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At least 1,333 records · Page 74

Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA

The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T–G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

59 BASIC BIOLOGICAL SCIENCES↗

Recovery of high specific activity molybdenum-99 from accelerator-induced fission on low-enriched uranium for technetium-99m generators

Abstract A new process was developed to recover high specific activity (no carrier added) 99 Mo from electron-accelerator irradiated U 3 O 8 or uranyl sulfate targets. The process leverages a novel solvent extraction scheme to recover Mo using di(2-ethylhexyl) phosphoric acid following uranium and transuranics removal with tri- n -butyl phosphate. An anion-exchange concentration column step provides a final purification, generating pure 99 Mo intended for making 99 Mo/ 99m Tc generators. The process was demonstrated with irradiated uranium targets resulting in more than 95% 99 Mo recovery and without presence of fission products or actinides in the product.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

An oceanic pathway for Madden–Julian Oscillation influence on Maritime Continent Tropical Cyclones

While the Madden–Julian Oscillation (MJO) has been shown to affect tropical cyclones (TCs) worldwide through its modulation of large-scale circulation in the atmosphere, little or no role for the ocean has been identified to date in this influence of MJO on TCs. Using observations and numerical model simulations, we demonstrate that MJO events substantially impact TCs over the Maritime Continent (MC) region through an oceanic pathway. While propagating across the MC region, MJO events cause significant sea surface cooling with an area-averaged value of about 0.35 ± 0.12 °C. Hence, TCs over the MC region immediately following the passage of MJO events encounter considerably cooler sea surface temperatures. Consequently, the enthalpy fluxes under the storms are reduced and the intensification rates decrease by more than 50% on average. These results highlight an important role played by the ocean in facilitating MJO-induced sub-seasonal variability in TC activity over the MC region.

54 ENVIRONMENTAL SCIENCES↗

Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4 CRBN , and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigating the Cuprates as a platform for high-order Van Hove singularities and flat-band physics

Abstract Beyond the two-dimensional saddle-point Van Hove singularities (VHSs) with logarithmic divergences in the density of states, recent studies have identified higher-order VHSs with faster-than-logarithmic divergences that can amplify electron correlation effects. Here we show that the cuprate high-Tc superconductors harbor high-order VHSs in their electronic spectra and unveil a new correlation that the cuprates with high-order VHSs display higher T c ’s. Our analysis indicates that the normal and higher-order VHSs can provide a straightforward new marker for identifying propensity of a material toward the occurrence of correlated phases such as the excitonic insulators and supermetals. Our study suggests cuprates and related high-T c superconductors as materials for exploring the interplay between high-order VHSs, superconducting transition temperatures, and electron correlation effects.

Markiewicz, Robert S. (ORCID:0000000207470713)↗

Gas-phase molybdenum-99 separation from uranium dioxide by fluoride volatility using nitrogen trifluoride

Production of the important 99m Tc medical isotope parent, molybdenum-99 ( 99 Mo), via the fissioning of high- and low-enriched uranium (HEU/LEU) targets followed by target dissolution in acid and solution-phase purification of 99 Mo is time-consuming, generates quantities of corrosive radioactive waste, and can result in the release of an array of radionuclides to the atmosphere. An alternative 99 Mo purification method has been devised that has the potential to alleviate many of these issues. Herein, we demonstrate the feasibility of a rapid Mo/Tc gas-phase separation from UO 2 . The results indicate that volatile [ 99 Mo]Mo can be captured downstream of the reacted solid mixture on a column bed (trap) of alumina; the majority of the captured [ 99 Mo]Mo can be subsequently eluted from the alumina trap with a few milliliters of water. >1.0 × 10 5 single pass decontamination of U and the collected [ 99 Mo]Mo product is demonstrated. This simple thermo-fluorination technique has the potential to provide a rapid methodology for routine 99 Mo production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Primary photodissociation mechanisms of pyruvic acid on S 1 : observation of methylhydroxycarbene and its chemical reaction in the gas phase

Pyruvic acid, a representative alpha-keto carboxylic acid, is one of the few organic molecules destroyed in the troposphere by solar radiation rather than by reactions with free radicals. To date, only its stable final products were identified, often with contribution from secondary chemistry, making it difficult to elucidate photodissociation mechanisms following excitation to the lowest singlet excited-state (S 1 ) and the role of the internal hydrogen bond in the most-stable Tc conformer. Using multiplexed photoionization mass spectrometry we report the first direct experimental evidence, via the observation of singlet methylhydroxycarbene (MHC) following 351 nm excitation, supporting the decarboxylation mechanism previously proposed. Decarboxylation to MHC + CO 2 represents 97–100% of product branching at 351 nm. We observe vinyl alcohol and acetaldehyde, which we attribute to isomerization of MHC. We also observe a 3 ± 2% yield of the Norrish Type I photoproducts CH 3 CO + DOCO, but only from d 1 -pyruvic acid. At 4 Torr pressure, we measure a photodissociation quantum yield of $1.0^{+0}_{–0.4}$, consistent with IUPAC recommendations. However, our measured product branching fractions disagree with IUPAC. In light of previous calculations, these results support a mechanism in which hydrogen transfer on the S 1 excited state occurs at least partially by tunneling, in competition with intersystem crossing to the T 1 state. Here, we present the first evidence of a bimolecular reaction of MHC in the gas phase, where MHC reacts with pyruvic acid to produce a C 4 H 8 O 2 product. This observation implies that some MHC produced from pyruvic acid in Earth's troposphere will be stabilized and participate in chemical reactions with O 2 and H 2 O, and should be considered in atmospheric modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stabilizing homogeneous CaMn6Sn6via oscillatory crystal growth: structural complexity in a kagome metal

CaMn6Sn6 is a member of the large family of Mn-based kagome metals derived by filling voids of the prototypical CoSn structure. We observed Ca-deficiency and structural complexity, with approximately 10% deficiency of calcium relative to the ideal 166 stoichiometry. These features are common in related Ca-based materials. We find that growth conditions stabilize different phases with varying Curie temperatures. Diffraction and magnetization measurements reveal that conventional growth profiles yield inhomogeneity both within and between crystals in a given batch, whereas an oscillatory temperature profile promotes homogeneous crystals that adopt a superstructure beyond the parent hexagonal structure type. We present the physical properties of crystals grown using the oscillatory approach. The crystals are highly conductive, with a c-axis residual resistivity ratio ρ(300 K)/ρ(2 K) exceeding 100 and a positive, linear magnetoresistance at base temperature. Magnetically, the crystals are quite similar to MgMn6Sn6, with easy-plane ferromagnetic behavior and a Curie temperature of TC ≈ 237 K. These results highlight the critical role of growth conditions in stabilizing homogeneous crystals of complex phases such as Ca0.9Mn6Sn6. The oscillatory growth approach provides an effective route for accessing the intrinsic properties of this complex material and may be broadly useful for the growth of related kagome systems.

May, Andrew [ORNL] (ORCID:0000000307778539)↗

The role of iron in magnetic damping of Mg(Al,Fe) 2 O 4 spinel ferrite thin films

© 2020 Author(s). We have investigated magnesium aluminum ferrite thin films with a range of iron concentrations and identified the optimal iron content to obtain high crystalline quality thin films with the low magnetic damping required for spin current-based applications. Epitaxial MgAl 2-x FexO4 films with 0.8 < x < 2.0 were grown by pulsed laser deposition on single crystal MgAl2O4 substrates and were characterized structurally and magnetically. We find that the x = 1.5 composition minimizes the room-temperature magnetic damping with a typical Gilbert damping parameter of α eff = 1.8 × 10-3. This minimized damping is governed by a competition between the more robust magnetic ordering with increased iron content, x, and the more defective structure due to larger film-substrate lattice mismatch with increased iron content. The temperature-dependent magnetization curves indicate that Tc is suppressed below room temperature for iron content x ≤ 1.2 and eventually suppressed entirely for x = 0.8. X-ray magnetic circular dichroism results indicate that for all x the magnetic moment is dominated by Fe 3 + cations distributed in a 60:40 ratio on the octahedral and tetrahedral sites, with minimal contribution from Fe 2 + cations. Films with x = 1.4-1.6 exhibit very strong ferromagnetic resonance and low Gilbert damping with α eff = (1.8-6) × 10-3, making them ideal candidates for microwave and spintronic applications.

36 MATERIALS SCIENCE↗

Room temperature multiferroicity and magnetodielectric coupling in 0–3 composite thin films

Magnetoelectric (ME) composite thin films are promising candidates for novel applications in future nanoelectronics, spintronics, memory and other multifunctional devices as they exhibit much higher ME coupling and transition temperatures (Tc) than well-known single phase multiferroics discovered to date. Among the three types of multiferroic composite nanostructures, (2-2) layered and (1-3) vertically aligned composite nanostructures exhibit comparatively smaller ME coupling due to different shortcomings which restrict their use in many applications. Here we study the morphological, piezoresponse force microscopic (PFM), ferroelectric, magnetic, and magnetodielectric properties of 0-3 (magnetic nanoparticles (0) homogeneously distributed in ferroelectric matrices (3)) multiferroic composite thin films. The Pb(Fe 0.5 Nb 0.5 )O 3 (PFN) - Ni 0.65 Zn 0.35 Fe 2 O 4 (NZFO) particulate composite films were synthesized by pulsed laser deposition (PLD). These particulate composite thin films are completely c-axis oriented with very low surface roughness. We observed magnetic and ferroelectric T c above room temperature (RT) for all composite thin films. The PFN-NZFO 0-3 composites exhibit large polarization, high saturated magnetization with low coercive field, low dielectric loss along with magnetodielectric coupling at RT. These nanocomposites might be utilized in next generation nano/microelectronics and spintronic devices.

36 MATERIALS SCIENCE↗

Low-loss superconducting titanium nitride grown using plasma-assisted molecular beam epitaxy

Titanium nitride (TiN) is a known superconducting material that is attractive for use as passive components in superconducting circuits for both conventional and quantum information devices. In contrast to conventional synthesis techniques, here, plasma-assisted molecular beam epitaxy is reported to produce high-quality TiN on bare silicon wafers. Using a rf-plasma source to crack the nitrogen molecules and a conventional high-temperature effusion cell for titanium, TiN growth is completed under nitrogen-rich conditions. The growth and nucleation is monitored in situ, while the structure and composition are characterized using x-ray diffraction, atomic force microscopy, x-ray photoelectron spectroscopy, secondary ion mass spectroscopy, and scanning transmission electron microscopy. The stoichiometric TiN (111) films sit on an amorphous nitride layer with low impurity concentrations. The films superconduct with Tc=5.4 K, and coplanar waveguide resonators are fabricated with a small center width of 6 μm that demonstrate single-photon quality factors approaching 1M and high-power quality factors over 5M without observing saturation.

Richardson, C. J. K. (ORCID:0000000188175347)↗

The scaling of kinetic and transport behaviors in the solution-phase chemistry of a plasma–liquid interface

The reactions at a plasma–liquid interface often involve species such as the solvated electron or the hydroxyl radical, which initiate the reduction or oxidation of solution-phase reactants (so-called scavengers) or are consumed by their own second-order recombination. Here, the mathematical scaling of the reaction–diffusion equations at the interface is used to obtain a characteristic time that can be used to determine the transition from highly efficient scavenger reduction or oxidation to lower efficiencies due to transport limitations. The characteristic time (tc) is validated using numerical solutions of the reaction–diffusion equations. When the scavenger kinetics are faster than second-order recombination, this characteristic transition time scales proportionally with the scavenger diffusivity (Ds) and the square of the scavenger bulk concentration (SB) and inversely proportional to the electron flux (J) squared; that is, t c = D s S B 2 F 2 /J 2 , where F is Faraday’s constant. However, when the scavenger kinetics are comparable or slower than second-order recombination, this scaling does not hold. Extending this analysis to three-dimensional systems shows that the profile of the electron flux on the surface affects the spatial location where reactions are most effective. Finally, the assessment of the implications of these behaviors for the reactor design highlights how effectively controlling the electron flux and solution transport may be necessary to improve the efficiency of scavenger reactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Analytical modeling of the evolution of the nonlinearity parameter of sensitized stainless steel

Austenitic stainless steels are subject to the precipitation of chromium carbides (M 23 C 6 ) during exposure to high temperatures, causing these alloys to be susceptible to intergranular corrosion due to chromium depletion along grain boundaries. The acoustic nonlinearity parameter, β, shows sensitivity to the formation of carbides in these alloys. The Thermo-Calc TC-PRISMA module was used to model the nucleation and growth of grain boundary M 23 C 6 carbides. The model was verified with scanning transmission electron microscopy analysis that allowed measurements of the grain boundary precipitates. The paper introduces a reduced-order model of the acoustic nonlinearity based on the formation of misfit dislocations at the interface of the grain boundary precipitate and matrix to explain the change in β during isothermal aging. Furthermore, a direct relationship between the radius of the M 23 C 6 grain boundary carbides and β was observed and verified with nonlinear ultrasound measurements on 304L and 316L stainless steels.

36 MATERIALS SCIENCE↗

Mechanism of enhanced critical fields and critical current densities of MgB2 wires with C/Dy$^{2}$O3 co-additions

A series of monofilamentary powder-in-tube MgB2 wires were fabricated with 2 mol. % C doping and co-additions of 0–3 wt. % Dy2O3. Irreversibility fields (μ0Hirr), upper critical fields (μ0Hc2), and transport critical currents were measured, and from these quantities, anisotropies (γ) and electronic diffusivities (Dπ,σ) were estimated. The addition of 1 wt. % Dy2O3 to already optimally C-doped MgB2 wires produced higher Hc2//ab, Hc2//c, and Hirr values at 4.2 K. In addition, the critical current density, Jc, increased with Dy2O3 concentration up to 1 wt. % where non-barrier Jc reached 4.35 × 104 A/cm2 at 4.2 K, 10 T. At higher temperatures, for example, 20 K and 5 T, co-additions of 2 mol. % C and 2 wt. % Dy2O3 improved non-barrier Jc by 40% and 93% compared to 2 and 3 mol. % C doping, respectively. On the other hand, measurements of Tc showed that C/Dy2O3 co-additions increase interband scattering rates at a lower rate than C doping does (assuming C doping levels giving similar levels of low-T μ0Hc2 increase as co-addition). Comparisons to a two-band model for μ0Hc2 in MgB2 allowed us to conclude that the increases in Hc2//ab, Hc2//c, and Hirr (as well as concomitant increases in high-field Jc) with Dy2O3 addition are consistent with increases primarily in intraband scattering. This suggests C/Dy2O3 co-addition to be a more promising candidate for improving non-barrier Jc of MgB2 at temperatures above 20 K.

36 MATERIALS SCIENCE↗

Critical behavior in a chiral molecular model

Understanding the condensed-phase behavior of chiral molecules is important in biology as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature of T = 0.985Tc, and our findings indicate that the free energy barrier for this transformation increases with system size as N2/3, where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.

Chemistry↗

Radiatively cooled quantum microwave amplifiers

Superconducting microwave amplifiers are essential for sensitive signal readout in superconducting quantum processors. Typically based on Josephson junctions, these amplifiers require operation at milli-Kelvin temperatures to achieve quantum-limited performance. Here, we demonstrate a quantum microwave amplifier that employs radiative cooling to operate at elevated temperatures and maintain near quantum-limited added noise. This kinetic-inductance-based parametric amplifier, patterned from a single layer of relatively high-Tc NbN thin film, maintains a high gain and meanwhile enables low added noise of 1.3 quanta when operated at 1.5 K. Remarkably, this represents only a 0.2 quanta increase compared to the performance at a base temperature of 0.1 K. Based on our findings, we also discuss the practicality of such an operating scheme for various quantum applications. By uplifting the parametric amplifiers from the mixing chamber without compromising readout efficiency, this work represents an important step toward more scalable microwave quantum technologies.

Physics↗

Xenon–metal pair formation in UO 2 investigated using DFT + U

A recent experimental study on a spent uranium dioxide (UO 2 ) fuel sample from Belgium Reactor 3 identified a unique pair structure formed by the noble metal phase (NMP) and fission gas [xenon (Xe)] precipitate. However, the fundamental mechanism behind this structure remains unclear. The present study aims to provide an understanding of the interaction between five different metal precipitates [molybdenum (Mo), ruthenium (Ru), palladium (Pd), technetium (Tc), and rhodium (Rh)] and the Xe fission gas atoms in UO 2 , by using density functional theory (DFT) in combination with the Hubbard U correction to compute the formation energies involved. All DFT + U calculations were performed with occupation matrix control to ensure antiferromagnetic ordering of UO 2 . The calculated formation and binding energies of the Xe and solid fission products in the NMP reveal that these metal precipitates form stable pair structures with Xe. Notably, the formation energy of Xe–metal pairs is lower than that of the isolated single defects in all instances, with Pd and Mo showing the most favorable binding energy, likely accounting for the observed pair structure formation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗