered evolutionary relationships between the ALC and rubisco. ALC localizes to carboxysomes and exhibits ATPase activity. Furthermore, the ALC induces rubisco aggregation in a manner similar to that of another carboxysomal protein, M35, and this activity is affected by ATP. An alc deletion mutant showed modified cell morphology when grown under enriched CO 2 and impaired regulation of carboxysome biogenesis, without affecting growth rate. Carbamylation of Fremyella recombinant rubisco was inhibited by RuBP, but this inhibition was not relieved by the ALC. Here, the ALC does not appear to function like a canonical Rca; instead, it exerts an effect on the response to CO 2 availability at the level of a metabolic module, the carboxysome, through rubisco network formation, and carboxysome organization.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Experimental Combustion and Flame Characterization of a Chemical Looping-Based Oxidative Dehydrogenation Byproduct Fuel Mixture Containing High CO2 Dilution

Abstract This study investigates the combustion performance of a CO2-rich fuel mixture containing ethane and methane as active species using a constant volume combustion chamber. This fuel is obtained as a byproduct of a chemical looping-based oxidative dehydrogenation (Cl-ODH) process ethylene production. The byproduct gas mixture has 40.79% CO2, 39.49% ethane, and 4.88% methane by weight with other minor compounds. Using this fuel for energy extraction would improve the process efficiency of the ethane to ethylene conversion. After initial combustion modeling, the gas fuel mixture was reduced to just the major species: CO2, ethane, and methane. The mixture was then tested for flammability limits and combustion performance under spark-ignition conditions. Effects of ambient conditions like temperatures between 300 and 400 K with initial pressures from 1 to 10 bar were tested. The effects of stoichiometry were tested to understand flame velocities and heat release. The fuel mixture showed an overall reduced flame velocity compared to gasoline. Instability in combustion was believed to be caused by the dissociation of ethane under elevated conditions. At higher pressures, the flame produces lower cumulative heat release. Simulations were also performed using a model tuned to replicate the operations of the combustion chamber used in the experiments. Heat release and unburnt fuel mass data were calculated to identify the discrepancies in the combustion completeness at elevated pressures. The effects of CO2 quenching the flame coupled with the increased dissociation of the fuel species can lead to up to more than 75% of the fuel mixture being unburnt. Data from this study were used to modify a small-scale spark-ignition engine to use this fuel and produce usable energy.

Energy & Fuels↗