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At least 667 records · Page 37

Unique Structural Features Relate to Evolutionary Adaptation of Cytochrome P450 in the Abyssal Zone

Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.

Biochemistry & Molecular Biology↗

In-space fabrication of thin-film structures

A conceptual study of physical vapor-deposition processes for in-space fabrication of thin-film structures is presented. Potential advantages of in-space fabrication are improved structural integrity and surface reflectivity of free-standing ultra-thin films and coatings. Free-standing thin-film structures can find use as photon propulsion devices (solar sails). Other applications of the concept involve free-standing shadow shields, or thermal control coatings of spacecraft surfaces. Use of expendables (such as booster and interstage structures) as source material for the physical vapor deposition process is considered. The practicability of producing thin, textured, aluminum films by physical vapor deposition and subsequent separation from a revolving substrate is demonstrated by laboratory experiments. Heating power requirement for the evaporation process is estimated for a specific mission.

Lippman, M. E.↗

Contribution of the graded region of a HgCdTe diode to its saturation current

Experimental results show that the contribution of the graded region to the current of Hg(1-x)Cd(x)Te diodes is not negligible, as compared to that of the p type bulk. The theoretical analysis reveals the influence of the electric field present outside the depletion region on the current generated by the graded region. The analysis shows the importance of the lifetime profile in the graded region, which is a function of the specific recombination mechanism and its dependence on the local dopant concentration. The effect of parameters such as substrate concentration, surface concentration, and junction depth on this current is discussed.

Schacham, S. E.↗

Pr-specific phytochrome phosphorylation in vitro by a protein kinase present in anti-phytochrome maize immunoprecipitates

Protein kinase activity has repeatedly been found to co-purify with the plant photoreceptor phytochrome, suggesting that light signals received by phytochrome may be transduced or modulated through protein phosphorylation. In this study immunoprecipitation techniques were used to characterize protein kinase activity associated with phytochrome from maize (Zea mays L.). A protein kinase that specifically phosphorylated phytochrome was present in washed anti-phytochrome immunoprecipitates of etiolated coleoptile proteins. No other substrate tested was phosphorylated by this kinase. Adding salts or detergents to disrupt low-affinity protein interactions reduced background phosphorylation in immunoprecipitates without affecting phytochrome phosphorylation, indicating that the protein kinase catalytic activity is either intrinsic to the phytochrome molecule or associated with it by high-affinity interactions. Red irradiation (of coleoptiles or extracts) sufficient to approach photoconversion saturation reduced phosphorylation of immunoprecipitated phytochrome. Subsequent far-red irradiation reversed the red-light effect. Phytochrome phosphorylation was stimulated about 10-fold by a co-immunoprecipitated factor. The stimulatory factor was highest in immunoprecipitates when Mg2+ was present in immunoprecipitation reactions but remained in the supernatant in the absence of Mg2+. These observations provide strong support for the hypothesis that phytochrome-associated protein kinase modulates light responses in vivo. Since only phytochrome was found to be phosphorylated, the co-immunoprecipitated protein kinase may function to regulate receptor activity.

NASA Discipline Plant Biology↗

Decoupling Thin Film CdTe Growth from Packaging: Toward Record Specific Power in Low Cost Polycrystalline PV: Preprint

There are critical material and scientific barriers to producing high efficiency, flexible, lightweight solar cells that maximize specific power in a cost-effective manner. GaAs solar cells produce the highest specific power of any photovoltaic (PV) technology due to their low weight and extremely high efficiency, but they are also among the most expensive to produce. This work explores a novel lift-off approach with thin-film solar cells, particularly CdTe, to achieve high specific power at low costs. Thin-film devices can be delaminated from their heavy, glass growth substrates post-growth by exploiting a mismatch in coefficient of thermal expansion between the two. This allows thin-film PV to be decoupled from high temperature growth requirements and repackaged using lightweight materials. Currently, the most consistent method of achieving complete delamination of CdTe films is to apply a glass handle at the back contact of the device using epoxy and submerge it in liquid nitrogen. By Tthen re-depositing a transparent front contact but be re-deposited and selectively etcheding to expose the back contact to produce, a functioning lifted-off devices have been produced. Effects of delamination and contributions to device functionality from CdCl2 and CdS layers are discussed. Reproducible delamination of high efficiency, thin-film solar cells over large areas will enable work to further improve device efficiency through passivation and reconstruction of the previously buried interface between the transparent contact and CdS.

14 SOLAR ENERGY↗

Numerical Simulation of Nanostructure Growth

Nanoscale structures, such as nanowires and carbon nanotubes (CNTs), are often grown in gaseous or plasma environments. Successful growth of these structures is defined by achieving a specified crystallinity or chirality, size or diameter, alignment, etc., which in turn depend on gas mixture ratios. pressure, flow rate, substrate temperature, and other operating conditions. To date, there has not been a rigorous growth model that addresses the specific concerns of crystalline nanowire growth, while demonstrating the correct trends of the processing conditions on growth rates. Most crystal growth models are based on the Burton, Cabrera, and Frank (BCF) method, where adatoms are incorporated into a growing crystal at surface steps or spirals. When the supersaturation of the vapor is high, islands nucleate to form steps, and these steps subsequently spread (grow). The overall bulk growth rate is determined by solving for the evolving motion of the steps. Our approach is to use a phase field model to simulate the growth of finite sized nanowire crystals, linking the free energy equation with the diffusion equation of the adatoms. The phase field method solves for an order parameter that defines the evolving steps in a concentration field. This eliminates the need for explicit front tracking/location, or complicated shadowing routines, both of which can be computationally expensive, particularly in higher dimensions. We will present results demonstrating the effect of process conditions, such as substrate temperature, vapor supersaturation, etc. on the evolving morphologies and overall growth rates of the nanostructures.

Hwang, Helen H.↗

Microfabricated Ion Traps on Sapphire for Larger Trap Areas and Higher Qubit Count

Surface ion traps are a promising platform for quantum computing due to their potential to store large numbers of ions that can be addressed by electrical and optical control signals in order to implement quantum algorithms. Increasing the power of the quantum computer requires increasing the number of ions, but this poses a significant challenge in that it leads to a non-linear increase in on-chip power dissipation. The primary contributor to this power scaling in current devices is the capacitance between the radio frequency (RF) electrode and the metal plane that shields the silicon substrate from the RF signals applied to it. Silicon has traditionally been chosen for the substrate material for compatibility with the processing required for multi-metal-level traps. In this work, we address these capacitance and fabrication challenges by replacing the commonly used silicon substrate with an insulating sapphire substrate to fabricate a multi-metal-level ion trap, while still employing common semiconductor manufacturing techniques. This change in substrate allows the design to remove the metal shielding from the device design, reducing the capacitance of the RF electrode. The electrical characteristics of these traps were measured, specifically trap impedance, capacitance, and voltage breakdown, and compared to nearly identical silicon trap devices. Finally, we used laser cutting techniques to shape a sapphire wafer into bowtie shapes matching silicon traps previously fabricated at Sandia National Labs to explore solutions for integrating sapphire substrates into non-rectangular ion trap designs.

97 MATHEMATICS AND COMPUTING↗

Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System

Leaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut, composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their roles in the detoxification of plant secondary compounds. In this study, we assessed if the bacterial communities associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus . Our findings suggest that the fungus garden and its associated microbial community influence the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores.

59 BASIC BIOLOGICAL SCIENCES↗

Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site

Abiraterone acetate is a first-line therapy for castration-resistant prostate cancer. This prodrug is deacetylated in vivo to abiraterone, which is a potent and specific inhibitor of cytochrome P450 17A1 (CYP17A1). CYP17A1 performs two sequential steps that are required for the biosynthesis of androgens that drive prostate cancer proliferation, analogous to estrogens in breast cancer. Abiraterone can be further metabolized in vivo on the steroid A ring to multiple metabolites that also inhibit CYP17A1. Despite its design as an active-site-directed substrate analog, abiraterone and its metabolites demonstrate mixed competitive/noncompetitive inhibition. To understand their binding, we solved the X-ray structures of CYP17A1 with three primary abiraterone metabolites. Despite different conformations of the steroid A ring and substituents, all three bound in the CYP17A1 active site with the steroid core packed against the I helix and the A ring C3 keto or hydroxyl oxygen forming a hydrogen bond with N202 similar to abiraterone itself. The structure of CYP17A1 with 3-keto, 5α-abiraterone was solved to 2.0 Å, the highest resolution to date for a CYP17A1 complex. This structure had additional electron density near the F/G loop, which is likely a second molecule of the inhibitor and which may explain the noncompetitive inhibition. Mutation of the adjacent Asn52 to Tyr positions its side chain in this space, maintains enzyme activity, and prevents binding of the peripheral ligand. Collectively, our findings provide further insight into abiraterone metabolite binding and CYP17A1 function.

59 BASIC BIOLOGICAL SCIENCES↗

Electronic Tongue for Quantitation of Contaminants in Water

An assembly of sensors, denoted an electronic tongue, is undergoing development as a prototype of compact devices for use in measuring concentrations of contaminants in water. Thus far, the electronic tongue has been tested on ions of Cu, Zn, Pb, and Fe and shown to respond to concentrations as low as about 10 parts per million. This electronic tongue is expected to be capable of measuring concentrations of other metal ions and organic compounds. Potential uses for electronic tongues include monitoring the chemical quality of water in a variety of natural, industrial, and laboratory settings; detecting micro-organisms indirectly by measuring microbially influenced corrosion; and characterizing compounds of interest to the pharmaceutical and food industries. This version of the electronic tongue includes a heater, a temperature sensor, an array of ion-specific electrodes, an oxidation/ reduction sensor pair, an electrical-conductivity sensor, and an array of galvanic cells, all on one compact ceramic substrate. Special-purpose electronic excitation and readout circuitry for the sensors has also been constructed. The main advantage of the electronic tongue, relative to electrodes of this type used traditionally to assess water quality, is extreme ruggedness. The types of measurements that can be performed by use of the sensors on the electronic tongue are quite varied. The best combination of types of measurements for a given application depends on the specific contaminants that one seeks to detect. Experimental studies to identify such combinations were in progress at the time of reporting the information for this article.

Buehler, Marlin↗

Thin-Film Solar Cells on Polymer Substrates for Space Power

Photovoltaic arrays have played a key role in power generation in space. The current technology will continue to evolve but is limited in the important mass specific power metric (MSP or power/weight ratio) because it is based on bulk crystal technology. Solar cells based on thin-film materials offer the promise of much higher MSP and much lower cost. However, for many space applications, a 20% or greater AM0 efficiency (eta) may be required. The leading thin-film materials, amorphous Si, CuInSe, and CdTe have seen significant advances in efficiency over the last decade but will not achieve the required efficiency in the near future. Several new technologies are herein described to maximize both device eta and MSP. We will discuss these technologies in the context of space exploration and commercialization. One novel approach involves the use of very lightweight polyimide substrates. We describe efforts to enable this advance including materials processing and device fabrication and characterization. Another approach involves stacking two cells on top of each other. These tandem devices more effectively utilize solar radiation by passing through non-absorbed longer wavelength light to a narrow-bandgap bottom cell material. Modeling of current devices in tandem format indicates that AM0 efficiencies near 20% can be achieved with potential for 25% in the near future. Several important technical issues need to be resolved to realize the benefits of lightweight technologies for solar arrays, such as: monolithic interconnects, lightweight array structures, and new ultra-light support and deployment mechanisms. Recent advances will be stressed.

Hepps, A. F.↗

Caged luciferins for bioluminescent activity-based sensing

Bioluminescence imaging is a powerful modality for in vivo imaging owing to its low background and high signal-to-noise ratio. Because bioluminescent emission occurs only upon the catalytic reaction between the luciferase enzyme and its luciferin substrate, caging luciferins with analyte-reactive triggers offers a general approach for activity-based sensing of specific biochemical processes in living systems across cell, tissue, and animal models. In this review, we summarize recent efforts in the development of synthetic caged luciferins for tracking enzyme, small molecule, and metal ion activity and their contributions to physiological and pathological processes.

59 BASIC BIOLOGICAL SCIENCES↗

Metabolism of Syringyl Lignin-Derived Compounds in Pseudomonas putida Enables Convergent Production of 2-Pyrone-4,6-Dicarboxylic Acid

Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (kcat/KM) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O2 consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.

2-pyrone-4,6-dicarboxylic acid↗

Towards chloroplastic nanofactories: formation of proteinaceous scaffolds for metabolic engineering

The evolution of eukaryotic lipid-bound organelles allows for specialized metabolism to occur within spatially distinct metabolic landscapes within the same cell. However, this strategy of compartmentalization is not unique to eukaryotic organisms. Many bacteria, spread across 45 different phyla, contain loci that encode for specialized bacterial microcompartments (BMCs) (Sutter et al., 2021). The formation of a BMC involves self-assembly from three families of shell proteins to form the outer shell membrane, in addition to the encapsulation of an enzymatic core packaged within the lumen of a BMC (Kerfeld et al., 2018). These proteinaceous organelles provide a competitive growth advantage by enabling organisms to process inaccessible substrates by sequestering metabolic intermediates (i.e. aldehydes) that would otherwise be toxic within the cytoplasm. While BMCs perform specific metabolic functions in their native organism, synthetic, empty BMC shells can form without the requirement of native cargo inside (Doron and Kerfeld, 2024). This provides a transferable and tunable platform of protein scaffolding for guiding metabolic engineering within a host organism of choice (Raba and Kerfeld, 2022).

59 BASIC BIOLOGICAL SCIENCES↗

Diffusion-assisted molecular beam epitaxy of CuCrO 2 thin films

Using molecular beam epitaxy (MBE) to grow multielemental oxides (MEOs) is generally challenging, partly due to difficulty in stoichiometry control. Occasionally, if one of the elements is volatile at the growth temperature, stoichiometry control can be greatly simplified using adsorption-controlled growth mode. Otherwise, stoichiometry control remains one of the main hurdles to achieving high-quality MEO film growths. Here, in this paper, we report another kind of self-limited growth mode, dubbed diffusion-assisted epitaxy, in which excess species diffuses into the substrate and leads to the desired stoichiometry, in a manner similar to the conventional adsorption-controlled epitaxy. Specifically, we demonstrate that using diffusion-assisted epitaxy, high-quality epitaxial CuCrO 2 films can be grown over a wide growth window without precise flux control using MBE.

36 MATERIALS SCIENCE↗

Design of a Nanophotonic Hybrid Coupler

This project aims to design and simulate a nanophotonic hybrid coupler for detecting vacuum ultraviolet (VUV) light with higher efficiency. VUV light is of significant interest because of its applications ranging from high energy physics to space science and electronic industry. However, current VUV photodetectors have very low efficiencies because most materials absorb in the VUV region (100-200 nm). To address this challenge, I have designed a plasmonic-dielectric coupler with wavelength shifting properties, enabling high Purcell enhancement and far-field confinement. The coupler consists of a cylindrical cSi resonator on top of a thin ZnO layer, and Ag and SiO2 are used as substrates. Simulations are done using the finite-difference time domain method to solve Maxwell’s equations, and specifically with Meep and Lumerical. The effectiveness of the coupler is characterized by the Purcell factor and far-field radiation. The Purcell factor reaches a maximum near 390 nm and is in the o rder of 10^4. Furthermore, the coupler also allows partial control of the directionality of the far-field radiation. With the presence of the resonator, the radiation is directed towards the coupled metalens. Overall, our design combines the advantages of plasmonic and dielectric couplers, along with the intrinsic wavelength shifting properties of materials to enhance VUV detection significantly, and such a device can be used in, for example, the DUNE project.

Zhou, Jiayang↗

PIE-Enabled Study of Aqueous Corrosion & Zr Hydriding in Cr-Coated Cladding: M3GV-23PN0101132

Chromium-coated zirconium alloy cladding is under investigation as an accident-tolerant fuel (ATF) concept to extend performance to higher burnups via improved oxidation resistance and reduced hydrogen pickup. However, hydrothermal corrosion behavior and hydrogen transport mechanisms governing in-service hydriding of these coatings remain poorly understood. In a collaborative study between Pacific Northwest National Laboratory (PNNL), Idaho National Laboratory (INL), and the University of Huddersfield, cold spray (CS) and physical vapor deposition (PVD) Cr-coated Optimized ZIRLO™ cladding samples were characterized after exposure to PWR-simulated water chemistry under both in-core (neutron irradiation) and out-of-core (aqueous-only) conditions at the MIT Research Reactor. Multi-scale characterization was performed independently at PNNL and INL to evaluate coating integrity, microstructural evolution, Cr/Zr interface chemistry, and hydride formation. Both laboratories observed a consistent divergence in hydriding behavior: out-of-core CS Cr-coated cladding exhibited elevated hydride concentrations exceeding those of uncoated cladding, whereas in-core CS samples showed substantially suppressed hydriding. In-core specimens also displayed irradiation-specific features, including nanoscale voids within the Cr coating and radiation-induced segregation clusters in the Zr substrate. CS coatings retained an interdiffusion-free Cr/Zr bond with no intermetallic layer, whereas PVD coatings exhibited inferior quality with visible cracks and pores. An automated image-based hydride quantification method systematically overestimated bulk hydrogen content relative to inert gas fusion measurements, underscoring the need for standardized sample preparation and reference standards. Interpretation of hydride nucleation and growth is complicated by the open inner-diameter of the specimens, which provides additional hydrogen pathways. The results motivate further foundational studies to support predictive models of hydrothermal corrosion and hydrogen transport in unirradiated and irradiated Cr-coated cladding.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Enhancing Coherence Limits in Superconducting Quantum Systems for Computing and Sensing

This talk will highlight recent efforts at the SQMS Center to develop qudit-based quantum computing architectures using superconducting three-dimensional (3D) cavities, as well as the use of these ultra-coherent cavities for quantum sensing. I will present systematic studies of materials and devices aimed at identifying and mitigating the dominant sources of decoherence—including two-level systems (TLS), quasiparticles, and other noise mechanisms—in both transmons and 3D cavities. These investigations include microwave loss characterization of niobium, tantalum, aluminum, their native oxides, and substrate materials such as silicon and sapphire. By combining measurements on qubits and cavities, we disentangle subsystem-specific loss mechanisms and establish a hierarchy of mitigation strategies, leading to transmon coherence times exceeding one millisecond. I will also discuss studies of quasiparticle dynamics, including quasiparticle bursts observed in qubits operated both above ground and at the Gran Sasso underground laboratory, and the observation that applied magnetic fields can suppress temporal T₁ fluctuations. Building on these advances, we demonstrate a record-coherence two-cell cavity-qudit system with coherence times exceeding 20 milliseconds. Leveraging tunable sideband interactions together with error-resilient protocols, including measurement-based error correction and post-selection, we achieve high-fidelity quantum state control, including the preparation of Fock states up to N=20 with fidelities above 95% and the generation of high-fidelity two-mode entangled states. Finally, I will discuss how these ultra-coherent quantum systems are enabling emerging quantum sensing applications, including searches for dark matter and gravitational waves.

Roy, Tanay [Fermilab] (ORCID:000000019442862X)↗