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DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography

The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO 2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn 4 Ca complex (Mn 4 CaO 5 ) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of O X from a new water molecule, which disappears on completion of the reaction, implicating it in the O—O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn 4 Ca cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Templated Liquid-Phase Epitaxy of InP Structures on Si

We demonstrate direct and over-dielectric heteroepitaxial growth of InP on Si substrates through templated liquid-phase epitaxy. Large grains (5 um) are indicated by electron channeling contrast imaging and epitaxy is confirmed by x-ray diffraction.We demonstrate direct and over-dielectric heteroepitaxial growth of InP on Si substrates through templated liquid-phase epitaxy. Large grains (5 um) are indicated by electron channeling contrast imaging and epitaxy is confirmed by x-ray diffraction.

CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SU↗

NASA NTRS1988

Phase-locked laser array

A phase-locked laser array comprises a substrate with two spaced-apart pluralities of channels extending towards different reflecting surfaces of the array. The axes of symmetry of the channels of one plurality are offset from the axes of symmetry of the channels of the second plurality. Coupling of light propagating in the optical waveguides over one plurality of channels into the waveguides over the second plurality of channels induces a zero phase difference between the laser oscillations of adjacent channels.

Botez, Dan↗

DOE OSTI2022

Coalescence of GaP on V-Groove Si

With an increase of control over crystalline defects, metallorganic vapor phase epitaxy (MOVPE)-grown III-V-on-Si multijunction solar cells have seen rapid increases in efficiency in recent years, pointing to a promising path to lower cost III-V solar cells. However, the cost of chemo-mechanical polishing the Si wafers to prepare them for epitaxy is high. The use of V-groove nanopatterns enables similar defect reduction to that achieved on planar wafers, but the nanopatterns can be fabricated with a low-cost process. While V-grooves offer advantages over planar Si, they add complexity to the growth process. In particular, coalescence can cause the formation of threading dislocations, and the highly-directional growth conditions required for coalescence are unusual for MOVPE. We have studied the coalescence of GaP films nucleated directly on V-groove Si by MOVPE. We observed that for optimized growth conditions (V/III=5,000 and T=800 C) two growth modes were possible, and the resulting morphology depended on the exact geometry of the SiNx cap used to cover the (0 0 1)-oriented Si at the tops of the grooves. For caps with a width >100 nm, noncoalescing, nano ridge-like growth terminating in f1 1 1g facets was observed. For narrower caps, coalescence with an RMS roughness of 0.2 nm as measured by atomic force microscopy was observed. We will discuss mechanisms responsible for this phenomenon, including the role of Si from the substrate surface. The dislocation dynamics of this system were studied with electron channeling contrast imaging (ECCI) and transmission electron microscopy (TEM). We find that V-grooves do not block dislocation glide; ECCI measurements show misfit dislocations greater than 10 micrometers long observed to continue perpendicularly across neighboring V-grooves. In addition, all threading dislocations appear to lie on f1 1 1g planes, consistent with the GaP relaxing via glided-in glissile dislocations. The dislocation dynamics and morphological evolution of the coalescence of GaP on Si, possible mechanisms behind the observed phenomenons, and further dislocation mitigation strategies for these materials will be presented.

dislocation dynamics↗

DOE OSTI2021

Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site

Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo 3 ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o 3 , and Cu B ), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71 I . In both structures, residue H98 I occupies two conformations. In conformation 1, H98 I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 I has flipped to form a hydrogen bond with E14 I at the N-terminal end of TM0. We propose that H98 I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98 I .

bioenergetics↗

NASA NTRS2009

Heat rejection sublimator

A sublimator includes a sublimation plate having a thermal element disposed adjacent to a feed water channel and a control point disposed between at least a portion of the thermal element and a large pore substrate. The control point includes a sintered metal material. A method of dissipating heat using a sublimator includes a sublimation plate having a thermal element and a control point. The thermal element is disposed adjacent to a feed water channel and the control point is disposed between at least a portion of the thermal element and a large pore substrate. The method includes controlling a flow rate of feed water to the large pore substrate at the control point and supplying heated coolant to the thermal element. Sublimation occurs in the large pore substrate and the controlling of the flow rate of feed water is independent of time. A sublimator includes a sublimation plate having a thermal element disposed adjacent to a feed water channel and a control point disposed between at least a portion of the thermal element and a large pore substrate. The control point restricts a flow rate of feed water from the feed water channel to the large pore substrate independent of time.

Dingell, Charles W.↗

DOE OSTI2022

Study of Carrier Mobilities in 4H-SiC MOSFETS Using Hall Analysis

The channel conduction in 4H-SiC metal–oxide–semiconductor field effect transistors (MOSFETs) are highly impacted by charge trapping and scattering at the interface. Even though nitridation reduces the interface trap density, scattering still plays a crucial role in increasing the channel resistance in these transistors. In this work, the dominant scattering mechanisms are distinguished for inversion layer electrons and holes using temperature and body-bias-dependent Hall measurements on nitrided lateral 4H-SiC MOSFETs. The effect of the transverse electric field (E eƒƒ ) on carrier mobility is analyzed under strong inversion condition where surface roughness scattering becomes prevalent. Power law dependencies of the electron and hole Hall mobility for surface roughness scattering are determined to be E$^{-1.8}_{eƒƒ}$ and E$^{-2.4}_{eƒƒ}$, respectively, analogous to those of silicon MOSFETs. Moreover, for n-channel MOSFETs, the effect of phonon scattering is observed at zero body bias, whereas in p-channel MOSFETs, it is observed only under negative body biases. Along with the identification of regimes governed by different scattering mechanisms, these results highlight the importance of the selection of substrate doping and of E eƒƒ in controlling the value of channel mobility in 4H-SiC MOSFETs.

36 MATERIALS SCIENCE↗

NASA NTRS1990

Low noise and conductively cooled microchannel plates

Microchannel plate (MCP) dynamic range has recently been enhanced for both very low and very high input flux conditions. Improvements in MCP manufacturing technology reported earlier have led to MCPs with substantially reduced radioisotope levels, giving dramatically lower internal background-counting rates. An update is given on the Galileo low noise MCP. Also, new results in increasing the MCP linear counting range for high input flux densities are presented. By bonding the active face of a very low resistance MCP (less than 1 megaohm) to a substrate providing a conductive path for heat transport, the bias current limit (hence, MCP output count rate limit) can be increased up to two orders of magnitude. Normal pulse-counting MCP operation was observed at bias currents of several mA when a curved-channel MCP (80:1) was bonded to a ceramic multianode substrate; the MCP temperature rise above ambient was less than 40 C.

Feller, W. B.↗

DOE OSTI2025

Spontaneous generation of athermal phonon bursts within bulk silicon causing excess noise, low energy background events, and quasiparticle poisoning in superconducting sensors

Solid state phonon detectors used in the search for dark matter and coherent neutrino nucleus interactions (CE $v$ NS) require excellent energy resolution (eV-scale or below) and low backgrounds. An unknown source of phonon bursts, the low energy excess (LEE), dominates other above-threshold backgrounds and generates excess shot noise from subthreshold bursts. Here, in this paper, we measure these phonon bursts for 12 days after cooldown in two nearly identical 1 cm 2 silicon detectors that differ only in the thickness of their substrate (1 vs 4 mm thick). We find that both the channel-correlated shot noise and near-threshold shared LEE relax with time since cooldown. Additionally, both the correlated shot noise and LEE rates scale linearly with substrate thickness. When combined with previous measurements of other silicon phonon detectors with different substrate geometries and mechanical support strategies, these measurements strongly suggest that the dominant source of both above and below threshold LEE is the bulk substrate. By monitoring the relation between bias power and excess phonon shot noise, we estimate that the energy scale for subthreshold noise events is 0.68 ± 0.38 meV. In our final dataset, we report a world-leading energy resolution of 258.5 ± 0.4 meV in the 1 mm thick detector. Simple calculations suggest that these silicon substrate phonon bursts are likely a significant source of quasiparticle poisoning in superconducting qubits operated in well shielded and vibration free environments.

Chang, C. L. [Argonne National Laboratory 1 , 9700↗

DOE OSTI2024

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗

NASA NTRS2008

Joining of Silicon Carbide: Diffusion Bond Optimization and Characterization

Joining and integration methods are critically needed as enabling technologies for the full utilization of advanced ceramic components in aerospace and aeronautics applications. One such application is a lean direct injector for a turbine engine to achieve low NOx emissions. In the application, several SiC substrates with different hole patterns to form fuel and combustion air channels are bonded to form the injector. Diffusion bonding is a joining approach that offers uniform bonds with high temperature capability, chemical stability, and high strength. Diffusion bonding was investigated with the aid of titanium foils and coatings as the interlayer between SiC substrates to aid bonding. The influence of such variables as interlayer type, interlayer thickness, substrate finish, and processing time were investigated. Optical microscopy, scanning electron microscopy, and electron microprobe analysis were used to characterize the bonds and to identify the reaction formed phases.

Halbig, Michael C.↗

NASA NTRS2005

In Situ Electrochemical Deposition of Microscopic Wires

A method of fabrication of wires having micron and submicron dimensions is built around electrochemical deposition of the wires in their final positions between electrodes in integrated circuits or other devices in which the wires are to be used. Heretofore, nanowires have been fabricated by a variety of techniques characterized by low degrees of controllability and low throughput rates, and it has been necessary to align and electrically connect the wires in their final positions by use of sophisticated equipment in expensive and tedious post-growth assembly processes. The present method is more economical, offers higher yields, enables control of wire widths, and eliminates the need for post-growth assembly. The wires fabricated by this method could be used as simple electrical conductors or as transducers in sensors. Depending upon electrodeposition conditions and the compositions of the electroplating solutions in specific applications, the wires could be made of metals, alloys, metal oxides, semiconductors, or electrically conductive polymers. In this method, one uses fabrication processes that are standard in the semiconductor industry. These include cleaning, dry etching, low-pressure chemical vapor deposition, lithography, dielectric deposition, electron-beam lithography, and metallization processes as well as the electrochemical deposition process used to form the wires. In a typical case of fabrication of a circuit that includes electrodes between which microscopic wires are to be formed on a silicon substrate, the fabrication processes follow a standard sequence until just before the fabrication of the microscopic wires. Then, by use of a thermal SiO-deposition technique, the electrodes and the substrate surface areas in the gaps between them are covered with SiO. Next, the SiO is electron-beam patterned, then reactive-ion etched to form channels having specified widths (typically about 1 m or less) that define the widths of the wires to be formed. Drops of an electroplating solution are placed on the substrate in the regions containing the channels thus formed, then the wires are electrodeposited from the solution onto the exposed portions of the electrodes and into the channels. The electrodeposition is a room-temperature, atmospheric-pressure process. The figure shows an example of palladium wires that were electrodeposited into 1-mm-wide channels between gold electrodes.

Yun, Minhee↗

NASA NTRS1972

Shielded silicon gate complementary MOS integrated circuit.

An electrostatic shield for complementary MOS integrated circuits was developed to minimize the adverse effects of stray electric fields created by the potentials in the metal interconnections. The process is compatible with silicon gate technology. N-doped polycrystalline silicon was used for all the gates and the shield. The effectiveness of the shield was demonstrated by constructing a special field plate over certain transistors. The threshold voltages obtained on an oriented silicon substrate ranged from 1.5 to 3 V for either channel. Integrated inverters performed satisfactorily from 3 to 15 V, limited at the low end by the threshold voltages and at the high end by the drain breakdown voltage of the n-channel transistors. The stability of the new structure with an n-doped silicon gate as measured by the shift in C-V curve under 200 C plus or minus 20 V temperature-bias conditions was better than conventional aluminum gate or p-doped silicon gate devices, presumably due to the doping of gate oxide with phosphorous.

Lin, H. C.↗

DOE OSTI2021

Structure and mechanism of Staphylococcus aureus oleate hydratase (OhyA)

Flavin adenine dinucleotide (FAD)-dependent bacterial oleate hydratases (OhyAs) catalyze the addition of water to isolated fatty acid carbon–carbon double bonds. Staphylococcus aureus uses OhyA to counteract the host innate immune response by inactivating antimicrobial unsaturated fatty acids. Mechanistic information explaining how OhyAs catalyze regiospecific and stereospecific hydration is required to understand their biological functions and the potential for engineering new products. In this study, we deduced the catalytic mechanism of OhyA from multiple structures of S. aureus OhyA in binary and ternary complexes with combinations of ligands along with biochemical analyses of relevant mutants. The substrate-free state shows Arg81 is the gatekeeper that controls fatty acid entrance to the active site. FAD binding engages the catalytic loop to simultaneously rotate Glu82 into its active conformation and Arg81 out of the hydrophobic substrate tunnel, allowing the fatty acid to rotate into the active site. FAD binding also dehydrates the active site, leaving a single water molecule connected to Glu82. This active site water is a hydronium ion based on the analysis of its hydrogen bond network in the OhyA•PEG400•FAD complex. We conclude that OhyA accelerates acid-catalyzed alkene hydration by positioning the fatty acid double bond to attack the active site hydronium ion, followed by the addition of water to the transient carbocation intermediate. Structural transitions within S. aureus OhyA channel oleate to the active site, curl oleate around the substrate water, and stabilize the hydroxylated product to inactivate antimicrobial fatty acids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Negative Capacitance MgZnO-Channel Thin-Film Transistor With Ferroelectric NiMgZnO in the Gate Stack

We demonstrate the negative capacitance thin-film transistor (NC-TFT) on glass substrate using the multifunctional MgZnO (MZO). The Mg 0.03 Zn 0.97 O semiconductor layer acts as the TFT channel for stable operation while the Ni-doped MZO, i.e. Ni 0.02 Mg 0.15 Zn 0.83 O (NMZO) serves as the ferroelectric layer in the NMZO/SiO 2 stacking gate dielectric structure. The subthreshold swing (SS) value is significantly reduced over the reference TFT without ferroelectric layer. The minimum SS value of the NC-TFT reaches 52 mV/dec while the on/off ratio of drain current ID reaches 10 9 .

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2025

Low energy backgrounds and excess noise in a two-channel low-threshold calorimeter

Here, we describe observations of low energy excess (LEE) events, background events observed in all light dark matter direct detection calorimeters, and noise in a transition edge sensor based two-channel silicon athermal phonon detector with 375 meV baseline energy resolution. We measure two distinct LEE populations: “shared” multichannel events with a pulse shape consistent with substrate athermal phonon events and sub-eV events that couple nearly exclusively to a single channel with a significantly faster pulse shape. These “singles” are consistent with events occurring within the aluminum athermal phonon collection fins. Similarly, our measured detector noise is higher than the theoretical expectation. Measured noise can be split into an uncorrelated component, consistent with shot noise from small energy depositions within the athermal phonon sensor itself, and a correlated component, consistent with shot noise from energy depositions within the silicon substrate's phonon system.

47 OTHER INSTRUMENTATION↗

NASA NTRS1997

Using Superconducting Thin Films in Microwave Lines

High temperature superconductors(HTS) and microwaves devices form the ideal partnership. The application of superconductors in microwave devices, components and systems allows the reduction in size, power consumption and insertion loss. The surface resistance of high-Tc superconductors has been found to be two orders of magnitude lower than normal conducting copper materials. The reduction in size and power requirements, which together both lead to a reduction in system mass, coupled with reasonably accessible operating temperatures, suggest that HTS microwave components should find ready application in satellite communications systems. At present, multi- channeling communication networks demand filters with narrow bandwidth in order to allow the available RF frequency spectrum to be partitioned into small frequency bands, -and possible variation of dielectric constant from substrate to substrate is undesirable. Microwave multiplexers demand the fabrication of two identical filters in each channel. Thus, the filter with tuning function is preferable. Tunable filters are the critical component for phased array antennas in order to electronically steer the radiated beam. To fabricate a tunable filter that uses an electric field for operation, one would like a material that provides a large change on dielectric constant for a given electric field, yet has a relatively low tangent in order to minimize the insertion loss of the device. Ferroelectrics have been the materials of choice. Their large dielectric constant sufficiently increases the coupling between microwave resonators and its dependence on electric field provides timability. Development of technology promises to diminish tangent loss. The use of thin ferroelectric films sufficiently decreases insertion losses keeping considerable potential for applications. NASA Lewis Research Center is the one of the leading centers in investigation of superconductors/ferroelectric tunable components for microwave devices. A large number of possible microwave devices were fabricated and tested on the basis of thin film multilayer superconductor-ferroelectric structures. In major cases the systems with edge-coupling scheme were investigated. Dr. Genkin has recently focused on the new potentialities which implements the using of thin ferroelectric films in filters fabricated with end-coupled microstrip lines. Numerical modeling shows that these systems have large potential for application in tunable narrow- and wide-bandpass filters in the frequency range 10-20 GHz. The phase shifter with end-coupled resonant sections was fabricated and tested. Experimental results show large tunability, particular in low voltages. The possible optimization of this structure promises to improve the obtained result and to reach the low level of insertion losses.

Genkin, Varery↗