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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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34 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

DNA parts and gene constructs for plant biodesign

Plant biodesign requires the knowledge of DNA parts (e.g., genes, promoters, terminators), along with their combinations (as gene constructs) linked to engineered traits. DNA parts with validated or predicted functions in plants have been deposited in various online databases. However, these existing databases focus on basic biological functions of individual DNA parts, leaving a gap between basic knowledge and bioengineering applications. To fill this knowledge gap, we have created a user-friendly, open-ended database as a knowledge graph linking DNA parts to gene constructs to traits. This database contains experimentally validated DNA parts and gene constructs documented in peer-reviewed publications. The DNA parts include 1) molecular components with biological functions, such as genes involved in various biological processes (e.g., metabolic and signal transduction pathways) and 2) molecular components with technical functions, such as gene expression, genome engineering and sequence splicing. The gene constructs deposited in this database include both single-gene and multi-gene constructs. This database allows users to submit DNA parts and gene construct compositions linked to engineered traits described in peer-reviewed publications, providing a public digital repository for sharing the biodesign information among the researchers in the fields of plant biotechnology and plant synthetic biology.

plant biodesign synthetic biology gene constructs ↗
DOE OSTI2024

Library Screening, In Vivo Confirmation, and Structural and Bioinformatic Analysis of Pentapeptide Sequences as Substrates for Protein Farnesyltransferase

Protein farnesylation is a post-translational modification where a 15-carbon farnesyl isoprenoid is appended to the C-terminal end of a protein by farnesyltransferase (FTase). This process often causes proteins to associate with the membrane and participate in signal transduction pathways. The most common substrates of FTase are proteins that have C-terminal tetrapeptide CaaX box sequences where the cysteine is the site of modification. However, recent work has shown that five amino acid sequences can also be recognized, including the pentapeptides CMIIM and CSLMQ. In this work, peptide libraries were initially used to systematically vary the residues in those two parental sequences using an assay based on Matrix Assisted Laser Desorption Ionization–Mass Spectrometry (MALDI-MS). In addition, 192 pentapeptide sequences from the human proteome were screened using that assay to discover additional extended CaaaX-box motifs. Selected hits from that screening effort were rescreened using an in vivo yeast reporter protein assay. The X-ray crystal structure of CMIIM bound to FTase was also solved, showing that the C-terminal tripeptide of that sequence interacted with the enzyme in a similar manner as the C-terminal tripeptide of CVVM, suggesting that the tripeptide comprises a common structural element for substrate recognition in both tetrapeptide and pentapeptide sequences. Molecular dynamics simulation of CMIIM bound to FTase further shed light on the molecular interactions involved, showing that a putative catalytically competent Zn(II)-thiolate species was able to form. Bioinformatic predictions of tetrapeptide (CaaX-box) reactivity correlated well with the reactivity of pentapeptides obtained from in vivo analysis, reinforcing the importance of the C-terminal tripeptide motif. This analysis provides a structural framework for understanding the reactivity of extended CaaaX-box motifs and a method that may be useful for predicting the reactivity of additional FTase substrates bearing CaaaX-box sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Glancing Angle Deposition in Gas Sensing: Bridging Morphological Innovations and Sensor Performances

Glancing Angle Deposition (GLAD) has emerged as a versatile and powerful nanofabrication technique for developing next-generation gas sensors by enabling precise control over nanostructure geometry, porosity, and material composition. Through dynamic substrate tilting and rotation, GLAD facilitates the fabrication of highly porous, anisotropic nanostructures, such as aligned, tilted, zigzag, helical, and multilayered nanorods, with tunable surface area and diffusion pathways optimized for gas detection. This review provides a comprehensive synthesis of recent advances in GLAD-based gas sensor design, focusing on how structural engineering and material integration converge to enhance sensor performance. Key materials strategies include the construction of heterojunctions and core–shell architectures, controlled doping, and nanoparticle decoration using noble metals or metal oxides to amplify charge transfer, catalytic activity, and redox responsiveness. GLAD-fabricated nanostructures have been effectively deployed across multiple gas sensing modalities, including resistive, capacitive, piezoelectric, and optical platforms, where their high aspect ratios, tailored porosity, and defect-rich surfaces facilitate enhanced gas adsorption kinetics and efficient signal transduction. These devices exhibit high sensitivity and selectivity toward a range of analytes, including NO2, CO, H2S, and volatile organic compounds (VOCs), with detection limits often reaching the parts-per-billion level. Emerging innovations, such as photo-assisted sensing and integration with artificial intelligence for data analysis and pattern recognition, further extend the capabilities of GLAD-based systems for multifunctional, real-time, and adaptive sensing. Finally, current challenges and future research directions are discussed, emphasizing the promise of GLAD as a scalable platform for next-generation gas sensing technologies.

Chemistry↗
DOE OSTI2025

Plant Defense Proteins: Recent Discoveries and Applications

Proteins play pivotal roles in safeguarding plants against numerous biotic and abiotic stresses. Understanding their biological functions and mechanisms of action is essential for advancing plant biology, agriculture, and biotechnology. This review considers the diversity and potential applications of plant defense proteins including pathogenesis-related (PR) proteins, chitinases, glucanases, protease inhibitors, lectins, and antimicrobial peptides. Recent advances, such as the omics technologies, have enabled the discovery of new plant defense proteins and regulatory networks that govern plant defense responses and unveiled numerous roles of plant defense proteins in stress perception, signal transduction, and immune priming. The molecular affinities and enzymatic activities of plant defense proteins are essential for their defense functions. Applications of plant defense proteins span agriculture, biotechnology, and medicine, including the development of resistant crop varieties, bio-based products, biopharmaceuticals, and functional foods. Future research directions include elucidating the structural bases of defense protein functions, exploring protein interactions with ligands and other proteins, and engineering defense proteins for enhanced efficacy. Overall, this review illuminates the significance of plant defense proteins against biotic stresses in plant biology and biotechnology, emphasizing their potential for sustainable agriculture and environmental management.

G-proteins↗
DOE OSTI2026

Transcriptomic data sets examining several stress responses in Zymomonas mobilis strains

We used RNA-seq to compare gene expression from Zymomonas mobilis ZM4 grown under various conditions: aerobic ± paraquat, anaerobic ± hydrogen peroxide, or an iron chelator. We analyzed two mutant strains lacking predicted transcription factors (ZMO_0442 and ZMO_1411) grown under aerobic or anaerobic conditions. We report the RNA-seq data from these experiments.

Bacterial Stress Response↗
DOE OSTI2025

An in vitro BRAF activation assay elucidates molecular mechanisms driving disassembly of the autoinhibited BRAF state

The RAF kinases (ARAF, BRAF, and CRAF) are essential components of the RAS-ERK signaling pathway, which controls vital cellular processes and is frequently dysregulated in human disease. Notably, mutations that alter BRAF function are prominent drivers of human cancer and certain RASopathy disorders, making BRAF an important target for therapeutic intervention. Despite extensive research, several aspects of BRAF regulation remain unclear. In this study, we developed an in vitro BRAF activation assay using purified autoinhibited BRAF:14-3-3 2 :MEK complexes. Our results show that fully processed, active-state KRAS alone can promote dimer-dependent BRAF activation. Moreover, we found that phosphatidylserine (PS)-containing liposomes synergized with KRAS to promote BRAF activation, achieving activity levels comparable to those observed with BRAF proteins that constitutively dimerize. In contrast, the SMP phosphatase complex had only a minimal effect on BRAF catalytic activity in this system but mediated the dephosphorylation of the negative regulatory pS365 14-3-3 binding site in a manner that was accelerated by the presence of KRAS alone or KRAS and 30% PS liposomes. Finally, we show that inhibitors blocking the BRAF RBD:KRAS interaction were able to suppress the in vitro activation of BRAF, underscoring the critical role of RAS binding in initiating the disassembly of the BRAF autoinhibited state. Thus, this assay provides valuable insights into the steps required for BRAF activation and can serve as an effective screening tool for identifying compounds that may inhibit this process and have therapeutic potential.

BRAF↗
DOE OSTI2025

Eucalyptus grandis MYB‐Like and RAN‐Like Zinc Finger Proteins Display Dual Roles in Regulating Plant Immunity and Symbiosis Pathways

Plant roots live in constant contact with diverse microbes in the soil. Plant fitness, therefore, relies on signaling pathways that mount an effective immune response against pathogens while fostering mutualistic symbioses. Plant pathways, and specifically immune genes that may act as "switches," discriminating between pathogenic or mutualistic fungi, remain largely unknown. Using Eucalyptus grandis as a model system, we investigate alterations to the root transcriptomic landscape during pre-symbiosis with either the pathogen Armillaria luteobubalina or the mutualistic fungus Pisolithus microcarpus. Comparative analyses identified three strongly counter-regulated genes that may act as immune switches to accommodate or to repress fungal colonization. We characterized two of these, a MYB-like and RAN-like zinc finger protein, using a transgenic approach and demonstrated that they have bifunctional roles in the regulation of cell death and a hypersensitive-like response, depending on the lifestyle of the associated fungus. Using co-expression network analysis, we identified hypothetical pathways correlated to these genes. We functionally validated these predictions using plants with transgenic roots with increased or decreased transcription of these genes, thereby showing the power of co-expression networks as an a priori approach to identify key immune response pathways in plants. Overall, our results demonstrate that prior to physical contact with microbes, MYB-like and RAN-like zinc finger proteins are key regulators of plant immune signaling that respond to fungal signals and enable or repress symbiotic establishment.

mycorrhizal fungi↗
DOE OSTI2026

Revealing the Full Potential of Glycolated Mixed Ionic-Electronic Semiconductors – Symmetric Monomer Polymerization to Boost Electrochemical Transistor Performance

Organic electrochemical transistors (OECTs) enable the transduction of ionic signals into electronic outputs, positioning them as ideal candidates for next-generation sensing and (bio)signal processing applications. Recent years have witnessed the development of various OECT channel materials, affording insights into structural fine-tuning to achieve optimal performance and/or stability. However, homocouplings, commonly present in alternating conjugated polymers, have largely been overlooked. This study investigates the effect of homocoupling on OECT materials by employing two synthesis methods – standard Stille polymerization and an alternative symmetric approach – to create the p-type enhancement-mode benchmark polymer pgBTTT. The impact of homocoupling, and its absence, is studied by comparing the bulk properties of the two polymers and evaluating their respective OECT metrics. The new, homocoupling-free polymer exhibits a notably improved OECT performance ( μC *), mainly due to an average 3-fold increase in electronic mobility (μ).

defects↗
DOE OSTI2025

Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus

Ammonia oxidizing archaea (AOA) are among the most abundant microorganisms on earth and are known to be a major source of nitrous oxide (N 2 O) emissions, although biochemical origins of this N 2 O remain unknown. Enzymological details of AOA nitrogen metabolism are broadly unavailable. We report the recombinant expression, purification, and characterization of a multicopper oxidase, Nmar_1354, from the AOA Nitrosopumilus maritimus . We show that Nmar_1354 selectively produces nitroxyl (HNO) by coupling the oxidation of the obligate nitrification intermediate hydroxylamine (NH 2 OH) to dioxygen (O 2 ) reduction. This HNO undergoes several downstream reactions, although the major fates are production of N 2 via reaction with NH 2 OH and dimerization with itself to yield N 2 O. These results afford one plausible enzymatic origin for N 2 O release by AOA. Moreover, these results reveal a physiologically relevant enzymatic reaction for producing HNO, an enigmatic nitrogen oxide speculated to be operative in cellular signaling and in energy transduction.

Voland, Robert W. (ORCID:0000000201061257)↗
DOE OSTI2024

Overcoming the fundamental limit of quantum transduction via intraband entanglement

A quantum transducer converts an input signal to an output probe at a distant frequency band while maintaining the quantum information with high fidelity, which is crucial for quantum networking and distributed quantum sensing and computing. In terms of microwave–optical quantum transduction, the state-of-the-art quantum transducers suffer low transduction efficiency from weak nonlinear coupling, wherein increasing pump power to enhance efficiency inevitably leads to thermal noise from heating. Moreover, we reveal that the efficiency-bandwidth product of a cavity electro-optical or electro-optomechanical transducer is fundamentally limited by pump power and nonlinear coupling coefficient, irrespective of cavity engineering efforts. To overcome this fundamental limit, we propose to noiselessly boost the transduction efficiency by consuming intraband entanglement (e.g., microwave–microwave or optical–optical entanglement in the case of microwave–optical transduction). Via a squeezer–coupler–antisqueezer sandwich structure, the protocol enhances the transduction efficiency to unity in the ideal lossless case, given an arbitrarily weak pump and nonlinear coupling. In practical cavity systems, our entanglement-assisted protocol surpasses the non-assisted fundamental limit of the efficiency-bandwidth product and reduces the threshold cooperativity for positive quantum capacity by a factor proportional to two-mode squeezing gain. Given a fixed cooperativity, our approach increases the broadband quantum capacity by orders of magnitude. The entanglement-assisted advantage is robust to ancilla loss and cavity detuning.

Shi, Haowei [Southern California U.] (ORCID:000000↗
DOE OSTI2026

How Do You Hear a Quantum Computer Whisper?

Quantum transduction is the process of upconverting microwave quantum signals into optical signals to develop quantum networks through optical fibers outside the dilution refrigerator, enabling connections between quantum technologies on the quantum internet. In this project, upconversion is achieved by directing an optical laser and the microwave quantum signal into an electro-optic bulk crystal. The crystal is housed within a Superconducting Radio Frequency (SRF) cavity designed to maximize the overlap between the microwave field and the crystal volume. In the presence of microwaves, the refractive index of the crystal changes through the Pockels effect. This change in refractive index modifies the propagation of the optical field within the crystal, allowing the quantum information carried by the microwave field to be transferred to the optical field. This study focuses on coupling laser light from suspended waveguide chips into the whispering-gallery modes (WGMs) of the crystal to enable transduction. The coupling efficiency between the optical field in the suspended waveguide and the WGM depends on the position of the laser spot on the crystal. To address this challenge, a feedback-based algorithm is being developed to fine-tune the waveguide position so that the optical signal is coupled efficiently into the crystal. After passing through the crystal, the optical signal is detected by a photodiode connected to an oscilloscope. The algorithm evaluates the coupling quality and iteratively adjusts the waveguide position to maximize coupling efficiency. The expected outcome is an automated waveguide alignment method that improves optical coupling and enables more efficient microwave-to-optical quantum transduction.

Karanastasis, Mihael [Fermilab]↗
DOE OSTI2024

Electrically interfaced Brillouin-active waveguide for microwave photonic measurements

New strategies for converting signals between optical and microwave domains could play a pivotal role in advancing both classical and quantum technologies. Traditional approaches to optical-to-microwave transduction typically perturb or destroy the information encoded on intensity of the light field, eliminating the possibility for further processing or distribution of these signals. In this paper, we introduce an optical-to-microwave conversion method that allows for both detection and spectral analysis of microwave photonic signals without degradation of their information content. This functionality is demonstrated using an optomechanical waveguide integrated with a piezoelectric transducer. Efficient electromechanical and optomechanical coupling within this system permits bidirectional optical-to-microwave conversion with a quantum efficiency of up to -54.16 dB. Leveraging the preservation of the optical field envelope in intramodal Brillouin scattering, we demonstrate a multi-channel microwave photonic filter by transmitting an optical signal through a series of electro-optomechanical waveguide segments, each with distinct resonance frequencies. Such electro-optomechanical systems could offer flexible strategies for remote sensing, channelization, and spectrum analysis in microwave photonics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Optimizing spectral phase transfer in four-wave mixing with gas-filled capillaries

Four-wave mixing (FWM) in gas-filled hollow-core capillaries, a nonlinear optical process that mixes signal and pump photon frequencies to generate idler frequency photons, offers a method for precise spectral phase transfer from signal to idler at ultrashort timescales and extreme powers. However, this regime is challenged by competing linear and nonlinear dynamics, leading to significant trade-offs between spectral phase transfer and conversion efficiency. Our computational investigation focuses on the upconversion of femtosecond pulses from the infrared (IR) to the ultraviolet (UV), a range notoriously difficult to manipulate. We explore an intermediate energy regime that strikes an optimal balance between FWM-mediated phase-transfer fidelity and nonlinear conversion efficiency. By adjusting the energy ratios and spectral phase profiles of the input signal, we achieve conversion efficiencies of approximately 5-15% while maintaining an effective quasi-linear spectral phase transfer. These findings will contribute to establishing first-principles and scaling laws essential for applications such as high-precision imaging, spectroscopy, quantum transduction, and distributed entangled interconnects, facilitating advanced control of ultrafast photonic and electronic wavepackets in quantum materials with unprecedented spatial and temporal precision.

Zhang, Hao↗
DOE OSTI2026

A 1-km photonic link connecting superconducting circuits in two dilution refrigerators

Superconducting quantum processors are a leading platform for implementing practical quantum computation algorithms. Although superconducting quantum processors with hundreds of qubits have been demonstrated, their further scale-up is constrained by the physical size and cooling power of dilution refrigerators. This constraint can be overcome by constructing a quantum network to interconnect qubits hosted in different refrigerators, which requires microwave-to-optical transducers to enable low-loss signal transmission over long distances. Although various designs and demonstrations have achieved high-efficiency and low-added-noise transducers, a coherent photonic link between separate refrigerators has not yet been realized. Here, in this work, we experimentally demonstrate coherent signal transfer between two superconducting circuits housed in separate dilution refrigerators, enabled by a pair of frequency-matched aluminium nitride electro-optic transducers connected via a 1-km telecom optical fibre. The optical frequency matching between two transducers is realized by an asymmetric photonic molecule design, and an overall 80 dB improvement in transduction efficiency over commercial electro-optic modulators is achieved, paving the way towards a fully quantum-enabled link. This work provides critical design guidelines for scalable superconducting quantum networks interconnected by photonic links.

nonlinear optics↗
DOE OSTI2024

Quantum computer-enabled receivers for optical communication

Abstract Optical communication is the standard for high-bandwidth information transfer in today’s digital age. The increasing demand for bandwidth has led to the maturation of coherent transceivers that use phase- and amplitude-modulated optical signals to encode more bits of information per transmitted pulse. Such encoding schemes achieve higher information density, but also require more complicated receivers to discriminate the signaling states. In fact, achieving the ultimate limit of optical communication capacity, especially in the low light regime, requires coherent joint detection of multiple pulses. Despite their superiority, such joint detection receivers are not in widespread use because of the difficulty of constructing them in the optical domain. In this work we describe how optomechanical transduction of phase information from coherent optical pulses to superconducting qubit states followed by the execution of trained short-depth variational quantum circuits can perform joint detection of communication codewords with error probabilities that surpass all classical, individual pulse detection receivers. Importantly, we utilize a model of optomechanical transduction that captures non-idealities such as thermal noise and loss in order to understand the transduction performance necessary to achieve a quantum advantage with such a scheme. We also execute the trained variational circuits on an IBM-Q device with the modeled transduced states as input to demonstrate that a quantum advantage is possible even with current levels of quantum computing hardware noise.

97 MATHEMATICS AND COMPUTING↗