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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Fluorescence-Enabled Self-Reporting for Redox Flow Batteries

Monitoring battery health is challenging. Self-reporting enables the rapid health assessment of redox flow batteries (RFBs) and provides insight into degradation mechanisms of electrochemically active molecules (redoxmers). In this study, we introduce fluorescence as an orthogonal property to probe this chemistry in situ. An established anolyte redoxmer, 2,1,3-benzothiadiazole, is rendered an efficient blue-green fluorophore through minimalistic derivatization. One of the derivatives is electrochemically reversible with a long lifetime and cycling stability in the charged state. Spectroscopic measurements on this new redoxmer reveal strong effects of the electrolyte cation on the fluorescence that are useful for probing the solvent microenvironment. Using this probe, we demonstrate proof-of-concept in situ crossover sensing and characterize the effects of electrolyte composition on this crossover. In this way, real-time tracing of redoxmers in a flow cell is demonstrated, paving the way to include still more self-reporting functions into the redoxmers.

25 ENERGY STORAGE↗
DOE OSTI2022

Imaging dark charge emitters in diamond via carrier-to-photon conversion

The application of color centers in wide-bandgap semiconductors to nanoscale sensing and quantum information processing largely rests on our knowledge of the surrounding crystalline lattice, often obscured by the countless classes of point defects the material can host. Here, we monitor the fluorescence from a negatively charged nitrogen-vacancy (NV – ) center in diamond as we illuminate its vicinity. Cyclic charge state conversion of neighboring point defects sensitive to the excitation beam leads to a position-dependent stream of photo-generated carriers whose capture by the probe NV – leads to a fluorescence change. This “charge-to-photon” conversion scheme allows us to image other individual point defects surrounding the probe NV, including nonfluorescent “single-charge emitters” that would otherwise remain unnoticed. Given the ubiquity of color center photochromism, this strategy may likely find extensions to material systems other than diamond.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Miniature fluorescence sensor for quantitative detection of brain tumour

Fluorescence-guided surgery has emerged as a vital tool for tumour resection procedures. As well as intraoperative tumour visualisation, 5-ALA-induced PpIX provides an avenue for quantitative tumour identification based on ratiometric fluorescence measurement. To this end, fluorescence imaging and fibre-based probes have enabled more precise demarcation between the cancerous and healthy tissues. These sensing approaches, which rely on collecting the fluorescence light from the tumour resection site and its “remote” spectral sensing, introduce challenges associated with optical losses. In this work, we demonstrate the viability of tumour detection at the resection site using a miniature fluorescence measurement system. Unlike the current bulky systems, which necessitate remote measurement, we have adopted a millimetre-sized spectral sensor chip for quantitative fluorescence measurements. A reliable measurement at the resection site requires a stable optical window between the tissue and the optoelectronic system. This is achieved using an antifouling diamond window, which provides stable optical transparency. The system achieved a sensitivity of 92.3% and specificity of 98.3% in detecting a surrogate tumour at a resolution of 1 × 1 mm 2 . In conclusion, as well as addressing losses associated with collecting and coupling fluorescence light in the current ‘remote’ sensing approaches, the small size of the system introduced in this work paves the way for its direct integration with the tumour resection tools with the aim of more accurate interoperative tumour identification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Does Selectivity of Molecular Catalysts Change with Time? Polymerization Imaged by Single-Molecule Spectroscopy

The chemoselectivity of molecular catalysts underpins much of modern synthetic organic chemistry. However, little is known about the selectivity of individual catalysts because this single-catalyst-level behavior is hidden by the bulk catalytic behavior. In this work, for the first time, the selectivity of individual molecular catalysts for two different reactions is imaged in real time at the single-catalyst level. This imaging is achieved through fluorescence microscopy paired with spectral probes that produce a snapshot of the instantaneous chemoselectivity of a single catalyst for either a single-chain-elongation or a single-chain-termination event during ruthenium-catalyzed polymerization. Superresolution imaging of multiple selectivity events, each at a different single-molecular ruthenium catalyst, indicates that catalyst selectivity may be unexpectedly spatially and time-variable.

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

A pipeline for targeted metagenomics of environmental bacteria

Background:Metagenomics and single cell genomics provide a window into the genetic repertoire of yet uncultivated microorganisms, but both methods are usually taxonomically untargeted. The combination of fluorescence in situ hybridization (FISH) and fluorescence activated cell sorting (FACS) has the potential to enrich taxonomically well-defined clades for genomic analyses. Methods:Cells hybridized with a taxon-specific FISH probe are enriched based on their fluorescence signal via flow cytometric cell sorting. A recently developed FISH procedure, the hybridization chain reaction (HCR)-FISH, provides the high signal intensities required for flow cytometric sorting while maintaining the integrity of the cellular DNA for subsequent genome sequencing. Sorted cells are subjected to shotgun sequencing, resulting in targeted metagenomes of low diversity. Results: Pure cultures of different taxonomic groups were used to (1) adapt and optimize the HCR-FISH protocol and (2) assess the effects of various cell fixation methods on both the signal intensity for cell sorting and the quality of subsequent genome amplification and sequencing. Best results were obtained for ethanol-fixed cells in terms of both HCR-FISH signal intensity and genome assembly quality. Our newly developed pipeline was successfully applied to a marine plankton sample from the North Sea yielding good quality metagenome assembled genomes from a yet uncultivated flavobacterial clade. Conclusions: With the developed pipeline, targeted metagenomes at various taxonomic levels can be efficiently retrieved from environmental samples. The resulting metagenome assembled genomes allow for the description of yet uncharacterized microbial clades.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High repetition rate mapping of the interaction between a laser plasma and magnetized background plasma via laser induced fluorescence

In this work, the laminar coupling of energy between a laser-produced plasma and a background magnetized plasma was investigated via planar laser induced fluorescence diagnostic and magnetic flux probes. Experiments performed on the Large Plasma Device at the University of California, Los Angeles, mapped out the two-dimensional spatiotemporal evolution of the laser-plasma (debris) ion velocity distribution function (VDF) to assess debris-background coupling in a sub-Alfvénic regime. The acquisition of these data necessitates high repetition rate (1 Hz) as each dataset is the accumulation of thousands of laser shots, which would not be feasible in single-shot experiments. Fully kinetic, three-dimensional particle-in-cell simulations are compared to the measured VDFs to provide a framework in which we can understand the coupling of a sub-Alfvénic plasma flow through a preformed, magnetized plasma. The simulations display the same departure from the expected gyromotion of the debris plasma as observed in the experimental data, and in conjunction with the measured magnetic field traces, have led to the direct observation of the collisionless coupling via laminar fields.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Direct observation of Mn distribution/speciation within and surrounding a basidiomycete fungus in the production of Mn-oxides important in toxic element containment

Biogenic manganese (Mn) oxides occur ubiquitously in the environment including the uranium (U) mill tailings at the Ningyo-toge U mine in Okayama, Japan, being important in the sequestration of radioactive radium (Ra). To understand the nanoscale processes in Mn oxides formation at the U mill tailings site, Mn 2+ absorption by a basidiomycete fungus, Coprinopsis urticicola, isolated from Ningyo-toge mine water samples, was investigated in the laboratory under controlled conditions utilizing electron microscopy, synchrotron-based X-ray analysis, and fluorescence microscopy with molecular pH probe. The fungus’ growth was first investigated in an agar-solidified medium supplemented with 1.0 mmol/L of Mn 2+ , ± Cu 2+ (50 – 200 µM), ± Zn 2+ (50 – 200 µM), or ± diphenyleneiodonium chloride (DPI) (50 – 100 µM) at 25 °C. The results revealed that Zn 2+ has no significant effects on the Mn oxides formation, whereas Cu 2+ and DPI significantly inhibit both fungal growth and Mn oxidation, indicating superoxide-mediated Mn oxidation. During the interaction of Mn 2+ with the fungi in solution medium at the initial pH of 5.67, a small fraction of Mn 2+ infiltrated into the fungal hyphae within 8 h, forming a few tens nm-sized concentrates of soluble Mn2+ in the intracellular pH of ~6.5, which can be released back to solution within a day as shown in a subsequent releasing experiment. After 1 day of incubation, Mn oxides began to precipitate on the hyphae, which were characterized to be fibrous nanocrystals with a hexagonal birnessite-structure, these forming spherical aggregates with a diameter of ~1.5 µm. When the fungi were reacted using the Ningyo-toge mine water, the Mn concentration decreased at a rate of 1.0 mmol·day-1 per unit dry weight. The nanoscale processes associated with the fungi derived from the Ningyo-toge mine area provides additional insights into the existing mechanisms of Mn oxidation by filamentous fungi at other U mill tailings sites under circumneutral pH conditions. Such processes add to the class of reactions important to the sequestration of toxic elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Reduction of Exciton Diffusion Length with Genetically Tuned Non-Photochemical Quenching in Plant Thylakoid Membranes

Non-photochemical quenching (NPQ) protects plants from excess light by dissipating excitation energy as heat. Limited exciton migration is a key feature of NPQ, reducing the energy flux to reaction centers; however, quantitative evidence for this mechanism in native thylakoid membranes has been lacking. Here, we investigate the correlation between NPQ activity and exciton diffusion length (LD) using Nicotiana benthamiana mutants with distinct NPQ capacities. NPQ under both light- and dark-acclimated conditions was quantified for each genotype via fluorescence lifetime snapshots, and exciton mobility was probed using transient absorption spectroscopy with exciton-exciton annihilation analysis. By comparing the relationship between chlorophyll fluorescence lifetime and LD across mutants, we observed that NPQ activation quantitatively limits the spatial range of exciton migration, thereby reducing the access to reaction centers. Our findings provide direct experimental evidence that NPQ modulates the dynamics of energy transport, advancing our understanding of photoprotective regulation in photosynthetic systems.

Diffusion↗
DOE OSTI2020

Does Selectivity of Molecular Catalysts Change with Time? Polymerization Imaged by Single‐Molecule Spectroscopy

Abstract The chemoselectivity of molecular catalysts underpins much of modern synthetic organic chemistry. However, little is known about the selectivity of individual catalysts because this single‐catalyst‐level behavior is hidden by the bulk catalytic behavior. Here, for the first time, the selectivity of individual molecular catalysts for two different reactions is imaged in real time at the single‐catalyst level. This imaging is achieved through fluorescence microscopy paired with spectral probes that produce a snapshot of the instantaneous chemoselectivity of a single catalyst for either a single‐chain‐elongation or a single‐chain‐termination event during ruthenium‐catalyzed polymerization. Superresolution imaging of multiple selectivity events, each at a different single‐molecular ruthenium catalyst, indicates that catalyst selectivity may be unexpectedly spatially and time‐variable.

Garcia, IV, Antonio↗
DOE OSTI2022

Complex pH-Dependent Interactions between Weak Polyelectrolyte Block Copolymer Micelles and Molecular Fluorophores

Amphiphilic block copolymers with weak polyelectrolyte blocks can assemble stimulus-responsive nanostructures and interfaces. Applications of these materials in drug delivery, biomimetics, and sensing largely rely on the well-understood swelling of polyelectrolyte chains upon deprotonation, often induced by changes in pH or ionic strength. This deprotonation can also tune interfacial interactions between the polyelectrolyte blocks and surrounding solution, an effect which is less studied than morphological swelling of polyelectrolytes but can be just as critical for intended function. Here, we investigate whether the pH-driven morphological response of polyelectrolyte-bearing nanostructures also affects the interactions of these nanostructures with molecules in solution, using micelles of a short-chain polybutadiene-block-poly(acrylic acid) (pBd–pAA) as a model system. Here we introduce a Förster resonance energy transfer (FRET) approach to probe interactions between micelles and fluorescent molecular solutes as a function of solution pH. As expected, the pAA corona of these pBd–pAA micelles increases in thickness monotonically as a function of pH. However, FRET efficiency, which provides a metric of the spatial proximity of fluorescently labeled micelles and freely diffusing fluorophores, exhibits complex nonmonotonic behavior as a function of pH, indicating that the average separation of micelles and acceptor fluorophores is not strictly correlated with micelle swelling. Dialysis experiments quantify the affinity of fluorophores for micelles as a function of pH, confirming that changes in FRET are driven almost entirely by the pH-dependent affinity of the pAA block for the investigated molecular fluorophores, not simply by a shape change of the pAA corona. This study provides key insights into the interfacial interactions between weak-polyelectrolyte-bearing nanostructures and molecular solutes, of importance for the development of their stimulus-responsive applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Safely probing the chemistry of Chernobyl nuclear fuel using micro-focus X-ray analysis

Detailed chemical analysis of the solidified molten fuel still residing in the stricken Chernobyl reactor unit 4 are inferred using multi-modal micro-focus X-ray analysis of a low-radioactivity proxy. A fascinating mixture of molten UO 2 , nuclear fuel cladding, concrete, stainless steel and other nuclear reactor components, these materials behaved like lava, solidifying to form a complex, highly radioactive glass-ceramic. Using element-specific chemical probes (micro-X-ray fluorescence and X-ray absorption spectroscopy), coupled with micro-diffraction analysis, the crystalline phase assemblage of simulants of these heterogeneous materials was established, which included “chernobylite” and a range of compositions in the (U 1-x Zr x )O 2 solid solution. Novel insight to nuclear accident fuel chemistry was obtained by establishing the oxidation state and local coordination of uranium not only in these crystalline phases, but uniquely in the amorphous fraction of the material, which varied depending on the history of the nuclear lava as it flowed through the reactor. This study demonstrates that micro-focus X-ray analysis of very small fractions of material can yield rich chemical information, which can be applied to nuclear-melt down materials to aid decommissioning and nuclear fuel management at nuclear accident sites.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

INSIGHTS INTO MARINE UNICELLULAR CYANOBACTERIAL AND NON-CYANOBACTERIAL DIAZOTROPHS THROUGH SINGLE-CELL ANALYSES

Nutrient availability affects primary productivity, and nitrogen (N) is the limiting nutrient over large regions of the ocean. Biological N fixation (BNF) is the conversion of atmospheric dinitrogen (N2) to bioavailable forms of N (ammonium and amino acids). A select group of Bacteria and Archaea, known as diazotrophs, are the only organisms capable of this conversion. BNF is a critical source of N in nutrient-depleted (oligotrophic) marine waters. As such, BNF studies are a fundamental component for better understanding primary productivity and carbon cycling, as well as parameterizing predictive future global ocean models. Unicellular diazotrophs are widespread in marine systems and, in some cases, important contributors of BNF. This dissertation investigates unicellular diazotrophs at the single-cell level, including: UCYN-A, a cyanobacterial diazotroph that lives in symbiosis with an algal host, non-cyanobacterial diazotrophs (NCDs), which are putative heterotrophs, as well as a specific NCD known as Gamma A, a commonly occurring organism throughout the tropics and subtropics that belongs to the class Gammaproteobacteria. The single-cell investigations used in these studies can provide high-resolution insights that are not possible from community-level analyses of BNF, such as the N2 fixation rate of individual cells and cell morphology. Singlecell nanoscale secondary ion mass spectrometry (nanoSIMS) analyses were used in chapter 2 and 3 to investigate the cell-specific N2 fixation rates of (2) UCYN-A in the viii cold waters of the Bering and Arctic Seas where N2 fixation was not previously believed to be possible, and (3) NCDs in the North Pacific Subtropical Gyre where we demonstrated the first direct evidence of NCD N2 fixation on open ocean particles. Chapter 4 focused on the uncultivated NCD, Gamma A, using geneFISH to visualize single cells in natural seawater samples. We successfully identified Gamma A by developing a fluorescent in situ hybridization (FISH) probe targeting the diazotrophic functional marker gene nifH, revealing Gamma A cells are most often attached to particles. Together these studies provide new insights into the distributions, activities, and physiologies of geographically widespread, unicellular diazotrophs, thus improving our understanding of their roles as sources of fixed N in the surface ocean.

Harding, K.↗
DOE OSTI2022

Robust, versatile DNA FISH probes for chromosome-specific repeats in Caenorhabditis elegans and Pristionchus pacificus

Repetitive DNA sequences are useful targets for chromosomal fluorescence in situ hybridization. We analyzed recent genome assemblies of Caenorhabditis elegans and Pristionchus pacificus to identify tandem repeats with a unique genomic localization. Based on these findings, we designed and validated sets of oligonucleotide probes for each species targeting at least 1 locus per chromosome. These probes yielded reliable fluorescent signals in different tissues and can easily be combined with the immunolocalization of cellular proteins. Synthesis and labeling of these probes are highly cost-effective and require no hands-on labor. The methods presented here can be easily applied in other model and nonmodel organisms with a sequenced genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Combining Multicolor FISH with Fluorescence Lifetime Imaging for Chromosomal Identification and Chromosomal Sub Structure Investigation

Understanding the structure of chromatin in chromosomes during normal and diseased state of cells is still one of the key challenges in structural biology. Using DAPI staining alone together with Fluorescence lifetime imaging (FLIM), the environment of chromatin in chromosomes can be explored. Fluorescence lifetime can be used to probe the environment of a fluorophore such as energy transfer, pH and viscosity. Multicolor FISH (M-FISH) is a technique that allows individual chromosome identification, classification as well as assessment of the entire genome. Here we describe a combined approach using DAPI as a DNA environment sensor together with FLIM and M-FISH to understand the nanometer structure of all 46 chromosomes in the nucleus covering the entire human genome at the single cell level. Upon DAPI binding to DNA minor groove followed by fluorescence lifetime measurement and imaging by multiphoton excitation, structural differences in the chromosomes can be studied and observed. This manuscript provides a blow by blow account of the protocol required to perform M-FISH-FLIM of whole chromosomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

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

Effect of indium alloying on the charge carrier dynamics of thick-shell InP/ZnSe quantum dots

In this work, thick-shell InP/ZnSe III–V/II–VI quantum dots (QDs) were synthesized with two distinct interfaces between the InP core and ZnSe shell: alloy and core/shell. Despite sharing similar optical properties in the spectral domain, these two QD systems have differing amounts of indium incorporation in the shell as determined by high-resolution energy-dispersive x-ray spectroscopy scanning transmission electron microscopy. Ultrafast fluorescence upconversion spectroscopy was used to probe the charge carrier dynamics of these two systems and shows substantial charge carrier trapping in both systems that prevents radiative recombination and reduces the photoluminescence quantum yield. The alloy and core/shell QDs show slight differences in the extent of charge carrier localization with more extensive trapping observed in the alloy nanocrystals. Despite the ability to grow a thick shell, structural defects caused by III–V/II–VI charge carrier imbalances still need to be mitigated to further improve InP QDs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Optimized CRISPR Interference System for Investigating Pseudomonas alloputida Genes Involved in Rhizosphere Microbiome Assembly

Pseudomonas alloputida KT2440 (formerly P. putida) has become both a well-known chassis organism for synthetic biology and a model organism for rhizosphere colonization. Here, we describe a CRISPR interference (CRISPRi) system in KT2440 for exploring microbe–microbe interactions in the rhizosphere and for use in industrial systems. Our CRISPRi system features three different promoter systems (XylS/P m , LacI/P lac , and AraC/P BAD ) and a dCas9 codon-optimized for Pseudomonads, all located on a mini-Tn7-based transposon that inserts into a neutral site in the genome. It also includes a suite of pSEVA-derived sgRNA expression vectors, where the expression is driven by synthetic promoters varying in strength. We compare the three promoter systems in terms of how well they can precisely modulate gene expression, and we discuss the impact of environmental factors, such as media choice, on the success of CRISPRi. We demonstrate that CRISPRi is functional in bacteria colonizing the rhizosphere, with repression of essential genes leading to a 10–100-fold reduction in P. alloputida cells per root. Finally, we show that CRISPRi can be used to modulate microbe–microbe interactions. When the gene pvdH is repressed and P. alloputida is unable to produce pyoverdine, it loses its ability to inhibit other microbes in vitro. Furthermore, our design is amendable for future CRISPRi-seq studies and in multispecies microbial communities, with the different promoter systems providing a means to control the level of gene expression in many different environments.

Bacteria↗
DOE OSTI2025

Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.

Cell signaling↗