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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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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Developing multi-gene CRISPRa/i programs to accelerate DBTL cycles in ABF hosts engineered for chemical production

This project developed and implemented a modular CRISPR activation and interference (CRISPRa/i) platform to accelerate strain optimization and pathway development for industrially relevant microbial hosts. By integrating multiplexed transcriptional perturbation tools with data-driven Design–Build–Test–Learn (DBTL) workflows, the team achieved reductions in cycle time and enhanced production of industrial aromatics, particularly 4-aminocinnamic acid (4-ACA), in Pseudomonas putida. Key accomplishments included: ● Development of a robust, tunable CRISPRa/i system in P. putida that enabled efficient multi-target gene regulation via guide RNA (gRNA) programs ● Completion of two full DBTL cycles, guided by machine learning (ML) models trained on transcriptomic and performance data, reducing engineering time by over 30% ● Optimization of multi-gene regulatory programs to balance expression of host and pathway modules, improve 4-ACA titers, and resolve metabolic bottlenecks ● Demonstration of system portability through a limited proof-of-concept extension in Acinetobacter baylyi, underscoring the generalizability of the approach ● Evaluation of strain performance on lignocellulosic biomass-derived substrates, demonstrating the feasibility of converting renewable carbon into aromatic building blocks These results illustrate the feasibility of applying ML-guided CRISPRa/i perturbation strategies to accelerate strain development in complex microbial systems. The resulting tools and datasets contribute to DOE objectives by improving platform predictability, reducing development costs, and enabling broader access to sustainable, economically viable bioproduction technologies.

09 BIOMASS FUELS↗
DOE OSTI2021

Study of the Synchrotron Photoionization Oxidation of Alpha-Angelica Lactone (AAL) Initiated by O( 3 P) at 298, 550, and 700 K

In recent years, biofuels have been receiving significant attention because of their potential for decreasing carbon emissions and providing a long-term renewable solution to unsustainable fossil fuels. Currently, lactones are some of the alternatives being produced. Many lactones occur in a range of natural substances and have many advantages over bioethanol. In this study, the oxidation of alpha-angelica lactone initiated by ground-state atomic oxygen, O( 3 P), was studied at 298, 550, and 700 K using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at the Lawrence Berkeley National Lab (LBNL). Photoionization spectra and kinetic time traces were measured to identify the primary products. Ketene, acetaldehyde, methyl vinyl ketone, methylglyoxal, dimethyl glyoxal, and 5-methyl-2,4-furandione were characterized as major reaction products, with ketene being the most abundant at all three temperatures. Possible reaction pathways for the formation of the observed primary products were computed using the CBS–QB3 composite method.

09 BIOMASS FUELS↗
DOE OSTI2020

Covalent Surface Modification Effects on Single‐Walled Carbon Nanotubes for Targeted Sensing and Optical Imaging

Abstract Optical nanoscale technologies often implement covalent or noncovalent strategies for the modification of nanoparticles, whereby both functionalizations are leveraged for multimodal applications but can affect the intrinsic fluorescence of nanoparticles. Specifically, single‐walled carbon nanotubes (SWCNTs) can enable real‐time imaging and cellular delivery; however, the introduction of covalent SWCNT sidewall functionalizations often attenuates SWCNT fluorescence. Recent advances in SWCNT covalent functionalization chemistries preserve the SWCNT's pristine graphitic lattice and intrinsic fluorescence, and here, such covalently functionalized SWCNTs maintain intrinsic fluorescence‐based molecular recognition of neurotransmitter and protein analytes. The covalently modified SWCNT nanosensor preserves its fluorescence response towards its analyte for certain nanosensors, presumably dependent on the intermolecular interactions between SWCNTs or the steric hindrance introduced by the covalent functionalization that hinders noncovalent interactions with the SWCNT surface. These SWCNT nanosensors are further functionalized via their covalent handles with a targeting ligand, biotin, to self‐assemble on passivated microscopy slides, and these dual‐functionalized SWCNT materials are explored for future use in multiplexed sensing and imaging applications.

Chio, Linda↗
DOE OSTI2020

Trace-Level, Multi-Gas Detection for Food Quality Assessment Based on Decorated Silicon Transistor Arrays

Multiplexed gas detection at room temperature is critical for practical applications, such as for tracking the complex chemical environments associated with food decomposition and spoilage. Here, an integrated array of multiple silicon-based, chemical-sensitive field effect transistors (CSFETs) is presented to realize selective, sensitive, and simultaneous measurement of gases typically associated with food spoilage. CSFETs decorated with sensing materials based on ruthenium, silver, and silicon oxide are used to obtain stable room-temperature responses to ammonia (NH 3 ), hydrogen sulfide (H 2 S), and humidity, respectively. For example, one multi-CSFET sensor signal changes from its baseline by 13.34 in response to 1 ppm of NH 3 , 724.45 under 1 ppm H 2 S, and 23.46 under 80% relative humidity, with sensitive detection down to 10 ppb of NH 3 and H 2 S. To demonstrate this sensor for practical applications, the CSFET sensor array is combined with a custom-printed circuit board into a compact, fully integrated, and portable system to conduct real-time monitoring of gases generated by decomposing food. By using existing silicon-based manufacturing methodologies, this room-temperature gas sensing array can be fabricated reproducibly and at low cost, making it an attractive platform for ambient gas measurement needed in food safety applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Solution-Deposited and Patternable Conductive Polymer Thin-Film Electrodes for Microbial Bioelectronics

Microbial bioelectronic devices integrate naturally occurring or synthetically engineered electroactive microbes with microelectronics. These devices have a broad range of potential applications, but engineering the biotic–abiotic interface for biocompatibility, adhesion, electron transfer, and maximum surface area remains a challenge. Prior approaches to interface modification lack simple processability, the ability to pattern the materials, and/or a significant enhancement in currents. We report a novel conductive polymer coating that significantly enhances current densities relative to unmodified electrodes in microbial bioelectronics is reported. The coating is based on a blend of poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (PEDOT:PSS) crosslinked with poly(2-hydroxyethylacrylate) (PHEA) along with a thin polydopamine (PDA) layer for adhesion to an underlying indium tin oxide (ITO) electrode. When used as an interface layer with the current-producing bacterium Shewanella oneidensis MR-1, this material produces a 178-fold increase in the current density compared to unmodified electrodes, a current gain that is higher than previously reported thin-film 2D coatings and 3D conductive polymer coatings. The chemistry, morphology, and electronic properties of the coatings are characterized and the implementation of these coated electrodes for use in microbial fuel cells, multiplexed bioelectronic devices, and organic electrochemical transistor based microbial sensors are demonstrated. It is envisioned that this simple coating will advance the development of microbial bioelectronic devices.

patterned bioelectronics↗
DOE OSTI2024

Chiral Kirigami for Bend‐Tolerant Reconfigurable Hologram with Continuously Variable Chirality Measures

Abstract Despite the commonality of static holograms, the holography with multiple information layers and reconfigurable grey‐scale images at communication frequencies remain a confluence of scientific challenges. One well‐known difficulty is the simultaneous modulation of phase and amplitude of electromagnetic wavefronts with a high modulation depth. A less appreciated challenge is scrambling of the information and images with hologram bending. Here, this work shows that chirality‐guided pixelation of plasmonic kirigami sheets enables tunable multiplexed holography at terahertz (THz) frequencies. The convex and concave structures with slanted Au strips exhibit gradual variations in geometries facilitating modulation of light ellipticity reaching 40 deg. Real‐time switching of 3D images of the letter “ M ” and the Mona Lisa demonstrates the possibility of complex grey‐scale information content and importance of continuously variable mirror asymmetry. Microscale chirality measures of each pixel experiences little change with bending while retaining controllable reconfigurability upon stretching, which translates to remarkable resilience of chiral holograms to bending. Simplicity of their design with local chirality measures opens the door to information technologies with fault‐tolerant THz encryption, wearable holographic devices, and new communication technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multicolor Inks of Black Phosphorus for Midwave‐Infrared Optoelectronics

Abstract Black phosphorus (bP) based ink with a bulk bandgap of 0.33 eV ( λ = 3.7 µm) has recently been shown to be promising for large‐area, high performance mid‐wave infrared (MWIR) optoelectronics. However, the development of multicolor bP inks expanding across the MWIR wavelength range has been challenging. Here a multicolor ink process based on bP with spectral emission tuned from 0.28 eV ( λ = 4.4 µm) to 0.8 eV ( λ = 1.5 µm) is demonstrated. Specifically, through the reduction of bP particle size distribution (i.e., lateral dimension and thickness), the optical bandgap systematically blueshifts, reaching up to 0.8 eV. Conversely, alloying bP with arsenic (bP 1− x As x ) induces a redshift in the bandgap to 0.28 eV. The ink processed films are passivated with an infrared‐transparent epoxy for stable infrared emission in ambient air. Utilizing these multicolor bP‐based inks as an infrared light source, a gas sensing system is demonstrated that selectively detects gases, such as CO 2 and CH 4 whose absorption band varies around 4.3 and 3.3 µm, respectively. The presented ink formulation sets the stage for the advancement of multiplex MWIR optoelectronics, including spectrometers and spectral imaging using a low‐cost material processing platform.

Kim, Jae Ik↗
DOE OSTI2023

Half‐Integer Topological Charge Polarization of Quasi‐Dirac Bound States in the Continuum

Abstract The non‐trivial polarization topology of bound states in the continuum (BICs) provides new strategies in nanophotonics. The polarization topology depends on the geometric parameters and energy‐momentum dispersion of the system and can be engineered to add specific functionalities for light molding. Herein, such a possibility is investigated by studying the topology of the polarization states associated with the optical field radiated by BICs when Dirac‐cone‐degeneracy is lifted. The opening of a pseudogap in the Dirac cone dispersion of square‐lattice dielectric photonic crystal slabs is achieved by tuning the slab thickness. First, the emergence of half‐integer topological charges without the requirement of BIC annihilation is theoretically shown, which instead occurs when in‐plane inversion symmetry is broken. Then, using spin‐to‐orbital angular momentum conversion, the theory of half‐integer topological charges mediated by BICs is demonstrated and experimentally proved. The same device is able to give rise to vortices with different orbital angular momentum depending on the way it is illuminated, thus improving the potential of optical multiplexing. In addition, the additive character of the topology‐induced phase‐vortex generation is finally demonstrated for both integer and half‐integer charges using also vortex states as input beams, which is of relevance for information delivery.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Up‐And‐Coming Advances in Optical and Microwave Nonreciprocity: From Classical to Quantum Realm

Reciprocity is a fundamental physical principle that roots in the time‐reversal symmetry of physical laws. It allows making predictions on any arbitrary complex system's response and operation and hence simplifies the analysis. However, there are many practical situations in which it is advantageous to break reciprocity, e.g., isolators preventing wave scattering back to lasers and generators, full‐duplex systems for multiplexing transmission and receiving in the same channel, nonreciprocal cavity excitation, and protection of fragile states of superconductor quantum computers from thermal noise. The most widespread approach to time‐reversal symmetry breaking and nonreciprocity based on magnetic field biasing suffers from bulkiness, cost ineffectiveness, and loss, motivating researchers and engineers to search for more practical approaches. Herein, the up‐and‐coming advances in optical nonreciprocity, including new materials (Weyl semimetals, topological insulators, metasurfaces), active structures, time‐modulation, parity‐time (PT)‐symmetry breaking, nonlinearity combined with a structural asymmetry, quantum nonlinearity, unidirectional gain and loss, chiral quantum states and valley polarization are overviewed. A general description of nonreciprocal systems is provided and the pros and cons of the mentioned approaches to nonreciprocity are discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Genome engineering allows selective conversions of terephthalaldehyde to multiple valorized products in bacterial cells

Deconstruction of polyethylene terephthalate (PET) plastic waste generates opportunities for valorization to alternative products. We recently designed an enzymatic cascade that could produce terephthalaldehyde (TPAL) from terephthalic acid. Here, we showed that the addition of TPAL to growing cultures of Escherichia coli wild-type strain MG1655 and an engineered strain for reduced aromatic aldehyde reduction (RARE) strain resulted in substantial reduction. We then investigated if we could mitigate this reduction using multiplex automatable genome engineering (MAGE) to create an E. coli strain with 10 additional knockouts in RARE. Encouragingly, we found this newly engineered strain enabled a 2.5-fold higher retention of TPAL over RARE after 24 h. We applied this new strain for the production of para-xylylenediamine (pXYL) and observed a 6.8-fold increase in pXYL titer compared with RARE. Altogether, our study demonstrates the potential of TPAL as a versatile intermediate in microbial biosynthesis of chemicals that derived from waste PET.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes

Abstract The discovery of new compounds with pharmacological properties is usually a lengthy, laborious and expensive process. Thus, there is increasing interest in developing workflows that allow for the rapid synthesis and evaluation of libraries of compounds with the aim of identifying leads for further drug development. Herein, we apply combinatorial synthesis to build a library of 90 iridium(III) complexes (81 of which are new) over two synthesise‐and‐test cycles, with the aim of identifying potential agents for photodynamic therapy. We demonstrate the power of this approach by identifying highly active complexes that are well‐tolerated in the dark but display very low nM phototoxicity against cancer cells. To build a detailed structure–activity relationship for this class of compounds we have used density functional theory (DFT) calculations to determine some key electronic parameters and study correlations with the experimental data. Finally, we present an optimised semi‐automated synthesise‐and‐test protocol to obtain multiplex data within 72 hours.

Kench, Timothy↗
DOE OSTI2024

A Semi‐Automated, High‐Throughput Approach for the Synthesis and Identification of Highly Photo‐Cytotoxic Iridium Complexes

Abstract The discovery of new compounds with pharmacological properties is usually a lengthy, laborious and expensive process. Thus, there is increasing interest in developing workflows that allow for the rapid synthesis and evaluation of libraries of compounds with the aim of identifying leads for further drug development. Herein, we apply combinatorial synthesis to build a library of 90 iridium(III) complexes (81 of which are new) over two synthesise‐and‐test cycles, with the aim of identifying potential agents for photodynamic therapy. We demonstrate the power of this approach by identifying highly active complexes that are well‐tolerated in the dark but display very low nM phototoxicity against cancer cells. To build a detailed structure–activity relationship for this class of compounds we have used density functional theory (DFT) calculations to determine some key electronic parameters and study correlations with the experimental data. Finally, we present an optimised semi‐automated synthesise‐and‐test protocol to obtain multiplex data within 72 hours.

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

Benchmark Dose Analysis of DNA Damage Biomarker Responses Provides Compound Potency and Adverse Outcome Pathway Information for the Topoisomerase II Inhibitor Class of Compounds

Genetic toxicology data have traditionally been utilized for hazard identification to provide a binary call for a compound's risk. Recent advances in the scientific field, especially with the development of high‐throughput methods to quantify DNA damage, have influenced a change of approach in genotoxicity assessment. The in vitro MultiFlow® DNA Damage Assay is one such method which multiplexes γH2AX, p53, phospho‐histone H3 biomarkers into a single‐flow cytometric analysis (Bryce et al., [2016]: Environ Mol Mutagen 57:546–558). This assay was used to study human TK6 cells exposed to each of eight topoisomerase II poisons for 4 and 24 hr. Using PROAST v65.5, the Benchmark Dose approach was applied to the resulting flow cytometric datasets. With “compound” serving as covariate, all eight compounds were combined into a single analysis, per time point and endpoint. The resulting 90% confidence intervals, plotted in Log scale, were considered as the potency rank for the eight compounds. The in vitro MultiFlow data showed a maximum confidence interval span of 1Log, which indicates data of good quality. Patterns observed in the compound potency rank were scrutinized by using the expert rule‐based software program Derek Nexus, developed by Lhasa Limited. Compound sub‐classification and structural alerts were considered contributory to the potencies observed for the topoisomerase II poisons studied herein. The Topo II poison Adverse Outcome Pathway was evaluated with MultiFlow endpoints serving as Key Events. The step‐wise approach described herein can be considered as a foundation for risk assessment of compounds within a specific mode of action of interest. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.

Wheeldon, Ryan P.↗
DOE OSTI2020

Reaction mechanisms of a cyclic ether intermediate: Ethyloxirane

Oxiranes are a class of cyclic ethers formed in abundance during low-temperature combustion of hydrocarbons and biofuels, either via chain-propagating steps that occur from unimolecular decomposition of β -hydroperoxyalkyl radicals ( β -˙QOOH) or from reactions of HOÓ with alkenes. Ethyloxirane is one of four alkyl-substituted cyclic ether isomers produced as an intermediate from n -butane oxidation. While rate coefficients for β -˙QOOH → ethyloxirane + ÓH are reported extensively, subsequent reaction mechanisms of the cyclic ether are not. As a result, chemical kinetics mechanisms commonly adopt simplified chemistry to describe ethyloxirane consumption by convoluting several elementary reactions into a single step, which may introduce mechanism truncation error—uncertainty derived from missing or incomplete chemistry. Here we provide fundamental insight on reaction mechanisms of ethyloxirane in support of ongoing efforts to minimize mechanism truncation error. Reaction mechanisms are inferred from the detection of products during chlorine atom-initiated oxidation experiments using multiplexed photoionization mass spectrometry conducted at 10 Torr and temperatures of 650 K and 800 K. To complement the experiments, calculations of stationary point energies were conducted using the ccCA-PS3 composite method on ˙R + O 2 potential energy surfaces for the four ethyloxiranyl radical isomers, which produced barrier heights for 24 reaction pathways. In addition to products from ˙QOOH → cyclic ether + ÓH and ˙R + O 2 → conjugate alkene + HOÓ, both of which were significant pathways and are prototypical to alkane oxidation, other species were identified from ring-opening of both ethyloxiranyl and ˙QOOH radicals. The latter occurs when the unpaired electron is localized on the ether group, causing the initial ˙QOOH structure to ring-open and form a resonance-stabilized ketohydroperoxide-type radical. The present work provides the first analysis of ethyloxirane oxidation chemistry, which reveals that consumption pathways are complex and may require an expansion of submechanisms to increase the fidelity of chemical kinetics mechanisms.

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

Isomer-Dependent Reaction Mechanisms of Cyclic Ether Intermediates: cis -23-Dimethyloxirane and trans -23-Dimethyloxirane.

Oxiranes are a class of cyclic ethers formed in abundance during low-temperature combustion of hydrocarbons and biofuels, either via chain-propagating steps that occur from unimolecular decomposition of β-hydroperoxyalkyl radicals (β-˙QOOH) or from reactions of HÒO with alkenes. The cis- and trans-isomers of 2,3-dimethyloxirane are intermediates of n-butane oxidation, and while rate coefficients for β-˙QOOH → 2,3-dimethyloxirane + OH are reported extensively, subsequent reaction mechanisms of the cyclic ethers are not. As a result, chemical kinetics mechanisms commonly adopt simplified chemistry to describe the consumption of 2,3-dimethyloxirane by convoluting several elementary reactions into a single step, which may introduce mechanism truncation error—uncertainty derived from missing or incomplete chemistry. The present research examines the isomerdependence of 2,3-dimethyloxirane reaction mechanisms in support of ongoing efforts to minimize mechanism truncation error. Reaction mechanisms are inferred via the detection of products from Cl-initiated oxidation of both cis-2,3-dimethyloxirane and trans-2,3-dimethyloxirane using multiplexed photoionization mass spectrometry (MPIMS). The experiments were conducted at 10 Torr and temperatures of 650 K and 800 K. To complement the experiments, the enthalpies of stationary points on the ˙R + O 2 surfaces were computed at the ccCA-PS3 level of theory. In total, 28 barrier heights were computed on the 2,3-dimethyloxiranylperoxy surfaces. Two notable aspects are low-lying pathways that form resonance-stabilized ketohydroperoxide-type radicals caused by ˙QOOH ring-opening when the unpaired electron is localized adjacent to the ether group, and cis-trans isomerization of ˙R and ˙QOOH radicals, via inversion, which enable reaction pathways otherwise restricted by stereochemistry. Several species were identified in the MPIMS experiments from ring opening of 2,3-dimethyloxiranyl radicals. Neither of the two conjugate alkene isomers prototypical of ˙R + O 2 reactions were detected. Products were also identified from decomposition of ketohydroperoxide-type radicals. The present work provides the first analysis of 2,3-dimethyloxirane oxidation chemistry and reveals that consumption pathways are complex and require the expansion of submechanisms in chemical kinetics mechanisms.

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

Flying Blind, or Just Flying Under the Radar? The Underappreciated Power of De Novo Methods of Mass Spectrometric Peptide Identification

Mass spectrometry-based proteomics is a popular and powerful method for precise and highly multiplexed protein identification. The most common method of analyzing untargeted proteomics data is called database searching, where the database is simply a collection of protein sequences from the target organism, derived from genome sequencing. Experimental peptide tandem mass spectra are compared to simplified models of theoretical spectra calculated from the translated genomic sequences. However, in several interesting application areas, such as forensics, archaeology, venomics and others, a genome sequence may not be available, or the correct genome sequence to use is not known. In these cases, de novo peptide identification can play an important role. De novo peptide identification infers peptide sequence directly from the tandem mass spectrum without reference to a sequence database, usually using graph-based or machine learning algorithms. In this review, we provide a basic overview of de novo peptide identification methods and applications, briefly covering de novo algorithms and tools, and focusing in more depth on recent applications from venomics, metaproteomics, forensics, and characterization of antibody drugs.

proteomics, mass spectrometry, forensics, de novo ↗