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Results for “amber suppression”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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8 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Application of Amber Suppression To Study the Role of Tyr M210 in Electron Transfer in Rhodobacter sphaeroides Photosynthetic Reaction Centers

The initial light-induced electron transfer (ET) steps in the bacterial photosynthetic reaction center (RC) have been extensively studied and provide a paradigm for connecting structure and function. Although RCs have local pseudo-C 2 symmetry, ET only occurs along the A branch of chromophores. Tyrosine M210 is a key symmetry-breaking residue adjacent to bacteriochlorophyll B A that bridges primary electron donor P and bacteriopheophytin acceptor H A . Here, we used amber suppression to incorporate phenylalanine variants with different electron-withdrawing/donating capabilities at position M210. X-ray data generally reveal no appreciable structural changes due to the mutations. P* decay and P + H A - formation are multi-exponential (~2-9, ~10-60, and ~100-300 ps) and temperature dependent. The 1020 nm transient-absorption band of P + B A - is barely resolved for a few variants at 295 K and for none at 77 K. The results indicate a change from two-step ET for wild-type RCs to dominance of one-step superexchange ET for the mutants. Resonance Stark spectroscopy reveals that the free energy of P + B A - changes by -57 to +66 meV among the phenylalanine variants. Because P+BA apparently lies above P* in all phenylalanine variants, the perturbations primarily affect the energy denominator for superexchange mixing. The findings deepen insight into primary ET in the bacterial RC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Electrostatic control of photoisomerization pathways in proteins

Rotation around a specific bond after photoexcitation is central to vision and emerging opportunities in optogenetics, super-resolution microscopy, and photoactive molecular devices. Competing roles for steric and electrostatic effects that govern bond-specific photoisomerization have been widely discussed, the latter originating from chromophore charge transfer upon excitation. We systematically altered the electrostatic properties of the green fluorescent protein chromophore in a photoswitchable variant, Dronpa2, using amber suppression to introduce electron-donating and electron-withdrawing groups to the phenolate ring. Through analysis of the absorption (color), fluorescence quantum yield, and energy barriers to ground- and excited-state isomerization, we evaluate the contributions of sterics and electrostatics quantitatively and demonstrate how electrostatic effects bias the pathway of chromophore photoisomerization, leading to a generalized framework to guide protein design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ancestral archaea expanded the genetic code with pyrrolysine

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Pressure dependence of intermediate-range order and elastic properties of glassy Baltic amber

Amber is a unique example of a fragile glass that has been extensively aged below its glass transition temperature, thus reaching a state that is not accessible under normal experimental conditions. In this paper, we studied the medium-range order of Baltic amber by x-ray diffraction (XRD) at high pressures. The pressure dependences of the low-angle XRD intensity between 0 and 5 Å -1 were measured from 0 to 7.3 GPa by the energy-dispersive XRD. The first diffraction peak at 1.1 Å -1 and ambient pressure has a doublet structure consisting of the first sharp diffraction peak (FSDP) at 1.05 Å -1 and the second feature at 1.40 Å -1 . The peak position and the width of the FSDP increase as the pressure increases, while the intensity of the FSDP decreases. Below P 0 = 2.4 GPa, the rapid increase of the FSDP peak position was observed, while above P 0 , the gradual increase was observed. Below P 0 , voids and holes in a relatively low-density state are suppressed, whereas above P 0 , the suppression becomes mild. Such a change suggests the crossover from the low- to high-density state at P 0 . There is a close correlation between the pressure dependence of XRD and previously reported sound velocity results. The correlation between the mean-square fluctuation of the shear modulus on the nanometer scale and fragility in amber and other glass formers is also discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Wafer-scale high-k SrTiO 3 dielectrics with rational barrier-layer design for low leakage and high charge density

High-k oxides such as SrTiO 3 promise large capacitance, but their dielectric response is often limited by leakage currents due to reduced bandgaps. We show that introducing a thin barrier layer beneath SrTiO 3 is a simple and effective way to suppress leakage and increase charge density. Using hybrid molecular beam epitaxy, we grew uniform SrTiO 3 films on Nb:SrTiO 3 , CaSnO 3 /Nb:SrTiO 3 , and 2-in. SiO 2 /p-Si stacks to directly compare how different barrier layers influence device behavior. Both CaSnO 3 and SiO 2 reduce leakage, but the ultra-wide-bandgap SiO 2 layer enables much higher operating voltages, yielding charge densities exceeding 5 × 10 13 cm −2 at room temperature—more than a fivefold enhancement compared to devices without a barrier layer. This improvement comes with a predictable trade-off: the lower dielectric constant of SiO 2 reduces overall capacitance, making its thickness an important design parameter. Together, these results demonstrate that rational barrier-layer engineering—including wafer-scale integration on Si—provides a clear pathway to achieving higher charge densities in SrTiO 3 -based dielectric devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Creep suppression and fatigue in bio-based composites manufactured via conventional and large format additive manufacturing processes

The emergence of novel extrusion-based additive manufacturing (AM) processes has prompted the development of new thermoplastic composite feedstocks, and broadening sustainability initiatives have driven the development of bio-based and recyclable material for AM feedstocks. Poly(lactic acid) (PLA) with wood flour (WF) is one composite system that has been demonstrated in numerous AM applications, as well as traditional processing methods (i.e., compression and injection molding); however, there has been a need to understand how the variation in processing methodology impacts the material performance of these bio-based feedstocks from a fundamental perspective, with particular emphasis on creep for an extended application use-life. Herein, PLA/WF is explored as a feedstock material for large format additive manufacturing (LFAM) and the performance of additively manufactured materials is compared to those produced via more traditional processing methods. It is also demonstrated that the addition of WF decreases the material’s coefficient of thermal expansion (CTE) while increasing its Young’s modulus, susceptibility to water uptake, and creep fatigue resistance. Essentially, the addition of 20 wt% WF results in a 92 % decrease in rubbery regime CTE while simultaneously resulting in a 14 % increase in modulus, 190 % increase in water uptake, and a 31 % decrease in residual strain after cyclic creep tests. The processing method was also found to play a large role in the final part performance, with the printed material increasing the crystallinity by 183 % and 214 % compared to its compression and injection molded counterparts. Furthermore, the porosity of printed samples increased by two orders of magnitude compared to samples prepared via traditional processing methods.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Mitigating cosmic-ray-like correlated events with a modular quantum processor

Quantum processors based on superconducting qubits are being scaled to larger qubit numbers, enabling the implementation of small-scale quantum error-correction codes. However, catastrophic chip-scale correlated errors have been observed in these processors, attributed to, e.g., cosmic ray impacts, which challenge conventional error-correction codes such as the surface code. These events are characterized by a temporary but pronounced suppression of the qubit-energy relaxation times. Here, in this study, we explore the potential for modular quantum computing architectures to mitigate such correlated energy decay events. We measure cosmic-ray-like events in a quantum processor comprising a motherboard and two flip-chip bonded daughterboard modules, each module containing two superconducting qubits. We monitor the appearance of correlated qubit decay events within a single module and across the physically separated modules. We find that while decay events within one module are strongly correlated (over 85%), events in separate modules only display approximately 2% correlations. We also report coincident decay events in the motherboard and in either of the two daughterboard modules, providing further insight into the nature of these decay events. These results suggest that modular architectures, combined with bespoke errorcorrection codes, offer a promising approach for protecting future quantum processors from chip-scale correlated errors.

Wu, Xuntao [Univ. of Chicago, IL (United States)] ↗
DOE OSTI2024

Super Resolving Unrolled Neural Networks for Remote Sensing

In remote sensing systems, the capabilities of the system are constrained by the complex interactions between size, weight, and power (SWAP) of potential designs. In electro-optical (EO) systems, examples of these critical parameters include the system’s sensitivity and resolution. Those parameters can be increased by ever larger optical apertures and focal planes but at the cost of more SWAP. Multi-image super resolution (MISR) techniques allow resolution to be enhanced via computation rather than more sophisticated optical hardware. These algorithms combine multiple images together into a single, higher resolution image, trading temporal resolution and computation for spatial resolution. Fielded MISR techniques, such as Drizzle, can require several hundred images to create a single super resolved image, implying reduced temporal resolution, increased data acquisition load, and limiting mission applications. Iterative techniques, such as model-based image reconstruction and compressive sensing, have been shown to create super resolved images using fewer images than Drizzle. They do this by posing an optimization problem that balances accuracy between a highly accurate physical model and an image model. In the case of super resolution, the physical model is defined by the relation between low resolution input images and the desired high resolution output image. The image model encodes some assumptions about the super resolved image. These assumptions are meant to suppress reconstruction artifacts that arise due to deterministic physical model error, stochastic measurement noise, and potential undersampling. In practice, the performance of iterative methods are limited by imaging models compatible with optimization. Deep learning-based methods can effectively learn image models of arbitrary complexity, but lack the theoretical explainability and robustness of iterative techniques. Consensus equilibrium (CE) generalizes the iterative techniques beyond optimization, enabling blackbox algorithms such as traditional and neural image denoisers to be used as the image model. CE-based approaches retain much of the explainability and robustness of iterative techniques while allowing the expressiveness of machine learning image models to be used. Additionally, by unrolling iterations of CE with an embedded image denoiser, the image denoiser can be further trained and specialized to the specific application with potentially higher quality reconstructions. Under this project, we demonstrated the feasibility of training an unrolled neural network based upon CE. While we didn’t train one, we showed that the CE process is differentiable and its gradient can be tractably computed. We also explored the usage of a variants of CE akin to generative neural works. Most importantly, we applied the CE framework to a number of problems including non-blind deconvolution, upsampling, single-image super resolution, MISR, event-based sensing, and saturated deconvolution. Our MISR prototype creates high quality reconstructions with an order of magnitude fewer images than previous approaches and, critically, produces these reconstructions fast enough for practical usage.

47 OTHER INSTRUMENTATION↗