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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 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism

Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular methods. Here, in this study, we describe a technical innovation combining bioorthogonal non-canonical amino acid tagging (BONCAT), stable isotope probing, and metaproteomics to improve the recovery of proteins from active community members and track isotope incorporation. Both click chemistry-enabled cell-sorting and direct protein pulldown coupled to metaproteomics improved recovery of isotopically labeled proteins during acetate oxidation within a full-scale anaerobic digester. Resulting labeled protein expression profiles revealed elevated activity of a rare and uncharacterized syntrophic bacterium belonging to the family Natronincolaceae. BONCAT-based capture of newly translated proteins provided direct molecular evidence for the expression of a previously hypothesized oxidative glycine pathway for syntrophic acetate oxidation by this microorganism, showcasing the potential of targeted metaproteomics to characterize rare and active cells central to community metabolism in natural and engineered ecosystems.

Friedline, Skyler [Univ. of British Columbia, Vanc↗
DOE OSTI2020

Integrative Quantitative-Phase and Airy Light-Sheet Imaging

Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free organelle recognition and metabolic information that are inaccessible by conventional methods. We report the fusion of these two modalities onto a standard inverted microscope that retains compatibility with microfluidics. We describe the utilization of an accelerating Airy-beam light-sheet yielding identical imaging areas with interferometry, and an application in unmasking the effects of cellular noise on metabolic compartmentalization.

Biological sciences, Biological techniques, Micros↗
DOE OSTI2021

Engineering an efficient and bright split Corynactis californica green fluorescent protein

Split green fluorescent protein (GFP) has been used in a panoply of cellular biology applications to study protein translocation, monitor protein solubility and aggregation, detect protein–protein interactions, enhance protein crystallization, and even map neuron contacts. Recent work shows the utility of split fluorescent proteins for large scale labeling of proteins in cells using CRISPR, but sets of efficient split fluorescent proteins that do not cross-react are needed for multiplexing experiments. We present a new monomeric split green fluorescent protein (ccGFP) engineered from a tetrameric GFP found in Corynactis californica, a bright red colonial anthozoan similar to sea anemones and scleractinian stony corals. Split ccGFP from C. californica complements up to threefold faster compared to the original Aequorea victoria split GFP and enable multiplexed labeling with existing A. victoria split YFP and CFP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

New thermal decomposition pathway for TATB

Abstract Understanding the thermal decomposition behavior of TATB (1,3,5-triamino-2,4,6-trinitrobenzene) is a major focus in energetic materials research because of safety issues. Previous research and modelling efforts have suggested benzo-monofurazan condensation producing H 2 O is the initiating decomposition step. However, early evolving CO 2 (m/z 44) along with H 2 O (m/z 18) evolution have been observed by mass spectrometric monitoring of head-space gases in both constant heating rate and isothermal decomposition studies. The source of the CO 2 has not been explained, until now. With the recent successful synthesis of 13 C 6 -TATB ( 13 C incorporated into the benzene ring), the same experiments have been used to show the source of the CO 2 is the early breakdown of the TATB ring, not adventitious C from impurities and/or adsorbed CO 2 . A shift in mass m/z 44 (CO 2 ) to m/z 45 is observed throughout the decomposition process indicating the isotopically labeled 13 C ring breakdown occurs at the onset of thermal decomposition along with furazan formation. Partially labeled (N 18 O 2 ) 3 -TATB confirms at least some of the oxygen comes from the nitro-groups. This finding has a significant bearing on decomposition computational models for prediction of energy release and deflagration to detonation transitions, with respect to conditions which currently do not recognize this oxidation step.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Exploration of the bio-analogous asymmetric C–C coupling mechanism in tandem CO 2 electroreduction

C–C coupling is a critical step of CO 2 fixation in constructing the carbon skeleton of value-added multicarbon products. The Wood–Ljungdahl pathway is an efficient natural process through which microbes transform CO 2 into methyl and carbonyl groups and subsequently couple them together. This asymmetric coupling mechanism remains largely unexplored in inorganic CO 2 electroreduction. Here we experimentally validate the asymmetric coupling pathway through isotope-labelled co-reduction experiments on a Cu surface where 13 CH 3 I and 12 CO are co-fed externally as the methyl and the carbonyl source, respectively. Isotope-labelled multicarbon oxygenates were detected, which confirms an electrocatalytic asymmetric coupling on the Cu surface. We further employed tandem Cu–Ag nanoparticle systems in which *CH x and *CO intermediates can be generated to achieve asymmetric C–C coupling for a practical CO 2 electroreduction. We found that the production of multicarbon oxygenates is correlated with the generation rate of two intermediate indicators, CH 4 and CO. By aligning their rates, the oxygenates generation rate can be maximized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Deep transfer operator learning for partial differential equations under conditional shift

Transfer learning enables the transfer of knowledge gained while learning to perform one task (source) to a related but different task (target), hence addressing the expense of data acquisition and labelling, potential computational power limitations and dataset distribution mismatches. Here, we propose a new transfer learning framework for task-specific learning (functional regression in partial differential equations) under conditional shift based on the deep operator network (DeepONet). Task-specific operator learning is accomplished by fine-tuning task-specific layers of the target DeepONet using a hybrid loss function that allows for the matching of individual target samples while also preserving the global properties of the conditional distribution of the target data. Inspired by conditional embedding operator theory, we minimize the statistical distance between labelled target data and the surrogate prediction on unlabelled target data by embedding conditional distributions onto a reproducing kernel Hilbert space. We demonstrate the advantages of our approach for various transfer learning scenarios involving nonlinear partial differential equations under diverse conditions due to shifts in the geometric domain and model dynamics. Our transfer learning framework enables fast and efficient learning of heterogeneous tasks despite considerable differences between the source and target domains.

42 ENGINEERING↗
DOE OSTI2021

Extracellular electron transfer across bio-nano interfaces for CO 2 electroreduction

Acetogenic bacteria represent a class of organisms capable of converting reducing equivalents and carbon dioxide into products with carbon–carbon bonds. Materials-based bio-electrochemical approaches are attractive for supplying biological organisms directly with grid-supplied electrons to convert carbon dioxide to value-added chemicals. Carbon nanotube-modified biocathodes have emerged as promising candidates for microbial electrosynthesis with high yields of carbon product formation, but a fundamental understanding of extracellular charge transfer at this electrode-biofilm interface is still lacking. Here, we utilize solid-state interfaces between semiconducting single-walled carbon nanotubes (s-SWCNT) and a model acetogenic bacterium for mechanistic studies of electro-catalytic CO 2 conversion to acetate. Studies of bacteria/s-SWCNT interactions in a transistor-based device suggest direct extracellular electron transfer (EET) at the bio-nano interface. Deuterium isotope labeling experiments confirmed that the availability of electrochemically produced H 2 as a redox mediator does not limit the efficiency of EET and CO 2 electro-reduction for C. ljungdahlii biofilms, suggesting the primary reducing equivalents are the electrons delivered across the electrode/bacterium interface or involvement of biological redox mediators. Additional isotope labeling studies demonstrate high Faradaic efficiency for CO 2 electro-reduction at the SWCNT/bacterium interface. These results provide important information about EET across the bacterium/material interface in a model biocathode.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell

Here, we report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.

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

Quantifying patterns in optical micrographs of one- and two-dimensional ellipsoidal particle assemblies

Current developments in colloidal science include the assembly of anisotropic colloids with broad geometric diversity. As the complexity of particle assemblies increases, the need for ubiquitous algorithms that quantitatively analyze images of the assemblies to deliver key information such as quantification of crystal structures becomes more urgent. This contribution describes algorithms capable of image analysis for classifying colloidal structures based on abstracted interparticle relationship information and quantitatively analyzing the abundance of each structure in mixed pattern assemblies. The algorithm parameters can be adjusted, allowing for the algorithms to be adapted for different image analyses. Three different ellipsoidal particle assembly images are presented to demonstrate the effectiveness of the algorithms: a one-dimensional (1D) particle chain assembly and two two-dimensional (2D) polymorphic crystals each consisting of assemblies of two distinct plane symmetry groups. Angle relationships between neighbouring particles are calculated and neighbour counts of each particle are determined. Combining these two parameters as rules for classification criteria allows for the labeling and quantification of each particle into a defined symmetry class within an assembly. The algorithms provide a labelled image comprising classification results and particle counts of each defined class. For multiple images or individual frames from a video, the script can be looped to achieve automatic processing. The yielded classification data allow for more in-depth image analysis of mixed pattern particle assemblies. Finally, we envision that these algorithms will have utility in quantitative analysis of images comprising ellipsoidal colloidal materials, nanoparticles, or biological matter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

One-bond 13 C– 13 C spin-coupling constants in saccharides: a comparison of experimental and calculated values by density functional theory using solid-state 13 C NMR and X-ray crystallography

Methyl aldohexopyranosides were 13 C-labeled at contiguous carbons, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13 C nuclear magnetic resonance (NMR) spectroscopy to examine the degree to which density functional theory (DFT) can calculate one-bond 13C–13C spin-coupling constants ( 1 J CC ) in saccharides with sufficient accuracy to permit their use in MA'AT analysis, a newly-reported hybrid DFT/NMR method that provides probability distributions of molecular torsion angles in solution (Zhang et al., J. Phys. Chem. B, 2017, 121, 3042–3058; Meredith et al., J. Chem. Inf. Model., 2022, 62, 3135–3141). Experimental 1 J CC values in crystalline samples of the doubly 13 C-labeled compounds were measured by solid-state 13 C NMR and compared to those calculated from five different DFT models: (1) 1 J CC values calculated from single structures identical to those observed in crystalline samples by X-ray crystallography (all atom refinement); (2) 1 J CC values calculated from the single structures in (1) but after Hirshfeld atom refinement (HAR); (3) 1 J CC values calculated from the single structures in (1) after DFT-optimization of hydrogen atoms only; and (4 and 5) 1 J CC values calculated in rotamers of torsion angle θ 2 (C1–C2–O2–O2H) or ω(C4–C5–C6–O6) from which either specific or generalized parameterized equations were obtained and used to calculate 1 J CC values in the specific θ 2 or ω rotamers observed in crystalline samples. Good qualitative agreement was observed between calculated 1 J CC values and those measured by solid-state 13 C NMR regardless of the DFT model, but in no cases were calculated 1 J CC values quantitative, differing (over-estimated) on average by 4–5% from experimental values. These findings, and those reported recently from solution NMR studies (Tetrault et al., J. Phys. Chem. B 2022, 126, 9506–9515), indicate that improvements in DFT calculations are needed before calculated 1 J CC values can be used directly as reliable constraints in MA'AT analyses of saccharides in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

On the mechanism of intermolecular nitrogen-atom transfer from a lattice-isolated diruthenium nitride intermediate

Catalyst confinement within microporous media provides the opportunity to site isolate reactive intermediates, enforce intermolecular functionalization chemistry by co-localizing reactive intermediates and substrates in molecular-scale interstices, and harness non-covalent host–guest interactions to achieve selectivities that are complementary to those accessible in solution. As part of an ongoing program to develop synthetically useful nitrogen-atom transfer (NAT) catalysts, we have demonstrated intermolecular benzylic amination of toluene at a Ru 2 nitride intermediate confined within the interstices of a Ru2-based metal–organic framework (MOF), Ru 3 (btc) 2 X 3 (btc = 1,3,5-benzenetricarboxylate, i.e., Ru-HKUST-1 for X = Cl). Nitride confinement within the extended MOF lattice enabled intermolecular C–H functionalization of benzylic C–H bonds in preference to nitride dimerization, which was encountered with soluble molecular analogues. Detailed study of the kinetic isotope effects (KIEs, i.e., k H /k D ) of C–H amination, assayed both as intramolecular effects using partially labeled toluene and as intermolecular effects using a mixture of per-labeled and unlabeled toluene, provided evidence for restricted substrate mobility on the time scale of interstitial NAT. Analysis of these KIEs as a function of material mesoporosity provided approximate experimental values for functionalization in the absence of mass transport barriers. Here, we disclose a combined experimental and computational investigation of the mechanism of NAT from a Ru 2 nitride to the C–H bond of toluene. Computed kinetic isotope effects for a H-atom abstraction (HAA)/radical rebound (RR) mechanism are in good agreement with experimental data obtained for C–H amination at the rapid diffusion limit. These results provide the first detailed analysis of the mechanism of intermolecular NAT to a C–H bond, bolster the use of KIEs as a probe of confinement effects on NAT within MOF lattices, and provide mechanistic insights unavailable by experiment because rate-determining mass transport obscured the underlying chemical kinetics.

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

Facet-dependent growth and dissolution of hematite resulting from autocatalytic interactions with Fe(II) and oxalic acid

The ability to simultaneously monitor the flux of iron atoms within the solution and solid phases can provide considerable insight into mechanisms of iron oxide mineral transformations. The autocatalytic interaction between hematite and Fe(II)-oxalate has long been of interest for its environmental and industrial relevance. In this study we take advantage of iron isotopic labelling and mass-sensitive imaging at the single particle scale to determine how changes in solution composition correlate with the morphologic evolution of faceted, micrometer-sized hematite platelets. Net dissolution is confirmed through analyses of aqueous iron chemistry, as well as by quantitative atomic force microscopy. Isotopic mapping techniques show that Fe(II) readily adsorbs to (001) and (012) surfaces in the absence of oxalate, but when oxalate is present selective dissolution of the (001) surface prevails and 57Fe deposition via recrystallization is not observed. Comparison between particle microtopographies following reaction with Fe(II), oxalate, and Fe(II)-oxalate show substantially different behavior, consistent with distinct mechanisms of interaction with hematite surfaces. The extensive characterization conducted on the coupled solution/solid dynamics in this system provides new insight for distinguishing crystal growth, dissolution, and recrystallization processes.

Taylor, Sandra D. [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2026

High-throughput Single-Cell Proteomics and Transcriptomics from the Same Cells with a Nanoliter-Scale Spin-Transfer Approach

Single-cell multiomic platforms provide a comprehensive snapshot of cellular states and cell types by offering critical insights into the spatiotemporal regulation of biomolecular networks at a systems level, thereby defining the basis of multicellularity. Here, we introduce nanoSPINS, an advanced platform that enables high-throughput profiling and integrative analysis of the transcriptome and proteome from the same single cells using RNA sequencing and isobaric labeling LC-MS-based proteomics, respectively. NanoSPINS can efficiently transfer mRNA-containing droplets across two microarrays via a centrifugation-based approach, while proteins are retained on the initial platform. Benchmarking of nanoSPINS on two cell lines demonstrates its ability to generate global proteomic and transcriptomic profiles that align well with previously established methodologies/platforms. The incorporation of isobaric TMTpro labeling into this single-cell multiomics platform significantly enhances the throughput of single-cell proteomic analyses. Through the high-throughput quantification of the proteome and transcriptome, nanoSPINS not only facilitates the identification of molecular features at both mRNA and protein level but also provides larger sample sizes for improved statistical power in clustering and differential abundance. Given the broad applicability of single-cell multiomics in biological research and clinical settings, we believe nanoSPINS represents a powerful platform for the characterization of heterogeneous cell populations.

multi 'omics↗
DOE OSTI2021

Graph Neural Network for Object Reconstruction in Liquid Argon Time Projection Chambers

This paper presents a graph neural network (GNN) technique for low-level reconstruction of neutrino interactions in a Liquid Argon Time Projection Chamber (LArTPC). GNNs are still a relatively novel technique, and have shown great promise for similar reconstruction tasks in the LHC. In this paper, a multihead attention message passing network is used to classify the relationship between detector hits by labelling graph edges, determining whether hits were produced by the same underlying particle, and if so, the particle type. The trained model is 84% accurate overall, and performs best on the EM shower and muon track classes. The model’s strengths and weaknesses are discussed, and plans for developing this technique further are summarised.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Taming the fixed-node error in diffusion Monte Carlo via range separation

By combining density-functional theory (DFT) and wave function theory via the range separation (RS) of the interelectronic Coulomb operator, we obtain accurate fixed-node diffusion Monte Carlo (FN-DMC) energies with compact multi-determinant trial wave functions. In particular, we combine here short-range exchange-correlation functionals with a flavor of selected configuration interaction known as configuration interaction using a perturbative selection made iteratively (CIPSI), a scheme that we label RS-DFT-CIPSI. One of the take-home messages of the present study is that RS-DFT-CIPSI trial wave functions yield lower fixed-node energies with more compact multi-determinant expansions than CIPSI, especially for small basis sets. Indeed, as the CIPSI component of RS-DFT-CIPSI is relieved from describing the short-range part of the correlation hole around the electron-electron coalescence points, the number of determinants in the trial wave function required to reach a given accuracy is significantly reduced as compared to a conventional CIPSI calculation. Importantly, by performing various numerical experiments, we evidence that the RS-DFT scheme essentially plays the role of a simple Jastrow factor by mimicking short-range correlation effects, hence avoiding the burden of performing a stochastic optimization. Considering the 55 atomization energies of the Gaussian-1 benchmark set of molecules, we show that using a fixed value of mu = 0.5 bohr(-1) provides effective error cancellations as well as compact trial wave functions, making the present method a good candidate for the accurate description of large chemical systems.

Scemama, Anthony↗
DOE OSTI2021

Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c</em

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.

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

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗